From f093a6ab2e0b101d01f8e2fdb51b94432fa69c68 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 2 Jan 2024 10:57:43 -0700
Subject: [PATCH 001/161] start with basics

---
 git_setup           | 91 +++++++++++++++++++++++++++++++++++++++++++++
 git_sparse_checkout | 69 ++++++++++++++++++++++++++++++++++
 show-tags           | 20 ++++++++++
 3 files changed, 180 insertions(+)
 create mode 100755 git_setup
 create mode 100755 git_sparse_checkout
 create mode 100755 show-tags

diff --git a/git_setup b/git_setup
new file mode 100755
index 0000000000..52901897d5
--- /dev/null
+++ b/git_setup
@@ -0,0 +1,91 @@
+#!/bin/bash
+# Script to fetch submodules for CAM
+# if argument -internal-only is supplied then only checkout CAM internal submodules, otherwise checkout everything needed for
+# cam as a top level repository
+#
+set -e
+script="install"
+function usage {
+    echo -e "\nusage: $script [-i/--internal-only]\n"
+}
+# Set default arguments
+internal_only=0
+
+# Process arguments
+while [ "$1" != "" ];
+do
+    case $1 in
+
+        # Only checkout CISM internal submodules
+        -i | -internal-only | --internal-only)
+            internal_only=1
+            ;;
+
+        *)
+            echo "$script: illegal option $1"
+            usage
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+########################
+
+# Start with sparse checkouts
+if ! test -f bash-scripts/bin/git_sparse_checkout; then
+  echo "Getting git_sparse_checkout script"
+  git clone -n https://github.com/frgomes/bash-scripts --depth 1
+  pushd bash-scripts 1>/dev/null
+  git checkout HEAD -- bin/git_sparse_checkout
+  popd 1>/dev/null
+fi
+
+
+
+
+
+
+./bash-scripts/bin/git_sparse_checkout  https://github.com/larson-group/clubb_release clubb_4ncar_20221129_59cb19f_branch src/physics/clubb -- src/CLUBB_core/ src/SILHS/
+git restore src/physics/clubb
+
+./bash-scripts/bin/git_sparse_checkout https://github.com/CFMIP/COSPv2.0 master src/physics/cosp2/src -- src/
+git restore src/physics/cosp2/src
+
+./bash-scripts/bin/git_sparse_checkout https://github.com/MPAS-Dev/MPAS-Model.git develop src/dynamics/mpas/dycore -- src/external/ src/operators/ src/tools/ \
+                      src/core_atmosphere/ src/framework/
+git restore src/dynamics/mpas/dycore
+
+submodules=('chem_proc' 'src/physics/carma/base' 'src/physics/pumas' 'src/physics/pumas-frozen' 'src/physics/ali_arms' 'src/atmos_phys' 'src/dynamics/fv3/atmos_cubed_sphere' 'src/hemco')
+for mod in "${submodules[@]}"
+do
+   echo "Initializing $mod"
+   git submodule update --init $mod
+done
+
+if [ ${internal_only} -eq 1 ]
+  then
+    exit 0
+fi
+
+
+submodules=('ccs_config' 'components/cice5' 'components/cice' 'components/cmeps' \
+           'components/cdeps' 'components/cpl7' 'share' 'libraries/mct' \
+           'libraries/parallelio' 'cime' 'libraries/FMS' 'components/mosart' \
+           'components/rtm')
+
+for mod in "${submodules[@]}"
+do
+   echo "Initializing $mod"
+   git submodule update --init --recursive $mod
+done
+
+sparse_submodules=('components/clm' 'components/cism')
+for mod in "${sparse_submodules[@]}"
+do
+   echo "Initializing $mod"
+   git submodule update --init $mod
+   pushd $mod 1>/dev/null
+   bash ./install -internal-only
+   popd 1>/dev/null
+done
diff --git a/git_sparse_checkout b/git_sparse_checkout
new file mode 100755
index 0000000000..ec80069c2a
--- /dev/null
+++ b/git_sparse_checkout
@@ -0,0 +1,69 @@
+#!/bin/bash -eu
+
+# see also: git_origin and git_clone
+
+function git_sparse_checkout {
+    local self=$(readlink -f "${BASH_SOURCE[0]}")
+    local app=$(basename $self)
+    local usage=\
+"USAGE: ${app} repository-URL [branch] [project-directory] [[--] [list-of-files-or-directories]]
+  where:
+    'repository-URL' is a valid URL pointing to a Git repository.
+    'branch' is a branch, atag or a commit id. Default: master.
+    'project-directory' is a folder to be created and populated. Default: the project name.
+    'list-of-files-or-directories' is a list of file names or directories separated by spaces.
+  Examples:
+    ${app} http://github.com/frgomes/bash-scripts -- README.md
+    ${app} http://github.com/frgomes/bash-scripts develop -- README.md bin/
+    ${app} http://github.com/frgomes/bash-scripts develop tmpdir -- README.md bin/ docs/"
+
+    # obtain repository-URL, e.g.: http://github.com/frgomes/bash-scripts
+    [[ $# != 0 ]] || (echo "${usage}" 1>&2 ; return 1)
+    local arg=${1}
+    [[ "${arg}" != "--" ]] || (echo "${usage}" 1>&2 ; return 1)
+    local url="${arg}"
+    [[ $# == 0 ]] || shift
+
+    # obtain branch, which the default is master for historical reasons
+    if [[ "${arg}" != "--" ]] ;then arg="${1:-master}" ;fi
+    if [[ "${arg}" == "--" ]] ;then
+      local tag=master
+    else
+      local tag="${arg}"
+      [[ $# == 0 ]] || shift
+    fi
+
+    # obtain the project directory, which defaults to the repository name
+    local prj=$(echo "$url" | sed 's:/:\n:g' | tail -1)
+
+    if [[ "${arg}" != "--" ]] ;then arg="${1:-.}" ;fi
+    if [[ "${arg}" == "--" || "${arg}" == "." ]] ;then
+      local dir=$(readlink -f "./${prj}")
+    else
+      local dir=$(readlink -f "${arg}")
+      [[ $# == 0 ]] || shift
+    fi
+
+    if [[ "${arg}" == "--" ]] ;then [[ $# == 0 ]] || shift; fi
+    if [[ "${1:-}" == "--" ]] ;then [[ $# == 0 ]] || shift; fi
+
+    # Note: any remaining arguments after these above are considered as a
+    # list of files or directories to be downloaded. Names of directories
+    # must be followed by a slash /.
+
+    local sparse=true
+    local opts='--depth=1'
+
+    # now perform the sparse checkout
+    mkdir -p "${dir}"
+    git -C "${dir}" init
+    git -C "${dir}" config core.sparseCheckout ${sparse}
+    for path in $* ;do
+        echo "${path}" >> ${dir}/.git/info/sparse-checkout
+    done
+    git -C "${dir}" remote add origin ${url}
+    git -C "${dir}" fetch ${opts} origin ${tag}
+    git -C "${dir}" checkout ${tag}
+}
+
+git_sparse_checkout $@
diff --git a/show-tags b/show-tags
new file mode 100755
index 0000000000..56c7d9c5e4
--- /dev/null
+++ b/show-tags
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+this_dir=$(pwd)
+printf "\nSubmodule status\n"
+printf "(currently checked out commit for each submodule)\n"
+printf "(when the submodule is initialized and a tag exists, the commit is shown as: 'most recent tag-commits since tag-commit hash')\n"
+printf "(when the submodule is not initialized, only the checked out commit is shown)\n\n"
+grep path .gitmodules | sed 's/.*= //' | while read x
+do
+  cd "$this_dir"
+  printf "$x\n   - current commit: "
+  if [ "$(ls -A $x)" ] ; then
+    cd "$x"
+    git describe --tags --always
+  else
+    git submodule status $x | sed 's/^-//' | awk '{ print $1 }'
+  fi
+done
+printf "\n"
+

From f530e88acee6e959e9345b35a7e00b71d81641bf Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 3 Jan 2024 17:20:30 -0700
Subject: [PATCH 002/161] module based method, sparse working

---
 git_setup               |  37 ++---
 git_setup.py            | 104 +++++++++++++
 git_sparse_checkout     |  10 +-
 modules/__init__.py     |   0
 modules/lstripreader.py |  44 ++++++
 modules/utils.py        | 325 ++++++++++++++++++++++++++++++++++++++++
 6 files changed, 501 insertions(+), 19 deletions(-)
 create mode 100644 git_setup.py
 create mode 100644 modules/__init__.py
 create mode 100644 modules/lstripreader.py
 create mode 100644 modules/utils.py

diff --git a/git_setup b/git_setup
index 52901897d5..a5b27b13f6 100755
--- a/git_setup
+++ b/git_setup
@@ -1,10 +1,10 @@
 #!/bin/bash
-# Script to fetch submodules for CAM
-# if argument -internal-only is supplied then only checkout CAM internal submodules, otherwise checkout everything needed for
-# cam as a top level repository
+# Script to fetch submodules for esm applications 
+# if argument -internal-only is supplied then only checkout internal submodules, otherwise checkout everything needed for
+# a top level repository
 #
 set -e
-script="install"
+script=$0
 function usage {
     echo -e "\nusage: $script [-i/--internal-only]\n"
 }
@@ -31,28 +31,31 @@ do
 done
 
 ########################
+declare -A submods
+submod_list=$(git config -f .gitmodules --list)
+
+while IFS= read -r line;
+do
+    readarray -d. -t strarr <<< "$line" 
+    if [[ "strarr[3]" == "path" ]]; then
+        echo "path is $strarr[4]"
+    fi
+done <<< "$submod_list"
+exit 0
 
 # Start with sparse checkouts
-if ! test -f bash-scripts/bin/git_sparse_checkout; then
+if ! test -f bin/git_sparse_checkout; then
   echo "Getting git_sparse_checkout script"
-  git clone -n https://github.com/frgomes/bash-scripts --depth 1
-  pushd bash-scripts 1>/dev/null
-  git checkout HEAD -- bin/git_sparse_checkout
-  popd 1>/dev/null
+  git clone https://github.com/jedwards4b/gitscripts --depth 1 bin
 fi
 
-
-
-
-
-
-./bash-scripts/bin/git_sparse_checkout  https://github.com/larson-group/clubb_release clubb_4ncar_20221129_59cb19f_branch src/physics/clubb -- src/CLUBB_core/ src/SILHS/
+./bin/git_sparse_checkout  https://github.com/larson-group/clubb_release clubb_4ncar_20221129_59cb19f_branch src/physics/clubb -- src/CLUBB_core/ src/SILHS/
 git restore src/physics/clubb
 
-./bash-scripts/bin/git_sparse_checkout https://github.com/CFMIP/COSPv2.0 master src/physics/cosp2/src -- src/
+./bin/git_sparse_checkout https://github.com/CFMIP/COSPv2.0 master src/physics/cosp2/src -- src/
 git restore src/physics/cosp2/src
 
-./bash-scripts/bin/git_sparse_checkout https://github.com/MPAS-Dev/MPAS-Model.git develop src/dynamics/mpas/dycore -- src/external/ src/operators/ src/tools/ \
+./bin/git_sparse_checkout https://github.com/MPAS-Dev/MPAS-Model.git develop src/dynamics/mpas/dycore -- src/external/ src/operators/ src/tools/ \
                       src/core_atmosphere/ src/framework/
 git restore src/dynamics/mpas/dycore
 
diff --git a/git_setup.py b/git_setup.py
new file mode 100644
index 0000000000..5d70486d63
--- /dev/null
+++ b/git_setup.py
@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+import os
+import shutil
+import logging
+from modules import utils
+from configparser import ConfigParser
+from modules.lstripreader import LstripReader
+
+def parse_submodules_desc_section(section, section_items):
+    """Create a dict for this submodule description"""
+    desc = {}
+    esmrequired_options = ("T:T", "I:T", "I:F", "T:F")
+    for item in section_items:
+        name = item[0].strip().lower()
+        desc[name] = item[1].strip()
+    if not "esmrequired" in desc:
+        desc["esmrequired"] = "I:T"
+    
+    if desc["esmrequired"] not in esmrequired_options:
+        val = desc["esmrequired"]
+        utils.fatal_error(f"esmrequired set to {val} which is not a supported option {esmrequired_options}")
+    return desc
+
+
+def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
+    # first create the module directory
+    if not os.path.isdir(path):
+        os.makedirs(path)
+    # Check first if the module is already defined
+    # and the sparse-checkout file exists
+    cmd = ("git", "rev-parse", "--show-toplevel")
+    topdir = utils.execute_subprocess(cmd, output_to_caller=True).rstrip()
+    topgit = os.path.join(topdir, ".git", "modules")
+    gitsparse = os.path.join(topgit, name, "info","sparse-checkout")
+    if os.path.isfile(gitsparse):
+        logging.warning(f"submodule {name} is already initialized")
+        return
+    
+    #initialize a new git repo and set the sparse checkout flag
+    cmd = ("git", "-C", path, "init")
+    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    cmd = ("git", "-C", path, "config", "core.sparseCheckout","true") 
+    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    # set the repository remote
+    cmd = ("git", "-C", path, "remote", "add", "origin", url) 
+    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    
+    if not os.path.isdir(topgit):
+        os.makedirs(topgit)
+    topgit = os.path.join(topgit,name)
+    
+    shutil.move(os.path.join(path, ".git"), topgit)
+
+    shutil.copy(os.path.join(path,sparsefile), gitsparse)
+        
+    with open(os.path.join(path, ".git"), "w") as f:
+        f.write("gitdir: " + os.path.relpath(topgit, path))
+
+    #Finally checkout the repo
+    cmd = ("git", "-C", path, "fetch", "--depth=1", "origin", "--tags")
+    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    cmd = ("git", "-C", path, "checkout", tag)
+    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    print(f"Successfully checked out {name}")
+    
+def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
+    root_dir = os.path.abspath(root_dir)
+
+    msg = 'In directory : {0}'.format(root_dir)
+    logging.info(msg)
+
+    file_path = os.path.join(root_dir, file_name)
+    if not os.path.exists(file_name):
+        msg = ('ERROR: submodules description file, "{0}", does not '
+               'exist in dir:\n    {1}'.format(file_name, root_dir))
+        utils.fatal_error(msg)
+    config = ConfigParser()
+    config.read_file(LstripReader(file_path), source=file_name)
+    for section in config.sections():
+        name = section[11:-1]
+        submodule_desc = parse_submodules_desc_section(section,config.items(section))
+        if submodule_desc["esmrequired"] not in esmrequired:
+            if "T:F" in esmrequired or submodule_desc["esmrequired"].startswith("I:"):
+                print(f"Skipping optional component {section}")
+                # TODO change to logging
+                #                logging.info(f"Skipping optional component {section}")
+            continue
+        if "esmsparse" in submodule_desc:
+            if "esmtag" in submodule_desc:
+                tag = submodule_desc["esmtag"]
+            else:
+                tag = "master"
+            submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
+                                      submodule_desc["esmsparse"], tag)
+
+
+
+
+
+esmrequired = ("I:T", "T:T")
+root_dir = os.getcwd()
+gitmodules = read_gitmodules_file(root_dir, esmrequired)
+
+    
diff --git a/git_sparse_checkout b/git_sparse_checkout
index ec80069c2a..9b52bb29a7 100755
--- a/git_sparse_checkout
+++ b/git_sparse_checkout
@@ -55,13 +55,19 @@ function git_sparse_checkout {
     local opts='--depth=1'
 
     # now perform the sparse checkout
+    
     mkdir -p "${dir}"
     git -C "${dir}" init
     git -C "${dir}" config core.sparseCheckout ${sparse}
+    git -C "${dir}" remote add origin ${url}
+    super=$(git rev-parse --show-toplevel)
+    pathtodotgit=$(realpath -m --relative-to=${dir} ${super})/.git
+    relpathfromsuper=$(realpath -m --relative-to=${super} ${dir})
+    mv ${dir}/.git  ${super}/.git/modules/${relpathfromsuper}
+    echo "gitdir: ${pathtodotgit}/modules/${relpathfromsuper}" > ${dir}/.git
     for path in $* ;do
-        echo "${path}" >> ${dir}/.git/info/sparse-checkout
+        echo "${path}" >> ${super}/.git/modules/${relpathfromsuper}/info/sparse-checkout
     done
-    git -C "${dir}" remote add origin ${url}
     git -C "${dir}" fetch ${opts} origin ${tag}
     git -C "${dir}" checkout ${tag}
 }
diff --git a/modules/__init__.py b/modules/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/lstripreader.py b/modules/lstripreader.py
new file mode 100644
index 0000000000..530abd297e
--- /dev/null
+++ b/modules/lstripreader.py
@@ -0,0 +1,44 @@
+
+class LstripReader(object):
+    "LstripReader formats .gitmodules files to be acceptable for configparser"
+    def __init__(self, filename):
+        with open(filename, 'r') as infile:
+            lines = infile.readlines()
+        self._lines = list()
+        self._num_lines = len(lines)
+        self._index = 0
+        for line in lines:
+            self._lines.append(line.lstrip())
+
+    def readlines(self):
+        """Return all the lines from this object's file"""
+        return self._lines
+
+    def readline(self, size=-1):
+        """Format and return the next line or raise StopIteration"""
+        try:
+            line = self.next()
+        except StopIteration:
+            line = ''
+
+        if (size > 0) and (len(line) < size):
+            return line[0:size]
+
+        return line
+
+    def __iter__(self):
+        """Begin an iteration"""
+        self._index = 0
+        return self
+
+    def next(self):
+        """Return the next line or raise StopIteration"""
+        if self._index >= self._num_lines:
+            raise StopIteration
+
+        self._index = self._index + 1
+        return self._lines[self._index - 1]
+
+    def __next__(self):
+        return self.next()
+
diff --git a/modules/utils.py b/modules/utils.py
new file mode 100644
index 0000000000..8271538797
--- /dev/null
+++ b/modules/utils.py
@@ -0,0 +1,325 @@
+#!/usr/bin/env python3
+"""
+Common public utilities for manic package
+
+"""
+
+import logging
+import os
+import subprocess
+import sys
+from threading import Timer
+
+LOCAL_PATH_INDICATOR = '.'
+# ---------------------------------------------------------------------
+#
+# screen and logging output and functions to massage text for output
+#
+# ---------------------------------------------------------------------
+
+
+def log_process_output(output):
+    """Log each line of process output at debug level so it can be
+    filtered if necessary. By default, output is a single string, and
+    logging.debug(output) will only put log info heading on the first
+    line. This makes it hard to filter with grep.
+
+    """
+    output = output.split('\n')
+    for line in output:
+        logging.debug(line)
+
+
+def printlog(msg, **kwargs):
+    """Wrapper script around print to ensure that everything printed to
+    the screen also gets logged.
+
+    """
+    logging.info(msg)
+    if kwargs:
+        print(msg, **kwargs)
+    else:
+        print(msg)
+    sys.stdout.flush()
+
+
+def last_n_lines(the_string, n_lines, truncation_message=None):
+    """Returns the last n lines of the given string
+
+    Args:
+        the_string: str
+        n_lines: int
+        truncation_message: str, optional
+
+    Returns a string containing the last n lines of the_string
+
+    If truncation_message is provided, the returned string begins with
+    the given message if and only if the string is greater than n lines
+    to begin with.
+    """
+
+    lines = the_string.splitlines(True)
+    if len(lines) <= n_lines:
+        return_val = the_string
+    else:
+        lines_subset = lines[-n_lines:]
+        str_truncated = ''.join(lines_subset)
+        if truncation_message:
+            str_truncated = truncation_message + '\n' + str_truncated
+        return_val = str_truncated
+
+    return return_val
+
+
+def indent_string(the_string, indent_level):
+    """Indents the given string by a given number of spaces
+
+    Args:
+       the_string: str
+       indent_level: int
+
+    Returns a new string that is the same as the_string, except that
+    each line is indented by 'indent_level' spaces.
+
+    In python3, this can be done with textwrap.indent.
+    """
+
+    lines = the_string.splitlines(True)
+    padding = ' ' * indent_level
+    lines_indented = [padding + line for line in lines]
+    return ''.join(lines_indented)
+
+# ---------------------------------------------------------------------
+#
+# error handling
+#
+# ---------------------------------------------------------------------
+
+
+def fatal_error(message):
+    """
+    Error output function
+    """
+    logging.error(message)
+    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
+
+
+# ---------------------------------------------------------------------
+#
+# Data conversion / manipulation
+#
+# ---------------------------------------------------------------------
+def str_to_bool(bool_str):
+    """Convert a sting representation of as boolean into a true boolean.
+
+    Conversion should be case insensitive.
+    """
+    value = None
+    str_lower = bool_str.lower()
+    if str_lower in ('true', 't'):
+        value = True
+    elif str_lower in ('false', 'f'):
+        value = False
+    if value is None:
+        msg = ('ERROR: invalid boolean string value "{0}". '
+               'Must be "true" or "false"'.format(bool_str))
+        fatal_error(msg)
+    return value
+
+
+REMOTE_PREFIXES = ['http://', 'https://', 'ssh://', 'git@']
+
+
+def is_remote_url(url):
+    """check if the user provided a local file path instead of a
+       remote. If so, it must be expanded to an absolute
+       path.
+
+    """
+    remote_url = False
+    for prefix in REMOTE_PREFIXES:
+        if url.startswith(prefix):
+            remote_url = True
+    return remote_url
+
+
+def split_remote_url(url):
+    """check if the user provided a local file path or a
+       remote. If remote, try to strip off protocol info.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        return url
+
+    for prefix in REMOTE_PREFIXES:
+        url = url.replace(prefix, '')
+
+    if '@' in url:
+        url = url.split('@')[1]
+
+    if ':' in url:
+        url = url.split(':')[1]
+
+    return url
+
+
+def expand_local_url(url, field):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
+    represent local copy only, don't work with the remotes.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        if url.strip() == LOCAL_PATH_INDICATOR:
+            pass
+        else:
+            url = os.path.expandvars(url)
+            url = os.path.expanduser(url)
+            if not os.path.isabs(url):
+                msg = ('WARNING: Externals description for "{0}" contains a '
+                       'url that is not remote and does not expand to an '
+                       'absolute path. Version control operations may '
+                       'fail.\n\nurl={1}'.format(field, url))
+                printlog(msg)
+            else:
+                url = os.path.normpath(url)
+    return url
+
+
+# ---------------------------------------------------------------------
+#
+# subprocess
+#
+# ---------------------------------------------------------------------
+
+# Give the user a helpful message if we detect that a command seems to
+# be hanging.
+_HANGING_SEC = 300
+
+
+def _hanging_msg(working_directory, command):
+    print("""
+
+Command '{command}'
+from directory {working_directory}
+has taken {hanging_sec} seconds. It may be hanging.
+
+The command will continue to run, but you may want to abort
+manage_externals with ^C and investigate. A possible cause of hangs is
+when svn or git require authentication to access a private
+repository. On some systems, svn and git requests for authentication
+information will not be displayed to the user. In this case, the program
+will appear to hang. Ensure you can run svn and git manually and access
+all repositories without entering your authentication information.
+
+""".format(command=command,
+           working_directory=working_directory,
+           hanging_sec=_HANGING_SEC))
+
+
+def execute_subprocess(commands, status_to_caller=False,
+                       output_to_caller=False):
+    """Wrapper around subprocess.check_output to handle common
+    exceptions.
+
+    check_output runs a command with arguments and waits
+    for it to complete.
+
+    check_output raises an exception on a nonzero return code.  if
+    status_to_caller is true, execute_subprocess returns the subprocess
+    return code, otherwise execute_subprocess treats non-zero return
+    status as an error and raises an exception.
+
+    """
+    cwd = os.getcwd()
+    msg = 'In directory: {0}\nexecute_subprocess running command:'.format(cwd)
+    logging.info(msg)
+    commands_str = ' '.join(commands)
+    logging.info(commands_str)
+    return_to_caller = status_to_caller or output_to_caller
+    status = -1
+    output = ''
+    hanging_timer = Timer(_HANGING_SEC, _hanging_msg,
+                          kwargs={"working_directory": cwd,
+                                  "command": commands_str})
+    hanging_timer.start()
+    try:
+        output = subprocess.check_output(commands, stderr=subprocess.STDOUT,
+                                         universal_newlines=True)
+        log_process_output(output)
+        status = 0
+    except OSError as error:
+        msg = failed_command_msg(
+            'Command execution failed. Does the executable exist?',
+            commands)
+        logging.error(error)
+        fatal_error(msg)
+    except ValueError as error:
+        msg = failed_command_msg(
+            'DEV_ERROR: Invalid arguments trying to run subprocess',
+            commands)
+        logging.error(error)
+        fatal_error(msg)
+    except subprocess.CalledProcessError as error:
+        # Only report the error if we are NOT returning to the
+        # caller. If we are returning to the caller, then it may be a
+        # simple status check. If returning, it is the callers
+        # responsibility determine if an error occurred and handle it
+        # appropriately.
+        if not return_to_caller:
+            msg_context = ('Process did not run successfully; '
+                           'returned status {0}'.format(error.returncode))
+            msg = failed_command_msg(msg_context, commands,
+                                     output=error.output)
+            logging.error(error)
+            logging.error(msg)
+            log_process_output(error.output)
+            fatal_error(msg)
+        status = error.returncode
+    finally:
+        hanging_timer.cancel()
+
+    if status_to_caller and output_to_caller:
+        ret_value = (status, output)
+    elif status_to_caller:
+        ret_value = status
+    elif output_to_caller:
+        ret_value = output
+    else:
+        ret_value = None
+
+    return ret_value
+
+
+def failed_command_msg(msg_context, command, output=None):
+    """Template for consistent error messages from subprocess calls.
+
+    If 'output' is given, it should provide the output from the failed
+    command
+    """
+
+    if output:
+        output_truncated = last_n_lines(output, 20,
+                                        truncation_message='[... Output truncated for brevity ...]')
+        errmsg = ('Failed with output:\n' +
+                  indent_string(output_truncated, 4) +
+                  '\nERROR: ')
+    else:
+        errmsg = ''
+
+    command_str = ' '.join(command)
+    errmsg += """In directory
+    {cwd}
+{context}:
+    {command}
+""".format(cwd=os.getcwd(), context=msg_context, command=command_str)
+
+    if output:
+        errmsg += 'See above for output from failed command.\n'
+
+    return errmsg

From e0cf1ff87ad4ff09ad950d39d8777b2df377456e Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 09:29:53 -0700
Subject: [PATCH 003/161] now works two ways

---
 git_setup.py            | 24 ++++++++---------
 modules/gitinterface.py | 58 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 12 deletions(-)
 create mode 100644 modules/gitinterface.py

diff --git a/git_setup.py b/git_setup.py
index 5d70486d63..56e3d2e39c 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -5,6 +5,7 @@
 from modules import utils
 from configparser import ConfigParser
 from modules.lstripreader import LstripReader
+from modules.gitinterface import GitInterface
 
 def parse_submodules_desc_section(section, section_items):
     """Create a dict for this submodule description"""
@@ -28,8 +29,10 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
         os.makedirs(path)
     # Check first if the module is already defined
     # and the sparse-checkout file exists
-    cmd = ("git", "rev-parse", "--show-toplevel")
-    topdir = utils.execute_subprocess(cmd, output_to_caller=True).rstrip()
+    fullpath = os.path.join(os.getcwd(),path)
+    git = GitInterface(os.getcwd())
+    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
+
     topgit = os.path.join(topdir, ".git", "modules")
     gitsparse = os.path.join(topgit, name, "info","sparse-checkout")
     if os.path.isfile(gitsparse):
@@ -37,13 +40,12 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
         return
     
     #initialize a new git repo and set the sparse checkout flag
-    cmd = ("git", "-C", path, "init")
-    status = utils.execute_subprocess(cmd, status_to_caller=True)
-    cmd = ("git", "-C", path, "config", "core.sparseCheckout","true") 
-    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    sprepo_git = GitInterface(os.path.join(topdir,path))
+    sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
     # set the repository remote
-    cmd = ("git", "-C", path, "remote", "add", "origin", url) 
-    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    cmd = ("remote", "add", "origin", url)
+    sprepo_git.git_operation("remote", "add", "origin", url)
     
     if not os.path.isdir(topgit):
         os.makedirs(topgit)
@@ -57,10 +59,8 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
         f.write("gitdir: " + os.path.relpath(topgit, path))
 
     #Finally checkout the repo
-    cmd = ("git", "-C", path, "fetch", "--depth=1", "origin", "--tags")
-    status = utils.execute_subprocess(cmd, status_to_caller=True)
-    cmd = ("git", "-C", path, "checkout", tag)
-    status = utils.execute_subprocess(cmd, status_to_caller=True)
+    sprepo_git.git_operation( "fetch", "--depth=1", "origin", "--tags")
+    sprepo_git.git_operation( "checkout", tag)
     print(f"Successfully checked out {name}")
     
 def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
diff --git a/modules/gitinterface.py b/modules/gitinterface.py
new file mode 100644
index 0000000000..105acd3d2c
--- /dev/null
+++ b/modules/gitinterface.py
@@ -0,0 +1,58 @@
+import os
+from modules import utils
+
+class GitInterface:
+    def __init__(self, repo_path):
+        self.repo_path = repo_path
+
+        try:
+            import git
+            self._use_module = True
+            try:
+                self.repo = git.Repo(repo_path)  # Initialize GitPython repo
+            except git.exc.InvalidGitRepositoryError:
+                self.git = git
+                self._init_git_repo()
+        except ImportError:
+            self._use_module = False
+            if not os.path.exists(os.path.join(repo_path,".git")):
+                self._init_git_repo()
+
+    def _git_command(self, operation, *args):
+        if self._use_module:
+            return getattr(self.repo.git, operation)(*args)
+        else:
+            return ["git", "-C",self.repo_path, operation] + list(args)
+
+    def _init_git_repo(self):
+        if self._use_module:
+            self.repo = self.git.Repo.init(self.repo_path)
+        else:
+            command = ("git", "-C", self.repo_path, "init")
+            utils.execute_subprocess(command)
+
+
+    def git_operation(self, operation, *args, **kwargs):
+        command = self._git_command(operation, *args)
+        if isinstance(command, list):
+            return utils.execute_subprocess(command, output_to_caller=True)
+        else:
+            return command
+
+    def config_get_value(self, section, name):
+        if self._use_module:
+            config = self.repo.config_reader()
+            return config.get_value(section, name)
+        else:
+            cmd = ("git","-C",self.repo_path,"config", "--get", f"{section}.{name}")
+            output = utils.execute_subprocess(cmd, output_to_caller=True)
+            return output.strip()
+
+    def config_set_value(self, section, name, value):
+        if self._use_module:
+            with self.repo.config_writer() as writer:
+                writer.set_value(section, name, value)
+            writer.release()  # Ensure changes are saved
+        else:
+            cmd = ("git","-C",self.repo_path,"config", f"{section}.{name}", value)
+            utils.execute_subprocess(cmd, output_to_caller=True)

From f36bc9a68a578667f83b59dbc339d96e6fdc6995 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 14:03:45 -0700
Subject: [PATCH 004/161] complete the tools

---
 git_setup.py            | 22 ++++++++++++++++++++--
 modules/gitinterface.py |  7 ++++++-
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index 56e3d2e39c..319e68cdf2 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -14,6 +14,9 @@ def parse_submodules_desc_section(section, section_items):
     for item in section_items:
         name = item[0].strip().lower()
         desc[name] = item[1].strip()
+        # e3sm needs to have ssh protocol urls, we don't
+        if name == "url" and desc[name].startswith("git@github"):
+            desc[name] = desc[name].replace("git@github.com:","https://github.com/")
     if not "esmrequired" in desc:
         desc["esmrequired"] = "I:T"
     
@@ -29,7 +32,6 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
         os.makedirs(path)
     # Check first if the module is already defined
     # and the sparse-checkout file exists
-    fullpath = os.path.join(os.getcwd(),path)
     git = GitInterface(os.getcwd())
     topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
 
@@ -62,6 +64,17 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
     sprepo_git.git_operation( "fetch", "--depth=1", "origin", "--tags")
     sprepo_git.git_operation( "checkout", tag)
     print(f"Successfully checked out {name}")
+
+def submodule_checkout(name, url, path, tag, esmrequired):
+    git = GitInterface(os.cwd())
+    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
+    repodir = os.path.join(topdir, path)
+    git.git_operation("submodule","update","--init")
+    # Look for a .gitmodules file in the newly checkedout repo
+    if os.path.exists(os.path.join(repodir,".gitmodules")):
+        # recursively handle this checkout
+        read_gitmodules_file(repodir, esmrequired)
+    return
     
 def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
     root_dir = os.path.abspath(root_dir)
@@ -92,7 +105,12 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
                 tag = "master"
             submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
                                       submodule_desc["esmsparse"], tag)
-
+            continue
+        Iesmrequired = []
+        for setting in esmrequired:
+            if setting.startswith("I:"):
+                Iesmrequired.append(setting) 
+        submodule_checkout(name, submodule_desc["url"], submodule_desc["path"], tag, Iesmrequired)
 
 
 
diff --git a/modules/gitinterface.py b/modules/gitinterface.py
index 105acd3d2c..06203bb9da 100644
--- a/modules/gitinterface.py
+++ b/modules/gitinterface.py
@@ -1,4 +1,5 @@
 import os
+import logging
 from modules import utils
 
 class GitInterface:
@@ -13,12 +14,16 @@ def __init__(self, repo_path):
             except git.exc.InvalidGitRepositoryError:
                 self.git = git
                 self._init_git_repo()
+            msg = "Using GitPython interface to git"
         except ImportError:
             self._use_module = False
             if not os.path.exists(os.path.join(repo_path,".git")):
                 self._init_git_repo()
-
+            msg = "Using shell interface to git"
+        logging.info(msg)
+                
     def _git_command(self, operation, *args):
+        logging.info(operation)
         if self._use_module:
             return getattr(self.repo.git, operation)(*args)
         else:

From 2beceaa56b02c1d607696a3d4259a54338214e35 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 15:45:11 -0700
Subject: [PATCH 005/161] more fixes

---
 git_setup.py            | 13 +++++++------
 modules/gitinterface.py |  1 +
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index 319e68cdf2..82c044cff2 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -66,14 +66,15 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
     print(f"Successfully checked out {name}")
 
 def submodule_checkout(name, url, path, tag, esmrequired):
-    git = GitInterface(os.cwd())
+    git = GitInterface(os.getcwd())
     topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
     repodir = os.path.join(topdir, path)
-    git.git_operation("submodule","update","--init")
+    git.git_operation("submodule","update","--init", name)
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir,".gitmodules")):
         # recursively handle this checkout
         read_gitmodules_file(repodir, esmrequired)
+    print(f"Successfully checked out {name}")
     return
     
 def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
@@ -98,11 +99,11 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
                 # TODO change to logging
                 #                logging.info(f"Skipping optional component {section}")
             continue
+        if "esmtag" in submodule_desc:
+            tag = submodule_desc["esmtag"]
+        else:
+            tag = "master"
         if "esmsparse" in submodule_desc:
-            if "esmtag" in submodule_desc:
-                tag = submodule_desc["esmtag"]
-            else:
-                tag = "master"
             submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
                                       submodule_desc["esmsparse"], tag)
             continue
diff --git a/modules/gitinterface.py b/modules/gitinterface.py
index 06203bb9da..baf98f35d8 100644
--- a/modules/gitinterface.py
+++ b/modules/gitinterface.py
@@ -40,6 +40,7 @@ def _init_git_repo(self):
     def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *args)
         if isinstance(command, list):
+            print(command)
             return utils.execute_subprocess(command, output_to_caller=True)
         else:
             return command

From a3fcaf20dad5a7bcbd5c4e3dc0ac916911172494 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 15:59:04 -0700
Subject: [PATCH 006/161] submodule needs path not name

---
 git_setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/git_setup.py b/git_setup.py
index 82c044cff2..79ee8f5517 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -69,10 +69,11 @@ def submodule_checkout(name, url, path, tag, esmrequired):
     git = GitInterface(os.getcwd())
     topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
     repodir = os.path.join(topdir, path)
-    git.git_operation("submodule","update","--init", name)
+    git.git_operation("submodule","update","--init", path)
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir,".gitmodules")):
         # recursively handle this checkout
+        print(
         read_gitmodules_file(repodir, esmrequired)
     print(f"Successfully checked out {name}")
     return

From eed05bd0e63cd08b9d8d6d388cdfc65764ba8204 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 16:06:35 -0700
Subject: [PATCH 007/161] improve error checking

---
 git_setup.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index 79ee8f5517..fc3616c268 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -73,9 +73,11 @@ def submodule_checkout(name, url, path, tag, esmrequired):
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir,".gitmodules")):
         # recursively handle this checkout
-        print(
         read_gitmodules_file(repodir, esmrequired)
-    print(f"Successfully checked out {name}")
+    if os.path.exists(os.path.join(repodir,".git")):
+        print(f"Successfully checked out {name}")
+    else:
+        utils.fatal_error(f"Failed to checkout {name}")
     return
     
 def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):

From 20431710b064b0cf4876de54065a38d962facb23 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 16:14:05 -0700
Subject: [PATCH 008/161] add more logging

---
 git_setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/git_setup.py b/git_setup.py
index fc3616c268..daf4181df7 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -73,6 +73,7 @@ def submodule_checkout(name, url, path, tag, esmrequired):
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir,".gitmodules")):
         # recursively handle this checkout
+        print(f"Recursively checking out submodules of {name}")
         read_gitmodules_file(repodir, esmrequired)
     if os.path.exists(os.path.join(repodir,".git")):
         print(f"Successfully checked out {name}")

From 9c35b88bcf355d48a262e82d04daba36ed4071aa Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 16:34:46 -0700
Subject: [PATCH 009/161] submodule always usees shell

---
 modules/gitinterface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gitinterface.py b/modules/gitinterface.py
index baf98f35d8..2fc7a131bc 100644
--- a/modules/gitinterface.py
+++ b/modules/gitinterface.py
@@ -24,7 +24,7 @@ def __init__(self, repo_path):
                 
     def _git_command(self, operation, *args):
         logging.info(operation)
-        if self._use_module:
+        if self._use_module and operation != "submodule":
             return getattr(self.repo.git, operation)(*args)
         else:
             return ["git", "-C",self.repo_path, operation] + list(args)

From 8c5dfcdc0e7eba4cf369e15e40f19a68de42f6a5 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 16:42:31 -0700
Subject: [PATCH 010/161] fix toplevel

---
 git_setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/git_setup.py b/git_setup.py
index daf4181df7..c22fa1355f 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -67,7 +67,8 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
 
 def submodule_checkout(name, url, path, tag, esmrequired):
     git = GitInterface(os.getcwd())
-    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
+    topdir = os.getcwd()
+#    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
     repodir = os.path.join(topdir, path)
     git.git_operation("submodule","update","--init", path)
     # Look for a .gitmodules file in the newly checkedout repo

From d431e3b7cc23672a7cd081c795ee0607e17beb3b Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 16:44:33 -0700
Subject: [PATCH 011/161] fix toplevel

---
 git_setup.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index c22fa1355f..5355b21069 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -65,11 +65,10 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
     sprepo_git.git_operation( "checkout", tag)
     print(f"Successfully checked out {name}")
 
-def submodule_checkout(name, url, path, tag, esmrequired):
+def submodule_checkout(root, name, url, path, tag, esmrequired):
     git = GitInterface(os.getcwd())
-    topdir = os.getcwd()
 #    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
-    repodir = os.path.join(topdir, path)
+    repodir = os.path.join(root, path)
     git.git_operation("submodule","update","--init", path)
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir,".gitmodules")):
@@ -116,7 +115,7 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
         for setting in esmrequired:
             if setting.startswith("I:"):
                 Iesmrequired.append(setting) 
-        submodule_checkout(name, submodule_desc["url"], submodule_desc["path"], tag, Iesmrequired)
+        submodule_checkout(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag, Iesmrequired)
 
 
 

From b6ee263ce6ee009f40288275866f45b471b8b6c8 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 4 Jan 2024 16:48:32 -0700
Subject: [PATCH 012/161] try again

---
 git_setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/git_setup.py b/git_setup.py
index 5355b21069..3be8e3dfce 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -73,7 +73,7 @@ def submodule_checkout(root, name, url, path, tag, esmrequired):
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir,".gitmodules")):
         # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name}")
+        print(f"Recursively checking out submodules of {name} {repodir}")
         read_gitmodules_file(repodir, esmrequired)
     if os.path.exists(os.path.join(repodir,".git")):
         print(f"Successfully checked out {name}")

From 996dfb6323dfd25e93c3a55ed1efb18d1f0b148a Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 5 Jan 2024 09:04:48 -0700
Subject: [PATCH 013/161] add command line options and support for update

---
 git_setup.py | 190 ++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 159 insertions(+), 31 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index 3be8e3dfce..8361fe9a8c 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -1,12 +1,119 @@
 #!/usr/bin/env python
+import sys
 import os
 import shutil
 import logging
+import argparse
 from modules import utils
 from configparser import ConfigParser
 from modules.lstripreader import LstripReader
 from modules.gitinterface import GitInterface
 
+from contextlib import contextmanager
+
+
+@contextmanager
+def pushd(new_dir):
+    previous_dir = os.getcwd()
+    os.chdir(new_dir)
+    try:
+        yield
+    finally:
+        os.chdir(previous_dir)
+
+def commandline_arguments(args=None):
+    description = '''
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    '''
+    parser = argparse.ArgumentParser(
+        description=description, 
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    #
+    # user options
+    #
+    parser.add_argument("components", nargs="*",
+                        help="Specific component(s) to checkout. By default, "
+                        "all required submodules are checked out.")
+
+    parser.add_argument('-C', '--path', default=os.getcwd(),
+                        help='Toplevel repository directory.  Defaults to current directory.')
+
+    parser.add_argument('-x', '--exclude', nargs='*',
+                        help='Component(s) listed in the gitmodules file which should be ignored.')
+
+    parser.add_argument('-o', '--optional', action='store_true', default=False,
+                        help='By default only the required submodules '
+                        'are checked out. This flag will also checkout the '
+                        'optional submodules relative to the toplevel directory.')
+
+    parser.add_argument('-S', '--status', action='store_true', default=False,
+                        help='Output the status of the repositories managed by '
+                        '%(prog)s. By default only summary information '
+                        'is provided. Use the verbose option to see details.')
+
+    parser.add_argument('-u', '--update', action='store_true', default=False,
+                        help='Update submodules to the tags defined in .gitmodules.')
+
+    parser.add_argument('-v', '--verbose', action='count', default=0,
+                        help='Output additional information to '
+                        'the screen and log file. This flag can be '
+                        'used up to two times, increasing the '
+                        'verbosity level each time.')
+
+    parser.add_argument('-V', '--version', action='store_true', default=False,
+                        help='Print manage_externals version and exit.')
+
+    #
+    # developer options
+    #
+    parser.add_argument('--backtrace', action='store_true',
+                        help='DEVELOPER: show exception backtraces as extra '
+                        'debugging output')
+
+    parser.add_argument('-d', '--debug', action='store_true', default=False,
+                        help='DEVELOPER: output additional debugging '
+                        'information to the screen and log file.')
+
+    logging_group = parser.add_mutually_exclusive_group()
+
+    logging_group.add_argument('--logging', dest='do_logging',
+                               action='store_true',
+                               help='DEVELOPER: enable logging.')
+    logging_group.add_argument('--no-logging', dest='do_logging',
+                               action='store_false', default=False,
+                               help='DEVELOPER: disable logging '
+                               '(this is the default)')
+    if args:
+        options = parser.parse_args(args)
+    else:
+        options = parser.parse_args()
+
+    if options.optional:
+        esmrequired = 'T:'
+    else:
+        esmrequired = 'T:T'
+        
+    if options.status:
+        action = 'status'
+    elif options.update:
+        action = 'update'
+    else:
+        action = 'install'
+
+    if options.version:
+        version_info = ''
+        version_file_path = os.path.join(os.path.dirname(__file__),'version.txt')
+        with open(version_file_path) as f:
+            version_info = f.readlines()[0].strip()
+        print(version_info)
+        sys.exit(0)
+
+
+        
+    return options.rootdir, esmrequired, options.components, options.exclude, options.verbose, action
+
+        
 def parse_submodules_desc_section(section, section_items):
     """Create a dict for this submodule description"""
     desc = {}
@@ -66,8 +173,7 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
     print(f"Successfully checked out {name}")
 
 def submodule_checkout(root, name, url, path, tag, esmrequired):
-    git = GitInterface(os.getcwd())
-#    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
+    git = GitInterface(root)
     repodir = os.path.join(root, path)
     git.git_operation("submodule","update","--init", path)
     # Look for a .gitmodules file in the newly checkedout repo
@@ -80,15 +186,26 @@ def submodule_checkout(root, name, url, path, tag, esmrequired):
     else:
         utils.fatal_error(f"Failed to checkout {name}")
     return
-    
-def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
+
+def submodule_update(root_dir, url, tag):
+    with pushd(root_dir):
+        git = GitInterface(root_dir)
+        # first make sure the url is correct
+        upstream = git.git_operation("ls-remote","--git-url")
+        if upstream != url:
+            # TODO - this needs to be a unique name
+            git.git_operation("remote","add","newbranch",url)
+        git.git_operation("checkout", tag)
+
+
+def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", gitmodulelist=None, action='install'):
     root_dir = os.path.abspath(root_dir)
 
     msg = 'In directory : {0}'.format(root_dir)
     logging.info(msg)
 
     file_path = os.path.join(root_dir, file_name)
-    if not os.path.exists(file_name):
+    if not os.path.exists(file_path):
         msg = ('ERROR: submodules description file, "{0}", does not '
                'exist in dir:\n    {1}'.format(file_name, root_dir))
         utils.fatal_error(msg)
@@ -97,31 +214,42 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules"):
     for section in config.sections():
         name = section[11:-1]
         submodule_desc = parse_submodules_desc_section(section,config.items(section))
-        if submodule_desc["esmrequired"] not in esmrequired:
-            if "T:F" in esmrequired or submodule_desc["esmrequired"].startswith("I:"):
-                print(f"Skipping optional component {section}")
-                # TODO change to logging
-                #                logging.info(f"Skipping optional component {section}")
-            continue
-        if "esmtag" in submodule_desc:
-            tag = submodule_desc["esmtag"]
-        else:
-            tag = "master"
-        if "esmsparse" in submodule_desc:
-            submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
-                                      submodule_desc["esmsparse"], tag)
-            continue
-        Iesmrequired = []
-        for setting in esmrequired:
-            if setting.startswith("I:"):
-                Iesmrequired.append(setting) 
-        submodule_checkout(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag, Iesmrequired)
-
-
-
-
-esmrequired = ("I:T", "T:T")
-root_dir = os.getcwd()
-gitmodules = read_gitmodules_file(root_dir, esmrequired)
 
+        if action == 'install':
+            # Recursively install submodules, honering esm tags in .gitmodules
+            if submodule_desc["esmrequired"] not in esmrequired:
+                if "T:F" in esmrequired or submodule_desc["esmrequired"].startswith("I:"):
+                    print(f"Skipping optional component {section}")
+                    # TODO change to logging
+                    #                logging.info(f"Skipping optional component {section}")
+                    continue
+            if "esmtag" in submodule_desc:
+                tag = submodule_desc["esmtag"]
+            else:
+                tag = "master"
+            if "esmsparse" in submodule_desc:
+                submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
+                                          submodule_desc["esmsparse"], tag)
+                continue
+            Iesmrequired = []
+            for setting in esmrequired:
+                if setting.startswith("I:"):
+                    Iesmrequired.append(setting) 
+                submodule_checkout(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag, Iesmrequired)
+
+        if action == 'update':
+            # update the submodules to the tags defined in .gitmodules
+            if "esmtag" in submodule_desc:
+                submod_dir = os.path.join(root_dir,submodule_desc['path'])
+                if os.path.exists(os.path.join(submod_dir,".git")):
+                    submodule_update(submod_dir, submodule_desc['url'], submodule_desc["esmtag"])
+
+                
+                
+
+if __name__ == '__main__':
+    root_dir, esmrequired, includelist, excludelist, verbose, action = commandline_arguments()
+    esmrequired = ("I:T", "T:T")
+    root_dir = os.getcwd()
+    read_gitmodules_file(root_dir, esmrequired, gitmodulelist, action, verbose)
     

From 647a8deea48c13ad9dbbb55fbcf294ff6eec6546 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 5 Jan 2024 10:23:07 -0700
Subject: [PATCH 014/161] fix new issues

---
 git_setup.py | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index 8361fe9a8c..82100a09c5 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -39,6 +39,11 @@ def commandline_arguments(args=None):
     parser.add_argument('-C', '--path', default=os.getcwd(),
                         help='Toplevel repository directory.  Defaults to current directory.')
 
+    parser.add_argument('-g', '--gitmodules', nargs='?',
+                        default='.gitmodules',
+                        help='The submodule description filename. '
+                        'Default: %(default)s.')
+
     parser.add_argument('-x', '--exclude', nargs='*',
                         help='Component(s) listed in the gitmodules file which should be ignored.')
 
@@ -109,9 +114,7 @@ def commandline_arguments(args=None):
         print(version_info)
         sys.exit(0)
 
-
-        
-    return options.rootdir, esmrequired, options.components, options.exclude, options.verbose, action
+    return options.path, options.gitmodules, esmrequired, options.components, options.exclude, options.verbose, action
 
         
 def parse_submodules_desc_section(section, section_items):
@@ -191,14 +194,15 @@ def submodule_update(root_dir, url, tag):
     with pushd(root_dir):
         git = GitInterface(root_dir)
         # first make sure the url is correct
-        upstream = git.git_operation("ls-remote","--git-url")
+        upstream = git.git_operation("ls-remote","--get-url").rstrip()
+        print(f"Here {upstream} and {url}")
         if upstream != url:
             # TODO - this needs to be a unique name
             git.git_operation("remote","add","newbranch",url)
         git.git_operation("checkout", tag)
 
 
-def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", gitmodulelist=None, action='install'):
+def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", includelist=None, excludelist=None, action='install'):
     root_dir = os.path.abspath(root_dir)
 
     msg = 'In directory : {0}'.format(root_dir)
@@ -213,6 +217,10 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", gitmodu
     config.read_file(LstripReader(file_path), source=file_name)
     for section in config.sections():
         name = section[11:-1]
+        if includelist and name not in includelist:
+            continue
+        if excludelist and name in excludelist:
+            continue
         submodule_desc = parse_submodules_desc_section(section,config.items(section))
 
         if action == 'install':
@@ -248,8 +256,6 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", gitmodu
                 
 
 if __name__ == '__main__':
-    root_dir, esmrequired, includelist, excludelist, verbose, action = commandline_arguments()
-    esmrequired = ("I:T", "T:T")
-    root_dir = os.getcwd()
-    read_gitmodules_file(root_dir, esmrequired, gitmodulelist, action, verbose)
+    root_dir, file_name, esmrequired, includelist, excludelist, verbose, action = commandline_arguments()
+    read_gitmodules_file(root_dir, file_name=file_name, esmrequired=esmrequired, includelist=includelist, excludelist=excludelist, action=action)
     

From fbb8eaf70bd134f8ec5de662294f033c1d18b8ed Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 5 Jan 2024 10:44:48 -0700
Subject: [PATCH 015/161] update esmrequired variable

---
 git_setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index 82100a09c5..baacdb3d7b 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -95,9 +95,9 @@ def commandline_arguments(args=None):
         options = parser.parse_args()
 
     if options.optional:
-        esmrequired = 'T:'
+        esmrequired = ('T:T','T:F','I:T')
     else:
-        esmrequired = 'T:T'
+        esmrequired = ('T:T','I:T')
         
     if options.status:
         action = 'status'

From e22d95b589470d1d4f93970951b555b1fdfa7462 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 5 Jan 2024 11:34:38 -0700
Subject: [PATCH 016/161] fix recursive issue

---
 git_setup.py            | 19 +++++++------------
 modules/gitinterface.py |  1 -
 2 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index baacdb3d7b..d8b0275348 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -183,7 +183,7 @@ def submodule_checkout(root, name, url, path, tag, esmrequired):
     if os.path.exists(os.path.join(repodir,".gitmodules")):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir}")
-        read_gitmodules_file(repodir, esmrequired)
+        read_gitmodules_file(repodir, ("I:T"))
     if os.path.exists(os.path.join(repodir,".git")):
         print(f"Successfully checked out {name}")
     else:
@@ -195,7 +195,6 @@ def submodule_update(root_dir, url, tag):
         git = GitInterface(root_dir)
         # first make sure the url is correct
         upstream = git.git_operation("ls-remote","--get-url").rstrip()
-        print(f"Here {upstream} and {url}")
         if upstream != url:
             # TODO - this needs to be a unique name
             git.git_operation("remote","add","newbranch",url)
@@ -226,11 +225,10 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", include
         if action == 'install':
             # Recursively install submodules, honering esm tags in .gitmodules
             if submodule_desc["esmrequired"] not in esmrequired:
-                if "T:F" in esmrequired or submodule_desc["esmrequired"].startswith("I:"):
-                    print(f"Skipping optional component {section}")
-                    # TODO change to logging
-                    #                logging.info(f"Skipping optional component {section}")
-                    continue
+                print(f"Skipping optional component {section}")
+                # TODO change to logging
+                #                logging.info(f"Skipping optional component {section}")
+                continue
             if "esmtag" in submodule_desc:
                 tag = submodule_desc["esmtag"]
             else:
@@ -239,11 +237,8 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", include
                 submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
                                           submodule_desc["esmsparse"], tag)
                 continue
-            Iesmrequired = []
-            for setting in esmrequired:
-                if setting.startswith("I:"):
-                    Iesmrequired.append(setting) 
-                submodule_checkout(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag, Iesmrequired)
+            
+            submodule_checkout(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag, esmrequired)
 
         if action == 'update':
             # update the submodules to the tags defined in .gitmodules
diff --git a/modules/gitinterface.py b/modules/gitinterface.py
index 2fc7a131bc..a4e2529256 100644
--- a/modules/gitinterface.py
+++ b/modules/gitinterface.py
@@ -40,7 +40,6 @@ def _init_git_repo(self):
     def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *args)
         if isinstance(command, list):
-            print(command)
             return utils.execute_subprocess(command, output_to_caller=True)
         else:
             return command

From 99d5439757f52b01fa0ae9f0924c472b255083eb Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 5 Jan 2024 13:52:33 -0700
Subject: [PATCH 017/161] add status flag support

---
 git_setup.py | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/git_setup.py b/git_setup.py
index d8b0275348..f5334faef9 100644
--- a/git_setup.py
+++ b/git_setup.py
@@ -200,7 +200,17 @@ def submodule_update(root_dir, url, tag):
             git.git_operation("remote","add","newbranch",url)
         git.git_operation("checkout", tag)
 
-
+def submodule_status(root_dir, name, url, path, tag):
+    with pushd(path):
+        git = GitInterface(os.path.join(root_dir,path))
+        atag = git.git_operation("describe","--tags","--always").rstrip()
+        if tag and atag != tag:
+            print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
+        elif tag:
+            print(f"Submodule {name} at tag {tag}")
+        else:
+            print(f"Submodule {name} has no tag defined in .gitmodules")
+            
 def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", includelist=None, excludelist=None, action='install'):
     root_dir = os.path.abspath(root_dir)
 
@@ -222,10 +232,19 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", include
             continue
         submodule_desc = parse_submodules_desc_section(section,config.items(section))
 
+        if action == 'status':
+            if "esmtag" in submodule_desc:
+                tag = submodule_desc["esmtag"]
+            else:
+                tag = None
+            submodule_status(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag)
+        
+        
         if action == 'install':
             # Recursively install submodules, honering esm tags in .gitmodules
             if submodule_desc["esmrequired"] not in esmrequired:
-                print(f"Skipping optional component {section}")
+                if 'T:F' in submodule_desc["esmrequired"]:
+                    print(f"Skipping optional component {section}")
                 # TODO change to logging
                 #                logging.info(f"Skipping optional component {section}")
                 continue
@@ -252,5 +271,6 @@ def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", include
 
 if __name__ == '__main__':
     root_dir, file_name, esmrequired, includelist, excludelist, verbose, action = commandline_arguments()
+    print(f"action is {action}")
     read_gitmodules_file(root_dir, file_name=file_name, esmrequired=esmrequired, includelist=includelist, excludelist=excludelist, action=action)
     

From 671bb1df07b611db05947f63572e38c2f6286a9a Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 09:28:06 -0700
Subject: [PATCH 018/161] add a gitmodules class

---
 git-fleximod.py       | 302 ++++++++++++++++++++++++++++++++++++++++++
 git_setup             |  94 -------------
 git_setup.py          | 276 --------------------------------------
 git_sparse_checkout   |  75 -----------
 modules/gitmodules.py |  53 ++++++++
 modules/utils.py      | 137 +++++++++++--------
 show-tags             |  20 ---
 7 files changed, 437 insertions(+), 520 deletions(-)
 create mode 100644 git-fleximod.py
 delete mode 100755 git_setup
 delete mode 100644 git_setup.py
 delete mode 100755 git_sparse_checkout
 create mode 100644 modules/gitmodules.py
 delete mode 100755 show-tags

diff --git a/git-fleximod.py b/git-fleximod.py
new file mode 100644
index 0000000000..ded13eb9db
--- /dev/null
+++ b/git-fleximod.py
@@ -0,0 +1,302 @@
+#!/usr/bin/env python
+import sys
+import os
+import shutil
+import logging
+import argparse
+from modules import utils
+from modules.gitinterface import GitInterface
+from modules.gitmodules import GitModules
+
+
+def commandline_arguments(args=None):
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=os.getcwd(),
+        help="Toplevel repository directory.  Defaults to current directory.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-S",
+        "--status",
+        action="store_true",
+        default=False,
+        help="Output the status of the repositories managed by "
+        "%(prog)s. By default only summary information "
+        "is provided. Use the verbose option to see details.",
+    )
+
+    parser.add_argument(
+        "-u",
+        "--update",
+        action="store_true",
+        default=False,
+        help="Update submodules to the tags defined in .gitmodules.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="store_true",
+        default=False,
+        help="Print manage_externals version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    logging_group = parser.add_mutually_exclusive_group()
+
+    logging_group.add_argument(
+        "--logging",
+        dest="do_logging",
+        action="store_true",
+        help="DEVELOPER: enable logging.",
+    )
+    logging_group.add_argument(
+        "--no-logging",
+        dest="do_logging",
+        action="store_false",
+        default=False,
+        help="DEVELOPER: disable logging " "(this is the default)",
+    )
+    if args:
+        options = parser.parse_args(args)
+    else:
+        options = parser.parse_args()
+
+    if options.optional:
+        esmrequired = ("T:T", "T:F", "I:T")
+    else:
+        esmrequired = ("T:T", "I:T")
+
+    if options.status:
+        action = "status"
+    elif options.update:
+        action = "update"
+    else:
+        action = "install"
+
+    if options.version:
+        version_info = ""
+        version_file_path = os.path.join(os.path.dirname(__file__), "version.txt")
+        with open(version_file_path) as f:
+            version_info = f.readlines()[0].strip()
+        print(version_info)
+        sys.exit(0)
+
+    return (
+        options.path,
+        options.gitmodules,
+        esmrequired,
+        options.components,
+        options.exclude,
+        options.verbose,
+        action,
+    )
+
+
+def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
+    # first create the module directory
+    if not os.path.isdir(path):
+        os.makedirs(path)
+    # Check first if the module is already defined
+    # and the sparse-checkout file exists
+    git = GitInterface(os.getcwd())
+    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
+
+    topgit = os.path.join(topdir, ".git", "modules")
+    gitsparse = os.path.join(topgit, name, "info", "sparse-checkout")
+    if os.path.isfile(gitsparse):
+        logging.warning("submodule {} is already initialized".format(name))
+        return
+
+    # initialize a new git repo and set the sparse checkout flag
+    sprepo_git = GitInterface(os.path.join(topdir, path))
+    sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
+    # set the repository remote
+    sprepo_git.git_operation("remote", "add", "origin", url)
+
+    if not os.path.isdir(topgit):
+        os.makedirs(topgit)
+    topgit = os.path.join(topgit, name)
+
+    shutil.move(os.path.join(path, ".git"), topgit)
+
+    shutil.copy(os.path.join(path, sparsefile), gitsparse)
+
+    with open(os.path.join(path, ".git"), "w") as f:
+        f.write("gitdir: " + os.path.relpath(topgit, path))
+
+    # Finally checkout the repo
+    sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
+    sprepo_git.git_operation("checkout", tag)
+    print(f"Successfully checked out {name}")
+
+
+def submodule_checkout(root, name, path):
+    git = GitInterface(root)
+    repodir = os.path.join(root, path)
+    git.git_operation("submodule", "update", "--init", path)
+    # Look for a .gitmodules file in the newly checkedout repo
+    if os.path.exists(os.path.join(repodir, ".gitmodules")):
+        # recursively handle this checkout
+        print(f"Recursively checking out submodules of {name} {repodir}")
+        gitmodules = GitModules(repodir)
+        submodules_install(gitmodules, repodir, ("I:T"))
+    if os.path.exists(os.path.join(repodir, ".git")):
+        print(f"Successfully checked out {name}")
+    else:
+        utils.fatal_error(f"Failed to checkout {name}")
+    return
+
+
+def submodules_status(gitmodules, root_dir):
+    for name in gitmodules.sections():
+        path = gitmodules.get(name, "path")
+        tag = gitmodules.git(name, "esmtag")
+        with utils.pushd(path):
+            git = GitInterface(os.path.join(root_dir, path))
+            atag = git.git_operation("describe", "--tags", "--always").rstrip()
+            if tag and atag != tag:
+                print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
+            elif tag:
+                print(f"Submodule {name} at tag {tag}")
+            else:
+                print(f"Submodule {name} has no tag defined in .gitmodules")
+
+
+def submodules_update(gitmodules, root_dir):
+    for name in gitmodules.sections():
+        esmtag = gitmodules.get(name, "esmtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        if os.path.exists(os.path.join(path, ".git")):
+            with utils.pushd(root_dir):
+                git = GitInterface(root_dir)
+                # first make sure the url is correct
+                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
+                if upstream != url:
+                    # TODO - this needs to be a unique name
+                    git.git_operation("remote", "add", "newbranch", url)
+                    git.git_operation("checkout", esmtag)
+
+
+def submodules_install(gitmodules, root_dir, requiredlist):
+    for name in gitmodules.sections():
+        esmrequired = gitmodules.get(name, "esmrequired")
+        esmsparse = gitmodules.get(name, "esmsparse")
+        esmtag = gitmodules.get(name, "esmtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        if esmrequired not in requiredlist:
+            if "T:F" in esmrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+        if esmsparse:
+            submodule_sparse_checkout(name, url, path, esmsparse, tag=esmtag)
+        else:
+            submodule_checkout(root_dir, name, path)
+
+
+def _main_func():
+    (
+        root_dir,
+        file_name,
+        esmrequired,
+        includelist,
+        excludelist,
+        verbose,
+        action,
+    ) = commandline_arguments()
+    if verbose:
+        print(f"action is {action}")
+    gitmodules = GitModules(
+        confpath=root_dir,
+        conffile=file_name,
+        includelist=includelist,
+        excludelist=excludelist,
+    )
+
+    if action == "update":
+        submodules_update(gitmodules, root_dir)
+    elif action == "install":
+        submodules_install(gitmodules, root_dir, esmrequired)
+    elif action == "status":
+        submodules_status(gitmodules, root_dir)
+    else:
+        utils.fatal_error(f"unrecognized action request {action}")
+
+
+if __name__ == "__main__":
+    _main_func()
diff --git a/git_setup b/git_setup
deleted file mode 100755
index a5b27b13f6..0000000000
--- a/git_setup
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/bin/bash
-# Script to fetch submodules for esm applications 
-# if argument -internal-only is supplied then only checkout internal submodules, otherwise checkout everything needed for
-# a top level repository
-#
-set -e
-script=$0
-function usage {
-    echo -e "\nusage: $script [-i/--internal-only]\n"
-}
-# Set default arguments
-internal_only=0
-
-# Process arguments
-while [ "$1" != "" ];
-do
-    case $1 in
-
-        # Only checkout CISM internal submodules
-        -i | -internal-only | --internal-only)
-            internal_only=1
-            ;;
-
-        *)
-            echo "$script: illegal option $1"
-            usage
-            exit 1
-            ;;
-    esac
-    shift
-done
-
-########################
-declare -A submods
-submod_list=$(git config -f .gitmodules --list)
-
-while IFS= read -r line;
-do
-    readarray -d. -t strarr <<< "$line" 
-    if [[ "strarr[3]" == "path" ]]; then
-        echo "path is $strarr[4]"
-    fi
-done <<< "$submod_list"
-exit 0
-
-# Start with sparse checkouts
-if ! test -f bin/git_sparse_checkout; then
-  echo "Getting git_sparse_checkout script"
-  git clone https://github.com/jedwards4b/gitscripts --depth 1 bin
-fi
-
-./bin/git_sparse_checkout  https://github.com/larson-group/clubb_release clubb_4ncar_20221129_59cb19f_branch src/physics/clubb -- src/CLUBB_core/ src/SILHS/
-git restore src/physics/clubb
-
-./bin/git_sparse_checkout https://github.com/CFMIP/COSPv2.0 master src/physics/cosp2/src -- src/
-git restore src/physics/cosp2/src
-
-./bin/git_sparse_checkout https://github.com/MPAS-Dev/MPAS-Model.git develop src/dynamics/mpas/dycore -- src/external/ src/operators/ src/tools/ \
-                      src/core_atmosphere/ src/framework/
-git restore src/dynamics/mpas/dycore
-
-submodules=('chem_proc' 'src/physics/carma/base' 'src/physics/pumas' 'src/physics/pumas-frozen' 'src/physics/ali_arms' 'src/atmos_phys' 'src/dynamics/fv3/atmos_cubed_sphere' 'src/hemco')
-for mod in "${submodules[@]}"
-do
-   echo "Initializing $mod"
-   git submodule update --init $mod
-done
-
-if [ ${internal_only} -eq 1 ]
-  then
-    exit 0
-fi
-
-
-submodules=('ccs_config' 'components/cice5' 'components/cice' 'components/cmeps' \
-           'components/cdeps' 'components/cpl7' 'share' 'libraries/mct' \
-           'libraries/parallelio' 'cime' 'libraries/FMS' 'components/mosart' \
-           'components/rtm')
-
-for mod in "${submodules[@]}"
-do
-   echo "Initializing $mod"
-   git submodule update --init --recursive $mod
-done
-
-sparse_submodules=('components/clm' 'components/cism')
-for mod in "${sparse_submodules[@]}"
-do
-   echo "Initializing $mod"
-   git submodule update --init $mod
-   pushd $mod 1>/dev/null
-   bash ./install -internal-only
-   popd 1>/dev/null
-done
diff --git a/git_setup.py b/git_setup.py
deleted file mode 100644
index f5334faef9..0000000000
--- a/git_setup.py
+++ /dev/null
@@ -1,276 +0,0 @@
-#!/usr/bin/env python
-import sys
-import os
-import shutil
-import logging
-import argparse
-from modules import utils
-from configparser import ConfigParser
-from modules.lstripreader import LstripReader
-from modules.gitinterface import GitInterface
-
-from contextlib import contextmanager
-
-
-@contextmanager
-def pushd(new_dir):
-    previous_dir = os.getcwd()
-    os.chdir(new_dir)
-    try:
-        yield
-    finally:
-        os.chdir(previous_dir)
-
-def commandline_arguments(args=None):
-    description = '''
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    '''
-    parser = argparse.ArgumentParser(
-        description=description, 
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-
-    #
-    # user options
-    #
-    parser.add_argument("components", nargs="*",
-                        help="Specific component(s) to checkout. By default, "
-                        "all required submodules are checked out.")
-
-    parser.add_argument('-C', '--path', default=os.getcwd(),
-                        help='Toplevel repository directory.  Defaults to current directory.')
-
-    parser.add_argument('-g', '--gitmodules', nargs='?',
-                        default='.gitmodules',
-                        help='The submodule description filename. '
-                        'Default: %(default)s.')
-
-    parser.add_argument('-x', '--exclude', nargs='*',
-                        help='Component(s) listed in the gitmodules file which should be ignored.')
-
-    parser.add_argument('-o', '--optional', action='store_true', default=False,
-                        help='By default only the required submodules '
-                        'are checked out. This flag will also checkout the '
-                        'optional submodules relative to the toplevel directory.')
-
-    parser.add_argument('-S', '--status', action='store_true', default=False,
-                        help='Output the status of the repositories managed by '
-                        '%(prog)s. By default only summary information '
-                        'is provided. Use the verbose option to see details.')
-
-    parser.add_argument('-u', '--update', action='store_true', default=False,
-                        help='Update submodules to the tags defined in .gitmodules.')
-
-    parser.add_argument('-v', '--verbose', action='count', default=0,
-                        help='Output additional information to '
-                        'the screen and log file. This flag can be '
-                        'used up to two times, increasing the '
-                        'verbosity level each time.')
-
-    parser.add_argument('-V', '--version', action='store_true', default=False,
-                        help='Print manage_externals version and exit.')
-
-    #
-    # developer options
-    #
-    parser.add_argument('--backtrace', action='store_true',
-                        help='DEVELOPER: show exception backtraces as extra '
-                        'debugging output')
-
-    parser.add_argument('-d', '--debug', action='store_true', default=False,
-                        help='DEVELOPER: output additional debugging '
-                        'information to the screen and log file.')
-
-    logging_group = parser.add_mutually_exclusive_group()
-
-    logging_group.add_argument('--logging', dest='do_logging',
-                               action='store_true',
-                               help='DEVELOPER: enable logging.')
-    logging_group.add_argument('--no-logging', dest='do_logging',
-                               action='store_false', default=False,
-                               help='DEVELOPER: disable logging '
-                               '(this is the default)')
-    if args:
-        options = parser.parse_args(args)
-    else:
-        options = parser.parse_args()
-
-    if options.optional:
-        esmrequired = ('T:T','T:F','I:T')
-    else:
-        esmrequired = ('T:T','I:T')
-        
-    if options.status:
-        action = 'status'
-    elif options.update:
-        action = 'update'
-    else:
-        action = 'install'
-
-    if options.version:
-        version_info = ''
-        version_file_path = os.path.join(os.path.dirname(__file__),'version.txt')
-        with open(version_file_path) as f:
-            version_info = f.readlines()[0].strip()
-        print(version_info)
-        sys.exit(0)
-
-    return options.path, options.gitmodules, esmrequired, options.components, options.exclude, options.verbose, action
-
-        
-def parse_submodules_desc_section(section, section_items):
-    """Create a dict for this submodule description"""
-    desc = {}
-    esmrequired_options = ("T:T", "I:T", "I:F", "T:F")
-    for item in section_items:
-        name = item[0].strip().lower()
-        desc[name] = item[1].strip()
-        # e3sm needs to have ssh protocol urls, we don't
-        if name == "url" and desc[name].startswith("git@github"):
-            desc[name] = desc[name].replace("git@github.com:","https://github.com/")
-    if not "esmrequired" in desc:
-        desc["esmrequired"] = "I:T"
-    
-    if desc["esmrequired"] not in esmrequired_options:
-        val = desc["esmrequired"]
-        utils.fatal_error(f"esmrequired set to {val} which is not a supported option {esmrequired_options}")
-    return desc
-
-
-def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
-    # first create the module directory
-    if not os.path.isdir(path):
-        os.makedirs(path)
-    # Check first if the module is already defined
-    # and the sparse-checkout file exists
-    git = GitInterface(os.getcwd())
-    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
-
-    topgit = os.path.join(topdir, ".git", "modules")
-    gitsparse = os.path.join(topgit, name, "info","sparse-checkout")
-    if os.path.isfile(gitsparse):
-        logging.warning(f"submodule {name} is already initialized")
-        return
-    
-    #initialize a new git repo and set the sparse checkout flag
-    sprepo_git = GitInterface(os.path.join(topdir,path))
-    sprepo_git.config_set_value("core", "sparseCheckout", "true")
-
-    # set the repository remote
-    cmd = ("remote", "add", "origin", url)
-    sprepo_git.git_operation("remote", "add", "origin", url)
-    
-    if not os.path.isdir(topgit):
-        os.makedirs(topgit)
-    topgit = os.path.join(topgit,name)
-    
-    shutil.move(os.path.join(path, ".git"), topgit)
-
-    shutil.copy(os.path.join(path,sparsefile), gitsparse)
-        
-    with open(os.path.join(path, ".git"), "w") as f:
-        f.write("gitdir: " + os.path.relpath(topgit, path))
-
-    #Finally checkout the repo
-    sprepo_git.git_operation( "fetch", "--depth=1", "origin", "--tags")
-    sprepo_git.git_operation( "checkout", tag)
-    print(f"Successfully checked out {name}")
-
-def submodule_checkout(root, name, url, path, tag, esmrequired):
-    git = GitInterface(root)
-    repodir = os.path.join(root, path)
-    git.git_operation("submodule","update","--init", path)
-    # Look for a .gitmodules file in the newly checkedout repo
-    if os.path.exists(os.path.join(repodir,".gitmodules")):
-        # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name} {repodir}")
-        read_gitmodules_file(repodir, ("I:T"))
-    if os.path.exists(os.path.join(repodir,".git")):
-        print(f"Successfully checked out {name}")
-    else:
-        utils.fatal_error(f"Failed to checkout {name}")
-    return
-
-def submodule_update(root_dir, url, tag):
-    with pushd(root_dir):
-        git = GitInterface(root_dir)
-        # first make sure the url is correct
-        upstream = git.git_operation("ls-remote","--get-url").rstrip()
-        if upstream != url:
-            # TODO - this needs to be a unique name
-            git.git_operation("remote","add","newbranch",url)
-        git.git_operation("checkout", tag)
-
-def submodule_status(root_dir, name, url, path, tag):
-    with pushd(path):
-        git = GitInterface(os.path.join(root_dir,path))
-        atag = git.git_operation("describe","--tags","--always").rstrip()
-        if tag and atag != tag:
-            print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
-        elif tag:
-            print(f"Submodule {name} at tag {tag}")
-        else:
-            print(f"Submodule {name} has no tag defined in .gitmodules")
-            
-def read_gitmodules_file(root_dir, esmrequired, file_name=".gitmodules", includelist=None, excludelist=None, action='install'):
-    root_dir = os.path.abspath(root_dir)
-
-    msg = 'In directory : {0}'.format(root_dir)
-    logging.info(msg)
-
-    file_path = os.path.join(root_dir, file_name)
-    if not os.path.exists(file_path):
-        msg = ('ERROR: submodules description file, "{0}", does not '
-               'exist in dir:\n    {1}'.format(file_name, root_dir))
-        utils.fatal_error(msg)
-    config = ConfigParser()
-    config.read_file(LstripReader(file_path), source=file_name)
-    for section in config.sections():
-        name = section[11:-1]
-        if includelist and name not in includelist:
-            continue
-        if excludelist and name in excludelist:
-            continue
-        submodule_desc = parse_submodules_desc_section(section,config.items(section))
-
-        if action == 'status':
-            if "esmtag" in submodule_desc:
-                tag = submodule_desc["esmtag"]
-            else:
-                tag = None
-            submodule_status(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag)
-        
-        
-        if action == 'install':
-            # Recursively install submodules, honering esm tags in .gitmodules
-            if submodule_desc["esmrequired"] not in esmrequired:
-                if 'T:F' in submodule_desc["esmrequired"]:
-                    print(f"Skipping optional component {section}")
-                # TODO change to logging
-                #                logging.info(f"Skipping optional component {section}")
-                continue
-            if "esmtag" in submodule_desc:
-                tag = submodule_desc["esmtag"]
-            else:
-                tag = "master"
-            if "esmsparse" in submodule_desc:
-                submodule_sparse_checkout(name, submodule_desc["url"], submodule_desc["path"],
-                                          submodule_desc["esmsparse"], tag)
-                continue
-            
-            submodule_checkout(root_dir, name, submodule_desc["url"], submodule_desc["path"], tag, esmrequired)
-
-        if action == 'update':
-            # update the submodules to the tags defined in .gitmodules
-            if "esmtag" in submodule_desc:
-                submod_dir = os.path.join(root_dir,submodule_desc['path'])
-                if os.path.exists(os.path.join(submod_dir,".git")):
-                    submodule_update(submod_dir, submodule_desc['url'], submodule_desc["esmtag"])
-
-                
-                
-
-if __name__ == '__main__':
-    root_dir, file_name, esmrequired, includelist, excludelist, verbose, action = commandline_arguments()
-    print(f"action is {action}")
-    read_gitmodules_file(root_dir, file_name=file_name, esmrequired=esmrequired, includelist=includelist, excludelist=excludelist, action=action)
-    
diff --git a/git_sparse_checkout b/git_sparse_checkout
deleted file mode 100755
index 9b52bb29a7..0000000000
--- a/git_sparse_checkout
+++ /dev/null
@@ -1,75 +0,0 @@
-#!/bin/bash -eu
-
-# see also: git_origin and git_clone
-
-function git_sparse_checkout {
-    local self=$(readlink -f "${BASH_SOURCE[0]}")
-    local app=$(basename $self)
-    local usage=\
-"USAGE: ${app} repository-URL [branch] [project-directory] [[--] [list-of-files-or-directories]]
-  where:
-    'repository-URL' is a valid URL pointing to a Git repository.
-    'branch' is a branch, atag or a commit id. Default: master.
-    'project-directory' is a folder to be created and populated. Default: the project name.
-    'list-of-files-or-directories' is a list of file names or directories separated by spaces.
-  Examples:
-    ${app} http://github.com/frgomes/bash-scripts -- README.md
-    ${app} http://github.com/frgomes/bash-scripts develop -- README.md bin/
-    ${app} http://github.com/frgomes/bash-scripts develop tmpdir -- README.md bin/ docs/"
-
-    # obtain repository-URL, e.g.: http://github.com/frgomes/bash-scripts
-    [[ $# != 0 ]] || (echo "${usage}" 1>&2 ; return 1)
-    local arg=${1}
-    [[ "${arg}" != "--" ]] || (echo "${usage}" 1>&2 ; return 1)
-    local url="${arg}"
-    [[ $# == 0 ]] || shift
-
-    # obtain branch, which the default is master for historical reasons
-    if [[ "${arg}" != "--" ]] ;then arg="${1:-master}" ;fi
-    if [[ "${arg}" == "--" ]] ;then
-      local tag=master
-    else
-      local tag="${arg}"
-      [[ $# == 0 ]] || shift
-    fi
-
-    # obtain the project directory, which defaults to the repository name
-    local prj=$(echo "$url" | sed 's:/:\n:g' | tail -1)
-
-    if [[ "${arg}" != "--" ]] ;then arg="${1:-.}" ;fi
-    if [[ "${arg}" == "--" || "${arg}" == "." ]] ;then
-      local dir=$(readlink -f "./${prj}")
-    else
-      local dir=$(readlink -f "${arg}")
-      [[ $# == 0 ]] || shift
-    fi
-
-    if [[ "${arg}" == "--" ]] ;then [[ $# == 0 ]] || shift; fi
-    if [[ "${1:-}" == "--" ]] ;then [[ $# == 0 ]] || shift; fi
-
-    # Note: any remaining arguments after these above are considered as a
-    # list of files or directories to be downloaded. Names of directories
-    # must be followed by a slash /.
-
-    local sparse=true
-    local opts='--depth=1'
-
-    # now perform the sparse checkout
-    
-    mkdir -p "${dir}"
-    git -C "${dir}" init
-    git -C "${dir}" config core.sparseCheckout ${sparse}
-    git -C "${dir}" remote add origin ${url}
-    super=$(git rev-parse --show-toplevel)
-    pathtodotgit=$(realpath -m --relative-to=${dir} ${super})/.git
-    relpathfromsuper=$(realpath -m --relative-to=${super} ${dir})
-    mv ${dir}/.git  ${super}/.git/modules/${relpathfromsuper}
-    echo "gitdir: ${pathtodotgit}/modules/${relpathfromsuper}" > ${dir}/.git
-    for path in $* ;do
-        echo "${path}" >> ${super}/.git/modules/${relpathfromsuper}/info/sparse-checkout
-    done
-    git -C "${dir}" fetch ${opts} origin ${tag}
-    git -C "${dir}" checkout ${tag}
-}
-
-git_sparse_checkout $@
diff --git a/modules/gitmodules.py b/modules/gitmodules.py
new file mode 100644
index 0000000000..3ef3ed87fd
--- /dev/null
+++ b/modules/gitmodules.py
@@ -0,0 +1,53 @@
+import os
+from configparser import ConfigParser
+
+from modules.lstripreader import LstripReader
+
+
+class GitModules(ConfigParser.ConfigParser):
+    def __init__(
+        self,
+        confpath=os.getcwd(),
+        conffile=".gitmodules",
+        includelist=None,
+        excludelist=None,
+    ):
+        ConfigParser.ConfigParser.__init__(self)
+        self.read_file(LstripReader(confpath), source=conffile)
+        self.conf_file = os.path.join(confpath, conffile)
+        self.includelist = includelist
+        self.excludelist = excludelist
+
+    def set(self, name, option, value):
+        section = f'submodule "{name}"'
+        if not self.has_section(section):
+            self.add_section(section)
+        ConfigParser.ConfigParser.set(self, section, option, str(value))
+
+    def get(self, name, option):
+        section = f'submodule "{name}"'
+        try:
+            return ConfigParser.ConfigParser.get(self, section, option)
+        except ConfigParser.NoOptionError:
+            return None
+
+    def save(self):
+        self.write(open(self.conf_file, "w"))
+
+    def __del__(self):
+        self.save()
+
+    def sections(self):
+        names = []
+        for section in ConfigParser.ConfigParser.sections(self):
+            name = section[11:-1]
+            if self.includelist and name not in self.includelist:
+                continue
+            if self.excludelist and name in self.excludelist:
+                continue
+            names.append(name)
+        return names
+
+    def items(self, name):
+        section = f'submodule "{name}"'
+        return ConfigParser.ConfigParser.items(section)
diff --git a/modules/utils.py b/modules/utils.py
index 8271538797..41c6bb25c8 100644
--- a/modules/utils.py
+++ b/modules/utils.py
@@ -10,12 +10,24 @@
 import sys
 from threading import Timer
 
-LOCAL_PATH_INDICATOR = '.'
+LOCAL_PATH_INDICATOR = "."
 # ---------------------------------------------------------------------
 #
-# screen and logging output and functions to massage text for output
+# functions to massage text for output and other useful utilities
 #
 # ---------------------------------------------------------------------
+from contextlib import contextmanager
+
+
+@contextmanager
+def pushd(new_dir):
+    """context for chdir. usage: with pushd(new_dir)"""
+    previous_dir = os.getcwd()
+    os.chdir(new_dir)
+    try:
+        yield
+    finally:
+        os.chdir(previous_dir)
 
 
 def log_process_output(output):
@@ -25,7 +37,7 @@ def log_process_output(output):
     line. This makes it hard to filter with grep.
 
     """
-    output = output.split('\n')
+    output = output.split("\n")
     for line in output:
         logging.debug(line)
 
@@ -63,9 +75,9 @@ def last_n_lines(the_string, n_lines, truncation_message=None):
         return_val = the_string
     else:
         lines_subset = lines[-n_lines:]
-        str_truncated = ''.join(lines_subset)
+        str_truncated = "".join(lines_subset)
         if truncation_message:
-            str_truncated = truncation_message + '\n' + str_truncated
+            str_truncated = truncation_message + "\n" + str_truncated
         return_val = str_truncated
 
     return return_val
@@ -85,9 +97,10 @@ def indent_string(the_string, indent_level):
     """
 
     lines = the_string.splitlines(True)
-    padding = ' ' * indent_level
+    padding = " " * indent_level
     lines_indented = [padding + line for line in lines]
-    return ''.join(lines_indented)
+    return "".join(lines_indented)
+
 
 # ---------------------------------------------------------------------
 #
@@ -116,24 +129,26 @@ def str_to_bool(bool_str):
     """
     value = None
     str_lower = bool_str.lower()
-    if str_lower in ('true', 't'):
+    if str_lower in ("true", "t"):
         value = True
-    elif str_lower in ('false', 'f'):
+    elif str_lower in ("false", "f"):
         value = False
     if value is None:
-        msg = ('ERROR: invalid boolean string value "{0}". '
-               'Must be "true" or "false"'.format(bool_str))
+        msg = (
+            'ERROR: invalid boolean string value "{0}". '
+            'Must be "true" or "false"'.format(bool_str)
+        )
         fatal_error(msg)
     return value
 
 
-REMOTE_PREFIXES = ['http://', 'https://', 'ssh://', 'git@']
+REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
 
 
 def is_remote_url(url):
     """check if the user provided a local file path instead of a
-       remote. If so, it must be expanded to an absolute
-       path.
+    remote. If so, it must be expanded to an absolute
+    path.
 
     """
     remote_url = False
@@ -145,7 +160,7 @@ def is_remote_url(url):
 
 def split_remote_url(url):
     """check if the user provided a local file path or a
-       remote. If remote, try to strip off protocol info.
+    remote. If remote, try to strip off protocol info.
 
     """
     remote_url = is_remote_url(url)
@@ -153,13 +168,13 @@ def split_remote_url(url):
         return url
 
     for prefix in REMOTE_PREFIXES:
-        url = url.replace(prefix, '')
+        url = url.replace(prefix, "")
 
-    if '@' in url:
-        url = url.split('@')[1]
+    if "@" in url:
+        url = url.split("@")[1]
 
-    if ':' in url:
-        url = url.split(':')[1]
+    if ":" in url:
+        url = url.split(":")[1]
 
     return url
 
@@ -181,10 +196,12 @@ def expand_local_url(url, field):
             url = os.path.expandvars(url)
             url = os.path.expanduser(url)
             if not os.path.isabs(url):
-                msg = ('WARNING: Externals description for "{0}" contains a '
-                       'url that is not remote and does not expand to an '
-                       'absolute path. Version control operations may '
-                       'fail.\n\nurl={1}'.format(field, url))
+                msg = (
+                    'WARNING: Externals description for "{0}" contains a '
+                    "url that is not remote and does not expand to an "
+                    "absolute path. Version control operations may "
+                    "fail.\n\nurl={1}".format(field, url)
+                )
                 printlog(msg)
             else:
                 url = os.path.normpath(url)
@@ -203,7 +220,8 @@ def expand_local_url(url, field):
 
 
 def _hanging_msg(working_directory, command):
-    print("""
+    print(
+        """
 
 Command '{command}'
 from directory {working_directory}
@@ -217,13 +235,15 @@ def _hanging_msg(working_directory, command):
 will appear to hang. Ensure you can run svn and git manually and access
 all repositories without entering your authentication information.
 
-""".format(command=command,
-           working_directory=working_directory,
-           hanging_sec=_HANGING_SEC))
+""".format(
+            command=command,
+            working_directory=working_directory,
+            hanging_sec=_HANGING_SEC,
+        )
+    )
 
 
-def execute_subprocess(commands, status_to_caller=False,
-                       output_to_caller=False):
+def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
     """Wrapper around subprocess.check_output to handle common
     exceptions.
 
@@ -237,32 +257,35 @@ def execute_subprocess(commands, status_to_caller=False,
 
     """
     cwd = os.getcwd()
-    msg = 'In directory: {0}\nexecute_subprocess running command:'.format(cwd)
+    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
     logging.info(msg)
-    commands_str = ' '.join(commands)
+    commands_str = " ".join(commands)
     logging.info(commands_str)
     return_to_caller = status_to_caller or output_to_caller
     status = -1
-    output = ''
-    hanging_timer = Timer(_HANGING_SEC, _hanging_msg,
-                          kwargs={"working_directory": cwd,
-                                  "command": commands_str})
+    output = ""
+    hanging_timer = Timer(
+        _HANGING_SEC,
+        _hanging_msg,
+        kwargs={"working_directory": cwd, "command": commands_str},
+    )
     hanging_timer.start()
     try:
-        output = subprocess.check_output(commands, stderr=subprocess.STDOUT,
-                                         universal_newlines=True)
+        output = subprocess.check_output(
+            commands, stderr=subprocess.STDOUT, universal_newlines=True
+        )
         log_process_output(output)
         status = 0
     except OSError as error:
         msg = failed_command_msg(
-            'Command execution failed. Does the executable exist?',
-            commands)
+            "Command execution failed. Does the executable exist?", commands
+        )
         logging.error(error)
         fatal_error(msg)
     except ValueError as error:
         msg = failed_command_msg(
-            'DEV_ERROR: Invalid arguments trying to run subprocess',
-            commands)
+            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
+        )
         logging.error(error)
         fatal_error(msg)
     except subprocess.CalledProcessError as error:
@@ -272,10 +295,11 @@ def execute_subprocess(commands, status_to_caller=False,
         # responsibility determine if an error occurred and handle it
         # appropriately.
         if not return_to_caller:
-            msg_context = ('Process did not run successfully; '
-                           'returned status {0}'.format(error.returncode))
-            msg = failed_command_msg(msg_context, commands,
-                                     output=error.output)
+            msg_context = (
+                "Process did not run successfully; "
+                "returned status {0}".format(error.returncode)
+            )
+            msg = failed_command_msg(msg_context, commands, output=error.output)
             logging.error(error)
             logging.error(msg)
             log_process_output(error.output)
@@ -304,22 +328,25 @@ def failed_command_msg(msg_context, command, output=None):
     """
 
     if output:
-        output_truncated = last_n_lines(output, 20,
-                                        truncation_message='[... Output truncated for brevity ...]')
-        errmsg = ('Failed with output:\n' +
-                  indent_string(output_truncated, 4) +
-                  '\nERROR: ')
+        output_truncated = last_n_lines(
+            output, 20, truncation_message="[... Output truncated for brevity ...]"
+        )
+        errmsg = (
+            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
+        )
     else:
-        errmsg = ''
+        errmsg = ""
 
-    command_str = ' '.join(command)
+    command_str = " ".join(command)
     errmsg += """In directory
     {cwd}
 {context}:
     {command}
-""".format(cwd=os.getcwd(), context=msg_context, command=command_str)
+""".format(
+        cwd=os.getcwd(), context=msg_context, command=command_str
+    )
 
     if output:
-        errmsg += 'See above for output from failed command.\n'
+        errmsg += "See above for output from failed command.\n"
 
     return errmsg
diff --git a/show-tags b/show-tags
deleted file mode 100755
index 56c7d9c5e4..0000000000
--- a/show-tags
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-this_dir=$(pwd)
-printf "\nSubmodule status\n"
-printf "(currently checked out commit for each submodule)\n"
-printf "(when the submodule is initialized and a tag exists, the commit is shown as: 'most recent tag-commits since tag-commit hash')\n"
-printf "(when the submodule is not initialized, only the checked out commit is shown)\n\n"
-grep path .gitmodules | sed 's/.*= //' | while read x
-do
-  cd "$this_dir"
-  printf "$x\n   - current commit: "
-  if [ "$(ls -A $x)" ] ; then
-    cd "$x"
-    git describe --tags --always
-  else
-    git submodule status $x | sed 's/^-//' | awk '{ print $1 }'
-  fi
-done
-printf "\n"
-

From 815e6cd0d9f00fdf1cd06bd67ca912006c8d3a46 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 10:34:47 -0700
Subject: [PATCH 019/161] now renamed git-fleximod for git interface

---
 git-fleximod.py => git-fleximod | 24 ++++++++++++++++++------
 modules/gitmodules.py           | 21 ++++++++++++---------
 2 files changed, 30 insertions(+), 15 deletions(-)
 rename git-fleximod.py => git-fleximod (92%)
 mode change 100644 => 100755

diff --git a/git-fleximod.py b/git-fleximod
old mode 100644
new mode 100755
similarity index 92%
rename from git-fleximod.py
rename to git-fleximod
index ded13eb9db..00fc2446c3
--- a/git-fleximod.py
+++ b/git-fleximod
@@ -8,6 +8,9 @@
 from modules.gitinterface import GitInterface
 from modules.gitmodules import GitModules
 
+logger = logging.getLogger(__name__)
+logger.propogate = False
+
 
 def commandline_arguments(args=None):
     description = """
@@ -135,9 +138,9 @@ def commandline_arguments(args=None):
         options = parser.parse_args()
 
     if options.optional:
-        esmrequired = ("T:T", "T:F", "I:T")
+        esmrequired = ["T:T", "T:F", "I:T"]
     else:
-        esmrequired = ("T:T", "I:T")
+        esmrequired = ["T:T", "I:T"]
 
     if options.status:
         action = "status"
@@ -177,7 +180,7 @@ def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
     topgit = os.path.join(topdir, ".git", "modules")
     gitsparse = os.path.join(topgit, name, "info", "sparse-checkout")
     if os.path.isfile(gitsparse):
-        logging.warning("submodule {} is already initialized".format(name))
+        logger.warning("submodule {} is already initialized".format(name))
         return
 
     # initialize a new git repo and set the sparse checkout flag
@@ -213,7 +216,7 @@ def submodule_checkout(root, name, path):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir}")
         gitmodules = GitModules(repodir)
-        submodules_install(gitmodules, repodir, ("I:T"))
+        submodules_install(gitmodules, repodir, ["I:T"])
     if os.path.exists(os.path.join(repodir, ".git")):
         print(f"Successfully checked out {name}")
     else:
@@ -253,19 +256,27 @@ def submodules_update(gitmodules, root_dir):
 
 
 def submodules_install(gitmodules, root_dir, requiredlist):
+    print(gitmodules.sections())
     for name in gitmodules.sections():
         esmrequired = gitmodules.get(name, "esmrequired")
         esmsparse = gitmodules.get(name, "esmsparse")
         esmtag = gitmodules.get(name, "esmtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
-        if esmrequired not in requiredlist:
-            if "T:F" in esmrequired:
+
+        if esmrequired and esmrequired not in requiredlist:
+            if "T:F" == esmrequired:
                 print("Skipping optional component {}".format(name))
             continue
         if esmsparse:
+            logger.debug(
+                f"Callng submodule_sparse_checkout({name} {url}, {path}, {esmsparse}, {esmtag}"
+            )
             submodule_sparse_checkout(name, url, path, esmsparse, tag=esmtag)
         else:
+            logger.debug(
+                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
+            )
             submodule_checkout(root_dir, name, path)
 
 
@@ -281,6 +292,7 @@ def _main_func():
     ) = commandline_arguments()
     if verbose:
         print(f"action is {action}")
+
     gitmodules = GitModules(
         confpath=root_dir,
         conffile=file_name,
diff --git a/modules/gitmodules.py b/modules/gitmodules.py
index 3ef3ed87fd..2858629270 100644
--- a/modules/gitmodules.py
+++ b/modules/gitmodules.py
@@ -4,7 +4,7 @@
 from modules.lstripreader import LstripReader
 
 
-class GitModules(ConfigParser.ConfigParser):
+class GitModules(ConfigParser):
     def __init__(
         self,
         confpath=os.getcwd(),
@@ -12,9 +12,9 @@ def __init__(
         includelist=None,
         excludelist=None,
     ):
-        ConfigParser.ConfigParser.__init__(self)
-        self.read_file(LstripReader(confpath), source=conffile)
+        ConfigParser.__init__(self)
         self.conf_file = os.path.join(confpath, conffile)
+        self.read_file(LstripReader(self.conf_file), source=conffile)
         self.includelist = includelist
         self.excludelist = excludelist
 
@@ -22,12 +22,15 @@ def set(self, name, option, value):
         section = f'submodule "{name}"'
         if not self.has_section(section):
             self.add_section(section)
-        ConfigParser.ConfigParser.set(self, section, option, str(value))
+        ConfigParser.set(self, section, option, str(value))
 
-    def get(self, name, option):
+    # pylint: disable=redefined-builtin, arguments-differ
+    def get(self, name, option, raw=False, vars=None, fallback=None):
         section = f'submodule "{name}"'
         try:
-            return ConfigParser.ConfigParser.get(self, section, option)
+            return ConfigParser.get(
+                self, section, option, raw=raw, vars=vars, fallback=fallback
+            )
         except ConfigParser.NoOptionError:
             return None
 
@@ -39,7 +42,7 @@ def __del__(self):
 
     def sections(self):
         names = []
-        for section in ConfigParser.ConfigParser.sections(self):
+        for section in ConfigParser.sections(self):
             name = section[11:-1]
             if self.includelist and name not in self.includelist:
                 continue
@@ -48,6 +51,6 @@ def sections(self):
             names.append(name)
         return names
 
-    def items(self, name):
+    def items(self, name, raw=False, vars=None):
         section = f'submodule "{name}"'
-        return ConfigParser.ConfigParser.items(section)
+        return ConfigParser.items(section, raw=raw, vars=vars)

From a6ce960bc9d102007608ab7dde8b9fd4ad590dec Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 11:41:25 -0700
Subject: [PATCH 020/161] clean up and refactor, rename to git-fleximod

---
 git-fleximod     | 48 ++++++++++++++++++++++++++++++++++--------------
 modules/utils.py | 13 +++++++++++++
 2 files changed, 47 insertions(+), 14 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 00fc2446c3..44a86c50bc 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -168,16 +168,14 @@ def commandline_arguments(args=None):
     )
 
 
-def submodule_sparse_checkout(name, url, path, sparsefile, tag="master"):
+def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
     # first create the module directory
     if not os.path.isdir(path):
         os.makedirs(path)
     # Check first if the module is already defined
     # and the sparse-checkout file exists
-    git = GitInterface(os.getcwd())
-    topdir = git.git_operation("rev-parse", "--show-toplevel").rstrip()
-
-    topgit = os.path.join(topdir, ".git", "modules")
+    git = GitInterface(root_dir)
+    topgit = os.path.join(root_dir, ".git", "modules")
     gitsparse = os.path.join(topgit, name, "info", "sparse-checkout")
     if os.path.isfile(gitsparse):
         logger.warning("submodule {} is already initialized".format(name))
@@ -227,7 +225,7 @@ def submodule_checkout(root, name, path):
 def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
-        tag = gitmodules.git(name, "esmtag")
+        tag = gitmodules.get(name, "esmtag")
         with utils.pushd(path):
             git = GitInterface(os.path.join(root_dir, path))
             atag = git.git_operation("describe", "--tags", "--always").rstrip()
@@ -236,7 +234,12 @@ def submodules_status(gitmodules, root_dir):
             elif tag:
                 print(f"Submodule {name} at tag {tag}")
             else:
-                print(f"Submodule {name} has no tag defined in .gitmodules")
+                print(
+                    f"Submodule {name} has no tag defined in .gitmodules, module at {atag}"
+                )
+            status = git.git_operation("status")
+            if "nothing to commit" not in status:
+                print(status)
 
 
 def submodules_update(gitmodules, root_dir):
@@ -245,18 +248,26 @@ def submodules_update(gitmodules, root_dir):
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         if os.path.exists(os.path.join(path, ".git")):
-            with utils.pushd(root_dir):
-                git = GitInterface(root_dir)
+            submoddir = os.path.join(root_dir, path)
+            with utils.pushd(submoddir):
+                git = GitInterface(submoddir)
                 # first make sure the url is correct
                 upstream = git.git_operation("ls-remote", "--get-url").rstrip()
+                newremote = "origin"
                 if upstream != url:
                     # TODO - this needs to be a unique name
-                    git.git_operation("remote", "add", "newbranch", url)
-                    git.git_operation("checkout", esmtag)
+                    remotes = git.git_operation("remote", "-v")
+                    newremote = "newremote"
+                    git.git_operation("remote", "add", newremote, url)
+
+                tags = git.git_operation("tag", "-l")
+                if esmtag not in tags:
+                    git.git_operation("fetch", newremote, "--tags")
+
+                git.git_operation("checkout", esmtag)
 
 
 def submodules_install(gitmodules, root_dir, requiredlist):
-    print(gitmodules.sections())
     for name in gitmodules.sections():
         esmrequired = gitmodules.get(name, "esmrequired")
         esmsparse = gitmodules.get(name, "esmsparse")
@@ -270,9 +281,9 @@ def submodules_install(gitmodules, root_dir, requiredlist):
             continue
         if esmsparse:
             logger.debug(
-                f"Callng submodule_sparse_checkout({name} {url}, {path}, {esmsparse}, {esmtag}"
+                f"Callng submodule_sparse_checkout({root_dir}, {name}, {url}, {path}, {esmsparse}, {esmtag}"
             )
-            submodule_sparse_checkout(name, url, path, esmsparse, tag=esmtag)
+            submodule_sparse_checkout(root_dir, name, url, path, esmsparse, tag=esmtag)
         else:
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
@@ -293,6 +304,15 @@ def _main_func():
     if verbose:
         print(f"action is {action}")
 
+    if not os.path.isfile(os.path.join(root_dir, file_name)):
+        file_path = utils.find_upwards(root_dir, file_name)
+
+        if file_path is None:
+            fatal_error(
+                "No {} found in {} or any of it's parents".format(file_name, root_dir)
+            )
+        root_dir = os.path.dirname(file_path)
+    print(f"root_dir is {root_dir}")
     gitmodules = GitModules(
         confpath=root_dir,
         conffile=file_name,
diff --git a/modules/utils.py b/modules/utils.py
index 41c6bb25c8..f0753367e5 100644
--- a/modules/utils.py
+++ b/modules/utils.py
@@ -9,6 +9,7 @@
 import subprocess
 import sys
 from threading import Timer
+from pathlib import Path
 
 LOCAL_PATH_INDICATOR = "."
 # ---------------------------------------------------------------------
@@ -55,6 +56,18 @@ def printlog(msg, **kwargs):
     sys.stdout.flush()
 
 
+def find_upwards(root_dir, filename):
+    """Find a file in root dir or any of it's parents"""
+    d = Path(root_dir)
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.exists():
+            return attempt
+        d = d.parent
+    return None
+
+
 def last_n_lines(the_string, n_lines, truncation_message=None):
     """Returns the last n lines of the given string
 

From 816158ceb02abca2b360811beba25a5c1b98c5e2 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 12:11:04 -0700
Subject: [PATCH 021/161] add version.txt and .pre-commit-config.yaml

---
 .pre-commit-config.yaml | 18 ++++++++++++++++++
 version.txt             |  1 +
 2 files changed, 19 insertions(+)
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 version.txt

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000..2f6089da72
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+exclude: ^utils/.*$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.11.1
+    hooks:
+      - id: pylint
+        args:
+          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/version.txt b/version.txt
new file mode 100644
index 0000000000..a3dce6cd3a
--- /dev/null
+++ b/version.txt
@@ -0,0 +1 @@
+v0.0.2

From 3be6537e39f7d9209be9b66b36756da022455612 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 15:21:15 -0700
Subject: [PATCH 022/161] fix issue in update

---
 git-fleximod | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 44a86c50bc..e5978cff6d 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -257,11 +257,20 @@ def submodules_update(gitmodules, root_dir):
                 if upstream != url:
                     # TODO - this needs to be a unique name
                     remotes = git.git_operation("remote", "-v")
-                    newremote = "newremote"
-                    git.git_operation("remote", "add", newremote, url)
+                    if url in remotes:
+                        for line in remotes:
+                            if url in line and "fetch" in line:
+                                newremote = line.split()[0]
+                                break
+                    else:
+                        i = 0
+                        while newremote in remotes:
+                            i = i + 1
+                            newremote = f"newremote.{i:02d}"
+                        git.git_operation("remote", "add", newremote, url)
 
                 tags = git.git_operation("tag", "-l")
-                if esmtag not in tags:
+                if esmtag and esmtag not in tags:
                     git.git_operation("fetch", newremote, "--tags")
 
                 git.git_operation("checkout", esmtag)

From d709c124c284c1ad007caed586db93914d78be47 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 15:47:38 -0700
Subject: [PATCH 023/161] make action a required subargument to look more like
 a git subcommand

---
 git-fleximod          | 38 +++++++++++++-------------------------
 modules/gitmodules.py |  3 ---
 2 files changed, 13 insertions(+), 28 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index e5978cff6d..d13f1b9f08 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -23,6 +23,14 @@ def commandline_arguments(args=None):
     #
     # user options
     #
+    choices = ["update", "install", "status"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="install",
+        help=f"Subcommand of fleximod, choices are {choices}",
+    )
+
     parser.add_argument(
         "components",
         nargs="*",
@@ -62,24 +70,6 @@ def commandline_arguments(args=None):
         "optional submodules relative to the toplevel directory.",
     )
 
-    parser.add_argument(
-        "-S",
-        "--status",
-        action="store_true",
-        default=False,
-        help="Output the status of the repositories managed by "
-        "%(prog)s. By default only summary information "
-        "is provided. Use the verbose option to see details.",
-    )
-
-    parser.add_argument(
-        "-u",
-        "--update",
-        action="store_true",
-        default=False,
-        help="Update submodules to the tags defined in .gitmodules.",
-    )
-
     parser.add_argument(
         "-v",
         "--verbose",
@@ -142,11 +132,8 @@ def commandline_arguments(args=None):
     else:
         esmrequired = ["T:T", "I:T"]
 
-    if options.status:
-        action = "status"
-    elif options.update:
-        action = "update"
-    else:
+    action = options.action
+    if not action:
         action = "install"
 
     if options.version:
@@ -226,8 +213,9 @@ def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "esmtag")
-        with utils.pushd(path):
-            git = GitInterface(os.path.join(root_dir, path))
+        newpath = os.path.join(root_dir, path)
+        with utils.pushd(newpath):
+            git = GitInterface(newpath)
             atag = git.git_operation("describe", "--tags", "--always").rstrip()
             if tag and atag != tag:
                 print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
diff --git a/modules/gitmodules.py b/modules/gitmodules.py
index 2858629270..5af10be406 100644
--- a/modules/gitmodules.py
+++ b/modules/gitmodules.py
@@ -37,9 +37,6 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
     def save(self):
         self.write(open(self.conf_file, "w"))
 
-    def __del__(self):
-        self.save()
-
     def sections(self):
         names = []
         for section in ConfigParser.sections(self):

From 83aea04a4366e246e5a107e88ef29aa347657e24 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 6 Jan 2024 16:02:03 -0700
Subject: [PATCH 024/161] add documentation

---
 modules/gitmodules.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/modules/gitmodules.py b/modules/gitmodules.py
index 5af10be406..9e38a5806c 100644
--- a/modules/gitmodules.py
+++ b/modules/gitmodules.py
@@ -12,6 +12,12 @@ def __init__(
         includelist=None,
         excludelist=None,
     ):
+        """
+        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
+        conffile: Name of the configuration file (defaults to .gitmodules).
+        includelist: Optional list of submodules to include.
+        excludelist: Optional list of submodules to exclude.
+        """
         ConfigParser.__init__(self)
         self.conf_file = os.path.join(confpath, conffile)
         self.read_file(LstripReader(self.conf_file), source=conffile)
@@ -19,6 +25,11 @@ def __init__(
         self.excludelist = excludelist
 
     def set(self, name, option, value):
+        """
+        Sets a configuration value for a specific submodule:
+        Ensures the appropriate section exists for the submodule.
+        Calls the parent class's set method to store the value.
+        """
         section = f'submodule "{name}"'
         if not self.has_section(section):
             self.add_section(section)
@@ -26,6 +37,11 @@ def set(self, name, option, value):
 
     # pylint: disable=redefined-builtin, arguments-differ
     def get(self, name, option, raw=False, vars=None, fallback=None):
+        """
+        Retrieves a configuration value for a specific submodule:
+        Uses the parent class's get method to access the value.
+        Handles potential errors if the section or option doesn't exist.
+        """
         section = f'submodule "{name}"'
         try:
             return ConfigParser.get(
@@ -38,6 +54,7 @@ def save(self):
         self.write(open(self.conf_file, "w"))
 
     def sections(self):
+        """Strip the submodule part out of section and just use the name"""
         names = []
         for section in ConfigParser.sections(self):
             name = section[11:-1]

From 905824aefcd187a25f4133826bd0a0a76edcfcdd Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 09:09:23 -0700
Subject: [PATCH 025/161] add README and License

---
 License   | 20 ++++++++++++++++++++
 README.md | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 License
 create mode 100644 README.md

diff --git a/License b/License
new file mode 100644
index 0000000000..2c6fe768c2
--- /dev/null
+++ b/License
@@ -0,0 +1,20 @@
+Copyright 2024 National Center for Atmospheric Sciences (NCAR)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+“Software�), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS�, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000..4ee56bc4a4
--- /dev/null
+++ b/README.md
@@ -0,0 +1,53 @@
+# git-fleximod
+
+Flexible Submodule Management for Git
+
+## Overview
+
+Git-fleximod is a Python-based tool that extends Git's submodule capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+
+## Installation
+
+    Install using pip:
+        pip install git-fleximod
+
+## Usage
+
+    Basic Usage:
+        git fleximod <command> [options]
+    Available Commands:
+        install: Install submodules according to configuration.
+        status: Display the status of submodules.
+        update: Update submodules to their latest commits.
+    Additional Options:
+        See git fleximod --help for more details.
+
+## Supported .gitmodules Variables
+
+    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxrequired: Mark a submodule's checkout behavior, with allowed values:
+      - T:T: Top-level and required (checked out only when this is the Toplevel module).
+      - T:F: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - I:T: Internal and required (always checked out).
+      - I:F: Internal and optional (checked out with --optional flag).
+    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+
+## Sparse Checkouts
+
+    To enable sparse checkout for a submodule, set the fxsparse variable
+    in the .gitmodules file to the path of a file containing the desired
+    sparse checkout paths. Git-fleximod will automatically configure
+    sparse checkout based on this file when applicable commands are run.
+
+## Examples
+
+    Installing submodules with optional ones: git fleximod install --optional
+    Checking out a specific tag for a submodule: git fleximod update --fxtag=v1.2.3 submodule-name
+
+## Contributing
+
+We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
+
+## License
+
+Git-fleximod is released under the MIT License.

From 3c723a86b39db2274c223e4a8ffb1d83f5b01ec1 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 10:56:42 -0700
Subject: [PATCH 026/161] update README

---
 README.md    | 34 +++++++++++++++++++++++++++++-----
 git-fleximod | 39 +++++++++++++++++++++------------------
 2 files changed, 50 insertions(+), 23 deletions(-)

diff --git a/README.md b/README.md
index 4ee56bc4a4..da725ab5f5 100644
--- a/README.md
+++ b/README.md
@@ -8,8 +8,9 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 
 ## Installation
 
-    Install using pip:
-        pip install git-fleximod
+#TODO    Install using pip:
+#        pip install git-fleximod
+  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
 
 ## Usage
 
@@ -18,7 +19,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
     Available Commands:
         install: Install submodules according to configuration.
         status: Display the status of submodules.
-        update: Update submodules to their latest commits.
+        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
     Additional Options:
         See git fleximod --help for more details.
 
@@ -38,11 +39,34 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
     in the .gitmodules file to the path of a file containing the desired
     sparse checkout paths. Git-fleximod will automatically configure
     sparse checkout based on this file when applicable commands are run.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set) for details on the format of this file.
 
 ## Examples
 
-    Installing submodules with optional ones: git fleximod install --optional
-    Checking out a specific tag for a submodule: git fleximod update --fxtag=v1.2.3 submodule-name
+    Installing submodules including optional ones: git fleximod install --optional
+    Update a specific submodule to the fxtag indicated in .gitmodules: git fleximod update submodule-name
+    Example .gitmodules entry:
+      [submodule "cosp2"]
+         path = src/physics/cosp2/src
+         url = https://github.com/CFMIP/COSPv2.0
+         fxsparse = ../.cosp_sparse_checkout
+         fxtag = v2.1.4cesm
+
+   This indicates that submodule named cosp2 at tag v2.1.4cesm should
+   be checked out into directory src/physics/cosp2/src relative to the
+   .gitmodules directory from the given url and that it should use the
+   sparse checkout as described in file ../.cosp_sparse_checkout relative
+   to the path directory.
+
+   [submodule "cime"]
+       path = cime
+       url = https://github.com/jedwards4b/cime
+       fxrequired = T:T
+       fxtag = cime6.0.198_rme01
+
+   This indicates that submodule cime should be checked out into a directory cime
+   at tag cime6.0.198_rme01 from url https://github.com/jedwards4b/cime, this should
+   only be done if this .gitmodules file is at the TopLevel of the repository clone.
 
 ## Contributing
 
diff --git a/git-fleximod b/git-fleximod
index d13f1b9f08..f03984f83c 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -128,9 +128,9 @@ def commandline_arguments(args=None):
         options = parser.parse_args()
 
     if options.optional:
-        esmrequired = ["T:T", "T:F", "I:T"]
+        fxrequired = ["T:T", "T:F", "I:T"]
     else:
-        esmrequired = ["T:T", "I:T"]
+        fxrequired = ["T:T", "I:T"]
 
     action = options.action
     if not action:
@@ -147,7 +147,7 @@ def commandline_arguments(args=None):
     return (
         options.path,
         options.gitmodules,
-        esmrequired,
+        fxrequired,
         options.components,
         options.exclude,
         options.verbose,
@@ -212,7 +212,7 @@ def submodule_checkout(root, name, path):
 def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
-        tag = gitmodules.get(name, "esmtag")
+        tag = gitmodules.get(name, "fxtag")
         newpath = os.path.join(root_dir, path)
         with utils.pushd(newpath):
             git = GitInterface(newpath)
@@ -232,9 +232,10 @@ def submodules_status(gitmodules, root_dir):
 
 def submodules_update(gitmodules, root_dir):
     for name in gitmodules.sections():
-        esmtag = gitmodules.get(name, "esmtag")
+        fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
+        print(f"name={name} path={path} url={url} fxtag={fxtag}")
         if os.path.exists(os.path.join(path, ".git")):
             submoddir = os.path.join(root_dir, path)
             with utils.pushd(submoddir):
@@ -258,29 +259,31 @@ def submodules_update(gitmodules, root_dir):
                         git.git_operation("remote", "add", newremote, url)
 
                 tags = git.git_operation("tag", "-l")
-                if esmtag and esmtag not in tags:
+                if fxtag and fxtag not in tags:
                     git.git_operation("fetch", newremote, "--tags")
-
-                git.git_operation("checkout", esmtag)
+                if fxtag:
+                    git.git_operation("checkout", fxtag)
+                else:
+                    print(f"No fxtag found for submodule {name}")
 
 
 def submodules_install(gitmodules, root_dir, requiredlist):
     for name in gitmodules.sections():
-        esmrequired = gitmodules.get(name, "esmrequired")
-        esmsparse = gitmodules.get(name, "esmsparse")
-        esmtag = gitmodules.get(name, "esmtag")
+        fxrequired = gitmodules.get(name, "fxrequired")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
 
-        if esmrequired and esmrequired not in requiredlist:
-            if "T:F" == esmrequired:
+        if fxrequired and fxrequired not in requiredlist:
+            if "T:F" == fxrequired:
                 print("Skipping optional component {}".format(name))
             continue
-        if esmsparse:
+        if fxsparse:
             logger.debug(
-                f"Callng submodule_sparse_checkout({root_dir}, {name}, {url}, {path}, {esmsparse}, {esmtag}"
+                f"Callng submodule_sparse_checkout({root_dir}, {name}, {url}, {path}, {fxsparse}, {fxtag}"
             )
-            submodule_sparse_checkout(root_dir, name, url, path, esmsparse, tag=esmtag)
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
         else:
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
@@ -292,7 +295,7 @@ def _main_func():
     (
         root_dir,
         file_name,
-        esmrequired,
+        fxrequired,
         includelist,
         excludelist,
         verbose,
@@ -320,7 +323,7 @@ def _main_func():
     if action == "update":
         submodules_update(gitmodules, root_dir)
     elif action == "install":
-        submodules_install(gitmodules, root_dir, esmrequired)
+        submodules_install(gitmodules, root_dir, fxrequired)
     elif action == "status":
         submodules_status(gitmodules, root_dir)
     else:

From 3903206397dfebfd0ca2f02a53761466b79cfc89 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 11:05:00 -0700
Subject: [PATCH 027/161] trying to improve markdown formatting

---
 README.md | 71 ++++++++++++++++++++++++++++++++++++-------------------
 1 file changed, 47 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index da725ab5f5..c5a885bd7e 100644
--- a/README.md
+++ b/README.md
@@ -43,30 +43,53 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 
 ## Examples
 
-    Installing submodules including optional ones: git fleximod install --optional
-    Update a specific submodule to the fxtag indicated in .gitmodules: git fleximod update submodule-name
-    Example .gitmodules entry:
-      [submodule "cosp2"]
-         path = src/physics/cosp2/src
-         url = https://github.com/CFMIP/COSPv2.0
-         fxsparse = ../.cosp_sparse_checkout
-         fxtag = v2.1.4cesm
-
-   This indicates that submodule named cosp2 at tag v2.1.4cesm should
-   be checked out into directory src/physics/cosp2/src relative to the
-   .gitmodules directory from the given url and that it should use the
-   sparse checkout as described in file ../.cosp_sparse_checkout relative
-   to the path directory.
-
-   [submodule "cime"]
-       path = cime
-       url = https://github.com/jedwards4b/cime
-       fxrequired = T:T
-       fxtag = cime6.0.198_rme01
-
-   This indicates that submodule cime should be checked out into a directory cime
-   at tag cime6.0.198_rme01 from url https://github.com/jedwards4b/cime, this should
-   only be done if this .gitmodules file is at the TopLevel of the repository clone.
+Here are some common usage examples:
+
+    Installing submodules, including optional ones:
+    Bash
+
+    git fleximod install --optional
+
+
+Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+Bash
+
+git fleximod update submodule-name
+
+Example .gitmodules entry:
+Ini, TOML
+
+[submodule "cosp2"]
+    path = src/physics/cosp2/src
+    url = https://github.com/CFMIP/COSPv2.0
+    fxsparse = ../.cosp_sparse_checkout
+    fxtag = v2.1.4cesm
+
+Explanation:
+
+    This entry indicates that the submodule named cosp2 at tag
+    v2.1.4cesm should be checked out into the directory
+    src/physics/cosp2/src relative to the .gitmodules directory.  It
+    should be checked out from the URL
+    https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+    described in the file ../.cosp_sparse_checkout relative to the
+    path directory.
+
+Additional example:
+Ini, TOML
+
+[submodule "cime"]
+    path = cime
+    url = https://github.com/jedwards4b/cime
+    fxrequired = T:T
+    fxtag = cime6.0.198_rme01
+
+
+Explanation:
+
+    This entry indicates that the submodule cime should be checked out into a directory named cime at tag cime6.0.198_rme01 from the URL https://github.com/jedwards4b/cime.
+    This should only be done if the .gitmodules file is at the top level of the repository clone.
 
 ## Contributing
 

From 8bd89cf9b7bdd710b0aa23def9a4b2f21c047b84 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 11:09:47 -0700
Subject: [PATCH 028/161] trying to improve markdown

---
 README.md | 66 +++++++++++++++++++++++++++----------------------------
 1 file changed, 32 insertions(+), 34 deletions(-)

diff --git a/README.md b/README.md
index c5a885bd7e..f3a0f889cb 100644
--- a/README.md
+++ b/README.md
@@ -46,27 +46,24 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 Here are some common usage examples:
 
     Installing submodules, including optional ones:
-    Bash
-
+    ```Bash
     git fleximod install --optional
-
-
-Updating a specific submodule to the fxtag indicated in .gitmodules:
-
-Bash
-
-git fleximod update submodule-name
-
-Example .gitmodules entry:
-Ini, TOML
-
-[submodule "cosp2"]
-    path = src/physics/cosp2/src
-    url = https://github.com/CFMIP/COSPv2.0
-    fxsparse = ../.cosp_sparse_checkout
-    fxtag = v2.1.4cesm
-
-Explanation:
+    ```
+
+    Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+    ```Bash
+    git fleximod update submodule-name
+    ```
+    Example .gitmodules entry:
+    ```Ini, TOML
+    [submodule "cosp2"]
+        path = src/physics/cosp2/src
+        url = https://github.com/CFMIP/COSPv2.0
+        fxsparse = ../.cosp_sparse_checkout
+        fxtag = v2.1.4cesm
+    ```
+    Explanation:
 
     This entry indicates that the submodule named cosp2 at tag
     v2.1.4cesm should be checked out into the directory
@@ -76,20 +73,21 @@ Explanation:
     described in the file ../.cosp_sparse_checkout relative to the
     path directory.
 
-Additional example:
-Ini, TOML
-
-[submodule "cime"]
-    path = cime
-    url = https://github.com/jedwards4b/cime
-    fxrequired = T:T
-    fxtag = cime6.0.198_rme01
-
-
-Explanation:
-
-    This entry indicates that the submodule cime should be checked out into a directory named cime at tag cime6.0.198_rme01 from the URL https://github.com/jedwards4b/cime.
-    This should only be done if the .gitmodules file is at the top level of the repository clone.
+    Additional example:
+    ```Ini, TOML
+    [submodule "cime"]
+        path = cime
+        url = https://github.com/jedwards4b/cime
+        fxrequired = T:T
+        fxtag = cime6.0.198_rme01
+    ```
+
+    Explanation:
+
+    This entry indicates that the submodule cime should be checked out
+    into a directory named cime at tag cime6.0.198_rme01 from the URL
+    https://github.com/jedwards4b/cime.  This should only be done if
+    the .gitmodules file is at the top level of the repository clone.
 
 ## Contributing
 

From e83bc7a865540751093c393f9edd8f66a450cf40 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 11:12:13 -0700
Subject: [PATCH 029/161] trying to improve markdown

---
 README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index f3a0f889cb..199d2064c0 100644
--- a/README.md
+++ b/README.md
@@ -46,17 +46,17 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 Here are some common usage examples:
 
     Installing submodules, including optional ones:
-    ```Bash
-    git fleximod install --optional
-    ```
+```bash
+  git fleximod install --optional
+```
 
     Updating a specific submodule to the fxtag indicated in .gitmodules:
 
-    ```Bash
+    ```bash
     git fleximod update submodule-name
     ```
     Example .gitmodules entry:
-    ```Ini, TOML
+    ```ini, toml
     [submodule "cosp2"]
         path = src/physics/cosp2/src
         url = https://github.com/CFMIP/COSPv2.0
@@ -74,7 +74,7 @@ Here are some common usage examples:
     path directory.
 
     Additional example:
-    ```Ini, TOML
+    ```ini, toml
     [submodule "cime"]
         path = cime
         url = https://github.com/jedwards4b/cime

From 967edf4ced928a444162079227637c794ed562e0 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 11:14:22 -0700
Subject: [PATCH 030/161] trying to improve markdown

---
 README.md | 49 ++++++++++++++++++++++++-------------------------
 1 file changed, 24 insertions(+), 25 deletions(-)

diff --git a/README.md b/README.md
index 199d2064c0..910858e79a 100644
--- a/README.md
+++ b/README.md
@@ -45,49 +45,48 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 
 Here are some common usage examples:
 
-    Installing submodules, including optional ones:
+Installing submodules, including optional ones:
 ```bash
   git fleximod install --optional
 ```
 
-    Updating a specific submodule to the fxtag indicated in .gitmodules:
+Updating a specific submodule to the fxtag indicated in .gitmodules:
 
-    ```bash
+```bash
     git fleximod update submodule-name
-    ```
-    Example .gitmodules entry:
-    ```ini, toml
+```
+Example .gitmodules entry:
+```ini, toml
     [submodule "cosp2"]
         path = src/physics/cosp2/src
         url = https://github.com/CFMIP/COSPv2.0
         fxsparse = ../.cosp_sparse_checkout
         fxtag = v2.1.4cesm
-    ```
-    Explanation:
-
-    This entry indicates that the submodule named cosp2 at tag
-    v2.1.4cesm should be checked out into the directory
-    src/physics/cosp2/src relative to the .gitmodules directory.  It
-    should be checked out from the URL
-    https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
-    described in the file ../.cosp_sparse_checkout relative to the
-    path directory.
-
-    Additional example:
-    ```ini, toml
+```
+Explanation:
+
+This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
+should be checked out into the directory src/physics/cosp2/src
+relative to the .gitmodules directory.  It should be checked out from
+the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+described in the file ../.cosp_sparse_checkout relative to the path
+directory.
+
+Additional example:
+```ini, toml
     [submodule "cime"]
         path = cime
         url = https://github.com/jedwards4b/cime
         fxrequired = T:T
         fxtag = cime6.0.198_rme01
-    ```
+```
 
-    Explanation:
+Explanation:
 
-    This entry indicates that the submodule cime should be checked out
-    into a directory named cime at tag cime6.0.198_rme01 from the URL
-    https://github.com/jedwards4b/cime.  This should only be done if
-    the .gitmodules file is at the top level of the repository clone.
+This entry indicates that the submodule cime should be checked out
+into a directory named cime at tag cime6.0.198_rme01 from the URL
+https://github.com/jedwards4b/cime.  This should only be done if
+the .gitmodules file is at the top level of the repository clone.
 
 ## Contributing
 

From 4926864512c75496530bc713ddadb26071f16ac9 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 13:17:00 -0700
Subject: [PATCH 031/161] add pip setup.py file

---
 setup.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 setup.py

diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000000..2d4cb3642b
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,26 @@
+import setuptools
+import os
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+with open("version.txt", "r") as fh:
+    version = fh.read()
+    cwd = os.getcwd()
+setuptools.setup(
+    name="git-fleximod",                     # This is the name of the package
+    version=version,                        # The initial release version
+    author="Jim Edwards",                     # Full name of the author
+    description="Extended support for git-submodule and git-sparse-checkout",
+    long_description=long_description,      # Long description read from the the readme file
+    long_description_content_type="text/markdown",
+    packages=setuptools.find_packages(),    # List of all python modules to be installed
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],                                      # Information to filter the project on PyPi website
+    python_requires='>=3.6',                # Minimum version requirement of the package
+    py_modules=['git-fleximod'],             # Name of the python package
+    package_dir={'git-fleximod':'.'},     # Directory of the source code of the package
+    install_requires=[]                     # Install other dependencies if any
+)

From d2b3985e4c0d43eb5afbf497f50fd67adde2d0e3 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 13:22:48 -0700
Subject: [PATCH 032/161] bug fix

---
 git-fleximod | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/git-fleximod b/git-fleximod
index f03984f83c..0f0fc36347 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -169,7 +169,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
         return
 
     # initialize a new git repo and set the sparse checkout flag
-    sprepo_git = GitInterface(os.path.join(topdir, path))
+    sprepo_git = GitInterface(os.path.join(root_dir, path))
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
 
     # set the repository remote

From 27375e88a3ee5d08ffc567f2d52f7ab6a7d1df7e Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 7 Jan 2024 14:23:55 -0700
Subject: [PATCH 033/161] improve messages

---
 git-fleximod | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 0f0fc36347..69491a5fde 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -235,7 +235,7 @@ def submodules_update(gitmodules, root_dir):
         fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
-        print(f"name={name} path={path} url={url} fxtag={fxtag}")
+        logger.info(f"name={name} path={path} url={url} fxtag={fxtag}")
         if os.path.exists(os.path.join(path, ".git")):
             submoddir = os.path.join(root_dir, path)
             with utils.pushd(submoddir):
@@ -261,10 +261,14 @@ def submodules_update(gitmodules, root_dir):
                 tags = git.git_operation("tag", "-l")
                 if fxtag and fxtag not in tags:
                     git.git_operation("fetch", newremote, "--tags")
-                if fxtag:
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                if fxtag and fxtag != atag:
+                    print(f"Updating {name} to {fxtag}")
                     git.git_operation("checkout", fxtag)
-                else:
+                elif not fxtag:
                     print(f"No fxtag found for submodule {name}")
+                else:
+                    print(f"submodule {name} up to date.")
 
 
 def submodules_install(gitmodules, root_dir, requiredlist):

From a17fe845273a99aa767558b88a020c1d82724f98 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 8 Jan 2024 12:03:03 -0700
Subject: [PATCH 034/161] fix some issues in sparse checkout

---
 git-fleximod | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 69491a5fde..51d0372655 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -162,11 +162,6 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # Check first if the module is already defined
     # and the sparse-checkout file exists
     git = GitInterface(root_dir)
-    topgit = os.path.join(root_dir, ".git", "modules")
-    gitsparse = os.path.join(topgit, name, "info", "sparse-checkout")
-    if os.path.isfile(gitsparse):
-        logger.warning("submodule {} is already initialized".format(name))
-        return
 
     # initialize a new git repo and set the sparse checkout flag
     sprepo_git = GitInterface(os.path.join(root_dir, path))
@@ -175,16 +170,31 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # set the repository remote
     sprepo_git.git_operation("remote", "add", "origin", url)
 
+
+    if os.path.isfile(os.path.join(root_dir, ".git")):
+        with open(os.path.join(root_dir, ".git")) as f:
+            gitpath = os.path.abspath(os.path.join(root_dir,f.read().split()[1]))
+        print(f"gitpath is {gitpath}")
+        topgit = os.path.join(gitpath, "modules")
+    else:                      
+        topgit = os.path.join(root_dir, ".git", "modules")
+    print(f"topgit is {topgit}")
     if not os.path.isdir(topgit):
         os.makedirs(topgit)
     topgit = os.path.join(topgit, name)
+    print(f"topgit is {topgit}")
+    if os.path.isdir(os.path.join(root_dir,path,".git")):
+        shutil.move(os.path.join(root_dir,path, ".git"), topgit)
+        with open(os.path.join(root_dir,path, ".git"), "w") as f:
+            f.write("gitdir: " + os.path.relpath(topgit, path))
+            
+    gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+    if os.path.isfile(gitsparse):
+        logger.warning("submodule {} is already initialized".format(name))
+        return
 
-    shutil.move(os.path.join(path, ".git"), topgit)
-
-    shutil.copy(os.path.join(path, sparsefile), gitsparse)
 
-    with open(os.path.join(path, ".git"), "w") as f:
-        f.write("gitdir: " + os.path.relpath(topgit, path))
+    shutil.copy(os.path.join(root_dir,path, sparsefile), gitsparse)
 
     # Finally checkout the repo
     sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")

From 8c9c123bd687e857a0d01205ddd0a3d9849fe6ec Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 8 Jan 2024 14:35:57 -0700
Subject: [PATCH 035/161] need to replace ssh with https

---
 git-fleximod | 39 +++++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 51d0372655..fbd6099a22 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -162,7 +162,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # Check first if the module is already defined
     # and the sparse-checkout file exists
     git = GitInterface(root_dir)
-
+    print(f"root_dir is {root_dir}")
     # initialize a new git repo and set the sparse checkout flag
     sprepo_git = GitInterface(os.path.join(root_dir, path))
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
@@ -170,7 +170,6 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # set the repository remote
     sprepo_git.git_operation("remote", "add", "origin", url)
 
-
     if os.path.isfile(os.path.join(root_dir, ".git")):
         with open(os.path.join(root_dir, ".git")) as f:
             gitpath = os.path.abspath(os.path.join(root_dir,f.read().split()[1]))
@@ -224,20 +223,23 @@ def submodules_status(gitmodules, root_dir):
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
         newpath = os.path.join(root_dir, path)
-        with utils.pushd(newpath):
-            git = GitInterface(newpath)
-            atag = git.git_operation("describe", "--tags", "--always").rstrip()
-            if tag and atag != tag:
-                print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
-            elif tag:
-                print(f"Submodule {name} at tag {tag}")
-            else:
-                print(
-                    f"Submodule {name} has no tag defined in .gitmodules, module at {atag}"
-                )
-            status = git.git_operation("status")
-            if "nothing to commit" not in status:
-                print(status)
+        if not os.path.exists(os.path.join(newpath, ".git")):
+            print(f"Submodule {name} not checked out")
+        else:
+            with utils.pushd(newpath):
+                git = GitInterface(newpath)
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                if tag and atag != tag:
+                    print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
+                elif tag:
+                    print(f"Submodule {name} at tag {tag}")
+                else:
+                    print(
+                        f"Submodule {name} has no tag defined in .gitmodules, module at {atag}"
+                    )
+                status = git.git_operation("status")
+                if "nothing to commit" not in status:
+                    print(status)
 
 
 def submodules_update(gitmodules, root_dir):
@@ -293,6 +295,11 @@ def submodules_install(gitmodules, root_dir, requiredlist):
             if "T:F" == fxrequired:
                 print("Skipping optional component {}".format(name))
             continue
+        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
+        # but cime has one since e3sm prefers ssh to https
+        if url.startswith("git@"):
+            url = url.replace("git@github.com:", "https://github.com")
+            
         if fxsparse:
             logger.debug(
                 f"Callng submodule_sparse_checkout({root_dir}, {name}, {url}, {path}, {fxsparse}, {fxtag}"

From 2752eccf37f28d3b7505d7d3c1faeb352c1a1bd0 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 8 Jan 2024 14:45:48 -0700
Subject: [PATCH 036/161] change from ssh to https

---
 git-fleximod | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index fbd6099a22..179bc2ca98 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -201,9 +201,12 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     print(f"Successfully checked out {name}")
 
 
-def submodule_checkout(root, name, path):
+def submodule_checkout(root, name, path, url=None):
     git = GitInterface(root)
     repodir = os.path.join(root, path)
+    # if url is provided update to the new url
+    if url:
+        git.git_operation("submodule", "set-url", path, url)
     git.git_operation("submodule", "update", "--init", path)
     # Look for a .gitmodules file in the newly checkedout repo
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
@@ -309,7 +312,7 @@ def submodules_install(gitmodules, root_dir, requiredlist):
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
-            submodule_checkout(root_dir, name, path)
+            submodule_checkout(root_dir, name, path, url=url)
 
 
 def _main_func():

From 2092f3ff672051f4c34de4986f7b59debbc30920 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 8 Jan 2024 14:58:44 -0700
Subject: [PATCH 037/161] fix ssh issue

---
 git-fleximod | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 179bc2ca98..0fcbc1feef 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -205,10 +205,19 @@ def submodule_checkout(root, name, path, url=None):
     git = GitInterface(root)
     repodir = os.path.join(root, path)
     # if url is provided update to the new url
+    tmpurl = None
     if url:
+        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
+        # but cime has one since e3sm prefers ssh to https
+        if url.startswith("git@"):
+            tmpurl = url
+            url = url.replace("git@github.com:", "https://github.com")            
         git.git_operation("submodule", "set-url", path, url)
     git.git_operation("submodule", "update", "--init", path)
     # Look for a .gitmodules file in the newly checkedout repo
+    if tmpurl:
+        git.git_operation("submodule", "set-url", path, tmpurl)
+        
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir}")
@@ -298,10 +307,6 @@ def submodules_install(gitmodules, root_dir, requiredlist):
             if "T:F" == fxrequired:
                 print("Skipping optional component {}".format(name))
             continue
-        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
-        # but cime has one since e3sm prefers ssh to https
-        if url.startswith("git@"):
-            url = url.replace("git@github.com:", "https://github.com")
             
         if fxsparse:
             logger.debug(
@@ -312,6 +317,7 @@ def submodules_install(gitmodules, root_dir, requiredlist):
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
+            
             submodule_checkout(root_dir, name, path, url=url)
 
 

From 4fd30a41f604b2bb6fbb8533429b60b4f1d0adc5 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 8 Jan 2024 15:07:31 -0700
Subject: [PATCH 038/161] remove debug print statments

---
 git-fleximod | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 0fcbc1feef..404b598f2b 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -162,7 +162,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # Check first if the module is already defined
     # and the sparse-checkout file exists
     git = GitInterface(root_dir)
-    print(f"root_dir is {root_dir}")
+
     # initialize a new git repo and set the sparse checkout flag
     sprepo_git = GitInterface(os.path.join(root_dir, path))
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
@@ -173,15 +173,14 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     if os.path.isfile(os.path.join(root_dir, ".git")):
         with open(os.path.join(root_dir, ".git")) as f:
             gitpath = os.path.abspath(os.path.join(root_dir,f.read().split()[1]))
-        print(f"gitpath is {gitpath}")
         topgit = os.path.join(gitpath, "modules")
     else:                      
         topgit = os.path.join(root_dir, ".git", "modules")
-    print(f"topgit is {topgit}")
+
     if not os.path.isdir(topgit):
         os.makedirs(topgit)
     topgit = os.path.join(topgit, name)
-    print(f"topgit is {topgit}")
+
     if os.path.isdir(os.path.join(root_dir,path,".git")):
         shutil.move(os.path.join(root_dir,path, ".git"), topgit)
         with open(os.path.join(root_dir,path, ".git"), "w") as f:

From 86a5a72abcbf9709a01ad01fa6c01229700a13f2 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 8 Jan 2024 16:59:21 -0700
Subject: [PATCH 039/161] fix issue with sparse checkout

---
 git-fleximod | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 404b598f2b..cb1c948d6c 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -170,21 +170,23 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # set the repository remote
     sprepo_git.git_operation("remote", "add", "origin", url)
 
+    superroot = git.git_operation("rev-parse", "--show-superproject-working-tree")
     if os.path.isfile(os.path.join(root_dir, ".git")):
         with open(os.path.join(root_dir, ".git")) as f:
             gitpath = os.path.abspath(os.path.join(root_dir,f.read().split()[1]))
-        topgit = os.path.join(gitpath, "modules")
+        topgit = os.path.abspath(os.path.join(gitpath, "modules"))
     else:                      
-        topgit = os.path.join(root_dir, ".git", "modules")
+        topgit = os.path.abspath(os.path.join(root_dir, ".git", "modules"))
 
     if not os.path.isdir(topgit):
         os.makedirs(topgit)
     topgit = os.path.join(topgit, name)
+    logger.debug(f"root_dir is {root_dir} topgit is {topgit} superroot is {superroot}")
 
     if os.path.isdir(os.path.join(root_dir,path,".git")):
         shutil.move(os.path.join(root_dir,path, ".git"), topgit)
         with open(os.path.join(root_dir,path, ".git"), "w") as f:
-            f.write("gitdir: " + os.path.relpath(topgit, path))
+            f.write("gitdir: " + os.path.relpath(topgit, os.path.join(root_dir,path)))
             
     gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
     if os.path.isfile(gitsparse):

From a9130f296d068f441994084f86c2fd376c66d6be Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 9 Jan 2024 09:42:17 -0700
Subject: [PATCH 040/161] more error checking

---
 git-fleximod          | 4 +++-
 modules/gitmodules.py | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index cb1c948d6c..2a00d41066 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -221,7 +221,7 @@ def submodule_checkout(root, name, path, url=None):
         
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name} {repodir}")
+        print(f"Recursively checking out submodules of {name} ")
         gitmodules = GitModules(repodir)
         submodules_install(gitmodules, repodir, ["I:T"])
     if os.path.exists(os.path.join(repodir, ".git")):
@@ -235,6 +235,8 @@ def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
+        if not path:
+            utils.fatal_error("No path found in .gitmodules for {}".format(name))
         newpath = os.path.join(root_dir, path)
         if not os.path.exists(os.path.join(newpath, ".git")):
             print(f"Submodule {name} not checked out")
diff --git a/modules/gitmodules.py b/modules/gitmodules.py
index 9e38a5806c..64b539a38f 100644
--- a/modules/gitmodules.py
+++ b/modules/gitmodules.py
@@ -51,7 +51,8 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
             return None
 
     def save(self):
-        self.write(open(self.conf_file, "w"))
+        print("Called gitmodules save, not expected")
+        #        self.write(open(self.conf_file, "w"))
 
     def sections(self):
         """Strip the submodule part out of section and just use the name"""

From 3ccf8a3adf15825ff440f9430c9cf3f56b99fe4b Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 9 Jan 2024 17:44:28 -0700
Subject: [PATCH 041/161] hack to prevent file corruption

---
 git-fleximod | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/git-fleximod b/git-fleximod
index 2a00d41066..e8a719aae7 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -203,6 +203,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
 
 
 def submodule_checkout(root, name, path, url=None):
+    shutil.copy(os.path.join(root,".gitmodules"), os.path.join(root,".save.gitmodules"))
     git = GitInterface(root)
     repodir = os.path.join(root, path)
     # if url is provided update to the new url
@@ -214,7 +215,9 @@ def submodule_checkout(root, name, path, url=None):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
         git.git_operation("submodule", "set-url", path, url)
-    git.git_operation("submodule", "update", "--init", path)
+    git.git_operation("submodule", "update", "--init", "--", path)
+    shutil.copy(os.path.join(root,".save.gitmodules"), os.path.join(root,".gitmodules"))
+
     # Look for a .gitmodules file in the newly checkedout repo
     if tmpurl:
         git.git_operation("submodule", "set-url", path, tmpurl)

From 840499c5601b1c944ac509b38558da0e8323ed9b Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 9 Jan 2024 18:01:01 -0700
Subject: [PATCH 042/161] ignore untracked files in submodules

---
 git-fleximod | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index e8a719aae7..04fcf20456 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -216,7 +216,8 @@ def submodule_checkout(root, name, path, url=None):
             url = url.replace("git@github.com:", "https://github.com")            
         git.git_operation("submodule", "set-url", path, url)
     git.git_operation("submodule", "update", "--init", "--", path)
-    shutil.copy(os.path.join(root,".save.gitmodules"), os.path.join(root,".gitmodules"))
+    
+    shutil.move(os.path.join(root,".save.gitmodules"), os.path.join(root,".gitmodules"))
 
     # Look for a .gitmodules file in the newly checkedout repo
     if tmpurl:
@@ -255,7 +256,7 @@ def submodules_status(gitmodules, root_dir):
                     print(
                         f"Submodule {name} has no tag defined in .gitmodules, module at {atag}"
                     )
-                status = git.git_operation("status")
+                status = git.git_operation("status","--ignore-submodules","untracked")
                 if "nothing to commit" not in status:
                     print(status)
 

From a25b257efc706ebc03468be128ec9c566791b05e Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 10 Jan 2024 05:24:18 -0700
Subject: [PATCH 043/161] a better solution to the file coruption issue

---
 git-fleximod          | 9 ++++-----
 modules/gitmodules.py | 6 ++++++
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 04fcf20456..9726059103 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -203,22 +203,21 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
 
 
 def submodule_checkout(root, name, path, url=None):
-    shutil.copy(os.path.join(root,".gitmodules"), os.path.join(root,".save.gitmodules"))
     git = GitInterface(root)
     repodir = os.path.join(root, path)
     # if url is provided update to the new url
     tmpurl = None
     if url:
         # ssh urls cause problems for those who dont have git accounts with ssh keys defined
-        # but cime has one since e3sm prefers ssh to https
+        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
+        # opened with a GitModules object we don't need to worry about restoring the file here
+        # it will be done by the GitModules class
         if url.startswith("git@"):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
         git.git_operation("submodule", "set-url", path, url)
     git.git_operation("submodule", "update", "--init", "--", path)
     
-    shutil.move(os.path.join(root,".save.gitmodules"), os.path.join(root,".gitmodules"))
-
     # Look for a .gitmodules file in the newly checkedout repo
     if tmpurl:
         git.git_operation("submodule", "set-url", path, tmpurl)
@@ -345,7 +344,7 @@ def _main_func():
         file_path = utils.find_upwards(root_dir, file_name)
 
         if file_path is None:
-            fatal_error(
+            utils.fatal_error(
                 "No {} found in {} or any of it's parents".format(file_name, root_dir)
             )
         root_dir = os.path.dirname(file_path)
diff --git a/modules/gitmodules.py b/modules/gitmodules.py
index 64b539a38f..fe05e3ca62 100644
--- a/modules/gitmodules.py
+++ b/modules/gitmodules.py
@@ -1,4 +1,5 @@
 import os
+import shutil
 from configparser import ConfigParser
 
 from modules.lstripreader import LstripReader
@@ -20,6 +21,8 @@ def __init__(
         """
         ConfigParser.__init__(self)
         self.conf_file = os.path.join(confpath, conffile)
+        # first create a backup of this file to be restored on deletion of the object
+        shutil.copy(self.conf_file, self.conf_file+".save")
         self.read_file(LstripReader(self.conf_file), source=conffile)
         self.includelist = includelist
         self.excludelist = excludelist
@@ -54,6 +57,9 @@ def save(self):
         print("Called gitmodules save, not expected")
         #        self.write(open(self.conf_file, "w"))
 
+    def __del__(self):
+        shutil.move(self.conf_file+".save", self.conf_file)
+            
     def sections(self):
         """Strip the submodule part out of section and just use the name"""
         names = []

From 657f110a761e2c49524e2f2dd64c139968b3ef2c Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 10 Jan 2024 10:48:30 -0700
Subject: [PATCH 044/161] awkward solution for ssh urls

---
 git-fleximod | 32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 9726059103..206359e39b 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -202,11 +202,14 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     print(f"Successfully checked out {name}")
 
 
-def submodule_checkout(root, name, path, url=None):
+def submodule_checkout(root, name, path, url=None, tag=None):
     git = GitInterface(root)
     repodir = os.path.join(root, path)
+
     # if url is provided update to the new url
     tmpurl = None
+
+    # Look for a .gitmodules file in the newly checkedout repo
     if url:
         # ssh urls cause problems for those who dont have git accounts with ssh keys defined
         # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
@@ -215,22 +218,31 @@ def submodule_checkout(root, name, path, url=None):
         if url.startswith("git@"):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
-        git.git_operation("submodule", "set-url", path, url)
-    git.git_operation("submodule", "update", "--init", "--", path)
-    
-    # Look for a .gitmodules file in the newly checkedout repo
-    if tmpurl:
-        git.git_operation("submodule", "set-url", path, tmpurl)
-        
+
+            git.git_operation("clone", "-b", tag, url, path)
+            print(f"Using {url} for {name}")
+            #            print(git.git_operation("submodule", "set-url", name, url))
+            #        if "cprnc" in repodir:
+            #            with open(os.path.join(root,".gitmodules"),"r") as f:
+            #                print(f.read())
+        print(f"calling update for {name}")
+    if not tmpurl:
+        logger.debug(git.git_operation("submodule", "update", "--init", "--", name))
+
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name} ")
+        print(f"Recursively checking out submodules of {name} {repodir} {url}")
         gitmodules = GitModules(repodir)
         submodules_install(gitmodules, repodir, ["I:T"])
     if os.path.exists(os.path.join(repodir, ".git")):
         print(f"Successfully checked out {name}")
     else:
         utils.fatal_error(f"Failed to checkout {name}")
+
+    
+    if tmpurl:
+        print(git.git_operation("restore", ".gitmodules"))
+        print(f"Using {tmpurl} for {name}")
     return
 
 
@@ -324,7 +336,7 @@ def submodules_install(gitmodules, root_dir, requiredlist):
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
             
-            submodule_checkout(root_dir, name, path, url=url)
+            submodule_checkout(root_dir, name, path, url=url, tag=fxtag)
 
 
 def _main_func():

From 4879c7530523b8b7a16c11a9c113755d8b0e4a85 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 10 Jan 2024 10:57:31 -0700
Subject: [PATCH 045/161] remove debug print statements

---
 git-fleximod | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/git-fleximod b/git-fleximod
index 206359e39b..f78dfa25e1 100755
--- a/git-fleximod
+++ b/git-fleximod
@@ -218,16 +218,10 @@ def submodule_checkout(root, name, path, url=None, tag=None):
         if url.startswith("git@"):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
-
             git.git_operation("clone", "-b", tag, url, path)
-            print(f"Using {url} for {name}")
-            #            print(git.git_operation("submodule", "set-url", name, url))
-            #        if "cprnc" in repodir:
-            #            with open(os.path.join(root,".gitmodules"),"r") as f:
-            #                print(f.read())
-        print(f"calling update for {name}")
+
     if not tmpurl:
-        logger.debug(git.git_operation("submodule", "update", "--init", "--", name))
+        logger.debug(git.git_operation("submodule", "update", "--init", "--", path))
 
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
@@ -239,10 +233,9 @@ def submodule_checkout(root, name, path, url=None, tag=None):
     else:
         utils.fatal_error(f"Failed to checkout {name}")
 
-    
     if tmpurl:
         print(git.git_operation("restore", ".gitmodules"))
-        print(f"Using {tmpurl} for {name}")
+
     return
 
 

From 661ba5efc813fa910e7fc43172a513a177d2e013 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 10 Jan 2024 17:29:53 -0700
Subject: [PATCH 046/161] update for distribution

---
 setup.py                                  | 25 +++++----
 {modules => src/fleximod}/__init__.py     |  0
 {modules => src/fleximod}/gitinterface.py | 13 +++--
 {modules => src/fleximod}/gitmodules.py   | 12 +++--
 {modules => src/fleximod}/lstripreader.py |  0
 {modules => src/fleximod}/utils.py        |  0
 src/fleximod/version.py                   |  1 +
 git-fleximod => src/git-fleximod          | 62 +++++++++++++----------
 version.txt                               |  1 -
 9 files changed, 70 insertions(+), 44 deletions(-)
 rename {modules => src/fleximod}/__init__.py (100%)
 rename {modules => src/fleximod}/gitinterface.py (87%)
 rename {modules => src/fleximod}/gitmodules.py (83%)
 rename {modules => src/fleximod}/lstripreader.py (100%)
 rename {modules => src/fleximod}/utils.py (100%)
 create mode 100644 src/fleximod/version.py
 rename git-fleximod => src/git-fleximod (90%)
 delete mode 100644 version.txt

diff --git a/setup.py b/setup.py
index 2d4cb3642b..1abf839259 100644
--- a/setup.py
+++ b/setup.py
@@ -1,26 +1,33 @@
 import setuptools
 import os
+from setuptools import setup, find_packages
+from distutils.util import convert_path
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
-with open("version.txt", "r") as fh:
-    version = fh.read()
-    cwd = os.getcwd()
+
+main_ns = {}
+ver_path = convert_path('src/fleximod/version.py')
+with open(ver_path) as ver_file:
+    exec(ver_file.read(), main_ns)
+
+    
 setuptools.setup(
-    name="git-fleximod",                     # This is the name of the package
-    version=version,                        # The initial release version
+    scripts=["src/git-fleximod"],                     # This is the name of the package
+    version=main_ns['__version__'],                        # The initial release version
     author="Jim Edwards",                     # Full name of the author
     description="Extended support for git-submodule and git-sparse-checkout",
     long_description=long_description,      # Long description read from the the readme file
     long_description_content_type="text/markdown",
-    packages=setuptools.find_packages(),    # List of all python modules to be installed
+    packages=['fleximod'],    # List of all python modules to be installed
+    package_dir={'fleximod': 'src/fleximod'},
+    package_data={"":['version.txt']},
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],                                      # Information to filter the project on PyPi website
     python_requires='>=3.6',                # Minimum version requirement of the package
-    py_modules=['git-fleximod'],             # Name of the python package
-    package_dir={'git-fleximod':'.'},     # Directory of the source code of the package
-    install_requires=[]                     # Install other dependencies if any
+#    py_modules=['git-fleximod'],             # Name of the python package
+    install_requires=["PyGit"]                     # Install other dependencies if any
 )
diff --git a/modules/__init__.py b/src/fleximod/__init__.py
similarity index 100%
rename from modules/__init__.py
rename to src/fleximod/__init__.py
diff --git a/modules/gitinterface.py b/src/fleximod/gitinterface.py
similarity index 87%
rename from modules/gitinterface.py
rename to src/fleximod/gitinterface.py
index a4e2529256..c127163dc6 100644
--- a/modules/gitinterface.py
+++ b/src/fleximod/gitinterface.py
@@ -1,11 +1,12 @@
 import os
 import logging
-from modules import utils
+from fleximod import utils
 
 class GitInterface:
-    def __init__(self, repo_path):
+    def __init__(self, repo_path, logger):
+        logger.debug("Initialize GitInterface for {}".format(repo_path))
         self.repo_path = repo_path
-
+        self.logger = logger
         try:
             import git
             self._use_module = True
@@ -20,10 +21,10 @@ def __init__(self, repo_path):
             if not os.path.exists(os.path.join(repo_path,".git")):
                 self._init_git_repo()
             msg = "Using shell interface to git"
-        logging.info(msg)
+        self.logger.info(msg)
                 
     def _git_command(self, operation, *args):
-        logging.info(operation)
+        self.logger.info(operation)
         if self._use_module and operation != "submodule":
             return getattr(self.repo.git, operation)(*args)
         else:
@@ -39,6 +40,7 @@ def _init_git_repo(self):
 
     def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *args)
+        self.logger.info(command)
         if isinstance(command, list):
             return utils.execute_subprocess(command, output_to_caller=True)
         else:
@@ -60,4 +62,5 @@ def config_set_value(self, section, name, value):
             writer.release()  # Ensure changes are saved
         else:
             cmd = ("git","-C",self.repo_path,"config", f"{section}.{name}", value)
+            self.logger.info(cmd)
             utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/modules/gitmodules.py b/src/fleximod/gitmodules.py
similarity index 83%
rename from modules/gitmodules.py
rename to src/fleximod/gitmodules.py
index fe05e3ca62..a6f7589319 100644
--- a/modules/gitmodules.py
+++ b/src/fleximod/gitmodules.py
@@ -1,13 +1,12 @@
 import os
 import shutil
 from configparser import ConfigParser
-
-from modules.lstripreader import LstripReader
-
+from fleximod.lstripreader import LstripReader
 
 class GitModules(ConfigParser):
     def __init__(
         self,
+        logger,
         confpath=os.getcwd(),
         conffile=".gitmodules",
         includelist=None,
@@ -19,6 +18,8 @@ def __init__(
         includelist: Optional list of submodules to include.
         excludelist: Optional list of submodules to exclude.
         """
+        self.logger = logger
+        self.logger.debug("Creating a GitModules object {} {} {} {}".format(confpath,conffile,includelist,excludelist))
         ConfigParser.__init__(self)
         self.conf_file = os.path.join(confpath, conffile)
         # first create a backup of this file to be restored on deletion of the object
@@ -33,6 +34,7 @@ def set(self, name, option, value):
         Ensures the appropriate section exists for the submodule.
         Calls the parent class's set method to store the value.
         """
+        self.logger.debug("set called {} {} {}".format(name,option,value))
         section = f'submodule "{name}"'
         if not self.has_section(section):
             self.add_section(section)
@@ -45,6 +47,7 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
         Uses the parent class's get method to access the value.
         Handles potential errors if the section or option doesn't exist.
         """
+        self.logger.debug("get called {} {}".format(name,option))
         section = f'submodule "{name}"'
         try:
             return ConfigParser.get(
@@ -58,10 +61,12 @@ def save(self):
         #        self.write(open(self.conf_file, "w"))
 
     def __del__(self):
+        self.logger.debug("Destroying GitModules object")
         shutil.move(self.conf_file+".save", self.conf_file)
             
     def sections(self):
         """Strip the submodule part out of section and just use the name"""
+        self.logger.debug("calling GitModules sections iterator")
         names = []
         for section in ConfigParser.sections(self):
             name = section[11:-1]
@@ -73,5 +78,6 @@ def sections(self):
         return names
 
     def items(self, name, raw=False, vars=None):
+        self.logger.debug("calling GitModules items for {}".format(name))
         section = f'submodule "{name}"'
         return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/modules/lstripreader.py b/src/fleximod/lstripreader.py
similarity index 100%
rename from modules/lstripreader.py
rename to src/fleximod/lstripreader.py
diff --git a/modules/utils.py b/src/fleximod/utils.py
similarity index 100%
rename from modules/utils.py
rename to src/fleximod/utils.py
diff --git a/src/fleximod/version.py b/src/fleximod/version.py
new file mode 100644
index 0000000000..8ce9b3623b
--- /dev/null
+++ b/src/fleximod/version.py
@@ -0,0 +1 @@
+__version__ = '0.1.3'
diff --git a/git-fleximod b/src/git-fleximod
similarity index 90%
rename from git-fleximod
rename to src/git-fleximod
index f78dfa25e1..dd2adb0f9d 100755
--- a/git-fleximod
+++ b/src/git-fleximod
@@ -4,13 +4,12 @@ import os
 import shutil
 import logging
 import argparse
-from modules import utils
-from modules.gitinterface import GitInterface
-from modules.gitmodules import GitModules
-
-logger = logging.getLogger(__name__)
-logger.propogate = False
-
+from fleximod import utils
+from fleximod.gitinterface import GitInterface
+from fleximod.gitmodules import GitModules
+from fleximod.version import __version__
+# logger variable is global
+logger = None
 
 def commandline_arguments(args=None):
     description = """
@@ -84,9 +83,9 @@ def commandline_arguments(args=None):
     parser.add_argument(
         "-V",
         "--version",
-        action="store_true",
-        default=False,
-        help="Print manage_externals version and exit.",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
     )
 
     #
@@ -136,14 +135,21 @@ def commandline_arguments(args=None):
     if not action:
         action = "install"
 
+    if options.debug:
+        level = logging.DEBUG
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level,
+        format="%(name)s - %(levelname)s - %(message)s",
+        handlers=[logging.FileHandler("fleximod.log"), logging.StreamHandler()],
+    )
     if options.version:
-        version_info = ""
-        version_file_path = os.path.join(os.path.dirname(__file__), "version.txt")
-        with open(version_file_path) as f:
-            version_info = f.readlines()[0].strip()
-        print(version_info)
-        sys.exit(0)
-
+        exit()
+    
     return (
         options.path,
         options.gitmodules,
@@ -161,10 +167,10 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
         os.makedirs(path)
     # Check first if the module is already defined
     # and the sparse-checkout file exists
-    git = GitInterface(root_dir)
+    git = GitInterface(root_dir, logger)
 
     # initialize a new git repo and set the sparse checkout flag
-    sprepo_git = GitInterface(os.path.join(root_dir, path))
+    sprepo_git = GitInterface(os.path.join(root_dir, path), logger)
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
 
     # set the repository remote
@@ -203,7 +209,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
 
 
 def submodule_checkout(root, name, path, url=None, tag=None):
-    git = GitInterface(root)
+    git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
 
     # if url is provided update to the new url
@@ -226,7 +232,7 @@ def submodule_checkout(root, name, path, url=None, tag=None):
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir} {url}")
-        gitmodules = GitModules(repodir)
+        gitmodules = GitModules(logger,confpath=repodir)
         submodules_install(gitmodules, repodir, ["I:T"])
     if os.path.exists(os.path.join(repodir, ".git")):
         print(f"Successfully checked out {name}")
@@ -250,7 +256,7 @@ def submodules_status(gitmodules, root_dir):
             print(f"Submodule {name} not checked out")
         else:
             with utils.pushd(newpath):
-                git = GitInterface(newpath)
+                git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
                 if tag and atag != tag:
                     print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
@@ -274,7 +280,7 @@ def submodules_update(gitmodules, root_dir):
         if os.path.exists(os.path.join(path, ".git")):
             submoddir = os.path.join(root_dir, path)
             with utils.pushd(submoddir):
-                git = GitInterface(submoddir)
+                git = GitInterface(submoddir, logger)
                 # first make sure the url is correct
                 upstream = git.git_operation("ls-remote", "--get-url").rstrip()
                 newremote = "origin"
@@ -342,8 +348,11 @@ def _main_func():
         verbose,
         action,
     ) = commandline_arguments()
-    if verbose:
-        print(f"action is {action}")
+    # Get a logger for the package
+    global logger
+    logger = logging.getLogger(__name__)
+        
+    logger.info(f"action is {action}")
 
     if not os.path.isfile(os.path.join(root_dir, file_name)):
         file_path = utils.find_upwards(root_dir, file_name)
@@ -353,8 +362,9 @@ def _main_func():
                 "No {} found in {} or any of it's parents".format(file_name, root_dir)
             )
         root_dir = os.path.dirname(file_path)
-    print(f"root_dir is {root_dir}")
+    logger.info(f"root_dir is {root_dir}")
     gitmodules = GitModules(
+        logger,
         confpath=root_dir,
         conffile=file_name,
         includelist=includelist,
diff --git a/version.txt b/version.txt
deleted file mode 100644
index a3dce6cd3a..0000000000
--- a/version.txt
+++ /dev/null
@@ -1 +0,0 @@
-v0.0.2

From b22bab6c5c359a9635493dd90cc8d17af03321b9 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 11 Jan 2024 11:03:15 -0700
Subject: [PATCH 047/161] fix error with version flag

---
 src/git-fleximod | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index dd2adb0f9d..d45acb14ed 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -147,7 +147,7 @@ def commandline_arguments(args=None):
         format="%(name)s - %(levelname)s - %(message)s",
         handlers=[logging.FileHandler("fleximod.log"), logging.StreamHandler()],
     )
-    if options.version:
+    if hasattr(options, 'version'):
         exit()
     
     return (

From e81099a63708e4e5cace47b6a1fe39bafee694b5 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 11 Jan 2024 11:04:10 -0700
Subject: [PATCH 048/161] update version to 0.1.4

---
 src/fleximod/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index 8ce9b3623b..7525d19930 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.1.3'
+__version__ = '0.1.4'

From 1a80e973560b86ccee228274dbb2b38e17037abc Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 15 Jan 2024 07:52:01 -0700
Subject: [PATCH 049/161] fix issues with rerunning

---
 src/fleximod/version.py |  2 +-
 src/git-fleximod        | 25 ++++++++++++++++++++++---
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index 7525d19930..2fb25139f1 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.1.4'
+__version__ = '0.1.6'
diff --git a/src/git-fleximod b/src/git-fleximod
index d45acb14ed..d7bc2c1202 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -8,6 +8,7 @@ from fleximod import utils
 from fleximod.gitinterface import GitInterface
 from fleximod.gitmodules import GitModules
 from fleximod.version import __version__
+from configparser import NoOptionError
 # logger variable is global
 logger = None
 
@@ -170,7 +171,21 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     git = GitInterface(root_dir, logger)
 
     # initialize a new git repo and set the sparse checkout flag
-    sprepo_git = GitInterface(os.path.join(root_dir, path), logger)
+    sprep_repo = os.path.join(root_dir, path)
+    sprepo_git = GitInterface(sprep_repo, logger)
+    if os.path.exists(os.path.join(sprep_repo,".git")):
+        try:
+            logger.info("Submodule {} found".format(name))
+            chk = sprepo_git.config_get_value("core", "sparseCheckout")
+            if chk == "true":
+                logger.info("Sparse submodule {} already checked out".format(name))
+                return
+        except NoOptionError:
+            logger.debug("Sparse submodule {} not present".format(name))
+        except Exception as e:
+            utils.fatal_error("Unexpected error {} occured.".format(e))
+
+
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
 
     # set the repository remote
@@ -211,7 +226,9 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
 def submodule_checkout(root, name, path, url=None, tag=None):
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
-
+    if os.path.exists(os.path.join(repodir, ".git")):
+        logger.info("Submodule {} already checked out".format(name))
+        return
     # if url is provided update to the new url
     tmpurl = None
 
@@ -225,7 +242,9 @@ def submodule_checkout(root, name, path, url=None, tag=None):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
             git.git_operation("clone", "-b", tag, url, path)
-
+            # Now need to move the .git dir to the submodule location
+            
+            
     if not tmpurl:
         logger.debug(git.git_operation("submodule", "update", "--init", "--", path))
 

From 13eb8b87bcfba34eb70c5bd3a39e570d2527a452 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 15 Jan 2024 07:53:10 -0700
Subject: [PATCH 050/161] update setup.py

---
 setup.cfg | 2 ++
 setup.py  | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 setup.cfg

diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000000..4f727fa0b1
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,2 @@
+[metadata]
+license_file = License
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 1abf839259..f891593865 100644
--- a/setup.py
+++ b/setup.py
@@ -16,6 +16,8 @@
     scripts=["src/git-fleximod"],                     # This is the name of the package
     version=main_ns['__version__'],                        # The initial release version
     author="Jim Edwards",                     # Full name of the author
+    maintainer="jedwards4b",
+    license="MIT License",
     description="Extended support for git-submodule and git-sparse-checkout",
     long_description=long_description,      # Long description read from the the readme file
     long_description_content_type="text/markdown",
@@ -29,5 +31,5 @@
     ],                                      # Information to filter the project on PyPi website
     python_requires='>=3.6',                # Minimum version requirement of the package
 #    py_modules=['git-fleximod'],             # Name of the python package
-    install_requires=["PyGit"]                     # Install other dependencies if any
+    install_requires=["GitPython"]                     # Install other dependencies if any
 )

From 5a590c541ca168c879d3726957c102f878af0f6d Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 15 Jan 2024 09:36:10 -0700
Subject: [PATCH 051/161] update version

---
 src/fleximod/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index 2fb25139f1..124e46203b 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.1.6'
+__version__ = '0.1.7'

From 8c92b14204c80b0b444a3155a1ce52e5dca8411b Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 17 Jan 2024 16:23:33 -0700
Subject: [PATCH 052/161] provide more info for status of uninstalled
 submodules

---
 src/fleximod/version.py |  2 +-
 src/git-fleximod        | 20 ++++++++++++++++++--
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index 124e46203b..c3bb2961b6 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.1.7'
+__version__ = '0.1.8'
diff --git a/src/git-fleximod b/src/git-fleximod
index d7bc2c1202..3e743c3f5c 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -127,7 +127,8 @@ def commandline_arguments(args=None):
     else:
         options = parser.parse_args()
 
-    if options.optional:
+# explicitly listing a component overrides the optional flag    
+    if options.optional or options.components:
         fxrequired = ["T:T", "T:F", "I:T"]
     else:
         fxrequired = ["T:T", "I:T"]
@@ -271,8 +272,23 @@ def submodules_status(gitmodules, root_dir):
         if not path:
             utils.fatal_error("No path found in .gitmodules for {}".format(name))
         newpath = os.path.join(root_dir, path)
+        logger.debug("newpath is {}".format(newpath))
         if not os.path.exists(os.path.join(newpath, ".git")):
-            print(f"Submodule {name} not checked out")
+            rootgit = GitInterface(root_dir, logger)
+            # submodule commands use path, not name
+            nhash = (rootgit.git_operation("submodule","status",path).split()[0])[1:]
+            url = gitmodules.get(name, "url")
+            tags = rootgit.git_operation("ls-remote","--tags",url)
+            atag = None
+            for htag in tags.split('\n'):
+                if tag in htag:
+                    atag = (htag.split()[1])[10:]
+                    break
+            if tag == atag:
+                print(f"Submodule {name} not checked out, aligned at tag {tag}")
+            else:
+                print(f"Submodule {name} not checked out, out of sync at tag {atag}, expected tag is {tag}")
+                
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)

From 43225eac86892d074453cbdc622124b2eedf48cf Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 18 Jan 2024 16:49:52 -0700
Subject: [PATCH 053/161] add test action

---
 escomp_install          | 25 +++++++++++++++++++
 src/fleximod/version.py |  2 +-
 src/git-fleximod        | 55 ++++++++++++++++++++++++-----------------
 3 files changed, 59 insertions(+), 23 deletions(-)
 create mode 100644 escomp_install

diff --git a/escomp_install b/escomp_install
new file mode 100644
index 0000000000..ae782e72a4
--- /dev/null
+++ b/escomp_install
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# updates git-fleximod in an ESCOMP model
+# this script should be run from the model root directory, it expects
+# git-fleximod to already be installed with the script in bin
+# and the classes in lib/python/site-packages
+import sys
+import shutil
+import os
+
+from glob import iglob
+
+fleximod_root = sys.argv[1]
+fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
+if os.path.isfile(fleximod_path):
+   with open(fleximod_path,"r") as f:
+        fleximod = f.readlines()
+   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
+        for line in fleximod:
+            f.write(line)
+            if "import argparse" in line:
+               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
+
+   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
+       shutil.copy(file,
+        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index c3bb2961b6..1c98a23a89 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.1.8'
+__version__ = '0.1.9'
diff --git a/src/git-fleximod b/src/git-fleximod
index 3e743c3f5c..fce79b8552 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -23,7 +23,7 @@ def commandline_arguments(args=None):
     #
     # user options
     #
-    choices = ["update", "install", "status"]
+    choices = ["update", "install", "status", "test"]
     parser.add_argument(
         "action",
         choices=choices,
@@ -107,21 +107,6 @@ def commandline_arguments(args=None):
         "information to the screen and log file.",
     )
 
-    logging_group = parser.add_mutually_exclusive_group()
-
-    logging_group.add_argument(
-        "--logging",
-        dest="do_logging",
-        action="store_true",
-        help="DEVELOPER: enable logging.",
-    )
-    logging_group.add_argument(
-        "--no-logging",
-        dest="do_logging",
-        action="store_false",
-        default=False,
-        help="DEVELOPER: disable logging " "(this is the default)",
-    )
     if args:
         options = parser.parse_args(args)
     else:
@@ -266,6 +251,7 @@ def submodule_checkout(root, name, path, url=None, tag=None):
 
 
 def submodules_status(gitmodules, root_dir):
+    testfails = 0
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
@@ -288,23 +274,27 @@ def submodules_status(gitmodules, root_dir):
                 print(f"Submodule {name} not checked out, aligned at tag {tag}")
             else:
                 print(f"Submodule {name} not checked out, out of sync at tag {atag}, expected tag is {tag}")
-                
+                testfails += 1
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
                 if tag and atag != tag:
                     print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
+                    testfails += 1
                 elif tag:
                     print(f"Submodule {name} at tag {tag}")
                 else:
                     print(
                         f"Submodule {name} has no tag defined in .gitmodules, module at {atag}"
                     )
+                    testfails += 1
+
                 status = git.git_operation("status","--ignore-submodules","untracked")
                 if "nothing to commit" not in status:
                     print(status)
-
+    
+    return testfails
 
 def submodules_update(gitmodules, root_dir):
     for name in gitmodules.sections():
@@ -372,7 +362,26 @@ def submodules_install(gitmodules, root_dir, requiredlist):
             
             submodule_checkout(root_dir, name, path, url=url, tag=fxtag)
 
+def submodules_test(gitmodules, root_dir):
+    # First check that fxtags are present and in sync with submodule hashes
+    testfails = submodules_status(gitmodules, root_dir)
+    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
+    # and that sparse checkout files exist
+    for name in gitmodules.sections():
+        url = gitmodules.get(name, "url")
+        fxurl = gitmodules.get(name, "fxurl")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        path = gitmodules.get(name, "path")
+        if not fxurl or url != fxurl:
+            print(f"submodule {name} url {url} not in sync with required {fxurl}")
+            testfails += 1
+        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
+            print(f"sparse submodule {name} sparse checkout file {fxsparse} not found")
+            testfails += 1
+    return testfails
+
 
+            
 def _main_func():
     (
         root_dir,
@@ -405,16 +414,18 @@ def _main_func():
         includelist=includelist,
         excludelist=excludelist,
     )
-
+    retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir)
     elif action == "install":
         submodules_install(gitmodules, root_dir, fxrequired)
     elif action == "status":
         submodules_status(gitmodules, root_dir)
+    elif action == "test":
+        retval = submodules_test(gitmodules, root_dir)
     else:
         utils.fatal_error(f"unrecognized action request {action}")
-
-
+    return(retval)
+        
 if __name__ == "__main__":
-    _main_func()
+    sys.exit(_main_func())

From bbb1b1d98b587ddb5dd455a9ce889c64d53f7151 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 30 Jan 2024 16:18:53 -0700
Subject: [PATCH 054/161] fix issue with status

---
 README.md        | 12 +++++++++++-
 src/git-fleximod | 19 ++++++++++---------
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 910858e79a..cec74c5a66 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,9 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
         install: Install submodules according to configuration.
         status: Display the status of submodules.
         update: Update submodules to the tag indicated in .gitmodules variable fxtag.
+        test: Make sure that fxtags and submodule hashes are consistant,
+              make sure that official urls (as defined by fxurl) are set
+              make sure that fxtags are defined for all submodules
     Additional Options:
         See git fleximod --help for more details.
 
@@ -32,6 +35,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
       - I:T: Internal and required (always checked out).
       - I:F: Internal and optional (checked out with --optional flag).
     fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+    fcurl
 
 ## Sparse Checkouts
 
@@ -39,7 +43,13 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
     in the .gitmodules file to the path of a file containing the desired
     sparse checkout paths. Git-fleximod will automatically configure
     sparse checkout based on this file when applicable commands are run.
-    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set) for details on the format of this file.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
+    for details on the format of this file.
+
+## Tests
+
+   The git fleximod test action is designed to be used by, for example, github workflows
+   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
 
 ## Examples
 
diff --git a/src/git-fleximod b/src/git-fleximod
index fce79b8552..9e2620d7f7 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -4,6 +4,7 @@ import os
 import shutil
 import logging
 import argparse
+import textwrap
 from fleximod import utils
 from fleximod.gitinterface import GitInterface
 from fleximod.gitmodules import GitModules
@@ -23,11 +24,11 @@ def commandline_arguments(args=None):
     #
     # user options
     #
-    choices = ["update", "install", "status", "test"]
+    choices = ["update", "checkout", "status", "test"]
     parser.add_argument(
         "action",
         choices=choices,
-        default="install",
+        default="checkout",
         help=f"Subcommand of fleximod, choices are {choices}",
     )
 
@@ -120,7 +121,7 @@ def commandline_arguments(args=None):
 
     action = options.action
     if not action:
-        action = "install"
+        action = "checkout"
 
     if options.debug:
         level = logging.DEBUG
@@ -238,7 +239,7 @@ def submodule_checkout(root, name, path, url=None, tag=None):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir} {url}")
         gitmodules = GitModules(logger,confpath=repodir)
-        submodules_install(gitmodules, repodir, ["I:T"])
+        submodules_checkout(gitmodules, repodir, ["I:T"])
     if os.path.exists(os.path.join(repodir, ".git")):
         print(f"Successfully checked out {name}")
     else:
@@ -290,9 +291,9 @@ def submodules_status(gitmodules, root_dir):
                     )
                     testfails += 1
 
-                status = git.git_operation("status","--ignore-submodules","untracked")
+                status = git.git_operation("status","--ignore-submodules")
                 if "nothing to commit" not in status:
-                    print(status)
+                    print(textwrap.indent(status,'    '))
     
     return testfails
 
@@ -337,7 +338,7 @@ def submodules_update(gitmodules, root_dir):
                     print(f"submodule {name} up to date.")
 
 
-def submodules_install(gitmodules, root_dir, requiredlist):
+def submodules_checkout(gitmodules, root_dir, requiredlist):
     for name in gitmodules.sections():
         fxrequired = gitmodules.get(name, "fxrequired")
         fxsparse = gitmodules.get(name, "fxsparse")
@@ -417,8 +418,8 @@ def _main_func():
     retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir)
-    elif action == "install":
-        submodules_install(gitmodules, root_dir, fxrequired)
+    elif action == "checkout":
+        submodules_checkout(gitmodules, root_dir, fxrequired)
     elif action == "status":
         submodules_status(gitmodules, root_dir)
     elif action == "test":

From af78aa4de1632ad1bcb8e94bfa7b272294108132 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 30 Jan 2024 16:38:50 -0700
Subject: [PATCH 055/161] update version

---
 src/fleximod/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index 1c98a23a89..7fd229a32b 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.1.9'
+__version__ = '0.2.0'

From 13a2f6b25dda439e74396073b52c3d748b838ea6 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 1 Feb 2024 12:21:58 -0700
Subject: [PATCH 056/161] cleaner format for status output, fix for special
 handling of ssh submodules, fix for 0 length log

---
 setup.cfg        |  5 ++++-
 setup.py         | 10 +++++++++-
 src/git-fleximod | 23 +++++++++++++++--------
 3 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 4f727fa0b1..9a13827a35 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,2 +1,5 @@
 [metadata]
-license_file = License
\ No newline at end of file
+license_file = License
+[build_manpages]
+manpages =
+    man/git-fleximod.1:object=parser:pyfile=bin/git-fleximod
diff --git a/setup.py b/setup.py
index f891593865..f68a4ea9b7 100644
--- a/setup.py
+++ b/setup.py
@@ -2,6 +2,7 @@
 import os
 from setuptools import setup, find_packages
 from distutils.util import convert_path
+from build_manpages import build_manpages, get_build_py_cmd, get_install_cmd
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
@@ -31,5 +32,12 @@
     ],                                      # Information to filter the project on PyPi website
     python_requires='>=3.6',                # Minimum version requirement of the package
 #    py_modules=['git-fleximod'],             # Name of the python package
-    install_requires=["GitPython"]                     # Install other dependencies if any
+    install_requires=["GitPython"],                     # Install other dependencies if any
+    cmdclass={
+      'build_manpages': build_manpages,
+      # Re-define build_py and install commands so the manual pages
+      # are automatically re-generated and installed
+      'build_py': get_build_py_cmd(),
+      'install': get_install_cmd(),
+  }
 )
diff --git a/src/git-fleximod b/src/git-fleximod
index 9e2620d7f7..f80d359c76 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -122,9 +122,11 @@ def commandline_arguments(args=None):
     action = options.action
     if not action:
         action = "checkout"
+    handlers=[logging.StreamHandler()]
 
     if options.debug:
         level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
     elif options.verbose:
         level = logging.INFO
     else:
@@ -133,8 +135,9 @@ def commandline_arguments(args=None):
     logging.basicConfig(
         level=level,
         format="%(name)s - %(levelname)s - %(message)s",
-        handlers=[logging.FileHandler("fleximod.log"), logging.StreamHandler()],
+        handlers=handlers
     )
+    
     if hasattr(options, 'version'):
         exit()
     
@@ -228,7 +231,11 @@ def submodule_checkout(root, name, path, url=None, tag=None):
         if url.startswith("git@"):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
-            git.git_operation("clone", "-b", tag, url, path)
+            git.git_operation("clone", url, path)
+            smgit = GitInterface(path, logger)
+            if not tag:
+                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
+            smgit.git_operation("checkout",tag)
             # Now need to move the .git dir to the submodule location
             
             
@@ -272,28 +279,28 @@ def submodules_status(gitmodules, root_dir):
                     atag = (htag.split()[1])[10:]
                     break
             if tag == atag:
-                print(f"Submodule {name} not checked out, aligned at tag {tag}")
+                print(f"e {name:>20} not checked out, aligned at tag {tag}")
             else:
-                print(f"Submodule {name} not checked out, out of sync at tag {atag}, expected tag is {tag}")
+                print(f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}")
                 testfails += 1
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
                 if tag and atag != tag:
-                    print(f"Submodule {name} {atag} is out of sync with .gitmodules {tag}")
+                    print(f"s {name:>20} {atag} is out of sync with .gitmodules {tag}")
                     testfails += 1
                 elif tag:
-                    print(f"Submodule {name} at tag {tag}")
+                    print(f"  {name:>20} at tag {tag}")
                 else:
                     print(
-                        f"Submodule {name} has no tag defined in .gitmodules, module at {atag}"
+                        f"e {name:>20} has no tag defined in .gitmodules, module at {atag}"
                     )
                     testfails += 1
 
                 status = git.git_operation("status","--ignore-submodules")
                 if "nothing to commit" not in status:
-                    print(textwrap.indent(status,'    '))
+                    print('M'+textwrap.indent(status,'                      '))
     
     return testfails
 

From c21372a088fa6a72c01397eb8c955b5e5cf411d8 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 1 Feb 2024 13:04:22 -0700
Subject: [PATCH 057/161] check for permission in fleximod.log file

---
 src/git-fleximod | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/git-fleximod b/src/git-fleximod
index f80d359c76..cbfa5f4f3d 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -125,6 +125,10 @@ def commandline_arguments(args=None):
     handlers=[logging.StreamHandler()]
 
     if options.debug:
+        try:
+            open("fleximod.log","w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
         level = logging.DEBUG
         handlers.append(logging.FileHandler("fleximod.log"))
     elif options.verbose:

From 07eb5dd3edcde5bfd1f125c85d6935bd0fa3b3cc Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 1 Feb 2024 14:02:34 -0700
Subject: [PATCH 058/161] fix issue with ssh submodule checkout

---
 src/git-fleximod | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index cbfa5f4f3d..2ebb2e5378 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -236,11 +236,28 @@ def submodule_checkout(root, name, path, url=None, tag=None):
             tmpurl = url
             url = url.replace("git@github.com:", "https://github.com")            
             git.git_operation("clone", url, path)
-            smgit = GitInterface(path, logger)
+            smgit = GitInterface(repodir, logger)
             if not tag:
                 tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
             smgit.git_operation("checkout",tag)
             # Now need to move the .git dir to the submodule location
+            rootdotgit = os.path.join(root,".git")
+            if os.path.isfile(rootdotgit):
+                with open(rootdotgit) as f:
+                    line = f.readline()
+                    if line.startswith("gitdir: "):
+                        rootdotgit = line[8:].rstrip()
+            
+            newpath = os.path.abspath(os.path.join(root,rootdotgit,"modules",path))
+            print(f"root is {root} rootdotgit is {rootdotgit} newpath is {newpath}")
+            if not os.path.isdir(os.path.join(newpath,os.pardir)):
+                os.makedirs(os.path.abspath(os.path.join(newpath,os.pardir)))
+
+            shutil.move(os.path.join(repodir,".git"), newpath) 
+            with open(os.path.join(repodir,".git"), "w") as f:
+                f.write("gitdir: "+newpath)
+            
+
             
             
     if not tmpurl:

From a12a5b051580b5f26048ab87ffe0521e4ba135ef Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 1 Feb 2024 14:22:41 -0700
Subject: [PATCH 059/161] add --force option and cowardly refusal

---
 src/git-fleximod | 41 +++++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index 2ebb2e5378..5489ae164f 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -60,6 +60,13 @@ def commandline_arguments(args=None):
         nargs="*",
         help="Component(s) listed in the gitmodules file which should be ignored.",
     )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository."
+    )
 
     parser.add_argument(
         "-o",
@@ -152,6 +159,7 @@ def commandline_arguments(args=None):
         options.components,
         options.exclude,
         options.verbose,
+        options.force,
         action,
     )
 
@@ -281,6 +289,7 @@ def submodule_checkout(root, name, path, url=None, tag=None):
 
 def submodules_status(gitmodules, root_dir):
     testfails = 0
+    localmods = 0
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
@@ -321,11 +330,17 @@ def submodules_status(gitmodules, root_dir):
 
                 status = git.git_operation("status","--ignore-submodules")
                 if "nothing to commit" not in status:
+                    localmods = localmods+1
                     print('M'+textwrap.indent(status,'                      '))
     
-    return testfails
+    return testfails, localmods
 
-def submodules_update(gitmodules, root_dir):
+def submodules_update(gitmodules, root_dir, force):
+    _,localmods = submodules_status(gitmodules, root_dir)
+    print("")
+    if localmods and not force:
+        print(f"Repository has local mods, cowardly refusing to continue, fix issues or use --force to override")
+        return
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
@@ -358,15 +373,20 @@ def submodules_update(gitmodules, root_dir):
                     git.git_operation("fetch", newremote, "--tags")
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
                 if fxtag and fxtag != atag:
-                    print(f"Updating {name} to {fxtag}")
+                    print(f"{name:>20} updated to {fxtag}")
                     git.git_operation("checkout", fxtag)
                 elif not fxtag:
-                    print(f"No fxtag found for submodule {name}")
+                    print(f"No fxtag found for submodule {name:>20}")
                 else:
-                    print(f"submodule {name} up to date.")
+                    print(f"{name:>20} up to date.")
 
 
-def submodules_checkout(gitmodules, root_dir, requiredlist):
+def submodules_checkout(gitmodules, root_dir, requiredlist, force):
+    _,localmods = submodules_status(gitmodules, root_dir)
+    print("")
+    if localmods and not force:
+        print(f"Repository has local mods, cowardly refusing to continue, fix issues or use --force to override")
+        return
     for name in gitmodules.sections():
         fxrequired = gitmodules.get(name, "fxrequired")
         fxsparse = gitmodules.get(name, "fxsparse")
@@ -393,7 +413,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist):
 
 def submodules_test(gitmodules, root_dir):
     # First check that fxtags are present and in sync with submodule hashes
-    testfails = submodules_status(gitmodules, root_dir)
+    testfails,localmods = submodules_status(gitmodules, root_dir)
     # Then make sure that urls are consistant with fxurls (not forks and not ssh)
     # and that sparse checkout files exist
     for name in gitmodules.sections():
@@ -407,7 +427,7 @@ def submodules_test(gitmodules, root_dir):
         if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
             print(f"sparse submodule {name} sparse checkout file {fxsparse} not found")
             testfails += 1
-    return testfails
+    return testfails+localmods
 
 
             
@@ -419,6 +439,7 @@ def _main_func():
         includelist,
         excludelist,
         verbose,
+        force,
         action,
     ) = commandline_arguments()
     # Get a logger for the package
@@ -445,9 +466,9 @@ def _main_func():
     )
     retval = 0
     if action == "update":
-        submodules_update(gitmodules, root_dir)
+        submodules_update(gitmodules, root_dir, force)
     elif action == "checkout":
-        submodules_checkout(gitmodules, root_dir, fxrequired)
+        submodules_checkout(gitmodules, root_dir, fxrequired, force)
     elif action == "status":
         submodules_status(gitmodules, root_dir)
     elif action == "test":

From ce22059f0f860c9e9f0961ee2637d21d967facfb Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 1 Feb 2024 14:37:08 -0700
Subject: [PATCH 060/161] start at root git dir unless --path flag is used

---
 src/git-fleximod | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index 5489ae164f..d0e6149f28 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -5,6 +5,7 @@ import shutil
 import logging
 import argparse
 import textwrap
+from pathlib import Path
 from fleximod import utils
 from fleximod.gitinterface import GitInterface
 from fleximod.gitmodules import GitModules
@@ -13,6 +14,17 @@ from configparser import NoOptionError
 # logger variable is global
 logger = None
 
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return attempt
+        d = d.parent
+    return None
+    
+
 def commandline_arguments(args=None):
     description = """
     %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
@@ -42,8 +54,8 @@ def commandline_arguments(args=None):
     parser.add_argument(
         "-C",
         "--path",
-        default=os.getcwd(),
-        help="Toplevel repository directory.  Defaults to current directory.",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
     )
 
     parser.add_argument(
@@ -430,6 +442,7 @@ def submodules_test(gitmodules, root_dir):
     return testfails+localmods
 
 
+
             
 def _main_func():
     (
@@ -455,6 +468,7 @@ def _main_func():
             utils.fatal_error(
                 "No {} found in {} or any of it's parents".format(file_name, root_dir)
             )
+
         root_dir = os.path.dirname(file_path)
     logger.info(f"root_dir is {root_dir}")
     gitmodules = GitModules(

From 8b7267959971c16d66803d92faa833055a8ff213 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 1 Feb 2024 14:43:10 -0700
Subject: [PATCH 061/161] remove test from visable options

---
 src/git-fleximod | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index d0e6149f28..da8431a174 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -41,7 +41,7 @@ def commandline_arguments(args=None):
         "action",
         choices=choices,
         default="checkout",
-        help=f"Subcommand of fleximod, choices are {choices}",
+        help=f"Subcommand of fleximod, choices are {choices[:-1]}",
     )
 
     parser.add_argument(

From a990864cef359b6a2f6e9a75f420ec05f669f894 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 17:34:21 -0700
Subject: [PATCH 062/161] update setup.cfg

---
 setup.cfg | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 9a13827a35..599646552c 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,4 +2,7 @@
 license_file = License
 [build_manpages]
 manpages =
-    man/git-fleximod.1:object=parser:pyfile=bin/git-fleximod
+    # solution 1: --split up the commandline_arguments parser
+    #man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
+    # solution 2 -- make parser global
+    man/git-fleximod.2:pyfile=src/git-fleximod:object=parser

From d2123b6022ad648ca78241a155fed93d13642ff4 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 17:34:43 -0700
Subject: [PATCH 063/161] updates for setup.py

---
 setup.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index f68a4ea9b7..53cc4e43ea 100644
--- a/setup.py
+++ b/setup.py
@@ -2,6 +2,8 @@
 import os
 from setuptools import setup, find_packages
 from distutils.util import convert_path
+from setuptools.command.build_py import build_py
+from setuptools.command.install import install
 from build_manpages import build_manpages, get_build_py_cmd, get_install_cmd
 
 with open("README.md", "r") as fh:
@@ -14,7 +16,8 @@
 
     
 setuptools.setup(
-    scripts=["src/git-fleximod"],                     # This is the name of the package
+    name="git-fleximod",                      # package name
+    #scripts=["src/git-fleximod"],                     # This is the name of the package
     version=main_ns['__version__'],                        # The initial release version
     author="Jim Edwards",                     # Full name of the author
     maintainer="jedwards4b",
@@ -38,6 +41,6 @@
       # Re-define build_py and install commands so the manual pages
       # are automatically re-generated and installed
       'build_py': get_build_py_cmd(),
-      'install': get_install_cmd(),
+      'install': get_install_cmd(install),
   }
 )

From 89dfbbe5e6a6d2ba532d4ec8a05ddd83ed3abb79 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 17:39:19 -0700
Subject: [PATCH 064/161] setup.cfg

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 599646552c..8df52e87a1 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,7 +2,7 @@
 license_file = License
 [build_manpages]
 manpages =
-    # solution 1: --split up the commandline_arguments parser
+    # solution 1: --split up the commandline_arguments parser --better
     #man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
     # solution 2 -- make parser global
     man/git-fleximod.2:pyfile=src/git-fleximod:object=parser

From 3fdff62ff545bf6fda5c7e475e7fc2c98f1e1f12 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 17:47:53 -0700
Subject: [PATCH 065/161] pointing to the better solution

---
 setup.cfg | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 8df52e87a1..7bd0d34d12 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,7 +2,7 @@
 license_file = License
 [build_manpages]
 manpages =
-    # solution 1: --split up the commandline_arguments parser --better
-    #man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
+    # solution 1: --split up the commandline_arguments parser
+    man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
     # solution 2 -- make parser global
-    man/git-fleximod.2:pyfile=src/git-fleximod:object=parser
+    #man/git-fleximod.2:pyfile=src/git-fleximod:object=parser

From 49e8fadbf834e1c03effd933e7bd5698b7555cc0 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 18:11:22 -0700
Subject: [PATCH 066/161] minimal changes required

---
 src/git-fleximod | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index d0e6149f28..26c00f5512 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -24,8 +24,7 @@ def find_root_dir(filename=".git"):
         d = d.parent
     return None
     
-
-def commandline_arguments(args=None):
+def get_parser():
     description = """
     %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
     """
@@ -127,6 +126,11 @@ def commandline_arguments(args=None):
         "information to the screen and log file.",
     )
 
+    return parser
+
+def commandline_arguments(args=None):
+    parser = get_parser()
+
     if args:
         options = parser.parse_args(args)
     else:

From 8c09b5b016629660613f0c0acb3889c5b8d5209b Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 18:22:59 -0700
Subject: [PATCH 067/161] updates to setup.cfg

---
 setup.cfg | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 7bd0d34d12..f6b737006f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,7 +2,4 @@
 license_file = License
 [build_manpages]
 manpages =
-    # solution 1: --split up the commandline_arguments parser
     man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
-    # solution 2 -- make parser global
-    #man/git-fleximod.2:pyfile=src/git-fleximod:object=parser

From a9bd103363ec9fe041daf4ee36bc915fe7209e15 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 18:23:22 -0700
Subject: [PATCH 068/161] minor changes

---
 setup.cfg | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/setup.cfg b/setup.cfg
index f6b737006f..7bd0d34d12 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,4 +2,7 @@
 license_file = License
 [build_manpages]
 manpages =
+    # solution 1: --split up the commandline_arguments parser
     man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
+    # solution 2 -- make parser global
+    #man/git-fleximod.2:pyfile=src/git-fleximod:object=parser

From 3b82247ef72c9c3f2f9e4d5697bbb735bb7181d2 Mon Sep 17 00:00:00 2001
From: Negin Sobhani <negin513@gmail.com>
Date: Thu, 1 Feb 2024 18:26:19 -0700
Subject: [PATCH 069/161] fix syntax and new function name

---
 setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 7bd0d34d12..66ff24ada6 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,7 +2,7 @@
 license_file = License
 [build_manpages]
 manpages =
-    # solution 1: --split up the commandline_arguments parser
-    man/git-fleximod.1:function:commandline_arguments:pyfile=src/git-fleximod
+    # solution 1: -- use parser function
+    man/git-fleximod.1:function=get_parser:pyfile=src/git-fleximod
     # solution 2 -- make parser global
     #man/git-fleximod.2:pyfile=src/git-fleximod:object=parser

From 23e0813eb3340dd410e989a48a7b753a69d0ae74 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 07:21:14 -0700
Subject: [PATCH 070/161] names were too similar, force needs to be optional

---
 src/git-fleximod | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index 1a55e91689..984ae9e1de 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -241,7 +241,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     print(f"Successfully checked out {name}")
 
 
-def submodule_checkout(root, name, path, url=None, tag=None):
+def single_submodule_checkout(root, name, path, url=None, tag=None, force=False):
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
     if os.path.exists(os.path.join(repodir, ".git")):
@@ -291,7 +291,7 @@ def submodule_checkout(root, name, path, url=None, tag=None):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir} {url}")
         gitmodules = GitModules(logger,confpath=repodir)
-        submodules_checkout(gitmodules, repodir, ["I:T"])
+        submodules_checkout(gitmodules, repodir, ["I:T"], force=force)
     if os.path.exists(os.path.join(repodir, ".git")):
         print(f"Successfully checked out {name}")
     else:
@@ -397,7 +397,7 @@ def submodules_update(gitmodules, root_dir, force):
                     print(f"{name:>20} up to date.")
 
 
-def submodules_checkout(gitmodules, root_dir, requiredlist, force):
+def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
     _,localmods = submodules_status(gitmodules, root_dir)
     print("")
     if localmods and not force:
@@ -425,7 +425,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force):
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
             
-            submodule_checkout(root_dir, name, path, url=url, tag=fxtag)
+            single_submodule_checkout(root_dir, name, path, url=url, tag=fxtag, force=force)
 
 def submodules_test(gitmodules, root_dir):
     # First check that fxtags are present and in sync with submodule hashes

From ae4c9c5962fe0ddbcc8043d9a647115dfb7e89e8 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 09:30:33 -0700
Subject: [PATCH 071/161] more cleanup

---
 setup.py         | 12 ++++++++----
 src/git-fleximod | 12 ++++++++----
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/setup.py b/setup.py
index 53cc4e43ea..259f9589cf 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,8 @@
-import setuptools
+import sys
 import os
+sys.path.insert(0,os.path.join(os.getenv("CONDA_PREFIX"),"lib","python3.12","site-packages"))
+
+import setuptools
 from setuptools import setup, find_packages
 from distutils.util import convert_path
 from setuptools.command.build_py import build_py
@@ -17,7 +20,7 @@
     
 setuptools.setup(
     name="git-fleximod",                      # package name
-    #scripts=["src/git-fleximod"],                     # This is the name of the package
+    scripts=["src/git-fleximod"],                     # This is the name of the package
     version=main_ns['__version__'],                        # The initial release version
     author="Jim Edwards",                     # Full name of the author
     maintainer="jedwards4b",
@@ -25,8 +28,9 @@
     description="Extended support for git-submodule and git-sparse-checkout",
     long_description=long_description,      # Long description read from the the readme file
     long_description_content_type="text/markdown",
-    packages=['fleximod'],    # List of all python modules to be installed
-    package_dir={'fleximod': 'src/fleximod'},
+    packages=find_packages(),    # List of all python modules to be installed
+    package_dir={'git-fleximod': 'src',
+                 'fleximod': 'src/fleximod'},
     package_data={"":['version.txt']},
     classifiers=[
         "Programming Language :: Python :: 3",
diff --git a/src/git-fleximod b/src/git-fleximod
index 984ae9e1de..0706a56236 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -273,7 +273,6 @@ def single_submodule_checkout(root, name, path, url=None, tag=None, force=False)
                         rootdotgit = line[8:].rstrip()
             
             newpath = os.path.abspath(os.path.join(root,rootdotgit,"modules",path))
-            print(f"root is {root} rootdotgit is {rootdotgit} newpath is {newpath}")
             if not os.path.isdir(os.path.join(newpath,os.pardir)):
                 os.makedirs(os.path.abspath(os.path.join(newpath,os.pardir)))
 
@@ -321,14 +320,17 @@ def submodules_status(gitmodules, root_dir):
             tags = rootgit.git_operation("ls-remote","--tags",url)
             atag = None
             for htag in tags.split('\n'):
-                if tag in htag:
+                if tag and tag in htag:
                     atag = (htag.split()[1])[10:]
                     break
-            if tag == atag:
+            if tag and tag == atag:
                 print(f"e {name:>20} not checked out, aligned at tag {tag}")
-            else:
+            elif tag:
                 print(f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}")
                 testfails += 1
+            else:
+                print(f"e {name:>20} has no fxtag defined in .gitmodules")
+                testfails +=1 
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
@@ -482,6 +484,8 @@ def _main_func():
         includelist=includelist,
         excludelist=excludelist,
     )
+    if not gitmodules.sections():
+        sys.exit("No submodule components found")
     retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir, force)

From 140529afedf13f88ba3673526917d6dd27750c3e Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 10:00:15 -0700
Subject: [PATCH 072/161] pre-commit cleanup

---
 setup.py                     |  51 ++++++------
 src/fleximod/gitinterface.py |  15 ++--
 src/fleximod/gitmodules.py   |  17 ++--
 src/fleximod/lstripreader.py |   7 +-
 src/fleximod/version.py      |   2 +-
 src/git-fleximod             | 150 +++++++++++++++++++----------------
 6 files changed, 129 insertions(+), 113 deletions(-)

diff --git a/setup.py b/setup.py
index 259f9589cf..8f8a49cbec 100644
--- a/setup.py
+++ b/setup.py
@@ -1,11 +1,13 @@
 import sys
 import os
-sys.path.insert(0,os.path.join(os.getenv("CONDA_PREFIX"),"lib","python3.12","site-packages"))
+
+sys.path.insert(
+    0, os.path.join(os.getenv("CONDA_PREFIX"), "lib", "python3.12", "site-packages")
+)
 
 import setuptools
-from setuptools import setup, find_packages
-from distutils.util import convert_path
-from setuptools.command.build_py import build_py
+from setuptools import find_packages
+from setuptools.util import convert_path
 from setuptools.command.install import install
 from build_manpages import build_manpages, get_build_py_cmd, get_install_cmd
 
@@ -13,38 +15,37 @@
     long_description = fh.read()
 
 main_ns = {}
-ver_path = convert_path('src/fleximod/version.py')
+ver_path = convert_path("src/fleximod/version.py")
 with open(ver_path) as ver_file:
     exec(ver_file.read(), main_ns)
 
-    
+
 setuptools.setup(
-    name="git-fleximod",                      # package name
-    scripts=["src/git-fleximod"],                     # This is the name of the package
-    version=main_ns['__version__'],                        # The initial release version
-    author="Jim Edwards",                     # Full name of the author
+    name="git-fleximod",  # package name
+    scripts=["src/git-fleximod"],  # This is the name of the package
+    version=main_ns["__version__"],  # The initial release version
+    author="Jim Edwards",  # Full name of the author
     maintainer="jedwards4b",
     license="MIT License",
     description="Extended support for git-submodule and git-sparse-checkout",
-    long_description=long_description,      # Long description read from the the readme file
+    long_description=long_description,  # Long description read from the the readme file
     long_description_content_type="text/markdown",
-    packages=find_packages(),    # List of all python modules to be installed
-    package_dir={'git-fleximod': 'src',
-                 'fleximod': 'src/fleximod'},
-    package_data={"":['version.txt']},
+    packages=find_packages(),  # List of all python modules to be installed
+    package_dir={"git-fleximod": "src", "fleximod": "src/fleximod"},
+    package_data={"": ["version.txt"]},
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
-    ],                                      # Information to filter the project on PyPi website
-    python_requires='>=3.6',                # Minimum version requirement of the package
-#    py_modules=['git-fleximod'],             # Name of the python package
-    install_requires=["GitPython"],                     # Install other dependencies if any
+    ],  # Information to filter the project on PyPi website
+    python_requires=">=3.6",  # Minimum version requirement of the package
+    #    py_modules=['git-fleximod'],             # Name of the python package
+    install_requires=["GitPython"],  # Install other dependencies if any
     cmdclass={
-      'build_manpages': build_manpages,
-      # Re-define build_py and install commands so the manual pages
-      # are automatically re-generated and installed
-      'build_py': get_build_py_cmd(),
-      'install': get_install_cmd(install),
-  }
+        "build_manpages": build_manpages,
+        # Re-define build_py and install commands so the manual pages
+        # are automatically re-generated and installed
+        "build_py": get_build_py_cmd(),
+        "install": get_install_cmd(install),
+    },
 )
diff --git a/src/fleximod/gitinterface.py b/src/fleximod/gitinterface.py
index c127163dc6..96bb9ac52b 100644
--- a/src/fleximod/gitinterface.py
+++ b/src/fleximod/gitinterface.py
@@ -1,7 +1,7 @@
 import os
-import logging
 from fleximod import utils
 
+
 class GitInterface:
     def __init__(self, repo_path, logger):
         logger.debug("Initialize GitInterface for {}".format(repo_path))
@@ -9,6 +9,7 @@ def __init__(self, repo_path, logger):
         self.logger = logger
         try:
             import git
+
             self._use_module = True
             try:
                 self.repo = git.Repo(repo_path)  # Initialize GitPython repo
@@ -18,17 +19,17 @@ def __init__(self, repo_path, logger):
             msg = "Using GitPython interface to git"
         except ImportError:
             self._use_module = False
-            if not os.path.exists(os.path.join(repo_path,".git")):
+            if not os.path.exists(os.path.join(repo_path, ".git")):
                 self._init_git_repo()
             msg = "Using shell interface to git"
         self.logger.info(msg)
-                
+
     def _git_command(self, operation, *args):
         self.logger.info(operation)
         if self._use_module and operation != "submodule":
             return getattr(self.repo.git, operation)(*args)
         else:
-            return ["git", "-C",self.repo_path, operation] + list(args)
+            return ["git", "-C", self.repo_path, operation] + list(args)
 
     def _init_git_repo(self):
         if self._use_module:
@@ -37,7 +38,7 @@ def _init_git_repo(self):
             command = ("git", "-C", self.repo_path, "init")
             utils.execute_subprocess(command)
 
-
+    # pylint: disable=unused-argument
     def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *args)
         self.logger.info(command)
@@ -51,7 +52,7 @@ def config_get_value(self, section, name):
             config = self.repo.config_reader()
             return config.get_value(section, name)
         else:
-            cmd = ("git","-C",self.repo_path,"config", "--get", f"{section}.{name}")
+            cmd = ("git", "-C", self.repo_path, "config", "--get", f"{section}.{name}")
             output = utils.execute_subprocess(cmd, output_to_caller=True)
             return output.strip()
 
@@ -61,6 +62,6 @@ def config_set_value(self, section, name, value):
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else:
-            cmd = ("git","-C",self.repo_path,"config", f"{section}.{name}", value)
+            cmd = ("git", "-C", self.repo_path, "config", f"{section}.{name}", value)
             self.logger.info(cmd)
             utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/src/fleximod/gitmodules.py b/src/fleximod/gitmodules.py
index a6f7589319..11a2457247 100644
--- a/src/fleximod/gitmodules.py
+++ b/src/fleximod/gitmodules.py
@@ -3,6 +3,7 @@
 from configparser import ConfigParser
 from fleximod.lstripreader import LstripReader
 
+
 class GitModules(ConfigParser):
     def __init__(
         self,
@@ -19,11 +20,15 @@ def __init__(
         excludelist: Optional list of submodules to exclude.
         """
         self.logger = logger
-        self.logger.debug("Creating a GitModules object {} {} {} {}".format(confpath,conffile,includelist,excludelist))
+        self.logger.debug(
+            "Creating a GitModules object {} {} {} {}".format(
+                confpath, conffile, includelist, excludelist
+            )
+        )
         ConfigParser.__init__(self)
         self.conf_file = os.path.join(confpath, conffile)
         # first create a backup of this file to be restored on deletion of the object
-        shutil.copy(self.conf_file, self.conf_file+".save")
+        shutil.copy(self.conf_file, self.conf_file + ".save")
         self.read_file(LstripReader(self.conf_file), source=conffile)
         self.includelist = includelist
         self.excludelist = excludelist
@@ -34,7 +39,7 @@ def set(self, name, option, value):
         Ensures the appropriate section exists for the submodule.
         Calls the parent class's set method to store the value.
         """
-        self.logger.debug("set called {} {} {}".format(name,option,value))
+        self.logger.debug("set called {} {} {}".format(name, option, value))
         section = f'submodule "{name}"'
         if not self.has_section(section):
             self.add_section(section)
@@ -47,7 +52,7 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
         Uses the parent class's get method to access the value.
         Handles potential errors if the section or option doesn't exist.
         """
-        self.logger.debug("get called {} {}".format(name,option))
+        self.logger.debug("get called {} {}".format(name, option))
         section = f'submodule "{name}"'
         try:
             return ConfigParser.get(
@@ -62,8 +67,8 @@ def save(self):
 
     def __del__(self):
         self.logger.debug("Destroying GitModules object")
-        shutil.move(self.conf_file+".save", self.conf_file)
-            
+        shutil.move(self.conf_file + ".save", self.conf_file)
+
     def sections(self):
         """Strip the submodule part out of section and just use the name"""
         self.logger.debug("calling GitModules sections iterator")
diff --git a/src/fleximod/lstripreader.py b/src/fleximod/lstripreader.py
index 530abd297e..01d5580ee8 100644
--- a/src/fleximod/lstripreader.py
+++ b/src/fleximod/lstripreader.py
@@ -1,8 +1,8 @@
-
 class LstripReader(object):
     "LstripReader formats .gitmodules files to be acceptable for configparser"
+
     def __init__(self, filename):
-        with open(filename, 'r') as infile:
+        with open(filename, "r") as infile:
             lines = infile.readlines()
         self._lines = list()
         self._num_lines = len(lines)
@@ -19,7 +19,7 @@ def readline(self, size=-1):
         try:
             line = self.next()
         except StopIteration:
-            line = ''
+            line = ""
 
         if (size > 0) and (len(line) < size):
             return line[0:size]
@@ -41,4 +41,3 @@ def next(self):
 
     def __next__(self):
         return self.next()
-
diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index 7fd229a32b..d3ec452c31 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = '0.2.0'
+__version__ = "0.2.0"
diff --git a/src/git-fleximod b/src/git-fleximod
index 0706a56236..aa587ea3a9 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -11,9 +11,11 @@ from fleximod.gitinterface import GitInterface
 from fleximod.gitmodules import GitModules
 from fleximod.version import __version__
 from configparser import NoOptionError
+
 # logger variable is global
 logger = None
 
+
 def find_root_dir(filename=".git"):
     d = Path.cwd()
     root = Path(d.root)
@@ -23,7 +25,8 @@ def find_root_dir(filename=".git"):
             return attempt
         d = d.parent
     return None
-    
+
+
 def get_parser():
     description = """
     %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
@@ -76,7 +79,7 @@ def get_parser():
         "--force",
         action="store_true",
         default=False,
-        help="Override cautions and update or checkout over locally modified repository."
+        help="Override cautions and update or checkout over locally modified repository.",
     )
 
     parser.add_argument(
@@ -128,6 +131,7 @@ def get_parser():
 
     return parser
 
+
 def commandline_arguments(args=None):
     parser = get_parser()
 
@@ -136,7 +140,7 @@ def commandline_arguments(args=None):
     else:
         options = parser.parse_args()
 
-# explicitly listing a component overrides the optional flag    
+    # explicitly listing a component overrides the optional flag
     if options.optional or options.components:
         fxrequired = ["T:T", "T:F", "I:T"]
     else:
@@ -145,11 +149,11 @@ def commandline_arguments(args=None):
     action = options.action
     if not action:
         action = "checkout"
-    handlers=[logging.StreamHandler()]
+    handlers = [logging.StreamHandler()]
 
     if options.debug:
         try:
-            open("fleximod.log","w")
+            open("fleximod.log", "w")
         except PermissionError:
             sys.exit("ABORT: Could not write file fleximod.log")
         level = logging.DEBUG
@@ -160,21 +164,18 @@ def commandline_arguments(args=None):
         level = logging.WARNING
     # Configure the root logger
     logging.basicConfig(
-        level=level,
-        format="%(name)s - %(levelname)s - %(message)s",
-        handlers=handlers
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
     )
-    
-    if hasattr(options, 'version'):
+
+    if hasattr(options, "version"):
         exit()
-    
+
     return (
         options.path,
         options.gitmodules,
         fxrequired,
         options.components,
         options.exclude,
-        options.verbose,
         options.force,
         action,
     )
@@ -191,7 +192,7 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # initialize a new git repo and set the sparse checkout flag
     sprep_repo = os.path.join(root_dir, path)
     sprepo_git = GitInterface(sprep_repo, logger)
-    if os.path.exists(os.path.join(sprep_repo,".git")):
+    if os.path.exists(os.path.join(sprep_repo, ".git")):
         try:
             logger.info("Submodule {} found".format(name))
             chk = sprepo_git.config_get_value("core", "sparseCheckout")
@@ -203,7 +204,6 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
         except Exception as e:
             utils.fatal_error("Unexpected error {} occured.".format(e))
 
-
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
 
     # set the repository remote
@@ -212,28 +212,31 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     superroot = git.git_operation("rev-parse", "--show-superproject-working-tree")
     if os.path.isfile(os.path.join(root_dir, ".git")):
         with open(os.path.join(root_dir, ".git")) as f:
-            gitpath = os.path.abspath(os.path.join(root_dir,f.read().split()[1]))
+            gitpath = os.path.abspath(os.path.join(root_dir, f.read().split()[1]))
         topgit = os.path.abspath(os.path.join(gitpath, "modules"))
-    else:                      
+    else:
         topgit = os.path.abspath(os.path.join(root_dir, ".git", "modules"))
 
     if not os.path.isdir(topgit):
         os.makedirs(topgit)
     topgit = os.path.join(topgit, name)
-    logger.debug(f"root_dir is {root_dir} topgit is {topgit} superroot is {superroot}")
+    logger.debug(
+        "root_dir is {} topgit is {} superroot is {}".format(
+            root_dir, topgit, superroot
+        )
+    )
+
+    if os.path.isdir(os.path.join(root_dir, path, ".git")):
+        shutil.move(os.path.join(root_dir, path, ".git"), topgit)
+        with open(os.path.join(root_dir, path, ".git"), "w") as f:
+            f.write("gitdir: " + os.path.relpath(topgit, os.path.join(root_dir, path)))
 
-    if os.path.isdir(os.path.join(root_dir,path,".git")):
-        shutil.move(os.path.join(root_dir,path, ".git"), topgit)
-        with open(os.path.join(root_dir,path, ".git"), "w") as f:
-            f.write("gitdir: " + os.path.relpath(topgit, os.path.join(root_dir,path)))
-            
     gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
     if os.path.isfile(gitsparse):
         logger.warning("submodule {} is already initialized".format(name))
         return
 
-
-    shutil.copy(os.path.join(root_dir,path, sparsefile), gitsparse)
+    shutil.copy(os.path.join(root_dir, path, sparsefile), gitsparse)
 
     # Finally checkout the repo
     sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
@@ -258,38 +261,35 @@ def single_submodule_checkout(root, name, path, url=None, tag=None, force=False)
         # it will be done by the GitModules class
         if url.startswith("git@"):
             tmpurl = url
-            url = url.replace("git@github.com:", "https://github.com")            
+            url = url.replace("git@github.com:", "https://github.com")
             git.git_operation("clone", url, path)
             smgit = GitInterface(repodir, logger)
             if not tag:
                 tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
-            smgit.git_operation("checkout",tag)
+            smgit.git_operation("checkout", tag)
             # Now need to move the .git dir to the submodule location
-            rootdotgit = os.path.join(root,".git")
+            rootdotgit = os.path.join(root, ".git")
             if os.path.isfile(rootdotgit):
                 with open(rootdotgit) as f:
                     line = f.readline()
                     if line.startswith("gitdir: "):
                         rootdotgit = line[8:].rstrip()
-            
-            newpath = os.path.abspath(os.path.join(root,rootdotgit,"modules",path))
-            if not os.path.isdir(os.path.join(newpath,os.pardir)):
-                os.makedirs(os.path.abspath(os.path.join(newpath,os.pardir)))
-
-            shutil.move(os.path.join(repodir,".git"), newpath) 
-            with open(os.path.join(repodir,".git"), "w") as f:
-                f.write("gitdir: "+newpath)
-            
-
-            
-            
+
+            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", path))
+            if not os.path.isdir(os.path.join(newpath, os.pardir)):
+                os.makedirs(os.path.abspath(os.path.join(newpath, os.pardir)))
+
+            shutil.move(os.path.join(repodir, ".git"), newpath)
+            with open(os.path.join(repodir, ".git"), "w") as f:
+                f.write("gitdir: " + newpath)
+
     if not tmpurl:
         logger.debug(git.git_operation("submodule", "update", "--init", "--", path))
 
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir} {url}")
-        gitmodules = GitModules(logger,confpath=repodir)
+        gitmodules = GitModules(logger, confpath=repodir)
         submodules_checkout(gitmodules, repodir, ["I:T"], force=force)
     if os.path.exists(os.path.join(repodir, ".git")):
         print(f"Successfully checked out {name}")
@@ -315,22 +315,23 @@ def submodules_status(gitmodules, root_dir):
         if not os.path.exists(os.path.join(newpath, ".git")):
             rootgit = GitInterface(root_dir, logger)
             # submodule commands use path, not name
-            nhash = (rootgit.git_operation("submodule","status",path).split()[0])[1:]
             url = gitmodules.get(name, "url")
-            tags = rootgit.git_operation("ls-remote","--tags",url)
+            tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
-            for htag in tags.split('\n'):
+            for htag in tags.split("\n"):
                 if tag and tag in htag:
                     atag = (htag.split()[1])[10:]
                     break
             if tag and tag == atag:
                 print(f"e {name:>20} not checked out, aligned at tag {tag}")
             elif tag:
-                print(f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}")
+                print(
+                    f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
+                )
                 testfails += 1
             else:
                 print(f"e {name:>20} has no fxtag defined in .gitmodules")
-                testfails +=1 
+                testfails += 1
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
@@ -346,24 +347,27 @@ def submodules_status(gitmodules, root_dir):
                     )
                     testfails += 1
 
-                status = git.git_operation("status","--ignore-submodules")
+                status = git.git_operation("status", "--ignore-submodules")
                 if "nothing to commit" not in status:
-                    localmods = localmods+1
-                    print('M'+textwrap.indent(status,'                      '))
-    
+                    localmods = localmods + 1
+                    print("M" + textwrap.indent(status, "                      "))
+
     return testfails, localmods
 
+
 def submodules_update(gitmodules, root_dir, force):
-    _,localmods = submodules_status(gitmodules, root_dir)
+    _, localmods = submodules_status(gitmodules, root_dir)
     print("")
     if localmods and not force:
-        print(f"Repository has local mods, cowardly refusing to continue, fix issues or use --force to override")
+        print(
+            "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
+        )
         return
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
-        logger.info(f"name={name} path={path} url={url} fxtag={fxtag}")
+        logger.info("name={} path={} url={} fxtag={}".format(name, path, url, fxtag))
         if os.path.exists(os.path.join(path, ".git")):
             submoddir = os.path.join(root_dir, path)
             with utils.pushd(submoddir):
@@ -400,10 +404,12 @@ def submodules_update(gitmodules, root_dir, force):
 
 
 def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
-    _,localmods = submodules_status(gitmodules, root_dir)
+    _, localmods = submodules_status(gitmodules, root_dir)
     print("")
     if localmods and not force:
-        print(f"Repository has local mods, cowardly refusing to continue, fix issues or use --force to override")
+        print(
+            "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
+        )
         return
     for name in gitmodules.sections():
         fxrequired = gitmodules.get(name, "fxrequired")
@@ -416,22 +422,28 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
             if "T:F" == fxrequired:
                 print("Skipping optional component {}".format(name))
             continue
-            
+
         if fxsparse:
             logger.debug(
-                f"Callng submodule_sparse_checkout({root_dir}, {name}, {url}, {path}, {fxsparse}, {fxtag}"
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
             )
             submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
         else:
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
-            
-            single_submodule_checkout(root_dir, name, path, url=url, tag=fxtag, force=force)
+
+            single_submodule_checkout(
+                root_dir, name, path, url=url, tag=fxtag, force=force
+            )
+
 
 def submodules_test(gitmodules, root_dir):
     # First check that fxtags are present and in sync with submodule hashes
-    testfails,localmods = submodules_status(gitmodules, root_dir)
+    testfails, localmods = submodules_status(gitmodules, root_dir)
+    print("")
     # Then make sure that urls are consistant with fxurls (not forks and not ssh)
     # and that sparse checkout files exist
     for name in gitmodules.sections():
@@ -440,16 +452,14 @@ def submodules_test(gitmodules, root_dir):
         fxsparse = gitmodules.get(name, "fxsparse")
         path = gitmodules.get(name, "path")
         if not fxurl or url != fxurl:
-            print(f"submodule {name} url {url} not in sync with required {fxurl}")
+            print(f"{name:>20} url {url} not in sync with required {fxurl}")
             testfails += 1
         if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
-            print(f"sparse submodule {name} sparse checkout file {fxsparse} not found")
+            print(f"{name:>20} sparse checkout file {fxsparse} not found")
             testfails += 1
-    return testfails+localmods
-
+    return testfails + localmods
 
 
-            
 def _main_func():
     (
         root_dir,
@@ -457,15 +467,14 @@ def _main_func():
         fxrequired,
         includelist,
         excludelist,
-        verbose,
         force,
         action,
     ) = commandline_arguments()
     # Get a logger for the package
     global logger
     logger = logging.getLogger(__name__)
-        
-    logger.info(f"action is {action}")
+
+    logger.info("action is {}".format(action))
 
     if not os.path.isfile(os.path.join(root_dir, file_name)):
         file_path = utils.find_upwards(root_dir, file_name)
@@ -476,7 +485,7 @@ def _main_func():
             )
 
         root_dir = os.path.dirname(file_path)
-    logger.info(f"root_dir is {root_dir}")
+    logger.info("root_dir is {}".format(root_dir))
     gitmodules = GitModules(
         logger,
         confpath=root_dir,
@@ -497,7 +506,8 @@ def _main_func():
         retval = submodules_test(gitmodules, root_dir)
     else:
         utils.fatal_error(f"unrecognized action request {action}")
-    return(retval)
-        
+    return retval
+
+
 if __name__ == "__main__":
     sys.exit(_main_func())

From 0a5cf50fb696f84ea5a71bcdb973a8972c14bb55 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 12:43:54 -0700
Subject: [PATCH 073/161] setup.py builds manpage but doesnt install

---
 .github/workflows/pre-commit | 13 ++++++
 setup.py                     | 76 +++++++++++++++++++-----------------
 2 files changed, 53 insertions(+), 36 deletions(-)
 create mode 100644 .github/workflows/pre-commit

diff --git a/.github/workflows/pre-commit b/.github/workflows/pre-commit
new file mode 100644
index 0000000000..1a6ad0082a
--- /dev/null
+++ b/.github/workflows/pre-commit
@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
diff --git a/setup.py b/setup.py
index 8f8a49cbec..048db75957 100644
--- a/setup.py
+++ b/setup.py
@@ -1,51 +1,55 @@
 import sys
 import os
 
+sys.path.insert(0, os.path.join(os.getenv("CONDA_PREFIX"), "lib", "python3.12"))
 sys.path.insert(
     0, os.path.join(os.getenv("CONDA_PREFIX"), "lib", "python3.12", "site-packages")
 )
 
 import setuptools
-from setuptools import find_packages
-from setuptools.util import convert_path
-from setuptools.command.install import install
+from setuptools import find_packages, convert_path
 from build_manpages import build_manpages, get_build_py_cmd, get_install_cmd
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
 main_ns = {}
-ver_path = convert_path("src/fleximod/version.py")
+ver_path = convert_path(
+    os.path.join(os.path.dirname(__file__), "src", "fleximod", "version.py")
+)
+print(f"ver_path is {ver_path}")
 with open(ver_path) as ver_file:
     exec(ver_file.read(), main_ns)
 
+if __name__ == "__main__":
+    with open("README.md", "r") as fh:
+        long_description = fh.read()
 
-setuptools.setup(
-    name="git-fleximod",  # package name
-    scripts=["src/git-fleximod"],  # This is the name of the package
-    version=main_ns["__version__"],  # The initial release version
-    author="Jim Edwards",  # Full name of the author
-    maintainer="jedwards4b",
-    license="MIT License",
-    description="Extended support for git-submodule and git-sparse-checkout",
-    long_description=long_description,  # Long description read from the the readme file
-    long_description_content_type="text/markdown",
-    packages=find_packages(),  # List of all python modules to be installed
-    package_dir={"git-fleximod": "src", "fleximod": "src/fleximod"},
-    package_data={"": ["version.txt"]},
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],  # Information to filter the project on PyPi website
-    python_requires=">=3.6",  # Minimum version requirement of the package
-    #    py_modules=['git-fleximod'],             # Name of the python package
-    install_requires=["GitPython"],  # Install other dependencies if any
-    cmdclass={
-        "build_manpages": build_manpages,
-        # Re-define build_py and install commands so the manual pages
-        # are automatically re-generated and installed
-        "build_py": get_build_py_cmd(),
-        "install": get_install_cmd(install),
-    },
-)
+    setuptools.setup(
+        name="git-fleximod",  # package name
+        scripts=["src/git-fleximod"],  # This is the name of the package
+        version=main_ns["__version__"],  # The initial release version
+        author="Jim Edwards",  # Full name of the author
+        maintainer="jedwards4b",
+        license="MIT License",
+        description="Extended support for git-submodule and git-sparse-checkout",
+        long_description=long_description,  # Long description read from the the readme file
+        long_description_content_type="text/markdown",
+        packages=find_packages(
+            where="src"
+        ),  # List of all python modules to be installed
+        package_dir={"": "src", "git-fleximod": "src", "fleximod": "src/fleximod"},
+        package_data={"": ["src/fleximod/version.txt", "man/git-fleximod.1"]},
+        classifiers=[
+            "Programming Language :: Python :: 3",
+            "License :: OSI Approved :: MIT License",
+            "Operating System :: OS Independent",
+        ],  # Information to filter the project on PyPi website
+        python_requires=">=3.6",  # Minimum version requirement of the package
+        #    py_modules=['git-fleximod'],             # Name of the python package
+        install_requires=["GitPython"],  # Install other dependencies if any
+        cmdclass={
+            "build_manpages": build_manpages,
+            # Re-define build_py and install commands so the manual pages
+            # are automatically re-generated and installed
+            "build_py": get_build_py_cmd(),
+            "install": get_install_cmd(),
+        },
+    )

From 64e26fc22df3c3faa7190eff289dce5accc88669 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 12:46:58 -0700
Subject: [PATCH 074/161] update version

---
 src/fleximod/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fleximod/version.py b/src/fleximod/version.py
index d3ec452c31..493f7415d7 100644
--- a/src/fleximod/version.py
+++ b/src/fleximod/version.py
@@ -1 +1 @@
-__version__ = "0.2.0"
+__version__ = "0.3.0"

From 2a2ab6503091b3336bf759a32c0874959a275dcd Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 12:58:20 -0700
Subject: [PATCH 075/161] update README

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index cec74c5a66..7c968e70b0 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
     Basic Usage:
         git fleximod <command> [options]
     Available Commands:
-        install: Install submodules according to configuration.
+        checkout: Checkout submodules according to git submodule hash configuration.
         status: Display the status of submodules.
         update: Update submodules to the tag indicated in .gitmodules variable fxtag.
         test: Make sure that fxtags and submodule hashes are consistant,
@@ -35,7 +35,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
       - I:T: Internal and required (always checked out).
       - I:F: Internal and optional (checked out with --optional flag).
     fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
-    fcurl
+    fxurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
 
 ## Sparse Checkouts
 
@@ -55,9 +55,9 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 
 Here are some common usage examples:
 
-Installing submodules, including optional ones:
+Checkout submodules, including optional ones:
 ```bash
-  git fleximod install --optional
+  git fleximod checkout --optional
 ```
 
 Updating a specific submodule to the fxtag indicated in .gitmodules:

From ad0a976b38cd8de97fdce0d04050e412cf2e3905 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 2 Feb 2024 17:15:26 -0700
Subject: [PATCH 076/161] add support for fxhash variable in .gitmodules

---
 src/git-fleximod | 72 +++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 59 insertions(+), 13 deletions(-)

diff --git a/src/git-fleximod b/src/git-fleximod
index aa587ea3a9..5182bb256a 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -181,7 +181,9 @@ def commandline_arguments(args=None):
     )
 
 
-def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
+def submodule_sparse_checkout(
+    root_dir, name, url, path, sparsefile, tag="master", fxhash=None
+):
     # first create the module directory
     if not os.path.isdir(path):
         os.makedirs(path)
@@ -239,12 +241,19 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     shutil.copy(os.path.join(root_dir, path, sparsefile), gitsparse)
 
     # Finally checkout the repo
-    sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
-    sprepo_git.git_operation("checkout", tag)
-    print(f"Successfully checked out {name}")
+    if fxhash:
+        sprepo_git.git_operation("fetch", "origin", "--tags")
+        sprepo_git.git_operation("checkout", fxhash)
+        print(f"Successfully checked out {name:>20} at {fxhash}")
+    else:
+        sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
+        sprepo_git.git_operation("checkout", tag)
+        print(f"Successfully checked out {name:>20} at {tag}")
 
 
-def single_submodule_checkout(root, name, path, url=None, tag=None, force=False):
+def single_submodule_checkout(
+    root, name, path, url=None, tag=None, force=False, fxhash=None
+):
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
     if os.path.exists(os.path.join(repodir, ".git")):
@@ -264,9 +273,12 @@ def single_submodule_checkout(root, name, path, url=None, tag=None, force=False)
             url = url.replace("git@github.com:", "https://github.com")
             git.git_operation("clone", url, path)
             smgit = GitInterface(repodir, logger)
-            if not tag:
+            if not tag and not fxhash:
                 tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
-            smgit.git_operation("checkout", tag)
+            if fxhash:
+                smgit.git_operation("checkout", fxhash)
+            else:
+                smgit.git_operation("checkout", tag)
             # Now need to move the .git dir to the submodule location
             rootdotgit = os.path.join(root, ".git")
             if os.path.isfile(rootdotgit):
@@ -308,6 +320,9 @@ def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
+        fxhash = gitmodules.get(name, "fxhash")
+        if tag and fxhash:
+            utils.fatal_error(f"{name:>20} cannot have both fxtag and fxhash")
         if not path:
             utils.fatal_error("No path found in .gitmodules for {}".format(name))
         newpath = os.path.join(root_dir, path)
@@ -329,21 +344,44 @@ def submodules_status(gitmodules, root_dir):
                     f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
                 )
                 testfails += 1
+            elif fxhash:
+                n = len(fxhash)
+                smhash = rootgit.git_operation(
+                    "ls-tree", "--object-only", f"--abbrev={n}", "HEAD", path
+                )
+                if smhash == fxhash:
+                    print(f"  {name:>20} not checked out, aligned at hash {fxhash}")
+                else:
+                    print(
+                        f"s {name:>20} not checked out, out of sync at hash {smhash}, expected hash is {fxhash}"
+                    )
+                    testfails += 1
             else:
-                print(f"e {name:>20} has no fxtag defined in .gitmodules")
+                print(f"e {name:>20} has no fxtag nor fxhash defined in .gitmodules")
                 testfails += 1
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                ahash = git.git_operation("status").partition("\n")[0].split()[-1]
                 if tag and atag != tag:
                     print(f"s {name:>20} {atag} is out of sync with .gitmodules {tag}")
                     testfails += 1
                 elif tag:
                     print(f"  {name:>20} at tag {tag}")
+                elif fxhash:
+                    rootgit = GitInterface(root_dir, logger)
+                    n = len(fxhash)
+                    if ahash.startswith(fxhash):
+                        print(f"  {name:>20} at hash {fxhash}")
+                    else:
+                        print(
+                            f"s {name:>20} {ahash} is out of sync with .gitmodules {fxhash}"
+                        )
+                        testfails += 1
                 else:
                     print(
-                        f"e {name:>20} has no tag defined in .gitmodules, module at {atag}"
+                        f"e {name:>20} has no fxtag nor fxhash defined in .gitmodules, module at {atag}"
                     )
                     testfails += 1
 
@@ -365,6 +403,7 @@ def submodules_update(gitmodules, root_dir, force):
         return
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
+        fxhash = gitmodules.get(name, "fxhash")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         logger.info("name={} path={} url={} fxtag={}".format(name, path, url, fxtag))
@@ -394,11 +433,15 @@ def submodules_update(gitmodules, root_dir, force):
                 if fxtag and fxtag not in tags:
                     git.git_operation("fetch", newremote, "--tags")
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                print(f"fxtag {fxtag} fxhash {fxhash}")
                 if fxtag and fxtag != atag:
                     print(f"{name:>20} updated to {fxtag}")
                     git.git_operation("checkout", fxtag)
-                elif not fxtag:
-                    print(f"No fxtag found for submodule {name:>20}")
+                elif fxhash:
+                    print(f"{name:>20} updated to {fxhash}")
+                    git.git_operation("checkout", fxhash)
+                elif not (fxtag or fxhash):
+                    print(f"No fxtag nor fxhash found for submodule {name:>20}")
                 else:
                     print(f"{name:>20} up to date.")
 
@@ -415,6 +458,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
         fxrequired = gitmodules.get(name, "fxrequired")
         fxsparse = gitmodules.get(name, "fxsparse")
         fxtag = gitmodules.get(name, "fxtag")
+        fxhash = gitmodules.get(name, "fxhash")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
 
@@ -429,14 +473,16 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
                     root_dir, name, url, path, fxsparse, fxtag
                 )
             )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+            submodule_sparse_checkout(
+                root_dir, name, url, path, fxsparse, tag=fxtag, fxhash=fxhash
+            )
         else:
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
 
             single_submodule_checkout(
-                root_dir, name, path, url=url, tag=fxtag, force=force
+                root_dir, name, path, url=url, tag=fxtag, force=force, fxhash=fxhash
             )
 
 

From bf56a97251d0f5e5e84910a56e4c8e3036d6b057 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 3 Feb 2024 11:27:03 -0700
Subject: [PATCH 077/161] working on poetry

---
 pyproject.toml                            | 28 ++++++++++++
 setup.cfg                                 |  8 ----
 setup.py                                  | 55 -----------------------
 src/{fleximod => }/__init__.py            |  0
 src/classes/__init__.py                   |  0
 src/{fleximod => classes}/gitinterface.py |  2 +-
 src/{fleximod => classes}/gitmodules.py   |  2 +-
 src/{fleximod => classes}/lstripreader.py |  0
 src/{fleximod => classes}/utils.py        |  0
 src/{fleximod => classes}/version.py      |  0
 src/git-fleximod                          | 11 ++---
 tbump.toml                                | 43 ++++++++++++++++++
 tests/__init__.py                         |  3 ++
 tests/test_import.py                      |  9 ++++
 14 files changed, 91 insertions(+), 70 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py
 rename src/{fleximod => }/__init__.py (100%)
 create mode 100644 src/classes/__init__.py
 rename src/{fleximod => classes}/gitinterface.py (98%)
 rename src/{fleximod => classes}/gitmodules.py (98%)
 rename src/{fleximod => classes}/lstripreader.py (100%)
 rename src/{fleximod => classes}/utils.py (100%)
 rename src/{fleximod => classes}/version.py (100%)
 create mode 100644 tbump.toml
 create mode 100644 tests/__init__.py
 create mode 100644 tests/test_import.py

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000..28e0e35a09
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,28 @@
+[tool.poetry]
+name = "git-fleximod"
+version = "0.3.0"
+description = "Extended support for git-submodule and git-sparse-checkout"
+authors = ["Jim Edwards <jedwards@ucar.edu>"]
+maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/jedwards4b/git-fleximod"
+keywords = ["git", "submodule", "sparse-checkout"]
+packages = [
+  { include = "src/git-fleximod" },
+  { include = "src/classes/*.py" },
+  { include = "License" },
+  { include = "tests" },
+
+]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+GitPython = "^3.1.0"
+
+[tools.poetry.urls]
+"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 66ff24ada6..0000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,8 +0,0 @@
-[metadata]
-license_file = License
-[build_manpages]
-manpages =
-    # solution 1: -- use parser function
-    man/git-fleximod.1:function=get_parser:pyfile=src/git-fleximod
-    # solution 2 -- make parser global
-    #man/git-fleximod.2:pyfile=src/git-fleximod:object=parser
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 048db75957..0000000000
--- a/setup.py
+++ /dev/null
@@ -1,55 +0,0 @@
-import sys
-import os
-
-sys.path.insert(0, os.path.join(os.getenv("CONDA_PREFIX"), "lib", "python3.12"))
-sys.path.insert(
-    0, os.path.join(os.getenv("CONDA_PREFIX"), "lib", "python3.12", "site-packages")
-)
-
-import setuptools
-from setuptools import find_packages, convert_path
-from build_manpages import build_manpages, get_build_py_cmd, get_install_cmd
-
-main_ns = {}
-ver_path = convert_path(
-    os.path.join(os.path.dirname(__file__), "src", "fleximod", "version.py")
-)
-print(f"ver_path is {ver_path}")
-with open(ver_path) as ver_file:
-    exec(ver_file.read(), main_ns)
-
-if __name__ == "__main__":
-    with open("README.md", "r") as fh:
-        long_description = fh.read()
-
-    setuptools.setup(
-        name="git-fleximod",  # package name
-        scripts=["src/git-fleximod"],  # This is the name of the package
-        version=main_ns["__version__"],  # The initial release version
-        author="Jim Edwards",  # Full name of the author
-        maintainer="jedwards4b",
-        license="MIT License",
-        description="Extended support for git-submodule and git-sparse-checkout",
-        long_description=long_description,  # Long description read from the the readme file
-        long_description_content_type="text/markdown",
-        packages=find_packages(
-            where="src"
-        ),  # List of all python modules to be installed
-        package_dir={"": "src", "git-fleximod": "src", "fleximod": "src/fleximod"},
-        package_data={"": ["src/fleximod/version.txt", "man/git-fleximod.1"]},
-        classifiers=[
-            "Programming Language :: Python :: 3",
-            "License :: OSI Approved :: MIT License",
-            "Operating System :: OS Independent",
-        ],  # Information to filter the project on PyPi website
-        python_requires=">=3.6",  # Minimum version requirement of the package
-        #    py_modules=['git-fleximod'],             # Name of the python package
-        install_requires=["GitPython"],  # Install other dependencies if any
-        cmdclass={
-            "build_manpages": build_manpages,
-            # Re-define build_py and install commands so the manual pages
-            # are automatically re-generated and installed
-            "build_py": get_build_py_cmd(),
-            "install": get_install_cmd(),
-        },
-    )
diff --git a/src/fleximod/__init__.py b/src/__init__.py
similarity index 100%
rename from src/fleximod/__init__.py
rename to src/__init__.py
diff --git a/src/classes/__init__.py b/src/classes/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/src/fleximod/gitinterface.py b/src/classes/gitinterface.py
similarity index 98%
rename from src/fleximod/gitinterface.py
rename to src/classes/gitinterface.py
index 96bb9ac52b..35c593a095 100644
--- a/src/fleximod/gitinterface.py
+++ b/src/classes/gitinterface.py
@@ -1,5 +1,5 @@
 import os
-from fleximod import utils
+from classes import utils
 
 
 class GitInterface:
diff --git a/src/fleximod/gitmodules.py b/src/classes/gitmodules.py
similarity index 98%
rename from src/fleximod/gitmodules.py
rename to src/classes/gitmodules.py
index 11a2457247..dd2e1fc948 100644
--- a/src/fleximod/gitmodules.py
+++ b/src/classes/gitmodules.py
@@ -1,7 +1,7 @@
 import os
 import shutil
 from configparser import ConfigParser
-from fleximod.lstripreader import LstripReader
+from classes.lstripreader import LstripReader
 
 
 class GitModules(ConfigParser):
diff --git a/src/fleximod/lstripreader.py b/src/classes/lstripreader.py
similarity index 100%
rename from src/fleximod/lstripreader.py
rename to src/classes/lstripreader.py
diff --git a/src/fleximod/utils.py b/src/classes/utils.py
similarity index 100%
rename from src/fleximod/utils.py
rename to src/classes/utils.py
diff --git a/src/fleximod/version.py b/src/classes/version.py
similarity index 100%
rename from src/fleximod/version.py
rename to src/classes/version.py
diff --git a/src/git-fleximod b/src/git-fleximod
index aa587ea3a9..1c06d0d3d0 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -6,10 +6,10 @@ import logging
 import argparse
 import textwrap
 from pathlib import Path
-from fleximod import utils
-from fleximod.gitinterface import GitInterface
-from fleximod.gitmodules import GitModules
-from fleximod.version import __version__
+from classes import utils
+from classes.gitinterface import GitInterface
+from classes.gitmodules import GitModules
+from classes.version import __version__
 from configparser import NoOptionError
 
 # logger variable is global
@@ -43,7 +43,7 @@ def get_parser():
         "action",
         choices=choices,
         default="checkout",
-        help=f"Subcommand of fleximod, choices are {choices[:-1]}",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
     )
 
     parser.add_argument(
@@ -394,6 +394,7 @@ def submodules_update(gitmodules, root_dir, force):
                 if fxtag and fxtag not in tags:
                     git.git_operation("fetch", newremote, "--tags")
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
+
                 if fxtag and fxtag != atag:
                     print(f"{name:>20} updated to {fxtag}")
                     git.git_operation("checkout", fxtag)
diff --git a/tbump.toml b/tbump.toml
new file mode 100644
index 0000000000..0e0a633036
--- /dev/null
+++ b/tbump.toml
@@ -0,0 +1,43 @@
+# Uncomment this if your project is hosted on GitHub:
+github_url = "https://github.com/jedwards4b/git-fleximod/"
+
+[version]
+current = "0.3.0"
+
+# Example of a semver regexp.
+# Make sure this matches current_version before
+# using tbump
+regex = '''
+  (?P<major>\d+)
+  \.
+  (?P<minor>\d+)
+  \.
+  (?P<patch>\d+)
+  '''
+
+[git]
+message_template = "Bump to {new_version}"
+tag_template = "v{new_version}"
+
+# For each file to patch, add a [[file]] config
+# section containing the path of the file, relative to the
+# tbump.toml location.
+[[file]]
+src = "src/classes/version.py"
+
+[[file]]
+src = "pyproject.toml"
+
+# You can specify a list of commands to
+# run after the files have been patched
+# and before the git commit is made
+
+#  [[before_commit]]
+#  name = "check changelog"
+#  cmd = "grep -q {new_version} Changelog.rst"
+
+# Or run some commands after the git tag and the branch
+# have been pushed:
+#  [[after_push]]
+#  name = "publish"
+#  cmd = "./publish.sh"
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000000..4d4c66c78e
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1,3 @@
+import sys, os
+
+sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/tests/test_import.py b/tests/test_import.py
new file mode 100644
index 0000000000..becf751441
--- /dev/null
+++ b/tests/test_import.py
@@ -0,0 +1,9 @@
+# pylint: disable=unused-import
+from classes import utils
+from classes.gitinterface import GitInterface
+from classes.gitmodules import GitModules
+from classes.version import __version__
+
+
+def test_import():
+    print("here")

From 4f3bb556e165f9f1087de841c9b408cedb62f4a3 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 3 Feb 2024 13:59:24 -0700
Subject: [PATCH 078/161] more poetry and sphinx

---
 doc/Makefile           |  20 +++++++
 doc/conf.py            |  26 +++++++++
 doc/index.rst          |  24 ++++++++
 doc/make.bat           |  35 ++++++++++++
 pyproject.toml         |   5 +-
 src/classes/cli.py     | 120 ++++++++++++++++++++++++++++++++++++++++
 src/classes/version.py |   1 -
 src/git-fleximod       | 122 +----------------------------------------
 tbump.toml             |   2 +-
 9 files changed, 232 insertions(+), 123 deletions(-)
 create mode 100644 doc/Makefile
 create mode 100644 doc/conf.py
 create mode 100644 doc/index.rst
 create mode 100644 doc/make.bat
 create mode 100644 src/classes/cli.py
 delete mode 100644 src/classes/version.py

diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000000..d4bb2cbb9e
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000000..423099eec9
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,26 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "git-fleximod"
+author = "Jim Edwards <jedwards@ucar.edu>"
+release = "0.4.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_argparse_cli"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000000..fa534d0d10
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,24 @@
+.. git-fleximod documentation master file, created by
+   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to git-fleximod's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+.. module:: sphinxcontrib.autoprogram
+.. sphinx_argparse_cli::
+   :module: classes.cli
+   :func: get_parser
+   :prog: git-fleximod
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000000..32bb24529f
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/pyproject.toml b/pyproject.toml
index 28e0e35a09..d49cbae72b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,10 @@ packages = [
   { include = "src/classes/*.py" },
   { include = "License" },
   { include = "tests" },
-
+  { include = "doc/*.rst" },
+  { include = "doc/Makefile" },
+  { include = "doc/make.bat" },
+  { include = "doc/conf.py" },
 ]
 
 [tool.poetry.dependencies]
diff --git a/src/classes/cli.py b/src/classes/cli.py
new file mode 100644
index 0000000000..437d9beec4
--- /dev/null
+++ b/src/classes/cli.py
@@ -0,0 +1,120 @@
+from pathlib import Path
+import argparse
+
+__version__ = "0.3.0"
+
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return attempt
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    choices = ["update", "checkout", "status", "test"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="checkout",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
+    )
+
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
diff --git a/src/classes/version.py b/src/classes/version.py
deleted file mode 100644
index 493f7415d7..0000000000
--- a/src/classes/version.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = "0.3.0"
diff --git a/src/git-fleximod b/src/git-fleximod
index 1c06d0d3d0..385515819c 100755
--- a/src/git-fleximod
+++ b/src/git-fleximod
@@ -3,137 +3,19 @@ import sys
 import os
 import shutil
 import logging
-import argparse
 import textwrap
-from pathlib import Path
 from classes import utils
+from classes import cli
 from classes.gitinterface import GitInterface
 from classes.gitmodules import GitModules
-from classes.version import __version__
 from configparser import NoOptionError
 
 # logger variable is global
 logger = None
 
 
-def find_root_dir(filename=".git"):
-    d = Path.cwd()
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return attempt
-        d = d.parent
-    return None
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    #
-    # user options
-    #
-    choices = ["update", "checkout", "status", "test"]
-    parser.add_argument(
-        "action",
-        choices=choices,
-        default="checkout",
-        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
-    )
-
-    parser.add_argument(
-        "components",
-        nargs="*",
-        help="Specific component(s) to checkout. By default, "
-        "all required submodules are checked out.",
-    )
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-
-    parser.add_argument(
-        "-x",
-        "--exclude",
-        nargs="*",
-        help="Component(s) listed in the gitmodules file which should be ignored.",
-    )
-    parser.add_argument(
-        "-f",
-        "--force",
-        action="store_true",
-        default=False,
-        help="Override cautions and update or checkout over locally modified repository.",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--optional",
-        action="store_true",
-        default=False,
-        help="By default only the required submodules "
-        "are checked out. This flag will also checkout the "
-        "optional submodules relative to the toplevel directory.",
-    )
-
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-
-    parser.add_argument(
-        "-V",
-        "--version",
-        action="version",
-        version=f"%(prog)s {__version__}",
-        help="Print version and exit.",
-    )
-
-    #
-    # developer options
-    #
-    parser.add_argument(
-        "--backtrace",
-        action="store_true",
-        help="DEVELOPER: show exception backtraces as extra " "debugging output",
-    )
-
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
-
-
 def commandline_arguments(args=None):
-    parser = get_parser()
+    parser = cli.get_parser()
 
     if args:
         options = parser.parse_args(args)
diff --git a/tbump.toml b/tbump.toml
index 0e0a633036..35521d04d1 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -23,7 +23,7 @@ tag_template = "v{new_version}"
 # section containing the path of the file, relative to the
 # tbump.toml location.
 [[file]]
-src = "src/classes/version.py"
+src = "src/classes/cli.py"
 
 [[file]]
 src = "pyproject.toml"

From 461ee4be93bc63eb9c735e03a7ce12c04ff3fe84 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 3 Feb 2024 14:02:07 -0700
Subject: [PATCH 079/161] Bump to 0.5.0

---
 pyproject.toml     | 2 +-
 src/classes/cli.py | 2 +-
 tbump.toml         | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d49cbae72b..8b4246e256 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.3.0"
+version = "0.5.0"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/src/classes/cli.py b/src/classes/cli.py
index 437d9beec4..65f70cdd34 100644
--- a/src/classes/cli.py
+++ b/src/classes/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.3.0"
+__version__ = "0.5.0"
 
 
 def find_root_dir(filename=".git"):
diff --git a/tbump.toml b/tbump.toml
index 35521d04d1..18e21a69f6 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.3.0"
+current = "0.5.0"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From f0ab8150ba149c42d4690aa8964754bd58225a11 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 4 Feb 2024 09:15:55 -0700
Subject: [PATCH 080/161] reformed to work with poetry

---
 {src => git_fleximod}/__init__.py                |  0
 {src/classes => git_fleximod}/cli.py             |  1 -
 src/git-fleximod => git_fleximod/git-fleximod.py | 12 ++++++------
 {src/classes => git_fleximod}/gitinterface.py    |  3 +--
 {src/classes => git_fleximod}/gitmodules.py      |  2 +-
 {src/classes => git_fleximod}/lstripreader.py    |  0
 {src/classes => git_fleximod}/utils.py           |  0
 pyproject.toml                                   | 16 ++++++----------
 src/classes/__init__.py                          |  0
 9 files changed, 14 insertions(+), 20 deletions(-)
 rename {src => git_fleximod}/__init__.py (100%)
 rename {src/classes => git_fleximod}/cli.py (99%)
 rename src/git-fleximod => git_fleximod/git-fleximod.py (98%)
 rename {src/classes => git_fleximod}/gitinterface.py (98%)
 rename {src/classes => git_fleximod}/gitmodules.py (98%)
 rename {src/classes => git_fleximod}/lstripreader.py (100%)
 rename {src/classes => git_fleximod}/utils.py (100%)
 delete mode 100644 src/classes/__init__.py

diff --git a/src/__init__.py b/git_fleximod/__init__.py
similarity index 100%
rename from src/__init__.py
rename to git_fleximod/__init__.py
diff --git a/src/classes/cli.py b/git_fleximod/cli.py
similarity index 99%
rename from src/classes/cli.py
rename to git_fleximod/cli.py
index 65f70cdd34..822b314387 100644
--- a/src/classes/cli.py
+++ b/git_fleximod/cli.py
@@ -3,7 +3,6 @@
 
 __version__ = "0.5.0"
 
-
 def find_root_dir(filename=".git"):
     d = Path.cwd()
     root = Path(d.root)
diff --git a/src/git-fleximod b/git_fleximod/git-fleximod.py
similarity index 98%
rename from src/git-fleximod
rename to git_fleximod/git-fleximod.py
index 385515819c..9e4969d6c1 100755
--- a/src/git-fleximod
+++ b/git_fleximod/git-fleximod.py
@@ -4,10 +4,10 @@
 import shutil
 import logging
 import textwrap
-from classes import utils
-from classes import cli
-from classes.gitinterface import GitInterface
-from classes.gitmodules import GitModules
+from git_fleximod import utils
+from git_fleximod import cli
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
 from configparser import NoOptionError
 
 # logger variable is global
@@ -343,7 +343,7 @@ def submodules_test(gitmodules, root_dir):
     return testfails + localmods
 
 
-def _main_func():
+def main():
     (
         root_dir,
         file_name,
@@ -393,4 +393,4 @@ def _main_func():
 
 
 if __name__ == "__main__":
-    sys.exit(_main_func())
+    sys.exit(main())
diff --git a/src/classes/gitinterface.py b/git_fleximod/gitinterface.py
similarity index 98%
rename from src/classes/gitinterface.py
rename to git_fleximod/gitinterface.py
index 35c593a095..eff155d54d 100644
--- a/src/classes/gitinterface.py
+++ b/git_fleximod/gitinterface.py
@@ -1,6 +1,5 @@
 import os
-from classes import utils
-
+from . import utils
 
 class GitInterface:
     def __init__(self, repo_path, logger):
diff --git a/src/classes/gitmodules.py b/git_fleximod/gitmodules.py
similarity index 98%
rename from src/classes/gitmodules.py
rename to git_fleximod/gitmodules.py
index dd2e1fc948..ae0ebe121c 100644
--- a/src/classes/gitmodules.py
+++ b/git_fleximod/gitmodules.py
@@ -1,7 +1,7 @@
 import os
 import shutil
 from configparser import ConfigParser
-from classes.lstripreader import LstripReader
+from .lstripreader import LstripReader
 
 
 class GitModules(ConfigParser):
diff --git a/src/classes/lstripreader.py b/git_fleximod/lstripreader.py
similarity index 100%
rename from src/classes/lstripreader.py
rename to git_fleximod/lstripreader.py
diff --git a/src/classes/utils.py b/git_fleximod/utils.py
similarity index 100%
rename from src/classes/utils.py
rename to git_fleximod/utils.py
diff --git a/pyproject.toml b/pyproject.toml
index 8b4246e256..6661789359 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,16 +8,12 @@ license = "MIT"
 readme = "README.md"
 homepage = "https://github.com/jedwards4b/git-fleximod"
 keywords = ["git", "submodule", "sparse-checkout"]
-packages = [
-  { include = "src/git-fleximod" },
-  { include = "src/classes/*.py" },
-  { include = "License" },
-  { include = "tests" },
-  { include = "doc/*.rst" },
-  { include = "doc/Makefile" },
-  { include = "doc/make.bat" },
-  { include = "doc/conf.py" },
-]
+
+[[tool.poetry.packages]]
+include = "git_fleximod"
+
+[tool.poetry.scripts]
+git-fleximod = "git_fleximod.git-fleximod:main"
 
 [tool.poetry.dependencies]
 python = "^3.8"
diff --git a/src/classes/__init__.py b/src/classes/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000

From 7b2a86dcfdcc039034c2ad2e2b69103ac5bf319f Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 4 Feb 2024 09:22:09 -0700
Subject: [PATCH 081/161] add a simple import test

---
 tests/test_import.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/tests/test_import.py b/tests/test_import.py
index becf751441..d5ca878de5 100644
--- a/tests/test_import.py
+++ b/tests/test_import.py
@@ -1,9 +1,8 @@
 # pylint: disable=unused-import
-from classes import utils
-from classes.gitinterface import GitInterface
-from classes.gitmodules import GitModules
-from classes.version import __version__
-
+from git_fleximod import cli
+from git_fleximod import utils
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
 
 def test_import():
     print("here")

From e7fdd39fd8df3b829196f276e21c7945fd71401e Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 4 Feb 2024 10:30:30 -0700
Subject: [PATCH 082/161] now includes man pages

---
 doc/index.rst  |  2 +-
 pyproject.toml | 13 +++++++++----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/doc/index.rst b/doc/index.rst
index fa534d0d10..0f9c1a7f7e 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -11,7 +11,7 @@ Welcome to git-fleximod's documentation!
    :caption: Contents:
 .. module:: sphinxcontrib.autoprogram
 .. sphinx_argparse_cli::
-   :module: classes.cli
+   :module: git_fleximod.cli
    :func: get_parser
    :prog: git-fleximod
 
diff --git a/pyproject.toml b/pyproject.toml
index 6661789359..17843e0b83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,18 +8,23 @@ license = "MIT"
 readme = "README.md"
 homepage = "https://github.com/jedwards4b/git-fleximod"
 keywords = ["git", "submodule", "sparse-checkout"]
-
-[[tool.poetry.packages]]
-include = "git_fleximod"
+packages = [
+{ include = "git_fleximod"},
+{ include = "doc"},
+]
 
 [tool.poetry.scripts]
 git-fleximod = "git_fleximod.git-fleximod:main"
+fsspec = "fsspec.fuse:main"
 
 [tool.poetry.dependencies]
 python = "^3.8"
 GitPython = "^3.1.0"
+sphinx = "^5.0.0"
+fsspec = "^2023.12.2"
+wheel = "^0.42.0"
 
-[tools.poetry.urls]
+[tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
 
 [build-system]

From 26739ada8bf21eda4aefabdf8219ade9e09e473e Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 5 Feb 2024 08:09:44 -0700
Subject: [PATCH 083/161] update tbump path

---
 tbump.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tbump.toml b/tbump.toml
index 18e21a69f6..c3720e25d7 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -23,7 +23,7 @@ tag_template = "v{new_version}"
 # section containing the path of the file, relative to the
 # tbump.toml location.
 [[file]]
-src = "src/classes/cli.py"
+src = "git_fleximod/cli.py"
 
 [[file]]
 src = "pyproject.toml"

From 25bcc7ea7ac8cf9e02c5dfbcd81f257c6f50b21a Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Mon, 5 Feb 2024 08:09:53 -0700
Subject: [PATCH 084/161] Bump to 0.6.0

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 822b314387..e1c6d2d5cd 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"
 
 def find_root_dir(filename=".git"):
     d = Path.cwd()
diff --git a/pyproject.toml b/pyproject.toml
index 17843e0b83..eabb7657e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.5.0"
+version = "0.6.0"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index c3720e25d7..b41ec17e20 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.5.0"
+current = "0.6.0"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From ed01cb7a0f07e1c79136b50f6448463a45538acb Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 5 Feb 2024 09:06:54 -0700
Subject: [PATCH 085/161] fix issue with hyphen

---
 .../{git-fleximod.py => git_fleximod.py}      |   0
 poetry.lock                                   | 682 ++++++++++++++++++
 pyproject.toml                                |   1 +
 3 files changed, 683 insertions(+)
 rename git_fleximod/{git-fleximod.py => git_fleximod.py} (100%)
 create mode 100644 poetry.lock

diff --git a/git_fleximod/git-fleximod.py b/git_fleximod/git_fleximod.py
similarity index 100%
rename from git_fleximod/git-fleximod.py
rename to git_fleximod/git_fleximod.py
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000000..6c31fac48a
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,682 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.dependencies]
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.2.2"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
+files = [
+    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
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+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.4"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
+    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.2"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.1"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
+    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["html5lib", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+
+[package.extras]
+test = ["flake8", "mypy", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-qthelp"
+version = "1.0.3"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.5"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.2.0"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
+    {file = "urllib3-2.2.0.tar.gz", hash = "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "wheel"
+version = "0.42.0"
+description = "A built-package format for Python"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "wheel-0.42.0-py3-none-any.whl", hash = "sha256:177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d"},
+    {file = "wheel-0.42.0.tar.gz", hash = "sha256:c45be39f7882c9d34243236f2d63cbd58039e360f85d0913425fbd7ceea617a8"},
+]
+
+[package.extras]
+test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
+
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.8"
+content-hash = "f20e29bada880bbb0aad20d2a7ac282d09c3e89d4aac06072cb82a9157f4023a"
diff --git a/pyproject.toml b/pyproject.toml
index eabb7657e5..c6ccff2624 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,6 +23,7 @@ GitPython = "^3.1.0"
 sphinx = "^5.0.0"
 fsspec = "^2023.12.2"
 wheel = "^0.42.0"
+pytest = "^8.0.0"
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"

From 69a5dc5ae30514b2cefe8ee827b6d2a5e4322db9 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 5 Feb 2024 09:07:10 -0700
Subject: [PATCH 086/161] Bump to 0.6.1

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index e1c6d2d5cd..39e83b97c0 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.6.0"
+__version__ = "0.6.1"
 
 def find_root_dir(filename=".git"):
     d = Path.cwd()
diff --git a/pyproject.toml b/pyproject.toml
index c6ccff2624..225f7b39b0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.6.0"
+version = "0.6.1"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index b41ec17e20..03b63f1540 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.6.0"
+current = "0.6.1"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From f456ca059ccd6bfacd15dce2b302eafb6c09ce2c Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 6 Feb 2024 11:45:42 -0700
Subject: [PATCH 087/161] fix issue with sparse checkout dir path

---
 git_fleximod/git_fleximod.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 9e4969d6c1..59656eeb08 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -65,8 +65,8 @@ def commandline_arguments(args=None):
 
 def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
     # first create the module directory
-    if not os.path.isdir(path):
-        os.makedirs(path)
+    if not os.path.isdir(os.path.join(root_dir,path)):
+        os.makedirs(os.path.join(root_dir,path))
     # Check first if the module is already defined
     # and the sparse-checkout file exists
     git = GitInterface(root_dir, logger)

From ac3e6ddc7f1fddc3066d81a61aa7a042683315cb Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 6 Feb 2024 13:12:28 -0700
Subject: [PATCH 088/161] Bump to 0.6.2

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 39e83b97c0..719b156206 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.6.1"
+__version__ = "0.6.2"
 
 def find_root_dir(filename=".git"):
     d = Path.cwd()
diff --git a/pyproject.toml b/pyproject.toml
index 225f7b39b0..f5828a58e7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.6.1"
+version = "0.6.2"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 03b63f1540..583cef45ae 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.6.1"
+current = "0.6.2"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 96ac371975428ddebf7744bf9304f7496c66a959 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 9 Feb 2024 14:41:10 -0700
Subject: [PATCH 089/161] add tests

---
 git_fleximod/gitinterface.py               | 11 +++++--
 poetry.lock                                | 13 +++++++-
 pyproject.toml                             |  3 +-
 tests/{test_import.py => test_a_import.py} |  0
 tests/test_checkout.py                     | 32 ++++++++++++++++++
 tests/test_sparse_checkout.py              | 38 ++++++++++++++++++++++
 6 files changed, 93 insertions(+), 4 deletions(-)
 rename tests/{test_import.py => test_a_import.py} (100%)
 create mode 100644 tests/test_checkout.py
 create mode 100644 tests/test_sparse_checkout.py

diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
index eff155d54d..4d4c4f4b9e 100644
--- a/git_fleximod/gitinterface.py
+++ b/git_fleximod/gitinterface.py
@@ -1,4 +1,5 @@
 import os
+import sys
 from . import utils
 
 class GitInterface:
@@ -26,7 +27,10 @@ def __init__(self, repo_path, logger):
     def _git_command(self, operation, *args):
         self.logger.info(operation)
         if self._use_module and operation != "submodule":
-            return getattr(self.repo.git, operation)(*args)
+            try:
+                return getattr(self.repo.git, operation)(*args)
+            except Exception as e:
+                sys.exit(e)
         else:
             return ["git", "-C", self.repo_path, operation] + list(args)
 
@@ -42,7 +46,10 @@ def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *args)
         self.logger.info(command)
         if isinstance(command, list):
-            return utils.execute_subprocess(command, output_to_caller=True)
+            try:
+                return utils.execute_subprocess(command, output_to_caller=True)
+            except Exception as e:
+                sys.exit(e)
         else:
             return command
 
diff --git a/poetry.lock b/poetry.lock
index 6c31fac48a..b59ed3942c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -404,6 +404,17 @@ files = [
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "pyfakefs"
+version = "5.3.5"
+description = "pyfakefs implements a fake file system that mocks the Python file system modules."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pyfakefs-5.3.5-py3-none-any.whl", hash = "sha256:751015c1de94e1390128c82b48cdedc3f088bbdbe4bc713c79d02a27f0f61e69"},
+    {file = "pyfakefs-5.3.5.tar.gz", hash = "sha256:7cdc500b35a214cb7a614e1940543acc6650e69a94ac76e30f33c9373bd9cf90"},
+]
+
 [[package]]
 name = "pygments"
 version = "2.17.2"
@@ -679,4 +690,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "f20e29bada880bbb0aad20d2a7ac282d09c3e89d4aac06072cb82a9157f4023a"
+content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
diff --git a/pyproject.toml b/pyproject.toml
index f5828a58e7..6d0fa42157 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,7 @@ packages = [
 ]
 
 [tool.poetry.scripts]
-git-fleximod = "git_fleximod.git-fleximod:main"
+git-fleximod = "git_fleximod.git_fleximod:main"
 fsspec = "fsspec.fuse:main"
 
 [tool.poetry.dependencies]
@@ -24,6 +24,7 @@ sphinx = "^5.0.0"
 fsspec = "^2023.12.2"
 wheel = "^0.42.0"
 pytest = "^8.0.0"
+pyfakefs = "^5.3.5"
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
diff --git a/tests/test_import.py b/tests/test_a_import.py
similarity index 100%
rename from tests/test_import.py
rename to tests/test_a_import.py
diff --git a/tests/test_checkout.py b/tests/test_checkout.py
new file mode 100644
index 0000000000..791587628b
--- /dev/null
+++ b/tests/test_checkout.py
@@ -0,0 +1,32 @@
+import pytest
+from pathlib import Path
+
+def test_basic_checkout(git_fleximod, test_repo):
+    # Prepare a simple .gitmodules
+    
+    gitmodules_content = """
+    [submodule "test_submodule"]
+        path = modules/test
+        url = https://github.com/ESMCI/mpi-serial.git
+        fxtag = MPIserial_2.4.0
+        fxurl = https://github.com/ESMCI/mpi-serial.git
+        fxrequired = T:T
+    """
+    (test_repo / ".gitmodules").write_text(gitmodules_content)
+    
+    # Run the command
+    result = git_fleximod("checkout")
+
+    # Assertions
+    assert result.returncode == 0
+    assert Path(test_repo / "modules/test").exists()   # Did the submodule directory get created?
+
+    status = git_fleximod("status")
+
+    assert "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0" in status.stdout
+
+    result = git_fleximod("update")
+    assert result.returncode == 0
+
+    status = git_fleximod("status")
+    assert "test_submodule at tag MPIserial_2.4.0" in status.stdout
diff --git a/tests/test_sparse_checkout.py b/tests/test_sparse_checkout.py
new file mode 100644
index 0000000000..0633802cb0
--- /dev/null
+++ b/tests/test_sparse_checkout.py
@@ -0,0 +1,38 @@
+import pytest
+from shutil import rmtree
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_sparse_checkout(git_fleximod, test_repo_base):
+    # Prepare a simple .gitmodules
+    gitmodules_content = (test_repo_base / ".gitmodules").read_text() + """
+    [submodule "test_sparse_submodule"]
+        path = modules/sparse_test
+        url = https://github.com/ESMCI/mpi-serial.git
+        fxtag = MPIserial_2.5.0
+        fxurl = https://github.com/ESMCI/mpi-serial.git
+        fxsparse = ../.sparse_file_list
+    """
+    (test_repo_base / ".gitmodules").write_text(gitmodules_content)
+
+    # Add the sparse checkout file
+    sparse_content = """m4
+"""
+    (test_repo_base / "modules" / ".sparse_file_list").write_text(sparse_content)
+
+    result = git_fleximod("checkout")
+    
+    # Assertions
+    assert result.returncode == 0
+    assert Path(test_repo_base / "modules/sparse_test").exists()   # Did the submodule directory get created?
+    assert Path(test_repo_base /  "modules/sparse_test/m4").exists()   # Did the submodule sparse directory get created?
+    assert not Path(test_repo_base /  "modules/sparse_test/README").exists()   # Did only the submodule sparse directory get created?
+    status = git_fleximod("status test_sparse_submodule")
+
+    assert "test_sparse_submodule at tag MPIserial_2.5.0" in status.stdout
+
+    result = git_fleximod("update")
+    assert result.returncode == 0
+
+    status = git_fleximod("status test_sparse_submodule")
+    assert "test_sparse_submodule at tag MPIserial_2.5.0" in status.stdout

From 8e04947c985c02063c246d20ac5b1ef4ecd18fd4 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 9 Feb 2024 15:51:58 -0700
Subject: [PATCH 090/161] add pytest to workflow

---
 .github/workflows/pytest.yaml | 73 +++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 .github/workflows/pytest.yaml

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
new file mode 100644
index 0000000000..8d2c2cb6ef
--- /dev/null
+++ b/.github/workflows/pytest.yaml
@@ -0,0 +1,73 @@
+# Run this job on pushes to `main`, and for pull requests. If you don't specify
+# `branches: [main], then this actions runs _twice_ on pull requests, which is
+# annoying.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
+      # reference the matrixe python version here.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
+      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
+      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
+      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
+      # mildly cleaner by using an environment variable, but I don't really care.
+      - name: cache poetry install
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-1.7.1
+
+      # Install Poetry. You could do this manually, or there are several actions that do this.
+      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
+      # Poetry's default install script, which feels correct. I pin the Poetry version here
+      # because Poetry does occasionally change APIs between versions and I don't want my
+      # actions to break if it does.
+      #
+      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
+      # venv as a `.venv` in your testing directory, which allows the next step to easily
+      # cache it.
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.7.1
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
+      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
+      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
+      - name: cache deps
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+
+      # Install dependencies. `--no-root` means "install all dependencies but not the project
+      # itself", which is what you want to avoid caching _your_ code. The `if` statement
+      # ensures this only runs on a cache miss.
+      - run: poetry install --no-interaction --no-root
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+
+      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
+      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
+      # pyproject.toml and makes that if you add things like console-scripts at some point that
+      # they'll be installed and working.
+      - run: poetry install --no-interaction
+
+      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
+      # so this line is super-simple. But it could be as complex as you need.
+      - run: poetry run pytest
+

From c1aef37f7b1e0b30399ed20d093a0756e658b25c Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 9 Feb 2024 15:52:42 -0700
Subject: [PATCH 091/161] add pytest to workflow

---
 .github/workflows/pytest.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
index 8d2c2cb6ef..4809a2787f 100644
--- a/.github/workflows/pytest.yaml
+++ b/.github/workflows/pytest.yaml
@@ -6,6 +6,7 @@ on:
   push:
     branches: [main]
   pull_request:
+    branches: [main]
 
 jobs:
   test:

From e8b6d3cc382785d787ee5fc482a974ef0c1be2b8 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 9 Feb 2024 15:55:32 -0700
Subject: [PATCH 092/161] add pytest fixtures

---
 tests/conftest.py | 51 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 tests/conftest.py

diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000000..1cb059dac6
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,51 @@
+import pytest 
+from git_fleximod.gitinterface import GitInterface
+import os
+import subprocess
+import logging
+from pathlib import Path
+
+@pytest.fixture(scope='session')
+def logger():
+    logging.basicConfig(
+        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+    )
+    logger = logging.getLogger(__name__)
+    return logger
+
+@pytest.fixture
+def test_repo_base(tmp_path, logger):
+    test_dir = tmp_path / "test_repo"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    #subprocess.run(["git", "init"], cwd=test_dir)
+    assert test_dir.joinpath(".git").is_dir()
+    return test_dir
+    
+@pytest.fixture(params=["modules/test"])
+def test_repo(request, test_repo_base, logger):
+    subrepo_path = request.param
+    gitp = GitInterface(str(test_repo_base), logger)
+    gitp.git_operation("submodule", "add", "--depth","1","--name","test_submodule", "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+    #    subprocess.run(
+    assert test_repo_base.joinpath(".gitmodules").is_file()
+    return test_repo_base
+
+@pytest.fixture
+def git_fleximod(test_repo):
+    def _run_fleximod(args, input=None):
+        cmd = ["git", "fleximod"] + args.split()
+        result = subprocess.run(cmd, cwd=test_repo, input=input, 
+                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
+                                text=True)
+        return result
+    return _run_fleximod
+
+    
+@pytest.fixture
+def deinit_submodule(test_repo, logger):
+    def _deinit(submodule_path):
+        gitp = GitInterface(str(test_repo), logger)
+        gitp.git_operation( "submodule", "deinit", "-f", submodule_path) 
+    yield _deinit 

From c1edd2c894d6f28903c70caa2ff5c7a6e892da26 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 11 Feb 2024 10:49:54 -0700
Subject: [PATCH 093/161] all working

---
 README.md                     | 18 +++++----
 git_fleximod/git_fleximod.py  |  7 ++--
 pyproject.toml                |  6 +++
 tests/conftest.py             | 73 +++++++++++++++++++++++++----------
 tests/test_checkout.py        | 54 ++++++++++++++------------
 tests/test_sparse_checkout.py | 52 ++++++++++++-------------
 6 files changed, 127 insertions(+), 83 deletions(-)

diff --git a/README.md b/README.md
index 7c968e70b0..259ba8b54f 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,10 @@
 # git-fleximod
 
-Flexible Submodule Management for Git
+Flexible, Enhanced Submodule Management for Git
 
 ## Overview
 
-Git-fleximod is a Python-based tool that extends Git's submodule capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
 
 ## Installation
 
@@ -30,10 +30,10 @@ Git-fleximod is a Python-based tool that extends Git's submodule capabilities, o
 
     fxtag: Specify a specific tag or branch to checkout for a submodule.
     fxrequired: Mark a submodule's checkout behavior, with allowed values:
-      - T:T: Top-level and required (checked out only when this is the Toplevel module).
-      - T:F: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
-      - I:T: Internal and required (always checked out).
-      - I:F: Internal and optional (checked out with --optional flag).
+      - ToplevelOnlyRequired: Top-level and required (checked out only when this is the Toplevel module).
+      - ToplevelOnlyOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - AlwaysRequired:       Always required (always checked out).
+      - AlwaysOptional:       Always optional (checked out with --optional flag).
     fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
     fxurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
 
@@ -71,6 +71,7 @@ Example .gitmodules entry:
         path = src/physics/cosp2/src
         url = https://github.com/CFMIP/COSPv2.0
         fxsparse = ../.cosp_sparse_checkout
+        fxrequired = AlwaysRequired
         fxtag = v2.1.4cesm
 ```
 Explanation:
@@ -80,14 +81,15 @@ should be checked out into the directory src/physics/cosp2/src
 relative to the .gitmodules directory.  It should be checked out from
 the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
 described in the file ../.cosp_sparse_checkout relative to the path
-directory.
+directory.  It should be checked out anytime this .gitmodules entry is
+read.
 
 Additional example:
 ```ini, toml
     [submodule "cime"]
         path = cime
         url = https://github.com/jedwards4b/cime
-        fxrequired = T:T
+        fxrequired = ToplevelOnlyRequired
         fxtag = cime6.0.198_rme01
 ```
 
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 1b6c357b94..df76127b38 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -24,9 +24,9 @@ def commandline_arguments(args=None):
 
     # explicitly listing a component overrides the optional flag
     if options.optional or options.components:
-        fxrequired = ["T:T", "T:F", "I:T"]
+        fxrequired = ["ToplevelOnlyRequired", "ToplevelOnlyOptional", "AlwaysRequired", "AlwaysOptional"]
     else:
-        fxrequired = ["T:T", "I:T"]
+        fxrequired = ["ToplevelOnlyRequired", "AlwaysRequired"]
 
     action = options.action
     if not action:
@@ -66,6 +66,7 @@ def commandline_arguments(args=None):
 def submodule_sparse_checkout(
     root_dir, name, url, path, sparsefile, tag="master", fxhash=None
 ):
+    logger.info("Called sparse_checkout for {}".format(name))
     # first create the module directory
     if not os.path.isdir(os.path.join(root_dir,path)):
         os.makedirs(os.path.join(root_dir,path))
@@ -344,7 +345,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
         url = gitmodules.get(name, "url")
 
         if fxrequired and fxrequired not in requiredlist:
-            if "T:F" == fxrequired:
+            if "Optional" in fxrequired:
                 print("Skipping optional component {}".format(name))
             continue
 
diff --git a/pyproject.toml b/pyproject.toml
index 6d0fa42157..772b154216 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,6 +29,12 @@ pyfakefs = "^5.3.5"
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
 
+[tool.pytest.ini_options]
+markers = [
+        "skip_after_first: only run on first iteration"
+]
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
diff --git a/tests/conftest.py b/tests/conftest.py
index 1cb059dac6..d6fec44f3e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -13,39 +13,72 @@ def logger():
     logger = logging.getLogger(__name__)
     return logger
 
+@pytest.fixture(params=[
+    {"subrepo_path": "modules/test", "submodule_name": "test_submodule", "gitmodules_content" : """
+    [submodule "test_submodule"]
+    path = modules/test
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelOnlyRequired
+"""},
+    {"subrepo_path": "modules/test_optional", "submodule_name": "test_optional", "gitmodules_content": """
+    [submodule "test_optional"]
+    path = modules/test_optional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelOnlyRequired
+"""},
+    {"subrepo_path": "modules/test_alwaysoptional", "submodule_name": "test_alwaysoptional", "gitmodules_content": """
+    [submodule "test_alwaysoptional"]
+    path = modules/test_alwaysoptional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.3.0
+    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysOptional
+"""},    
+    {"subrepo_path": "modules/test_sparse", "submodule_name": "test_sparse", "gitmodules_content": """
+    [submodule "test_sparse"]
+    path = modules/test_sparse
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.5.0
+    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysRequired
+    fxsparse = ../.sparse_file_list
+"""},
+])
+
+def shared_repos(request):
+    return request.param
+
+@pytest.fixture
+def test_repo(shared_repos, test_repo_base, logger): 
+    subrepo_path = shared_repos["subrepo_path"]
+    submodule_name = shared_repos["submodule_name"]
+
+    gitp = GitInterface(str(test_repo_base), logger)
+    gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+    assert test_repo_base.joinpath(".gitmodules").is_file()
+    return test_repo_base
+
 @pytest.fixture
 def test_repo_base(tmp_path, logger):
-    test_dir = tmp_path / "test_repo"
+    test_dir = tmp_path / "testrepo"
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
-    #subprocess.run(["git", "init"], cwd=test_dir)
     assert test_dir.joinpath(".git").is_dir()
+    (test_dir / "modules").mkdir()
     return test_dir
     
-@pytest.fixture(params=["modules/test"])
-def test_repo(request, test_repo_base, logger):
-    subrepo_path = request.param
-    gitp = GitInterface(str(test_repo_base), logger)
-    gitp.git_operation("submodule", "add", "--depth","1","--name","test_submodule", "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
-    #    subprocess.run(
-    assert test_repo_base.joinpath(".gitmodules").is_file()
-    return test_repo_base
-
 @pytest.fixture
-def git_fleximod(test_repo):
+def git_fleximod(test_repo_base):
     def _run_fleximod(args, input=None):
         cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=test_repo, input=input, 
+        result = subprocess.run(cmd, cwd=test_repo_base, input=input, 
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
                                 text=True)
         return result
     return _run_fleximod
 
-    
-@pytest.fixture
-def deinit_submodule(test_repo, logger):
-    def _deinit(submodule_path):
-        gitp = GitInterface(str(test_repo), logger)
-        gitp.git_operation( "submodule", "deinit", "-f", submodule_path) 
-    yield _deinit 
diff --git a/tests/test_checkout.py b/tests/test_checkout.py
index 791587628b..6d17ce18fd 100644
--- a/tests/test_checkout.py
+++ b/tests/test_checkout.py
@@ -1,32 +1,38 @@
 import pytest
 from pathlib import Path
 
-def test_basic_checkout(git_fleximod, test_repo):
-    # Prepare a simple .gitmodules
-    
-    gitmodules_content = """
-    [submodule "test_submodule"]
+@pytest.fixture(params=[
+    {"subrepo_path": "modules/test", "submodule_name": "test_submodule", "gitmodules_content" : """                                                                                                                                                                                      [submodule "test_submodule"]
         path = modules/test
         url = https://github.com/ESMCI/mpi-serial.git
         fxtag = MPIserial_2.4.0
         fxurl = https://github.com/ESMCI/mpi-serial.git
-        fxrequired = T:T
-    """
-    (test_repo / ".gitmodules").write_text(gitmodules_content)
+        fxrequired = ToplevelOnlyRequired
+"""},
+])
+def test_config(request):                
+    return request.param
+                
+def test_basic_checkout(git_fleximod, test_repo, test_config):
+    # Prepare a simple .gitmodules
+    gm = test_config['gitmodules_content']
+    file_path = (test_repo / ".gitmodules")
+    if not file_path.exists():
+        file_path.write_text(gm)
     
-    # Run the command
-    result = git_fleximod("checkout")
-
-    # Assertions
-    assert result.returncode == 0
-    assert Path(test_repo / "modules/test").exists()   # Did the submodule directory get created?
-
-    status = git_fleximod("status")
-
-    assert "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0" in status.stdout
-
-    result = git_fleximod("update")
-    assert result.returncode == 0
-
-    status = git_fleximod("status")
-    assert "test_submodule at tag MPIserial_2.4.0" in status.stdout
+        # Run the command
+        result = git_fleximod("checkout test_submodule")
+        
+        # Assertions
+        assert result.returncode == 0
+        assert Path(test_repo / "modules/test").exists()   # Did the submodule directory get created?
+        
+        status = git_fleximod("status")
+        
+        assert "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0" in status.stdout
+        
+        result = git_fleximod("update")
+        assert result.returncode == 0
+        
+        status = git_fleximod("status")
+        assert "test_submodule at tag MPIserial_2.4.0" in status.stdout
diff --git a/tests/test_sparse_checkout.py b/tests/test_sparse_checkout.py
index 0633802cb0..7276e18d35 100644
--- a/tests/test_sparse_checkout.py
+++ b/tests/test_sparse_checkout.py
@@ -3,36 +3,32 @@
 from pathlib import Path
 from git_fleximod.gitinterface import GitInterface
 
-def test_sparse_checkout(git_fleximod, test_repo_base):
-    # Prepare a simple .gitmodules
-    gitmodules_content = (test_repo_base / ".gitmodules").read_text() + """
-    [submodule "test_sparse_submodule"]
-        path = modules/sparse_test
-        url = https://github.com/ESMCI/mpi-serial.git
-        fxtag = MPIserial_2.5.0
-        fxurl = https://github.com/ESMCI/mpi-serial.git
-        fxsparse = ../.sparse_file_list
-    """
-    (test_repo_base / ".gitmodules").write_text(gitmodules_content)
+def test_sparse_checkout(shared_repos, git_fleximod, test_repo_base):
+    repo_name = shared_repos["submodule_name"]
+    if repo_name == "test_sparse":
+        gm = shared_repos["gitmodules_content"]
+        (test_repo_base / ".gitmodules").write_text(gm)
 
-    # Add the sparse checkout file
-    sparse_content = """m4
+        # Add the sparse checkout file
+        sparse_content = """m4
 """
-    (test_repo_base / "modules" / ".sparse_file_list").write_text(sparse_content)
 
-    result = git_fleximod("checkout")
-    
-    # Assertions
-    assert result.returncode == 0
-    assert Path(test_repo_base / "modules/sparse_test").exists()   # Did the submodule directory get created?
-    assert Path(test_repo_base /  "modules/sparse_test/m4").exists()   # Did the submodule sparse directory get created?
-    assert not Path(test_repo_base /  "modules/sparse_test/README").exists()   # Did only the submodule sparse directory get created?
-    status = git_fleximod("status test_sparse_submodule")
-
-    assert "test_sparse_submodule at tag MPIserial_2.5.0" in status.stdout
+        (test_repo_base / "modules" / ".sparse_file_list").write_text(sparse_content)
 
-    result = git_fleximod("update")
-    assert result.returncode == 0
+        result = git_fleximod(f"checkout {repo_name}")
+    
+        # Assertions
+        assert result.returncode == 0
+        assert Path(test_repo_base / f"modules/{repo_name}").exists()   # Did the submodule directory get created?
+        assert Path(test_repo_base /  f"modules/{repo_name}/m4").exists()   # Did the submodule sparse directory get created?
+        assert not Path(test_repo_base /  f"modules/{repo_name}/README").exists()   # Did only the submodule sparse directory get created?
+        status = git_fleximod(f"status {repo_name}")
+        
+        assert f"{repo_name} at tag MPIserial_2.5.0" in status.stdout
+        
+        result = git_fleximod(f"update {repo_name}")
+        assert result.returncode == 0
+        
+        status = git_fleximod(f"status {repo_name}")
+        assert f"{repo_name} at tag MPIserial_2.5.0" in status.stdout
 
-    status = git_fleximod("status test_sparse_submodule")
-    assert "test_sparse_submodule at tag MPIserial_2.5.0" in status.stdout

From 03156218c7ddf4387fd5a8b74b8550ddae7d08da Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 11 Feb 2024 11:47:20 -0700
Subject: [PATCH 094/161] clean up and combine tests

---
 tests/conftest.py             | 50 +++++++++++++++++++++++-----------
 tests/test_checkout.py        | 51 +++++++++++++++--------------------
 tests/test_sparse_checkout.py | 34 -----------------------
 3 files changed, 57 insertions(+), 78 deletions(-)
 delete mode 100644 tests/test_sparse_checkout.py

diff --git a/tests/conftest.py b/tests/conftest.py
index d6fec44f3e..ffff68956d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -14,7 +14,11 @@ def logger():
     return logger
 
 @pytest.fixture(params=[
-    {"subrepo_path": "modules/test", "submodule_name": "test_submodule", "gitmodules_content" : """
+    {"subrepo_path": "modules/test",
+     "submodule_name": "test_submodule",
+     "status1" : "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_submodule at tag MPIserial_2.4.0",
+     "gitmodules_content" : """
     [submodule "test_submodule"]
     path = modules/test
     url = https://github.com/ESMCI/mpi-serial.git
@@ -22,7 +26,11 @@ def logger():
     fxurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelOnlyRequired
 """},
-    {"subrepo_path": "modules/test_optional", "submodule_name": "test_optional", "gitmodules_content": """
+    {"subrepo_path": "modules/test_optional",
+     "submodule_name": "test_optional",
+     "status1" : "test_optional d82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_optional at tag MPIserial_2.4.0",
+     "gitmodules_content": """
     [submodule "test_optional"]
     path = modules/test_optional
     url = https://github.com/ESMCI/mpi-serial.git
@@ -30,7 +38,11 @@ def logger():
     fxurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelOnlyRequired
 """},
-    {"subrepo_path": "modules/test_alwaysoptional", "submodule_name": "test_alwaysoptional", "gitmodules_content": """
+    {"subrepo_path": "modules/test_alwaysoptional",
+     "submodule_name": "test_alwaysoptional",
+     "status1" : "test_alwaysoptional d82ce7c is out of sync with .gitmodules MPIserial_2.3.0",
+     "status2" : "test_alwaysoptional at tag MPIserial_2.3.0",
+     "gitmodules_content": """
     [submodule "test_alwaysoptional"]
     path = modules/test_alwaysoptional
     url = https://github.com/ESMCI/mpi-serial.git
@@ -38,7 +50,11 @@ def logger():
     fxurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysOptional
 """},    
-    {"subrepo_path": "modules/test_sparse", "submodule_name": "test_sparse", "gitmodules_content": """
+    {"subrepo_path": "modules/test_sparse",
+     "submodule_name": "test_sparse",
+     "status1" : "test_sparse at tag MPIserial_2.5.0",
+     "status2" : "test_sparse at tag MPIserial_2.5.0",
+     "gitmodules_content": """
     [submodule "test_sparse"]
     path = modules/test_sparse
     url = https://github.com/ESMCI/mpi-serial.git
@@ -53,30 +69,34 @@ def shared_repos(request):
     return request.param
 
 @pytest.fixture
-def test_repo(shared_repos, test_repo_base, logger): 
+def test_repo(shared_repos, tmp_path, logger):
     subrepo_path = shared_repos["subrepo_path"]
     submodule_name = shared_repos["submodule_name"]
-
-    gitp = GitInterface(str(test_repo_base), logger)
-    gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
-    assert test_repo_base.joinpath(".gitmodules").is_file()
-    return test_repo_base
-
-@pytest.fixture
-def test_repo_base(tmp_path, logger):
     test_dir = tmp_path / "testrepo"
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
     assert test_dir.joinpath(".git").is_dir()
     (test_dir / "modules").mkdir()
+    if "sparse" in submodule_name:
+        (test_dir / subrepo_path).mkdir()
+        # Add the sparse checkout file
+        sparse_content = """m4
+"""
+        (test_dir / "modules" / ".sparse_file_list").write_text(sparse_content)
+    else:
+        gitp = GitInterface(str(test_dir), logger)
+        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        assert test_dir.joinpath(".gitmodules").is_file()
+        
+        
     return test_dir
     
 @pytest.fixture
-def git_fleximod(test_repo_base):
+def git_fleximod(test_repo):
     def _run_fleximod(args, input=None):
         cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=test_repo_base, input=input, 
+        result = subprocess.run(cmd, cwd=test_repo, input=input, 
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
                                 text=True)
         return result
diff --git a/tests/test_checkout.py b/tests/test_checkout.py
index 6d17ce18fd..38bc5f9b28 100644
--- a/tests/test_checkout.py
+++ b/tests/test_checkout.py
@@ -1,38 +1,31 @@
 import pytest
 from pathlib import Path
-
-@pytest.fixture(params=[
-    {"subrepo_path": "modules/test", "submodule_name": "test_submodule", "gitmodules_content" : """                                                                                                                                                                                      [submodule "test_submodule"]
-        path = modules/test
-        url = https://github.com/ESMCI/mpi-serial.git
-        fxtag = MPIserial_2.4.0
-        fxurl = https://github.com/ESMCI/mpi-serial.git
-        fxrequired = ToplevelOnlyRequired
-"""},
-])
-def test_config(request):                
-    return request.param
                 
-def test_basic_checkout(git_fleximod, test_repo, test_config):
+def test_basic_checkout(git_fleximod, test_repo, shared_repos):
     # Prepare a simple .gitmodules
-    gm = test_config['gitmodules_content']
+    gm = shared_repos['gitmodules_content']
     file_path = (test_repo / ".gitmodules")
-    if not file_path.exists():
-        file_path.write_text(gm)
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+
+    file_path.write_text(gm)
     
-        # Run the command
-        result = git_fleximod("checkout test_submodule")
-        
-        # Assertions
-        assert result.returncode == 0
-        assert Path(test_repo / "modules/test").exists()   # Did the submodule directory get created?
-        
-        status = git_fleximod("status")
+    # Run the command
+    result = git_fleximod(f"checkout {repo_name}")
+    
+    # Assertions
+    assert result.returncode == 0
+    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    if "sparse" in repo_name:
+        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
+        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
+    
+    status = git_fleximod(f"status {repo_name}")
         
-        assert "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0" in status.stdout
+    assert shared_repos["status1"] in status.stdout
         
-        result = git_fleximod("update")
-        assert result.returncode == 0
+    result = git_fleximod(f"update {repo_name}")
+    assert result.returncode == 0
         
-        status = git_fleximod("status")
-        assert "test_submodule at tag MPIserial_2.4.0" in status.stdout
+    status = git_fleximod(f"status {repo_name}")
+    assert shared_repos["status2"] in status.stdout
diff --git a/tests/test_sparse_checkout.py b/tests/test_sparse_checkout.py
deleted file mode 100644
index 7276e18d35..0000000000
--- a/tests/test_sparse_checkout.py
+++ /dev/null
@@ -1,34 +0,0 @@
-import pytest
-from shutil import rmtree
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
-
-def test_sparse_checkout(shared_repos, git_fleximod, test_repo_base):
-    repo_name = shared_repos["submodule_name"]
-    if repo_name == "test_sparse":
-        gm = shared_repos["gitmodules_content"]
-        (test_repo_base / ".gitmodules").write_text(gm)
-
-        # Add the sparse checkout file
-        sparse_content = """m4
-"""
-
-        (test_repo_base / "modules" / ".sparse_file_list").write_text(sparse_content)
-
-        result = git_fleximod(f"checkout {repo_name}")
-    
-        # Assertions
-        assert result.returncode == 0
-        assert Path(test_repo_base / f"modules/{repo_name}").exists()   # Did the submodule directory get created?
-        assert Path(test_repo_base /  f"modules/{repo_name}/m4").exists()   # Did the submodule sparse directory get created?
-        assert not Path(test_repo_base /  f"modules/{repo_name}/README").exists()   # Did only the submodule sparse directory get created?
-        status = git_fleximod(f"status {repo_name}")
-        
-        assert f"{repo_name} at tag MPIserial_2.5.0" in status.stdout
-        
-        result = git_fleximod(f"update {repo_name}")
-        assert result.returncode == 0
-        
-        status = git_fleximod(f"status {repo_name}")
-        assert f"{repo_name} at tag MPIserial_2.5.0" in status.stdout
-

From 9602eb0b777c3e174027bc9ea121da907879bac6 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 11 Feb 2024 14:43:38 -0700
Subject: [PATCH 095/161] all tests passing

---
 tests/conftest.py | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index ffff68956d..a6ba850893 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -16,8 +16,10 @@ def logger():
 @pytest.fixture(params=[
     {"subrepo_path": "modules/test",
      "submodule_name": "test_submodule",
-     "status1" : "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_submodule at tag MPIserial_2.4.0",
+     "status3" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status4" : "test_submodule at tag MPIserial_2.4.0",
      "gitmodules_content" : """
     [submodule "test_submodule"]
     path = modules/test
@@ -28,20 +30,24 @@ def logger():
 """},
     {"subrepo_path": "modules/test_optional",
      "submodule_name": "test_optional",
-     "status1" : "test_optional d82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_optional at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
+     "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
     [submodule "test_optional"]
     path = modules/test_optional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelOnlyRequired
+    fxrequired = ToplevelOnlyOptional
 """},
     {"subrepo_path": "modules/test_alwaysoptional",
      "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional d82ce7c is out of sync with .gitmodules MPIserial_2.3.0",
+     "status1" : "test_alwaysoptional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.3.0",
      "status2" : "test_alwaysoptional at tag MPIserial_2.3.0",
+     "status3" : "test_alwaysoptional not checked out, aligned at tag MPIserial_2.3.0",
+     "status4" : "test_alwaysoptional at tag MPIserial_2.3.0",
      "gitmodules_content": """
     [submodule "test_alwaysoptional"]
     path = modules/test_alwaysoptional
@@ -54,6 +60,8 @@ def logger():
      "submodule_name": "test_sparse",
      "status1" : "test_sparse at tag MPIserial_2.5.0",
      "status2" : "test_sparse at tag MPIserial_2.5.0",
+     "status3" : "test_sparse at tag MPIserial_2.5.0",
+     "status4" : "test_sparse at tag MPIserial_2.5.0",
      "gitmodules_content": """
     [submodule "test_sparse"]
     path = modules/test_sparse
@@ -84,13 +92,18 @@ def test_repo(shared_repos, tmp_path, logger):
         sparse_content = """m4
 """
         (test_dir / "modules" / ".sparse_file_list").write_text(sparse_content)
+        gitp.git_operation("add","modules/.sparse_file_list")
     else:
         gitp = GitInterface(str(test_dir), logger)
         gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
         assert test_dir.joinpath(".gitmodules").is_file()
+        gitp.git_operation("add",subrepo_path)
+    gitp.git_operation("commit","-a","-m","\"add submod\"")
+    test_dir2 = tmp_path / "testrepo2"
+    gitp.git_operation("clone",test_dir,test_dir2)
+    return test_dir2    
         
-        
-    return test_dir
+
     
 @pytest.fixture
 def git_fleximod(test_repo):

From b5c4515d0e9d1a48de659f96da99e6a8f3c20ed5 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 11 Feb 2024 15:52:38 -0700
Subject: [PATCH 096/161] thought it was working??

---
 tests/test_required.py | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 tests/test_required.py

diff --git a/tests/test_required.py b/tests/test_required.py
new file mode 100644
index 0000000000..0997db69f7
--- /dev/null
+++ b/tests/test_required.py
@@ -0,0 +1,33 @@
+import pytest
+from pathlib import Path
+                
+def test_required(git_fleximod, test_repo, shared_repos):
+    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    repo_name = shared_repos["submodule_name"]
+
+    status = git_fleximod(f"status {repo_name}")
+    print(f"stdout is {status.stdout}")
+    if file_path.exists():
+        with file_path.open("r") as f:
+            gitmodules_content = f.read()
+            # add the entry if it does not exist
+        if repo_name not in gitmodules_content:
+            file_path.write_text(gitmodules_content+gm)
+        # or if it is incomplete
+        elif gm not in gitmodules_content:
+                file_path.write_text(gm)
+    else:
+        file_path.write_text(gm)
+    status = git_fleximod(f"status {repo_name}")
+    result = git_fleximod("checkout")
+    assert result.returncode == 0
+    status = git_fleximod(f"status {repo_name}")
+    assert shared_repos["status3"] in status.stdout
+    if "not checked out" in status.stdout:
+        status = git_fleximod(f"checkout {repo_name}")
+        assert result.returncode == 0
+    status = git_fleximod(f"update {repo_name}")
+    assert result.returncode == 0
+    status = git_fleximod(f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout

From a3ce6116065af2e8e86bd3d7d6de06bc215a6e58 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 13 Feb 2024 15:50:55 -0700
Subject: [PATCH 097/161] test_complex is still a work in progress

---
 tests/conftest.py      | 18 +++++++++++++-----
 tests/test_checkout.py |  2 +-
 tests/test_complex.py  | 35 +++++++++++++++++++++++++++++++++++
 tests/test_required.py | 11 ++++-------
 4 files changed, 53 insertions(+), 13 deletions(-)
 create mode 100644 tests/test_complex.py

diff --git a/tests/conftest.py b/tests/conftest.py
index a6ba850893..9bd6a758b2 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -13,7 +13,7 @@ def logger():
     logger = logging.getLogger(__name__)
     return logger
 
-@pytest.fixture(params=[
+all_repos=[
     {"subrepo_path": "modules/test",
      "submodule_name": "test_submodule",
      "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
@@ -71,11 +71,21 @@ def logger():
     fxrequired = AlwaysRequired
     fxsparse = ../.sparse_file_list
 """},
-])
+]
+@pytest.fixture(params=all_repos)
 
 def shared_repos(request):
     return request.param
 
+@pytest.fixture
+def get_all_repos():
+    return all_repos
+
+def write_sparse_checkout_file(fp):
+    sparse_content = """m4
+"""
+    fp.write_text(sparse_content)
+
 @pytest.fixture
 def test_repo(shared_repos, tmp_path, logger):
     subrepo_path = shared_repos["subrepo_path"]
@@ -89,9 +99,7 @@ def test_repo(shared_repos, tmp_path, logger):
     if "sparse" in submodule_name:
         (test_dir / subrepo_path).mkdir()
         # Add the sparse checkout file
-        sparse_content = """m4
-"""
-        (test_dir / "modules" / ".sparse_file_list").write_text(sparse_content)
+        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
         gitp.git_operation("add","modules/.sparse_file_list")
     else:
         gitp = GitInterface(str(test_dir), logger)
diff --git a/tests/test_checkout.py b/tests/test_checkout.py
index 38bc5f9b28..fd8ffc1996 100644
--- a/tests/test_checkout.py
+++ b/tests/test_checkout.py
@@ -14,7 +14,7 @@ def test_basic_checkout(git_fleximod, test_repo, shared_repos):
     result = git_fleximod(f"checkout {repo_name}")
     
     # Assertions
-    assert result.returncode == 0
+    assert result.returncode == 0 
     assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
     if "sparse" in repo_name:
         assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
diff --git a/tests/test_complex.py b/tests/test_complex.py
new file mode 100644
index 0000000000..628a92d837
--- /dev/null
+++ b/tests/test_complex.py
@@ -0,0 +1,35 @@
+import pytest
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_complex_checkout(git_fleximod, get_all_repos, test_repo, request, logger):
+    gitp = None
+    for repo in get_all_repos:
+        repo_name = repo["submodule_name"]
+        gm = repo["gitmodules_content"]
+        if "shared_repos0" in request.node.name:
+            if not gitp:
+                gitp = GitInterface(str(test_repo), logger)
+            file_path = (test_repo / ".gitmodules")
+            if file_path.exists():
+                with file_path.open("r") as f:
+                    gitmodules_content = f.read()
+                    print(f"content={gitmodules_content}")
+                    print(f"gm={gm}")
+                    # add the entry if it does not exist
+                    if repo_name not in gitmodules_content:
+                        file_path.write_text(gitmodules_content+gm)
+                    # or if it is incomplete
+                    elif gm not in gitmodules_content:
+                        file_path.write_text(gm)
+                        
+            else:
+                file_path.write_text(gm)
+            if "sparse" in repo_name:
+                print(f"writing sparse_file_list in {test_repo}")
+                write_sparse_checkout_file(test_repo / "modules" / ".sparse_file_list")
+                gitp.git_operation("add","modules/.sparse_file_list")
+            gitp.git_operation("commit","-a","-m","\"add submod\"")
+
+            
+    assert(False)
diff --git a/tests/test_required.py b/tests/test_required.py
index 0997db69f7..b4d99c5642 100644
--- a/tests/test_required.py
+++ b/tests/test_required.py
@@ -5,17 +5,14 @@ def test_required(git_fleximod, test_repo, shared_repos):
     file_path = (test_repo / ".gitmodules")
     gm = shared_repos["gitmodules_content"]
     repo_name = shared_repos["submodule_name"]
-
-    status = git_fleximod(f"status {repo_name}")
-    print(f"stdout is {status.stdout}")
     if file_path.exists():
         with file_path.open("r") as f:
             gitmodules_content = f.read()
             # add the entry if it does not exist
-        if repo_name not in gitmodules_content:
-            file_path.write_text(gitmodules_content+gm)
-        # or if it is incomplete
-        elif gm not in gitmodules_content:
+            if repo_name not in gitmodules_content:
+                file_path.write_text(gitmodules_content+gm)
+            # or if it is incomplete
+            elif gm not in gitmodules_content:
                 file_path.write_text(gm)
     else:
         file_path.write_text(gm)

From 8af16188fe7c531f3e651000505c06751784e988 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Tue, 13 Feb 2024 16:08:33 -0700
Subject: [PATCH 098/161] update should checkout if needed

---
 git_fleximod/git_fleximod.py                  | 34 +++++++++++++++++--
 ...arse_checkout.py => test_sparse_update.py} |  7 +---
 tests/{test_checkout.py => test_update.py}    |  7 +---
 3 files changed, 33 insertions(+), 15 deletions(-)
 rename tests/{test_sparse_checkout.py => test_sparse_update.py} (86%)
 rename tests/{test_checkout.py => test_update.py} (82%)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 1b6c357b94..593a8b3b22 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -275,7 +275,7 @@ def submodules_status(gitmodules, root_dir):
     return testfails, localmods
 
 
-def submodules_update(gitmodules, root_dir, force):
+def submodules_update(gitmodules, root_dir, requiredlist, force):
     _, localmods = submodules_status(gitmodules, root_dir)
     print("")
     if localmods and not force:
@@ -289,6 +289,34 @@ def submodules_update(gitmodules, root_dir, force):
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         logger.info("name={} path={} url={} fxtag={}".format(name, path, url, fxtag))
+        if not os.path.exists(os.path.join(path, ".git")):
+            fxrequired = gitmodules.get(name, "fxrequired")
+            fxsparse = gitmodules.get(name, "fxsparse")
+
+            if fxrequired and fxrequired not in requiredlist:
+                if "T:F" == fxrequired:
+                    print("Skipping optional component {}".format(name))
+                continue
+
+            if fxsparse:
+                logger.debug(
+                    "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                        root_dir, name, url, path, fxsparse, fxtag
+                    )
+                )
+                submodule_sparse_checkout(
+                    root_dir, name, url, path, fxsparse, tag=fxtag, fxhash=fxhash
+                )
+            else:
+                logger.debug(
+                    "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
+                )
+                
+                single_submodule_checkout(
+                    root_dir, name, path, url=url, tag=fxtag, force=force, fxhash=fxhash
+                )
+
+
         if os.path.exists(os.path.join(path, ".git")):
             submoddir = os.path.join(root_dir, path)
             with utils.pushd(submoddir):
@@ -326,7 +354,7 @@ def submodules_update(gitmodules, root_dir, force):
                 else:
                     print(f"{name:>20} up to date.")
 
-
+# checkout is done by update if required so this function may be depricated
 def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
     _, localmods = submodules_status(gitmodules, root_dir)
     print("")
@@ -424,7 +452,7 @@ def main():
         sys.exit("No submodule components found")
     retval = 0
     if action == "update":
-        submodules_update(gitmodules, root_dir, force)
+        submodules_update(gitmodules, root_dir, fxrequired, force)
     elif action == "checkout":
         submodules_checkout(gitmodules, root_dir, fxrequired, force)
     elif action == "status":
diff --git a/tests/test_sparse_checkout.py b/tests/test_sparse_update.py
similarity index 86%
rename from tests/test_sparse_checkout.py
rename to tests/test_sparse_update.py
index 0633802cb0..1e6ee83ba1 100644
--- a/tests/test_sparse_checkout.py
+++ b/tests/test_sparse_update.py
@@ -20,7 +20,7 @@ def test_sparse_checkout(git_fleximod, test_repo_base):
 """
     (test_repo_base / "modules" / ".sparse_file_list").write_text(sparse_content)
 
-    result = git_fleximod("checkout")
+    result = git_fleximod("update")
     
     # Assertions
     assert result.returncode == 0
@@ -31,8 +31,3 @@ def test_sparse_checkout(git_fleximod, test_repo_base):
 
     assert "test_sparse_submodule at tag MPIserial_2.5.0" in status.stdout
 
-    result = git_fleximod("update")
-    assert result.returncode == 0
-
-    status = git_fleximod("status test_sparse_submodule")
-    assert "test_sparse_submodule at tag MPIserial_2.5.0" in status.stdout
diff --git a/tests/test_checkout.py b/tests/test_update.py
similarity index 82%
rename from tests/test_checkout.py
rename to tests/test_update.py
index 791587628b..baaea76035 100644
--- a/tests/test_checkout.py
+++ b/tests/test_update.py
@@ -15,7 +15,7 @@ def test_basic_checkout(git_fleximod, test_repo):
     (test_repo / ".gitmodules").write_text(gitmodules_content)
     
     # Run the command
-    result = git_fleximod("checkout")
+    result = git_fleximod("update")
 
     # Assertions
     assert result.returncode == 0
@@ -23,10 +23,5 @@ def test_basic_checkout(git_fleximod, test_repo):
 
     status = git_fleximod("status")
 
-    assert "test_submodule d82ce7c is out of sync with .gitmodules MPIserial_2.4.0" in status.stdout
-
-    result = git_fleximod("update")
-    assert result.returncode == 0
-
     status = git_fleximod("status")
     assert "test_submodule at tag MPIserial_2.4.0" in status.stdout

From 7c47c05ffbd4d329e94ada655c9a467e8f968585 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 14 Feb 2024 09:18:43 -0700
Subject: [PATCH 099/161] restructure of tests working

---
 tests/conftest.py        | 20 +++++++++++++++-----
 tests/test_b_update.py   |  4 ++--
 tests/test_c_required.py | 12 ++++--------
 tests/test_d_complex.py  | 34 +++-------------------------------
 4 files changed, 24 insertions(+), 46 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 9bd6a758b2..fd3678f9ee 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -18,7 +18,7 @@ def logger():
      "submodule_name": "test_submodule",
      "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_submodule at tag MPIserial_2.4.0",
-     "status3" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status3" : "test_submodule at tag MPIserial_2.4.0",
      "status4" : "test_submodule at tag MPIserial_2.4.0",
      "gitmodules_content" : """
     [submodule "test_submodule"]
@@ -84,6 +84,7 @@ def get_all_repos():
 def write_sparse_checkout_file(fp):
     sparse_content = """m4
 """
+    print(f"writing sparse_file_list \n")
     fp.write_text(sparse_content)
 
 @pytest.fixture
@@ -110,14 +111,23 @@ def test_repo(shared_repos, tmp_path, logger):
     test_dir2 = tmp_path / "testrepo2"
     gitp.git_operation("clone",test_dir,test_dir2)
     return test_dir2    
-        
 
+
+@pytest.fixture
+def complex_repo(tmp_path, logger):
+    test_dir = tmp_path / "testcomplex"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test")
+    gitp.git_operation("fetch", "origin", "main")
+    return test_dir
     
 @pytest.fixture
-def git_fleximod(test_repo):
-    def _run_fleximod(args, input=None):
+def git_fleximod():
+    def _run_fleximod(path, args, input=None):
         cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=test_repo, input=input, 
+        result = subprocess.run(cmd, cwd=path, input=input, 
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
                                 text=True)
         return result
diff --git a/tests/test_b_update.py b/tests/test_b_update.py
index e03daa3974..159f1cfae0 100644
--- a/tests/test_b_update.py
+++ b/tests/test_b_update.py
@@ -11,7 +11,7 @@ def test_basic_checkout(git_fleximod, test_repo, shared_repos):
     file_path.write_text(gm)
     
     # Run the command
-    result = git_fleximod(f"update {repo_name}")
+    result = git_fleximod(test_repo, f"update {repo_name}")
 
     # Assertions
     assert result.returncode == 0 
@@ -20,7 +20,7 @@ def test_basic_checkout(git_fleximod, test_repo, shared_repos):
         assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
         assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
     
-    status = git_fleximod(f"status {repo_name}")
+    status = git_fleximod(test_repo, f"status {repo_name}")
         
     assert shared_repos["status2"] in status.stdout
         
diff --git a/tests/test_c_required.py b/tests/test_c_required.py
index b4d99c5642..d6cc040b8d 100644
--- a/tests/test_c_required.py
+++ b/tests/test_c_required.py
@@ -16,15 +16,11 @@ def test_required(git_fleximod, test_repo, shared_repos):
                 file_path.write_text(gm)
     else:
         file_path.write_text(gm)
-    status = git_fleximod(f"status {repo_name}")
-    result = git_fleximod("checkout")
+    result = git_fleximod(test_repo, "update")
     assert result.returncode == 0
-    status = git_fleximod(f"status {repo_name}")
+    status = git_fleximod(test_repo, f"status {repo_name}")
     assert shared_repos["status3"] in status.stdout
-    if "not checked out" in status.stdout:
-        status = git_fleximod(f"checkout {repo_name}")
-        assert result.returncode == 0
-    status = git_fleximod(f"update {repo_name}")
+    status = git_fleximod(test_repo, f"update {repo_name}")
     assert result.returncode == 0
-    status = git_fleximod(f"status {repo_name}")
+    status = git_fleximod(test_repo, f"status {repo_name}")
     assert shared_repos["status4"] in status.stdout
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
index 628a92d837..2983b0193f 100644
--- a/tests/test_d_complex.py
+++ b/tests/test_d_complex.py
@@ -2,34 +2,6 @@
 from pathlib import Path
 from git_fleximod.gitinterface import GitInterface
 
-def test_complex_checkout(git_fleximod, get_all_repos, test_repo, request, logger):
-    gitp = None
-    for repo in get_all_repos:
-        repo_name = repo["submodule_name"]
-        gm = repo["gitmodules_content"]
-        if "shared_repos0" in request.node.name:
-            if not gitp:
-                gitp = GitInterface(str(test_repo), logger)
-            file_path = (test_repo / ".gitmodules")
-            if file_path.exists():
-                with file_path.open("r") as f:
-                    gitmodules_content = f.read()
-                    print(f"content={gitmodules_content}")
-                    print(f"gm={gm}")
-                    # add the entry if it does not exist
-                    if repo_name not in gitmodules_content:
-                        file_path.write_text(gitmodules_content+gm)
-                    # or if it is incomplete
-                    elif gm not in gitmodules_content:
-                        file_path.write_text(gm)
-                        
-            else:
-                file_path.write_text(gm)
-            if "sparse" in repo_name:
-                print(f"writing sparse_file_list in {test_repo}")
-                write_sparse_checkout_file(test_repo / "modules" / ".sparse_file_list")
-                gitp.git_operation("add","modules/.sparse_file_list")
-            gitp.git_operation("commit","-a","-m","\"add submod\"")
-
-            
-    assert(False)
+def test_complex_checkout(git_fleximod, complex_repo, logger):
+    status = git_fleximod(complex_repo, "status")
+    print(status)

From e6d4838ebeee5a7ce408aa098d9cfab0cd34d405 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 16 Feb 2024 17:40:26 -0700
Subject: [PATCH 100/161] all tests are passing and complete

---
 README.md                    |   6 +-
 git_fleximod/git_fleximod.py | 167 +++++++++++++++++++----------------
 tests/conftest.py            |  13 +--
 tests/test_c_required.py     |   4 +
 tests/test_d_complex.py      |  62 ++++++++++++-
 5 files changed, 167 insertions(+), 85 deletions(-)

diff --git a/README.md b/README.md
index 259ba8b54f..94d85c4150 100644
--- a/README.md
+++ b/README.md
@@ -30,8 +30,8 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
 
     fxtag: Specify a specific tag or branch to checkout for a submodule.
     fxrequired: Mark a submodule's checkout behavior, with allowed values:
-      - ToplevelOnlyRequired: Top-level and required (checked out only when this is the Toplevel module).
-      - ToplevelOnlyOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
+      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
       - AlwaysRequired:       Always required (always checked out).
       - AlwaysOptional:       Always optional (checked out with --optional flag).
     fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
@@ -89,7 +89,7 @@ Additional example:
     [submodule "cime"]
         path = cime
         url = https://github.com/jedwards4b/cime
-        fxrequired = ToplevelOnlyRequired
+        fxrequired = ToplevelRequired
         fxtag = cime6.0.198_rme01
 ```
 
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index f81e713814..08f31fa778 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -12,7 +12,8 @@
 
 # logger variable is global
 logger = None
-
+def fxrequired_allowed_values():
+    return ['ToplevelRequired', 'ToplevelOptional', 'AlwaysRequired', 'AlwaysOptional']
 
 def commandline_arguments(args=None):
     parser = cli.get_parser()
@@ -24,9 +25,9 @@ def commandline_arguments(args=None):
 
     # explicitly listing a component overrides the optional flag
     if options.optional or options.components:
-        fxrequired = ["ToplevelOnlyRequired", "ToplevelOnlyOptional", "AlwaysRequired", "AlwaysOptional"]
+        fxrequired = ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
     else:
-        fxrequired = ["ToplevelOnlyRequired", "AlwaysRequired"]
+        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
 
     action = options.action
     if not action:
@@ -67,12 +68,16 @@ def submodule_sparse_checkout(
     root_dir, name, url, path, sparsefile, tag="master", fxhash=None
 ):
     logger.info("Called sparse_checkout for {}".format(name))
+    rgit = GitInterface(root_dir, logger)
+    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    if superroot:
+        gitroot = superroot
+    else:
+        gitroot = root_dir
+    assert(os.path.isdir(os.path.join(gitroot,".git")))
     # first create the module directory
     if not os.path.isdir(os.path.join(root_dir,path)):
         os.makedirs(os.path.join(root_dir,path))
-    # Check first if the module is already defined
-    # and the sparse-checkout file exists
-    git = GitInterface(root_dir, logger)
 
     # initialize a new git repo and set the sparse checkout flag
     sprep_repo = os.path.join(root_dir, path)
@@ -92,36 +97,39 @@ def submodule_sparse_checkout(
     sprepo_git.config_set_value("core", "sparseCheckout", "true")
 
     # set the repository remote
-    sprepo_git.git_operation("remote", "add", "origin", url)
 
-    superroot = git.git_operation("rev-parse", "--show-superproject-working-tree")
-    if os.path.isfile(os.path.join(root_dir, ".git")):
+    logger.info("Setting remote origin in {}/{}".format(root_dir,path))
+    status = sprepo_git.git_operation("remote", "-v")
+    if url not in status:
+        sprepo_git.git_operation("remote", "add", "origin", url)
+    
+    topgit = os.path.join(gitroot,".git")
+    
+    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
         with open(os.path.join(root_dir, ".git")) as f:
-            gitpath = os.path.abspath(os.path.join(root_dir, f.read().split()[1]))
-        topgit = os.path.abspath(os.path.join(gitpath, "modules"))
+            gitpath = os.path.relpath(os.path.join(root_dir, f.read().split()[1]), start=os.path.join(root_dir,path))
+        topgit = os.path.join(gitpath, "modules")
     else:
-        topgit = os.path.abspath(os.path.join(root_dir, ".git", "modules"))
-
-    if not os.path.isdir(topgit):
-        os.makedirs(topgit)
-    topgit = os.path.join(topgit, name)
-    logger.debug(
-        "root_dir is {} topgit is {} superroot is {}".format(
-            root_dir, topgit, superroot
-        )
-    )
-
+        topgit = os.path.relpath(os.path.join(root_dir, ".git", "modules"), start=os.path.join(root_dir,path))
+    
+    with utils.pushd(sprep_repo):
+        if not os.path.isdir(topgit):
+            os.makedirs(topgit)
+    topgit += os.sep + name
+    
     if os.path.isdir(os.path.join(root_dir, path, ".git")):
-        shutil.move(os.path.join(root_dir, path, ".git"), topgit)
-        with open(os.path.join(root_dir, path, ".git"), "w") as f:
-            f.write("gitdir: " + os.path.relpath(topgit, os.path.join(root_dir, path)))
-
-    gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
-    if os.path.isfile(gitsparse):
-        logger.warning("submodule {} is already initialized".format(name))
-        return
-
-    shutil.copy(os.path.join(root_dir, path, sparsefile), gitsparse)
+        with utils.pushd(sprep_repo):
+            shutil.move(".git", topgit)
+            with open(".git", "w") as f:
+                f.write("gitdir: " + os.path.relpath(topgit))
+            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
+            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+        if os.path.isfile(gitsparse):
+            logger.warning("submodule {} is already initialized {}".format(name, topgit))
+            return
+
+        with utils.pushd(sprep_repo):
+            shutil.copy(sparsefile, gitsparse)
 
     # Finally checkout the repo
     if fxhash:
@@ -132,28 +140,31 @@ def submodule_sparse_checkout(
         sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
         sprepo_git.git_operation("checkout", tag)
         print(f"Successfully checked out {name:>20} at {tag}")
-
+    rgit.config_set_value(f'submodule "{name}"',"active","true")
+    rgit.config_set_value(f'submodule "{name}"',"url",url)
 
 def single_submodule_checkout(
-    root, name, path, url=None, tag=None, force=False, fxhash=None
+        root, name, path, url=None, tag=None, force=False, fxhash=None, optional=False
 ):
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
-    if os.path.exists(os.path.join(repodir, ".git")):
-        logger.info("Submodule {} already checked out".format(name))
-        return
+    logger.info("Checkout {} into {}/{}".format(name,root,path))
     # if url is provided update to the new url
     tmpurl = None
+    repo_exists = False
+    if os.path.exists(os.path.join(repodir, ".git")):
+        logger.info("Submodule {} already checked out".format(name))
+        repo_exists = True
 
     # Look for a .gitmodules file in the newly checkedout repo
-    if url:
+    if not repo_exists and url:
         # ssh urls cause problems for those who dont have git accounts with ssh keys defined
         # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
         # opened with a GitModules object we don't need to worry about restoring the file here
         # it will be done by the GitModules class
         if url.startswith("git@"):
             tmpurl = url
-            url = url.replace("git@github.com:", "https://github.com")
+            url = url.replace("git@github.com:", "https://github.com/")
             git.git_operation("clone", url, path)
             smgit = GitInterface(repodir, logger)
             if not tag and not fxhash:
@@ -170,26 +181,26 @@ def single_submodule_checkout(
                     if line.startswith("gitdir: "):
                         rootdotgit = line[8:].rstrip()
 
-            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", path))
-            if not os.path.isdir(os.path.join(newpath, os.pardir)):
-                os.makedirs(os.path.abspath(os.path.join(newpath, os.pardir)))
-
+            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
             shutil.move(os.path.join(repodir, ".git"), newpath)
             with open(os.path.join(repodir, ".git"), "w") as f:
-                f.write("gitdir: " + newpath)
+                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
 
-    if not tmpurl:
+    if not repo_exists or not tmpurl:
         logger.debug(git.git_operation("submodule", "update", "--init", "--", path))
 
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name} {repodir} {url}")
         gitmodules = GitModules(logger, confpath=repodir)
-        submodules_checkout(gitmodules, repodir, ["I:T"], force=force)
+        requiredlist = ["AlwaysRequired"]
+        if optional:
+            requiredlist.append("AlwaysOptional")
+        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
     if os.path.exists(os.path.join(repodir, ".git")):
-        print(f"Successfully checked out {name}")
+        print(f"Successfully checked out {name} {repodir}")
     else:
-        utils.fatal_error(f"Failed to checkout {name}")
+        utils.fatal_error(f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}")
 
     if tmpurl:
         print(git.git_operation("restore", ".gitmodules"))
@@ -289,33 +300,37 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
         fxhash = gitmodules.get(name, "fxhash")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
-        logger.info("name={} path={} url={} fxtag={}".format(name, path, url, fxtag))
-        if not os.path.exists(os.path.join(path, ".git")):
-            fxrequired = gitmodules.get(name, "fxrequired")
-            fxsparse = gitmodules.get(name, "fxsparse")
-
-            if fxrequired and fxrequired not in requiredlist:
-                if "T:F" == fxrequired:
-                    print("Skipping optional component {}".format(name))
-                continue
-
-            if fxsparse:
-                logger.debug(
-                    "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                        root_dir, name, url, path, fxsparse, fxtag
-                    )
-                )
-                submodule_sparse_checkout(
-                    root_dir, name, url, path, fxsparse, tag=fxtag, fxhash=fxhash
-                )
-            else:
-                logger.debug(
-                    "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
+        logger.info("name={} path={} url={} fxtag={} requiredlist={}".format(name,os.path.join(root_dir, path), url, fxtag, requiredlist))
+#        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+        fxrequired = gitmodules.get(name, "fxrequired")
+        assert(fxrequired in fxrequired_allowed_values())
+        rgit = GitInterface(root_dir, logger)
+        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+            
+        fxsparse = gitmodules.get(name, "fxsparse")
+            
+        if fxrequired and (superroot and "Toplevel" in fxrequired) or fxrequired not in requiredlist:
+            if "ToplevelOptional" == fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
                 )
+            )
+            submodule_sparse_checkout(
+                root_dir, name, url, path, fxsparse, tag=fxtag, fxhash=fxhash
+            )
+        else:
+            logger.info(
+                "Calling submodule_checkout({},{},{},{})".format(root_dir, name, path,url)
+            )
                 
-                single_submodule_checkout(
-                    root_dir, name, path, url=url, tag=fxtag, force=force, fxhash=fxhash
-                )
+            single_submodule_checkout(
+                root_dir, name, path, url=url, tag=fxtag, force=force,
+                fxhash=fxhash, optional=("AlwaysOptional" in requiredlist)
+            )
 
 
         if os.path.exists(os.path.join(path, ".git")):
@@ -371,7 +386,6 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
         fxhash = gitmodules.get(name, "fxhash")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
-
         if fxrequired and fxrequired not in requiredlist:
             if "Optional" in fxrequired:
                 print("Skipping optional component {}".format(name))
@@ -392,7 +406,8 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
             )
 
             single_submodule_checkout(
-                root_dir, name, path, url=url, tag=fxtag, force=force, fxhash=fxhash
+                root_dir, name, path, url=url, tag=fxtag, force=force, fxhash=fxhash,
+                optional = "AlwaysOptional" in requiredlist
             )
 
 
@@ -441,7 +456,7 @@ def main():
             )
 
         root_dir = os.path.dirname(file_path)
-    logger.info("root_dir is {}".format(root_dir))
+    logger.info("root_dir is {} includelist={} excludelist={}".format(root_dir, includelist, excludelist))
     gitmodules = GitModules(
         logger,
         confpath=root_dir,
diff --git a/tests/conftest.py b/tests/conftest.py
index fd3678f9ee..b88fa61d27 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -26,7 +26,7 @@ def logger():
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelOnlyRequired
+    fxrequired = ToplevelRequired
 """},
     {"subrepo_path": "modules/test_optional",
      "submodule_name": "test_optional",
@@ -35,12 +35,12 @@ def logger():
      "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
      "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
-    [submodule "test_optional"]
+     [submodule "test_optional"]
     path = modules/test_optional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelOnlyOptional
+    fxrequired = ToplevelOptional
 """},
     {"subrepo_path": "modules/test_alwaysoptional",
      "submodule_name": "test_alwaysoptional",
@@ -84,7 +84,6 @@ def get_all_repos():
 def write_sparse_checkout_file(fp):
     sparse_content = """m4
 """
-    print(f"writing sparse_file_list \n")
     fp.write_text(sparse_content)
 
 @pytest.fixture
@@ -119,8 +118,9 @@ def complex_repo(tmp_path, logger):
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test")
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
     gitp.git_operation("fetch", "origin", "main")
+    gitp.git_operation("checkout", "main")
     return test_dir
     
 @pytest.fixture
@@ -130,6 +130,9 @@ def _run_fleximod(path, args, input=None):
         result = subprocess.run(cmd, cwd=path, input=input, 
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
                                 text=True)
+        if result.returncode:
+            print(result.stdout)
+            print(result.stderr)
         return result
     return _run_fleximod
 
diff --git a/tests/test_c_required.py b/tests/test_c_required.py
index d6cc040b8d..89ab8d294d 100644
--- a/tests/test_c_required.py
+++ b/tests/test_c_required.py
@@ -20,6 +20,10 @@ def test_required(git_fleximod, test_repo, shared_repos):
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
     assert shared_repos["status3"] in status.stdout
+    status = git_fleximod(test_repo, f"update --optional")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
     status = git_fleximod(test_repo, f"update {repo_name}")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
index 2983b0193f..fdce516274 100644
--- a/tests/test_d_complex.py
+++ b/tests/test_d_complex.py
@@ -4,4 +4,64 @@
 
 def test_complex_checkout(git_fleximod, complex_repo, logger):
     status = git_fleximod(complex_repo, "status")
-    print(status)
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+    
+    # This should checkout and update test_submodule and complex_sub
+    result = git_fleximod(complex_repo, "update")    
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex")
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+    # update a single optional submodule
+
+    result = git_fleximod(complex_repo, "update ToplevelOptional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+
+
+    # Finally update optional
+    result = git_fleximod(complex_repo, "update --optional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
+    
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex" )
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+

From 194d845ad2131c7ce50e1f5a14fc5476799c87fb Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 17 Feb 2024 08:08:57 -0700
Subject: [PATCH 101/161] add git user info to tests

---
 .github/workflows/pytest.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
index 4809a2787f..0868dd9a33 100644
--- a/.github/workflows/pytest.yaml
+++ b/.github/workflows/pytest.yaml
@@ -70,5 +70,8 @@ jobs:
 
       # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
       # so this line is super-simple. But it could be as complex as you need.
-      - run: poetry run pytest
+      - run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+          poetry run pytest
 

From d64c5c6dd311364cc98ffc5ca39be425437e377c Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 17 Feb 2024 08:14:37 -0700
Subject: [PATCH 102/161] remove checkout user option

---
 git_fleximod/cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 719b156206..80dbd58d5a 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -25,11 +25,11 @@ def get_parser():
     #
     # user options
     #
-    choices = ["update", "checkout", "status", "test"]
+    choices = ["update", "status", "test"]
     parser.add_argument(
         "action",
         choices=choices,
-        default="checkout",
+        default="update",
         help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
     )
 

From 6bac7946376f7ae85511b4ed02ad4881f9e0440d Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sat, 17 Feb 2024 09:43:54 -0700
Subject: [PATCH 103/161] remove fxhash, putting hash in tag works fine

---
 git_fleximod/git_fleximod.py | 87 +++++++++++-------------------------
 tests/conftest.py            | 10 ++---
 2 files changed, 32 insertions(+), 65 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 08f31fa778..7a4470e246 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -31,7 +31,7 @@ def commandline_arguments(args=None):
 
     action = options.action
     if not action:
-        action = "checkout"
+        action = "update"
     handlers = [logging.StreamHandler()]
 
     if options.debug:
@@ -65,7 +65,7 @@ def commandline_arguments(args=None):
 
 
 def submodule_sparse_checkout(
-    root_dir, name, url, path, sparsefile, tag="master", fxhash=None
+    root_dir, name, url, path, sparsefile, tag="master"
 ):
     logger.info("Called sparse_checkout for {}".format(name))
     rgit = GitInterface(root_dir, logger)
@@ -132,19 +132,14 @@ def submodule_sparse_checkout(
             shutil.copy(sparsefile, gitsparse)
 
     # Finally checkout the repo
-    if fxhash:
-        sprepo_git.git_operation("fetch", "origin", "--tags")
-        sprepo_git.git_operation("checkout", fxhash)
-        print(f"Successfully checked out {name:>20} at {fxhash}")
-    else:
-        sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
-        sprepo_git.git_operation("checkout", tag)
-        print(f"Successfully checked out {name:>20} at {tag}")
+    sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
+    sprepo_git.git_operation("checkout", tag)
+    print(f"Successfully checked out {name:>20} at {tag}")
     rgit.config_set_value(f'submodule "{name}"',"active","true")
     rgit.config_set_value(f'submodule "{name}"',"url",url)
 
 def single_submodule_checkout(
-        root, name, path, url=None, tag=None, force=False, fxhash=None, optional=False
+        root, name, path, url=None, tag=None, force=False, optional=False
 ):
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
@@ -167,12 +162,9 @@ def single_submodule_checkout(
             url = url.replace("git@github.com:", "https://github.com/")
             git.git_operation("clone", url, path)
             smgit = GitInterface(repodir, logger)
-            if not tag and not fxhash:
+            if not tag:
                 tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
-            if fxhash:
-                smgit.git_operation("checkout", fxhash)
-            else:
-                smgit.git_operation("checkout", tag)
+            smgit.git_operation("checkout", tag)
             # Now need to move the .git dir to the submodule location
             rootdotgit = os.path.join(root, ".git")
             if os.path.isfile(rootdotgit):
@@ -214,9 +206,6 @@ def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
-        fxhash = gitmodules.get(name, "fxhash")
-        if tag and fxhash:
-            utils.fatal_error(f"{name:>20} cannot have both fxtag and fxhash")
         if not path:
             utils.fatal_error("No path found in .gitmodules for {}".format(name))
         newpath = os.path.join(root_dir, path)
@@ -234,48 +223,33 @@ def submodules_status(gitmodules, root_dir):
             if tag and tag == atag:
                 print(f"e {name:>20} not checked out, aligned at tag {tag}")
             elif tag:
-                print(
-                    f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
-                )
-                testfails += 1
-            elif fxhash:
-                n = len(fxhash)
-                smhash = rootgit.git_operation(
-                    "ls-tree", "--object-only", f"--abbrev={n}", "HEAD", path
-                )
-                if smhash == fxhash:
-                    print(f"  {name:>20} not checked out, aligned at hash {fxhash}")
+                ahash = rootgit.git_operation("submodule", "status", "{}".format(path)).rstrip()
+                ahash = ahash[1:len(tag)+1]
+                if tag == ahash:
+                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
                 else:
                     print(
-                        f"s {name:>20} not checked out, out of sync at hash {smhash}, expected hash is {fxhash}"
+                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
                     )
                     testfails += 1
             else:
-                print(f"e {name:>20} has no fxtag nor fxhash defined in .gitmodules")
+                print(f"e {name:>20} has no fxtag defined in .gitmodules")
                 testfails += 1
         else:
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
                 ahash = git.git_operation("status").partition("\n")[0].split()[-1]
-                if tag and atag != tag:
-                    print(f"s {name:>20} {atag} is out of sync with .gitmodules {tag}")
-                    testfails += 1
-                elif tag:
+                if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
-                elif fxhash:
-                    rootgit = GitInterface(root_dir, logger)
-                    n = len(fxhash)
-                    if ahash.startswith(fxhash):
-                        print(f"  {name:>20} at hash {fxhash}")
-                    else:
-                        print(
-                            f"s {name:>20} {ahash} is out of sync with .gitmodules {fxhash}"
-                        )
-                        testfails += 1
+                elif tag and ahash == tag:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif tag:
+                    print(f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}")
+                    testfails += 1
                 else:
                     print(
-                        f"e {name:>20} has no fxtag nor fxhash defined in .gitmodules, module at {atag}"
+                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
                     )
                     testfails += 1
 
@@ -297,7 +271,6 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
         return
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
-        fxhash = gitmodules.get(name, "fxhash")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         logger.info("name={} path={} url={} fxtag={} requiredlist={}".format(name,os.path.join(root_dir, path), url, fxtag, requiredlist))
@@ -320,7 +293,7 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 )
             )
             submodule_sparse_checkout(
-                root_dir, name, url, path, fxsparse, tag=fxtag, fxhash=fxhash
+                root_dir, name, url, path, fxsparse, tag=fxtag
             )
         else:
             logger.info(
@@ -329,7 +302,7 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 
             single_submodule_checkout(
                 root_dir, name, path, url=url, tag=fxtag, force=force,
-                fxhash=fxhash, optional=("AlwaysOptional" in requiredlist)
+                optional=("AlwaysOptional" in requiredlist)
             )
 
 
@@ -362,11 +335,8 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 if fxtag and fxtag != atag:
                     print(f"{name:>20} updated to {fxtag}")
                     git.git_operation("checkout", fxtag)
-                elif fxhash:
-                    print(f"{name:>20} updated to {fxhash}")
-                    git.git_operation("checkout", fxhash)
-                elif not (fxtag or fxhash):
-                    print(f"No fxtag nor fxhash found for submodule {name:>20}")
+                elif not fxtag:
+                    print(f"No fxtag found for submodule {name:>20}")
                 else:
                     print(f"{name:>20} up to date.")
 
@@ -383,7 +353,6 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
         fxrequired = gitmodules.get(name, "fxrequired")
         fxsparse = gitmodules.get(name, "fxsparse")
         fxtag = gitmodules.get(name, "fxtag")
-        fxhash = gitmodules.get(name, "fxhash")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         if fxrequired and fxrequired not in requiredlist:
@@ -398,7 +367,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
                 )
             )
             submodule_sparse_checkout(
-                root_dir, name, url, path, fxsparse, tag=fxtag, fxhash=fxhash
+                root_dir, name, url, path, fxsparse, tag=fxtag
             )
         else:
             logger.debug(
@@ -406,7 +375,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
             )
 
             single_submodule_checkout(
-                root_dir, name, path, url=url, tag=fxtag, force=force, fxhash=fxhash,
+                root_dir, name, path, url=url, tag=fxtag, force=force,
                 optional = "AlwaysOptional" in requiredlist
             )
 
@@ -469,8 +438,6 @@ def main():
     retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir, fxrequired, force)
-    elif action == "checkout":
-        submodules_checkout(gitmodules, root_dir, fxrequired, force)
     elif action == "status":
         submodules_status(gitmodules, root_dir)
     elif action == "test":
diff --git a/tests/conftest.py b/tests/conftest.py
index b88fa61d27..5fed907c4f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -44,15 +44,15 @@ def logger():
 """},
     {"subrepo_path": "modules/test_alwaysoptional",
      "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.3.0",
-     "status2" : "test_alwaysoptional at tag MPIserial_2.3.0",
-     "status3" : "test_alwaysoptional not checked out, aligned at tag MPIserial_2.3.0",
-     "status4" : "test_alwaysoptional at tag MPIserial_2.3.0",
+     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+     "status2" : "test_alwaysoptional at hash e5cf35c",
+     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
+     "status4" : "test_alwaysoptional at hash e5cf35c",
      "gitmodules_content": """
     [submodule "test_alwaysoptional"]
     path = modules/test_alwaysoptional
     url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.3.0
+    fxtag = e5cf35c
     fxurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysOptional
 """},    

From 678bae800ca818a0dd458dbc39334007da8f973d Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Sun, 18 Feb 2024 10:09:05 -0700
Subject: [PATCH 104/161] update version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 772b154216..e8c7bd58ba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.6.2"
+version = "0.7.0"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]

From 8d0ed18d3a7f30048aa4b302eb607e27bf1d45ff Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 22 Feb 2024 09:25:59 -0700
Subject: [PATCH 105/161] add translater from manage_externals

---
 git_fleximod/gitinterface.py |  22 ++--
 git_fleximod/gitmodules.py   |  39 +++---
 git_fleximod/metoflexi.py    | 242 +++++++++++++++++++++++++++++++++++
 pyproject.toml               |   1 +
 4 files changed, 281 insertions(+), 23 deletions(-)
 create mode 100755 git_fleximod/metoflexi.py

diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
index 4d4c4f4b9e..203c500304 100644
--- a/git_fleximod/gitinterface.py
+++ b/git_fleximod/gitinterface.py
@@ -1,25 +1,31 @@
 import os
 import sys
 from . import utils
+from pathlib import Path
 
 class GitInterface:
     def __init__(self, repo_path, logger):
         logger.debug("Initialize GitInterface for {}".format(repo_path))
-        self.repo_path = repo_path
+        if isinstance(repo_path, str):
+            self.repo_path = Path(repo_path).resolve()
+        elif isinstance(repo_path, Path):
+            self.repo_path = repo_path.resolve()
+        else:
+            raise TypeError("repo_path must be a str or Path object")
         self.logger = logger
         try:
             import git
 
             self._use_module = True
             try:
-                self.repo = git.Repo(repo_path)  # Initialize GitPython repo
+                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
             except git.exc.InvalidGitRepositoryError:
                 self.git = git
                 self._init_git_repo()
             msg = "Using GitPython interface to git"
         except ImportError:
             self._use_module = False
-            if not os.path.exists(os.path.join(repo_path, ".git")):
+            if not (repo_path / ".git").exists():
                 self._init_git_repo()
             msg = "Using shell interface to git"
         self.logger.info(msg)
@@ -32,13 +38,13 @@ def _git_command(self, operation, *args):
             except Exception as e:
                 sys.exit(e)
         else:
-            return ["git", "-C", self.repo_path, operation] + list(args)
+            return ["git", "-C", str(self.repo_path), operation] + list(args)
 
     def _init_git_repo(self):
         if self._use_module:
-            self.repo = self.git.Repo.init(self.repo_path)
+            self.repo = self.git.Repo.init(str(self.repo_path))
         else:
-            command = ("git", "-C", self.repo_path, "init")
+            command = ("git", "-C", str(self.repo_path), "init")
             utils.execute_subprocess(command)
 
     # pylint: disable=unused-argument
@@ -58,7 +64,7 @@ def config_get_value(self, section, name):
             config = self.repo.config_reader()
             return config.get_value(section, name)
         else:
-            cmd = ("git", "-C", self.repo_path, "config", "--get", f"{section}.{name}")
+            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
             output = utils.execute_subprocess(cmd, output_to_caller=True)
             return output.strip()
 
@@ -68,6 +74,6 @@ def config_set_value(self, section, name, value):
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else:
-            cmd = ("git", "-C", self.repo_path, "config", f"{section}.{name}", value)
+            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
             self.logger.info(cmd)
             utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
index ae0ebe121c..68c82d066f 100644
--- a/git_fleximod/gitmodules.py
+++ b/git_fleximod/gitmodules.py
@@ -1,14 +1,14 @@
-import os
 import shutil
-from configparser import ConfigParser
+from pathlib import Path
+from configparser import RawConfigParser, ConfigParser
 from .lstripreader import LstripReader
 
 
-class GitModules(ConfigParser):
+class GitModules(RawConfigParser):
     def __init__(
         self,
         logger,
-        confpath=os.getcwd(),
+        confpath=Path.cwd(),
         conffile=".gitmodules",
         includelist=None,
         excludelist=None,
@@ -25,25 +25,32 @@ def __init__(
                 confpath, conffile, includelist, excludelist
             )
         )
-        ConfigParser.__init__(self)
-        self.conf_file = os.path.join(confpath, conffile)
-        # first create a backup of this file to be restored on deletion of the object
-        shutil.copy(self.conf_file, self.conf_file + ".save")
-        self.read_file(LstripReader(self.conf_file), source=conffile)
+        super().__init__()
+        self.conf_file = (Path(confpath) / Path(conffile))
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
         self.includelist = includelist
         self.excludelist = excludelist
+        self.isdirty = False
+        
+    def reload(self):
+        self.clear()
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
 
+        
     def set(self, name, option, value):
         """
         Sets a configuration value for a specific submodule:
         Ensures the appropriate section exists for the submodule.
         Calls the parent class's set method to store the value.
         """
+        self.isdirty = True
         self.logger.debug("set called {} {} {}".format(name, option, value))
         section = f'submodule "{name}"'
         if not self.has_section(section):
             self.add_section(section)
-        ConfigParser.set(self, section, option, str(value))
+        super().set(section, option, str(value))
 
     # pylint: disable=redefined-builtin, arguments-differ
     def get(self, name, option, raw=False, vars=None, fallback=None):
@@ -62,12 +69,14 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
             return None
 
     def save(self):
-        print("Called gitmodules save, not expected")
-        #        self.write(open(self.conf_file, "w"))
-
+        if self.isdirty:
+            self.logger.info("Writing {}".format(self.conf_file))
+            with open(self.conf_file, "w") as fd:
+                self.write(fd)
+        self.isdirty = False
+        
     def __del__(self):
-        self.logger.debug("Destroying GitModules object")
-        shutil.move(self.conf_file + ".save", self.conf_file)
+        self.save()
 
     def sections(self):
         """Strip the submodule part out of section and just use the name"""
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
new file mode 100755
index 0000000000..1d56bc9ad8
--- /dev/null
+++ b/git_fleximod/metoflexi.py
@@ -0,0 +1,242 @@
+#!/usr/bin/env python
+from configparser import ConfigParser
+import sys
+import shutil
+from pathlib import Path
+import argparse
+import logging
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from git_fleximod import utils
+
+logger = None
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return attempt
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument('-e', '--externals', nargs='?',
+                        default='Externals.cfg',
+                        help='The externals description filename. '
+                        'Default: %(default)s.')
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
+
+def commandline_arguments(args=None):
+    parser = get_parser()
+
+    options = parser.parse_args(args)
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    return(
+        options.path,
+        options.gitmodules,
+        options.externals
+        )
+
+class ExternalRepoTranslator:
+    """
+    Translates external repositories configured in an INI-style externals file.
+    """
+
+    def __init__(self, rootpath, gitmodules, externals):
+        self.rootpath = rootpath
+        if gitmodules:
+            self.gitmodules = GitModules(logger, confpath=rootpath)
+        self.externals = (rootpath / Path(externals)).resolve()
+        print(f"Translating {self.externals}")
+        self.git = GitInterface(rootpath, logger)
+        
+#    def __del__(self):
+#        if (self.rootpath / "save.gitignore"):
+            
+
+    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+        """
+        Translates a single repository based on configuration details.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            tag (str): The tag to use for the external repository.
+            url (str): The URL of the external repository.
+            path (str): The relative path within the main repository for the external repository.
+            efile (str): The external file or file containing submodules.
+            hash_ (str): The commit hash to checkout (if applicable).
+            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
+            protocol (str): The protocol to use (e.g., 'git', 'http').
+        """
+        assert protocol != "svn", "SVN protocol is not currently supported"
+        print(f"Translating repository {section}")
+        if efile:
+            file_path = Path(path) / Path(efile)
+            newroot = (self.rootpath / file_path).parent.resolve()
+            if not newroot.exists():
+                newroot.mkdir(parents=True)
+            logger.info("Newroot is {}".format(newroot))
+            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
+            newt.translate_repo()
+        if protocol == "externals_only":
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+
+            return
+        
+        newpath = (self.rootpath / Path(path))
+        if newpath.exists():
+            shutil.rmtree(newpath)
+        logger.info("Creating directory {}".format(newpath))
+        newpath.mkdir(parents=True)
+        if tag:
+            logger.info("cloning {}".format(section))
+            try:
+                self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+            except:
+                self.git.git_operation("clone", url, path)
+                with utils.pushd(newpath):
+                    ngit = GitInterface(newpath, logger)
+                    ngit.git_operation("checkout", tag)
+
+        if (newpath / ".gitignore").exists():
+            logger.info("Moving .gitignore file in {}".format(newpath))
+            (newpath / ".gitignore").rename((newpath / "save.gitignore"))
+            
+        if hash_:
+            self.git.git_operation("clone", url, path)
+            git = GitInterface(newpath, logger)
+            git.git_operation("fetch", "origin")
+            git.git_operation("checkout", hash_)
+        if sparse:
+            print("setting as sparse submodule {}".format(section))
+            sparsefile = (newpath / Path(sparse))
+            newfile = (newpath / ".git" / "info" / "sparse-checkout")
+            print(f"sparsefile {sparsefile} newfile {newfile}")
+            shutil.copy(sparsefile, newfile)
+        logger.info("adding submodule {}".format(section))
+        self.gitmodules.save()
+        self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
+        self.git.git_operation("submodule","absorbgitdirs")
+        self.gitmodules.reload()
+        if tag:
+            self.gitmodules.set(section, "fxtag", tag)
+        if hash_:
+           self.gitmodules.set(section, "fxtag", hash_)
+            
+        self.gitmodules.set(section, "fxurl", url)
+        if sparse:
+            self.gitmodules.set(section, "fxsparse", sparse)
+        self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+    
+        
+    def translate_repo(self):
+        """
+        Translates external repositories defined within an external file.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            external_file (str): The path to the external file containing repository definitions.
+        """
+        econfig = ConfigParser()
+        econfig.read((self.rootpath / Path(self.externals)))
+
+        for section in econfig.sections():
+            if section == "externals_description":
+                logger.info("skipping section {}".format(section))
+                return
+            logger.info("Translating section {}".format(section))
+            tag = econfig.get(section, "tag", raw=False, fallback=None)
+            url = econfig.get(section, "repo_url", raw=False, fallback=None)
+            path = econfig.get(section, "local_path", raw=False, fallback=None)
+            efile = econfig.get(section, "externals", raw=False, fallback=None)
+            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
+            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
+            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
+
+            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
+
+
+
+def _main():
+    rootpath, gitmodules, externals = commandline_arguments()
+    global logger
+    logger = logging.getLogger(__name__)
+    with utils.pushd(rootpath):
+        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
+        logger.info("Translating {}".format(rootpath))
+        t.translate_repo()
+
+        
+if __name__ == "__main__":
+    sys.exit(_main())
diff --git a/pyproject.toml b/pyproject.toml
index e8c7bd58ba..212b014d97 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,6 +15,7 @@ packages = [
 
 [tool.poetry.scripts]
 git-fleximod = "git_fleximod.git_fleximod:main"
+me2flexi = "git_fleximod.metoflexi:_main"
 fsspec = "fsspec.fuse:main"
 
 [tool.poetry.dependencies]

From 91df5a0ea5f8601c01c0462cf7e9a8aca84f2aa3 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Wed, 28 Feb 2024 16:00:42 -0700
Subject: [PATCH 106/161] update README and improve me2flexi

---
 README.md                    | 5 ++---
 git_fleximod/git_fleximod.py | 5 +++--
 git_fleximod/metoflexi.py    | 6 +++---
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 94d85c4150..c17c5b6f7a 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,6 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
     Basic Usage:
         git fleximod <command> [options]
     Available Commands:
-        checkout: Checkout submodules according to git submodule hash configuration.
         status: Display the status of submodules.
         update: Update submodules to the tag indicated in .gitmodules variable fxtag.
         test: Make sure that fxtags and submodule hashes are consistant,
@@ -55,9 +54,9 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
 
 Here are some common usage examples:
 
-Checkout submodules, including optional ones:
+Update all submodules, including optional ones:
 ```bash
-  git fleximod checkout --optional
+  git fleximod update --optional
 ```
 
 Updating a specific submodule to the fxtag indicated in .gitmodules:
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 7a4470e246..1f60b1822b 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -132,8 +132,9 @@ def submodule_sparse_checkout(
             shutil.copy(sparsefile, gitsparse)
 
     # Finally checkout the repo
-    sprepo_git.git_operation("fetch", "--depth=1", "origin", "--tags")
+    sprepo_git.git_operation("fetch", "origin", "--tags")
     sprepo_git.git_operation("checkout", tag)
+        
     print(f"Successfully checked out {name:>20} at {tag}")
     rgit.config_set_value(f'submodule "{name}"',"active","true")
     rgit.config_set_value(f'submodule "{name}"',"url",url)
@@ -242,7 +243,7 @@ def submodules_status(gitmodules, root_dir):
                 ahash = git.git_operation("status").partition("\n")[0].split()[-1]
                 if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
-                elif tag and ahash == tag:
+                elif tag and ahash[:len(tag)] == tag:
                     print(f"  {name:>20} at hash {ahash}")
                 elif tag:
                     print(f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}")
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
index 1d56bc9ad8..b607ad925d 100755
--- a/git_fleximod/metoflexi.py
+++ b/git_fleximod/metoflexi.py
@@ -168,9 +168,9 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
                     ngit = GitInterface(newpath, logger)
                     ngit.git_operation("checkout", tag)
 
-        if (newpath / ".gitignore").exists():
-            logger.info("Moving .gitignore file in {}".format(newpath))
-            (newpath / ".gitignore").rename((newpath / "save.gitignore"))
+#        if (newpath / ".gitignore").exists():
+#            logger.info("Moving .gitignore file in {}".format(newpath))
+#            (newpath / ".gitignore").rename((newpath / "save.gitignore"))
             
         if hash_:
             self.git.git_operation("clone", url, path)

From b7914f26c22704b0aa984bad0978eeb7d88e55e0 Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 29 Feb 2024 15:25:23 -0700
Subject: [PATCH 107/161] correcting version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 212b014d97..cbbe83a401 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.0"
+version = "0.6.2"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]

From ff3fcb9587fabfe28e924b2249bcee89bb68d97c Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Thu, 29 Feb 2024 15:25:38 -0700
Subject: [PATCH 108/161] Bump to 0.7.0

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 80dbd58d5a..f9cd67cff7 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.6.2"
+__version__ = "0.7.0"
 
 def find_root_dir(filename=".git"):
     d = Path.cwd()
diff --git a/pyproject.toml b/pyproject.toml
index cbbe83a401..212b014d97 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.6.2"
+version = "0.7.0"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 583cef45ae..568226dfa1 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.6.2"
+current = "0.7.0"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From fd53786233fd742ec7959908cc8a543dd5315d8f Mon Sep 17 00:00:00 2001
From: James Edwards <jedwards@ucar.edu>
Date: Fri, 1 Mar 2024 07:09:45 -0700
Subject: [PATCH 109/161] code cleanup

---
 git_fleximod/git_fleximod.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 1f60b1822b..8f2b1199e2 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -184,14 +184,14 @@ def single_submodule_checkout(
 
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name} {repodir} {url}")
+        print(f"Recursively checking out submodules of {name}")
         gitmodules = GitModules(logger, confpath=repodir)
         requiredlist = ["AlwaysRequired"]
         if optional:
             requiredlist.append("AlwaysOptional")
         submodules_checkout(gitmodules, repodir, requiredlist, force=force)
     if os.path.exists(os.path.join(repodir, ".git")):
-        print(f"Successfully checked out {name} {repodir}")
+        print(f"Successfully checked out {name:>20}")
     else:
         utils.fatal_error(f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}")
 
@@ -207,6 +207,8 @@ def submodules_status(gitmodules, root_dir):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
+        required = gitmodules.get(name, "fxrequired")
+        level = required and "Toplevel" in required 
         if not path:
             utils.fatal_error("No path found in .gitmodules for {}".format(name))
         newpath = os.path.join(root_dir, path)
@@ -217,6 +219,8 @@ def submodules_status(gitmodules, root_dir):
             url = gitmodules.get(name, "url")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
+            if level:
+                continue
             for htag in tags.split("\n"):
                 if tag and tag in htag:
                     atag = (htag.split()[1])[10:]

From 0c26ad0ce55a4d080ef211662e9f0d544c4ceada Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 14 Mar 2024 12:43:23 -0600
Subject: [PATCH 110/161] update cleanup

---
 git_fleximod/git_fleximod.py | 12 +++---
 git_fleximod/metoflexi.py    | 84 +++++++++++++++++-------------------
 2 files changed, 46 insertions(+), 50 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 8f2b1199e2..69301e72d5 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -201,7 +201,7 @@ def single_submodule_checkout(
     return
 
 
-def submodules_status(gitmodules, root_dir):
+def submodules_status(gitmodules, root_dir, toplevel=False):
     testfails = 0
     localmods = 0
     for name in gitmodules.sections():
@@ -219,7 +219,7 @@ def submodules_status(gitmodules, root_dir):
             url = gitmodules.get(name, "url")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
-            if level:
+            if not toplevel and level:
                 continue
             for htag in tags.split("\n"):
                 if tag and tag in htag:
@@ -268,18 +268,20 @@ def submodules_status(gitmodules, root_dir):
 
 def submodules_update(gitmodules, root_dir, requiredlist, force):
     _, localmods = submodules_status(gitmodules, root_dir)
-    print("")
+
     if localmods and not force:
         print(
             "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
         )
         return
+    elif not localmods:
+        return
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         logger.info("name={} path={} url={} fxtag={} requiredlist={}".format(name,os.path.join(root_dir, path), url, fxtag, requiredlist))
-#        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
         fxrequired = gitmodules.get(name, "fxrequired")
         assert(fxrequired in fxrequired_allowed_values())
         rgit = GitInterface(root_dir, logger)
@@ -444,7 +446,7 @@ def main():
     if action == "update":
         submodules_update(gitmodules, root_dir, fxrequired, force)
     elif action == "status":
-        submodules_status(gitmodules, root_dir)
+        submodules_status(gitmodules, root_dir, toplevel=True)
     elif action == "test":
         retval = submodules_test(gitmodules, root_dir)
     else:
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
index b607ad925d..1a4f84213a 100755
--- a/git_fleximod/metoflexi.py
+++ b/git_fleximod/metoflexi.py
@@ -150,53 +150,47 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-
-            return
-        
-        newpath = (self.rootpath / Path(path))
-        if newpath.exists():
-            shutil.rmtree(newpath)
-        logger.info("Creating directory {}".format(newpath))
-        newpath.mkdir(parents=True)
-        if tag:
-            logger.info("cloning {}".format(section))
-            try:
-                self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
-            except:
+        else:
+            newpath = (self.rootpath / Path(path))
+            if newpath.exists():
+                shutil.rmtree(newpath)
+                logger.info("Creating directory {}".format(newpath))
+            newpath.mkdir(parents=True)
+            if tag:
+                logger.info("cloning {}".format(section))
+                try:
+                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                except:
+                    self.git.git_operation("clone", url, path)
+                    with utils.pushd(newpath):
+                        ngit = GitInterface(newpath, logger)
+                        ngit.git_operation("checkout", tag)
+            if hash_:
                 self.git.git_operation("clone", url, path)
-                with utils.pushd(newpath):
-                    ngit = GitInterface(newpath, logger)
-                    ngit.git_operation("checkout", tag)
-
-#        if (newpath / ".gitignore").exists():
-#            logger.info("Moving .gitignore file in {}".format(newpath))
-#            (newpath / ".gitignore").rename((newpath / "save.gitignore"))
-            
-        if hash_:
-            self.git.git_operation("clone", url, path)
-            git = GitInterface(newpath, logger)
-            git.git_operation("fetch", "origin")
-            git.git_operation("checkout", hash_)
-        if sparse:
-            print("setting as sparse submodule {}".format(section))
-            sparsefile = (newpath / Path(sparse))
-            newfile = (newpath / ".git" / "info" / "sparse-checkout")
-            print(f"sparsefile {sparsefile} newfile {newfile}")
-            shutil.copy(sparsefile, newfile)
-        logger.info("adding submodule {}".format(section))
-        self.gitmodules.save()
-        self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
-        self.git.git_operation("submodule","absorbgitdirs")
-        self.gitmodules.reload()
-        if tag:
-            self.gitmodules.set(section, "fxtag", tag)
-        if hash_:
-           self.gitmodules.set(section, "fxtag", hash_)
+                git = GitInterface(newpath, logger)
+                git.git_operation("fetch", "origin")
+                git.git_operation("checkout", hash_)
+            if sparse:
+                print("setting as sparse submodule {}".format(section))
+                sparsefile = (newpath / Path(sparse))
+                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                print(f"sparsefile {sparsefile} newfile {newfile}")
+                shutil.copy(sparsefile, newfile)
+        
+            logger.info("adding submodule {}".format(section))        
+            self.gitmodules.save()
+            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
+            self.git.git_operation("submodule","absorbgitdirs")
+            self.gitmodules.reload()
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
             
-        self.gitmodules.set(section, "fxurl", url)
-        if sparse:
-            self.gitmodules.set(section, "fxsparse", sparse)
-        self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+            self.gitmodules.set(section, "fxurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
     
         
     def translate_repo(self):

From 17dc6d3a0abbc7a6f69c79197f6892501b7e2e8d Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 14 Mar 2024 12:45:58 -0600
Subject: [PATCH 111/161] update cleanup

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index c17c5b6f7a..f8afb40b37 100644
--- a/README.md
+++ b/README.md
@@ -35,6 +35,8 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
       - AlwaysOptional:       Always optional (checked out with --optional flag).
     fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
     fxurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+           **NOTE** the fxurl variable is only used to identify the official project repository and should not be
+           changed by users.  Use the url variable to change to a fork if desired.
 
 ## Sparse Checkouts
 

From a56b7f7cec1372dec15962865123f9d14f8fd4bf Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 14 Mar 2024 14:33:45 -0600
Subject: [PATCH 112/161] all tests passing

---
 git_fleximod/git_fleximod.py | 52 +++++++++++++++++++++++++++++++-----
 1 file changed, 46 insertions(+), 6 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 69301e72d5..db788c1484 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -67,6 +67,24 @@ def commandline_arguments(args=None):
 def submodule_sparse_checkout(
     root_dir, name, url, path, sparsefile, tag="master"
 ):
+    """
+    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
+    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
+    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
+    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time 
+    and disk space consuming.
+    
+    Parameters:
+    root_dir (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    url (str): The URL of the submodule.
+    path (str): The path to the submodule.
+    sparsefile (str): The sparse file for the submodule.
+    tag (str, optional): The tag to checkout. Defaults to "master".
+
+    Returns:
+    None
+    """
     logger.info("Called sparse_checkout for {}".format(name))
     rgit = GitInterface(root_dir, logger)
     superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
@@ -140,8 +158,24 @@ def submodule_sparse_checkout(
     rgit.config_set_value(f'submodule "{name}"',"url",url)
 
 def single_submodule_checkout(
-        root, name, path, url=None, tag=None, force=False, optional=False
+    root, name, path, url=None, tag=None, force=False, optional=False
 ):
+    """
+    This function checks out a single git submodule.
+
+    Parameters:
+    root (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    path (str): The path to the submodule.
+    url (str, optional): The URL of the submodule. Defaults to None.
+    tag (str, optional): The tag to checkout. Defaults to None.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
     logger.info("Checkout {} into {}/{}".format(name,root,path))
@@ -204,6 +238,7 @@ def single_submodule_checkout(
 def submodules_status(gitmodules, root_dir, toplevel=False):
     testfails = 0
     localmods = 0
+    needsupdate = 0
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
@@ -219,6 +254,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             url = gitmodules.get(name, "url")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
+            needsupdate += 1
             if not toplevel and level:
                 continue
             for htag in tags.split("\n"):
@@ -252,6 +288,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                 elif tag:
                     print(f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}")
                     testfails += 1
+                    needsupdate += 1
                 else:
                     print(
                         f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
@@ -263,19 +300,20 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                     localmods = localmods + 1
                     print("M" + textwrap.indent(status, "                      "))
 
-    return testfails, localmods
+    return testfails, localmods, needsupdate
 
 
 def submodules_update(gitmodules, root_dir, requiredlist, force):
-    _, localmods = submodules_status(gitmodules, root_dir)
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
 
     if localmods and not force:
         print(
             "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
         )
         return
-    elif not localmods:
+    if needsupdate == 0:
         return
+    
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
@@ -349,13 +387,15 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
 
 # checkout is done by update if required so this function may be depricated
 def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
-    _, localmods = submodules_status(gitmodules, root_dir)
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
     print("")
     if localmods and not force:
         print(
             "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
         )
         return
+    if not needsupdate:
+        return
     for name in gitmodules.sections():
         fxrequired = gitmodules.get(name, "fxrequired")
         fxsparse = gitmodules.get(name, "fxsparse")
@@ -389,7 +429,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
 
 def submodules_test(gitmodules, root_dir):
     # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods = submodules_status(gitmodules, root_dir)
+    testfails, localmods, _ = submodules_status(gitmodules, root_dir)
     print("")
     # Then make sure that urls are consistant with fxurls (not forks and not ssh)
     # and that sparse checkout files exist

From c31e17f4fbb17aaffd8afdd1475b19dcfb074409 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 14 Mar 2024 14:48:01 -0600
Subject: [PATCH 113/161] more cleanup and comments

---
 git_fleximod/git_fleximod.py | 34 ++++++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index db788c1484..89b0a6e031 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -387,8 +387,21 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
 
 # checkout is done by update if required so this function may be depricated
 def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    """
+    This function checks out all git submodules based on the provided parameters.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+    requiredlist (list): The list of required modules.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
     print("")
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
     if localmods and not force:
         print(
             "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
@@ -426,10 +439,23 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
                 optional = "AlwaysOptional" in requiredlist
             )
 
-
 def submodules_test(gitmodules, root_dir):
+    """
+    This function tests the git submodules based on the provided parameters.
+
+    It first checks that fxtags are present and in sync with submodule hashes.
+    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
+    and that sparse checkout files exist.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+
+    Returns:
+    int: The number of test failures.
+    """
     # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods, _ = submodules_status(gitmodules, root_dir)
+    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
     print("")
     # Then make sure that urls are consistant with fxurls (not forks and not ssh)
     # and that sparse checkout files exist
@@ -444,7 +470,7 @@ def submodules_test(gitmodules, root_dir):
         if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
             print(f"{name:>20} sparse checkout file {fxsparse} not found")
             testfails += 1
-    return testfails + localmods
+    return testfails + localmods + needsupdate
 
 
 def main():

From 82428601f52b15b27f67031ad093d91554d09d3e Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 19 Mar 2024 13:00:01 -0600
Subject: [PATCH 114/161] fix py3.11 issue in gitinterface

---
 git_fleximod/gitinterface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
index 203c500304..93ae38ecde 100644
--- a/git_fleximod/gitinterface.py
+++ b/git_fleximod/gitinterface.py
@@ -25,7 +25,7 @@ def __init__(self, repo_path, logger):
             msg = "Using GitPython interface to git"
         except ImportError:
             self._use_module = False
-            if not (repo_path / ".git").exists():
+            if not (self.repo_path / ".git").exists():
                 self._init_git_repo()
             msg = "Using shell interface to git"
         self.logger.info(msg)

From 3fba38563fd5a9ceec5d0abcd210ae90676b6309 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 28 Mar 2024 13:09:57 -0600
Subject: [PATCH 115/161] explain M flag

---
 git_fleximod/git_fleximod.py | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 89b0a6e031..ebb719d4b7 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -307,9 +307,7 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
     _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
 
     if localmods and not force:
-        print(
-            "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
-        )
+        local_mods_output()
         return
     if needsupdate == 0:
         return
@@ -385,6 +383,22 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 else:
                     print(f"{name:>20} up to date.")
 
+def local_mods_output():
+    text = '''\
+    The submodules labeled with 'M' above are not in a clean state.
+    The following are options for how to proceed:
+    (1) Go into each submodule which is not in a clean state and issue a 'git status'
+        Either revert or commit your changes so that the submodule is in a clean state.
+    (2) use the --force option to git-fleximod
+    (3) you can name the particular submodules to update using the git-fleximod command line
+    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
+        then rerun git-fleximod update.
+'''
+    print(text)
+    
+    
+
+                    
 # checkout is done by update if required so this function may be depricated
 def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
     """
@@ -403,9 +417,7 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
     print("")
     _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
     if localmods and not force:
-        print(
-            "Repository has local mods, cowardly refusing to continue, fix issues or use --force to override"
-        )
+        local_mods_output()
         return
     if not needsupdate:
         return
@@ -512,7 +524,11 @@ def main():
     if action == "update":
         submodules_update(gitmodules, root_dir, fxrequired, force)
     elif action == "status":
-        submodules_status(gitmodules, root_dir, toplevel=True)
+        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        if tfails + lmods + updates > 0:
+            print(f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n")
+            if lmods > 0:
+                local_mods_output()                
     elif action == "test":
         retval = submodules_test(gitmodules, root_dir)
     else:

From b4e07beb2fef9e4c62514a9b7fe4b86e99e043b2 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 28 Mar 2024 13:37:26 -0600
Subject: [PATCH 116/161] fixes issue with ssh access to github (should not be
 required)

---
 git_fleximod/git_fleximod.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index ebb719d4b7..a0d3a76137 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -185,7 +185,6 @@ def single_submodule_checkout(
     if os.path.exists(os.path.join(repodir, ".git")):
         logger.info("Submodule {} already checked out".format(name))
         repo_exists = True
-
     # Look for a .gitmodules file in the newly checkedout repo
     if not repo_exists and url:
         # ssh urls cause problems for those who dont have git accounts with ssh keys defined
@@ -209,7 +208,11 @@ def single_submodule_checkout(
                         rootdotgit = line[8:].rstrip()
 
             newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
-            shutil.move(os.path.join(repodir, ".git"), newpath)
+            if os.path.exists(newpath):
+                shutil.rmtree(os.path.join(repodir,".git"))
+            else:
+                shutil.move(os.path.join(repodir, ".git"), newpath)
+
             with open(os.path.join(repodir, ".git"), "w") as f:
                 f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
 
@@ -252,6 +255,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             rootgit = GitInterface(root_dir, logger)
             # submodule commands use path, not name
             url = gitmodules.get(name, "url")
+            url = url.replace("git@github.com:", "https://github.com/")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
             needsupdate += 1
@@ -445,7 +449,6 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
-
             single_submodule_checkout(
                 root_dir, name, path, url=url, tag=fxtag, force=force,
                 optional = "AlwaysOptional" in requiredlist

From 3a9201dce1a482de86d7a00e6958cd8ce310b4ef Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 28 Mar 2024 13:59:06 -0600
Subject: [PATCH 117/161] better error handling for not a tag

---
 git_fleximod/git_fleximod.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index a0d3a76137..8e479fc30c 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -227,9 +227,7 @@ def single_submodule_checkout(
         if optional:
             requiredlist.append("AlwaysOptional")
         submodules_checkout(gitmodules, repodir, requiredlist, force=force)
-    if os.path.exists(os.path.join(repodir, ".git")):
-        print(f"Successfully checked out {name:>20}")
-    else:
+    if not os.path.exists(os.path.join(repodir, ".git")):
         utils.fatal_error(f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}")
 
     if tmpurl:
@@ -380,8 +378,11 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                     git.git_operation("fetch", newremote, "--tags")
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
                 if fxtag and fxtag != atag:
-                    print(f"{name:>20} updated to {fxtag}")
-                    git.git_operation("checkout", fxtag)
+                    try:
+                        git.git_operation("checkout", fxtag)
+                        print(f"{name:>20} updated to {fxtag}")
+                    except Exception as error:
+                        print(error)
                 elif not fxtag:
                     print(f"No fxtag found for submodule {name:>20}")
                 else:

From ad6b84ee19be4983561fbfff5d9d9abe24fda74e Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 28 Mar 2024 14:15:45 -0600
Subject: [PATCH 118/161] Bump to 0.7.3

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index f9cd67cff7..169a1b3384 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.7.0"
+__version__ = "0.7.3"
 
 def find_root_dir(filename=".git"):
     d = Path.cwd()
diff --git a/pyproject.toml b/pyproject.toml
index 212b014d97..bb4d89a307 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.0"
+version = "0.7.3"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 568226dfa1..7338278fb6 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.0"
+current = "0.7.3"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From fd0ce7ad12f73b7932b98c6531b127767a7a2a19 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 28 Mar 2024 14:40:25 -0600
Subject: [PATCH 119/161] set python 3.7 as min version requirement

---
 git_fleximod/git_fleximod.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 8e479fc30c..3c0ae0764e 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -1,5 +1,9 @@
 #!/usr/bin/env python
 import sys
+MIN_PYTHON = (3, 7)
+if sys.version_info < MIN_PYTHON:
+    sys.exit("Python %s.%s or later is required."%MIN_PYTHON)
+
 import os
 import shutil
 import logging

From ca419c61c810d57f0f7b4ab0de165ad30e28360d Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 29 Mar 2024 14:53:16 -0600
Subject: [PATCH 120/161] rename fxurl

---
 git_fleximod/git_fleximod.py | 165 ++++++++++++++++++++++-------------
 1 file changed, 105 insertions(+), 60 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 3c0ae0764e..e4e18ee25e 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 import sys
+
 MIN_PYTHON = (3, 7)
 if sys.version_info < MIN_PYTHON:
-    sys.exit("Python %s.%s or later is required."%MIN_PYTHON)
+    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
 
 import os
 import shutil
@@ -16,8 +17,11 @@
 
 # logger variable is global
 logger = None
+
+
 def fxrequired_allowed_values():
-    return ['ToplevelRequired', 'ToplevelOptional', 'AlwaysRequired', 'AlwaysOptional']
+    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
+
 
 def commandline_arguments(args=None):
     parser = cli.get_parser()
@@ -29,7 +33,12 @@ def commandline_arguments(args=None):
 
     # explicitly listing a component overrides the optional flag
     if options.optional or options.components:
-        fxrequired = ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
+        fxrequired = [
+            "ToplevelRequired",
+            "ToplevelOptional",
+            "AlwaysRequired",
+            "AlwaysOptional",
+        ]
     else:
         fxrequired = ["ToplevelRequired", "AlwaysRequired"]
 
@@ -68,16 +77,14 @@ def commandline_arguments(args=None):
     )
 
 
-def submodule_sparse_checkout(
-    root_dir, name, url, path, sparsefile, tag="master"
-):
+def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
     """
     This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
     in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
     Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
-    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time 
+    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
     and disk space consuming.
-    
+
     Parameters:
     root_dir (str): The root directory for the git operation.
     name (str): The name of the submodule.
@@ -96,10 +103,10 @@ def submodule_sparse_checkout(
         gitroot = superroot
     else:
         gitroot = root_dir
-    assert(os.path.isdir(os.path.join(gitroot,".git")))
+    assert os.path.isdir(os.path.join(gitroot, ".git"))
     # first create the module directory
-    if not os.path.isdir(os.path.join(root_dir,path)):
-        os.makedirs(os.path.join(root_dir,path))
+    if not os.path.isdir(os.path.join(root_dir, path)):
+        os.makedirs(os.path.join(root_dir, path))
 
     # initialize a new git repo and set the sparse checkout flag
     sprep_repo = os.path.join(root_dir, path)
@@ -120,25 +127,31 @@ def submodule_sparse_checkout(
 
     # set the repository remote
 
-    logger.info("Setting remote origin in {}/{}".format(root_dir,path))
+    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
     status = sprepo_git.git_operation("remote", "-v")
     if url not in status:
         sprepo_git.git_operation("remote", "add", "origin", url)
-    
-    topgit = os.path.join(gitroot,".git")
-    
+
+    topgit = os.path.join(gitroot, ".git")
+
     if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
         with open(os.path.join(root_dir, ".git")) as f:
-            gitpath = os.path.relpath(os.path.join(root_dir, f.read().split()[1]), start=os.path.join(root_dir,path))
+            gitpath = os.path.relpath(
+                os.path.join(root_dir, f.read().split()[1]),
+                start=os.path.join(root_dir, path),
+            )
         topgit = os.path.join(gitpath, "modules")
     else:
-        topgit = os.path.relpath(os.path.join(root_dir, ".git", "modules"), start=os.path.join(root_dir,path))
-    
+        topgit = os.path.relpath(
+            os.path.join(root_dir, ".git", "modules"),
+            start=os.path.join(root_dir, path),
+        )
+
     with utils.pushd(sprep_repo):
         if not os.path.isdir(topgit):
             os.makedirs(topgit)
     topgit += os.sep + name
-    
+
     if os.path.isdir(os.path.join(root_dir, path, ".git")):
         with utils.pushd(sprep_repo):
             shutil.move(".git", topgit)
@@ -147,7 +160,9 @@ def submodule_sparse_checkout(
             #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
             gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
         if os.path.isfile(gitsparse):
-            logger.warning("submodule {} is already initialized {}".format(name, topgit))
+            logger.warning(
+                "submodule {} is already initialized {}".format(name, topgit)
+            )
             return
 
         with utils.pushd(sprep_repo):
@@ -156,10 +171,11 @@ def submodule_sparse_checkout(
     # Finally checkout the repo
     sprepo_git.git_operation("fetch", "origin", "--tags")
     sprepo_git.git_operation("checkout", tag)
-        
+
     print(f"Successfully checked out {name:>20} at {tag}")
-    rgit.config_set_value(f'submodule "{name}"',"active","true")
-    rgit.config_set_value(f'submodule "{name}"',"url",url)
+    rgit.config_set_value(f'submodule "{name}"', "active", "true")
+    rgit.config_set_value(f'submodule "{name}"', "url", url)
+
 
 def single_submodule_checkout(
     root, name, path, url=None, tag=None, force=False, optional=False
@@ -182,7 +198,7 @@ def single_submodule_checkout(
     # function implementation...
     git = GitInterface(root, logger)
     repodir = os.path.join(root, path)
-    logger.info("Checkout {} into {}/{}".format(name,root,path))
+    logger.info("Checkout {} into {}/{}".format(name, root, path))
     # if url is provided update to the new url
     tmpurl = None
     repo_exists = False
@@ -213,7 +229,7 @@ def single_submodule_checkout(
 
             newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
             if os.path.exists(newpath):
-                shutil.rmtree(os.path.join(repodir,".git"))
+                shutil.rmtree(os.path.join(repodir, ".git"))
             else:
                 shutil.move(os.path.join(repodir, ".git"), newpath)
 
@@ -232,7 +248,9 @@ def single_submodule_checkout(
             requiredlist.append("AlwaysOptional")
         submodules_checkout(gitmodules, repodir, requiredlist, force=force)
     if not os.path.exists(os.path.join(repodir, ".git")):
-        utils.fatal_error(f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}")
+        utils.fatal_error(
+            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
+        )
 
     if tmpurl:
         print(git.git_operation("restore", ".gitmodules"))
@@ -248,7 +266,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
         required = gitmodules.get(name, "fxrequired")
-        level = required and "Toplevel" in required 
+        level = required and "Toplevel" in required
         if not path:
             utils.fatal_error("No path found in .gitmodules for {}".format(name))
         newpath = os.path.join(root_dir, path)
@@ -270,8 +288,10 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             if tag and tag == atag:
                 print(f"e {name:>20} not checked out, aligned at tag {tag}")
             elif tag:
-                ahash = rootgit.git_operation("submodule", "status", "{}".format(path)).rstrip()
-                ahash = ahash[1:len(tag)+1]
+                ahash = rootgit.git_operation(
+                    "submodule", "status", "{}".format(path)
+                ).rstrip()
+                ahash = ahash[1 : len(tag) + 1]
                 if tag == ahash:
                     print(f"e {name:>20} not checked out, aligned at hash {ahash}")
                 else:
@@ -289,10 +309,12 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                 ahash = git.git_operation("status").partition("\n")[0].split()[-1]
                 if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
-                elif tag and ahash[:len(tag)] == tag:
+                elif tag and ahash[: len(tag)] == tag:
                     print(f"  {name:>20} at hash {ahash}")
                 elif tag:
-                    print(f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}")
+                    print(
+                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
+                    )
                     testfails += 1
                     needsupdate += 1
                 else:
@@ -317,21 +339,29 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
         return
     if needsupdate == 0:
         return
-    
+
     for name in gitmodules.sections():
         fxtag = gitmodules.get(name, "fxtag")
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
-        logger.info("name={} path={} url={} fxtag={} requiredlist={}".format(name,os.path.join(root_dir, path), url, fxtag, requiredlist))
+        logger.info(
+            "name={} path={} url={} fxtag={} requiredlist={}".format(
+                name, os.path.join(root_dir, path), url, fxtag, requiredlist
+            )
+        )
         #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
         fxrequired = gitmodules.get(name, "fxrequired")
-        assert(fxrequired in fxrequired_allowed_values())
+        assert fxrequired in fxrequired_allowed_values()
         rgit = GitInterface(root_dir, logger)
         superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-            
+
         fxsparse = gitmodules.get(name, "fxsparse")
-            
-        if fxrequired and (superroot and "Toplevel" in fxrequired) or fxrequired not in requiredlist:
+
+        if (
+            fxrequired
+            and (superroot and "Toplevel" in fxrequired)
+            or fxrequired not in requiredlist
+        ):
             if "ToplevelOptional" == fxrequired:
                 print("Skipping optional component {}".format(name))
             continue
@@ -341,20 +371,24 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                     root_dir, name, url, path, fxsparse, fxtag
                 )
             )
-            submodule_sparse_checkout(
-                root_dir, name, url, path, fxsparse, tag=fxtag
-            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
         else:
             logger.info(
-                "Calling submodule_checkout({},{},{},{})".format(root_dir, name, path,url)
+                "Calling submodule_checkout({},{},{},{})".format(
+                    root_dir, name, path, url
+                )
             )
-                
+
             single_submodule_checkout(
-                root_dir, name, path, url=url, tag=fxtag, force=force,
-                optional=("AlwaysOptional" in requiredlist)
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional=("AlwaysOptional" in requiredlist),
             )
 
-
         if os.path.exists(os.path.join(path, ".git")):
             submoddir = os.path.join(root_dir, path)
             with utils.pushd(submoddir):
@@ -392,8 +426,9 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 else:
                     print(f"{name:>20} up to date.")
 
+
 def local_mods_output():
-    text = '''\
+    text = """\
     The submodules labeled with 'M' above are not in a clean state.
     The following are options for how to proceed:
     (1) Go into each submodule which is not in a clean state and issue a 'git status'
@@ -402,12 +437,10 @@ def local_mods_output():
     (3) you can name the particular submodules to update using the git-fleximod command line
     (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
         then rerun git-fleximod update.
-'''
+"""
     print(text)
-    
-    
 
-                    
+
 # checkout is done by update if required so this function may be depricated
 def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
     """
@@ -447,18 +480,22 @@ def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
                     root_dir, name, url, path, fxsparse, fxtag
                 )
             )
-            submodule_sparse_checkout(
-                root_dir, name, url, path, fxsparse, tag=fxtag
-            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
         else:
             logger.debug(
                 "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
             )
             single_submodule_checkout(
-                root_dir, name, path, url=url, tag=fxtag, force=force,
-                optional = "AlwaysOptional" in requiredlist
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional="AlwaysOptional" in requiredlist,
             )
 
+
 def submodules_test(gitmodules, root_dir):
     """
     This function tests the git submodules based on the provided parameters.
@@ -481,10 +518,12 @@ def submodules_test(gitmodules, root_dir):
     # and that sparse checkout files exist
     for name in gitmodules.sections():
         url = gitmodules.get(name, "url")
-        fxurl = gitmodules.get(name, "fxurl")
+        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
         fxsparse = gitmodules.get(name, "fxsparse")
         path = gitmodules.get(name, "path")
-        if not fxurl or url != fxurl:
+        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
+        url = url[:-4] if url.endswith(".git") else url
+        if not fxurl or url.lower() != fxurl.lower():
             print(f"{name:>20} url {url} not in sync with required {fxurl}")
             testfails += 1
         if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
@@ -518,7 +557,11 @@ def main():
             )
 
         root_dir = os.path.dirname(file_path)
-    logger.info("root_dir is {} includelist={} excludelist={}".format(root_dir, includelist, excludelist))
+    logger.info(
+        "root_dir is {} includelist={} excludelist={}".format(
+            root_dir, includelist, excludelist
+        )
+    )
     gitmodules = GitModules(
         logger,
         confpath=root_dir,
@@ -534,9 +577,11 @@ def main():
     elif action == "status":
         tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
         if tfails + lmods + updates > 0:
-            print(f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n")
+            print(
+                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
+            )
             if lmods > 0:
-                local_mods_output()                
+                local_mods_output()
     elif action == "test":
         retval = submodules_test(gitmodules, root_dir)
     else:

From 152bad98fecc769308c782db5c80d95e51b33f61 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 3 Apr 2024 09:05:06 -0600
Subject: [PATCH 121/161] fix tests on izumi

---
 git_fleximod/git_fleximod.py | 4 ++--
 git_fleximod/utils.py        | 2 +-
 tests/conftest.py            | 8 ++++----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index e4e18ee25e..7957001b84 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -100,9 +100,9 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     rgit = GitInterface(root_dir, logger)
     superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
     if superroot:
-        gitroot = superroot
+        gitroot = superroot.strip()
     else:
-        gitroot = root_dir
+        gitroot = root_dir.strip()
     assert os.path.isdir(os.path.join(gitroot, ".git"))
     # first create the module directory
     if not os.path.isdir(os.path.join(root_dir, path)):
diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py
index f0753367e5..7cc1de38cc 100644
--- a/git_fleximod/utils.py
+++ b/git_fleximod/utils.py
@@ -272,7 +272,7 @@ def execute_subprocess(commands, status_to_caller=False, output_to_caller=False)
     cwd = os.getcwd()
     msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
     logging.info(msg)
-    commands_str = " ".join(commands)
+    commands_str = " ".join(str(element) for element in commands)
     logging.info(commands_str)
     return_to_caller = status_to_caller or output_to_caller
     status = -1
diff --git a/tests/conftest.py b/tests/conftest.py
index 5fed907c4f..942a0efb97 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -25,7 +25,7 @@ def logger():
     path = modules/test
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
-    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelRequired
 """},
     {"subrepo_path": "modules/test_optional",
@@ -39,7 +39,7 @@ def logger():
     path = modules/test_optional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
-    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelOptional
 """},
     {"subrepo_path": "modules/test_alwaysoptional",
@@ -53,7 +53,7 @@ def logger():
     path = modules/test_alwaysoptional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = e5cf35c
-    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysOptional
 """},    
     {"subrepo_path": "modules/test_sparse",
@@ -67,7 +67,7 @@ def logger():
     path = modules/test_sparse
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.5.0
-    fxurl = https://github.com/ESMCI/mpi-serial.git
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysRequired
     fxsparse = ../.sparse_file_list
 """},

From 5a1e5f64b813208fb6c62dfdab6e466a5b4ef8d6 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 3 Apr 2024 09:50:57 -0600
Subject: [PATCH 122/161] fix issue in metoflexi

---
 git_fleximod/metoflexi.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
index 1a4f84213a..cc347db2dd 100755
--- a/git_fleximod/metoflexi.py
+++ b/git_fleximod/metoflexi.py
@@ -17,7 +17,7 @@ def find_root_dir(filename=".git"):
     while d != root:
         attempt = d / filename
         if attempt.is_dir():
-            return attempt
+            return d
         d = d.parent
     return None
 
@@ -146,7 +146,7 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
             if hash_:
                 self.gitmodules.set(section, "fxtag", hash_)
             
-            self.gitmodules.set(section, "fxurl", url)
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
@@ -187,7 +187,7 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
             if hash_:
                 self.gitmodules.set(section, "fxtag", hash_)
             
-            self.gitmodules.set(section, "fxurl", url)
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")

From 5398ef43fc6cdacdc894b7e6567bc9fb28b26da6 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 23 Apr 2024 15:18:24 -0600
Subject: [PATCH 123/161] if submodule does not exist add it

---
 git_fleximod/git_fleximod.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 7957001b84..adf575f9cb 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -235,10 +235,13 @@ def single_submodule_checkout(
 
             with open(os.path.join(repodir, ".git"), "w") as f:
                 f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
+                
+    if not os.path.exists(repodir):
+        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
 
     if not repo_exists or not tmpurl:
-        logger.debug(git.git_operation("submodule", "update", "--init", "--", path))
-
+        git.git_operation("submodule", "update", "--init", "--", path)
+            
     if os.path.exists(os.path.join(repodir, ".gitmodules")):
         # recursively handle this checkout
         print(f"Recursively checking out submodules of {name}")
@@ -311,6 +314,8 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                     print(f"  {name:>20} at tag {tag}")
                 elif tag and ahash[: len(tag)] == tag:
                     print(f"  {name:>20} at hash {ahash}")
+                elif atag == ahash:
+                    print(f"  {name:>20} at hash {ahash}")
                 elif tag:
                     print(
                         f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"

From 46a74ac7f75b5d086fb1f3b3ffb117ae76cc46d4 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 23 Apr 2024 16:44:14 -0600
Subject: [PATCH 124/161] create parent if it doesnt exist

---
 git_fleximod/git_fleximod.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index adf575f9cb..103cc82a50 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -237,6 +237,9 @@ def single_submodule_checkout(
                 f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
                 
     if not os.path.exists(repodir):
+        parent = os.path.dirname(repodir)
+        if not os.path.isdir(parent):
+            os.makedirs(parent)
         git.git_operation("submodule", "add", "--name", name, "--", url, path) 
 
     if not repo_exists or not tmpurl:

From eb932b015072ba3ec8cc7fadf5a387058f79fc4c Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 23 Apr 2024 16:49:47 -0600
Subject: [PATCH 125/161] Bump to 0.7.4

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 169a1b3384..1fb959dad0 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 import argparse
 
-__version__ = "0.7.3"
+__version__ = "0.7.4"
 
 def find_root_dir(filename=".git"):
     d = Path.cwd()
diff --git a/pyproject.toml b/pyproject.toml
index bb4d89a307..2484552e4f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.3"
+version = "0.7.4"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 7338278fb6..d4b8eaee11 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.3"
+current = "0.7.4"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 32bf4b5d9eae057e24bdcedd45215f2a102c3acb Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Tue, 14 May 2024 10:45:10 -0600
Subject: [PATCH 126/161] Update externals to match cesm2_3_alpha17f

---
 Externals.cfg                         | 25 +++++++++----------------
 cime_config/testdefs/testlist_cam.xml |  2 +-
 2 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index ffe2c4b012..f967878539 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -1,5 +1,5 @@
 [ccs_config]
-tag = ccs_config_cesm0.0.85
+tag = ccs_config_cesm0.0.106
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm
 local_path = ccs_config
@@ -13,7 +13,7 @@ local_path = components/cice5
 required = True
 
 [cice6]
-tag = cesm_cice6_4_1_10
+tag = cesm_cice6_5_0_7
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CICE
 local_path = components/cice
@@ -21,14 +21,14 @@ externals = Externals.cfg
 required = True
 
 [cmeps]
-tag = cmeps0.14.59
+tag = cmeps0.14.60
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.31
+tag = cdeps1.0.33
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -36,7 +36,7 @@ externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl77.0.7
+tag = cpl77.0.8
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
@@ -49,13 +49,6 @@ repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
 required = True
 
-[mct]
-tag = MCT_2.11.0
-protocol = git
-repo_url = https://github.com/MCSclimate/MCT
-local_path = libraries/mct
-required = True
-
 [parallelio]
 tag = pio2_6_2
 protocol = git
@@ -71,7 +64,7 @@ local_path = cime
 required = True
 
 [cism]
-tag = cismwrap_2_1_96
+tag = cismwrap_2_1_100
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
 local_path = components/cism
@@ -79,7 +72,7 @@ externals = Externals_CISM.cfg
 required = True
 
 [clm]
-tag = ctsm5.1.dev145
+tag = ctsm5.2.005
 protocol = git
 repo_url = https://github.com/ESCOMP/CTSM
 local_path = components/clm
@@ -95,14 +88,14 @@ externals = Externals_FMS.cfg
 required = True
 
 [mosart]
-tag = mosart1_0_48
+tag = mosart1_0_49
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
 local_path = components/mosart
 required = True
 
 [rtm]
-tag = rtm1_0_78
+tag = rtm1_0_79
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
 local_path = components/rtm
diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
index 05983cca7b..98813e6993 100644
--- a/cime_config/testdefs/testlist_cam.xml
+++ b/cime_config/testdefs/testlist_cam.xml
@@ -1444,7 +1444,7 @@
       <machine name="izumi" compiler="nag" category="prealpha"/>
     </machines>
   </test>
-  <test compset="FGRAYRAD" grid="f09_f09_mg17" name="ERP_D_Ln9_Vmct" testmods="cam/outfrq9s">
+  <test compset="FGRAYRAD" grid="f09_f09_mg17" name="ERP_D_Ln9" testmods="cam/outfrq9s">
     <machines>
       <machine name="izumi" compiler="nag" category="prebeta"/>
     </machines>

From c2a1d37eb9d7a79d8dffb54bb1a4fa3b471ef841 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Tue, 14 May 2024 11:22:48 -0600
Subject: [PATCH 127/161] put back in MCT since makefile mods would be required

---
 Externals.cfg                         | 7 +++++++
 cime_config/testdefs/testlist_cam.xml | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index f967878539..ad6907e697 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -49,6 +49,13 @@ repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
 required = True
 
+[mct]
+tag = MCT_2.11.0
+protocol = git
+repo_url = https://github.com/MCSclimate/MCT
+local_path = libraries/mct
+required = True
+
 [parallelio]
 tag = pio2_6_2
 protocol = git
diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
index 98813e6993..05983cca7b 100644
--- a/cime_config/testdefs/testlist_cam.xml
+++ b/cime_config/testdefs/testlist_cam.xml
@@ -1444,7 +1444,7 @@
       <machine name="izumi" compiler="nag" category="prealpha"/>
     </machines>
   </test>
-  <test compset="FGRAYRAD" grid="f09_f09_mg17" name="ERP_D_Ln9" testmods="cam/outfrq9s">
+  <test compset="FGRAYRAD" grid="f09_f09_mg17" name="ERP_D_Ln9_Vmct" testmods="cam/outfrq9s">
     <machines>
       <machine name="izumi" compiler="nag" category="prebeta"/>
     </machines>

From 94121295e57a1d6e713b8e3ba84261d9e9cfebe6 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 14 May 2024 13:48:01 -0600
Subject: [PATCH 128/161] update documentation

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index f8afb40b37..d1ef632f28 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
         status: Display the status of submodules.
         update: Update submodules to the tag indicated in .gitmodules variable fxtag.
         test: Make sure that fxtags and submodule hashes are consistant,
-              make sure that official urls (as defined by fxurl) are set
+              make sure that official urls (as defined by fxDONOTUSEurl) are set
               make sure that fxtags are defined for all submodules
     Additional Options:
         See git fleximod --help for more details.
@@ -34,8 +34,8 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
       - AlwaysRequired:       Always required (always checked out).
       - AlwaysOptional:       Always optional (checked out with --optional flag).
     fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
-    fxurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
-           **NOTE** the fxurl variable is only used to identify the official project repository and should not be
+    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
            changed by users.  Use the url variable to change to a fork if desired.
 
 ## Sparse Checkouts

From 0c922db8c47af355779d96b5a3c1b3702d7a6353 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Tue, 14 May 2024 15:49:34 -0600
Subject: [PATCH 129/161] Increase wall clock times

---
 cime_config/testdefs/testlist_cam.xml | 28 +++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
index 05983cca7b..575729a37c 100644
--- a/cime_config/testdefs/testlist_cam.xml
+++ b/cime_config/testdefs/testlist_cam.xml
@@ -73,7 +73,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
 
@@ -83,7 +83,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
 
@@ -93,7 +93,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam_short"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
 
@@ -1811,7 +1811,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:30:00</option>
+      <option name="wallclock">00:90:00</option>
       <option name="comment">CAM7 dev low top ~40 km</option>
     </options>
   </test>
@@ -1829,7 +1829,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:60:00</option>
       <option name="comment">CAM7 dev mid top ~80 km</option>
     </options>
   </test>
@@ -2033,7 +2033,7 @@
       <machine name="derecho" compiler="intel" category="camchem_hco"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:60:00</option>
       <option name="comment">FCSD CAM-chem f19 with HEMCO exact restart/PE tests</option>
     </options>
   </test>
@@ -2390,7 +2390,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:30:00</option>
     </options>
   </test>
   <test compset="FWHIST_BGC" grid="f09_f09_mg17" name="ERP_Ld3" testmods="cam/reduced_hist1d">
@@ -2415,7 +2415,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:80:00</option>
     </options>
   </test>
   <test compset="FWHIST" grid="f09_f09_mg17" name="SMS_D_Ln9" testmods="cam/reduced_hist3s">
@@ -2424,7 +2424,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
   <test compset="FX2000" grid="f19_f19_mg17" name="SMS_D_Ln9"   testmods="cam/outfrq9s">
@@ -2450,7 +2450,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:30:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
   <test compset="FXHIST" grid="f19_f19_mg17" name="SMS_D_Ln9" testmods="cam/outfrq9s_amie">
@@ -2459,7 +2459,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:30:00</option>
     </options>
   </test>
   <test compset="QPX2000" grid="f19_f19_mg17" name="SMS_D_Ln9_P240x3" testmods="cam/outfrq9s_ltr">
@@ -2725,7 +2725,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
   <test compset="FWscHIST" grid="f09_f09_mg17" name="ERP_Ld3" testmods="cam/outfrq3d">
@@ -2748,7 +2748,7 @@
       <machine name="derecho" compiler="intel" category="ghg_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:30:00</option>
       <option name="comment">Checks that exact restarts occur when crossing the December 16th date boundary with WACCM-SC chemistry in low top configuration</option>
     </options>
   </test>
@@ -2800,7 +2800,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:30:00</option>
       <option name="comment">WACCM w/ RRTMGP</option>
     </options>
   </test>

From 4d797696cf47d5cab0eb18dba692cc746e35d45f Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Thu, 16 May 2024 13:08:22 -0600
Subject: [PATCH 130/161] revert times back for regression tests to original
 times

---
 cime_config/testdefs/testlist_cam.xml | 28 +++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
index 575729a37c..05983cca7b 100644
--- a/cime_config/testdefs/testlist_cam.xml
+++ b/cime_config/testdefs/testlist_cam.xml
@@ -73,7 +73,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:10:00</option>
     </options>
   </test>
 
@@ -83,7 +83,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:10:00</option>
     </options>
   </test>
 
@@ -93,7 +93,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam_short"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
 
@@ -1811,7 +1811,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:90:00</option>
+      <option name="wallclock">00:30:00</option>
       <option name="comment">CAM7 dev low top ~40 km</option>
     </options>
   </test>
@@ -1829,7 +1829,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment">CAM7 dev mid top ~80 km</option>
     </options>
   </test>
@@ -2033,7 +2033,7 @@
       <machine name="derecho" compiler="intel" category="camchem_hco"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment">FCSD CAM-chem f19 with HEMCO exact restart/PE tests</option>
     </options>
   </test>
@@ -2390,7 +2390,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:30:00</option>
+      <option name="wallclock">00:10:00</option>
     </options>
   </test>
   <test compset="FWHIST_BGC" grid="f09_f09_mg17" name="ERP_Ld3" testmods="cam/reduced_hist1d">
@@ -2415,7 +2415,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:80:00</option>
+      <option name="wallclock">00:40:00</option>
     </options>
   </test>
   <test compset="FWHIST" grid="f09_f09_mg17" name="SMS_D_Ln9" testmods="cam/reduced_hist3s">
@@ -2424,7 +2424,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
   <test compset="FX2000" grid="f19_f19_mg17" name="SMS_D_Ln9"   testmods="cam/outfrq9s">
@@ -2450,7 +2450,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:30:00</option>
     </options>
   </test>
   <test compset="FXHIST" grid="f19_f19_mg17" name="SMS_D_Ln9" testmods="cam/outfrq9s_amie">
@@ -2459,7 +2459,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:30:00</option>
+      <option name="wallclock">00:10:00</option>
     </options>
   </test>
   <test compset="QPX2000" grid="f19_f19_mg17" name="SMS_D_Ln9_P240x3" testmods="cam/outfrq9s_ltr">
@@ -2725,7 +2725,7 @@
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
     <options>
-      <option name="wallclock">00:60:00</option>
+      <option name="wallclock">00:10:00</option>
     </options>
   </test>
   <test compset="FWscHIST" grid="f09_f09_mg17" name="ERP_Ld3" testmods="cam/outfrq3d">
@@ -2748,7 +2748,7 @@
       <machine name="derecho" compiler="intel" category="ghg_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:30:00</option>
+      <option name="wallclock">00:10:00</option>
       <option name="comment">Checks that exact restarts occur when crossing the December 16th date boundary with WACCM-SC chemistry in low top configuration</option>
     </options>
   </test>
@@ -2800,7 +2800,7 @@
       <machine name="derecho" compiler="intel" category="aux_cam"/>
     </machines>
     <options>
-      <option name="wallclock">00:30:00</option>
+      <option name="wallclock">00:10:00</option>
       <option name="comment">WACCM w/ RRTMGP</option>
     </options>
   </test>

From 6d958488d99059327aed1e362112cffbc26378e6 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Thu, 16 May 2024 16:34:40 -0600
Subject: [PATCH 131/161] ChangeLog for cam6_3_161

---
 doc/ChangeLog | 115 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 114 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 9f4f0d348d..3a5c46527d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,6 +1,120 @@
 
 ===============================================================
 
+Tag name: cam6_3_161
+Originator(s): cacraig
+Date: May 16, 2024
+One-line Summary: Update to alpha17 externals
+Github PR URL: https://github.com/ESCOMP/CAM/pull/1031
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+ - Update externals to match externals which will be used in cesm2_3_beta17: https://github.com/ESCOMP/CAM/issues/985
+ - Bring in ccs_config0.0.99: https://github.com/ESCOMP/CAM/issues/1021
+ - Unable to compile cam6_3_154 with nvhpc/24.3 on Derecho: https://github.com/ESCOMP/CAM/issues/1025
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist: N/A
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by: nusbaume
+
+List all files eliminated: N/A
+
+List all files added and what they do: N/A
+
+List all existing files that have been modified, and describe the changes:
+M       Externals.cfg
+          - update externals to match cesm2_3_beta17
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+NOTE - most tests have namelist differences due to mediator namelist changes
+
+derecho/intel/aux_cam:
+  ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+     - pre-existing failure
+
+  ERP_Lh12.f19_f19_mg17.FW4madSD.derecho_intel.cam-outfrq3h (Overall: FAIL) details:
+     - Bug during CREATE_NEWCASE in CTSM code - will go away when CTSM external is updated post git-fleximod
+
+  SMS_D_Ln9.T42_T42.FSCAM.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+     - Bug in med.F90 - Will go away when CICE external is updated post git-fleximod
+
+  ERP_Ln9.ne30_ne30_mg17.FCnudged.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+    FAIL ERP_Ln9.ne30_ne30_mg17.FCnudged.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD failed to initialize
+  SMS_D_Ln9.ne16_ne16_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: PEND) details:
+    PEND SMS_D_Ln9.ne16_ne16_mg17.FX2000.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD
+  SMS_D_Ln9_P1280x1.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.FHIST.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+    FAIL SMS_D_Ln9_P1280x1.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.FHIST.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD time=2
+  SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+    FAIL SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD time=1
+      - Bugs reported to CTSM and will be fixed when CTSM external is updated post git-fleximod
+
+  ERP_D_Ln9.ne30pg3_ne30pg3_mg17.F2000dev.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.derecho_intel.cam-outfrq9s_rrtmgp (Overall: DIFF) details:
+  ERP_Ld3.f09_f09_mg17.FWHIST.derecho_intel.cam-reduced_hist1d (Overall: DIFF) details:
+  ERP_Ln9.C96_C96_mg17.F2000climo.derecho_intel.cam-outfrq9s_mg3 (Overall: DIFF) details:
+  ERP_Ln9.f09_f09_mg17.F1850.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_Ln9.f09_f09_mg17.F2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_Ln9.f09_f09_mg17.F2000dev.derecho_intel.cam-outfrq9s_mg3 (Overall: DIFF) details:
+  ERP_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_Ln9.f09_f09_mg17.FHIST_BDRD.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_Ln9.f19_f19_mg17.FWsc1850.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERP_Ln9.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERS_Ld3.f10_f10_mg37.F1850.derecho_intel.cam-outfrq1d_14dec_ghg_cam_dev (Overall: DIFF) details:
+  ERS_Ln9.f09_f09_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERS_Ln9.f19_f19_mg17.FSPCAMS.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERS_Ln9.f19_f19_mg17.FXSD.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  ERS_Ln9_P288x1.mpasa120_mpasa120.F2000climo.derecho_intel.cam-outfrq9s_mpasa120 (Overall: DIFF) details:
+  ERS_Ln9_P36x1.mpasa480_mpasa480.F2000climo.derecho_intel.cam-outfrq9s_mpasa480 (Overall: DIFF) details:
+  SMS_D_Ln9.f09_f09_mg17.FCts2nudged.derecho_intel.cam-outfrq9s_leapday (Overall: DIFF) details:
+  SMS_D_Ln9.f09_f09_mg17.FCvbsxHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  SMS_D_Ln9.f09_f09_mg17.FSD.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  SMS_D_Ln9.f19_f19_mg17.FWma2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  SMS_D_Ln9.f19_f19_mg17.FWma2000climo.derecho_intel.cam-outfrq9s_waccm_ma_mam4 (Overall: DIFF) details:
+  SMS_D_Ln9.f19_f19_mg17.FXHIST.derecho_intel.cam-outfrq9s_amie (Overall: DIFF) details:
+  SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  SMS_D_Ln9_P1280x1.ne30pg3_ne30pg3_mg17.FCLTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+  SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+  SMS_Ld1.f09_f09_mg17.FW2000climo.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+  SMS_Ld1.f19_f19.F2000dev.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+  SMS_Ld1.ne30pg3_ne30pg3_mg17.FC2010climo.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+  SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+  SMS_Lm13.f10_f10_mg37.F2000climo.derecho_intel.cam-outfrq1m (Overall: DIFF) details:
+  SMS_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-nudging (Overall: DIFF) details:
+  SMS_Ln9.f09_f09_mg17.FW1850.derecho_intel.cam-reduced_hist3s (Overall: DIFF) details:
+  SMS_Ln9.f19_f19.F2000climo.derecho_intel.cam-silhs (Overall: DIFF) details:
+  SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s_nochem (Overall: DIFF) details:
+  SMS_Ln9.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s_rrtmgp (Overall: DIFF) details:
+    - Answer changes due to updated externals
+
+izumi/nag/aux_cam: all B4B, except:
+  DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+     - pre-existing failure
+
+izumi/gnu/aux_cam: all BFB except:
+  SMS_P48x1_D_Ln9.f19_f19_mg17.FW4madSD.izumi_gnu.cam-outfrq9s (Overall: FAIL) details:
+     - Bug during CREATE_NEWCASE in CTSM code - will go away when CTSM external is updated post git-fleximod
+
+    SMS_D_Ln9.f10_f10_mg37.2000_CAM%DEV%GHGMAM4_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV_SESP.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+     - answer changes due to updated externals
+
+
+CAM tag used for the baseline comparison tests if different than previous
+tag: cam6_3_159 as cam6_3_160 did not run regression tests
+
+
+===============================================================
+===============================================================
+
 Tag name: cam6_3_160
 Originator(s): cacraig, jedwards
 Date: April 29, 2024
@@ -461,7 +575,6 @@ derecho/intel/aux_cam:
   SMS_Ld1.f09_f09_mg17.FW2000climo.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
   SMS_Ld1.f19_f19.F2000dev.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
   SMS_Ld1.ne30pg3_ne30pg3_mg17.FC2010climo.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
-  SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
   SMS_Lm13.f10_f10_mg37.F2000climo.derecho_intel.cam-outfrq1m (Overall: DIFF) details:
   SMS_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-nudging (Overall: DIFF) details:
   SMS_Ln9.f09_f09_mg17.FW1850.derecho_intel.cam-reduced_hist3s (Overall: DIFF) details:

From 8593b17b3685cd33237f41b27bb30e7658c16655 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 07:45:25 -0600
Subject: [PATCH 132/161] add submodules

---
 .gitignore                          |  24 ----
 .gitmodules                         | 199 ++++++++++++++++++++++++++++
 ccs_config                          |   1 +
 chem_proc                           |   1 +
 cime                                |   1 +
 components/cdeps                    |   1 +
 components/cice                     |   1 +
 components/cism                     |   1 +
 components/clm                      |   1 +
 components/cmeps                    |   1 +
 components/mizuRoute                |   1 +
 components/mosart                   |   1 +
 components/rtm                      |   1 +
 libraries/FMS                       |   1 +
 libraries/mct                       |   1 +
 libraries/parallelio                |   1 +
 share                               |   1 +
 src/atmos_phys                      |   1 +
 src/chemistry/geoschem/geoschem_src |   1 +
 src/dynamics/fv3                    |   1 +
 src/dynamics/mpas/dycore            |   1 +
 src/hemco                           |   1 +
 src/physics/ali_arms                |   1 +
 src/physics/carma/base              |   1 +
 src/physics/clubb                   |   1 +
 src/physics/cosp2/src               |   1 +
 src/physics/pumas                   |   1 +
 src/physics/pumas-frozen            |   1 +
 src/physics/rrtmgp/data             |   1 +
 src/physics/rrtmgp/ext              |   1 +
 30 files changed, 227 insertions(+), 24 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 ccs_config
 create mode 160000 chem_proc
 create mode 160000 cime
 create mode 160000 components/cdeps
 create mode 160000 components/cice
 create mode 160000 components/cism
 create mode 160000 components/clm
 create mode 160000 components/cmeps
 create mode 160000 components/mizuRoute
 create mode 160000 components/mosart
 create mode 160000 components/rtm
 create mode 160000 libraries/FMS
 create mode 160000 libraries/mct
 create mode 160000 libraries/parallelio
 create mode 160000 share
 create mode 160000 src/atmos_phys
 create mode 160000 src/chemistry/geoschem/geoschem_src
 create mode 160000 src/dynamics/fv3
 create mode 160000 src/dynamics/mpas/dycore
 create mode 160000 src/hemco
 create mode 160000 src/physics/ali_arms
 create mode 160000 src/physics/carma/base
 create mode 160000 src/physics/clubb
 create mode 160000 src/physics/cosp2/src
 create mode 160000 src/physics/pumas
 create mode 160000 src/physics/pumas-frozen
 create mode 160000 src/physics/rrtmgp/data
 create mode 160000 src/physics/rrtmgp/ext

diff --git a/.gitignore b/.gitignore
index e24b6fa55e..ca3a7df6c0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,27 +1,3 @@
-# Ignore externals
-ccs_config
-chem_proc
-cime
-components
-manage_externals.log
-src/physics/ali_arms/
-src/physics/carma/base
-src/physics/clubb
-src/physics/cosp2/src
-src/physics/silhs
-src/chemistry/geoschem/geoschem_src
-src/physics/pumas
-src/physics/pumas-frozen
-src/physics/rrtmgp/data
-src/physics/rrtmgp/ext
-src/dynamics/fv3
-libraries/FMS
-libraries/mct
-libraries/parallelio
-src/atmos_phys
-src/dynamics/mpas/dycore
-share
-src/hemco
 # Ignore compiled python
 buildnmlc
 buildcppc
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000..4b2a94beb3
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,199 @@
+[submodule "chem_proc"]
+	path = chem_proc
+	url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
+        fxrequired = AlwaysRequired
+        fxtag = chem_proc5_0_05
+	fxDONOTUSEurl = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
+
+[submodule "carma"]
+	path = src/physics/carma/base
+	url = https://github.com/ESCOMP/CARMA_base.git
+        fxrequired = AlwaysRequired
+        fxtag = carma4_01
+        fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git
+
+[submodule "pumas"]
+	path = src/physics/pumas
+	url = https://github.com/ESCOMP/PUMAS
+        fxrequired = AlwaysRequired
+        fxtag = pumas_cam-release_v1.36
+        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
+
+[submodule "pumas-frozen"]
+	path = src/physics/pumas-frozen
+	url = https://github.com/ESCOMP/PUMAS
+        fxrequired = AlwaysRequired
+        fxtag = pumas_cam-release_v1.17_rename
+        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
+
+[submodule "ali_arms"]
+	path = src/physics/ali_arms
+	url = https://github.com/ESCOMP/ALI-ARMS
+        fxrequired = AlwaysRequired
+        fxtag = ALI_ARMS_v1.0.1
+        fxDONOTUSEurl = https://github.com/ESCOMP/ALI-ARMS
+
+[submodule "atmos_phys"]
+	path = src/atmos_phys
+	url = https://github.com/ESCOMP/atmospheric_physics
+        fxtag = atmos_phys0_02_006
+        fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
+
+[submodule "fv3"]
+	path = src/dynamics/fv3
+	url = https://github.com/ESCOMP/CAM_FV3_interface.git
+        fxrequired = AlwaysRequired
+        fxtag = fv3int_022824
+	fxDONOTUSEurl = https://github.com/ESCOMP/CAM_FV3_interface.git
+        
+[submodule "geoschem"]
+	path = src/chemistry/geoschem/geoschem_src
+	url = https://github.com/geoschem/geos-chem.git
+        fxrequired = AlwaysRequired
+        fxtag = 14.1.2
+        fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
+
+[submodule "hemco"]
+	path = src/hemco
+	url = https://github.com/ESCOMP/HEMCO_CESM.git
+        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm 
+        fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
+
+[submodule "rte-rrtmgp"]
+	path = src/physics/rrtmgp/ext
+	url = https://github.com/earth-system-radiation/rte-rrtmgp.git
+        fxrequired = AlwaysRequired
+        fxtag = v1.7
+        fxDONOTUSEurl = https://github.com/earth-system-radiation/rte-rrtmgp.git
+
+[submodule "rrtmgp-data"]
+	path = src/physics/rrtmgp/data
+	url = https://github.com/earth-system-radiation/rrtmgp-data.git
+        fxrequired = AlwaysRequired
+        fxtag = v1.8
+        fxDONOTUSEurl = https://github.com/earth-system-radiation/rrtmgp-data.git
+
+[submodule "mpas"]
+	path = src/dynamics/mpas/dycore
+	url = https://github.com/MPAS-Dev/MPAS-Model.git
+        fxrequired = AlwaysRequired
+        fxsparse = ../.mpas_sparse_checkout
+        fxtag = b8c33daa
+	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
+
+[submodule "cosp2"]
+	path = src/physics/cosp2/src
+	url = https://github.com/CFMIP/COSPv2.0
+        fxrequired = AlwaysRequired
+        fxsparse = ../.cosp_sparse_checkout
+        fxtag = v2.1.4cesm
+	fxDONOTUSEurl = https://github.com/CFMIP/COSPv2.0
+
+[submodule "clubb"]
+	path = src/physics/clubb
+	url = https://github.com/larson-group/clubb_release
+        fxrequired = AlwaysRequired
+        fxsparse = ../.clubb_sparse_checkout 
+        fxtag = clubb_4ncar_20231115_5406350
+        fxDONOTUSEurl = https://github.com/larson-group/clubb_release
+
+[submodule "cism"]
+path = components/cism
+url = https://github.com/ESCOMP/CISM-wrapper
+fxtag = cismwrap_2_2_001
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+
+[submodule "rtm"]
+path = components/rtm
+url = https://github.com/ESCOMP/RTM
+fxtag = rtm1_0_79
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/RTM
+
+[submodule "mosart"]
+path = components/mosart
+url = https://github.com/ESCOMP/MOSART
+fxtag = mosart1_0_49
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
+
+[submodule "mizuRoute"]
+path = components/mizuRoute
+url = https://github.com/ESCOMP/mizuRoute
+fxtag = cesm-coupling.n02_v2.1.2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
+        
+[submodule "ccs_config"]
+path = ccs_config
+url = https://github.com/ESMCI/ccs_config_cesm.git
+fxtag = ccs_config_cesm0.0.106
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
+
+[submodule "cime"]
+path = cime
+url = https://github.com/ESMCI/cime
+fxtag = cime6.0.246
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESMCI/cime
+
+[submodule "cmeps"]
+path = components/cmeps
+url = https://github.com/ESCOMP/CMEPS.git
+fxtag = cmeps0.14.63
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
+
+[submodule "cdeps"]
+path = components/cdeps
+url = https://github.com/ESCOMP/CDEPS.git
+fxtag = cdeps1.0.34
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+
+[submodule "share"]
+path = share
+url = https://github.com/ESCOMP/CESM_share
+fxtag = share1.0.19
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
+
+[submodule "mct"]
+path = libraries/mct
+url = https://github.com/MCSclimate/MCT
+fxtag = MCT_2.11.0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/MCSclimate/MCT
+
+[submodule "parallelio"]
+path = libraries/parallelio
+url = https://github.com/NCAR/ParallelIO
+fxtag = pio2_6_2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+
+[submodule "cice"]
+path = components/cice
+url = https://github.com/ESCOMP/CESM_CICE
+fxtag = cesm_cice6_5_0_9
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+
+[submodule "clm"]
+path = components/clm
+url = https://github.com/ESCOMP/CTSM
+fxtag = ctsm5.2.007
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
+
+[submodule "fms"]
+path = libraries/FMS
+url = https://github.com/ESCOMP/FMS_interface
+fxtag = fi_240516
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
+
diff --git a/ccs_config b/ccs_config
new file mode 160000
index 0000000000..f90e10502c
--- /dev/null
+++ b/ccs_config
@@ -0,0 +1 @@
+Subproject commit f90e10502c7246c2b45e373b7dd5e0da6cba0828
diff --git a/chem_proc b/chem_proc
new file mode 160000
index 0000000000..944f506033
--- /dev/null
+++ b/chem_proc
@@ -0,0 +1 @@
+Subproject commit 944f506033d88a5dd1ee4556a932d2c90023cbfc
diff --git a/cime b/cime
new file mode 160000
index 0000000000..422ddaa770
--- /dev/null
+++ b/cime
@@ -0,0 +1 @@
+Subproject commit 422ddaa770a3cea6e83a60c9700ebce77acaceed
diff --git a/components/cdeps b/components/cdeps
new file mode 160000
index 0000000000..7a522c828c
--- /dev/null
+++ b/components/cdeps
@@ -0,0 +1 @@
+Subproject commit 7a522c828c32dc35777992653f281ec525509c4a
diff --git a/components/cice b/components/cice
new file mode 160000
index 0000000000..bdf6ea04d6
--- /dev/null
+++ b/components/cice
@@ -0,0 +1 @@
+Subproject commit bdf6ea04d6133434fcaa4de5336de106f01290d0
diff --git a/components/cism b/components/cism
new file mode 160000
index 0000000000..c05dd5c4fc
--- /dev/null
+++ b/components/cism
@@ -0,0 +1 @@
+Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928
diff --git a/components/clm b/components/clm
new file mode 160000
index 0000000000..6aebaad42f
--- /dev/null
+++ b/components/clm
@@ -0,0 +1 @@
+Subproject commit 6aebaad42f1db6d8be2c84205adce60a884cc254
diff --git a/components/cmeps b/components/cmeps
new file mode 160000
index 0000000000..6384ff4e4a
--- /dev/null
+++ b/components/cmeps
@@ -0,0 +1 @@
+Subproject commit 6384ff4e4a6bc82a678f9419a43ffbd5d53ac209
diff --git a/components/mizuRoute b/components/mizuRoute
new file mode 160000
index 0000000000..0a62ee6185
--- /dev/null
+++ b/components/mizuRoute
@@ -0,0 +1 @@
+Subproject commit 0a62ee6185bdc9b99cd88ed5f15ea850602c43a2
diff --git a/components/mosart b/components/mosart
new file mode 160000
index 0000000000..1c22a8c547
--- /dev/null
+++ b/components/mosart
@@ -0,0 +1 @@
+Subproject commit 1c22a8c5478b714cf5b7c54b3e5cf7bad09fd9b2
diff --git a/components/rtm b/components/rtm
new file mode 160000
index 0000000000..88503adbc2
--- /dev/null
+++ b/components/rtm
@@ -0,0 +1 @@
+Subproject commit 88503adbc275fb2ccbb6b598e460deaeb140e515
diff --git a/libraries/FMS b/libraries/FMS
new file mode 160000
index 0000000000..270433531d
--- /dev/null
+++ b/libraries/FMS
@@ -0,0 +1 @@
+Subproject commit 270433531d33c64da7944d80564fe39a84917d26
diff --git a/libraries/mct b/libraries/mct
new file mode 160000
index 0000000000..e36024c5dd
--- /dev/null
+++ b/libraries/mct
@@ -0,0 +1 @@
+Subproject commit e36024c5ddf482625ae6bd9474eff7d8f393f87c
diff --git a/libraries/parallelio b/libraries/parallelio
new file mode 160000
index 0000000000..6539ef05ae
--- /dev/null
+++ b/libraries/parallelio
@@ -0,0 +1 @@
+Subproject commit 6539ef05ae7584ec570a56fdab9f7dfb336c2b80
diff --git a/share b/share
new file mode 160000
index 0000000000..4b9dc4871a
--- /dev/null
+++ b/share
@@ -0,0 +1 @@
+Subproject commit 4b9dc4871a259f00f35bb47708d876cb7dcdf75c
diff --git a/src/atmos_phys b/src/atmos_phys
new file mode 160000
index 0000000000..4944547f04
--- /dev/null
+++ b/src/atmos_phys
@@ -0,0 +1 @@
+Subproject commit 4944547f04b1457d78bf7d3c0becddcfe0deabb9
diff --git a/src/chemistry/geoschem/geoschem_src b/src/chemistry/geoschem/geoschem_src
new file mode 160000
index 0000000000..20e2402baf
--- /dev/null
+++ b/src/chemistry/geoschem/geoschem_src
@@ -0,0 +1 @@
+Subproject commit 20e2402baf56c682cc04af74adb139efdb6ca000
diff --git a/src/dynamics/fv3 b/src/dynamics/fv3
new file mode 160000
index 0000000000..38b889fcff
--- /dev/null
+++ b/src/dynamics/fv3
@@ -0,0 +1 @@
+Subproject commit 38b889fcfff1e316ef5b4d4d02ecc47c801b8669
diff --git a/src/dynamics/mpas/dycore b/src/dynamics/mpas/dycore
new file mode 160000
index 0000000000..f084b36f8a
--- /dev/null
+++ b/src/dynamics/mpas/dycore
@@ -0,0 +1 @@
+Subproject commit f084b36f8ac82eb1e76c426d3572339c36523c77
diff --git a/src/hemco b/src/hemco
new file mode 160000
index 0000000000..3bd9df0970
--- /dev/null
+++ b/src/hemco
@@ -0,0 +1 @@
+Subproject commit 3bd9df097069ff0158a1d104483c445b69f1426d
diff --git a/src/physics/ali_arms b/src/physics/ali_arms
new file mode 160000
index 0000000000..825e7f20e2
--- /dev/null
+++ b/src/physics/ali_arms
@@ -0,0 +1 @@
+Subproject commit 825e7f20e2dd368b95b1e3cb2562ab571318bb4d
diff --git a/src/physics/carma/base b/src/physics/carma/base
new file mode 160000
index 0000000000..2123b52f97
--- /dev/null
+++ b/src/physics/carma/base
@@ -0,0 +1 @@
+Subproject commit 2123b52f97daaeb546753cbbef56c6f1b70ba608
diff --git a/src/physics/clubb b/src/physics/clubb
new file mode 160000
index 0000000000..a7eaa45389
--- /dev/null
+++ b/src/physics/clubb
@@ -0,0 +1 @@
+Subproject commit a7eaa4538926587250da0bd37653f5cf70aad174
diff --git a/src/physics/cosp2/src b/src/physics/cosp2/src
new file mode 160000
index 0000000000..241f1b7f4f
--- /dev/null
+++ b/src/physics/cosp2/src
@@ -0,0 +1 @@
+Subproject commit 241f1b7f4f64dbabe8d1c042ce27466a0b6972ee
diff --git a/src/physics/pumas b/src/physics/pumas
new file mode 160000
index 0000000000..d2683f278f
--- /dev/null
+++ b/src/physics/pumas
@@ -0,0 +1 @@
+Subproject commit d2683f278fd6de65c326354673124ad3cf34f047
diff --git a/src/physics/pumas-frozen b/src/physics/pumas-frozen
new file mode 160000
index 0000000000..d2683f278f
--- /dev/null
+++ b/src/physics/pumas-frozen
@@ -0,0 +1 @@
+Subproject commit d2683f278fd6de65c326354673124ad3cf34f047
diff --git a/src/physics/rrtmgp/data b/src/physics/rrtmgp/data
new file mode 160000
index 0000000000..aafa333a60
--- /dev/null
+++ b/src/physics/rrtmgp/data
@@ -0,0 +1 @@
+Subproject commit aafa333a60c06fca2fbf219fbd17e7f432b43e3f
diff --git a/src/physics/rrtmgp/ext b/src/physics/rrtmgp/ext
new file mode 160000
index 0000000000..41c5fcd950
--- /dev/null
+++ b/src/physics/rrtmgp/ext
@@ -0,0 +1 @@
+Subproject commit 41c5fcd950fed09b8afe186dede266824eca7fd3

From aff830f7dfec1956a90b594460eb59ae026d5534 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 07:49:30 -0600
Subject: [PATCH 133/161] update externals, waiting for clm tag

---
 ccs_config                          | 2 +-
 chem_proc                           | 2 +-
 components/cdeps                    | 2 +-
 components/mizuRoute                | 2 +-
 components/mosart                   | 2 +-
 libraries/mct                       | 2 +-
 libraries/parallelio                | 2 +-
 src/chemistry/geoschem/geoschem_src | 2 +-
 src/dynamics/mpas/dycore            | 2 +-
 src/hemco                           | 2 +-
 src/physics/carma/base              | 2 +-
 src/physics/clubb                   | 2 +-
 src/physics/cosp2/src               | 2 +-
 src/physics/pumas                   | 2 +-
 src/physics/pumas-frozen            | 2 +-
 src/physics/rrtmgp/data             | 2 +-
 src/physics/rrtmgp/ext              | 2 +-
 17 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/ccs_config b/ccs_config
index f90e10502c..2ff978f92a 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit f90e10502c7246c2b45e373b7dd5e0da6cba0828
+Subproject commit 2ff978f92a5ac9a6ab243e5c14d06a7e2d2f5799
diff --git a/chem_proc b/chem_proc
index 944f506033..ed4ba1b27e 160000
--- a/chem_proc
+++ b/chem_proc
@@ -1 +1 @@
-Subproject commit 944f506033d88a5dd1ee4556a932d2c90023cbfc
+Subproject commit ed4ba1b27e40c8d5af6657ec49a3e3cc8e6f8b5f
diff --git a/components/cdeps b/components/cdeps
index 7a522c828c..7476950699 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 7a522c828c32dc35777992653f281ec525509c4a
+Subproject commit 7476950699909813d1938a34bd8d71bf5bfbf1e9
diff --git a/components/mizuRoute b/components/mizuRoute
index 0a62ee6185..81c720c7ee 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit 0a62ee6185bdc9b99cd88ed5f15ea850602c43a2
+Subproject commit 81c720c7ee51f9c69f2934f696078c42f4493565
diff --git a/components/mosart b/components/mosart
index 1c22a8c547..8c682b1b7f 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit 1c22a8c5478b714cf5b7c54b3e5cf7bad09fd9b2
+Subproject commit 8c682b1b7f15d146816de302e0d359da3e957056
diff --git a/libraries/mct b/libraries/mct
index e36024c5dd..82b0071e69 160000
--- a/libraries/mct
+++ b/libraries/mct
@@ -1 +1 @@
-Subproject commit e36024c5ddf482625ae6bd9474eff7d8f393f87c
+Subproject commit 82b0071e69d14330b75d23b0bc68543ebea9aadc
diff --git a/libraries/parallelio b/libraries/parallelio
index 6539ef05ae..f52ade0756 160000
--- a/libraries/parallelio
+++ b/libraries/parallelio
@@ -1 +1 @@
-Subproject commit 6539ef05ae7584ec570a56fdab9f7dfb336c2b80
+Subproject commit f52ade075619b32fa141993b5665b0fe099befc2
diff --git a/src/chemistry/geoschem/geoschem_src b/src/chemistry/geoschem/geoschem_src
index 20e2402baf..28345ee76e 160000
--- a/src/chemistry/geoschem/geoschem_src
+++ b/src/chemistry/geoschem/geoschem_src
@@ -1 +1 @@
-Subproject commit 20e2402baf56c682cc04af74adb139efdb6ca000
+Subproject commit 28345ee76e5631d6d14869a36dc73e9dd6e0ce1e
diff --git a/src/dynamics/mpas/dycore b/src/dynamics/mpas/dycore
index f084b36f8a..b8c33daa4b 160000
--- a/src/dynamics/mpas/dycore
+++ b/src/dynamics/mpas/dycore
@@ -1 +1 @@
-Subproject commit f084b36f8ac82eb1e76c426d3572339c36523c77
+Subproject commit b8c33daa4b124f116b0ba1b1386968c4c15b42e4
diff --git a/src/hemco b/src/hemco
index 3bd9df0970..83127485c1 160000
--- a/src/hemco
+++ b/src/hemco
@@ -1 +1 @@
-Subproject commit 3bd9df097069ff0158a1d104483c445b69f1426d
+Subproject commit 83127485c149846ba79d5472ae131acd7bda0544
diff --git a/src/physics/carma/base b/src/physics/carma/base
index 2123b52f97..bf165cd84e 160000
--- a/src/physics/carma/base
+++ b/src/physics/carma/base
@@ -1 +1 @@
-Subproject commit 2123b52f97daaeb546753cbbef56c6f1b70ba608
+Subproject commit bf165cd84ef94087d9a5669a5ad47838ab24c0ef
diff --git a/src/physics/clubb b/src/physics/clubb
index a7eaa45389..50cee042e5 160000
--- a/src/physics/clubb
+++ b/src/physics/clubb
@@ -1 +1 @@
-Subproject commit a7eaa4538926587250da0bd37653f5cf70aad174
+Subproject commit 50cee042e588fefd3fe58c2a1d638affec8c0389
diff --git a/src/physics/cosp2/src b/src/physics/cosp2/src
index 241f1b7f4f..34d8eef3d2 160000
--- a/src/physics/cosp2/src
+++ b/src/physics/cosp2/src
@@ -1 +1 @@
-Subproject commit 241f1b7f4f64dbabe8d1c042ce27466a0b6972ee
+Subproject commit 34d8eef3d231a87c0f73e565f6b5d548876b294a
diff --git a/src/physics/pumas b/src/physics/pumas
index d2683f278f..84f27d8042 160000
--- a/src/physics/pumas
+++ b/src/physics/pumas
@@ -1 +1 @@
-Subproject commit d2683f278fd6de65c326354673124ad3cf34f047
+Subproject commit 84f27d804207e79e344e8deec98b471207f9b1f0
diff --git a/src/physics/pumas-frozen b/src/physics/pumas-frozen
index d2683f278f..be3cad3a12 160000
--- a/src/physics/pumas-frozen
+++ b/src/physics/pumas-frozen
@@ -1 +1 @@
-Subproject commit d2683f278fd6de65c326354673124ad3cf34f047
+Subproject commit be3cad3a12d25918f5016b509b15057f84aab608
diff --git a/src/physics/rrtmgp/data b/src/physics/rrtmgp/data
index aafa333a60..df02975ab9 160000
--- a/src/physics/rrtmgp/data
+++ b/src/physics/rrtmgp/data
@@ -1 +1 @@
-Subproject commit aafa333a60c06fca2fbf219fbd17e7f432b43e3f
+Subproject commit df02975ab93165b34a59f0d04b4ae6148fe5127c
diff --git a/src/physics/rrtmgp/ext b/src/physics/rrtmgp/ext
index 41c5fcd950..4d8c5df4c6 160000
--- a/src/physics/rrtmgp/ext
+++ b/src/physics/rrtmgp/ext
@@ -1 +1 @@
-Subproject commit 41c5fcd950fed09b8afe186dede266824eca7fd3
+Subproject commit 4d8c5df4c63434aaab854afd1b02f5986d41dfb3

From dbbb17ffd56271971f3f85ad7728b18c6d202c06 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 07:51:15 -0600
Subject: [PATCH 134/161] remove manage externals

---
 Externals.cfg                                 |  118 -
 Externals_CAM.cfg                             |  105 -
 manage_externals/.dir_locals.el               |   12 -
 manage_externals/.github/ISSUE_TEMPLATE.md    |    6 -
 .../.github/PULL_REQUEST_TEMPLATE.md          |   17 -
 .../.github/workflows/bumpversion.yml         |   19 -
 manage_externals/.github/workflows/tests.yml  |   30 -
 manage_externals/.gitignore                   |   17 -
 manage_externals/.travis.yml                  |   18 -
 manage_externals/LICENSE.txt                  |   34 -
 manage_externals/README.md                    |  231 --
 manage_externals/README_FIRST                 |   54 -
 manage_externals/checkout_externals           |   36 -
 manage_externals/manic/__init__.py            |    9 -
 manage_externals/manic/checkout.py            |  446 ----
 .../manic/externals_description.py            |  830 --------
 manage_externals/manic/externals_status.py    |  164 --
 manage_externals/manic/global_constants.py    |   18 -
 manage_externals/manic/repository.py          |   98 -
 manage_externals/manic/repository_factory.py  |   30 -
 manage_externals/manic/repository_git.py      |  849 --------
 manage_externals/manic/repository_svn.py      |  288 ---
 manage_externals/manic/sourcetree.py          |  425 ----
 manage_externals/manic/utils.py               |  330 ---
 manage_externals/test/.coveragerc             |    7 -
 manage_externals/test/.gitignore              |    7 -
 manage_externals/test/.pylint.rc              |  426 ----
 manage_externals/test/Makefile                |  124 --
 manage_externals/test/README.md               |   53 -
 manage_externals/test/doc/.gitignore          |    2 -
 manage_externals/test/doc/Makefile            |   20 -
 manage_externals/test/doc/conf.py             |  172 --
 manage_externals/test/doc/develop.rst         |  202 --
 manage_externals/test/doc/index.rst           |   22 -
 manage_externals/test/doc/testing.rst         |  123 --
 manage_externals/test/repos/README.md         |   33 -
 .../test/repos/container.git/HEAD             |    1 -
 .../test/repos/container.git/config           |    6 -
 .../test/repos/container.git/description      |    1 -
 .../test/repos/container.git/info/exclude     |    6 -
 .../41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801 |  Bin 133 -> 0 bytes
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 .../repos/container.git/refs/heads/master     |    1 -
 manage_externals/test/repos/error/readme.txt  |    3 -
 .../test/repos/mixed-cont-ext.git/HEAD        |    1 -
 .../test/repos/mixed-cont-ext.git/config      |    6 -
 .../test/repos/mixed-cont-ext.git/description |    1 -
 .../repos/mixed-cont-ext.git/info/exclude     |    6 -
 .../00/437ac2000d5f06fb8a572a01a5bbdae98b17cb |  Bin 172 -> 0 bytes
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 .../test/repos/simple-ext.git/refs/tags/tag1  |    1 -
 .../test/repos/simple-ext.git/refs/tags/tag2  |    1 -
 manage_externals/test/requirements.txt        |    5 -
 manage_externals/test/test_sys_checkout.py    | 1896 -----------------
 .../test/test_sys_repository_git.py           |  238 ---
 .../test/test_unit_externals_description.py   |  478 -----
 .../test/test_unit_externals_status.py        |  299 ---
 manage_externals/test/test_unit_repository.py |  208 --
 .../test/test_unit_repository_git.py          |  811 -------
 .../test/test_unit_repository_svn.py          |  501 -----
 manage_externals/test/test_unit_utils.py      |  350 ---
 138 files changed, 10270 deletions(-)
 delete mode 100644 Externals.cfg
 delete mode 100644 Externals_CAM.cfg
 delete mode 100644 manage_externals/.dir_locals.el
 delete mode 100644 manage_externals/.github/ISSUE_TEMPLATE.md
 delete mode 100644 manage_externals/.github/PULL_REQUEST_TEMPLATE.md
 delete mode 100644 manage_externals/.github/workflows/bumpversion.yml
 delete mode 100644 manage_externals/.github/workflows/tests.yml
 delete mode 100644 manage_externals/.gitignore
 delete mode 100644 manage_externals/.travis.yml
 delete mode 100644 manage_externals/LICENSE.txt
 delete mode 100644 manage_externals/README.md
 delete mode 100644 manage_externals/README_FIRST
 delete mode 100755 manage_externals/checkout_externals
 delete mode 100644 manage_externals/manic/__init__.py
 delete mode 100755 manage_externals/manic/checkout.py
 delete mode 100644 manage_externals/manic/externals_description.py
 delete mode 100644 manage_externals/manic/externals_status.py
 delete mode 100644 manage_externals/manic/global_constants.py
 delete mode 100644 manage_externals/manic/repository.py
 delete mode 100644 manage_externals/manic/repository_factory.py
 delete mode 100644 manage_externals/manic/repository_git.py
 delete mode 100644 manage_externals/manic/repository_svn.py
 delete mode 100644 manage_externals/manic/sourcetree.py
 delete mode 100644 manage_externals/manic/utils.py
 delete mode 100644 manage_externals/test/.coveragerc
 delete mode 100644 manage_externals/test/.gitignore
 delete mode 100644 manage_externals/test/.pylint.rc
 delete mode 100644 manage_externals/test/Makefile
 delete mode 100644 manage_externals/test/README.md
 delete mode 100644 manage_externals/test/doc/.gitignore
 delete mode 100644 manage_externals/test/doc/Makefile
 delete mode 100644 manage_externals/test/doc/conf.py
 delete mode 100644 manage_externals/test/doc/develop.rst
 delete mode 100644 manage_externals/test/doc/index.rst
 delete mode 100644 manage_externals/test/doc/testing.rst
 delete mode 100644 manage_externals/test/repos/README.md
 delete mode 100644 manage_externals/test/repos/container.git/HEAD
 delete mode 100644 manage_externals/test/repos/container.git/config
 delete mode 100644 manage_externals/test/repos/container.git/description
 delete mode 100644 manage_externals/test/repos/container.git/info/exclude
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 delete mode 100644 manage_externals/test/repos/mixed-cont-ext.git/config
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diff --git a/Externals.cfg b/Externals.cfg
deleted file mode 100644
index ad6907e697..0000000000
--- a/Externals.cfg
+++ /dev/null
@@ -1,118 +0,0 @@
-[ccs_config]
-tag = ccs_config_cesm0.0.106
-protocol = git
-repo_url = https://github.com/ESMCI/ccs_config_cesm
-local_path = ccs_config
-required = True
-
-[cice5]
-tag = cice5_20220204
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_CICE5
-local_path = components/cice5
-required = True
-
-[cice6]
-tag = cesm_cice6_5_0_7
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_CICE
-local_path = components/cice
-externals = Externals.cfg
-required = True
-
-[cmeps]
-tag = cmeps0.14.60
-protocol = git
-repo_url = https://github.com/ESCOMP/CMEPS.git
-local_path = components/cmeps
-required = True
-
-[cdeps]
-tag = cdeps1.0.33
-protocol = git
-repo_url = https://github.com/ESCOMP/CDEPS.git
-local_path = components/cdeps
-externals =  Externals_CDEPS.cfg
-required = True
-
-[cpl7]
-tag = cpl77.0.8
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
-local_path = components/cpl7
-required = True
-
-[share]
-tag = share1.0.18
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_share
-local_path = share
-required = True
-
-[mct]
-tag = MCT_2.11.0
-protocol = git
-repo_url = https://github.com/MCSclimate/MCT
-local_path = libraries/mct
-required = True
-
-[parallelio]
-tag = pio2_6_2
-protocol = git
-repo_url = https://github.com/NCAR/ParallelIO
-local_path = libraries/parallelio
-required = True
-
-[cime]
-tag = cime6.0.236_httpsbranch01
-protocol = git
-repo_url = https://github.com/ESMCI/cime
-local_path = cime
-required = True
-
-[cism]
-tag = cismwrap_2_1_100
-protocol = git
-repo_url = https://github.com/ESCOMP/CISM-wrapper
-local_path = components/cism
-externals = Externals_CISM.cfg
-required = True
-
-[clm]
-tag = ctsm5.2.005
-protocol = git
-repo_url = https://github.com/ESCOMP/CTSM
-local_path = components/clm
-externals = Externals_CLM.cfg
-required = True
-
-[fms]
-tag = fi_230818
-protocol = git
-repo_url = https://github.com/ESCOMP/FMS_interface
-local_path = libraries/FMS
-externals = Externals_FMS.cfg
-required = True
-
-[mosart]
-tag = mosart1_0_49
-protocol = git
-repo_url = https://github.com/ESCOMP/MOSART
-local_path = components/mosart
-required = True
-
-[rtm]
-tag = rtm1_0_79
-protocol = git
-repo_url = https://github.com/ESCOMP/RTM
-local_path = components/rtm
-required = True
-
-[cam]
-local_path = .
-protocol = externals_only
-externals = Externals_CAM.cfg
-required = True
-
-[externals_description]
-schema_version = 1.0.0
diff --git a/Externals_CAM.cfg b/Externals_CAM.cfg
deleted file mode 100644
index a1c76e7db5..0000000000
--- a/Externals_CAM.cfg
+++ /dev/null
@@ -1,105 +0,0 @@
-[chem_proc]
-local_path = chem_proc
-protocol = git
-repo_url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
-tag = chem_proc5_0_05
-required = True
-
-[carma]
-local_path = src/physics/carma/base
-protocol = git
-repo_url = https://github.com/ESCOMP/CARMA_base.git
-tag = carma4_01
-required = True
-
-[cosp2]
-local_path = src/physics/cosp2/src
-protocol = git
-repo_url = https://github.com/CFMIP/COSPv2.0
-sparse = ../.cosp_sparse_checkout
-tag = v2.1.4cesm
-required = True
-
-[clubb]
-local_path = src/physics/clubb
-protocol = git
-repo_url = https://github.com/larson-group/clubb_release
-sparse = ../.clubb_sparse_checkout
-tag = clubb_4ncar_20231115_5406350
-required = True
-
-[pumas]
-local_path = src/physics/pumas
-protocol = git
-repo_url = https://github.com/ESCOMP/PUMAS
-tag = pumas_cam-release_v1.36
-required = True
-
-[pumas-frozen]
-local_path = src/physics/pumas-frozen
-protocol = git
-repo_url = https://github.com/ESCOMP/PUMAS
-tag = pumas_cam-release_v1.17_rename
-required = True
-
-[ali_arms]
-local_path = src/physics/ali_arms
-protocol = git
-repo_url = https://github.com/ESCOMP/ALI-ARMS
-tag = ALI_ARMS_v1.0.1
-required = True
-
-[atmos_phys]
-tag = atmos_phys0_02_006
-protocol = git
-repo_url = https://github.com/ESCOMP/atmospheric_physics
-required = True
-local_path = src/atmos_phys
-
-[fv3]
-tag = fv3int_022824
-protocol = git
-repo_url = https://github.com/ESCOMP/CAM_FV3_interface.git
-local_path = src/dynamics/fv3
-externals = Externals_FV3.cfg
-required = True
-
-[mpas]
-local_path = src/dynamics/mpas/dycore
-protocol = git
-repo_url = https://github.com/MPAS-Dev/MPAS-Model.git
-sparse = ../.mpas_sparse_checkout
-hash = b8c33daa
-required = True
-
-[geoschem]
-local_path = src/chemistry/geoschem/geoschem_src
-protocol = git
-repo_url = https://github.com/geoschem/geos-chem.git
-tag = 14.1.2
-required = True
-
-[hemco]
-local_path = src/hemco
-tag = hemco-cesm1_2_1_hemco3_6_3_cesm
-protocol = git
-repo_url = https://github.com/ESCOMP/HEMCO_CESM.git
-required = True
-externals = Externals_HCO.cfg
-
-[rte-rrtmgp]
-local_path = src/physics/rrtmgp/ext
-protocol = git
-repo_url = https://github.com/earth-system-radiation/rte-rrtmgp.git
-tag = v1.7
-required = True
-
-[rrtmgp-data]
-local_path = src/physics/rrtmgp/data
-protocol = git
-repo_url = https://github.com/earth-system-radiation/rrtmgp-data.git
-tag = v1.8
-required = True
-
-[externals_description]
-schema_version = 1.0.0
diff --git a/manage_externals/.dir_locals.el b/manage_externals/.dir_locals.el
deleted file mode 100644
index a370490e92..0000000000
--- a/manage_externals/.dir_locals.el
+++ /dev/null
@@ -1,12 +0,0 @@
-; -*- mode: Lisp -*-
-
-((python-mode
-  . (
-     ;; fill the paragraph to 80 columns when using M-q
-     (fill-column . 80)
-
-     ;; Use 4 spaces to indent in Python
-     (python-indent-offset . 4)
-     (indent-tabs-mode . nil)
-     )))
-
diff --git a/manage_externals/.github/ISSUE_TEMPLATE.md b/manage_externals/.github/ISSUE_TEMPLATE.md
deleted file mode 100644
index 8ecb2ae64b..0000000000
--- a/manage_externals/.github/ISSUE_TEMPLATE.md
+++ /dev/null
@@ -1,6 +0,0 @@
-### Summary of Issue:
-### Expected behavior and actual behavior:
-### Steps to reproduce the problem (should include model description file(s) or link to publi c repository):
-### What is the changeset ID of the code, and the machine you are using:
-### have you modified the code? If so, it must be committed and available for testing:
-### Screen output or log file showing the error message and context:
diff --git a/manage_externals/.github/PULL_REQUEST_TEMPLATE.md b/manage_externals/.github/PULL_REQUEST_TEMPLATE.md
deleted file mode 100644
index b68b1fb5e2..0000000000
--- a/manage_externals/.github/PULL_REQUEST_TEMPLATE.md
+++ /dev/null
@@ -1,17 +0,0 @@
-[ 50 character, one line summary ]
-
-[ Description of the changes in this commit. It should be enough
-  information for someone not following this development to understand. 
-  Lines should be wrapped at about 72 characters. ]
-
-User interface changes?: [ No/Yes ]
-[ If yes, describe what changed, and steps taken to ensure backward compatibilty ]
-
-Fixes: [Github issue #s] And brief description of each issue.
-
-Testing:
-  test removed:
-  unit tests:
-  system tests:
-  manual testing:
-
diff --git a/manage_externals/.github/workflows/bumpversion.yml b/manage_externals/.github/workflows/bumpversion.yml
deleted file mode 100644
index f4dc9b7ca5..0000000000
--- a/manage_externals/.github/workflows/bumpversion.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-name: Bump version
-on:
-  push:
-    branches:
-      - main
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Bump version and push tag
-        id: tag_version
-        uses: mathieudutour/github-tag-action@v5.5
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          create_annotated_tag: true
-          default_bump: patch
-          dry_run: false
-          tag_prefix: manic-
diff --git a/manage_externals/.github/workflows/tests.yml b/manage_externals/.github/workflows/tests.yml
deleted file mode 100644
index dd75b91b49..0000000000
--- a/manage_externals/.github/workflows/tests.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# This is a workflow to compile the cmeps source without cime
-name: Test Manic
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  test-manic:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Test Manic
-        run: |
-          pushd test
-          git config --global user.email "devnull@example.com"
-          git config --global user.name "GITHUB tester"
-          git config --global protocol.file.allow always
-          make utest
-          make stest
-          popd
-
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
diff --git a/manage_externals/.gitignore b/manage_externals/.gitignore
deleted file mode 100644
index a71ac0cd75..0000000000
--- a/manage_externals/.gitignore
+++ /dev/null
@@ -1,17 +0,0 @@
-# directories that are checked out by the tool
-cime/
-cime_config/
-components/
-
-# generated local files
-*.log
-
-# editor files
-*~
-*.bak
-
-# generated python files
-*.pyc
-
-# test tmp file
-test/tmp
diff --git a/manage_externals/.travis.yml b/manage_externals/.travis.yml
deleted file mode 100644
index d9b24c584d..0000000000
--- a/manage_externals/.travis.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-language: python
-os: linux
-python:
-  - "3.4"
-  - "3.5"
-  - "3.6"
-  - "3.7"
-  - "3.8"
-install:
-  - pip install -r test/requirements.txt
-before_script:
-  - git --version
-script:
-  - cd test; make test
-  - cd test; make lint
-after_success:
-  - cd test; make coverage
-  - cd test; coveralls
diff --git a/manage_externals/LICENSE.txt b/manage_externals/LICENSE.txt
deleted file mode 100644
index 665ee03fbc..0000000000
--- a/manage_externals/LICENSE.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-Copyright (c) 2017-2018, University Corporation for Atmospheric Research (UCAR)
-All rights reserved.
-
-Developed by: 
-              University Corporation for Atmospheric Research - National Center for Atmospheric Research
-              https://www2.cesm.ucar.edu/working-groups/sewg
-
-Permission is hereby granted, free of charge, to any person obtaining 
-a copy of this software and associated documentation files (the "Software"), 
-to deal with the Software without restriction, including without limitation 
-the rights to use, copy, modify, merge, publish, distribute, sublicense, 
-and/or sell copies of the Software, and to permit persons to whom 
-the Software is furnished to do so, subject to the following conditions:
-
-    - Redistributions of source code must retain the above copyright notice, 
-      this list of conditions and the following disclaimers.
-    - Redistributions in binary form must reproduce the above copyright notice, 
-      this list of conditions and the following disclaimers in the documentation 
-      and/or other materials provided with the distribution.
-    - Neither the names of [Name of Development Group, UCAR], 
-      nor the names of its contributors may be used to endorse or promote 
-      products derived from this Software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-POSSIBILITY OF SUCH DAMAGE.		
diff --git a/manage_externals/README.md b/manage_externals/README.md
deleted file mode 100644
index 9475301b5d..0000000000
--- a/manage_externals/README.md
+++ /dev/null
@@ -1,231 +0,0 @@
--- AUTOMATICALLY GENERATED FILE. DO NOT EDIT --
-
-[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master)
-```
-usage: checkout_externals [-h] [-e [EXTERNALS]] [-o] [-S] [-v] [--backtrace]
-                          [-d] [--no-logging]
-
-checkout_externals manages checking out groups of externals from revision
-control based on a externals description file. By default only the
-required externals are checkout out.
-
-Operations performed by manage_externals utilities are explicit and
-data driven. checkout_externals will always make the working copy *exactly*
-match what is in the externals file when modifying the working copy of
-a repository.
-
-If checkout_externals isn't doing what you expected, double check the contents
-of the externals description file.
-
-Running checkout_externals without the '--status' option will always attempt to
-synchronize the working copy to exactly match the externals description.
-
-optional arguments:
-  -h, --help            show this help message and exit
-  -e [EXTERNALS], --externals [EXTERNALS]
-                        The externals description filename. Default:
-                        Externals.cfg.
-  -o, --optional        By default only the required externals are checked
-                        out. This flag will also checkout the optional
-                        externals.
-  -S, --status          Output status of the repositories managed by
-                        checkout_externals. By default only summary
-                        information is provided. Use verbose output to see
-                        details.
-  -v, --verbose         Output additional information to the screen and log
-                        file. This flag can be used up to two times,
-                        increasing the verbosity level each time.
-  --backtrace           DEVELOPER: show exception backtraces as extra
-                        debugging output
-  -d, --debug           DEVELOPER: output additional debugging information to
-                        the screen and log file.
-  --no-logging          DEVELOPER: disable logging.
-
-```
-NOTE: checkout_externals *MUST* be run from the root of the source tree it
-is managing. For example, if you cloned a repository with:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-Then the root of the source tree is /path/to/some-project-dev. If you
-obtained a sub-project via a checkout of another project:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-and you need to checkout the sub-project externals, then the root of the
-source tree is /path/to/some-project-dev. Do *NOT* run checkout_externals
-from within /path/to/some-project-dev/sub-project
-
-The root of the source tree will be referred to as `${SRC_ROOT}` below.
-
-# Supported workflows
-
-  * Checkout all required components from the default externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals
-
-  * To update all required components to the current values in the
-    externals description file, re-run checkout_externals:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals
-
-    If there are *any* modifications to *any* working copy according
-    to the git or svn 'status' command, checkout_externals
-    will not update any external repositories. Modifications
-    include: modified files, added files, removed files, or missing
-    files.
-
-    To avoid this safety check, edit the externals description file
-    and comment out the modified external block.
-
-  * Checkout all required components from a user specified externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals --externals my-externals.cfg
-
-  * Status summary of the repositories managed by checkout_externals:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals --status
-
-              ./cime
-          s   ./components/cism
-              ./components/mosart
-          e-o ./components/rtm
-           M  ./src/fates
-          e-o ./tools/PTCLM
-
-    where:
-      * column one indicates the status of the repository in relation
-        to the externals description file.
-      * column two indicates whether the working copy has modified files.
-      * column three shows how the repository is managed, optional or required
-
-    Column one will be one of these values:
-      * s : out-of-sync : repository is checked out at a different commit
-            compared with the externals description
-      * e : empty : directory does not exist - checkout_externals has not been run
-      * ? : unknown : directory exists but .git or .svn directories are missing
-
-    Column two will be one of these values:
-      * M : Modified : modified, added, deleted or missing files
-      *   : blank / space : clean
-      * - : dash : no meaningful state, for empty repositories
-
-    Column three will be one of these values:
-      * o : optional : optionally repository
-      *   : blank / space : required repository
-
-  * Detailed git or svn status of the repositories managed by checkout_externals:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals --status --verbose
-
-# Externals description file
-
-  The externals description contains a list of the external
-  repositories that are used and their version control locations. The
-  file format is the standard ini/cfg configuration file format. Each
-  external is defined by a section containing the component name in
-  square brackets:
-
-  * name (string) : component name, e.g. [cime], [cism], etc.
-
-  Each section has the following keyword-value pairs:
-
-  * required (boolean) : whether the component is a required checkout,
-    'true' or 'false'.
-
-  * local_path (string) : component path *relative* to where
-    checkout_externals is called.
-
-  * protoctol (string) : version control protocol that is used to
-    manage the component.  Valid values are 'git', 'svn',
-    'externals_only'.
-
-    Switching an external between different protocols is not
-    supported, e.g. from svn to git. To switch protocols, you need to
-    manually move the old working copy to a new location.
-
-    Note: 'externals_only' will only process the external's own
-    external description file without trying to manage a repository
-    for the component. This is used for retreiving externals for
-    standalone components like cam and clm. If the source root of the
-    externals_only component is the same as the main source root, then
-    the local path must be set to '.', the unix current working
-    directory, e. g. 'local_path = .'
-
-  * repo_url (string) : URL for the repository location, examples:
-    * https://svn-ccsm-models.cgd.ucar.edu/glc
-    * git@github.com:esmci/cime.git
-    * /path/to/local/repository
-    * .
-
-    NOTE: To operate on only the local clone and and ignore remote
-    repositories, set the url to '.' (the unix current path),
-    i.e. 'repo_url = .' . This can be used to checkout a local branch
-    instead of the upstream branch.
-
-    If a repo url is determined to be a local path (not a network url)
-    then user expansion, e.g. ~/, and environment variable expansion,
-    e.g. $HOME or $REPO_ROOT, will be performed.
-
-    Relative paths are difficult to get correct, especially for mixed
-    use repos. It is advised that local paths expand to absolute paths.
-    If relative paths are used, they should be relative to one level
-    above local_path. If local path is 'src/foo', the the relative url
-    should be relative to 'src'.
-
-  * tag (string) : tag to checkout
-
-  * hash (string) : the git hash to checkout. Only applies to git
-    repositories.
-
-  * branch (string) : branch to checkout from the specified
-    repository. Specifying a branch on a remote repository means that
-    checkout_externals will checkout the version of the branch in the remote,
-    not the the version in the local repository (if it exists).
-
-    Note: one and only one of tag, branch hash must be supplied.
-
-  * externals (string) : used to make manage_externals aware of
-    sub-externals required by an external. This is a relative path to
-    the external's root directory. For example, the main externals
-    description has an external checkout out at 'src/useful_library'.
-    useful_library requires additional externals to be complete.
-    Those additional externals are managed from the source root by the
-    externals description file pointed 'useful_library/sub-xternals.cfg',
-    Then the main 'externals' field in the top level repo should point to
-    'sub-externals.cfg'.
-    Note that by default, `checkout_externals` will clone an external's
-    submodules. As a special case, the entry, `externals = None`, will
-    prevent this behavior. For more control over which externals are
-    checked out, create an externals file (and see the `from_submodule`
-    configuration entry below).
-
-  * from_submodule (True / False) : used to pull the repo_url, local_path,
-    and hash properties for this external from the .gitmodules file in
-    this repository. Note that the section name (the entry in square
-    brackets) must match the name in the .gitmodules file.
-    If from_submodule is True, the protocol must be git and no repo_url,
-    local_path, hash, branch, or tag entries are allowed.
-    Default: False
-
-  * sparse (string) : used to control a sparse checkout. This optional
-    entry should point to a filename (path relative to local_path) that
-    contains instructions on which repository paths to include (or
-    exclude) from the working tree.
-    See the "SPARSE CHECKOUT" section of https://git-scm.com/docs/git-read-tree
-    Default: sparse checkout is disabled
-
-  * Lines begining with '#' or ';' are comments and will be ignored.
-
-# Obtaining this tool, reporting issues, etc.
-
-  The master repository for manage_externals is
-  https://github.com/ESMCI/manage_externals. Any issues with this tool
-  should be reported there.
diff --git a/manage_externals/README_FIRST b/manage_externals/README_FIRST
deleted file mode 100644
index c8a47d7806..0000000000
--- a/manage_externals/README_FIRST
+++ /dev/null
@@ -1,54 +0,0 @@
-CESM is comprised of a number of different components that are
-developed and managed independently. Each component may have
-additional 'external' dependancies and optional parts that are also
-developed and managed independently.
-
-The checkout_externals.py tool manages retreiving and updating the
-components and their externals so you have a complete set of source
-files for the model.
-
-checkout_externals.py relies on a model description file that
-describes what components are needed, where to find them and where to
-put them in the source tree. The default file is called "CESM.xml"
-regardless of whether you are checking out CESM or a standalone
-component.
-
-checkout_externals requires access to git and svn repositories that
-require authentication. checkout_externals may pass through
-authentication requests, but it will not cache them for you. For the
-best and most robust user experience, you should have svn and git
-working without password authentication. See:
-
-    https://help.github.com/articles/connecting-to-github-with-ssh/
-
-    ?svn ref?
-
-NOTE: checkout_externals.py *MUST* be run from the root of the source
-tree it is managing. For example, if you cloned CLM with:
-
-    $ git clone git@github.com/ncar/clm clm-dev
-
-Then the root of the source tree is /path/to/cesm-dev. If you obtained
-CLM via an svn checkout of CESM and you need to checkout the CLM
-externals, then the root of the source tree for CLM is:
-
-    /path/to/cesm-dev/components/clm
-
-The root of the source tree will be referred to as ${SRC_ROOT} below.
-
-To get started quickly, checkout all required components from the
-default model description file:
-
-    $ cd ${SRC_ROOT}
-    $ ./checkout_cesm/checkout_externals.py
-
-For additional information about using checkout model, please see:
-
-    ${SRC_ROOT}/checkout_cesm/README
-
-or run:
-
-    $ cd ${SRC_ROOT}
-    $ ./checkout_cesm/checkout_externals.py --help
-
-
diff --git a/manage_externals/checkout_externals b/manage_externals/checkout_externals
deleted file mode 100755
index 48bce24010..0000000000
--- a/manage_externals/checkout_externals
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env python3
-
-"""Main driver wrapper around the manic/checkout utility.
-
-Tool to assemble external respositories represented in an externals
-description file.
-
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import sys
-import traceback
-
-import manic
-
-if sys.hexversion < 0x02070000:
-    print(70 * '*')
-    print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0]))
-    print('It appears that you are running python {0}'.format(
-        '.'.join(str(x) for x in sys.version_info[0:3])))
-    print(70 * '*')
-    sys.exit(1)
-
-
-if __name__ == '__main__':
-    ARGS = manic.checkout.commandline_arguments()
-    try:
-        RET_STATUS, _ = manic.checkout.main(ARGS)
-        sys.exit(RET_STATUS)
-    except Exception as error:  # pylint: disable=broad-except
-        manic.printlog(str(error))
-        if ARGS.backtrace:
-            traceback.print_exc()
-        sys.exit(1)
diff --git a/manage_externals/manic/__init__.py b/manage_externals/manic/__init__.py
deleted file mode 100644
index 11badedd3b..0000000000
--- a/manage_externals/manic/__init__.py
+++ /dev/null
@@ -1,9 +0,0 @@
-"""Public API for the manage_externals library
-"""
-
-from manic import checkout
-from manic.utils import printlog
-
-__all__ = [
-    'checkout', 'printlog',
-]
diff --git a/manage_externals/manic/checkout.py b/manage_externals/manic/checkout.py
deleted file mode 100755
index 3f5537adce..0000000000
--- a/manage_externals/manic/checkout.py
+++ /dev/null
@@ -1,446 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-Tool to assemble repositories represented in a model-description file.
-
-If loaded as a module (e.g., in a component's buildcpp), it can be used
-to check the validity of existing subdirectories and load missing sources.
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import argparse
-import logging
-import os
-import os.path
-import sys
-
-from manic.externals_description import create_externals_description
-from manic.externals_description import read_externals_description_file
-from manic.externals_status import check_safe_to_update_repos
-from manic.sourcetree import SourceTree
-from manic.utils import printlog, fatal_error
-from manic.global_constants import VERSION_SEPERATOR, LOG_FILE_NAME
-
-if sys.hexversion < 0x02070000:
-    print(70 * '*')
-    print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0]))
-    print('It appears that you are running python {0}'.format(
-        VERSION_SEPERATOR.join(str(x) for x in sys.version_info[0:3])))
-    print(70 * '*')
-    sys.exit(1)
-
-
-# ---------------------------------------------------------------------
-#
-# User input
-#
-# ---------------------------------------------------------------------
-def commandline_arguments(args=None):
-    """Process the command line arguments
-
-    Params: args - optional args. Should only be used during systems
-    testing.
-
-    Returns: processed command line arguments
-    """
-    description = '''
-
-%(prog)s manages checking out groups of externals from revision
-control based on an externals description file. By default only the
-required externals are checkout out.
-
-Running %(prog)s without the '--status' option will always attempt to
-synchronize the working copy to exactly match the externals description.
-'''
-
-    epilog = '''
-```
-NOTE: %(prog)s *MUST* be run from the root of the source tree it
-is managing. For example, if you cloned a repository with:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-Then the root of the source tree is /path/to/some-project-dev. If you
-obtained a sub-project via a checkout of another project:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-and you need to checkout the sub-project externals, then the root of the
-source tree remains /path/to/some-project-dev. Do *NOT* run %(prog)s
-from within /path/to/some-project-dev/sub-project
-
-The root of the source tree will be referred to as `${SRC_ROOT}` below.
-
-
-# Supported workflows
-
-  * Checkout all required components from the default externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s
-
-  * To update all required components to the current values in the
-    externals description file, re-run %(prog)s:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s
-
-    If there are *any* modifications to *any* working copy according
-    to the git or svn 'status' command, %(prog)s
-    will not update any external repositories. Modifications
-    include: modified files, added files, removed files, or missing
-    files.
-
-    To avoid this safety check, edit the externals description file
-    and comment out the modified external block.
-
-  * Checkout all required components from a user specified externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s --externals my-externals.cfg
-
-  * Status summary of the repositories managed by %(prog)s:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s --status
-
-              ./cime
-          s   ./components/cism
-              ./components/mosart
-          e-o ./components/rtm
-           M  ./src/fates
-          e-o ./tools/PTCLM
-
-
-    where:
-      * column one indicates the status of the repository in relation
-        to the externals description file.
-      * column two indicates whether the working copy has modified files.
-      * column three shows how the repository is managed, optional or required
-
-    Column one will be one of these values:
-      * s : out-of-sync : repository is checked out at a different commit
-            compared with the externals description
-      * e : empty : directory does not exist - %(prog)s has not been run
-      * ? : unknown : directory exists but .git or .svn directories are missing
-
-    Column two will be one of these values:
-      * M : Modified : modified, added, deleted or missing files
-      *   : blank / space : clean
-      * - : dash : no meaningful state, for empty repositories
-
-    Column three will be one of these values:
-      * o : optional : optionally repository
-      *   : blank / space : required repository
-
-  * Detailed git or svn status of the repositories managed by %(prog)s:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s --status --verbose
-
-# Externals description file
-
-  The externals description contains a list of the external
-  repositories that are used and their version control locations. The
-  file format is the standard ini/cfg configuration file format. Each
-  external is defined by a section containing the component name in
-  square brackets:
-
-  * name (string) : component name, e.g. [cime], [cism], etc.
-
-  Each section has the following keyword-value pairs:
-
-  * required (boolean) : whether the component is a required checkout,
-    'true' or 'false'.
-
-  * local_path (string) : component path *relative* to where
-    %(prog)s is called.
-
-  * protoctol (string) : version control protocol that is used to
-    manage the component.  Valid values are 'git', 'svn',
-    'externals_only'.
-
-    Switching an external between different protocols is not
-    supported, e.g. from svn to git. To switch protocols, you need to
-    manually move the old working copy to a new location.
-
-    Note: 'externals_only' will only process the external's own
-    external description file without trying to manage a repository
-    for the component. This is used for retrieving externals for
-    standalone components like cam and ctsm which also serve as
-    sub-components within a larger project. If the source root of the
-    externals_only component is the same as the main source root, then
-    the local path must be set to '.', the unix current working
-    directory, e. g. 'local_path = .'
-
-  * repo_url (string) : URL for the repository location, examples:
-    * https://svn-ccsm-models.cgd.ucar.edu/glc
-    * git@github.com:esmci/cime.git
-    * /path/to/local/repository
-    * .
-
-    NOTE: To operate on only the local clone and and ignore remote
-    repositories, set the url to '.' (the unix current path),
-    i.e. 'repo_url = .' . This can be used to checkout a local branch
-    instead of the upstream branch.
-
-    If a repo url is determined to be a local path (not a network url)
-    then user expansion, e.g. ~/, and environment variable expansion,
-    e.g. $HOME or $REPO_ROOT, will be performed.
-
-    Relative paths are difficult to get correct, especially for mixed
-    use repos. It is advised that local paths expand to absolute paths.
-    If relative paths are used, they should be relative to one level
-    above local_path. If local path is 'src/foo', the the relative url
-    should be relative to 'src'.
-
-  * tag (string) : tag to checkout
-
-  * hash (string) : the git hash to checkout. Only applies to git
-    repositories.
-
-  * branch (string) : branch to checkout from the specified
-    repository. Specifying a branch on a remote repository means that
-    %(prog)s will checkout the version of the branch in the remote,
-    not the the version in the local repository (if it exists).
-
-    Note: one and only one of tag, branch hash must be supplied.
-
-  * externals (string) : used to make manage_externals aware of
-    sub-externals required by an external. This is a relative path to
-    the external's root directory. For example, if LIBX is often used
-    as a sub-external, it might have an externals file (for its
-    externals) called Externals_LIBX.cfg. To use libx as a standalone
-    checkout, it would have another file, Externals.cfg with the
-    following entry:
-
-    [ libx ]
-    local_path = .
-    protocol = externals_only
-    externals = Externals_LIBX.cfg
-    required = True
-
-    Now, %(prog)s will process Externals.cfg and also process
-    Externals_LIBX.cfg as if it was a sub-external.
-
-    Note that by default, checkout_externals will clone an external's
-    submodules. As a special case, the entry, "externals = None", will
-    prevent this behavior. For more control over which externals are
-    checked out, create an externals file (and see the from_submodule
-    configuration entry below).
-
-  * from_submodule (True / False) : used to pull the repo_url, local_path,
-    and hash properties for this external from the .gitmodules file in
-    this repository. Note that the section name (the entry in square
-    brackets) must match the name in the .gitmodules file.
-    If from_submodule is True, the protocol must be git and no repo_url,
-    local_path, hash, branch, or tag entries are allowed.
-    Default: False
-
-  * sparse (string) : used to control a sparse checkout. This optional
-    entry should point to a filename (path relative to local_path) that
-    contains instructions on which repository paths to include (or
-    exclude) from the working tree.
-    See the "SPARSE CHECKOUT" section of https://git-scm.com/docs/git-read-tree
-    Default: sparse checkout is disabled
-
-  * Lines beginning with '#' or ';' are comments and will be ignored.
-
-# Obtaining this tool, reporting issues, etc.
-
-  The master repository for manage_externals is
-  https://github.com/ESMCI/manage_externals. Any issues with this tool
-  should be reported there.
-
-# Troubleshooting
-
-Operations performed by manage_externals utilities are explicit and
-data driven. %(prog)s will always attempt to make the working copy
-*exactly* match what is in the externals file when modifying the
-working copy of a repository.
-
-If %(prog)s is not doing what you expected, double check the contents
-of the externals description file or examine the output of
-./manage_externals/%(prog)s --status
-
-'''
-
-    parser = argparse.ArgumentParser(
-        description=description, epilog=epilog,
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-
-    #
-    # user options
-    #
-    parser.add_argument("components", nargs="*",
-                        help="Specific component(s) to checkout. By default, "
-                        "all required externals are checked out.")
-
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
-
-    parser.add_argument('-x', '--exclude', nargs='*',
-                        help='Component(s) listed in the externals file which should be ignored.')
-
-    parser.add_argument('-o', '--optional', action='store_true', default=False,
-                        help='By default only the required externals '
-                        'are checked out. This flag will also checkout the '
-                        'optional externals.')
-
-    parser.add_argument('-S', '--status', action='store_true', default=False,
-                        help='Output the status of the repositories managed by '
-                        '%(prog)s. By default only summary information '
-                        'is provided. Use the verbose option to see details.')
-
-    parser.add_argument('-v', '--verbose', action='count', default=0,
-                        help='Output additional information to '
-                        'the screen and log file. This flag can be '
-                        'used up to two times, increasing the '
-                        'verbosity level each time.')
-
-    parser.add_argument('--svn-ignore-ancestry', action='store_true', default=False,
-                        help='By default, subversion will abort if a component is '
-                        'already checked out and there is no common ancestry with '
-                        'the new URL. This flag passes the "--ignore-ancestry" flag '
-                        'to the svn switch call. (This is not recommended unless '
-                        'you are sure about what you are doing.)')
-
-    #
-    # developer options
-    #
-    parser.add_argument('--backtrace', action='store_true',
-                        help='DEVELOPER: show exception backtraces as extra '
-                        'debugging output')
-
-    parser.add_argument('-d', '--debug', action='store_true', default=False,
-                        help='DEVELOPER: output additional debugging '
-                        'information to the screen and log file.')
-
-    logging_group = parser.add_mutually_exclusive_group()
-
-    logging_group.add_argument('--logging', dest='do_logging',
-                               action='store_true',
-                               help='DEVELOPER: enable logging.')
-    logging_group.add_argument('--no-logging', dest='do_logging',
-                               action='store_false', default=False,
-                               help='DEVELOPER: disable logging '
-                               '(this is the default)')
-
-    if args:
-        options = parser.parse_args(args)
-    else:
-        options = parser.parse_args()
-    return options
-
-def _dirty_local_repo_msg(program_name, config_file):
-    return """The external repositories labeled with 'M' above are not in a clean state.
-The following are four options for how to proceed:
-(1) Go into each external that is not in a clean state and issue either a 'git status' or
-    an 'svn status' command (depending on whether the external is managed by git or
-    svn). Either revert or commit your changes so that all externals are in a clean
-    state. (To revert changes in git, follow the instructions given when you run 'git
-    status'.) (Note, though, that it is okay to have untracked files in your working
-    directory.) Then rerun {program_name}.
-(2) Alternatively, you do not have to rely on {program_name}. Instead, you can manually
-    update out-of-sync externals (labeled with 's' above) as described in the
-    configuration file {config_file}. (For example, run 'git fetch' and 'git checkout'
-    commands to checkout the appropriate tags for each external, as given in
-    {config_file}.)
-(3) You can also use {program_name} to manage most, but not all externals: You can specify
-    one or more externals to ignore using the '-x' or '--exclude' argument to
-    {program_name}. Excluding externals labeled with 'M' will allow {program_name} to
-    update the other, non-excluded externals.
-(4) As a last resort, if you are confident that there is no work that needs to be saved
-    from a given external, you can remove that external (via "rm -rf [directory]") and
-    then rerun the {program_name} tool. This option is mainly useful as a workaround for
-    issues with this tool (such as https://github.com/ESMCI/manage_externals/issues/157).
-The external repositories labeled with '?' above are not under version
-control using the expected protocol. If you are sure you want to switch
-protocols, and you don't have any work you need to save from this
-directory, then run "rm -rf [directory]" before rerunning the
-{program_name} tool.
-""".format(program_name=program_name, config_file=config_file)
-# ---------------------------------------------------------------------
-#
-# main
-#
-# ---------------------------------------------------------------------
-def main(args):
-    """
-    Function to call when module is called from the command line.
-    Parse externals file and load required repositories or all repositories if
-    the --all option is passed.
-
-    Returns a tuple (overall_status, tree_status). overall_status is 0
-    on success, non-zero on failure. tree_status is a dict mapping local path
-    to ExternalStatus -- if no checkout is happening. If checkout is happening, tree_status
-    is None.
-    """
-    if args.do_logging:
-        logging.basicConfig(filename=LOG_FILE_NAME,
-                            format='%(levelname)s : %(asctime)s : %(message)s',
-                            datefmt='%Y-%m-%d %H:%M:%S',
-                            level=logging.DEBUG)
-
-    program_name = os.path.basename(sys.argv[0])
-    logging.info('Beginning of %s', program_name)
-
-    load_all = False
-    if args.optional:
-        load_all = True
-
-    root_dir = os.path.abspath(os.getcwd())
-    model_data = read_externals_description_file(root_dir, args.externals)
-    ext_description = create_externals_description(
-        model_data, components=args.components, exclude=args.exclude)
-
-    for comp in args.components:
-        if comp not in ext_description.keys():
-            # Note we can't print out the list of found externals because
-            # they were filtered in create_externals_description above.
-            fatal_error(
-                "No component {} found in {}".format(
-                    comp, args.externals))
-
-    source_tree = SourceTree(root_dir, ext_description, svn_ignore_ancestry=args.svn_ignore_ancestry)
-    if args.components:
-        components_str = 'specified components'
-    else:
-        components_str = 'required & optional components'
-    printlog('Checking local status of ' + components_str + ': ', end='')
-    tree_status = source_tree.status(print_progress=True)
-    printlog('')
-
-    if args.status:
-        # user requested status-only
-        for comp in sorted(tree_status):
-            tree_status[comp].log_status_message(args.verbose)
-    else:
-        # checkout / update the external repositories.
-        safe_to_update = check_safe_to_update_repos(tree_status)
-        if not safe_to_update:
-            # print status
-            for comp in sorted(tree_status):
-                tree_status[comp].log_status_message(args.verbose)
-            # exit gracefully
-            printlog('-' * 70)
-            printlog(_dirty_local_repo_msg(program_name, args.externals))
-            printlog('-' * 70)
-        else:
-            if not args.components:
-                source_tree.checkout(args.verbose, load_all)
-            for comp in args.components:
-                source_tree.checkout(args.verbose, load_all, load_comp=comp)
-            printlog('')
-            # New tree status is unknown, don't return anything.
-            tree_status = None
-
-    logging.info('%s completed without exceptions.', program_name)
-    # NOTE(bja, 2017-11) tree status is used by the systems tests
-    return 0, tree_status
diff --git a/manage_externals/manic/externals_description.py b/manage_externals/manic/externals_description.py
deleted file mode 100644
index 546e7fdcb4..0000000000
--- a/manage_externals/manic/externals_description.py
+++ /dev/null
@@ -1,830 +0,0 @@
-#!/usr/bin/env python3
-
-"""Model description
-
-Model description is the representation of the various externals
-included in the model. It processes in input data structure, and
-converts it into a standard interface that is used by the rest of the
-system.
-
-To maintain backward compatibility, externals description files should
-follow semantic versioning rules, http://semver.org/
-
-
-
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import logging
-import os
-import os.path
-import re
-
-# ConfigParser in python2 was renamed to configparser in python3.
-# In python2, ConfigParser returns byte strings, str, instead of unicode.
-# We need unicode to be compatible with xml and json parser and python3.
-try:
-    # python2
-    from ConfigParser import SafeConfigParser as config_parser
-    from ConfigParser import MissingSectionHeaderError
-    from ConfigParser import NoSectionError, NoOptionError
-
-    USE_PYTHON2 = True
-
-    def config_string_cleaner(text):
-        """convert strings into unicode
-        """
-        return text.decode('utf-8')
-except ImportError:
-    # python3
-    from configparser import ConfigParser as config_parser
-    from configparser import MissingSectionHeaderError
-    from configparser import NoSectionError, NoOptionError
-
-    USE_PYTHON2 = False
-
-    def config_string_cleaner(text):
-        """Python3 already uses unicode strings, so just return the string
-        without modification.
-
-        """
-        return text
-
-from .utils import printlog, fatal_error, str_to_bool, expand_local_url
-from .utils import execute_subprocess
-from .global_constants import EMPTY_STR, PPRINTER, VERSION_SEPERATOR
-
-#
-# Globals
-#
-DESCRIPTION_SECTION = 'externals_description'
-VERSION_ITEM = 'schema_version'
-
-
-def read_externals_description_file(root_dir, file_name):
-    """Read a file containing an externals description and
-    create its internal representation.
-
-    """
-    root_dir = os.path.abspath(root_dir)
-    msg = 'In directory : {0}'.format(root_dir)
-    logging.info(msg)
-    printlog('Processing externals description file : {0} ({1})'.format(file_name,
-                                                                        root_dir))
-
-    file_path = os.path.join(root_dir, file_name)
-    if not os.path.exists(file_name):
-        if file_name.lower() == "none":
-            msg = ('INTERNAL ERROR: Attempt to read externals file '
-                   'from {0} when not configured'.format(file_path))
-        else:
-            msg = ('ERROR: Model description file, "{0}", does not '
-                   'exist at path:\n    {1}\nDid you run from the root of '
-                   'the source tree?'.format(file_name, file_path))
-
-        fatal_error(msg)
-
-    externals_description = None
-    if file_name == ExternalsDescription.GIT_SUBMODULES_FILENAME:
-        externals_description = _read_gitmodules_file(root_dir, file_name)
-    else:
-        try:
-            config = config_parser()
-            config.read(file_path)
-            externals_description = config
-        except MissingSectionHeaderError:
-            # not a cfg file
-            pass
-
-    if externals_description is None:
-        msg = 'Unknown file format!'
-        fatal_error(msg)
-
-    return externals_description
-
-class LstripReader(object):
-    "LstripReader formats .gitmodules files to be acceptable for configparser"
-    def __init__(self, filename):
-        with open(filename, 'r') as infile:
-            lines = infile.readlines()
-        self._lines = list()
-        self._num_lines = len(lines)
-        self._index = 0
-        for line in lines:
-            self._lines.append(line.lstrip())
-
-    def readlines(self):
-        """Return all the lines from this object's file"""
-        return self._lines
-
-    def readline(self, size=-1):
-        """Format and return the next line or raise StopIteration"""
-        try:
-            line = self.next()
-        except StopIteration:
-            line = ''
-
-        if (size > 0) and (len(line) < size):
-            return line[0:size]
-
-        return line
-
-    def __iter__(self):
-        """Begin an iteration"""
-        self._index = 0
-        return self
-
-    def next(self):
-        """Return the next line or raise StopIteration"""
-        if self._index >= self._num_lines:
-            raise StopIteration
-
-        self._index = self._index + 1
-        return self._lines[self._index - 1]
-
-    def __next__(self):
-        return self.next()
-
-def git_submodule_status(repo_dir):
-    """Run the git submodule status command to obtain submodule hashes.
-        """
-    # This function is here instead of GitRepository to avoid a dependency loop
-    cmd = 'git -C {repo_dir} submodule status'.format(
-        repo_dir=repo_dir).split()
-    git_output = execute_subprocess(cmd, output_to_caller=True)
-    submodules = {}
-    submods = git_output.split('\n')
-    for submod in submods:
-        if submod:
-            status = submod[0]
-            items = submod[1:].split(' ')
-            if len(items) > 2:
-                tag = items[2]
-            else:
-                tag = None
-
-            submodules[items[1]] = {'hash':items[0], 'status':status, 'tag':tag}
-
-    return submodules
-
-def parse_submodules_desc_section(section_items, file_path):
-    """Find the path and url for this submodule description"""
-    path = None
-    url = None
-    for item in section_items:
-        name = item[0].strip().lower()
-        if name == 'path':
-            path = item[1].strip()
-        elif name == 'url':
-            url = item[1].strip()
-        elif name == 'branch':
-            # We do not care about branch since we have a hash - silently ignore
-            pass
-        else:
-            msg = 'WARNING: Ignoring unknown {} property, in {}'
-            msg = msg.format(item[0], file_path) # fool pylint
-            logging.warning(msg)
-
-    return path, url
-
-def _read_gitmodules_file(root_dir, file_name):
-    # pylint: disable=deprecated-method
-    # Disabling this check because the method is only used for python2
-    # pylint: disable=too-many-locals
-    # pylint: disable=too-many-branches
-    # pylint: disable=too-many-statements
-    """Read a .gitmodules file and convert it to be compatible with an
-    externals description.
-    """
-    root_dir = os.path.abspath(root_dir)
-    msg = 'In directory : {0}'.format(root_dir)
-    logging.info(msg)
-
-    file_path = os.path.join(root_dir, file_name)
-    if not os.path.exists(file_name):
-        msg = ('ERROR: submodules description file, "{0}", does not '
-               'exist in dir:\n    {1}'.format(file_name, root_dir))
-        fatal_error(msg)
-
-    submodules_description = None
-    externals_description = None
-    try:
-        config = config_parser()
-        if USE_PYTHON2:
-            config.readfp(LstripReader(file_path), filename=file_name)
-        else:
-            config.read_file(LstripReader(file_path), source=file_name)
-
-        submodules_description = config
-    except MissingSectionHeaderError:
-        # not a cfg file
-        pass
-
-    if submodules_description is None:
-        msg = 'Unknown file format!'
-        fatal_error(msg)
-    else:
-        # Convert the submodules description to an externals description
-        externals_description = config_parser()
-        # We need to grab all the commit hashes for this repo
-        submods = git_submodule_status(root_dir)
-        for section in submodules_description.sections():
-            if section[0:9] == 'submodule':
-                sec_name = section[9:].strip(' "')
-                externals_description.add_section(sec_name)
-                section_items = submodules_description.items(section)
-                path, url = parse_submodules_desc_section(section_items,
-                                                          file_path)
-
-                if path is None:
-                    msg = 'Submodule {} missing path'.format(sec_name)
-                    fatal_error(msg)
-
-                if url is None:
-                    msg = 'Submodule {} missing url'.format(sec_name)
-                    fatal_error(msg)
-
-                externals_description.set(sec_name,
-                                          ExternalsDescription.PATH, path)
-                externals_description.set(sec_name,
-                                          ExternalsDescription.PROTOCOL, 'git')
-                externals_description.set(sec_name,
-                                          ExternalsDescription.REPO_URL, url)
-                externals_description.set(sec_name,
-                                          ExternalsDescription.REQUIRED, 'True')
-                if sec_name in submods:
-                    submod_name = sec_name
-                else:
-                    # The section name does not have to match the path
-                    submod_name = path
-
-                if submod_name in submods:
-                    git_hash = submods[submod_name]['hash']
-                    externals_description.set(sec_name,
-                                              ExternalsDescription.HASH,
-                                              git_hash)
-                else:
-                    emsg = "submodule status has no section, '{}'"
-                    emsg += "\nCheck section names in externals config file"
-                    fatal_error(emsg.format(submod_name))
-
-        # Required items
-        externals_description.add_section(DESCRIPTION_SECTION)
-        externals_description.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.0')
-
-    return externals_description
-
-def create_externals_description(
-        model_data, model_format='cfg', components=None, exclude=None, parent_repo=None):
-    """Create the a externals description object from the provided data
-        
-    components: list of component names to include, None to include all. If a
-                name isn't found, it is silently omitted from the return value.
-    exclude: list of component names to skip.
-    """
-    externals_description = None
-    if model_format == 'dict':
-        externals_description = ExternalsDescriptionDict(
-            model_data, components=components, exclude=exclude)
-    elif model_format == 'cfg':
-        major, _, _ = get_cfg_schema_version(model_data)
-        if major == 1:
-            externals_description = ExternalsDescriptionConfigV1(
-                model_data, components=components, exclude=exclude, parent_repo=parent_repo)
-        else:
-            msg = ('Externals description file has unsupported schema '
-                   'version "{0}".'.format(major))
-            fatal_error(msg)
-    else:
-        msg = 'Unknown model data format "{0}"'.format(model_format)
-        fatal_error(msg)
-    return externals_description
-
-
-def get_cfg_schema_version(model_cfg):
-    """Extract the major, minor, patch version of the config file schema
-
-    Params:
-    model_cfg - config parser object containing the externas description data
-
-    Returns:
-    major = integer major version
-    minor = integer minor version
-    patch = integer patch version
-    """
-    semver_str = ''
-    try:
-        semver_str = model_cfg.get(DESCRIPTION_SECTION, VERSION_ITEM)
-    except (NoSectionError, NoOptionError):
-        msg = ('externals description file must have the required '
-               'section: "{0}" and item "{1}"'.format(DESCRIPTION_SECTION,
-                                                      VERSION_ITEM))
-        fatal_error(msg)
-
-    # NOTE(bja, 2017-11) Assume we don't care about the
-    # build/pre-release metadata for now!
-    version_list = re.split(r'[-+]', semver_str)
-    version_str = version_list[0]
-    version = version_str.split(VERSION_SEPERATOR)
-    try:
-        major = int(version[0].strip())
-        minor = int(version[1].strip())
-        patch = int(version[2].strip())
-    except ValueError:
-        msg = ('Config file schema version must have integer digits for '
-               'major, minor and patch versions. '
-               'Received "{0}"'.format(version_str))
-        fatal_error(msg)
-    return major, minor, patch
-
-
-class ExternalsDescription(dict):
-    """Base externals description class that is independent of the user input
-    format. Different input formats can all be converted to this
-    representation to provide a consistent represtentation for the
-    rest of the objects in the system.
-
-    NOTE(bja, 2018-03): do NOT define _schema_major etc at the class
-    level in the base class. The nested/recursive nature of externals
-    means different schema versions may be present in a single run!
-
-    All inheriting classes must overwrite:
-        self._schema_major and self._input_major
-        self._schema_minor and self._input_minor
-        self._schema_patch and self._input_patch
-
-    where _schema_x is the supported schema, _input_x is the user
-    input value.
-
-    """
-    # keywords defining the interface into the externals description data; these
-    # are brought together by the schema below.
-    EXTERNALS = 'externals'  # path to externals file.
-    BRANCH = 'branch'
-    SUBMODULE = 'from_submodule'
-    HASH = 'hash'
-    NAME = 'name'
-    PATH = 'local_path'
-    PROTOCOL = 'protocol'
-    REPO = 'repo'
-    REPO_URL = 'repo_url'
-    REQUIRED = 'required'
-    TAG = 'tag'
-    SPARSE = 'sparse'
-
-    PROTOCOL_EXTERNALS_ONLY = 'externals_only'
-    PROTOCOL_GIT = 'git'
-    PROTOCOL_SVN = 'svn'
-    GIT_SUBMODULES_FILENAME = '.gitmodules'
-    KNOWN_PRROTOCOLS = [PROTOCOL_GIT, PROTOCOL_SVN, PROTOCOL_EXTERNALS_ONLY]
-
-    # v1 xml keywords
-    _V1_TREE_PATH = 'TREE_PATH'
-    _V1_ROOT = 'ROOT'
-    _V1_TAG = 'TAG'
-    _V1_BRANCH = 'BRANCH'
-    _V1_REQ_SOURCE = 'REQ_SOURCE'
-
-    # Dictionary keys are component names. The corresponding values are laid out
-    # according to this schema.
-    _source_schema = {REQUIRED: True,
-                      PATH: 'string',
-                      EXTERNALS: 'string',
-                      SUBMODULE : True,
-                      REPO: {PROTOCOL: 'string',
-                             REPO_URL: 'string',
-                             TAG: 'string',
-                             BRANCH: 'string',
-                             HASH: 'string',
-                             SPARSE: 'string',
-                            }
-                     }
-
-    def __init__(self, parent_repo=None):
-        """Convert the xml into a standardized dict that can be used to
-        construct the source objects
-
-        """
-        dict.__init__(self)
-
-        self._schema_major = None
-        self._schema_minor = None
-        self._schema_patch = None
-        self._input_major = None
-        self._input_minor = None
-        self._input_patch = None
-        self._parent_repo = parent_repo
-
-    def _verify_schema_version(self):
-        """Use semantic versioning rules to verify we can process this schema.
-
-        """
-        known = '{0}.{1}.{2}'.format(self._schema_major,
-                                     self._schema_minor,
-                                     self._schema_patch)
-        received = '{0}.{1}.{2}'.format(self._input_major,
-                                        self._input_minor,
-                                        self._input_patch)
-
-        if self._input_major != self._schema_major:
-            # should never get here, the factory should handle this correctly!
-            msg = ('DEV_ERROR: version "{0}" parser received '
-                   'version "{1}" input.'.format(known, received))
-            fatal_error(msg)
-
-        if self._input_minor > self._schema_minor:
-            msg = ('Incompatible schema version:\n'
-                   '  User supplied schema version "{0}" is too new."\n'
-                   '  Can only process version "{1}" files and '
-                   'older.'.format(received, known))
-            fatal_error(msg)
-
-        if self._input_patch > self._schema_patch:
-            # NOTE(bja, 2018-03) ignoring for now... Not clear what
-            # conditions the test is needed.
-            pass
-
-    def _check_user_input(self):
-        """Run a series of checks to attempt to validate the user input and
-        detect errors as soon as possible.
-
-        NOTE(bja, 2018-03) These checks are called *after* the file is
-        read. That means the schema check can not occur here.
-
-        Note: the order is important. check_optional will create
-        optional with null data. run check_data first to ensure
-        required data was provided correctly by the user.
-
-        """
-        self._check_data()
-        self._check_optional()
-        self._validate()
-
-    def _check_data(self):
-        # pylint: disable=too-many-branches,too-many-statements
-        """Check user supplied data is valid where possible.
-        """
-        for ext_name in self.keys():
-            if (self[ext_name][self.REPO][self.PROTOCOL]
-                    not in self.KNOWN_PRROTOCOLS):
-                msg = 'Unknown repository protocol "{0}" in "{1}".'.format(
-                    self[ext_name][self.REPO][self.PROTOCOL], ext_name)
-                fatal_error(msg)
-
-            if (self[ext_name][self.REPO][self.PROTOCOL] ==
-                    self.PROTOCOL_SVN):
-                if self.HASH in self[ext_name][self.REPO]:
-                    msg = ('In repo description for "{0}". svn repositories '
-                           'may not include the "hash" keyword.'.format(
-                               ext_name))
-                    fatal_error(msg)
-
-            if ((self[ext_name][self.REPO][self.PROTOCOL] != self.PROTOCOL_GIT)
-                    and (self.SUBMODULE in self[ext_name])):
-                msg = ('self.SUBMODULE is only supported with {0} protocol, '
-                       '"{1}" is defined as an {2} repository')
-                fatal_error(msg.format(self.PROTOCOL_GIT, ext_name,
-                                       self[ext_name][self.REPO][self.PROTOCOL]))
-
-            if (self[ext_name][self.REPO][self.PROTOCOL] !=
-                    self.PROTOCOL_EXTERNALS_ONLY):
-                ref_count = 0
-                found_refs = ''
-                if self.TAG in self[ext_name][self.REPO]:
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.TAG, self[ext_name][self.REPO][self.TAG],
-                        found_refs)
-                if self.BRANCH in self[ext_name][self.REPO]:
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.BRANCH, self[ext_name][self.REPO][self.BRANCH],
-                        found_refs)
-                if self.HASH in self[ext_name][self.REPO]:
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.HASH, self[ext_name][self.REPO][self.HASH],
-                        found_refs)
-                if (self.SUBMODULE in self[ext_name] and
-                        self[ext_name][self.SUBMODULE]):
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.SUBMODULE,
-                        self[ext_name][self.SUBMODULE], found_refs)
-
-                if ref_count > 1:
-                    msg = 'Model description is over specified! '
-                    if self.SUBMODULE in self[ext_name]:
-                        msg += ('from_submodule is not compatible with '
-                                '"tag", "branch", or "hash" ')
-                    else:
-                        msg += (' Only one of "tag", "branch", or "hash" '
-                                'may be specified ')
-
-                    msg += 'for repo description of "{0}".'.format(ext_name)
-                    msg = '{0}\nFound: {1}'.format(msg, found_refs)
-                    fatal_error(msg)
-                elif ref_count < 1:
-                    msg = ('Model description is under specified! One of '
-                           '"tag", "branch", or "hash" must be specified for '
-                           'repo description of "{0}"'.format(ext_name))
-                    fatal_error(msg)
-
-                if (self.REPO_URL not in self[ext_name][self.REPO] and
-                        (self.SUBMODULE not in self[ext_name] or
-                         not self[ext_name][self.SUBMODULE])):
-                    msg = ('Model description is under specified! Must have '
-                           '"repo_url" in repo '
-                           'description for "{0}"'.format(ext_name))
-                    fatal_error(msg)
-
-                if (self.SUBMODULE in self[ext_name] and
-                        self[ext_name][self.SUBMODULE]):
-                    if self.REPO_URL in self[ext_name][self.REPO]:
-                        msg = ('Model description is over specified! '
-                               'from_submodule keyword is not compatible '
-                               'with {0} keyword for'.format(self.REPO_URL))
-                        msg = '{0} repo description of "{1}"'.format(msg,
-                                                                     ext_name)
-                        fatal_error(msg)
-
-                    if self.PATH in self[ext_name]:
-                        msg = ('Model description is over specified! '
-                               'from_submodule keyword is not compatible with '
-                               '{0} keyword for'.format(self.PATH))
-                        msg = '{0} repo description of "{1}"'.format(msg,
-                                                                     ext_name)
-                        fatal_error(msg)
-
-                if self.REPO_URL in self[ext_name][self.REPO]:
-                    url = expand_local_url(
-                        self[ext_name][self.REPO][self.REPO_URL], ext_name)
-                    self[ext_name][self.REPO][self.REPO_URL] = url
-
-    def _check_optional(self):
-        # pylint: disable=too-many-branches
-        """Some fields like externals, repo:tag repo:branch are
-        (conditionally) optional. We don't want the user to be
-        required to enter them in every externals description file, but
-        still want to validate the input. Check conditions and add
-        default values if appropriate.
-
-        """
-        submod_desc = None      # Only load submodules info once
-        for field in self:
-            # truely optional
-            if self.EXTERNALS not in self[field]:
-                self[field][self.EXTERNALS] = EMPTY_STR
-
-            # git and svn repos must tags and branches for validation purposes.
-            if self.TAG not in self[field][self.REPO]:
-                self[field][self.REPO][self.TAG] = EMPTY_STR
-            if self.BRANCH not in self[field][self.REPO]:
-                self[field][self.REPO][self.BRANCH] = EMPTY_STR
-            if self.HASH not in self[field][self.REPO]:
-                self[field][self.REPO][self.HASH] = EMPTY_STR
-            if self.REPO_URL not in self[field][self.REPO]:
-                self[field][self.REPO][self.REPO_URL] = EMPTY_STR
-            if self.SPARSE not in self[field][self.REPO]:
-                self[field][self.REPO][self.SPARSE] = EMPTY_STR
-
-            # from_submodule has a complex relationship with other fields
-            if self.SUBMODULE in self[field]:
-                # User wants to use submodule information, is it available?
-                if self._parent_repo is None:
-                    # No parent == no submodule information
-                    PPRINTER.pprint(self[field])
-                    msg = 'No parent submodule for "{0}"'.format(field)
-                    fatal_error(msg)
-                elif self._parent_repo.protocol() != self.PROTOCOL_GIT:
-                    PPRINTER.pprint(self[field])
-                    msg = 'Parent protocol, "{0}", does not support submodules'
-                    fatal_error(msg.format(self._parent_repo.protocol()))
-                else:
-                    args = self._repo_config_from_submodule(field, submod_desc)
-                    repo_url, repo_path, ref_hash, submod_desc = args
-
-                    if repo_url is None:
-                        msg = ('Cannot checkout "{0}" as a submodule, '
-                               'repo not found in {1} file')
-                        fatal_error(msg.format(field,
-                                               self.GIT_SUBMODULES_FILENAME))
-                    # Fill in submodule fields
-                    self[field][self.REPO][self.REPO_URL] = repo_url
-                    self[field][self.REPO][self.HASH] = ref_hash
-                    self[field][self.PATH] = repo_path
-
-                if self[field][self.SUBMODULE]:
-                    # We should get everything from the parent submodule
-                    # configuration.
-                    pass
-                # No else (from _submodule = False is the default)
-            else:
-                # Add the default value (not using submodule information)
-                self[field][self.SUBMODULE] = False
-
-    def _repo_config_from_submodule(self, field, submod_desc):
-        """Find the external config information for a repository from
-        its submodule configuration information.
-        """
-        if submod_desc is None:
-            repo_path = os.getcwd() # Is this always correct?
-            submod_file = self._parent_repo.submodules_file(repo_path=repo_path)
-            if submod_file is None:
-                msg = ('Cannot checkout "{0}" from submodule information\n'
-                       '       Parent repo, "{1}" does not have submodules')
-                fatal_error(msg.format(field, self._parent_repo.name()))
-
-            printlog(
-                'Processing submodules description file : {0} ({1})'.format(
-                    submod_file, repo_path))
-            submod_model_data= _read_gitmodules_file(repo_path, submod_file)
-            submod_desc = create_externals_description(submod_model_data)
-
-        # Can we find our external?
-        repo_url = None
-        repo_path = None
-        ref_hash = None
-        for ext_field in submod_desc:
-            if field == ext_field:
-                ext = submod_desc[ext_field]
-                repo_url = ext[self.REPO][self.REPO_URL]
-                repo_path = ext[self.PATH]
-                ref_hash = ext[self.REPO][self.HASH]
-                break
-
-        return repo_url, repo_path, ref_hash, submod_desc
-
-    def _validate(self):
-        """Validate that the parsed externals description contains all necessary
-        fields.
-
-        """
-        def print_compare_difference(data_a, data_b, loc_a, loc_b):
-            """Look through the data structures and print the differences.
-
-            """
-            for item in data_a:
-                if item in data_b:
-                    if not isinstance(data_b[item], type(data_a[item])):
-                        printlog("    {item}: {loc} = {val} ({val_type})".format(
-                            item=item, loc=loc_a, val=data_a[item],
-                            val_type=type(data_a[item])))
-                        printlog("    {item}  {loc} = {val} ({val_type})".format(
-                            item=' ' * len(item), loc=loc_b, val=data_b[item],
-                            val_type=type(data_b[item])))
-                else:
-                    printlog("    {item}: {loc} = {val} ({val_type})".format(
-                        item=item, loc=loc_a, val=data_a[item],
-                        val_type=type(data_a[item])))
-                    printlog("    {item}  {loc} missing".format(
-                        item=' ' * len(item), loc=loc_b))
-
-        def validate_data_struct(schema, data):
-            """Compare a data structure against a schema and validate all required
-            fields are present.
-
-            """
-            is_valid = False
-            in_ref = True
-            valid = True
-            if isinstance(schema, dict) and isinstance(data, dict):
-                # Both are dicts, recursively verify that all fields
-                # in schema are present in the data.
-                for key in schema:
-                    in_ref = in_ref and (key in data)
-                    if in_ref:
-                        valid = valid and (
-                            validate_data_struct(schema[key], data[key]))
-
-                is_valid = in_ref and valid
-            else:
-                # non-recursive structure. verify data and schema have
-                # the same type.
-                is_valid = isinstance(data, type(schema))
-
-            if not is_valid:
-                printlog("  Unmatched schema and input:")
-                if isinstance(schema, dict):
-                    print_compare_difference(schema, data, 'schema', 'input')
-                    print_compare_difference(data, schema, 'input', 'schema')
-                else:
-                    printlog("    schema = {0} ({1})".format(
-                        schema, type(schema)))
-                    printlog("    input = {0} ({1})".format(data, type(data)))
-
-            return is_valid
-
-        for field in self:
-            valid = validate_data_struct(self._source_schema, self[field])
-            if not valid:
-                PPRINTER.pprint(self._source_schema)
-                PPRINTER.pprint(self[field])
-                msg = 'ERROR: source for "{0}" did not validate'.format(field)
-                fatal_error(msg)
-
-
-class ExternalsDescriptionDict(ExternalsDescription):
-    """Create a externals description object from a dictionary using the API
-    representations. Primarily used to simplify creating model
-    description files for unit testing.
-
-    """
-
-    def __init__(self, model_data, components=None, exclude=None):
-        """Parse a native dictionary into a externals description.
-        """
-        ExternalsDescription.__init__(self)
-        self._schema_major = 1
-        self._schema_minor = 0
-        self._schema_patch = 0
-        self._input_major = 1
-        self._input_minor = 0
-        self._input_patch = 0
-        self._verify_schema_version()
-        if components:
-            for key in list(model_data.keys()):
-                if key not in components:
-                    del model_data[key]
-
-        if exclude:
-            for key in list(model_data.keys()):
-                if key in exclude:
-                    del model_data[key]
-
-        self.update(model_data)
-        self._check_user_input()
-
-
-class ExternalsDescriptionConfigV1(ExternalsDescription):
-    """Create a externals description object from a config_parser object,
-    schema version 1.
-
-    """
-
-    def __init__(self, model_data, components=None, exclude=None, parent_repo=None):
-        """Convert the config data into a standardized dict that can be used to
-        construct the source objects
-
-        components: list of component names to include, None to include all.
-        exclude: list of component names to skip.
-        """
-        ExternalsDescription.__init__(self, parent_repo=parent_repo)
-        self._schema_major = 1
-        self._schema_minor = 1
-        self._schema_patch = 0
-        self._input_major, self._input_minor, self._input_patch = \
-            get_cfg_schema_version(model_data)
-        self._verify_schema_version()
-        self._remove_metadata(model_data)
-        self._parse_cfg(model_data, components=components, exclude=exclude)
-        self._check_user_input()
-
-    @staticmethod
-    def _remove_metadata(model_data):
-        """Remove the metadata section from the model configuration file so
-        that it is simpler to look through the file and construct the
-        externals description.
-
-        """
-        model_data.remove_section(DESCRIPTION_SECTION)
-
-    def _parse_cfg(self, cfg_data, components=None, exclude=None):
-        """Parse a config_parser object into a externals description.
-
-        components: list of component names to include, None to include all.
-        exclude: list of component names to skip.
-        """
-        def list_to_dict(input_list, convert_to_lower_case=True):
-            """Convert a list of key-value pairs into a dictionary.
-            """
-            output_dict = {}
-            for item in input_list:
-                key = config_string_cleaner(item[0].strip())
-                value = config_string_cleaner(item[1].strip())
-                if convert_to_lower_case:
-                    key = key.lower()
-                output_dict[key] = value
-            return output_dict
-
-        for section in cfg_data.sections():
-            name = config_string_cleaner(section.lower().strip())
-            if (components and name not in components) or (exclude and name in exclude):
-                continue
-            self[name] = {}
-            self[name].update(list_to_dict(cfg_data.items(section)))
-            self[name][self.REPO] = {}
-            loop_keys = self[name].copy().keys()
-            for item in loop_keys:
-                if item in self._source_schema:
-                    if isinstance(self._source_schema[item], bool):
-                        self[name][item] = str_to_bool(self[name][item])
-                elif item in self._source_schema[self.REPO]:
-                    self[name][self.REPO][item] = self[name][item]
-                    del self[name][item]
-                else:
-                    msg = ('Invalid input: "{sect}" contains unknown '
-                           'item "{item}".'.format(sect=name, item=item))
-                    fatal_error(msg)
diff --git a/manage_externals/manic/externals_status.py b/manage_externals/manic/externals_status.py
deleted file mode 100644
index 6bc29e9732..0000000000
--- a/manage_externals/manic/externals_status.py
+++ /dev/null
@@ -1,164 +0,0 @@
-"""ExternalStatus
-
-Class to store status and state information about repositories and
-create a string representation.
-
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-from .global_constants import EMPTY_STR
-from .utils import printlog, indent_string
-from .global_constants import VERBOSITY_VERBOSE, VERBOSITY_DUMP
-
-
-class ExternalStatus(object):
-    """Class to represent the status of a given source repository or tree.
-
-    Individual repositories determine their own status in the
-    Repository objects. This object is just resposible for storing the
-    information and passing it up to a higher level for reporting or
-    global decisions.
-
-    There are two states of concern:
-
-    * If the repository is in-sync with the externals description file.
-
-    * If the repostiory working copy is clean and there are no pending
-    transactions (e.g. add, remove, rename, untracked files).
-
-    """
-    # sync_state and clean_state can be one of the following:
-    DEFAULT = '-'  # not set yet (sync_state).  clean_state can be this if sync_state is EMPTY.
-    UNKNOWN = '?'
-    EMPTY = 'e'
-    MODEL_MODIFIED = 's'  # repo version != externals (sync_state only)
-    DIRTY = 'M'       # repo is dirty (clean_state only)
-    STATUS_OK = ' '   # repo is clean (clean_state) or matches externals version (sync_state)
-    STATUS_ERROR = '!'
-
-    # source_type can be one of the following:
-    OPTIONAL = 'o'
-    STANDALONE = 's'
-    MANAGED = ' '
-
-    def __init__(self):
-        self.sync_state = self.DEFAULT
-        self.clean_state = self.DEFAULT
-        self.source_type = self.DEFAULT
-        self.path = EMPTY_STR
-        self.current_version = EMPTY_STR
-        self.expected_version = EMPTY_STR
-        self.status_output = EMPTY_STR
-
-    def log_status_message(self, verbosity):
-        """Write status message to the screen and log file
-        """
-        printlog(self._default_status_message())
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog(self._verbose_status_message())
-        if verbosity >= VERBOSITY_DUMP:
-            printlog(self._dump_status_message())
-
-    def __repr__(self):
-        return self._default_status_message()
-
-    def _default_status_message(self):
-        """Return the default terse status message string
-        """
-        return '{sync}{clean}{src_type} {path}'.format(
-            sync=self.sync_state, clean=self.clean_state,
-            src_type=self.source_type, path=self.path)
-
-    def _verbose_status_message(self):
-        """Return the verbose status message string
-        """
-        clean_str = self.DEFAULT
-        if self.clean_state == self.STATUS_OK:
-            clean_str = 'clean sandbox'
-        elif self.clean_state == self.DIRTY:
-            clean_str = 'modified sandbox'
-
-        sync_str = 'on {0}'.format(self.current_version)
-        if self.sync_state != self.STATUS_OK:
-            sync_str = '{current} --> {expected}'.format(
-                current=self.current_version, expected=self.expected_version)
-        return '        {clean}, {sync}'.format(clean=clean_str, sync=sync_str)
-
-    def _dump_status_message(self):
-        """Return the dump status message string
-        """
-        return indent_string(self.status_output, 12)
-
-    def safe_to_update(self):
-        """Report if it is safe to update a repository. Safe is defined as:
-
-        * If a repository is empty, it is safe to update.
-
-        * If a repository exists and has a clean working copy state
-        with no pending transactions.
-
-        """
-        safe_to_update = False
-        repo_exists = self.exists()
-        if not repo_exists:
-            safe_to_update = True
-        else:
-            # If the repo exists, it must be in ok or modified
-            # sync_state. Any other sync_state at this point
-            # represents a logic error that should have been handled
-            # before now!
-            sync_safe = ((self.sync_state == ExternalStatus.STATUS_OK) or
-                         (self.sync_state == ExternalStatus.MODEL_MODIFIED))
-            if sync_safe:
-                # The clean_state must be STATUS_OK to update. Otherwise we
-                # are dirty or there was a missed error previously.
-                if self.clean_state == ExternalStatus.STATUS_OK:
-                    safe_to_update = True
-        return safe_to_update
-
-    def exists(self):
-        """Determine if the repo exists. This is indicated by:
-
-        * sync_state is not EMPTY
-
-            * if the sync_state is empty, then the valid states for
-              clean_state are default, empty or unknown. Anything else
-              and there was probably an internal logic error.
-
-        NOTE(bja, 2017-10) For the moment we are considering a
-        sync_state of default or unknown to require user intervention,
-        but we may want to relax this convention. This is probably a
-        result of a network error or internal logic error but more
-        testing is needed.
-
-        """
-        is_empty = (self.sync_state == ExternalStatus.EMPTY)
-        clean_valid = ((self.clean_state == ExternalStatus.DEFAULT) or
-                       (self.clean_state == ExternalStatus.EMPTY) or
-                       (self.clean_state == ExternalStatus.UNKNOWN))
-
-        if is_empty and clean_valid:
-            exists = False
-        else:
-            exists = True
-        return exists
-
-
-def check_safe_to_update_repos(tree_status):
-    """Check if *ALL* repositories are in a safe state to update. We don't
-    want to do a partial update of the repositories then die, leaving
-    the model in an inconsistent state.
-
-    Note: if there is an update to do, the repositories will by
-    definiation be out of synce with the externals description, so we
-    can't use that as criteria for updating.
-
-    """
-    safe_to_update = True
-    for comp in tree_status:
-        stat = tree_status[comp]
-        safe_to_update &= stat.safe_to_update()
-
-    return safe_to_update
diff --git a/manage_externals/manic/global_constants.py b/manage_externals/manic/global_constants.py
deleted file mode 100644
index 0e91cffc90..0000000000
--- a/manage_externals/manic/global_constants.py
+++ /dev/null
@@ -1,18 +0,0 @@
-"""Globals shared across modules
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import pprint
-
-EMPTY_STR = ''
-LOCAL_PATH_INDICATOR = '.'
-VERSION_SEPERATOR = '.'
-LOG_FILE_NAME = 'manage_externals.log'
-PPRINTER = pprint.PrettyPrinter(indent=4)
-
-VERBOSITY_DEFAULT = 0
-VERBOSITY_VERBOSE = 1
-VERBOSITY_DUMP = 2
diff --git a/manage_externals/manic/repository.py b/manage_externals/manic/repository.py
deleted file mode 100644
index ea4230fb7b..0000000000
--- a/manage_externals/manic/repository.py
+++ /dev/null
@@ -1,98 +0,0 @@
-"""Base class representation of a repository
-"""
-
-from .externals_description import ExternalsDescription
-from .utils import fatal_error
-from .global_constants import EMPTY_STR
-
-
-class Repository(object):
-    """
-    Class to represent and operate on a repository description.
-    """
-
-    def __init__(self, component_name, repo):
-        """
-        Parse repo externals description
-        """
-        self._name = component_name
-        self._protocol = repo[ExternalsDescription.PROTOCOL]
-        self._tag = repo[ExternalsDescription.TAG]
-        self._branch = repo[ExternalsDescription.BRANCH]
-        self._hash = repo[ExternalsDescription.HASH]
-        self._url = repo[ExternalsDescription.REPO_URL]
-        self._sparse = repo[ExternalsDescription.SPARSE]
-
-        if self._url is EMPTY_STR:
-            fatal_error('repo must have a URL')
-
-        if ((self._tag is EMPTY_STR) and (self._branch is EMPTY_STR) and
-                (self._hash is EMPTY_STR)):
-            fatal_error('{0} repo must have a branch, tag or hash element')
-
-        ref_count = 0
-        if self._tag is not EMPTY_STR:
-            ref_count += 1
-        if self._branch is not EMPTY_STR:
-            ref_count += 1
-        if self._hash is not EMPTY_STR:
-            ref_count += 1
-        if ref_count != 1:
-            fatal_error('repo {0} must have exactly one of '
-                        'tag, branch or hash.'.format(self._name))
-
-    def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive):  # pylint: disable=unused-argument
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly update the source.
-        If the repo destination directory does not exist, checkout the correce
-        branch or tag.
-        NB: <recursive> is include as an argument for compatibility with
-            git functionality (repository_git.py)
-        """
-        msg = ('DEV_ERROR: checkout method must be implemented in all '
-               'repository classes! {0}'.format(self.__class__.__name__))
-        fatal_error(msg)
-
-    def status(self, stat, repo_dir_path):  # pylint: disable=unused-argument
-        """Report the status of the repo
-
-        """
-        msg = ('DEV_ERROR: status method must be implemented in all '
-               'repository classes! {0}'.format(self.__class__.__name__))
-        fatal_error(msg)
-
-    def submodules_file(self, repo_path=None):
-        # pylint: disable=no-self-use,unused-argument
-        """Stub for use by non-git VC systems"""
-        return None
-
-    def url(self):
-        """Public access of repo url.
-        """
-        return self._url
-
-    def tag(self):
-        """Public access of repo tag
-        """
-        return self._tag
-
-    def branch(self):
-        """Public access of repo branch.
-        """
-        return self._branch
-
-    def hash(self):
-        """Public access of repo hash.
-        """
-        return self._hash
-
-    def name(self):
-        """Public access of repo name.
-        """
-        return self._name
-
-    def protocol(self):
-        """Public access of repo protocol.
-        """
-        return self._protocol
diff --git a/manage_externals/manic/repository_factory.py b/manage_externals/manic/repository_factory.py
deleted file mode 100644
index 18c73ffc4b..0000000000
--- a/manage_externals/manic/repository_factory.py
+++ /dev/null
@@ -1,30 +0,0 @@
-"""Factory for creating and initializing the appropriate repository class
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-from .repository_git import GitRepository
-from .repository_svn import SvnRepository
-from .externals_description import ExternalsDescription
-from .utils import fatal_error
-
-
-def create_repository(component_name, repo_info, svn_ignore_ancestry=False):
-    """Determine what type of repository we have, i.e. git or svn, and
-    create the appropriate object.
-
-    Can return None (e.g. if protocol is 'externals_only').
-    """
-    protocol = repo_info[ExternalsDescription.PROTOCOL].lower()
-    if protocol == 'git':
-        repo = GitRepository(component_name, repo_info)
-    elif protocol == 'svn':
-        repo = SvnRepository(component_name, repo_info, ignore_ancestry=svn_ignore_ancestry)
-    elif protocol == 'externals_only':
-        repo = None
-    else:
-        msg = 'Unknown repo protocol "{0}"'.format(protocol)
-        fatal_error(msg)
-    return repo
diff --git a/manage_externals/manic/repository_git.py b/manage_externals/manic/repository_git.py
deleted file mode 100644
index adc666cc57..0000000000
--- a/manage_externals/manic/repository_git.py
+++ /dev/null
@@ -1,849 +0,0 @@
-"""Class for interacting with git repositories
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import copy
-import os
-
-from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR
-from .global_constants import VERBOSITY_VERBOSE
-from .repository import Repository
-from .externals_status import ExternalStatus
-from .externals_description import ExternalsDescription, git_submodule_status
-from .utils import expand_local_url, split_remote_url, is_remote_url
-from .utils import fatal_error, printlog
-from .utils import execute_subprocess
-
-
-class GitRepository(Repository):
-    """Class to represent and operate on a repository description.
-
-    For testing purpose, all system calls to git should:
-
-    * be isolated in separate functions with no application logic
-      * of the form:
-         - cmd = 'git -C {dirname} ...'.format(dirname=dirname).split()
-         - value = execute_subprocess(cmd, output_to_caller={T|F},
-                                      status_to_caller={T|F})
-         - return value
-      * be static methods (not rely on self)
-      * name as _git_subcommand_args(user_args)
-
-    This convention allows easy unit testing of the repository logic
-    by mocking the specific calls to return predefined results.
-
-    """
-
-    def __init__(self, component_name, repo):
-        """
-        repo: ExternalsDescription.
-        """
-        Repository.__init__(self, component_name, repo)
-        self._gitmodules = None
-        self._submods = None
-
-    # ----------------------------------------------------------------
-    #
-    # Public API, defined by Repository
-    #
-    # ----------------------------------------------------------------
-    def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive):
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly update the source.
-        If the repo destination directory does not exist, checkout the correct
-        branch or tag.
-        """
-        repo_dir_path = os.path.join(base_dir_path, repo_dir_name)
-        repo_dir_exists = os.path.exists(repo_dir_path)
-        if (repo_dir_exists and not os.listdir(
-                repo_dir_path)) or not repo_dir_exists:
-            self._clone_repo(base_dir_path, repo_dir_name, verbosity)
-        self._checkout_ref(repo_dir_path, verbosity, recursive)
-        gmpath = os.path.join(repo_dir_path,
-                              ExternalsDescription.GIT_SUBMODULES_FILENAME)
-        if os.path.exists(gmpath):
-            self._gitmodules = gmpath
-            self._submods = git_submodule_status(repo_dir_path)
-        else:
-            self._gitmodules = None
-            self._submods = None
-
-    def status(self, stat, repo_dir_path):
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly update the source.
-        If the repo destination directory does not exist, checkout the correct
-        branch or tag.
-        """
-        self._check_sync(stat, repo_dir_path)
-        if os.path.exists(repo_dir_path):
-            self._status_summary(stat, repo_dir_path)
-
-    def submodules_file(self, repo_path=None):
-        if repo_path is not None:
-            gmpath = os.path.join(repo_path,
-                                  ExternalsDescription.GIT_SUBMODULES_FILENAME)
-            if os.path.exists(gmpath):
-                self._gitmodules = gmpath
-                self._submods = git_submodule_status(repo_path)
-
-        return self._gitmodules
-
-    # ----------------------------------------------------------------
-    #
-    # Internal work functions
-    #
-    # ----------------------------------------------------------------
-    def _clone_repo(self, base_dir_path, repo_dir_name, verbosity):
-        """Clones repo_dir_name into base_dir_path.
-        """
-        self._git_clone(self._url, os.path.join(base_dir_path, repo_dir_name),
-                        verbosity=verbosity)
-
-    def _current_ref(self, dirname):
-        """Determine the *name* associated with HEAD at dirname.
-
-        If we're on a tag, then returns the tag name; otherwise, returns
-        the current hash. Returns an empty string if no reference can be
-        determined (e.g., if we're not actually in a git repository).
-
-        If we're on a branch, then the branch name is also included in
-        the returned string (in addition to the tag / hash).
-        """
-        ref_found = False
-
-        # If we're exactly at a tag, use that as the current ref
-        tag_found, tag_name = self._git_current_tag(dirname)
-        if tag_found:
-            current_ref = tag_name
-            ref_found = True
-
-        if not ref_found:
-            # Otherwise, use current hash as the current ref
-            hash_found, hash_name = self._git_current_hash(dirname)
-            if hash_found:
-                current_ref = hash_name
-                ref_found = True
-
-        if ref_found:
-            # If we're on a branch, include branch name in current ref
-            branch_found, branch_name = self._git_current_branch(dirname)
-            if branch_found:
-                current_ref = "{} (branch {})".format(current_ref, branch_name)
-        else:
-            # If we still can't find a ref, return empty string. This
-            # can happen if we're not actually in a git repo
-            current_ref = ''
-
-        return current_ref
-
-    def _check_sync(self, stat, repo_dir_path):
-        """Determine whether a git repository is in-sync with the model
-        description.
-
-        Because repos can have multiple remotes, the only criteria is
-        whether the branch or tag is the same.
-
-        """
-        if not os.path.exists(repo_dir_path):
-            # NOTE(bja, 2017-10) condition should have been determined
-            # by _Source() object and should never be here!
-            stat.sync_state = ExternalStatus.STATUS_ERROR
-        else:
-            git_dir = os.path.join(repo_dir_path, '.git')
-            if not os.path.exists(git_dir):
-                # NOTE(bja, 2017-10) directory exists, but no git repo
-                # info.... Can't test with subprocess git command
-                # because git will move up directory tree until it
-                # finds the parent repo git dir!
-                stat.sync_state = ExternalStatus.UNKNOWN
-            else:
-                self._check_sync_logic(stat, repo_dir_path)
-
-    def _check_sync_logic(self, stat, repo_dir_path):
-        """Compare the underlying hashes of the currently checkout ref and the
-        expected ref.
-
-        Output: sets the sync_state as well as the current and
-        expected ref in the input status object.
-
-        """
-        def compare_refs(current_ref, expected_ref):
-            """Compare the current and expected ref.
-
-            """
-            if current_ref == expected_ref:
-                status = ExternalStatus.STATUS_OK
-            else:
-                status = ExternalStatus.MODEL_MODIFIED
-            return status
-
-        # get the full hash of the current commit
-        _, current_ref = self._git_current_hash(repo_dir_path)
-
-        if self._branch:
-            if self._url == LOCAL_PATH_INDICATOR:
-                expected_ref = self._branch
-            else:
-                remote_name = self._remote_name_for_url(self._url,
-                                                        repo_dir_path)
-                if not remote_name:
-                    # git doesn't know about this remote. by definition
-                    # this is a modified state.
-                    expected_ref = "unknown_remote/{0}".format(self._branch)
-                else:
-                    expected_ref = "{0}/{1}".format(remote_name, self._branch)
-        elif self._hash:
-            expected_ref = self._hash
-        elif self._tag:
-            expected_ref = self._tag
-        else:
-            msg = 'In repo "{0}": none of branch, hash or tag are set'.format(
-                self._name)
-            fatal_error(msg)
-
-        # record the *names* of the current and expected branches
-        stat.current_version = self._current_ref(repo_dir_path)
-        stat.expected_version = copy.deepcopy(expected_ref)
-
-        if current_ref == EMPTY_STR:
-            stat.sync_state = ExternalStatus.UNKNOWN
-        else:
-            # get the underlying hash of the expected ref
-            revparse_status, expected_ref_hash = self._git_revparse_commit(
-                expected_ref, repo_dir_path)
-            if revparse_status:
-                # We failed to get the hash associated with
-                # expected_ref. Maybe we should assign this to some special
-                # status, but for now we're just calling this out-of-sync to
-                # remain consistent with how this worked before.
-                stat.sync_state = ExternalStatus.MODEL_MODIFIED
-            else:
-                # compare the underlying hashes
-                stat.sync_state = compare_refs(current_ref, expected_ref_hash)
-
-    @classmethod
-    def _remote_name_for_url(cls, remote_url, dirname):
-        """Return the remote name matching remote_url (or None)
-
-        """
-        git_output = cls._git_remote_verbose(dirname)
-        git_output = git_output.splitlines()
-        for line in git_output:
-            data = line.strip()
-            if not data:
-                continue
-            data = data.split()
-            name = data[0].strip()
-            url = data[1].strip()
-            if remote_url == url:
-                return name
-        return None
-
-    def _create_remote_name(self):
-        """The url specified in the externals description file was not known
-        to git. We need to add it, which means adding a unique and
-        safe name....
-
-        The assigned name needs to be safe for git to use, e.g. can't
-        look like a path 'foo/bar' and work with both remote and local paths.
-
-        Remote paths include but are not limited to: git, ssh, https,
-        github, gitlab, bitbucket, custom server, etc.
-
-        Local paths can be relative or absolute. They may contain
-        shell variables, e.g. ${REPO_ROOT}/repo_name, or username
-        expansion, i.e. ~/ or ~someuser/.
-
-        Relative paths must be at least one layer of redirection, i.e.
-        container/../ext_repo, but may be many layers deep, e.g.
-        container/../../../../../ext_repo
-
-        NOTE(bja, 2017-11)
-
-            The base name below may not be unique, for example if the
-            user has local paths like:
-
-            /path/to/my/repos/nice_repo
-            /path/to/other/repos/nice_repo
-
-            But the current implementation should cover most common
-            use cases for remotes and still provide usable names.
-
-        """
-        url = copy.deepcopy(self._url)
-        if is_remote_url(url):
-            url = split_remote_url(url)
-        else:
-            url = expand_local_url(url, self._name)
-        url = url.split('/')
-        repo_name = url[-1]
-        base_name = url[-2]
-        # repo name should nominally already be something that git can
-        # deal with. We need to remove other possibly troublesome
-        # punctuation, e.g. /, $, from the base name.
-        unsafe_characters = '!@#$%^&*()[]{}\\/,;~'
-        for unsafe in unsafe_characters:
-            base_name = base_name.replace(unsafe, '')
-        remote_name = "{0}_{1}".format(base_name, repo_name)
-        return remote_name
-
-    def _checkout_ref(self, repo_dir, verbosity, submodules):
-        """Checkout the user supplied reference
-        if <submodules> is True, recursively initialize and update
-        the repo's submodules
-        """
-        # import pdb; pdb.set_trace()
-        if self._url.strip() == LOCAL_PATH_INDICATOR:
-            self._checkout_local_ref(verbosity, submodules, repo_dir)
-        else:
-            self._checkout_external_ref(verbosity, submodules, repo_dir)
-
-        if self._sparse:
-            self._sparse_checkout(repo_dir, verbosity)
-
-
-    def _checkout_local_ref(self, verbosity, submodules, dirname):
-        """Checkout the reference considering the local repo only. Do not
-        fetch any additional remotes or specify the remote when
-        checkout out the ref.
-        if <submodules> is True, recursively initialize and update
-        the repo's submodules
-        """
-        if self._tag:
-            ref = self._tag
-        elif self._branch:
-            ref = self._branch
-        else:
-            ref = self._hash
-
-        self._check_for_valid_ref(ref, remote_name=None,
-                                  dirname=dirname)
-        self._git_checkout_ref(ref, verbosity, submodules, dirname)
-
-    def _checkout_external_ref(self, verbosity, submodules, dirname):
-        """Checkout the reference from a remote repository into dirname.
-        if <submodules> is True, recursively initialize and update
-        the repo's submodules. 
-        Note that this results in a 'detached HEAD' state if checking out
-        a branch, because we check out the remote branch rather than the
-        local. See https://github.com/ESMCI/manage_externals/issues/34 for 
-        more discussion.
-        """
-        if self._tag:
-            ref = self._tag
-        elif self._branch:
-            ref = self._branch
-        else:
-            ref = self._hash
-
-        remote_name = self._remote_name_for_url(self._url, dirname)
-        if not remote_name:
-            remote_name = self._create_remote_name()
-            self._git_remote_add(remote_name, self._url, dirname)
-        self._git_fetch(remote_name, dirname)
-
-        # NOTE(bja, 2018-03) we need to send separate ref and remote
-        # name to check_for_vaild_ref, but the combined name to
-        # checkout_ref!
-        self._check_for_valid_ref(ref, remote_name, dirname)
-
-        if self._branch:
-            # Prepend remote name to branch. This means we avoid various
-            # special cases if the local branch is not tracking the remote or
-            # cannot be trivially fast-forwarded to match; but, it also
-            # means we end up in a 'detached HEAD' state.
-            ref = '{0}/{1}'.format(remote_name, ref)
-        self._git_checkout_ref(ref, verbosity, submodules, dirname)
-
-    def _sparse_checkout(self, repo_dir, verbosity):
-        """Use git read-tree to thin the working tree."""
-        cmd = ['cp', os.path.join(repo_dir, self._sparse),
-               os.path.join(repo_dir,
-                            '.git/info/sparse-checkout')]
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-        self._git_sparse_checkout(verbosity, repo_dir)
-
-    def _check_for_valid_ref(self, ref, remote_name, dirname):
-        """Try some basic sanity checks on the user supplied reference so we
-        can provide a more useful error message than calledprocess
-        error...
-
-        remote_name can be NOne
-        """
-        is_tag = self._ref_is_tag(ref, dirname)
-        is_branch = self._ref_is_branch(ref, remote_name, dirname)
-        is_hash = self._ref_is_hash(ref, dirname)
-
-        is_valid = is_tag or is_branch or is_hash
-        if not is_valid:
-            msg = ('In repo "{0}": reference "{1}" does not appear to be a '
-                   'valid tag, branch or hash! Please verify the reference '
-                   'name (e.g. spelling), is available from: {2} '.format(
-                       self._name, ref, self._url))
-            fatal_error(msg)
-
-        if is_tag:
-            is_unique_tag, msg = self._is_unique_tag(ref, remote_name,
-                                                     dirname)
-            if not is_unique_tag:
-                msg = ('In repo "{0}": tag "{1}" {2}'.format(
-                    self._name, self._tag, msg))
-                fatal_error(msg)
-
-        return is_valid
-
-    def _is_unique_tag(self, ref, remote_name, dirname):
-        """Verify that a reference is a valid tag and is unique (not a branch)
-
-        Tags may be tag names, or SHA id's. It is also possible that a
-        branch and tag have the some name.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_tag = self._ref_is_tag(ref, dirname)
-        is_branch = self._ref_is_branch(ref, remote_name, dirname)
-        is_hash = self._ref_is_hash(ref, dirname)
-
-        msg = ''
-        is_unique_tag = False
-        if is_tag and not is_branch:
-            # unique tag
-            msg = 'is ok'
-            is_unique_tag = True
-        elif is_tag and is_branch:
-            msg = ('is both a branch and a tag. git may checkout the branch '
-                   'instead of the tag depending on your version of git.')
-            is_unique_tag = False
-        elif not is_tag and is_branch:
-            msg = ('is a branch, and not a tag. If you intended to checkout '
-                   'a branch, please change the externals description to be '
-                   'a branch. If you intended to checkout a tag, it does not '
-                   'exist. Please check the name.')
-            is_unique_tag = False
-        else:  # not is_tag and not is_branch:
-            if is_hash:
-                # probably a sha1 or HEAD, etc, we call it a tag
-                msg = 'is ok'
-                is_unique_tag = True
-            else:
-                # undetermined state.
-                msg = ('does not appear to be a valid tag, branch or hash! '
-                       'Please check the name and repository.')
-                is_unique_tag = False
-
-        return is_unique_tag, msg
-
-    def _ref_is_tag(self, ref, dirname):
-        """Verify that a reference is a valid tag according to git.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-        """
-        is_tag = False
-        value = self._git_showref_tag(ref, dirname)
-        if value == 0:
-            is_tag = True
-        return is_tag
-
-    def _ref_is_branch(self, ref, remote_name, dirname):
-        """Verify if a ref is any kind of branch (local, tracked remote,
-        untracked remote).
-
-        remote_name can be None.
-        """
-        local_branch = False
-        remote_branch = False
-        if remote_name:
-            remote_branch = self._ref_is_remote_branch(ref, remote_name,
-                                                       dirname)
-        local_branch = self._ref_is_local_branch(ref, dirname)
-
-        is_branch = False
-        if local_branch or remote_branch:
-            is_branch = True
-        return is_branch
-
-    def _ref_is_local_branch(self, ref, dirname):
-        """Verify that a reference is a valid branch according to git.
-
-        show-ref branch returns local branches that have been
-        previously checked out. It will not necessarily pick up
-        untracked remote branches.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_branch = False
-        value = self._git_showref_branch(ref, dirname)
-        if value == 0:
-            is_branch = True
-        return is_branch
-
-    def _ref_is_remote_branch(self, ref, remote_name, dirname):
-        """Verify that a reference is a valid branch according to git.
-
-        show-ref branch returns local branches that have been
-        previously checked out. It will not necessarily pick up
-        untracked remote branches.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_branch = False
-        value = self._git_lsremote_branch(ref, remote_name, dirname)
-        if value == 0:
-            is_branch = True
-        return is_branch
-
-    def _ref_is_commit(self, ref, dirname):
-        """Verify that a reference is a valid commit according to git.
-
-        This could be a tag, branch, sha1 id, HEAD and potentially others...
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-        """
-        is_commit = False
-        value, _ = self._git_revparse_commit(ref, dirname)
-        if value == 0:
-            is_commit = True
-        return is_commit
-
-    def _ref_is_hash(self, ref, dirname):
-        """Verify that a reference is a valid hash according to git.
-
-        Git doesn't seem to provide an exact way to determine if user
-        supplied reference is an actual hash. So we verify that the
-        ref is a valid commit and return the underlying commit
-        hash. Then check that the commit hash begins with the user
-        supplied string.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_hash = False
-        status, git_output = self._git_revparse_commit(ref, dirname)
-        if status == 0:
-            if git_output.strip().startswith(ref):
-                is_hash = True
-        return is_hash
-
-    def _status_summary(self, stat, repo_dir_path):
-        """Determine the clean/dirty status of a git repository
-
-        """
-        git_output = self._git_status_porcelain_v1z(repo_dir_path)
-        is_dirty = self._status_v1z_is_dirty(git_output)
-        if is_dirty:
-            stat.clean_state = ExternalStatus.DIRTY
-        else:
-            stat.clean_state = ExternalStatus.STATUS_OK
-
-        # Now save the verbose status output incase the user wants to
-        # see it.
-        stat.status_output = self._git_status_verbose(repo_dir_path)
-
-    @staticmethod
-    def _status_v1z_is_dirty(git_output):
-        """Parse the git status output from --porcelain=v1 -z and determine if
-        the repo status is clean or dirty. Dirty means:
-
-        * modified files
-        * missing files
-        * added files
-        * removed
-        * renamed
-        * unmerged
-
-        Whether untracked files are considered depends on how the status
-        command was run (i.e., whether it was run with the '-u' option).
-
-        NOTE: Based on the above definition, the porcelain status
-        should be an empty string to be considered 'clean'. Of course
-        this assumes we only get an empty string from an status
-        command on a clean checkout, and not some error
-        condition... Could alse use 'git diff --quiet'.
-
-        """
-        is_dirty = False
-        if git_output:
-            is_dirty = True
-        return is_dirty
-
-    # ----------------------------------------------------------------
-    #
-    # system call to git for information gathering
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _git_current_hash(dirname):
-        """Return the full hash of the currently checked-out version.
-
-        Returns a tuple, (hash_found, hash), where hash_found is a
-        logical specifying whether a hash was found for HEAD (False
-        could mean we're not in a git repository at all). (If hash_found
-        is False, then hash is ''.)
-        """
-        status, git_output = GitRepository._git_revparse_commit("HEAD",
-                                                                dirname)
-        hash_found = not status
-        if not hash_found:
-            git_output = ''
-        return hash_found, git_output
-
-    @staticmethod
-    def _git_current_remote_branch(dirname):
-        """Determines the name of the current remote branch, if any.
-
-        if dir is None, uses the cwd.
-
-        Returns a tuple, (branch_found, branch_name), where branch_found
-        is a bool specifying whether a branch name was found for
-        HEAD. (If branch_found is False, then branch_name is '').
-        branch_name is in the format '$remote/$branch', e.g. 'origin/foo'.
-        """
-        branch_found = False
-        branch_name = ''
-        
-        cmd = 'git -C {dirname} log -n 1 --pretty=%d HEAD'.format(
-            dirname=dirname).split()
-        status, git_output = execute_subprocess(cmd,
-                                                output_to_caller=True,
-                                                status_to_caller=True)
-        branch_found = 'HEAD,' in git_output
-        if branch_found:
-            # git_output is of the form " (HEAD, origin/blah)"
-            branch_name = git_output.split(',')[1].strip()[:-1]
-        return branch_found, branch_name
-    
-    @staticmethod
-    def _git_current_branch(dirname):
-        """Determines the name of the current local branch.
-
-        Returns a tuple, (branch_found, branch_name), where branch_found
-        is a bool specifying whether a branch name was found for
-        HEAD. (If branch_found is False, then branch_name is ''.)
-        Note that currently we check out the remote branch rather than
-        the local, so this command does not return the just-checked-out
-        branch. See _git_current_remote_branch.
-        """
-        cmd = 'git -C {dirname} symbolic-ref --short -q HEAD'.format(
-            dirname=dirname).split()
-        status, git_output = execute_subprocess(cmd,
-                                                output_to_caller=True,
-                                                status_to_caller=True)
-        branch_found = not status
-        if branch_found:
-            git_output = git_output.strip()
-        else:
-            git_output = ''
-        return branch_found, git_output
-
-    @staticmethod
-    def _git_current_tag(dirname):
-        """Determines the name tag corresponding to HEAD (if any).
-
-        if dirname is None, uses the cwd.
-
-        Returns a tuple, (tag_found, tag_name), where tag_found is a
-        bool specifying whether we found a tag name corresponding to
-        HEAD. (If tag_found is False, then tag_name is ''.)
-        """
-        cmd = 'git -C {dirname} describe --exact-match --tags HEAD'.format(
-            dirname=dirname).split()
-        status, git_output = execute_subprocess(cmd,
-                                                output_to_caller=True,
-                                                status_to_caller=True)
-        tag_found = not status
-        if tag_found:
-            git_output = git_output.strip()
-        else:
-            git_output = ''
-        return tag_found, git_output
-
-    @staticmethod
-    def _git_showref_tag(ref, dirname):
-        """Run git show-ref check if the user supplied ref is a tag.
-
-        could also use git rev-parse --quiet --verify tagname^{tag}
-        """
-        cmd = ('git -C {dirname} show-ref --quiet --verify refs/tags/{ref}'
-               .format(dirname=dirname, ref=ref).split())
-        status = execute_subprocess(cmd, status_to_caller=True)
-        return status
-
-    @staticmethod
-    def _git_showref_branch(ref, dirname):
-        """Run git show-ref check if the user supplied ref is a local or
-        tracked remote branch.
-
-        """
-        cmd = ('git -C {dirname} show-ref --quiet --verify refs/heads/{ref}'
-               .format(dirname=dirname, ref=ref).split())
-        status = execute_subprocess(cmd, status_to_caller=True)
-        return status
-
-    @staticmethod
-    def _git_lsremote_branch(ref, remote_name, dirname):
-        """Run git ls-remote to check if the user supplied ref is a remote
-        branch that is not being tracked
-
-        """
-        cmd = ('git -C {dirname} ls-remote --exit-code --heads '
-               '{remote_name} {ref}').format(
-                   dirname=dirname, remote_name=remote_name, ref=ref).split()
-        status = execute_subprocess(cmd, status_to_caller=True)
-        return status
-
-    @staticmethod
-    def _git_revparse_commit(ref, dirname):
-        """Run git rev-parse to detect if a reference is a SHA, HEAD or other
-        valid commit.
-
-        """
-        cmd = ('git -C {dirname} rev-parse --quiet --verify {ref}^{commit}'
-               .format(dirname=dirname, ref=ref, commit='{commit}').split())
-        status, git_output = execute_subprocess(cmd, status_to_caller=True,
-                                                output_to_caller=True)
-        git_output = git_output.strip()
-        return status, git_output
-
-    @staticmethod
-    def _git_status_porcelain_v1z(dirname):
-        """Run git status to obtain repository information.
-
-        This is run with '--untracked=no' to ignore untracked files.
-
-        The machine-portable format that is guaranteed not to change
-        between git versions or *user configuration*.
-
-        """
-        cmd = ('git -C {dirname} status --untracked-files=no --porcelain -z'
-               .format(dirname=dirname)).split()
-        git_output = execute_subprocess(cmd, output_to_caller=True)
-        return git_output
-
-    @staticmethod
-    def _git_status_verbose(dirname):
-        """Run the git status command to obtain repository information.
-        """
-        cmd = 'git -C {dirname} status'.format(dirname=dirname).split()
-        git_output = execute_subprocess(cmd, output_to_caller=True)
-        return git_output
-
-    @staticmethod
-    def _git_remote_verbose(dirname):
-        """Run the git remote command to obtain repository information.
-
-        Returned string is of the form:
-        myfork  git@github.com:johnpaulalex/manage_externals_jp.git (fetch)
-        myfork  git@github.com:johnpaulalex/manage_externals_jp.git (push)
-        """
-        cmd = 'git -C {dirname} remote --verbose'.format(
-            dirname=dirname).split()
-        return execute_subprocess(cmd, output_to_caller=True)
-
-    @staticmethod
-    def has_submodules(repo_dir_path):
-        """Return True iff the repository at <repo_dir_path> has a 
-        '.gitmodules' file
-        """
-        fname = os.path.join(repo_dir_path,
-                             ExternalsDescription.GIT_SUBMODULES_FILENAME)
-
-        return os.path.exists(fname)
-
-    # ----------------------------------------------------------------
-    #
-    # system call to git for sideffects modifying the working tree
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _git_clone(url, repo_dir_name, verbosity):
-        """Clones url into repo_dir_name.
-        """
-        cmd = 'git clone --quiet {url} {repo_dir_name}'.format(
-            url=url, repo_dir_name=repo_dir_name).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_remote_add(name, url, dirname):
-        """Run the git remote command for the side effect of adding a remote
-        """
-        cmd = 'git -C {dirname} remote add {name} {url}'.format(
-            dirname=dirname, name=name, url=url).split()
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_fetch(remote_name, dirname):
-        """Run the git fetch command for the side effect of updating the repo
-        """
-        cmd = 'git -C {dirname} fetch --quiet --tags {remote_name}'.format(
-            dirname=dirname, remote_name=remote_name).split()
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_checkout_ref(ref, verbosity, submodules, dirname):
-        """Run the git checkout command for the side effect of updating the repo
-
-        Param: ref is a reference to a local or remote object in the
-        form 'origin/my_feature', or 'tag1'.
-
-        """
-        cmd = 'git -C {dirname} checkout --quiet {ref}'.format(
-            dirname=dirname, ref=ref).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-        if submodules:
-            GitRepository._git_update_submodules(verbosity, dirname)
-
-    @staticmethod
-    def _git_sparse_checkout(verbosity, dirname):
-        """Configure repo via read-tree."""
-        cmd = 'git -C {dirname} config core.sparsecheckout true'.format(
-            dirname=dirname).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-        cmd = 'git -C {dirname} read-tree -mu HEAD'.format(
-            dirname=dirname).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_update_submodules(verbosity, dirname):
-        """Run git submodule update for the side effect of updating this
-        repo's submodules.
-        """
-        # First, verify that we have a .gitmodules file
-        if os.path.exists(
-                os.path.join(dirname,
-                             ExternalsDescription.GIT_SUBMODULES_FILENAME)):
-            cmd = ('git -C {dirname} submodule update --init --recursive'
-                   .format(dirname=dirname)).split()
-            if verbosity >= VERBOSITY_VERBOSE:
-                printlog('    {0}'.format(' '.join(cmd)))
-
-            execute_subprocess(cmd)
diff --git a/manage_externals/manic/repository_svn.py b/manage_externals/manic/repository_svn.py
deleted file mode 100644
index 922855d34e..0000000000
--- a/manage_externals/manic/repository_svn.py
+++ /dev/null
@@ -1,288 +0,0 @@
-"""Class for interacting with svn repositories
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import re
-import xml.etree.ElementTree as ET
-
-from .global_constants import EMPTY_STR, VERBOSITY_VERBOSE
-from .repository import Repository
-from .externals_status import ExternalStatus
-from .utils import fatal_error, indent_string, printlog
-from .utils import execute_subprocess
-
-
-class SvnRepository(Repository):
-    """
-    Class to represent and operate on a repository description.
-
-    For testing purpose, all system calls to svn should:
-
-    * be isolated in separate functions with no application logic
-      * of the form:
-         - cmd = ['svn', ...]
-         - value = execute_subprocess(cmd, output_to_caller={T|F},
-                                      status_to_caller={T|F})
-         - return value
-      * be static methods (not rely on self)
-      * name as _svn_subcommand_args(user_args)
-
-    This convention allows easy unit testing of the repository logic
-    by mocking the specific calls to return predefined results.
-
-    """
-    RE_URLLINE = re.compile(r'^URL:')
-
-    def __init__(self, component_name, repo, ignore_ancestry=False):
-        """
-        Parse repo (a <repo> XML element).
-        """
-        Repository.__init__(self, component_name, repo)
-        self._ignore_ancestry = ignore_ancestry
-        if self._url.endswith('/'):
-            # there is already a '/' separator in the URL; no need to add another
-            url_sep = ''
-        else:
-            url_sep = '/'
-        if self._branch:
-            self._url = self._url + url_sep + self._branch
-        elif self._tag:
-            self._url = self._url + url_sep + self._tag
-        else:
-            msg = "DEV_ERROR in svn repository. Shouldn't be here!"
-            fatal_error(msg)
-
-    # ----------------------------------------------------------------
-    #
-    # Public API, defined by Repository
-    #
-    # ----------------------------------------------------------------
-    def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive):  # pylint: disable=unused-argument
-        """Checkout or update the working copy
-
-        If the repo destination directory exists, switch the sandbox to
-        match the externals description.
-
-        If the repo destination directory does not exist, checkout the
-        correct branch or tag.
-        NB: <recursive> is include as an argument for compatibility with
-            git functionality (repository_git.py)
-
-        """
-        repo_dir_path = os.path.join(base_dir_path, repo_dir_name)
-        if os.path.exists(repo_dir_path):
-            cwd = os.getcwd()
-            os.chdir(repo_dir_path)
-            self._svn_switch(self._url, self._ignore_ancestry, verbosity)
-            # svn switch can lead to a conflict state, but it gives a
-            # return code of 0. So now we need to make sure that we're
-            # in a clean (non-conflict) state.
-            self._abort_if_dirty(repo_dir_path,
-                                 "Expected clean state following switch")
-            os.chdir(cwd)
-        else:
-            self._svn_checkout(self._url, repo_dir_path, verbosity)
-
-    def status(self, stat, repo_dir_path):
-        """
-        Check and report the status of the repository
-        """
-        self._check_sync(stat, repo_dir_path)
-        if os.path.exists(repo_dir_path):
-            self._status_summary(stat, repo_dir_path)
-
-    # ----------------------------------------------------------------
-    #
-    # Internal work functions
-    #
-    # ----------------------------------------------------------------
-    def _check_sync(self, stat, repo_dir_path):
-        """Check to see if repository directory exists and is at the expected
-        url.  Return: status object
-
-        """
-        if not os.path.exists(repo_dir_path):
-            # NOTE(bja, 2017-10) this state should have been handled by
-            # the source object and we never get here!
-            stat.sync_state = ExternalStatus.STATUS_ERROR
-        else:
-            svn_output = self._svn_info(repo_dir_path)
-            if not svn_output:
-                # directory exists, but info returned nothing. .svn
-                # directory removed or incomplete checkout?
-                stat.sync_state = ExternalStatus.UNKNOWN
-            else:
-                stat.sync_state, stat.current_version = \
-                    self._check_url(svn_output, self._url)
-            stat.expected_version = '/'.join(self._url.split('/')[3:])
-
-    def _abort_if_dirty(self, repo_dir_path, message):
-        """Check if the repo is in a dirty state; if so, abort with a
-        helpful message.
-
-        """
-
-        stat = ExternalStatus()
-        self._status_summary(stat, repo_dir_path)
-        if stat.clean_state != ExternalStatus.STATUS_OK:
-            status = self._svn_status_verbose(repo_dir_path)
-            status = indent_string(status, 4)
-            errmsg = """In directory
-    {cwd}
-
-svn status now shows:
-{status}
-
-ERROR: {message}
-
-One possible cause of this problem is that there may have been untracked
-files in your working directory that had the same name as tracked files
-in the new revision.
-
-To recover: Clean up the above directory (resolving conflicts, etc.),
-then rerun checkout_externals.
-""".format(cwd=repo_dir_path, message=message, status=status)
-
-            fatal_error(errmsg)
-
-    @staticmethod
-    def _check_url(svn_output, expected_url):
-        """Determine the svn url from svn info output and return whether it
-        matches the expected value.
-
-        """
-        url = None
-        for line in svn_output.splitlines():
-            if SvnRepository.RE_URLLINE.match(line):
-                url = line.split(': ')[1].strip()
-                break
-        if not url:
-            status = ExternalStatus.UNKNOWN
-        elif url == expected_url:
-            status = ExternalStatus.STATUS_OK
-        else:
-            status = ExternalStatus.MODEL_MODIFIED
-
-        if url:
-            current_version = '/'.join(url.split('/')[3:])
-        else:
-            current_version = EMPTY_STR
-
-        return status, current_version
-
-    def _status_summary(self, stat, repo_dir_path):
-        """Report whether the svn repository is in-sync with the model
-        description and whether the sandbox is clean or dirty.
-
-        """
-        svn_output = self._svn_status_xml(repo_dir_path)
-        is_dirty = self.xml_status_is_dirty(svn_output)
-        if is_dirty:
-            stat.clean_state = ExternalStatus.DIRTY
-        else:
-            stat.clean_state = ExternalStatus.STATUS_OK
-
-        # Now save the verbose status output incase the user wants to
-        # see it.
-        stat.status_output = self._svn_status_verbose(repo_dir_path)
-
-    @staticmethod
-    def xml_status_is_dirty(svn_output):
-        """Parse svn status xml output and determine if the working copy is
-        clean or dirty. Dirty is defined as:
-
-        * modified files
-        * added files
-        * deleted files
-        * missing files
-
-        Unversioned files do not affect the clean/dirty status.
-
-        'external' is also an acceptable state
-
-        """
-        # pylint: disable=invalid-name
-        SVN_EXTERNAL = 'external'
-        SVN_UNVERSIONED = 'unversioned'
-        # pylint: enable=invalid-name
-
-        is_dirty = False
-        try:
-            xml_status = ET.fromstring(svn_output)
-        except BaseException:
-            fatal_error(
-                "SVN returned invalid XML message {}".format(svn_output))
-        xml_target = xml_status.find('./target')
-        entries = xml_target.findall('./entry')
-        for entry in entries:
-            status = entry.find('./wc-status')
-            item = status.get('item')
-            if item == SVN_EXTERNAL:
-                continue
-            if item == SVN_UNVERSIONED:
-                continue
-            is_dirty = True
-            break
-        return is_dirty
-
-    # ----------------------------------------------------------------
-    #
-    # system call to svn for information gathering
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _svn_info(repo_dir_path):
-        """Return results of svn info command
-        """
-        cmd = ['svn', 'info', repo_dir_path]
-        output = execute_subprocess(cmd, output_to_caller=True)
-        return output
-
-    @staticmethod
-    def _svn_status_verbose(repo_dir_path):
-        """capture the full svn status output
-        """
-        cmd = ['svn', 'status', repo_dir_path]
-        svn_output = execute_subprocess(cmd, output_to_caller=True)
-        return svn_output
-
-    @staticmethod
-    def _svn_status_xml(repo_dir_path):
-        """
-        Get status of the subversion sandbox in repo_dir
-        """
-        cmd = ['svn', 'status', '--xml', repo_dir_path]
-        svn_output = execute_subprocess(cmd, output_to_caller=True)
-        return svn_output
-
-    # ----------------------------------------------------------------
-    #
-    # system call to svn for sideffects modifying the working tree
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _svn_checkout(url, repo_dir_path, verbosity):
-        """
-        Checkout a subversion repository (repo_url) to checkout_dir.
-        """
-        cmd = ['svn', 'checkout', '--quiet', url, repo_dir_path]
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _svn_switch(url, ignore_ancestry, verbosity):
-        """
-        Switch branches for in an svn sandbox
-        """
-        cmd = ['svn', 'switch', '--quiet']
-        if ignore_ancestry:
-            cmd.append('--ignore-ancestry')
-        cmd.append(url)
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
diff --git a/manage_externals/manic/sourcetree.py b/manage_externals/manic/sourcetree.py
deleted file mode 100644
index cf2a5b7569..0000000000
--- a/manage_externals/manic/sourcetree.py
+++ /dev/null
@@ -1,425 +0,0 @@
-"""
-Classes to represent an externals config file (SourceTree) and the components
-within it (_External).
-"""
-
-import errno
-import logging
-import os
-
-from .externals_description import ExternalsDescription
-from .externals_description import read_externals_description_file
-from .externals_description import create_externals_description
-from .repository_factory import create_repository
-from .repository_git import GitRepository
-from .externals_status import ExternalStatus
-from .utils import fatal_error, printlog
-from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR
-from .global_constants import VERBOSITY_VERBOSE
-
-class _External(object):
-    """
-    A single component hosted in an external repository (and any children).
-
-    The component may or may not be checked-out upon construction.
-    """
-    # pylint: disable=R0902
-
-    def __init__(self, root_dir, name, local_path, required, subexternals_path,
-                 repo, svn_ignore_ancestry, subexternal_sourcetree):
-        """Create a single external component (checked out or not).
-
-        Input:
-            root_dir : string - the (checked-out) parent repo's root dir.
-            local_path : string - this external's (checked-out) subdir relative
-            to root_dir, e.g. "components/mom"
-            repo: Repository - the repo object for this external. Can be None (e.g. if this external just refers to another external file).
-
-            name : string - name of this external (as named by the parent 
-            reference).  May or may not correspond to something in the path.
-
-            ext_description : dict - source ExternalsDescription object
-
-            svn_ignore_ancestry : bool - use --ignore-externals with svn switch
-
-            subexternals_path: string - path to sub-externals config file, if any. Relative to local_path, or special value 'none'.
-            subexternal_sourcetree: SourceTree - corresponding to subexternals_path, if subexternals_path exists (it might not, if it is not checked out yet).
-        """
-        self._name = name
-        self._required = required
-        
-        self._stat = None  # Populated in status()
-
-        self._local_path = local_path
-        # _repo_dir_path : full repository directory, e.g.
-        # "<root_dir>/components/mom"
-        repo_dir = os.path.join(root_dir, local_path)
-        self._repo_dir_path = os.path.abspath(repo_dir)
-        # _base_dir_path : base directory *containing* the repository, e.g.
-        # "<root_dir>/components"
-        self._base_dir_path = os.path.dirname(self._repo_dir_path)
-        # _repo_dir_name : base_dir_path + repo_dir_name = repo_dir_path
-        # e.g., "mom"
-        self._repo_dir_name = os.path.basename(self._repo_dir_path)
-        self._repo = repo
-
-        # Does this component have subcomponents aka an externals config?
-        self._subexternals_path = subexternals_path
-        self._subexternal_sourcetree = subexternal_sourcetree
-        
-
-    def get_name(self):
-        """
-        Return the external object's name
-        """
-        return self._name
-
-    def get_local_path(self):
-        """
-        Return the external object's path
-        """
-        return self._local_path
-
-    def get_repo_dir_path(self):
-        return self._repo_dir_path
-
-    def get_subexternals_path(self):
-        return self._subexternals_path
-
-    def get_repo(self):
-        return self._repo
-    
-    def status(self, force=False, print_progress=False):
-        """
-        Returns status of this component and all subcomponents.
-
-        Returns a dict mapping our local path (not component name!) to an
-        ExternalStatus dict. Any subcomponents will have their own top-level
-        path keys.  Note the return value includes entries for this and all 
-        subcomponents regardless of whether they are locally installed or not.
-
-        Side-effect: If self._stat is empty or force is True, calculates _stat.
-        """
-        calc_stat = force or not self._stat
-
-        if calc_stat:
-            self._stat = ExternalStatus()
-            self._stat.path = self.get_local_path()
-            if not self._required:
-                self._stat.source_type = ExternalStatus.OPTIONAL
-            elif self._local_path == LOCAL_PATH_INDICATOR:
-                # LOCAL_PATH_INDICATOR, '.' paths, are standalone
-                # component directories that are not managed by
-                # checkout_subexternals.
-                self._stat.source_type = ExternalStatus.STANDALONE
-            else:
-                # managed by checkout_subexternals
-                self._stat.source_type = ExternalStatus.MANAGED
-
-        subcomponent_stats = {}
-        if not os.path.exists(self._repo_dir_path):
-            if calc_stat:
-                # No local repository.
-                self._stat.sync_state = ExternalStatus.EMPTY
-                msg = ('status check: repository directory for "{0}" does not '
-                       'exist.'.format(self._name))
-                logging.info(msg)
-                self._stat.current_version = 'not checked out'
-                # NOTE(bja, 2018-01) directory doesn't exist, so we cannot
-                # use repo to determine the expected version. We just take
-                # a best-guess based on the assumption that only tag or
-                # branch should be set, but not both.
-                if not self._repo:
-                    self._stat.expected_version = 'unknown'
-                else:
-                    self._stat.expected_version = self._repo.tag() + self._repo.branch()
-        else:
-            # Merge local repository state (e.g. clean/dirty) into self._stat.
-            if calc_stat and self._repo:
-                self._repo.status(self._stat, self._repo_dir_path)
-
-            # Status of subcomponents, if any.
-            if self._subexternals_path and self._subexternal_sourcetree:
-                cwd = os.getcwd()
-                # SourceTree.status() expects to be called from the correct
-                # root directory.
-                os.chdir(self._repo_dir_path)
-                subcomponent_stats = self._subexternal_sourcetree.status(self._local_path, force=force, print_progress=print_progress)
-                os.chdir(cwd)
-
-        # Merge our status + subcomponent statuses into one return dict keyed
-        # by component path.
-        all_stats = {}
-        # don't add the root component because we don't manage it
-        # and can't provide useful info about it.
-        if self._local_path != LOCAL_PATH_INDICATOR:
-            # store the stats under the local_path, not comp name so
-            # it will be sorted correctly
-            all_stats[self._stat.path] = self._stat
-
-        if subcomponent_stats:
-            all_stats.update(subcomponent_stats)
-
-        return all_stats
-
-    def checkout(self, verbosity):
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly updateit.
-        If the repo destination directory does not exist, checkout the correct
-        branch or tag.
-        Does not check out sub-externals, see SourceTree.checkout().
-        """
-        # Make sure we are in correct location
-        if not os.path.exists(self._repo_dir_path):
-            # repository directory doesn't exist. Need to check it
-            # out, and for that we need the base_dir_path to exist
-            try:
-                os.makedirs(self._base_dir_path)
-            except OSError as error:
-                if error.errno != errno.EEXIST:
-                    msg = 'Could not create directory "{0}"'.format(
-                        self._base_dir_path)
-                    fatal_error(msg)
-
-        if not self._stat:
-            self.status()
-            assert self._stat
-            
-        if self._stat.source_type != ExternalStatus.STANDALONE:
-            if verbosity >= VERBOSITY_VERBOSE:
-                # NOTE(bja, 2018-01) probably do not want to pass
-                # verbosity in this case, because if (verbosity ==
-                # VERBOSITY_DUMP), then the previous status output would
-                # also be dumped, adding noise to the output.
-                self._stat.log_status_message(VERBOSITY_VERBOSE)
-
-        if self._repo:
-            if self._stat.sync_state == ExternalStatus.STATUS_OK:
-                # If we're already in sync, avoid showing verbose output
-                # from the checkout command, unless the verbosity level
-                # is 2 or more.
-                checkout_verbosity = verbosity - 1
-            else:
-                checkout_verbosity = verbosity
-
-            self._repo.checkout(self._base_dir_path, self._repo_dir_name,
-                                checkout_verbosity, self.clone_recursive())
-
-    def replace_subexternal_sourcetree(self, sourcetree):
-        self._subexternal_sourcetree = sourcetree
-
-    def clone_recursive(self):
-        'Return True iff any .gitmodules files should be processed'
-        # Try recursive .gitmodules unless there is an externals entry
-        recursive = not self._subexternals_path
-
-        return recursive
-
-
-class SourceTree(object):
-    """
-    SourceTree represents a group of managed externals.
-
-    Those externals may not be checked out locally yet, they might only
-    have Repository objects pointing to their respective repositories.
-    """
-
-    @classmethod
-    def from_externals_file(cls, parent_repo_dir_path, parent_repo,
-                            externals_path):
-        """Creates a SourceTree representing the given externals file.
-        
-        Looks up a git submodules file as an optional backup if there is no
-        externals file specified.
-
-        Returns None if there is no externals file (i.e. it's None or 'none'),
-        or if the externals file hasn't been checked out yet.
-
-        parent_repo_dir_path: parent repo root dir
-        parent_repo: parent repo.
-        externals_path: path to externals file, relative to parent_repo_dir_path.
-        """
-        if not os.path.exists(parent_repo_dir_path):
-            # NOTE(bja, 2017-10) repository has not been checked out
-            # yet, can't process the externals file. Assume we are
-            # checking status before code is checkoud out and this
-            # will be handled correctly later.
-            return None
-
-        if externals_path.lower() == 'none':
-            # With explicit 'none', do not look for git submodules file.
-            return None
-
-        cwd = os.getcwd()
-        os.chdir(parent_repo_dir_path)
-        
-        if not externals_path:
-            if GitRepository.has_submodules(parent_repo_dir_path):
-                externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME
-            else:
-                return None
-
-        if not os.path.exists(externals_path):
-            # NOTE(bja, 2017-10) this check is redundant with the one
-            # in read_externals_description_file!
-            msg = ('Externals description file "{0}" '
-                   'does not exist! In directory: {1}'.format(
-                       externals_path, parent_repo_dir_path))
-            fatal_error(msg)
-
-        externals_root = parent_repo_dir_path
-        # model_data is a dict-like object which mirrors the file format.
-        model_data = read_externals_description_file(externals_root,
-                                                     externals_path)
-        # ext_description is another dict-like object (see ExternalsDescription)
-        ext_description = create_externals_description(model_data,
-                                                       parent_repo=parent_repo)
-        externals_sourcetree = SourceTree(externals_root, ext_description)
-        os.chdir(cwd)
-        return externals_sourcetree
-    
-    def __init__(self, root_dir, ext_description, svn_ignore_ancestry=False):
-        """
-        Build a SourceTree object from an ExternalDescription.
-
-        root_dir: the (checked-out) parent repo root dir.
-        """
-        self._root_dir = os.path.abspath(root_dir)
-        self._all_components = {}  # component_name -> _External
-        self._required_compnames = []
-        for comp, desc in ext_description.items():
-            local_path = desc[ExternalsDescription.PATH]
-            required = desc[ExternalsDescription.REQUIRED]
-            repo_info = desc[ExternalsDescription.REPO]
-            subexternals_path = desc[ExternalsDescription.EXTERNALS]
-
-            repo = create_repository(comp,
-                                     repo_info,
-                                     svn_ignore_ancestry=svn_ignore_ancestry)
-
-            sourcetree = None
-            # Treat a .gitmodules file as a backup externals config
-            if not subexternals_path:
-                parent_repo_dir_path = os.path.abspath(os.path.join(root_dir,
-                                                             local_path))
-                if GitRepository.has_submodules(parent_repo_dir_path):
-                    subexternals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME
-            
-            # Might return None (if the subexternal isn't checked out yet, or subexternal is None or 'none')
-            subexternal_sourcetree = SourceTree.from_externals_file(
-                os.path.join(self._root_dir, local_path),
-                repo,
-                subexternals_path)
-            src = _External(self._root_dir, comp, local_path, required,
-                            subexternals_path, repo, svn_ignore_ancestry,
-                            subexternal_sourcetree)
-            
-            self._all_components[comp] = src
-            if required:
-                self._required_compnames.append(comp)
-
-    def status(self, relative_path_base=LOCAL_PATH_INDICATOR,
-               force=False, print_progress=False):
-        """Return a dictionary of local path->ExternalStatus.
-
-        Notes about the returned dictionary:
-          * It is keyed by local path (e.g. 'components/mom'), not by
-            component name (e.g. 'mom').
-          * It contains top-level keys for all traversed components, whether
-            discovered by recursion or top-level.
-          * It contains entries for all components regardless of whether they
-            are locally installed or not, or required or optional.
-x        """
-        load_comps = self._all_components.keys()
-
-        summary = {}  # Holds merged statuses from all components.
-        for comp in load_comps:
-            if print_progress:
-                printlog('{0}, '.format(comp), end='')
-            stat = self._all_components[comp].status(force=force,
-                                                     print_progress=print_progress)
-
-            # Returned status dictionary is keyed by local path; prepend
-            # relative_path_base if not already there.
-            stat_final = {}
-            for name in stat.keys():
-                if stat[name].path.startswith(relative_path_base):
-                    stat_final[name] = stat[name]
-                else:
-                    modified_path = os.path.join(relative_path_base,
-                                                 stat[name].path)
-                    stat_final[modified_path] = stat[name]
-                    stat_final[modified_path].path = modified_path
-            summary.update(stat_final)
-
-        return summary
-
-    def _find_installed_optional_components(self):
-        """Returns a list of installed optional component names, if any."""
-        installed_comps = []
-        for comp_name, ext in self._all_components.items():
-            if comp_name in self._required_compnames:
-                continue
-            # Note that in practice we expect this status to be cached.
-            path_to_stat = ext.status()
-
-            # If any part of this component exists locally, consider it
-            # installed and therefore eligible for updating.
-            if any(s.sync_state != ExternalStatus.EMPTY
-                   for s in path_to_stat.values()):
-                installed_comps.append(comp_name)
-        return installed_comps
-
-    def checkout(self, verbosity, load_all, load_comp=None):
-        """
-        Checkout or update indicated components into the configured subdirs.
-
-        If load_all is True, checkout all externals (required + optional), recursively.
-        If load_all is False and load_comp is set, checkout load_comp (and any required subexternals, plus any optional subexternals that are already checked out, recursively)
-        If load_all is False and load_comp is None, checkout all required externals, plus any optionals that are already checked out, recursively.
-        """
-        if load_all:
-            tmp_comps = self._all_components.keys()
-        elif load_comp is not None:
-            tmp_comps = [load_comp]
-        else:
-            local_optional_compnames = self._find_installed_optional_components()
-            tmp_comps = self._required_compnames + local_optional_compnames
-            if local_optional_compnames:
-                printlog('Found locally installed optional components: ' +
-                         ', '.join(local_optional_compnames))
-                bad_compnames = set(local_optional_compnames) - set(self._all_components.keys())
-                if bad_compnames:
-                    printlog('Internal error: found locally installed components that are not in the global list of all components: ' + ','.join(bad_compnames))
-
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('Checking out externals: ')
-        else:
-            printlog('Checking out externals: ', end='')
-
-        # Sort by path so that if paths are nested the
-        # parent repo is checked out first.
-        load_comps = sorted(tmp_comps, key=lambda comp: self._all_components[comp].get_local_path())
-
-        # checkout.
-        for comp_name in load_comps:
-            if verbosity < VERBOSITY_VERBOSE:
-                printlog('{0}, '.format(comp_name), end='')
-            else:
-                # verbose output handled by the _External object, just
-                # output a newline
-                printlog(EMPTY_STR)
-            c = self._all_components[comp_name]
-            # Does not recurse.
-            c.checkout(verbosity)
-            # Recursively check out subexternals, if any. Returns None
-            # if there's no subexternals path.
-            component_subexternal_sourcetree = SourceTree.from_externals_file(
-                    c.get_repo_dir_path(),
-                    c.get_repo(),
-                    c.get_subexternals_path())
-            c.replace_subexternal_sourcetree(component_subexternal_sourcetree)
-            if component_subexternal_sourcetree:
-                component_subexternal_sourcetree.checkout(verbosity, load_all)
-        printlog('')
diff --git a/manage_externals/manic/utils.py b/manage_externals/manic/utils.py
deleted file mode 100644
index 9c63ffe65e..0000000000
--- a/manage_externals/manic/utils.py
+++ /dev/null
@@ -1,330 +0,0 @@
-#!/usr/bin/env python3
-"""
-Common public utilities for manic package
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import logging
-import os
-import subprocess
-import sys
-from threading import Timer
-
-from .global_constants import LOCAL_PATH_INDICATOR
-
-# ---------------------------------------------------------------------
-#
-# screen and logging output and functions to massage text for output
-#
-# ---------------------------------------------------------------------
-
-
-def log_process_output(output):
-    """Log each line of process output at debug level so it can be
-    filtered if necessary. By default, output is a single string, and
-    logging.debug(output) will only put log info heading on the first
-    line. This makes it hard to filter with grep.
-
-    """
-    output = output.split('\n')
-    for line in output:
-        logging.debug(line)
-
-
-def printlog(msg, **kwargs):
-    """Wrapper script around print to ensure that everything printed to
-    the screen also gets logged.
-
-    """
-    logging.info(msg)
-    if kwargs:
-        print(msg, **kwargs)
-    else:
-        print(msg)
-    sys.stdout.flush()
-
-
-def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
-    """
-
-    lines = the_string.splitlines(True)
-    if len(lines) <= n_lines:
-        return_val = the_string
-    else:
-        lines_subset = lines[-n_lines:]
-        str_truncated = ''.join(lines_subset)
-        if truncation_message:
-            str_truncated = truncation_message + '\n' + str_truncated
-        return_val = str_truncated
-
-    return return_val
-
-
-def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
-    """
-
-    lines = the_string.splitlines(True)
-    padding = ' ' * indent_level
-    lines_indented = [padding + line for line in lines]
-    return ''.join(lines_indented)
-
-# ---------------------------------------------------------------------
-#
-# error handling
-#
-# ---------------------------------------------------------------------
-
-
-def fatal_error(message):
-    """
-    Error output function
-    """
-    logging.error(message)
-    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
-
-
-# ---------------------------------------------------------------------
-#
-# Data conversion / manipulation
-#
-# ---------------------------------------------------------------------
-def str_to_bool(bool_str):
-    """Convert a sting representation of as boolean into a true boolean.
-
-    Conversion should be case insensitive.
-    """
-    value = None
-    str_lower = bool_str.lower()
-    if str_lower in ('true', 't'):
-        value = True
-    elif str_lower in ('false', 'f'):
-        value = False
-    if value is None:
-        msg = ('ERROR: invalid boolean string value "{0}". '
-               'Must be "true" or "false"'.format(bool_str))
-        fatal_error(msg)
-    return value
-
-
-REMOTE_PREFIXES = ['http://', 'https://', 'ssh://', 'git@']
-
-
-def is_remote_url(url):
-    """check if the user provided a local file path instead of a
-       remote. If so, it must be expanded to an absolute
-       path.
-
-    """
-    remote_url = False
-    for prefix in REMOTE_PREFIXES:
-        if url.startswith(prefix):
-            remote_url = True
-    return remote_url
-
-
-def split_remote_url(url):
-    """check if the user provided a local file path or a
-       remote. If remote, try to strip off protocol info.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        return url
-
-    for prefix in REMOTE_PREFIXES:
-        url = url.replace(prefix, '')
-
-    if '@' in url:
-        url = url.split('@')[1]
-
-    if ':' in url:
-        url = url.split(':')[1]
-
-    return url
-
-
-def expand_local_url(url, field):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
-    represent local copy only, don't work with the remotes.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        if url.strip() == LOCAL_PATH_INDICATOR:
-            pass
-        else:
-            url = os.path.expandvars(url)
-            url = os.path.expanduser(url)
-            if not os.path.isabs(url):
-                msg = ('WARNING: Externals description for "{0}" contains a '
-                       'url that is not remote and does not expand to an '
-                       'absolute path. Version control operations may '
-                       'fail.\n\nurl={1}'.format(field, url))
-                printlog(msg)
-            else:
-                url = os.path.normpath(url)
-    return url
-
-
-# ---------------------------------------------------------------------
-#
-# subprocess
-#
-# ---------------------------------------------------------------------
-
-# Give the user a helpful message if we detect that a command seems to
-# be hanging.
-_HANGING_SEC = 300
-
-
-def _hanging_msg(working_directory, command):
-    print("""
-
-Command '{command}'
-from directory {working_directory}
-has taken {hanging_sec} seconds. It may be hanging.
-
-The command will continue to run, but you may want to abort
-manage_externals with ^C and investigate. A possible cause of hangs is
-when svn or git require authentication to access a private
-repository. On some systems, svn and git requests for authentication
-information will not be displayed to the user. In this case, the program
-will appear to hang. Ensure you can run svn and git manually and access
-all repositories without entering your authentication information.
-
-""".format(command=command,
-           working_directory=working_directory,
-           hanging_sec=_HANGING_SEC))
-
-
-def execute_subprocess(commands, status_to_caller=False,
-                       output_to_caller=False):
-    """Wrapper around subprocess.check_output to handle common
-    exceptions.
-
-    check_output runs a command with arguments and waits
-    for it to complete.
-
-    check_output raises an exception on a nonzero return code.  if
-    status_to_caller is true, execute_subprocess returns the subprocess
-    return code, otherwise execute_subprocess treats non-zero return
-    status as an error and raises an exception.
-
-    """
-    cwd = os.getcwd()
-    msg = 'In directory: {0}\nexecute_subprocess running command:'.format(cwd)
-    logging.info(msg)
-    commands_str = ' '.join(commands)
-    logging.info(commands_str)
-    return_to_caller = status_to_caller or output_to_caller
-    status = -1
-    output = ''
-    hanging_timer = Timer(_HANGING_SEC, _hanging_msg,
-                          kwargs={"working_directory": cwd,
-                                  "command": commands_str})
-    hanging_timer.start()
-    try:
-        output = subprocess.check_output(commands, stderr=subprocess.STDOUT,
-                                         universal_newlines=True)
-        log_process_output(output)
-        status = 0
-    except OSError as error:
-        msg = failed_command_msg(
-            'Command execution failed. Does the executable exist?',
-            commands)
-        logging.error(error)
-        fatal_error(msg)
-    except ValueError as error:
-        msg = failed_command_msg(
-            'DEV_ERROR: Invalid arguments trying to run subprocess',
-            commands)
-        logging.error(error)
-        fatal_error(msg)
-    except subprocess.CalledProcessError as error:
-        # Only report the error if we are NOT returning to the
-        # caller. If we are returning to the caller, then it may be a
-        # simple status check. If returning, it is the callers
-        # responsibility determine if an error occurred and handle it
-        # appropriately.
-        if not return_to_caller:
-            msg_context = ('Process did not run successfully; '
-                           'returned status {0}'.format(error.returncode))
-            msg = failed_command_msg(msg_context, commands,
-                                     output=error.output)
-            logging.error(error)
-            logging.error(msg)
-            log_process_output(error.output)
-            fatal_error(msg)
-        status = error.returncode
-    finally:
-        hanging_timer.cancel()
-
-    if status_to_caller and output_to_caller:
-        ret_value = (status, output)
-    elif status_to_caller:
-        ret_value = status
-    elif output_to_caller:
-        ret_value = output
-    else:
-        ret_value = None
-
-    return ret_value
-
-
-def failed_command_msg(msg_context, command, output=None):
-    """Template for consistent error messages from subprocess calls.
-
-    If 'output' is given, it should provide the output from the failed
-    command
-    """
-
-    if output:
-        output_truncated = last_n_lines(output, 20,
-                                        truncation_message='[... Output truncated for brevity ...]')
-        errmsg = ('Failed with output:\n' +
-                  indent_string(output_truncated, 4) +
-                  '\nERROR: ')
-    else:
-        errmsg = ''
-
-    command_str = ' '.join(command)
-    errmsg += """In directory
-    {cwd}
-{context}:
-    {command}
-""".format(cwd=os.getcwd(), context=msg_context, command=command_str)
-
-    if output:
-        errmsg += 'See above for output from failed command.\n'
-
-    return errmsg
diff --git a/manage_externals/test/.coveragerc b/manage_externals/test/.coveragerc
deleted file mode 100644
index 8b681888b8..0000000000
--- a/manage_externals/test/.coveragerc
+++ /dev/null
@@ -1,7 +0,0 @@
-[run]
-branch = True
-omit = test_unit_*.py
-       test_sys_*.py
-       /usr/*
-       .local/*
-       */site-packages/*
\ No newline at end of file
diff --git a/manage_externals/test/.gitignore b/manage_externals/test/.gitignore
deleted file mode 100644
index dd5795998f..0000000000
--- a/manage_externals/test/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-# virtual environments
-env_python*
-
-# python code coverage tool output
-.coverage
-htmlcov
-
diff --git a/manage_externals/test/.pylint.rc b/manage_externals/test/.pylint.rc
deleted file mode 100644
index 64abd03e42..0000000000
--- a/manage_externals/test/.pylint.rc
+++ /dev/null
@@ -1,426 +0,0 @@
-[MASTER]
-
-# A comma-separated list of package or module names from where C extensions may
-# be loaded. Extensions are loading into the active Python interpreter and may
-# run arbitrary code
-extension-pkg-whitelist=
-
-# Add files or directories to the blacklist. They should be base names, not
-# paths.
-ignore=.git,.svn,env2
-
-# Add files or directories matching the regex patterns to the blacklist. The
-# regex matches against base names, not paths.
-ignore-patterns=
-
-# Python code to execute, usually for sys.path manipulation such as
-# pygtk.require().
-#init-hook=
-
-# Use multiple processes to speed up Pylint.
-jobs=1
-
-# List of plugins (as comma separated values of python modules names) to load,
-# usually to register additional checkers.
-load-plugins=
-
-# Pickle collected data for later comparisons.
-persistent=yes
-
-# Specify a configuration file.
-#rcfile=
-
-# Allow loading of arbitrary C extensions. Extensions are imported into the
-# active Python interpreter and may run arbitrary code.
-unsafe-load-any-extension=no
-
-
-[MESSAGES CONTROL]
-
-# Only show warnings with the listed confidence levels. Leave empty to show
-# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED
-confidence=
-
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifiers separated by comma (,) or put this
-# option multiple times (only on the command line, not in the configuration
-# file where it should appear only once).You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
-# you want to run only the similarities checker, you can use "--disable=all
-# --enable=similarities". If you want to run only the classes checker, but have
-# no Warning level messages displayed, use"--disable=all --enable=classes
-# --disable=W"
-disable=bad-continuation,useless-object-inheritance
-
-
-# Enable the message, report, category or checker with the given id(s). You can
-# either give multiple identifier separated by comma (,) or put this option
-# multiple time (only on the command line, not in the configuration file where
-# it should appear only once). See also the "--disable" option for examples.
-enable=
-
-
-[REPORTS]
-
-# Python expression which should return a note less than 10 (10 is the highest
-# note). You have access to the variables errors warning, statement which
-# respectively contain the number of errors / warnings messages and the total
-# number of statements analyzed. This is used by the global evaluation report
-# (RP0004).
-evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
-
-# Template used to display messages. This is a python new-style format string
-# used to format the message information. See doc for all details
-msg-template={msg_id}:{line:3d},{column:2d}: {msg} ({symbol})
-
-# Set the output format. Available formats are text, parseable, colorized, json
-# and msvs (visual studio).You can also give a reporter class, eg
-# mypackage.mymodule.MyReporterClass.
-output-format=text
-
-# Tells whether to display a full report or only the messages
-#reports=yes
-
-# Activate the evaluation score.
-score=yes
-
-
-[REFACTORING]
-
-# Maximum number of nested blocks for function / method body
-max-nested-blocks=5
-
-
-[BASIC]
-
-# Naming hint for argument names
-argument-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct argument names
-argument-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Naming hint for attribute names
-attr-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct attribute names
-attr-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Bad variable names which should always be refused, separated by a comma
-bad-names=foo,bar,baz,toto,tutu,tata
-
-# Naming hint for class attribute names
-class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
-# Regular expression matching correct class attribute names
-class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
-# Naming hint for class names
-class-name-hint=[A-Z_][a-zA-Z0-9]+$
-
-# Regular expression matching correct class names
-class-rgx=[A-Z_][a-zA-Z0-9]+$
-
-# Naming hint for constant names
-const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
-# Regular expression matching correct constant names
-const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
-# Minimum line length for functions/classes that require docstrings, shorter
-# ones are exempt.
-docstring-min-length=-1
-
-# Naming hint for function names
-function-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct function names
-function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Good variable names which should always be accepted, separated by a comma
-good-names=i,j,k,ex,Run,_
-
-# Include a hint for the correct naming format with invalid-name
-include-naming-hint=no
-
-# Naming hint for inline iteration names
-inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
-
-# Regular expression matching correct inline iteration names
-inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
-
-# Naming hint for method names
-method-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct method names
-method-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Naming hint for module names
-module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
-# Regular expression matching correct module names
-module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
-# Colon-delimited sets of names that determine each other's naming style when
-# the name regexes allow several styles.
-name-group=
-
-# Regular expression which should only match function or class names that do
-# not require a docstring.
-no-docstring-rgx=^_
-
-# List of decorators that produce properties, such as abc.abstractproperty. Add
-# to this list to register other decorators that produce valid properties.
-property-classes=abc.abstractproperty
-
-# Naming hint for variable names
-variable-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct variable names
-variable-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-
-[FORMAT]
-
-# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
-expected-line-ending-format=
-
-# Regexp for a line that is allowed to be longer than the limit.
-ignore-long-lines=^\s*(# )?<?https?://\S+>?$
-
-# Number of spaces of indent required inside a hanging  or continued line.
-indent-after-paren=4
-
-# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
-# tab).
-indent-string='    '
-
-# Maximum number of characters on a single line.
-max-line-length=100
-
-# Maximum number of lines in a module
-max-module-lines=1000
-
-# List of optional constructs for which whitespace checking is disabled. `dict-
-# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
-# `trailing-comma` allows a space between comma and closing bracket: (a, ).
-# `empty-line` allows space-only lines.
-no-space-check=trailing-comma,dict-separator
-
-# Allow the body of a class to be on the same line as the declaration if body
-# contains single statement.
-single-line-class-stmt=no
-
-# Allow the body of an if to be on the same line as the test if there is no
-# else.
-single-line-if-stmt=no
-
-
-[LOGGING]
-
-# Logging modules to check that the string format arguments are in logging
-# function parameter format
-logging-modules=logging
-
-
-[MISCELLANEOUS]
-
-# List of note tags to take in consideration, separated by a comma.
-notes=FIXME,XXX,TODO
-
-
-[SIMILARITIES]
-
-# Ignore comments when computing similarities.
-ignore-comments=yes
-
-# Ignore docstrings when computing similarities.
-ignore-docstrings=yes
-
-# Ignore imports when computing similarities.
-ignore-imports=no
-
-# Minimum lines number of a similarity.
-min-similarity-lines=4
-
-
-[SPELLING]
-
-# Spelling dictionary name. Available dictionaries: none. To make it working
-# install python-enchant package.
-spelling-dict=
-
-# List of comma separated words that should not be checked.
-spelling-ignore-words=
-
-# A path to a file that contains private dictionary; one word per line.
-spelling-private-dict-file=
-
-# Tells whether to store unknown words to indicated private dictionary in
-# --spelling-private-dict-file option instead of raising a message.
-spelling-store-unknown-words=no
-
-
-[TYPECHECK]
-
-# List of decorators that produce context managers, such as
-# contextlib.contextmanager. Add to this list to register other decorators that
-# produce valid context managers.
-contextmanager-decorators=contextlib.contextmanager
-
-# List of members which are set dynamically and missed by pylint inference
-# system, and so shouldn't trigger E1101 when accessed. Python regular
-# expressions are accepted.
-generated-members=
-
-# Tells whether missing members accessed in mixin class should be ignored. A
-# mixin class is detected if its name ends with "mixin" (case insensitive).
-ignore-mixin-members=yes
-
-# This flag controls whether pylint should warn about no-member and similar
-# checks whenever an opaque object is returned when inferring. The inference
-# can return multiple potential results while evaluating a Python object, but
-# some branches might not be evaluated, which results in partial inference. In
-# that case, it might be useful to still emit no-member and other checks for
-# the rest of the inferred objects.
-ignore-on-opaque-inference=yes
-
-# List of class names for which member attributes should not be checked (useful
-# for classes with dynamically set attributes). This supports the use of
-# qualified names.
-ignored-classes=optparse.Values,thread._local,_thread._local
-
-# List of module names for which member attributes should not be checked
-# (useful for modules/projects where namespaces are manipulated during runtime
-# and thus existing member attributes cannot be deduced by static analysis. It
-# supports qualified module names, as well as Unix pattern matching.
-ignored-modules=
-
-# Show a hint with possible names when a member name was not found. The aspect
-# of finding the hint is based on edit distance.
-missing-member-hint=yes
-
-# The minimum edit distance a name should have in order to be considered a
-# similar match for a missing member name.
-missing-member-hint-distance=1
-
-# The total number of similar names that should be taken in consideration when
-# showing a hint for a missing member.
-missing-member-max-choices=1
-
-
-[VARIABLES]
-
-# List of additional names supposed to be defined in builtins. Remember that
-# you should avoid to define new builtins when possible.
-additional-builtins=
-
-# Tells whether unused global variables should be treated as a violation.
-allow-global-unused-variables=yes
-
-# List of strings which can identify a callback function by name. A callback
-# name must start or end with one of those strings.
-callbacks=cb_,_cb
-
-# A regular expression matching the name of dummy variables (i.e. expectedly
-# not used).
-dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
-
-# Argument names that match this expression will be ignored. Default to name
-# with leading underscore
-ignored-argument-names=_.*|^ignored_|^unused_
-
-# Tells whether we should check for unused import in __init__ files.
-init-import=no
-
-# List of qualified module names which can have objects that can redefine
-# builtins.
-redefining-builtins-modules=six.moves,future.builtins
-
-
-[CLASSES]
-
-# List of method names used to declare (i.e. assign) instance attributes.
-defining-attr-methods=__init__,__new__,setUp
-
-# List of member names, which should be excluded from the protected access
-# warning.
-exclude-protected=_asdict,_fields,_replace,_source,_make
-
-# List of valid names for the first argument in a class method.
-valid-classmethod-first-arg=cls
-
-# List of valid names for the first argument in a metaclass class method.
-valid-metaclass-classmethod-first-arg=mcs
-
-
-[DESIGN]
-
-# Maximum number of arguments for function / method
-max-args=5
-
-# Maximum number of attributes for a class (see R0902).
-max-attributes=7
-
-# Maximum number of boolean expressions in a if statement
-max-bool-expr=5
-
-# Maximum number of branch for function / method body
-max-branches=12
-
-# Maximum number of locals for function / method body
-max-locals=15
-
-# Maximum number of parents for a class (see R0901).
-max-parents=7
-
-# Maximum number of public methods for a class (see R0904).
-max-public-methods=20
-
-# Maximum number of return / yield for function / method body
-max-returns=6
-
-# Maximum number of statements in function / method body
-max-statements=50
-
-# Minimum number of public methods for a class (see R0903).
-min-public-methods=2
-
-
-[IMPORTS]
-
-# Allow wildcard imports from modules that define __all__.
-allow-wildcard-with-all=no
-
-# Analyse import fallback blocks. This can be used to support both Python 2 and
-# 3 compatible code, which means that the block might have code that exists
-# only in one or another interpreter, leading to false positives when analysed.
-analyse-fallback-blocks=no
-
-# Deprecated modules which should not be used, separated by a comma
-deprecated-modules=regsub,TERMIOS,Bastion,rexec
-
-# Create a graph of external dependencies in the given file (report RP0402 must
-# not be disabled)
-ext-import-graph=
-
-# Create a graph of every (i.e. internal and external) dependencies in the
-# given file (report RP0402 must not be disabled)
-import-graph=
-
-# Create a graph of internal dependencies in the given file (report RP0402 must
-# not be disabled)
-int-import-graph=
-
-# Force import order to recognize a module as part of the standard
-# compatibility libraries.
-known-standard-library=
-
-# Force import order to recognize a module as part of a third party library.
-known-third-party=enchant
-
-
-[EXCEPTIONS]
-
-# Exceptions that will emit a warning when being caught. Defaults to
-# "Exception"
-overgeneral-exceptions=Exception
diff --git a/manage_externals/test/Makefile b/manage_externals/test/Makefile
deleted file mode 100644
index 293e360757..0000000000
--- a/manage_externals/test/Makefile
+++ /dev/null
@@ -1,124 +0,0 @@
-python = not-set
-verbose = not-set
-debug = not-set
-
-ifneq ($(python), not-set)
-PYTHON=$(python)
-else
-PYTHON=python
-endif
-
-# we need the python path to point one level up to access the package
-# and executables
-PYPATH=PYTHONPATH=..:
-
-# common args for running tests
-TEST_ARGS=-m unittest discover
-
-ifeq ($(debug), not-set)
-    ifeq ($(verbose), not-set)
-        # summary only output
-        TEST_ARGS+=--buffer
-    else
-        # show individual test summary
-        TEST_ARGS+=--buffer --verbose
-    endif
-else
-    # show detailed test output
-    TEST_ARGS+=--verbose
-endif
-
-
-# auto reformat the code
-AUTOPEP8=autopep8
-AUTOPEP8_ARGS=--aggressive --in-place 
-
-# run lint
-PYLINT=pylint
-PYLINT_ARGS=-j 2 --rcfile=.pylint.rc
-
-# code coverage
-COVERAGE=coverage
-COVERAGE_ARGS=--rcfile=.coveragerc
-
-# source files
-SRC = \
-	../checkout_externals \
-	../manic/*.py
-
-CHECKOUT_EXE = ../checkout_externals
-
-TEST_DIR = .
-
-README = ../README.md
-
-#
-# testing
-#
-.PHONY : utest
-utest : FORCE
-	$(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_unit_*.py'
-
-.PHONY : stest
-stest : FORCE
-	$(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_sys_*.py'
-
-.PHONY : test
-test : utest stest
-
-#
-# documentation
-#
-.PHONY : readme
-readme : $(CHECKOUT_EXE)
-	printf "%s\n\n" "-- AUTOMATICALLY GENERATED FILE. DO NOT EDIT --" > $(README)
-	printf "%s" '[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)' >> $(README)
-	printf "%s" '[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master)' >> $(README)
-	printf "\n%s\n" '```' >> $(README)
-	$(CHECKOUT_EXE) --help >> $(README)
-
-#
-# coding standards
-#
-.PHONY : style
-style : FORCE
-	$(AUTOPEP8) $(AUTOPEP8_ARGS) --recursive $(SRC) $(TEST_DIR)/test_*.py
-
-.PHONY : lint
-lint : FORCE
-	$(PYLINT) $(PYLINT_ARGS) $(SRC) $(TEST_DIR)/test_*.py
-
-.PHONY : stylint
-stylint : style lint
-
-.PHONY : coverage
-# Need to use a single coverage run with a single pattern rather than
-# using two separate commands with separate patterns for test_unit_*.py
-# and test_sys_*.py: The latter clobbers some results from the first
-# run, even if we use the --append flag to 'coverage run'.
-coverage : FORCE
-	$(PYPATH) $(COVERAGE) erase
-	$(PYPATH) $(COVERAGE) run $(COVERAGE_ARGS) $(TEST_ARGS) --pattern 'test_*.py'
-	$(PYPATH) $(COVERAGE) html
-
-#
-# virtual environment creation
-#
-.PHONY : env
-env : FORCE
-	$(PYPATH) virtualenv --python $(PYTHON) $@_$(PYTHON)
-	. $@_$(PYTHON)/bin/activate; pip install -r requirements.txt
-
-#
-# utilites
-#
-.PHONY : clean
-clean : FORCE
-	-rm -rf *~ *.pyc tmp fake htmlcov
-
-.PHONY : clobber
-clobber : clean
-	-rm -rf env_*
-
-FORCE : 
-
diff --git a/manage_externals/test/README.md b/manage_externals/test/README.md
deleted file mode 100644
index 1e8f2eaa77..0000000000
--- a/manage_externals/test/README.md
+++ /dev/null
@@ -1,53 +0,0 @@
-# Testing for checkout_externals
-
-## Unit tests
-
-```SH
-    cd checkout_externals/test
-    make utest
-```
-
-## System tests
-
-```SH
-    cd checkout_externals/test
-    make stest
-```
-
-Example to run a single test:
-```SH
-    cd checkout_externals
-    python -m unittest test.test_sys_checkout.TestSysCheckout.test_container_simple_required
-```
-
-## Static analysis
-
-checkout_externals is difficult to test thoroughly because it relies
-on git and svn, and svn requires a live network connection and
-repository. Static analysis will help catch bugs in code paths that
-are not being executed, but it requires conforming to community
-standards and best practices. autopep8 and pylint should be run
-regularly for automatic code formatting and linting.
-
-```SH
-    cd checkout_externals/test
-    make lint
-```
-
-The canonical formatting for the code is whatever autopep8
-generates. All issues identified by pylint should be addressed.
-
-
-## Code coverage
-
-All changes to the code should include maintaining existing tests and
-writing new tests for new or changed functionality. To ensure test
-coverage, run the code coverage tool:
-
-```SH
-    cd checkout_externals/test
-    make coverage
-    open -a Firefox.app htmlcov/index.html
-```
-
-
diff --git a/manage_externals/test/doc/.gitignore b/manage_externals/test/doc/.gitignore
deleted file mode 100644
index d4e11e5ea0..0000000000
--- a/manage_externals/test/doc/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-_build
-
diff --git a/manage_externals/test/doc/Makefile b/manage_externals/test/doc/Makefile
deleted file mode 100644
index 18f4d5bf99..0000000000
--- a/manage_externals/test/doc/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = ManageExternals
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/manage_externals/test/doc/conf.py b/manage_externals/test/doc/conf.py
deleted file mode 100644
index 469c0b0dc5..0000000000
--- a/manage_externals/test/doc/conf.py
+++ /dev/null
@@ -1,172 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# Manage Externals documentation build configuration file, created by
-# sphinx-quickstart on Wed Nov 29 10:53:25 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'Manage Externals'
-copyright = u'2017, CSEG at NCAR'
-author = u'CSEG at NCAR'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = u'1.0.0'
-# The full version, including alpha/beta/rc tags.
-release = u'1.0.0'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# This is required for the alabaster theme
-# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
-html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-    ]
-}
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'ManageExternalsdoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'ManageExternals.tex', u'Manage Externals Documentation',
-     u'CSEG at NCAR', 'manual'),
-]
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'manageexternals', u'Manage Externals Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'ManageExternals', u'Manage Externals Documentation',
-     author, 'ManageExternals', 'One line description of project.',
-     'Miscellaneous'),
-]
-
-
-
diff --git a/manage_externals/test/doc/develop.rst b/manage_externals/test/doc/develop.rst
deleted file mode 100644
index b817b7b093..0000000000
--- a/manage_externals/test/doc/develop.rst
+++ /dev/null
@@ -1,202 +0,0 @@
-Developer Guidelines
-====================
-
-The manage externals utilities are a light weight replacement for svn
-externals that will work with git repositories pulling in a mixture of
-git and svn dependencies.
-
-Given an externals description and a working copy:
-
-* *checkout_externals* attempts to make the working copy agree with the
-  externals description
-
-* *generate_externals* attempts to make the externals description agree
-  with the working copy.
-
-For these operations utilities should:
-
-* operate consistently across git and svn
-
-* operate simply with minimal user complexity
-
-* robustly across a wide range of repository states
-
-* provide explicit error messages when a problem occurs
-
-* leave the working copy in a valid state
-  
-The utilities in manage externals are **NOT** generic wrappers around
-revision control operations or a replacement for common tasks. Users
-are expected to:
-
-* create branches prior to starting development
-  
-* add remotes and push changes
-
-* create tags
-  
-* delete branches
-
-These types of tasks are often highly workflow dependent, e.g. branch
-naming conventions may vary between repositories, have the potential
-to destroy user data, introduce significant code complexit and 'edge
-cases' that are extremely difficult to detect and test, and often
-require subtle decision making, especially if a problem occurs.
-
-Users who want to automate these types are encouraged to create their
-own tools. The externals description files are explicitly versioned
-and the internal APIs are intended to be stable for these purposes.
-
-Core Design Principles
------------------------
-
-1. Users can, and are actively encouraged to, modify the externals
-   directories using revision control outside of manage_externals
-   tools. You can't make any assumptions about the state of the
-   working copy. Examples: adding a remote, creating a branch,
-   switching to a branch, deleting the directory entirely.
-      
-2. Give that the user can do anything, the manage externals library
-   can not preserve state between calls. The only information it can
-   rely on is what it expectes based on the content of the externals
-   description file, and what the actual state of the directory tree
-   is.
-
-3. Do *not* do anything that will possibly destroy user data!
-
-   a. Do not remove files from the file system. We are operating on
-      user supplied input. If you don't call 'rm', you can't
-      accidentally remove the user's data. Thinking of calling
-      ``shutil.rmtree(user_input)``? What if the user accidentally
-      specified user_input such that it resolves to their home
-      directory.... Yeah. Don't go there.
-
-   b. Rely on git and svn to do their job as much as possible. Don't
-      duplicate functionality. Examples:
-
-      i. We require the working copies to be 'clean' as reported by
-         ``git status`` and ``svn status``. What if there are misc
-         editor files floating around that prevent an update? Use the
-         git and svn ignore functionality so they are not
-         reported. Don't try to remove them from manage_externals or
-         determine if they are 'safe' to ignore.
-
-      ii. Do not use '--force'. Ever. This is a sign you are doing
-          something dangerous, it may not be what the user
-          wants. Remember, they are encouraged to modify their repo.
-
-4. There are often multiple ways to obtain a particular piece of
-   information from git. Scraping screen output is brittle and
-   generally not considered a stable API across different versions of
-   git. Given a choice between:
-          
-    a. a lower level git 'plumbing' command that processes a
-       specific request and returns a sucess/failure status.
-
-    b. high level git command that produces a bunch of output
-       that must be processed.
-
-   We always prefer the former. It almost always involves
-   writing and maintaining less code and is more likely to be
-   stable.
-
-5. Backward compatibility is critical. We have *nested*
-   repositories. They are trivially easy to change versions. They may
-   have very different versions of the top level manage_externals. The
-   ability to read and work with old model description files is
-   critical to avoid problems for users. We also have automated tools
-   (testdb) that must generate and read external description
-   files. Backward compatibility will make staging changes vastly
-   simpler.
-   
-Model Users
------------
-
-Consider the needs of the following model userswhen developing manage_externals:
-
-* Users who will checkout the code once, and never change versions.
-
-* Users who will checkout the code once, then work for several years,
-  never updating. before trying to update or request integration.
-
-* Users develope code but do not use revision control beyond the
-  initial checkout. If they have modified or untracked files in the
-  repo, they may be irreplacable. Don't destroy user data.
-
-* Intermediate users who are working with multiple repos or branches
-  on a regular basis. They may only use manage_externals weekly or
-  monthly. Keep the user interface and documentation simple and
-  explicit. The more command line options they have to remember or
-  look up, the more frustrated they git.
-  
-* Software engineers who use the tools multiple times a day. It should
-  get out of their way.
-
-User Interface
---------------
-
-Basic operation for the most standard use cases should be kept as
-simple as possible. Many users will only rarely run the manage
-utilities. Even advanced users don't like reading a lot of help
-documentation or struggling to remember commands and piece together
-what they need to run. Having many command line options, even if not
-needed, is exteremly frustrating and overwhelming for most users. A few
-simple, explicitly named commands are better than a single command
-with many options.
-
-How will users get help if something goes wrong? This is a custom,
-one-off solution. Searching the internet for manage_externals, will
-only return the user doc for this project at best. There isn't likely
-to be a stackoverflow question or blog post where someone else already
-answered a user's question. And very few people outside this community
-will be able to provide help if something goes wrong. The sooner we
-kick users out of these utilities and into standard version control
-tools, the better off they are going to be if they run into a problem.
-  
-Repositories
-------------
-
-There are three basic types of repositories that must be considered:
-
-* container repositories - repositories that are always top level
-  repositories, and have a group of externals that must be managed.
-
-* simple repositories - repositories that are externals to another
-  repository, and do not have any of their own externals that will be
-  managed.
-
-* mixed use repositories - repositories that can act as a top level
-  container repository or as an external to a top level
-  container. They may also have their own sub-externals that are
-  required. They may have different externals needs depening on
-  whether they are top level or not.
-
-Repositories must be able to checkout and switch to both branches and
-tags.
-
-Development
-===========
-
-The functionality to manage externals is broken into a library of core
-functionality and applications built with the library.
-
-The core library is called 'manic', pseduo-homophone of (man)age
-(ex)ternals that is: short, pronounceable and spell-checkable. It is
-also no more or less meaningful to an unfamiliar user than a random
-jumble of letters forming an acronym.
-
-The core architecture of manic is:
-
-* externals description - an abstract description on an external,
-  including of how to obtain it, where to obtain it, where it goes in
-  the working tree.
-
-* externals - the software object representing an external.
-  
-* source trees - collection of externals
-  
-* repository wrappers - object oriented wrappers around repository
-  operations. So the higher level management of the soure tree and
-  external does not have to be concerned with how a particular
-  external is obtained and managed.
-  
diff --git a/manage_externals/test/doc/index.rst b/manage_externals/test/doc/index.rst
deleted file mode 100644
index 9ab287ad8c..0000000000
--- a/manage_externals/test/doc/index.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-.. Manage Externals documentation master file, created by
-   sphinx-quickstart on Wed Nov 29 10:53:25 2017.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to Manage Externals's documentation!
-============================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-
-   develop.rst
-   testing.rst
-   
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/manage_externals/test/doc/testing.rst b/manage_externals/test/doc/testing.rst
deleted file mode 100644
index 623f0e431c..0000000000
--- a/manage_externals/test/doc/testing.rst
+++ /dev/null
@@ -1,123 +0,0 @@
-Testing
-=======
-
-The manage_externals package has an automated test suite. All pull
-requests are expected to pass 100% of the automated tests, as well as
-be pep8 and lint 'clean' and maintain approximately constant (at a
-minimum) level of code coverage.
-
-Quick Start
------------
-
-Do nothing approach
-~~~~~~~~~~~~~~~~~~~
-
-When you create a pull request on GitHub, Travis-CI continuous
-integration testing will run the test suite in both python2 and
-python3. Test results, lint results, and code coverage results are
-available online.
-
-Do something approach
-~~~~~~~~~~~~~~~~~~~~~
-
-In the test directory, run:
-
-.. code-block:: shell
-
-    make env
-    make lint
-    make test
-    make coverage
-
- 
-Automated Testing
------------------
-
-The manage_externals manic library and executables are developed to be
-python2 and python3 compatible using only the standard library. The
-test suites meet the same requirements. But additional tools are
-required to provide lint and code coverage metrics and generate
-documentation. The requirements are maintained in the requirements.txt
-file, and can be automatically installed into an isolated environment
-via Makefile.
-
-Bootstrap requirements:
-
-* python2 - version 2.7.x or later
-
-* python3 - version 3.6 tested other versions may work
-
-* pip and virtualenv for python2 and python3
-
-Note: all make rules can be of the form ``make python=pythonX rule``
-or ``make rule`` depending if you want to use the default system
-python or specify a specific version.
-
-The Makefile in the test directory has the following rules:
-
-* ``make python=pythonX env`` - create a python virtual environment
-  for python2 or python3 and install all required packages. These
-  packages are required to run lint or coverage.
-
-* ``make style`` - runs autopep8
-
-* ``make lint`` - runs autopep8 and pylint
-
-* ``make test`` - run the full test suite
-
-* ``make utest`` - run jus the unit tests
-
-* ``make stest`` - run jus the system integration tests
-
-* ``make coverage`` - run the full test suite through the code
-  coverage tool and generate an html report.
-
-* ``make readme`` - automatically generate the README files.
-
-* ``make clean`` - remove editor and pyc files
-
-* ``make clobber`` - remove all generated test files, including
-  virtual environments, coverage reports, and temporary test
-  repository directories.
-
-Unit Tests
-----------
-
-Unit tests are probably not 'true unit tests' for the pedantic, but
-are pragmatic unit tests. They cover small practicle code blocks:
-functions, class methods, and groups of functions and class methods.
-
-System Integration Tests
-------------------------
-
-NOTE(bja, 2017-11) The systems integration tests currently do not include svn repositories.
-
-The manage_externals package is extremely tedious and error prone to test manually.
-
-Combinations that must be tested to ensure basic functionality are:
-
-* container repository pulling in simple externals
-
-* container repository pulling in mixed externals with sub-externals.
-
-* mixed repository acting as a container, pulling in simple externals and sub-externals
-
-Automatic system tests are handled the same way manual testing is done:
-
-* clone a test repository
-
-* create an externals description file for the test
-
-* run the executable with the desired args
-
-* check the results
-
-* potentially modify the repo (checkout a different branch)
-
-* rerun and test
-
-* etc
-
-The automated system stores small test repositories in the main repo
-by adding them as bare repositories. These repos are cloned via a
-subprocess call to git and manipulated during the tests. 
diff --git a/manage_externals/test/repos/README.md b/manage_externals/test/repos/README.md
deleted file mode 100644
index 8a3502c35f..0000000000
--- a/manage_externals/test/repos/README.md
+++ /dev/null
@@ -1,33 +0,0 @@
-Git repositories for testing git-related behavior.  For usage and terminology notes, see test/test_sys_checkout.py.
-
-To list files and view file contents at HEAD:
-```
-cd <repo_dir>
-git ls-tree --full-tree -r --name-only HEAD
-git cat-file -p HEAD:<filename>
-```
-
-File contents at a glance:
-```
-container.git/
-  readme.txt
-
-simple-ext.git/
-  (has branches: feature2, feature3)
-  (has tags: tag1, tag2)
-  readme.txt
-  simple_subdir/subdir_file.txt
-
-simple-ext-fork.git/
-  (has tags: abandoned-feature, forked-feature-v1, tag1)
-  (has branch: feature2)
-  readme.txt
-
-mixed-cont-ext.git/
-  (has branch: new-feature)
-  readme.txt
-  sub-externals.cfg ('simp_branch' section refers to 'feature2' branch in simple-ext.git/ repo)
-
-error/
-   (no git repo here, just a readme.txt in the clear)
-```
diff --git a/manage_externals/test/repos/container.git/HEAD b/manage_externals/test/repos/container.git/HEAD
deleted file mode 100644
index cb089cd89a..0000000000
--- a/manage_externals/test/repos/container.git/HEAD
+++ /dev/null
@@ -1 +0,0 @@
-ref: refs/heads/master
diff --git a/manage_externals/test/repos/container.git/config b/manage_externals/test/repos/container.git/config
deleted file mode 100644
index e6da231579..0000000000
--- a/manage_externals/test/repos/container.git/config
+++ /dev/null
@@ -1,6 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
-	ignorecase = true
-	precomposeunicode = true
diff --git a/manage_externals/test/repos/container.git/description b/manage_externals/test/repos/container.git/description
deleted file mode 100644
index 498b267a8c..0000000000
--- a/manage_externals/test/repos/container.git/description
+++ /dev/null
@@ -1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/container.git/info/exclude b/manage_externals/test/repos/container.git/info/exclude
deleted file mode 100644
index a5196d1be8..0000000000
--- a/manage_externals/test/repos/container.git/info/exclude
+++ /dev/null
@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~
diff --git a/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801 b/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801
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diff --git a/manage_externals/test/repos/container.git/refs/heads/master b/manage_externals/test/repos/container.git/refs/heads/master
deleted file mode 100644
index 3ae00f3af0..0000000000
--- a/manage_externals/test/repos/container.git/refs/heads/master
+++ /dev/null
@@ -1 +0,0 @@
-715b8f3e4afe1802a178e1d603af404ba45d59de
diff --git a/manage_externals/test/repos/error/readme.txt b/manage_externals/test/repos/error/readme.txt
deleted file mode 100644
index 6b5753377e..0000000000
--- a/manage_externals/test/repos/error/readme.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-Invalid or corrupted git repository (.git dir exists, but is empty) for error
-testing.
- 
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/HEAD b/manage_externals/test/repos/mixed-cont-ext.git/HEAD
deleted file mode 100644
index cb089cd89a..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/HEAD
+++ /dev/null
@@ -1 +0,0 @@
-ref: refs/heads/master
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/config b/manage_externals/test/repos/mixed-cont-ext.git/config
deleted file mode 100644
index e6da231579..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/config
+++ /dev/null
@@ -1,6 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
-	ignorecase = true
-	precomposeunicode = true
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/description b/manage_externals/test/repos/mixed-cont-ext.git/description
deleted file mode 100644
index 498b267a8c..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/description
+++ /dev/null
@@ -1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/info/exclude b/manage_externals/test/repos/mixed-cont-ext.git/info/exclude
deleted file mode 100644
index a5196d1be8..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/info/exclude
+++ /dev/null
@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~
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diff --git a/manage_externals/test/repos/simple-ext-fork.git/objects/c5/32bc8fde96fa63103a52057f0baffcc9f00c6b b/manage_externals/test/repos/simple-ext-fork.git/objects/c5/32bc8fde96fa63103a52057f0baffcc9f00c6b
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diff --git a/manage_externals/test/repos/simple-ext-fork.git/packed-refs b/manage_externals/test/repos/simple-ext-fork.git/packed-refs
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index b8f9e86308..0000000000
--- a/manage_externals/test/repos/simple-ext-fork.git/packed-refs
+++ /dev/null
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diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1 b/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1
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diff --git a/manage_externals/test/repos/simple-ext.git/HEAD b/manage_externals/test/repos/simple-ext.git/HEAD
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index cb089cd89a..0000000000
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diff --git a/manage_externals/test/repos/simple-ext.git/config b/manage_externals/test/repos/simple-ext.git/config
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index e6da231579..0000000000
--- a/manage_externals/test/repos/simple-ext.git/config
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-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
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diff --git a/manage_externals/test/repos/simple-ext.git/description b/manage_externals/test/repos/simple-ext.git/description
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index 498b267a8c..0000000000
--- a/manage_externals/test/repos/simple-ext.git/description
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-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/simple-ext.git/info/exclude b/manage_externals/test/repos/simple-ext.git/info/exclude
deleted file mode 100644
index a5196d1be8..0000000000
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-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
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diff --git a/manage_externals/test/repos/simple-ext.git/objects/36/418b4e5665956a90725c9a1b5a8e551c5f3d48 b/manage_externals/test/repos/simple-ext.git/objects/36/418b4e5665956a90725c9a1b5a8e551c5f3d48
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GIT binary patch
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GIT binary patch
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diff --git a/manage_externals/test/repos/simple-ext.git/objects/60/b1cc1a38d63a4bcaa1e767262bbe23dbf9f5f5 b/manage_externals/test/repos/simple-ext.git/objects/60/b1cc1a38d63a4bcaa1e767262bbe23dbf9f5f5
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diff --git a/manage_externals/test/repos/simple-ext.git/objects/c5/b315915742133dbdfbeed0753e481b55c1d364 b/manage_externals/test/repos/simple-ext.git/objects/c5/b315915742133dbdfbeed0753e481b55c1d364
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diff --git a/manage_externals/test/repos/simple-ext.git/objects/df/312890f93ba4d2c694208599b665c4a08afeff b/manage_externals/test/repos/simple-ext.git/objects/df/312890f93ba4d2c694208599b665c4a08afeff
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/heads/feature2 b/manage_externals/test/repos/simple-ext.git/refs/heads/feature2
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/heads/feature3 b/manage_externals/test/repos/simple-ext.git/refs/heads/feature3
deleted file mode 100644
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/heads/master b/manage_externals/test/repos/simple-ext.git/refs/heads/master
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/tags/tag1 b/manage_externals/test/repos/simple-ext.git/refs/tags/tag1
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index ee595be8bd..0000000000
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/tags/tag2 b/manage_externals/test/repos/simple-ext.git/refs/tags/tag2
deleted file mode 100644
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diff --git a/manage_externals/test/requirements.txt b/manage_externals/test/requirements.txt
deleted file mode 100644
index d66f6f1e67..0000000000
--- a/manage_externals/test/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-pylint>=1.7.0
-autopep8>=1.3.0
-coverage>=4.4.0
-coveralls>=1.2.0
-sphinx>=1.6.0
diff --git a/manage_externals/test/test_sys_checkout.py b/manage_externals/test/test_sys_checkout.py
deleted file mode 100644
index ab4f77e88f..0000000000
--- a/manage_externals/test/test_sys_checkout.py
+++ /dev/null
@@ -1,1896 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Terminology: 
-  * 'container': a repo that has externals
-  * 'simple': a repo that has no externals, but is referenced as an external by another repo.
-  * 'mixed': a repo that both has externals and is referenced as an external by another repo.
-
-  * 'clean': the local repo matches the version in the externals and has no local modifications.
-  * 'empty': the external isn't checked out at all.
-
-Note: this script assume the path to the manic and
-checkout_externals module is already in the python path. This is
-usually handled by the makefile. If you call it directly, you may need
-to adjust your path.
-
-NOTE(bja, 2017-11) If a test fails, we want to keep the repo for that
-test. But the tests will keep running, so we need a unique name. Also,
-tearDown is always called after each test. I haven't figured out how
-to determine if an assertion failed and whether it is safe to clean up
-the test repos.
-
-So the solution is:
-
-* assign a unique id to each test repo.
-
-* never cleanup during the run.
-
-* Erase any existing repos at the begining of the module in
-setUpModule.
-"""
-
-# NOTE(bja, 2017-11) pylint complains that the module is too big, but
-# I'm still working on how to break up the tests and still have the
-# temporary directory be preserved....
-# pylint: disable=too-many-lines
-
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import logging
-import os
-import os.path
-import shutil
-import unittest
-
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import DESCRIPTION_SECTION, VERSION_ITEM
-from manic.externals_description import git_submodule_status
-from manic.externals_status import ExternalStatus
-from manic.repository_git import GitRepository
-from manic.utils import printlog, execute_subprocess
-from manic.global_constants import LOCAL_PATH_INDICATOR, VERBOSITY_DEFAULT
-from manic.global_constants import LOG_FILE_NAME
-from manic import checkout
-
-# ConfigParser was renamed in python2 to configparser. In python2,
-# ConfigParser returns byte strings, str, instead of unicode. We need
-# unicode to be compatible with xml and json parser and python3.
-try:
-    # python2
-    from ConfigParser import SafeConfigParser as config_parser
-except ImportError:
-    # python3
-    from configparser import ConfigParser as config_parser
-
-# ---------------------------------------------------------------------
-#
-# Global constants
-#
-# ---------------------------------------------------------------------
-
-
-# Module-wide root directory for all the per-test subdirs we'll create on
-# the fly (which are placed under wherever $CWD is when the test runs).
-# Set by setupModule().
-module_tmp_root_dir = None
-TMP_REPO_DIR_NAME = 'tmp'  # subdir under $CWD
-
-# subdir under test/ that holds all of our checked-in repositories (which we
-# will clone for these tests).
-BARE_REPO_ROOT_NAME = 'repos'
-
-# Environment var referenced by checked-in externals file in mixed-cont-ext.git,
-# which should be pointed to the fully-resolved BARE_REPO_ROOT_NAME directory.
-# We explicitly clear this after every test, via tearDown().
-MIXED_CONT_EXT_ROOT_ENV_VAR = 'MANIC_TEST_BARE_REPO_ROOT'
-
-# Subdirs under bare repo root, each holding a repository. For more info
-# on the contents of these repositories, see test/repos/README.md. In these
-# tests the 'parent' repos are cloned as a starting point, whereas the 'child'
-# repos are checked out when the tests run checkout_externals.
-CONTAINER_REPO = 'container.git'     # Parent repo
-SIMPLE_REPO = 'simple-ext.git'       # Child repo
-SIMPLE_FORK_REPO = 'simple-ext-fork.git'  # Child repo
-MIXED_REPO = 'mixed-cont-ext.git'    # Both parent and child
-
-# Standard (arbitrary) external names for test configs
-TAG_SECTION = 'simp_tag'
-BRANCH_SECTION = 'simp_branch'
-HASH_SECTION = 'simp_hash'
-
-# All the configs we construct check out their externals into these local paths.
-EXTERNALS_PATH = 'externals'
-SUB_EXTERNALS_PATH = 'src'  # For mixed test repos, 
-
-# For testing behavior with '.' instead of an explicit paths.
-SIMPLE_LOCAL_ONLY_NAME = '.'
-
-# Externals files.
-CFG_NAME = 'externals.cfg'  # We construct this on a per-test basis.
-CFG_SUB_NAME = 'sub-externals.cfg' # Already exists in mixed-cont-ext repo.
-
-# Arbitrary text file in all the test repos.
-README_NAME = 'readme.txt'  
-
-# Branch that exists in both the simple and simple-fork repos.
-REMOTE_BRANCH_FEATURE2 = 'feature2'
-
-SVN_TEST_REPO = 'https://github.com/escomp/cesm'
-
-# Disable too-many-public-methods error
-# pylint: disable=R0904
-
-def setUpModule():  # pylint: disable=C0103
-    """Setup for all tests in this module. It is called once per module!
-    """
-    logging.basicConfig(filename=LOG_FILE_NAME,
-                        format='%(levelname)s : %(asctime)s : %(message)s',
-                        datefmt='%Y-%m-%d %H:%M:%S',
-                        level=logging.DEBUG)
-    repo_root = os.path.join(os.getcwd(), TMP_REPO_DIR_NAME)
-    repo_root = os.path.abspath(repo_root)
-    # delete if it exists from previous runs
-    try:
-        shutil.rmtree(repo_root)
-    except BaseException:
-        pass
-    # create clean dir for this run
-    os.mkdir(repo_root)
-
-    # Make available to all tests in this file.
-    global module_tmp_root_dir
-    assert module_tmp_root_dir == None, module_tmp_root_dir
-    module_tmp_root_dir = repo_root
-
-
-class RepoUtils(object):
-    """Convenience methods for interacting with git repos."""
-    @staticmethod
-    def create_branch(repo_base_dir, external_name, branch, with_commit=False):
-        """Create branch and optionally (with_commit) add a single commit.
-        """
-        # pylint: disable=R0913
-        cwd = os.getcwd()
-        repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name)
-        os.chdir(repo_root)
-        cmd = ['git', 'checkout', '-b', branch, ]
-        execute_subprocess(cmd)
-        if with_commit:
-            msg = 'start work on {0}'.format(branch)
-            with open(README_NAME, 'a') as handle:
-                handle.write(msg)
-            cmd = ['git', 'add', README_NAME, ]
-            execute_subprocess(cmd)
-            cmd = ['git', 'commit', '-m', msg, ]
-            execute_subprocess(cmd)
-        os.chdir(cwd)
-
-    @staticmethod
-    def create_commit(repo_base_dir, external_name):
-        """Make a commit to the given external.
-        
-        This is used to test sync state changes from local commits on
-        detached heads and tracking branches.
-        """
-        cwd = os.getcwd()
-        repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name)
-        os.chdir(repo_root)
-
-        msg = 'work on great new feature!'
-        with open(README_NAME, 'a') as handle:
-            handle.write(msg)
-        cmd = ['git', 'add', README_NAME, ]
-        execute_subprocess(cmd)
-        cmd = ['git', 'commit', '-m', msg, ]
-        execute_subprocess(cmd)
-        os.chdir(cwd)
-
-    @staticmethod
-    def clone_test_repo(bare_root, test_id, parent_repo_name, dest_dir_in):
-        """Clone repo at <bare_root>/<parent_repo_name> into dest_dir_in or local per-test-subdir.
-
-        Returns output dir.
-        """
-        parent_repo_dir = os.path.join(bare_root, parent_repo_name)
-        if dest_dir_in is None:
-            # create unique subdir for this test
-            test_dir_name = test_id
-            print("Test repository name: {0}".format(test_dir_name))
-            dest_dir = os.path.join(module_tmp_root_dir, test_dir_name)
-        else:
-            dest_dir = dest_dir_in
-
-        # pylint: disable=W0212
-        GitRepository._git_clone(parent_repo_dir, dest_dir, VERBOSITY_DEFAULT)
-        return dest_dir
-
-    @staticmethod
-    def add_file_to_repo(under_test_dir, filename, tracked):
-        """Add a file to the repository so we can put it into a dirty state
-
-        """
-        cwd = os.getcwd()
-        os.chdir(under_test_dir)
-        with open(filename, 'w') as tmp:
-            tmp.write('Hello, world!')
-
-        if tracked:
-            # NOTE(bja, 2018-01) brittle hack to obtain repo dir and
-            # file name
-            path_data = filename.split('/')
-            repo_dir = os.path.join(path_data[0], path_data[1])
-            os.chdir(repo_dir)
-            tracked_file = path_data[2]
-            cmd = ['git', 'add', tracked_file]
-            execute_subprocess(cmd)
-
-        os.chdir(cwd)
-
-class GenerateExternalsDescriptionCfgV1(object):
-    """Building blocks to create ExternalsDescriptionCfgV1 files.
-
-    Basic usage: create_config() multiple create_*(), then write_config().
-    Optionally after that: write_with_*().
-    """
-
-    def __init__(self, bare_root):
-        self._schema_version = '1.1.0'
-        self._config = None
-
-        # directory where we have test repositories (which we will clone for
-        # tests)
-        self._bare_root = bare_root
-
-    def write_config(self, dest_dir, filename=CFG_NAME):
-        """Write self._config to disk
-
-        """
-        dest_path = os.path.join(dest_dir, filename)
-        with open(dest_path, 'w') as configfile:
-            self._config.write(configfile)
-
-    def create_config(self):
-        """Create an config object and add the required metadata section
-
-        """
-        self._config = config_parser()
-        self.create_metadata()
-
-    def create_metadata(self):
-        """Create the metadata section of the config file
-        """
-        self._config.add_section(DESCRIPTION_SECTION)
-
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM,
-                         self._schema_version)
-
-    def url_for_repo_path(self, repo_path, repo_path_abs=None):
-        if repo_path_abs is not None:
-            return repo_path_abs
-        else:
-            return os.path.join(self._bare_root, repo_path)
-        
-    def create_section(self, repo_path, name, tag='', branch='',
-                       ref_hash='', required=True, path=EXTERNALS_PATH,
-                       sub_externals='', repo_path_abs=None, from_submodule=False,
-                       sparse='', nested=False):
-        # pylint: disable=too-many-branches
-        """Create a config ExternalsDescription section with the given name.
-
-        Autofills some items and handles some optional items.
-
-        repo_path_abs overrides repo_path (which is relative to the bare repo)
-        path is a subdir under repo_path to check out to.
-        """
-        # pylint: disable=R0913
-        self._config.add_section(name)
-        if not from_submodule:
-            if nested:
-                self._config.set(name, ExternalsDescription.PATH, path)
-            else:
-                self._config.set(name, ExternalsDescription.PATH,
-                                 os.path.join(path, name))
-
-        self._config.set(name, ExternalsDescription.PROTOCOL,
-                         ExternalsDescription.PROTOCOL_GIT)
-
-        # from_submodules is incompatible with some other options, turn them off
-        if (from_submodule and
-                ((repo_path_abs is not None) or tag or ref_hash or branch)):
-            printlog('create_section: "from_submodule" is incompatible with '
-                     '"repo_url", "tag", "hash", and "branch" options;\n'
-                     'Ignoring those options for {}'.format(name))
-            repo_url = None
-            tag = ''
-            ref_hash = ''
-            branch = ''
-
-        repo_url = self.url_for_repo_path(repo_path, repo_path_abs)
-
-        if not from_submodule:
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        self._config.set(name, ExternalsDescription.REQUIRED, str(required))
-
-        if tag:
-            self._config.set(name, ExternalsDescription.TAG, tag)
-
-        if branch:
-            self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-        if ref_hash:
-            self._config.set(name, ExternalsDescription.HASH, ref_hash)
-
-        if sub_externals:
-            self._config.set(name, ExternalsDescription.EXTERNALS,
-                             sub_externals)
-
-        if sparse:
-            self._config.set(name, ExternalsDescription.SPARSE, sparse)
-
-        if from_submodule:
-            self._config.set(name, ExternalsDescription.SUBMODULE, "True")
-
-    def create_section_reference_to_subexternal(self, name):
-        """Just a reference to another externals file.
-
-        """
-        # pylint: disable=R0913
-        self._config.add_section(name)
-        self._config.set(name, ExternalsDescription.PATH, LOCAL_PATH_INDICATOR)
-
-        self._config.set(name, ExternalsDescription.PROTOCOL,
-                         ExternalsDescription.PROTOCOL_EXTERNALS_ONLY)
-
-        self._config.set(name, ExternalsDescription.REPO_URL,
-                         LOCAL_PATH_INDICATOR)
-
-        self._config.set(name, ExternalsDescription.REQUIRED, str(True))
-
-        self._config.set(name, ExternalsDescription.EXTERNALS, CFG_SUB_NAME)
-
-    def create_svn_external(self, name, tag='', branch=''):
-        """Create a config section for an svn repository.
-
-        """
-        self._config.add_section(name)
-        self._config.set(name, ExternalsDescription.PATH,
-                         os.path.join(EXTERNALS_PATH, name))
-
-        self._config.set(name, ExternalsDescription.PROTOCOL,
-                         ExternalsDescription.PROTOCOL_SVN)
-
-        self._config.set(name, ExternalsDescription.REPO_URL, SVN_TEST_REPO)
-
-        self._config.set(name, ExternalsDescription.REQUIRED, str(True))
-
-        if tag:
-            self._config.set(name, ExternalsDescription.TAG, tag)
-
-        if branch:
-            self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-    def write_with_git_branch(self, dest_dir, name, branch, new_remote_repo_path=None):
-        """Update fields in our config and write it to disk.
-
-        name is the key of the ExternalsDescription in self._config to update.
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-        if new_remote_repo_path:
-            if new_remote_repo_path == SIMPLE_LOCAL_ONLY_NAME:
-                repo_url = SIMPLE_LOCAL_ONLY_NAME
-            else:
-                repo_url = os.path.join(self._bare_root, new_remote_repo_path)
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        try:
-            # remove the tag if it existed
-            self._config.remove_option(name, ExternalsDescription.TAG)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_with_svn_branch(self, dest_dir, name, branch):
-        """Update a repository branch, and potentially the remote.
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-        try:
-            # remove the tag if it existed
-            self._config.remove_option(name, ExternalsDescription.TAG)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_with_tag_and_remote_repo(self, dest_dir, name, tag, new_remote_repo_path,
-                                       remove_branch=True):
-        """Update a repository tag and the remote.
-
-        NOTE(bja, 2017-11) remove_branch=False should result in an
-        overspecified external with both a branch and tag. This is
-        used for error condition testing.
-
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.TAG, tag)
-
-        if new_remote_repo_path:
-            repo_url = os.path.join(self._bare_root, new_remote_repo_path)
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        try:
-            # remove the branch if it existed
-            if remove_branch:
-                self._config.remove_option(name, ExternalsDescription.BRANCH)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_without_branch_tag(self, dest_dir, name):
-        """Update a repository protocol, and potentially the remote
-        """
-        # pylint: disable=R0913
-        try:
-            # remove the branch if it existed
-            self._config.remove_option(name, ExternalsDescription.BRANCH)
-        except BaseException:
-            pass
-
-        try:
-            # remove the tag if it existed
-            self._config.remove_option(name, ExternalsDescription.TAG)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_without_repo_url(self, dest_dir, name):
-        """Update a repository protocol, and potentially the remote
-        """
-        # pylint: disable=R0913
-        try:
-            # remove the repo url if it existed
-            self._config.remove_option(name, ExternalsDescription.REPO_URL)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_with_protocol(self, dest_dir, name, protocol, repo_path=None):
-        """Update a repository protocol, and potentially the remote
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.PROTOCOL, protocol)
-
-        if repo_path:
-            repo_url = os.path.join(self._bare_root, repo_path)
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        self.write_config(dest_dir)
-
-
-def _execute_checkout_in_dir(dirname, args, debug_env=''):
-    """Execute the checkout command in the appropriate repo dir with the
-    specified additional args. 
-
-    args should be a list of strings.
-    debug_env shuld be a string of the form 'FOO=bar' or the empty string. 
-
-    Note that we are calling the command line processing and main
-    routines and not using a subprocess call so that we get code
-    coverage results! Note this means that environment variables are passed
-    to checkout_externals via os.environ; debug_env is just used to aid
-    manual reproducibility of a given call.
-
-    Returns (overall_status, tree_status)
-    where overall_status is 0 for success, nonzero otherwise.
-    and tree_status is set if --status was passed in, None otherwise.
-
-    Note this command executes the checkout command, it doesn't
-    necessarily do any checking out (e.g. if --status is passed in).
-    """
-    cwd = os.getcwd()
-
-    # Construct a command line for reproducibility; this command is not
-    # actually executed in the test.
-    os.chdir(dirname)
-    cmdline = ['--externals', CFG_NAME, ]
-    cmdline += args
-    manual_cmd = ('Running equivalent of:\n'
-                  'pushd {dirname}; '
-                  '{debug_env} /path/to/checkout_externals {args}'.format(
-                      dirname=dirname, debug_env=debug_env,
-                      args=' '.join(cmdline)))
-    printlog(manual_cmd)
-    options = checkout.commandline_arguments(cmdline)
-    overall_status, tree_status = checkout.main(options)
-    os.chdir(cwd)
-    return overall_status, tree_status
-        
-class BaseTestSysCheckout(unittest.TestCase):
-    """Base class of reusable systems level test setup for
-    checkout_externals
-
-    """
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic.
-    # pylint: disable=invalid-name
-
-    # Command-line args for checkout_externals, used in execute_checkout_in_dir()
-    status_args = ['--status']
-    checkout_args = []
-    optional_args = ['--optional']
-    verbose_args = ['--status', '--verbose']
-
-    def setUp(self):
-        """Setup for all individual checkout_externals tests
-        """
-        # directory we want to return to after the test system and
-        # checkout_externals are done cd'ing all over the place.
-        self._return_dir = os.getcwd()
-
-        self._test_id = self.id().split('.')[-1]
-
-        # find root
-        if os.path.exists(os.path.join(os.getcwd(), 'checkout_externals')):
-            root_dir = os.path.abspath(os.getcwd())
-        else:
-            # maybe we are in a subdir, search up
-            root_dir = os.path.abspath(os.path.join(os.getcwd(), os.pardir))
-            while os.path.basename(root_dir):
-                if os.path.exists(os.path.join(root_dir, 'checkout_externals')):
-                    break
-                root_dir = os.path.dirname(root_dir)
-
-        if not os.path.exists(os.path.join(root_dir, 'checkout_externals')):
-            raise RuntimeError('Cannot find checkout_externals')
-
-        # path to the executable
-        self._checkout = os.path.join(root_dir, 'checkout_externals')
-
-        # directory where we have test repositories (which we will clone for
-        # tests)
-        self._bare_root = os.path.abspath(
-            os.path.join(root_dir, 'test', BARE_REPO_ROOT_NAME))
-
-        # set the input file generator
-        self._generator = GenerateExternalsDescriptionCfgV1(self._bare_root)
-        # set the input file generator for secondary externals
-        self._sub_generator = GenerateExternalsDescriptionCfgV1(self._bare_root)
-
-    def tearDown(self):
-        """Tear down for individual tests
-        """
-        # return to our common starting point
-        os.chdir(self._return_dir)
-        
-        # (in case this was set) Don't pollute environment of other tests.
-        os.environ.pop(MIXED_CONT_EXT_ROOT_ENV_VAR,
-                       None)  # Don't care if key wasn't set.
-
-    def clone_test_repo(self, parent_repo_name, dest_dir_in=None):
-        """Clones repo under self._bare_root"""
-        return RepoUtils.clone_test_repo(self._bare_root, self._test_id,
-                                         parent_repo_name, dest_dir_in)
-
-    def execute_checkout_in_dir(self, dirname, args, debug_env=''):
-        overall_status, tree_status = _execute_checkout_in_dir(dirname, args,
-                                                               debug_env=debug_env)
-        self.assertEqual(overall_status, 0)
-        return tree_status
-
-    def execute_checkout_with_status(self, dirname, args, debug_env=''):
-        """Calls checkout a second time to get status if needed."""
-        tree_status = self.execute_checkout_in_dir(
-            dirname, args, debug_env=debug_env)
-        if tree_status is None:
-            tree_status = self.execute_checkout_in_dir(dirname,
-                                                       self.status_args,
-                                                       debug_env=debug_env)
-            self.assertNotEqual(tree_status, None)
-        return tree_status
-    
-    def _check_sync_clean(self, ext_status, expected_sync_state,
-                          expected_clean_state):
-        self.assertEqual(ext_status.sync_state, expected_sync_state)
-        self.assertEqual(ext_status.clean_state, expected_clean_state)
-
-    @staticmethod
-    def _external_path(section_name, base_path=EXTERNALS_PATH):
-        return './{0}/{1}'.format(base_path, section_name)
-        
-    def _check_file_exists(self, repo_dir, pathname):
-        "Check that <pathname> exists in <repo_dir>"
-        self.assertTrue(os.path.exists(os.path.join(repo_dir, pathname)))
-
-    def _check_file_absent(self, repo_dir, pathname):
-        "Check that <pathname> does not exist in <repo_dir>"
-        self.assertFalse(os.path.exists(os.path.join(repo_dir, pathname)))
-
-
-class TestSysCheckout(BaseTestSysCheckout):
-    """Run systems level tests of checkout_externals
-    """
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic.
-    # pylint: disable=invalid-name
-
-    # ----------------------------------------------------------------
-    #
-    # Run systems tests
-    #
-    # ----------------------------------------------------------------
-    def test_required_bytag(self):
-        """Check out a required external pointing to a git tag."""
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                       tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        local_path_rel = self._external_path(TAG_SECTION)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        local_path_abs = os.path.join(cloned_repo_dir, local_path_rel)
-        self.assertFalse(os.path.exists(local_path_abs))
-
-        # after checkout, the external is 'clean' aka at the correct version.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # Actually checked out the desired repo.
-        self.assertEqual('origin', GitRepository._remote_name_for_url(
-            # Which url to look up
-            self._generator.url_for_repo_path(SIMPLE_REPO),
-            # Which directory has the local checked-out repo.
-            dirname=local_path_abs))
-        
-        # Actually checked out the desired tag.
-        (tag_found, tag_name) = GitRepository._git_current_tag(local_path_abs)
-        self.assertEqual(tag_name, 'tag1')
-
-        # Check existence of some simp_tag files
-        tag_path = os.path.join('externals', TAG_SECTION)
-        self._check_file_exists(cloned_repo_dir,
-                                os.path.join(tag_path, README_NAME))
-        # Subrepo should not exist (not referenced by configs).
-        self._check_file_absent(cloned_repo_dir, os.path.join(tag_path,
-                                                             'simple_subdir',
-                                                             'subdir_file.txt'))
-        
-    def test_required_bybranch(self):
-        """Check out a required external pointing to a git branch."""
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        local_path_rel = self._external_path(BRANCH_SECTION)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        local_path_abs = os.path.join(cloned_repo_dir, local_path_rel)
-        self.assertFalse(os.path.exists(local_path_abs))
-
-        # after checkout, the external is 'clean' aka at the correct version.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertTrue(os.path.exists(local_path_abs))
-
-        # Actually checked out the desired repo.
-        self.assertEqual('origin', GitRepository._remote_name_for_url(
-            # Which url to look up
-            self._generator.url_for_repo_path(SIMPLE_REPO),
-            # Which directory has the local checked-out repo.
-            dirname=local_path_abs))
-
-        # Actually checked out the desired branch. 
-        (branch_found, branch_name) = GitRepository._git_current_remote_branch(
-            local_path_abs)
-        self.assertEquals(branch_name, 'origin/' + REMOTE_BRANCH_FEATURE2)
-        
-    def test_required_byhash(self):
-        """Check out a required external pointing to a git hash."""
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, HASH_SECTION,
-                                       ref_hash='60b1cc1a38d63')
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        local_path_rel = self._external_path(HASH_SECTION)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        local_path_abs = os.path.join(cloned_repo_dir, local_path_rel)
-        self.assertFalse(os.path.exists(local_path_abs))
-
-        # after checkout, the externals are 'clean' aka at their correct version.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # Actually checked out the desired repo.
-        self.assertEqual('origin', GitRepository._remote_name_for_url(
-            # Which url to look up
-            self._generator.url_for_repo_path(SIMPLE_REPO),
-            # Which directory has the local checked-out repo.
-            dirname=local_path_abs))
-
-        # Actually checked out the desired hash.
-        (hash_found, hash_name) = GitRepository._git_current_hash(
-            local_path_abs)
-        self.assertTrue(hash_name.startswith('60b1cc1a38d63'),
-                        msg=hash_name)
-        
-    def test_container_nested_required(self):
-        """Verify that a container with nested subrepos generates the correct initial status.
-        Tests over all possible permutations
-        """
-        # Output subdirs for each of the externals, to test that one external can be
-        # checked out in a subdir of another.
-        NESTED_SUBDIR = ['./fred', './fred/wilma', './fred/wilma/barney']
-
-        # Assert that each type of external (e.g. tag vs branch) can be at any parent level
-        # (e.g. child/parent/grandparent).
-        orders = [[0, 1, 2], [1, 2, 0], [2, 0, 1],
-                  [0, 2, 1], [2, 1, 0], [1, 0, 2]]
-        for n, order in enumerate(orders):
-            dest_dir = os.path.join(module_tmp_root_dir, self._test_id,
-                                    "test"+str(n))
-            cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO,
-                                                   dest_dir_in=dest_dir)
-            self._generator.create_config()
-            # We happen to check out each section via a different reference (tag/branch/hash) but
-            # those don't really matter, we just need to check out three repos into a nested set of
-            # directories.
-            self._generator.create_section(
-                SIMPLE_REPO, TAG_SECTION, nested=True,
-                tag='tag1', path=NESTED_SUBDIR[order[0]])
-            self._generator.create_section(
-                SIMPLE_REPO, BRANCH_SECTION, nested=True,
-                branch=REMOTE_BRANCH_FEATURE2, path=NESTED_SUBDIR[order[1]])
-            self._generator.create_section(
-                SIMPLE_REPO, HASH_SECTION, nested=True,
-                ref_hash='60b1cc1a38d63', path=NESTED_SUBDIR[order[2]])
-            self._generator.write_config(cloned_repo_dir)
-
-            # all externals start out 'empty' aka not checked out.
-            tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                                self.status_args)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]],
-                                   ExternalStatus.EMPTY,
-                                   ExternalStatus.DEFAULT)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]],
-                                   ExternalStatus.EMPTY,
-                                   ExternalStatus.DEFAULT)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]],
-                                   ExternalStatus.EMPTY,
-                                   ExternalStatus.DEFAULT)
-
-            # after checkout, all the repos are 'clean'.
-            tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                     self.checkout_args)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]],
-                                   ExternalStatus.STATUS_OK,
-                                   ExternalStatus.STATUS_OK)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]],
-                                   ExternalStatus.STATUS_OK,
-                                   ExternalStatus.STATUS_OK)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]],
-                                   ExternalStatus.STATUS_OK,
-                                   ExternalStatus.STATUS_OK)
-            
-    def test_container_simple_optional(self):
-        """Verify that container with an optional simple subrepos generates
-        the correct initial status.
-
-        """
-        # create repo and externals config.
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, 'simp_req',
-                            tag='tag1')
-
-        self._generator.create_section(SIMPLE_REPO, 'simp_opt',
-                            tag='tag1', required=False)
-
-        self._generator.write_config(cloned_repo_dir)
-
-        # all externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        req_status = tree[self._external_path('simp_req')]
-        self._check_sync_clean(req_status,
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self.assertEqual(req_status.source_type, ExternalStatus.MANAGED)
-
-        opt_status = tree[self._external_path('simp_opt')]
-        self._check_sync_clean(opt_status,
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL)
-
-        # after checkout, required external is clean, optional is still empty.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        req_status = tree[self._external_path('simp_req')]
-        self._check_sync_clean(req_status,
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertEqual(req_status.source_type, ExternalStatus.MANAGED)
-        
-        opt_status = tree[self._external_path('simp_opt')]
-        self._check_sync_clean(opt_status,
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL)
-
-        # after checking out optionals, the optional external is also clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.optional_args)
-        req_status = tree[self._external_path('simp_req')]        
-        self._check_sync_clean(req_status,
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertEqual(req_status.source_type, ExternalStatus.MANAGED)
-
-        opt_status = tree[self._external_path('simp_opt')]
-        self._check_sync_clean(opt_status,
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL)
-
-    def test_container_simple_verbose(self):
-        """Verify that verbose status matches non-verbose.
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # after checkout, all externals should be 'clean'.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # 'Verbose' status should tell the same story.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.verbose_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_simple_dirty(self):
-        """Verify that a container with a new tracked file is marked dirty.
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # checkout, should start out clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # add a tracked file to the simp_tag external, should be dirty.
-        RepoUtils.add_file_to_repo(cloned_repo_dir,
-                                   'externals/{0}/tmp.txt'.format(TAG_SECTION),
-                                   tracked=True)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.DIRTY)
-
-        # Re-checkout; simp_tag should still be dirty.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.DIRTY)
-
-    def test_container_simple_untracked(self):
-        """Verify that a container with simple subrepos and a untracked files
-        is not considered 'dirty' and will attempt an update.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                       tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # checkout, should start out clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # add an untracked file to the simp_tag external, should stay clean.
-        RepoUtils.add_file_to_repo(cloned_repo_dir,
-                                   'externals/{0}/tmp.txt'.format(TAG_SECTION),
-                                   tracked=False)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        
-        # After checkout, the external should still be 'clean'.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_simple_detached_sync(self):
-        """Verify that a container with simple subrepos generates the correct
-        out of sync status when making commits from a detached head
-        state. 
-
-        For more info about 'detached head' state: https://www.cloudbees.com/blog/git-detached-head
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        
-        self._generator.create_section(SIMPLE_REPO, 'simp_hash',
-                                 ref_hash='60b1cc1a38d63')
-        
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-
-        # checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # Commit on top of the tag and hash (creating the detached head state in those two
-        # externals' repos)
-        # The branch commit does not create the detached head state, but here for completeness.
-        RepoUtils.create_commit(cloned_repo_dir, TAG_SECTION)
-        RepoUtils.create_commit(cloned_repo_dir, HASH_SECTION)
-        RepoUtils.create_commit(cloned_repo_dir, BRANCH_SECTION)
-
-        # sync status of all three should be 'modified' (uncommitted changes)
-        # clean status is 'ok' (matches externals version)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # after checkout, all externals should be totally clean (no uncommitted changes,
-        # and matches externals version).
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_remote_branch(self):
-        """Verify that a container with remote branch change works
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the branch external to point to a different remote with the same branch,
-        # then simp_branch should be out of sync
-        self._generator.write_with_git_branch(cloned_repo_dir,
-                                              name=BRANCH_SECTION,
-                                              branch=REMOTE_BRANCH_FEATURE2,
-                                              new_remote_repo_path=SIMPLE_FORK_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # checkout new externals, now simp_branch should be clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_remote_tag_same_branch(self):
-        """Verify that a container with remote tag change works. The new tag
-        should not be in the original repo, only the new remote
-        fork. The new tag is automatically fetched because it is on
-        the branch.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the config file to point to a different remote with
-        # the new tag replacing the old branch. Tag MUST NOT be in the original
-        # repo! status of simp_branch should then be out of sync
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='forked-feature-v1',
-                                                       new_remote_repo_path=SIMPLE_FORK_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # checkout new externals, then should be synced.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_remote_tag_fetch_all(self):
-        """Verify that a container with remote tag change works. The new tag
-        should not be in the original repo, only the new remote
-        fork. It should also not be on a branch that will be fetched,
-        and therefore not fetched by default with 'git fetch'. It will
-        only be retrieved by 'git fetch --tags'
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the config file to point to a different remote with
-        # the new tag instead of the old branch. Tag MUST NOT be in the original
-        # repo! status of simp_branch should then be out of sync.
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='abandoned-feature',
-                                                       new_remote_repo_path=SIMPLE_FORK_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # checkout new externals, should be clean again.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_preserve_dot(self):
-        """Verify that after inital checkout, modifying an external git repo
-        url to '.' and the current branch will leave it unchanged.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the config file to point to a different remote with
-        # the same branch.
-        self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION,
-                                              branch=REMOTE_BRANCH_FEATURE2,
-                                              new_remote_repo_path=SIMPLE_FORK_REPO)
-        # after checkout, should be clean again.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # update branch to point to a new branch that only exists in
-        # the local fork
-        RepoUtils.create_branch(cloned_repo_dir, external_name=BRANCH_SECTION,
-                                branch='private-feature', with_commit=True)
-        self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION,
-                                              branch='private-feature',
-                                              new_remote_repo_path=SIMPLE_LOCAL_ONLY_NAME)
-        # after checkout, should be clean again.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_mixed_subrepo(self):
-        """Verify container with mixed subrepo.
-
-        The mixed subrepo has a sub-externals file with different
-        sub-externals on different branches.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        self._generator.create_config()
-        self._generator.create_section(MIXED_REPO, 'mixed_req',
-                                       branch='master', sub_externals=CFG_SUB_NAME)
-        self._generator.write_config(cloned_repo_dir)
-
-        # The subrepo has a repo_url that uses this environment variable.
-        # It'll be cleared in tearDown().
-        os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root
-        debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root 
-        
-        # inital checkout: all requireds are clean, and optional is empty.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args,
-                                                 debug_env=debug_env)
-        mixed_req_path = self._external_path('mixed_req')
-        self._check_sync_clean(tree[mixed_req_path],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        sub_ext_base_path = "{0}/{1}/{2}".format(EXTERNALS_PATH, 'mixed_req', SUB_EXTERNALS_PATH)
-        # The already-checked-in subexternals file has a 'simp_branch' section
-        self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # update the mixed-use external to point to different branch
-        # status should become out of sync for mixed_req, but sub-externals
-        # are still in sync
-        self._generator.write_with_git_branch(cloned_repo_dir, name='mixed_req',
-                                              branch='new-feature',
-                                              new_remote_repo_path=MIXED_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args,
-                                            debug_env=debug_env)
-        self._check_sync_clean(tree[mixed_req_path],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # run the checkout. Now the mixed use external and its sub-externals should be clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args,
-                                                 debug_env=debug_env)
-        self._check_sync_clean(tree[mixed_req_path],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        
-    def test_container_component(self):
-        """Verify that optional component checkout works
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        # create the top level externals file
-        self._generator.create_config()
-        # Optional external, by tag.
-        self._generator.create_section(SIMPLE_REPO, 'simp_opt',
-                                       tag='tag1', required=False)
-
-        # Required external, by branch.
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-
-        # Required external, by hash.
-        self._generator.create_section(SIMPLE_REPO, HASH_SECTION,
-                                       ref_hash='60b1cc1a38d63')
-        self._generator.write_config(cloned_repo_dir)
-        
-        # inital checkout, first try a nonexistent component argument noref
-        checkout_args = ['simp_opt', 'noref']
-        checkout_args.extend(self.checkout_args)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, checkout_args)
-
-        # Now explicitly check out one optional component..
-        # Explicitly listed component (opt) should be present, the other two not.
-        checkout_args = ['simp_opt']
-        checkout_args.extend(self.checkout_args)
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 checkout_args)
-        self._check_sync_clean(tree[self._external_path('simp_opt')],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-
-        # Check out a second component, this one required.
-        # Explicitly listed component (branch) should be present, the still-unlisted one (tag) not.
-        checkout_args.append(BRANCH_SECTION)
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 checkout_args)
-        self._check_sync_clean(tree[self._external_path('simp_opt')],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-
-
-    def test_container_exclude_component(self):
-        """Verify that exclude component checkout works
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        
-        self._generator.create_section(SIMPLE_REPO, 'simp_hash',
-                                 ref_hash='60b1cc1a38d63')
-        
-        self._generator.write_config(cloned_repo_dir)
-
-        # inital checkout should result in all externals being clean except excluded TAG_SECTION.
-        checkout_args = ['--exclude', TAG_SECTION]
-        checkout_args.extend(self.checkout_args)
-        tree = self.execute_checkout_with_status(cloned_repo_dir, checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_subexternal(self):
-        """Verify that an externals file can be brought in as a reference.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(MIXED_REPO)
-
-        self._generator.create_config()
-        self._generator.create_section_reference_to_subexternal('mixed_base')
-        self._generator.write_config(cloned_repo_dir)
-
-        # The subrepo has a repo_url that uses this environment variable.
-        # It'll be cleared in tearDown().
-        os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root
-        debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root 
-
-        # After checkout, confirm required's are clean and the referenced
-        # subexternal's contents are also clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args,
-                                                 debug_env=debug_env)
-        
-        self._check_sync_clean(
-            tree[self._external_path(BRANCH_SECTION, base_path=SUB_EXTERNALS_PATH)],
-            ExternalStatus.STATUS_OK,
-            ExternalStatus.STATUS_OK)
-
-    def test_container_sparse(self):
-        """Verify that 'full' container with simple subrepo
-        can run a sparse checkout and generate the correct initial status.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        # Create a file to list filenames to checkout.
-        sparse_filename = 'sparse_checkout'
-        with open(os.path.join(cloned_repo_dir, sparse_filename), 'w') as sfile:
-            sfile.write(README_NAME)
-
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                       tag='tag2')
-
-        # Same tag as above, but with a sparse file too.
-        sparse_relpath = '../../' + sparse_filename
-        self._generator.create_section(SIMPLE_REPO, 'simp_sparse',
-                                       tag='tag2', sparse=sparse_relpath)
-
-        self._generator.write_config(cloned_repo_dir)
-
-        # inital checkout, confirm required's are clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path('simp_sparse')],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # Check existence of some files - full set in TAG_SECTION, and sparse set
-        # in 'simp_sparse'.
-        subrepo_path = os.path.join('externals', TAG_SECTION)
-        self._check_file_exists(cloned_repo_dir,
-                                os.path.join(subrepo_path, README_NAME))
-        self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path,
-                                                             'simple_subdir',
-                                                             'subdir_file.txt'))
-        subrepo_path = os.path.join('externals', 'simp_sparse')
-        self._check_file_exists(cloned_repo_dir,
-                                os.path.join(subrepo_path, README_NAME))
-        self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path,
-                                                             'simple_subdir',
-                                                             'subdir_file.txt'))
-
-
-class TestSysCheckoutSVN(BaseTestSysCheckout):
-    """Run systems level tests of checkout_externals accessing svn repositories
-
-    SVN tests - these tests use the svn repository interface. Since
-    they require an active network connection, they are significantly
-    slower than the git tests. But svn testing is critical. So try to
-    design the tests to only test svn repository functionality
-    (checkout, switch) and leave generic testing of functionality like
-    'optional' to the fast git tests.
-
-    Example timing as of 2017-11:
-
-      * All other git and unit tests combined take between 4-5 seconds
-
-      * Just checking if svn is available for a single test takes 2 seconds.
-
-      * The single svn test typically takes between 10 and 25 seconds
-        (depending on the network)!
-
-    NOTE(bja, 2017-11) To enable CI testing we can't use a real remote
-    repository that restricts access and it seems inappropriate to hit
-    a random open source repo. For now we are just hitting one of our
-    own github repos using the github svn server interface. This
-    should be "good enough" for basic checkout and swich
-    functionality. But if additional svn functionality is required, a
-    better solution will be necessary. I think eventually we want to
-    create a small local svn repository on the fly (doesn't require an
-    svn server or network connection!) and use it for testing.
-
-    """
-
-    @staticmethod
-    def _svn_branch_name():
-        return './{0}/svn_branch'.format(EXTERNALS_PATH)
-
-    @staticmethod
-    def _svn_tag_name():
-        return './{0}/svn_tag'.format(EXTERNALS_PATH)
-    
-    def _check_tag_branch_svn_tag_clean(self, tree):
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._svn_branch_name()],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._svn_tag_name()],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    @staticmethod
-    def _have_svn_access():
-        """Check if we have svn access so we can enable tests that use svn.
-
-        """
-        have_svn = False
-        cmd = ['svn', 'ls', SVN_TEST_REPO, ]
-        try:
-            execute_subprocess(cmd)
-            have_svn = True
-        except BaseException:
-            pass
-        return have_svn
-
-    def _skip_if_no_svn_access(self):
-        """Function decorator to disable svn tests when svn isn't available
-        """
-        have_svn = self._have_svn_access()
-        if not have_svn:
-            raise unittest.SkipTest("No svn access")
-
-    def test_container_simple_svn(self):
-        """Verify that a container repo can pull in an svn branch and svn tag.
-
-        """
-        self._skip_if_no_svn_access()
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        self._generator.create_config()
-        # Git repo.
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION, tag='tag1')
-
-        # Svn repos.
-        self._generator.create_svn_external('svn_branch', branch='trunk')
-        self._generator.create_svn_external('svn_tag', tag='tags/cesm2.0.beta07')
-
-        self._generator.write_config(cloned_repo_dir)
-
-        # checkout, make sure all sections are clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_tag_branch_svn_tag_clean(tree)
-
-        # update description file to make the tag into a branch and
-        # trigger a switch
-        self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag',
-                                              'trunk')
-
-        # checkout, again the results should be clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_tag_branch_svn_tag_clean(tree)
-
-        # add an untracked file to the repo
-        tracked = False
-        RepoUtils.add_file_to_repo(cloned_repo_dir,
-                                   'externals/svn_branch/tmp.txt', tracked)
-
-        # run a no-op checkout.
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update description file to make the branch into a tag and
-        # trigger a modified sync status
-        self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag',
-                                              'tags/cesm2.0.beta07')
-
-        self.execute_checkout_in_dir(cloned_repo_dir,self.checkout_args)
-
-        # verify status is still clean and unmodified, last
-        # checkout modified the working dir state.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.verbose_args)
-        self._check_tag_branch_svn_tag_clean(tree)
-
-class TestSubrepoCheckout(BaseTestSysCheckout):
-    # Need to store information at setUp time for checking
-    # pylint: disable=too-many-instance-attributes
-    """Run tests to ensure proper handling of repos with submodules.
-
-    By default, submodules in git repositories are checked out. A git
-    repository checked out as a submodule is treated as if it was
-    listed in an external with the same properties as in the source
-    .gitmodules file.
-    """
-
-    def setUp(self):
-        """Setup for all submodule checkout tests
-        Create a repo with two submodule repositories.
-        """
-
-        # Run the basic setup
-        super().setUp()
-        # create test repo
-        # We need to do this here (rather than have a static repo) because
-        # git submodules do not allow for variables in .gitmodules files
-        self._test_repo_name = 'test_repo_with_submodules'
-        self._bare_branch_name = 'subrepo_branch'
-        self._config_branch_name = 'subrepo_config_branch'
-        self._container_extern_name = 'externals_container.cfg'
-        self._my_test_dir = os.path.join(module_tmp_root_dir, self._test_id)
-        self._repo_dir = os.path.join(self._my_test_dir, self._test_repo_name)
-        self._checkout_dir = 'repo_with_submodules'
-        check_dir = self.clone_test_repo(CONTAINER_REPO,
-                                         dest_dir_in=self._repo_dir)
-        self.assertTrue(self._repo_dir == check_dir)
-        # Add the submodules
-        cwd = os.getcwd()
-        fork_repo_dir = os.path.join(self._bare_root, SIMPLE_FORK_REPO)
-        simple_repo_dir = os.path.join(self._bare_root, SIMPLE_REPO)
-        self._simple_ext_fork_name = os.path.splitext(SIMPLE_FORK_REPO)[0]
-        self._simple_ext_name = os.path.join('sourc',
-                                             os.path.splitext(SIMPLE_REPO)[0])
-        os.chdir(self._repo_dir)
-        # Add a branch with a subrepo
-        cmd = ['git', 'branch', self._bare_branch_name, 'master']
-        execute_subprocess(cmd)
-        cmd = ['git', 'checkout', self._bare_branch_name]
-        execute_subprocess(cmd)
-        cmd = ['git', 'submodule', 'add', fork_repo_dir]
-        execute_subprocess(cmd)
-        cmd = ['git', 'commit', '-am', "'Added simple-ext-fork as a submodule'"]
-        execute_subprocess(cmd)
-        # Save the fork repo hash for comparison
-        os.chdir(self._simple_ext_fork_name)
-        self._fork_hash_check = self.get_git_hash()
-        os.chdir(self._repo_dir)
-        # Now, create a branch to test from_sbmodule
-        cmd = ['git', 'branch',
-               self._config_branch_name, self._bare_branch_name]
-        execute_subprocess(cmd)
-        cmd = ['git', 'checkout', self._config_branch_name]
-        execute_subprocess(cmd)
-        cmd = ['git', 'submodule', 'add', '--name', SIMPLE_REPO,
-               simple_repo_dir, self._simple_ext_name]
-        execute_subprocess(cmd)
-        # Checkout feature2
-        os.chdir(self._simple_ext_name)
-        cmd = ['git', 'branch', 'feature2', 'origin/feature2']
-        execute_subprocess(cmd)
-        cmd = ['git', 'checkout', 'feature2']
-        execute_subprocess(cmd)
-        # Save the fork repo hash for comparison
-        self._simple_hash_check = self.get_git_hash()
-        os.chdir(self._repo_dir)
-        self.write_externals_config(filename=self._container_extern_name,
-                                    dest_dir=self._repo_dir, from_submodule=True)
-        cmd = ['git', 'add', self._container_extern_name]
-        execute_subprocess(cmd)
-        cmd = ['git', 'commit', '-am', "'Added simple-ext as a submodule'"]
-        execute_subprocess(cmd)
-        # Reset to master
-        cmd = ['git', 'checkout', 'master']
-        execute_subprocess(cmd)
-        os.chdir(cwd)
-
-    @staticmethod
-    def get_git_hash(revision="HEAD"):
-        """Return the hash for <revision>"""
-        cmd = ['git', 'rev-parse', revision]
-        git_out = execute_subprocess(cmd, output_to_caller=True)
-        return git_out.strip()
-
-    def write_externals_config(self, name='', dest_dir=None,
-                               filename=CFG_NAME,
-                               branch_name=None, sub_externals=None,
-                               from_submodule=False):
-        # pylint: disable=too-many-arguments
-        """Create a container externals file with only simple externals.
-
-        """
-        self._generator.create_config()
-
-        if dest_dir is None:
-            dest_dir = self._my_test_dir
-
-        if from_submodule:
-            self._generator.create_section(SIMPLE_FORK_REPO,
-                                           self._simple_ext_fork_name,
-                                           from_submodule=True)
-            self._generator.create_section(SIMPLE_REPO,
-                                           self._simple_ext_name,
-                                           branch='feature3', path='',
-                                           from_submodule=False)
-        else:
-            if branch_name is None:
-                branch_name = 'master'
-
-            self._generator.create_section(self._test_repo_name,
-                                           self._checkout_dir,
-                                           branch=branch_name,
-                                           path=name, sub_externals=sub_externals,
-                                           repo_path_abs=self._repo_dir)
-
-        self._generator.write_config(dest_dir, filename=filename)
-
-    def idempotence_check(self, checkout_dir):
-        """Verify that calling checkout_externals and
-        checkout_externals --status does not cause errors"""
-        cwd = os.getcwd()
-        os.chdir(checkout_dir)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.status_args)
-        os.chdir(cwd)
-
-    def test_submodule_checkout_bare(self):
-        """Verify that a git repo with submodule is properly checked out
-        This test if for where there is no 'externals' keyword in the
-        parent repo.
-        Correct behavior is that the submodule is checked out using
-        normal git submodule behavior.
-        """
-        simple_ext_fork_tag = "(tag1)"
-        simple_ext_fork_status = " "
-        self.write_externals_config(branch_name=self._bare_branch_name)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        cwd = os.getcwd()
-        checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir)
-        fork_file = os.path.join(checkout_dir,
-                                 self._simple_ext_fork_name, "readme.txt")
-        self.assertTrue(os.path.exists(fork_file))
-
-        submods = git_submodule_status(checkout_dir)
-        print('checking status of', checkout_dir, ':', submods)
-        self.assertEqual(len(submods.keys()), 1)
-        self.assertTrue(self._simple_ext_fork_name in submods)
-        submod = submods[self._simple_ext_fork_name]
-        self.assertTrue('hash' in submod)
-        self.assertEqual(submod['hash'], self._fork_hash_check)
-        self.assertTrue('status' in submod)
-        self.assertEqual(submod['status'], simple_ext_fork_status)
-        self.assertTrue('tag' in submod)
-        self.assertEqual(submod['tag'], simple_ext_fork_tag)
-        self.idempotence_check(checkout_dir)
-
-    def test_submodule_checkout_none(self):
-        """Verify that a git repo with submodule is properly checked out
-        This test is for when 'externals=None' is in parent repo's
-        externals cfg file.
-        Correct behavior is the submodle is not checked out.
-        """
-        self.write_externals_config(branch_name=self._bare_branch_name,
-                                    sub_externals="none")
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        cwd = os.getcwd()
-        checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir)
-        fork_file = os.path.join(checkout_dir,
-                                 self._simple_ext_fork_name, "readme.txt")
-        self.assertFalse(os.path.exists(fork_file))
-        os.chdir(cwd)
-        self.idempotence_check(checkout_dir)
-
-    def test_submodule_checkout_config(self): # pylint: disable=too-many-locals
-        """Verify that a git repo with submodule is properly checked out
-        This test if for when the 'from_submodule' keyword is used in the
-        parent repo.
-        Correct behavior is that the submodule is checked out using
-        normal git submodule behavior.
-        """
-        tag_check = None # Not checked out as submodule
-        status_check = "-" # Not checked out as submodule
-        self.write_externals_config(branch_name=self._config_branch_name,
-                                    sub_externals=self._container_extern_name)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        cwd = os.getcwd()
-        checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir)
-        fork_file = os.path.join(checkout_dir,
-                                 self._simple_ext_fork_name, "readme.txt")
-        self.assertTrue(os.path.exists(fork_file))
-        os.chdir(checkout_dir)
-        # Check submodule status
-        submods = git_submodule_status(checkout_dir)
-        self.assertEqual(len(submods.keys()), 2)
-        self.assertTrue(self._simple_ext_fork_name in submods)
-        submod = submods[self._simple_ext_fork_name]
-        self.assertTrue('hash' in submod)
-        self.assertEqual(submod['hash'], self._fork_hash_check)
-        self.assertTrue('status' in submod)
-        self.assertEqual(submod['status'], status_check)
-        self.assertTrue('tag' in submod)
-        self.assertEqual(submod['tag'], tag_check)
-        self.assertTrue(self._simple_ext_name in submods)
-        submod = submods[self._simple_ext_name]
-        self.assertTrue('hash' in submod)
-        self.assertEqual(submod['hash'], self._simple_hash_check)
-        self.assertTrue('status' in submod)
-        self.assertEqual(submod['status'], status_check)
-        self.assertTrue('tag' in submod)
-        self.assertEqual(submod['tag'], tag_check)
-        # Check fork repo status
-        os.chdir(self._simple_ext_fork_name)
-        self.assertEqual(self.get_git_hash(), self._fork_hash_check)
-        os.chdir(checkout_dir)
-        os.chdir(self._simple_ext_name)
-        hash_check = self.get_git_hash('origin/feature3')
-        self.assertEqual(self.get_git_hash(), hash_check)
-        os.chdir(cwd)
-        self.idempotence_check(checkout_dir)
-
-class TestSysCheckoutErrors(BaseTestSysCheckout):
-    """Run systems level tests of error conditions in checkout_externals
-
-    Error conditions - these tests are designed to trigger specific
-    error conditions and ensure that they are being handled as
-    runtime errors (and hopefully usefull error messages) instead of
-    the default internal message that won't mean anything to the
-    user, e.g. key error, called process error, etc.
-
-    These are not 'expected failures'. They are pass when a
-    RuntimeError is raised, fail if any other error is raised (or no
-    error is raised).
-
-    """
-
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic.
-    # pylint: disable=invalid-name
-
-    def test_error_unknown_protocol(self):
-        """Verify that a runtime error is raised when the user specified repo
-        protocol is not known.
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION,
-                                            'this-protocol-does-not-exist')
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_switch_protocol(self):
-        """Verify that a runtime error is raised when the user switches
-        protocols, git to svn.
-
-        TODO(bja, 2017-11) This correctly results in an error, but it
-        isn't a helpful error message.
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION, 'svn')
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_unknown_tag(self):
-        """Verify that a runtime error is raised when the user specified tag
-        does not exist.
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='this-tag-does-not-exist',
-                                                       new_remote_repo_path=SIMPLE_REPO)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_overspecify_tag_branch(self):
-        """Verify that a runtime error is raised when the user specified both
-        tag and a branch
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='this-tag-does-not-exist',
-                                                       new_remote_repo_path=SIMPLE_REPO,
-                                                       remove_branch=False)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_underspecify_tag_branch(self):
-        """Verify that a runtime error is raised when the user specified
-        neither a tag or a branch
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_without_branch_tag(cloned_repo_dir, BRANCH_SECTION)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_missing_url(self):
-        """Verify that a runtime error is raised when the user specified
-        neither a tag or a branch
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_without_repo_url(cloned_repo_dir,
-                                               BRANCH_SECTION)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_sys_repository_git.py b/manage_externals/test/test_sys_repository_git.py
deleted file mode 100644
index 7e5fb5020d..0000000000
--- a/manage_externals/test/test_sys_repository_git.py
+++ /dev/null
@@ -1,238 +0,0 @@
-#!/usr/bin/env python3
-
-"""Tests of some of the functionality in repository_git.py that actually
-interacts with git repositories.
-
-We're calling these "system" tests because we expect them to be a lot
-slower than most of the unit tests.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import shutil
-import tempfile
-import unittest
-
-from manic.repository_git import GitRepository
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.utils import execute_subprocess
-
-# NOTE(wjs, 2018-04-09) I find a mix of camel case and underscores to be
-# more readable for unit test names, so I'm disabling pylint's naming
-# convention check
-# pylint: disable=C0103
-
-# Allow access to protected members
-# pylint: disable=W0212
-
-
-class GitTestCase(unittest.TestCase):
-    """Adds some git-specific unit test functionality on top of TestCase"""
-
-    def assertIsHash(self, maybe_hash):
-        """Assert that the string given by maybe_hash really does look
-        like a git hash.
-        """
-
-        # Ensure it is non-empty
-        self.assertTrue(maybe_hash, msg="maybe_hash is empty")
-
-        # Ensure it has a single string
-        self.assertEqual(1, len(maybe_hash.split()),
-                         msg="maybe_hash has multiple strings: {}".format(maybe_hash))
-
-        # Ensure that the only characters in the string are ones allowed
-        # in hashes
-        allowed_chars_set = set('0123456789abcdef')
-        self.assertTrue(set(maybe_hash) <= allowed_chars_set,
-                        msg="maybe_hash has non-hash characters: {}".format(maybe_hash))
-
-
-class TestGitTestCase(GitTestCase):
-    """Tests GitTestCase"""
-
-    def test_assertIsHash_true(self):
-        """Ensure that assertIsHash passes for something that looks
-        like a hash"""
-        self.assertIsHash('abc123')
-
-    def test_assertIsHash_empty(self):
-        """Ensure that assertIsHash raises an AssertionError for an
-        empty string"""
-        with self.assertRaises(AssertionError):
-            self.assertIsHash('')
-
-    def test_assertIsHash_multipleStrings(self):
-        """Ensure that assertIsHash raises an AssertionError when
-        given multiple strings"""
-        with self.assertRaises(AssertionError):
-            self.assertIsHash('abc123 def456')
-
-    def test_assertIsHash_badChar(self):
-        """Ensure that assertIsHash raises an AssertionError when given a
-        string that has a character that doesn't belong in a hash
-        """
-        with self.assertRaises(AssertionError):
-            self.assertIsHash('abc123g')
-
-
-class TestGitRepositoryGitCommands(GitTestCase):
-    """Test some git commands in RepositoryGit
-
-    It's silly that we need to create a repository in order to test
-    these git commands. Much or all of the git functionality that is
-    currently in repository_git.py should eventually be moved to a
-    separate module that is solely responsible for wrapping git
-    commands; that would allow us to test it independently of this
-    repository class.
-    """
-
-    # ========================================================================
-    # Test helper functions
-    # ========================================================================
-
-    def setUp(self):
-        # directory we want to return to after the test system and
-        # checkout_externals are done cd'ing all over the place.
-        self._return_dir = os.getcwd()
-
-        self._tmpdir = tempfile.mkdtemp()
-        os.chdir(self._tmpdir)
-
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG:
-                 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: '',
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    def tearDown(self):
-        # return to our common starting point
-        os.chdir(self._return_dir)
-
-        shutil.rmtree(self._tmpdir, ignore_errors=True)
-
-    @staticmethod
-    def make_cwd_git_repo():
-        """Turn the current directory into an empty git repository"""
-        execute_subprocess(['git', 'init'])
-
-    @staticmethod
-    def add_cwd_git_commit():
-        """Add a git commit in the current directory"""
-        with open('README', 'a') as myfile:
-            myfile.write('more info')
-        execute_subprocess(['git', 'add', 'README'])
-        execute_subprocess(['git', 'commit', '-m', 'my commit message'])
-
-    @staticmethod
-    def checkout_cwd_git_branch(branchname):
-        """Checkout a new branch in the current directory"""
-        execute_subprocess(['git', 'checkout', '-b', branchname])
-
-    @staticmethod
-    def make_cwd_git_tag(tagname):
-        """Make a lightweight tag at the current commit"""
-        execute_subprocess(['git', 'tag', '-m', 'making a tag', tagname])
-
-    @staticmethod
-    def checkout_cwd_ref(refname):
-        """Checkout the given refname in the current directory"""
-        execute_subprocess(['git', 'checkout', refname])
-
-    # ========================================================================
-    # Begin actual tests
-    # ========================================================================
-
-    def test_currentHash_returnsHash(self):
-        """Ensure that the _git_current_hash function returns a hash"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        hash_found, myhash = self._repo._git_current_hash(os.getcwd())
-        self.assertTrue(hash_found)
-        self.assertIsHash(myhash)
-
-    def test_currentHash_outsideGitRepo(self):
-        """Ensure that the _git_current_hash function returns False when
-        outside a git repository"""
-        hash_found, myhash = self._repo._git_current_hash(os.getcwd())
-        self.assertFalse(hash_found)
-        self.assertEqual('', myhash)
-
-    def test_currentBranch_onBranch(self):
-        """Ensure that the _git_current_branch function returns the name
-        of the branch"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.checkout_cwd_git_branch('foo')
-        branch_found, mybranch = self._repo._git_current_branch(os.getcwd())
-        self.assertTrue(branch_found)
-        self.assertEqual('foo', mybranch)
-
-    def test_currentBranch_notOnBranch(self):
-        """Ensure that the _git_current_branch function returns False
-        when not on a branch"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.make_cwd_git_tag('mytag')
-        self.checkout_cwd_ref('mytag')
-        branch_found, mybranch = self._repo._git_current_branch(os.getcwd())
-        self.assertFalse(branch_found)
-        self.assertEqual('', mybranch)
-
-    def test_currentBranch_outsideGitRepo(self):
-        """Ensure that the _git_current_branch function returns False
-        when outside a git repository"""
-        branch_found, mybranch = self._repo._git_current_branch(os.getcwd())
-        self.assertFalse(branch_found)
-        self.assertEqual('', mybranch)
-
-    def test_currentTag_onTag(self):
-        """Ensure that the _git_current_tag function returns the name of
-        the tag"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.make_cwd_git_tag('some_tag')
-        tag_found, mytag = self._repo._git_current_tag(os.getcwd())            
-        self.assertTrue(tag_found)
-        self.assertEqual('some_tag', mytag)
-
-    def test_currentTag_notOnTag(self):
-        """Ensure tha the _git_current_tag function returns False when
-        not on a tag"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.make_cwd_git_tag('some_tag')
-        self.add_cwd_git_commit()
-        tag_found, mytag = self._repo._git_current_tag(os.getcwd())
-        self.assertFalse(tag_found)
-        self.assertEqual('', mytag)
-
-    def test_currentTag_outsideGitRepo(self):
-        """Ensure that the _git_current_tag function returns False when
-        outside a git repository"""
-        tag_found, mytag = self._repo._git_current_tag(os.getcwd())
-        self.assertFalse(tag_found)
-        self.assertEqual('', mytag)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_externals_description.py b/manage_externals/test/test_unit_externals_description.py
deleted file mode 100644
index 30e5288499..0000000000
--- a/manage_externals/test/test_unit_externals_description.py
+++ /dev/null
@@ -1,478 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import os.path
-import shutil
-import unittest
-
-try:
-    # python2
-    from ConfigParser import SafeConfigParser as config_parser
-
-    def config_string_cleaner(text):
-        """convert strings into unicode
-        """
-        return text.decode('utf-8')
-except ImportError:
-    # python3
-    from configparser import ConfigParser as config_parser
-
-    def config_string_cleaner(text):
-        """Python3 already uses unicode strings, so just return the string
-        without modification.
-
-        """
-        return text
-
-from manic.externals_description import DESCRIPTION_SECTION, VERSION_ITEM
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.externals_description import ExternalsDescriptionConfigV1
-from manic.externals_description import get_cfg_schema_version
-from manic.externals_description import read_externals_description_file
-from manic.externals_description import create_externals_description
-
-from manic.global_constants import EMPTY_STR
-
-
-class TestCfgSchemaVersion(unittest.TestCase):
-    """Test that schema identification for the externals description
-    returns the correct results.
-
-    """
-
-    def setUp(self):
-        """Reusable config object
-        """
-        self._config = config_parser()
-        self._config.add_section('section1')
-        self._config.set('section1', 'keword', 'value')
-
-        self._config.add_section(DESCRIPTION_SECTION)
-
-    def test_schema_version_valid(self):
-        """Test that schema identification returns the correct version for a
-        valid tag.
-
-        """
-        version_str = '2.1.3'
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, version_str)
-        major, minor, patch = get_cfg_schema_version(self._config)
-        expected_major = 2
-        expected_minor = 1
-        expected_patch = 3
-        self.assertEqual(expected_major, major)
-        self.assertEqual(expected_minor, minor)
-        self.assertEqual(expected_patch, patch)
-
-    def test_schema_section_missing(self):
-        """Test that an error is returned if the schema section is missing
-        from the input file.
-
-        """
-        self._config.remove_section(DESCRIPTION_SECTION)
-        with self.assertRaises(RuntimeError):
-            get_cfg_schema_version(self._config)
-
-    def test_schema_version_missing(self):
-        """Test that a externals description file without a version raises a
-        runtime error.
-
-        """
-        # Note: the default setup method shouldn't include a version
-        # keyword, but remove it just to be future proof....
-        self._config.remove_option(DESCRIPTION_SECTION, VERSION_ITEM)
-        with self.assertRaises(RuntimeError):
-            get_cfg_schema_version(self._config)
-
-    def test_schema_version_not_int(self):
-        """Test that a externals description file a version that doesn't
-        decompose to integer major, minor and patch versions raises
-        runtime error.
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, 'unknown')
-        with self.assertRaises(RuntimeError):
-            get_cfg_schema_version(self._config)
-
-
-class TestModelDescritionConfigV1(unittest.TestCase):
-    """Test that parsing config/ini fileproduces a correct dictionary
-    for the externals description.
-
-    """
-    # pylint: disable=R0902
-
-    def setUp(self):
-        """Boiler plate construction of string containing xml for multiple components.
-        """
-        self._comp1_name = 'comp1'
-        self._comp1_path = 'path/to/comp1'
-        self._comp1_protocol = 'svn'
-        self._comp1_url = 'https://svn.somewhere.com/path/of/comp1'
-        self._comp1_tag = 'a_nice_tag_v1'
-        self._comp1_is_required = 'True'
-        self._comp1_externals = ''
-
-        self._comp2_name = 'comp2'
-        self._comp2_path = 'path/to/comp2'
-        self._comp2_protocol = 'git'
-        self._comp2_url = '/local/clone/of/comp2'
-        self._comp2_branch = 'a_very_nice_branch'
-        self._comp2_is_required = 'False'
-        self._comp2_externals = 'path/to/comp2.cfg'
-
-    def _setup_comp1(self, config):
-        """Boiler plate construction of xml string for componet 1
-        """
-        config.add_section(self._comp1_name)
-        config.set(self._comp1_name, 'local_path', self._comp1_path)
-        config.set(self._comp1_name, 'protocol', self._comp1_protocol)
-        config.set(self._comp1_name, 'repo_url', self._comp1_url)
-        config.set(self._comp1_name, 'tag', self._comp1_tag)
-        config.set(self._comp1_name, 'required', self._comp1_is_required)
-
-    def _setup_comp2(self, config):
-        """Boiler plate construction of xml string for componet 2
-        """
-        config.add_section(self._comp2_name)
-        config.set(self._comp2_name, 'local_path', self._comp2_path)
-        config.set(self._comp2_name, 'protocol', self._comp2_protocol)
-        config.set(self._comp2_name, 'repo_url', self._comp2_url)
-        config.set(self._comp2_name, 'branch', self._comp2_branch)
-        config.set(self._comp2_name, 'required', self._comp2_is_required)
-        config.set(self._comp2_name, 'externals', self._comp2_externals)
-
-    @staticmethod
-    def _setup_externals_description(config):
-        """Add the required exernals description section
-        """
-
-        config.add_section(DESCRIPTION_SECTION)
-        config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.1')
-
-    def _check_comp1(self, model):
-        """Test that component one was constructed correctly.
-        """
-        self.assertTrue(self._comp1_name in model)
-        comp1 = model[self._comp1_name]
-        self.assertEqual(comp1[ExternalsDescription.PATH], self._comp1_path)
-        self.assertTrue(comp1[ExternalsDescription.REQUIRED])
-        repo = comp1[ExternalsDescription.REPO]
-        self.assertEqual(repo[ExternalsDescription.PROTOCOL],
-                         self._comp1_protocol)
-        self.assertEqual(repo[ExternalsDescription.REPO_URL], self._comp1_url)
-        self.assertEqual(repo[ExternalsDescription.TAG], self._comp1_tag)
-        self.assertEqual(EMPTY_STR, comp1[ExternalsDescription.EXTERNALS])
-
-    def _check_comp2(self, model):
-        """Test that component two was constucted correctly.
-        """
-        self.assertTrue(self._comp2_name in model)
-        comp2 = model[self._comp2_name]
-        self.assertEqual(comp2[ExternalsDescription.PATH], self._comp2_path)
-        self.assertFalse(comp2[ExternalsDescription.REQUIRED])
-        repo = comp2[ExternalsDescription.REPO]
-        self.assertEqual(repo[ExternalsDescription.PROTOCOL],
-                         self._comp2_protocol)
-        self.assertEqual(repo[ExternalsDescription.REPO_URL], self._comp2_url)
-        self.assertEqual(repo[ExternalsDescription.BRANCH], self._comp2_branch)
-        self.assertEqual(self._comp2_externals,
-                         comp2[ExternalsDescription.EXTERNALS])
-
-    def test_one_tag_required(self):
-        """Test that a component source with a tag is correctly parsed.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        model = ExternalsDescriptionConfigV1(config)
-        print(model)
-        self._check_comp1(model)
-
-    def test_one_branch_externals(self):
-        """Test that a component source with a branch is correctly parsed.
-        """
-        config = config_parser()
-        self._setup_comp2(config)
-        self._setup_externals_description(config)
-        model = ExternalsDescriptionConfigV1(config)
-        print(model)
-        self._check_comp2(model)
-
-    def test_two_sources(self):
-        """Test that multiple component sources are correctly parsed.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_comp2(config)
-        self._setup_externals_description(config)
-        model = ExternalsDescriptionConfigV1(config)
-        print(model)
-        self._check_comp1(model)
-        self._check_comp2(model)
-
-    def test_cfg_v1_reject_unknown_item(self):
-        """Test that a v1 description object will reject unknown items
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        config.set(self._comp1_name, 'junk', 'foobar')
-        with self.assertRaises(RuntimeError):
-            ExternalsDescriptionConfigV1(config)
-
-    def test_cfg_v1_reject_v2(self):
-        """Test that a v1 description object won't try to parse a v2 file.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        config.set(DESCRIPTION_SECTION, VERSION_ITEM, '2.0.1')
-        with self.assertRaises(RuntimeError):
-            ExternalsDescriptionConfigV1(config)
-
-    def test_cfg_v1_reject_v1_too_new(self):
-        """Test that a v1 description object won't try to parse a v2 file.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.100.0')
-        with self.assertRaises(RuntimeError):
-            ExternalsDescriptionConfigV1(config)
-
-
-class TestReadExternalsDescription(unittest.TestCase):
-    """Test the application logic of read_externals_description_file
-    """
-    TMP_FAKE_DIR = 'fake'
-
-    def setUp(self):
-        """Setup directory for tests
-        """
-        if not os.path.exists(self.TMP_FAKE_DIR):
-            os.makedirs(self.TMP_FAKE_DIR)
-
-    def tearDown(self):
-        """Cleanup tmp stuff on the file system
-        """
-        if os.path.exists(self.TMP_FAKE_DIR):
-            shutil.rmtree(self.TMP_FAKE_DIR)
-
-    def test_no_file_error(self):
-        """Test that a runtime error is raised when the file does not exist
-
-        """
-        root_dir = os.getcwd()
-        filename = 'this-file-should-not-exist'
-        with self.assertRaises(RuntimeError):
-            read_externals_description_file(root_dir, filename)
-
-    def test_no_dir_error(self):
-        """Test that a runtime error is raised when the file does not exist
-
-        """
-        root_dir = '/path/to/some/repo'
-        filename = 'externals.cfg'
-        with self.assertRaises(RuntimeError):
-            read_externals_description_file(root_dir, filename)
-
-    def test_no_invalid_error(self):
-        """Test that a runtime error is raised when the file format is invalid
-
-        """
-        root_dir = os.getcwd()
-        filename = 'externals.cfg'
-        file_path = os.path.join(root_dir, filename)
-        file_path = os.path.abspath(file_path)
-        contents = """
-<source_tree version='1.0.0'>
-invalid file format
-</sourc_tree>"""
-        with open(file_path, 'w') as fhandle:
-            fhandle.write(contents)
-        with self.assertRaises(RuntimeError):
-            read_externals_description_file(root_dir, filename)
-        os.remove(file_path)
-
-
-class TestCreateExternalsDescription(unittest.TestCase):
-    """Test the application logic of creat_externals_description
-    """
-
-    def setUp(self):
-        """Create config object used as basis for all tests
-        """
-        self._config = config_parser()
-        self._gmconfig = config_parser()
-        self.setup_config()
-
-    def setup_config(self):
-        """Boiler plate construction of xml string for componet 1
-        """
-        # Create a standard externals config with a single external
-        name = 'test'
-        self._config.add_section(name)
-        self._config.set(name, ExternalsDescription.PATH, 'externals')
-        self._config.set(name, ExternalsDescription.PROTOCOL, 'git')
-        self._config.set(name, ExternalsDescription.REPO_URL, '/path/to/repo')
-        self._config.set(name, ExternalsDescription.TAG, 'test_tag')
-        self._config.set(name, ExternalsDescription.REQUIRED, 'True')
-
-        self._config.add_section(DESCRIPTION_SECTION)
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.0')
-
-        # Create a .gitmodules test
-        name = 'submodule "gitmodules_test"'
-        self._gmconfig.add_section(name)
-        self._gmconfig.set(name, "path", 'externals/test')
-        self._gmconfig.set(name, "url", '/path/to/repo')
-        # NOTE(goldy, 2019-03) Should test other possible keywords such as
-        # fetchRecurseSubmodules, ignore, and shallow
-
-    @staticmethod
-    def setup_dict_config():
-        """Create the full container dictionary with simple and mixed use
-        externals
-
-        """
-        rdatat = {ExternalsDescription.PROTOCOL: 'git',
-                  ExternalsDescription.REPO_URL: 'simple-ext.git',
-                  ExternalsDescription.TAG: 'tag1'}
-        rdatab = {ExternalsDescription.PROTOCOL: 'git',
-                  ExternalsDescription.REPO_URL: 'simple-ext.git',
-                  ExternalsDescription.BRANCH: 'feature2'}
-        rdatam = {ExternalsDescription.PROTOCOL: 'git',
-                  ExternalsDescription.REPO_URL: 'mixed-cont-ext.git',
-                  ExternalsDescription.BRANCH: 'master'}
-        desc = {'simp_tag': {ExternalsDescription.REQUIRED: True,
-                             ExternalsDescription.PATH: 'simp_tag',
-                             ExternalsDescription.EXTERNALS: EMPTY_STR,
-                             ExternalsDescription.REPO: rdatat},
-                'simp_branch' : {ExternalsDescription.REQUIRED: True,
-                                 ExternalsDescription.PATH: 'simp_branch',
-                                 ExternalsDescription.EXTERNALS: EMPTY_STR,
-                                 ExternalsDescription.REPO: rdatab},
-                'simp_opt': {ExternalsDescription.REQUIRED: False,
-                             ExternalsDescription.PATH: 'simp_opt',
-                             ExternalsDescription.EXTERNALS: EMPTY_STR,
-                             ExternalsDescription.REPO: rdatat},
-                'mixed_req': {ExternalsDescription.REQUIRED: True,
-                              ExternalsDescription.PATH: 'mixed_req',
-                              ExternalsDescription.EXTERNALS: 'sub-ext.cfg',
-                              ExternalsDescription.REPO: rdatam}}
-
-        return desc
-
-    def test_cfg_v1_ok(self):
-        """Test that a correct cfg v1 object is created by create_externals_description
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.3')
-        ext = create_externals_description(self._config, model_format='cfg')
-        self.assertIsInstance(ext, ExternalsDescriptionConfigV1)
-
-    def test_cfg_v1_unknown_version(self):
-        """Test that a config file with unknown schema version is rejected by
-        create_externals_description.
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '100.0.3')
-        with self.assertRaises(RuntimeError):
-            create_externals_description(self._config, model_format='cfg')
-
-    def test_dict(self):
-        """Test that a correct cfg v1 object is created by create_externals_description
-
-        """
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL: '/path/to/repo',
-                 ExternalsDescription.TAG: 'tagv1',
-                }
-
-        desc = {
-            'test': {
-                ExternalsDescription.REQUIRED: False,
-                ExternalsDescription.PATH: '../fake',
-                ExternalsDescription.EXTERNALS: EMPTY_STR,
-                ExternalsDescription.REPO: rdata, },
-        }
-
-        ext = create_externals_description(desc, model_format='dict')
-        self.assertIsInstance(ext, ExternalsDescriptionDict)
-
-    def test_cfg_component_dict(self):
-        """Verify that create_externals_description works with a dictionary
-        """
-        # create the top level externals file
-        desc = self.setup_dict_config()
-        # Check external with all repos
-        external = create_externals_description(desc, model_format='dict')
-        self.assertIsInstance(external, ExternalsDescriptionDict)
-        self.assertTrue('simp_tag' in external)
-        self.assertTrue('simp_branch' in external)
-        self.assertTrue('simp_opt' in external)
-        self.assertTrue('mixed_req' in external)
-
-    def test_cfg_exclude_component_dict(self):
-        """Verify that exclude component checkout works with a dictionary
-        """
-        # create the top level externals file
-        desc = self.setup_dict_config()
-        # Test an excluded repo
-        external = create_externals_description(desc, model_format='dict',
-                                                exclude=['simp_tag',
-                                                         'simp_opt'])
-        self.assertIsInstance(external, ExternalsDescriptionDict)
-        self.assertFalse('simp_tag' in external)
-        self.assertTrue('simp_branch' in external)
-        self.assertFalse('simp_opt' in external)
-        self.assertTrue('mixed_req' in external)
-
-    def test_cfg_opt_component_dict(self):
-        """Verify that exclude component checkout works with a dictionary
-        """
-        # create the top level externals file
-        desc = self.setup_dict_config()
-        # Test an excluded repo
-        external = create_externals_description(desc, model_format='dict',
-                                                components=['simp_tag',
-                                                            'simp_opt'])
-        self.assertIsInstance(external, ExternalsDescriptionDict)
-        self.assertTrue('simp_tag' in external)
-        self.assertFalse('simp_branch' in external)
-        self.assertTrue('simp_opt' in external)
-        self.assertFalse('mixed_req' in external)
-
-    def test_cfg_unknown_version(self):
-        """Test that a runtime error is raised when an unknown file version is
-        received
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '123.456.789')
-        with self.assertRaises(RuntimeError):
-            create_externals_description(self._config, model_format='cfg')
-
-    def test_cfg_unknown_format(self):
-        """Test that a runtime error is raised when an unknown format string is
-        received
-
-        """
-        with self.assertRaises(RuntimeError):
-            create_externals_description(self._config, model_format='unknown')
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_externals_status.py b/manage_externals/test/test_unit_externals_status.py
deleted file mode 100644
index f019514e9e..0000000000
--- a/manage_externals/test/test_unit_externals_status.py
+++ /dev/null
@@ -1,299 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for the manic external status reporting module.
-
-Note: this script assumes the path to the manic package is already in
-the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import unittest
-
-from manic.externals_status import ExternalStatus
-
-
-class TestStatusObject(unittest.TestCase):
-    """Verify that the Status object behaives as expected.
-    """
-
-    def test_exists_empty_all(self):
-        """If the repository sync-state is empty (doesn't exist), and there is no
-        clean state, then it is considered not to exist.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.EMPTY
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertFalse(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertFalse(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertFalse(exists)
-
-        # this state represtens an internal logic error in how the
-        # repo status was determined.
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        # this state represtens an internal logic error in how the
-        # repo status was determined.
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_default_all(self):
-        """If the repository sync-state is default, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.DEFAULT
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_unknown_all(self):
-        """If the repository sync-state is unknown, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_modified_all(self):
-        """If the repository sync-state is modified, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.MODEL_MODIFIED
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_ok_all(self):
-        """If the repository sync-state is ok, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.STATUS_OK
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_update_ok_all(self):
-        """If the repository in-sync is ok, then it is safe to
-        update only if clean state is ok
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.STATUS_OK
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertTrue(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_modified_all(self):
-        """If the repository in-sync is modified, then it is safe to
-        update only if clean state is ok
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.MODEL_MODIFIED
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertTrue(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_unknown_all(self):
-        """If the repository in-sync is unknown, then it is not safe to
-        update, regardless of the clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_default_all(self):
-        """If the repository in-sync is default, then it is not safe to
-        update, regardless of the clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_empty_all(self):
-        """If the repository in-sync is empty, then it is not safe to
-        update, regardless of the clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_repository.py b/manage_externals/test/test_unit_repository.py
deleted file mode 100644
index 1b93861834..0000000000
--- a/manage_externals/test/test_unit_repository.py
+++ /dev/null
@@ -1,208 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import unittest
-
-from manic.repository_factory import create_repository
-from manic.repository_git import GitRepository
-from manic.repository_svn import SvnRepository
-from manic.repository import Repository
-from manic.externals_description import ExternalsDescription
-from manic.global_constants import EMPTY_STR
-
-
-class TestCreateRepositoryDict(unittest.TestCase):
-    """Test the create_repository functionality to ensure it returns the
-    propper type of repository and errors for unknown repository
-    types.
-
-    """
-
-    def setUp(self):
-        """Common data needed for all tests in this class
-        """
-        self._name = 'test_name'
-        self._repo = {ExternalsDescription.PROTOCOL: None,
-                      ExternalsDescription.REPO_URL: 'junk_root',
-                      ExternalsDescription.TAG: 'junk_tag',
-                      ExternalsDescription.BRANCH: EMPTY_STR,
-                      ExternalsDescription.HASH: EMPTY_STR,
-                      ExternalsDescription.SPARSE: EMPTY_STR, }
-
-    def test_create_repo_git(self):
-        """Verify that several possible names for the 'git' protocol
-        create git repository objects.
-
-        """
-        protocols = ['git', 'GIT', 'Git', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            repo = create_repository(self._name, self._repo)
-            self.assertIsInstance(repo, GitRepository)
-
-    def test_create_repo_svn(self):
-        """Verify that several possible names for the 'svn' protocol
-        create svn repository objects.
-        """
-        protocols = ['svn', 'SVN', 'Svn', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            repo = create_repository(self._name, self._repo)
-            self.assertIsInstance(repo, SvnRepository)
-
-    def test_create_repo_externals_only(self):
-        """Verify that an externals only repo returns None.
-        """
-        protocols = ['externals_only', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            repo = create_repository(self._name, self._repo)
-            self.assertEqual(None, repo)
-
-    def test_create_repo_unsupported(self):
-        """Verify that an unsupported protocol generates a runtime error.
-        """
-        protocols = ['not_a_supported_protocol', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            with self.assertRaises(RuntimeError):
-                create_repository(self._name, self._repo)
-
-
-class TestRepository(unittest.TestCase):
-    """Test the externals description processing used to create the Repository
-    base class shared by protocol specific repository classes.
-
-    """
-
-    def test_tag(self):
-        """Test creation of a repository object with a tag
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        tag = 'test_tag'
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.BRANCH: EMPTY_STR,
-                     ExternalsDescription.HASH: EMPTY_STR,
-                     ExternalsDescription.SPARSE: EMPTY_STR, }
-        repo = Repository(name, repo_info)
-        print(repo.__dict__)
-        self.assertEqual(repo.tag(), tag)
-        self.assertEqual(repo.url(), url)
-
-    def test_branch(self):
-        """Test creation of a repository object with a branch
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = 'test_branch'
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: EMPTY_STR,
-                     ExternalsDescription.HASH: EMPTY_STR,
-                     ExternalsDescription.SPARSE: EMPTY_STR, }
-        repo = Repository(name, repo_info)
-        print(repo.__dict__)
-        self.assertEqual(repo.branch(), branch)
-        self.assertEqual(repo.url(), url)
-
-    def test_hash(self):
-        """Test creation of a repository object with a hash
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        ref = 'deadc0de'
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: EMPTY_STR,
-                     ExternalsDescription.TAG: EMPTY_STR,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        repo = Repository(name, repo_info)
-        print(repo.__dict__)
-        self.assertEqual(repo.hash(), ref)
-        self.assertEqual(repo.url(), url)
-
-    def test_tag_branch(self):
-        """Test creation of a repository object with a tag and branch raises a
-        runtimer error.
-
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = 'test_branch'
-        tag = 'test_tag'
-        ref = EMPTY_STR
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        with self.assertRaises(RuntimeError):
-            Repository(name, repo_info)
-
-    def test_tag_branch_hash(self):
-        """Test creation of a repository object with a tag, branch and hash raises a
-        runtimer error.
-
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = 'test_branch'
-        tag = 'test_tag'
-        ref = 'deadc0de'
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        with self.assertRaises(RuntimeError):
-            Repository(name, repo_info)
-
-    def test_no_tag_no_branch(self):
-        """Test creation of a repository object without a tag or branch raises a
-        runtimer error.
-
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = EMPTY_STR
-        tag = EMPTY_STR
-        ref = EMPTY_STR
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        with self.assertRaises(RuntimeError):
-            Repository(name, repo_info)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_repository_git.py b/manage_externals/test/test_unit_repository_git.py
deleted file mode 100644
index 1c01098acf..0000000000
--- a/manage_externals/test/test_unit_repository_git.py
+++ /dev/null
@@ -1,811 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-# pylint: disable=too-many-lines,protected-access
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import shutil
-import unittest
-
-from manic.repository_git import GitRepository
-from manic.externals_status import ExternalStatus
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.global_constants import EMPTY_STR
-
-# NOTE(bja, 2017-11) order is important here. origin should be a
-# subset of other to trap errors on processing remotes!
-GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM = '''
-upstream	/path/to/other/repo (fetch)
-upstream	/path/to/other/repo (push)
-other	/path/to/local/repo2 (fetch)
-other	/path/to/local/repo2 (push)
-origin	/path/to/local/repo (fetch)
-origin	/path/to/local/repo (push)
-'''
-
-
-class TestGitRepositoryCurrentRef(unittest.TestCase):
-    """test the current_ref command on a git repository
-    """
-
-    def setUp(self):
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG:
-                 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    #
-    # mock methods replacing git system calls
-    #
-    @staticmethod
-    def _git_current_branch(branch_found, branch_name):
-        """Return a function that takes the place of
-        repo._git_current_branch, which returns the given output."""
-        def my_git_current_branch(dirname):
-            """mock function that can take the place of repo._git_current_branch"""
-            return branch_found, branch_name
-        return my_git_current_branch
-
-    @staticmethod
-    def _git_current_tag(tag_found, tag_name):
-        """Return a function that takes the place of
-        repo._git_current_tag, which returns the given output."""
-        def my_git_current_tag(dirname):
-            """mock function that can take the place of repo._git_current_tag"""
-            return tag_found, tag_name
-        return my_git_current_tag
-
-    @staticmethod
-    def _git_current_hash(hash_found, hash_name):
-        """Return a function that takes the place of
-        repo._git_current_hash, which returns the given output."""
-        def my_git_current_hash(dirname):
-            """mock function that can take the place of repo._git_current_hash"""
-            return hash_found, hash_name
-        return my_git_current_hash
-
-    # ------------------------------------------------------------------------
-    # Begin tests
-    # ------------------------------------------------------------------------
-
-    def test_ref_branch(self):
-        """Test that we correctly identify we are on a branch
-        """
-        self._repo._git_current_branch = self._git_current_branch(
-            True, 'feature3')
-        self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag')
-        self._repo._git_current_hash = self._git_current_hash(True, 'abc123')
-        expected = 'foo_tag (branch feature3)'
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, expected)
-
-    def test_ref_detached_tag(self):
-        """Test that we correctly identify that the ref is detached at a tag
-        """
-        self._repo._git_current_branch = self._git_current_branch(False, '')
-        self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag')
-        self._repo._git_current_hash = self._git_current_hash(True, 'abc123')
-        expected = 'foo_tag'
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, expected)
-
-    def test_ref_detached_hash(self):
-        """Test that we can identify ref is detached at a hash
-
-        """
-        self._repo._git_current_branch = self._git_current_branch(False, '')
-        self._repo._git_current_tag = self._git_current_tag(False, '')
-        self._repo._git_current_hash = self._git_current_hash(True, 'abc123')
-        expected = 'abc123'
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, expected)
-
-    def test_ref_none(self):
-        """Test that we correctly identify that we're not in a git repo.
-        """
-        self._repo._git_current_branch = self._git_current_branch(False, '')
-        self._repo._git_current_tag = self._git_current_tag(False, '')
-        self._repo._git_current_hash = self._git_current_hash(False, '')
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, EMPTY_STR)
-
-
-class TestGitRepositoryCheckSync(unittest.TestCase):
-    """Test whether the GitRepository _check_sync_logic functionality is
-    correct.
-
-    Note: there are a lot of combinations of state:
-
-    - external description - tag, branch
-
-    - working copy
-      - doesn't exist (not checked out)
-      - exists, no git info - incorrect protocol, e.g. svn, or tarball?
-      - exists, git info
-        - as expected:
-        - different from expected:
-           - detached tag,
-           - detached hash,
-           - detached branch (compare remote and branch),
-           - tracking branch (compare remote and branch),
-             - same remote
-             - different remote
-           - untracked branch
-
-    Test list:
-      - doesn't exist
-      - exists no git info
-
-      - num_external * (working copy expected + num_working copy different)
-      - total tests = 16
-
-    """
-
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic. Also complains about too many public methods, but it
-    # doesn't really make sense to break this up.
-    # pylint: disable=invalid-name,too-many-public-methods
-
-    TMP_FAKE_DIR = 'fake'
-    TMP_FAKE_GIT_DIR = os.path.join(TMP_FAKE_DIR, '.git')
-
-    def setUp(self):
-        """Setup reusable git repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG: 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: self.TMP_FAKE_DIR,
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-        # The unit tests here don't care about the result of
-        # _current_ref, but we replace it here so that we don't need to
-        # worry about calling a possibly slow and possibly
-        # error-producing command (since _current_ref calls various git
-        # functions):
-        self._repo._current_ref = self._current_ref_empty
-        self._create_tmp_git_dir()
-
-        # We have to override this class method rather than the self._repo
-        # instance method because it is called via
-        # GitRepository._remote_name_for_url, which is itself a @classmethod
-        # calls cls._git_remote_verbose().
-        self._orignal_git_remote_verbose = GitRepository._git_remote_verbose
-        GitRepository._git_remote_verbose = self._git_remote_origin_upstream        
-    def tearDown(self):
-        """Cleanup tmp stuff on the file system
-        """
-        self._remove_tmp_git_dir()
-
-        GitRepository._git_remote_verbose = self._orignal_git_remote_verbose
-
-    def _create_tmp_git_dir(self):
-        """Create a temporary fake git directory for testing purposes.
-        """
-        if not os.path.exists(self.TMP_FAKE_GIT_DIR):
-            os.makedirs(self.TMP_FAKE_GIT_DIR)
-
-    def _remove_tmp_git_dir(self):
-        """Remove the temporary fake git directory
-        """
-        if os.path.exists(self.TMP_FAKE_DIR):
-            shutil.rmtree(self.TMP_FAKE_DIR)
-
-    #
-    # mock methods replacing git system calls
-    #
-    @staticmethod
-    def _current_ref_empty(dirname):
-        """Return an empty string.
-
-        Drop-in for GitRepository._current_ref
-        """
-        return EMPTY_STR
-
-    @staticmethod
-    def _git_remote_origin_upstream(dirname):
-        """Return an info string that is a checkout hash.
-
-        Drop-in for GitRepository._git_remote_verbose.
-        """
-        return GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM
-
-    @staticmethod
-    def _git_current_hash(myhash):
-        """Return a function that takes the place of repo._git_current_hash,
-        which returns the given hash
-        """
-        def my_git_current_hash(dirname):
-            """mock function that can take the place of repo._git_current_hash"""
-            return 0, myhash
-        return my_git_current_hash
-
-    def _git_revparse_commit(self, expected_ref, mystatus, myhash):
-        """Return a function that takes the place of
-        repo._git_revparse_commit, which returns a tuple:
-        (mystatus, myhash).
-
-        Expects the passed-in ref to equal expected_ref
-
-        status = 0 implies success, non-zero implies failure
-        """
-        def my_git_revparse_commit(ref, dirname):
-            """mock function that can take the place of repo._git_revparse_commit"""
-            self.assertEqual(expected_ref, ref)
-            return mystatus, myhash
-        return my_git_revparse_commit
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where working copy doesn't exist or is invalid
-    #
-    # ----------------------------------------------------------------
-    def test_sync_dir_not_exist(self):
-        """Test that a directory that doesn't exist returns an error status
-
-        Note: the Repository classes should be prevented from ever
-        working on an empty directory by the _Source object.
-
-        """
-        stat = ExternalStatus()
-        self._repo._check_sync(stat, 'invalid_directory_name')
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_ERROR)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_dir_exist_no_git_info(self):
-        """Test that a non-existent git repo returns an unknown status
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 1, '')
-        self._repo._check_sync(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.UNKNOWN)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ------------------------------------------------------------------------
-    #
-    # Tests where version in configuration file is not a valid reference
-    #
-    # ------------------------------------------------------------------------
-
-    def test_sync_invalid_reference(self):
-        """Test that an invalid reference returns out-of-sync
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 1, '')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where external description specifies a tag
-    #
-    # ----------------------------------------------------------------
-    def test_sync_tag_on_same_hash(self):
-        """Test expect tag on same hash --> status ok
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_tag_on_different_hash(self):
-        """Test expect tag on a different hash --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('def456')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where external description specifies a hash
-    #
-    # ----------------------------------------------------------------
-    def test_sync_hash_on_same_hash(self):
-        """Test expect hash on same hash --> status ok
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = ''
-        self._repo._hash = 'abc'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'abc', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_hash_on_different_hash(self):
-        """Test expect hash on a different hash --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = ''
-        self._repo._hash = 'abc'
-        self._repo._git_current_hash = self._git_current_hash('def456')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'abc', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where external description specifies a branch
-    #
-    # ----------------------------------------------------------------
-    def test_sync_branch_on_same_hash(self):
-        """Test expect branch on same hash --> status ok
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('origin/feature-2', 0, 'abc123'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_branch_on_diff_hash(self):
-        """Test expect branch on diff hash --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('origin/feature-2', 0, 'def456'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_branch_diff_remote(self):
-        """Test _remote_name_for_url with a different remote
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._url = '/path/to/other/repo'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('upstream/feature-2', 0, 'def456'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        # The test passes if _git_revparse_commit is called with the
-        # expected argument
-
-    def test_sync_branch_diff_remote2(self):
-        """Test _remote_name_for_url with a different remote
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._url = '/path/to/local/repo2'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('other/feature-2', 0, 'def789'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        # The test passes if _git_revparse_commit is called with the
-        # expected argument
-
-    def test_sync_branch_on_unknown_remote(self):
-        """Test expect branch, but remote is unknown --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._url = '/path/to/unknown/repo'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('unknown_remote/feature-2', 1, ''))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_branch_on_untracked_local(self):
-        """Test expect branch, on untracked branch in local repo --> status ok
-
-        Setting the externals description to '.' indicates that the
-        user only wants to consider the current local repo state
-        without fetching from remotes. This is required to preserve
-        the current branch of a repository during an update.
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature3'
-        self._repo._tag = ''
-        self._repo._url = '.'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('feature3', 0, 'abc123'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-
-class TestGitStatusPorcelain(unittest.TestCase):
-    """Test parsing of output from git status --porcelain=v1 -z
-    """
-    # pylint: disable=C0103
-    GIT_STATUS_PORCELAIN_V1_ALL = (
-        r' D INSTALL\0MM Makefile\0M README.md\0R  cmakelists.txt\0'
-        r'CMakeLists.txt\0D  commit-message-template.txt\0A  stuff.txt\0'
-        r'?? junk.txt')
-
-    GIT_STATUS_PORCELAIN_CLEAN = r''
-
-    def test_porcelain_status_dirty(self):
-        """Verify that git status output is considered dirty when there are
-        listed files.
-
-        """
-        git_output = self.GIT_STATUS_PORCELAIN_V1_ALL
-        is_dirty = GitRepository._status_v1z_is_dirty(git_output)
-        self.assertTrue(is_dirty)
-
-    def test_porcelain_status_clean(self):
-        """Verify that git status output is considered clean when there are no
-        listed files.
-
-        """
-        git_output = self.GIT_STATUS_PORCELAIN_CLEAN
-        is_dirty = GitRepository._status_v1z_is_dirty(git_output)
-        self.assertFalse(is_dirty)
-
-
-class TestGitCreateRemoteName(unittest.TestCase):
-    """Test the create_remote_name method on the GitRepository class
-    """
-
-    def setUp(self):
-        """Common infrastructure for testing _create_remote_name
-        """
-        self._rdata = {ExternalsDescription.PROTOCOL: 'git',
-                       ExternalsDescription.REPO_URL:
-                       'empty',
-                       ExternalsDescription.TAG:
-                       'very_useful_tag',
-                       ExternalsDescription.BRANCH: EMPTY_STR,
-                       ExternalsDescription.HASH: EMPTY_STR,
-                       ExternalsDescription.SPARSE: EMPTY_STR, }
-        self._repo = GitRepository('test', self._rdata)
-
-    def test_remote_git_proto(self):
-        """Test remote with git protocol
-        """
-        self._repo._url = 'git@git.github.com:very_nice_org/useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'very_nice_org_useful_repo')
-
-    def test_remote_https_proto(self):
-        """Test remote with git protocol
-        """
-        self._repo._url = 'https://www.github.com/very_nice_org/useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'very_nice_org_useful_repo')
-
-    def test_remote_local_abs(self):
-        """Test remote with git protocol
-        """
-        self._repo._url = '/path/to/local/repositories/useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'repositories_useful_repo')
-
-    def test_remote_local_rel(self):
-        """Test remote with git protocol
-        """
-        os.environ['TEST_VAR'] = '/my/path/to/repos'
-        self._repo._url = '${TEST_VAR}/../../useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'path_useful_repo')
-        del os.environ['TEST_VAR']
-
-
-class TestVerifyTag(unittest.TestCase):
-    """Test logic verifying that a tag exists and is unique
-
-    """
-
-    def setUp(self):
-        """Setup reusable git repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG: 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'tmp',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    @staticmethod
-    def _shell_true(*args, **kwargs):
-        return 0
-
-    @staticmethod
-    def _shell_false(*args, **kwargs):
-        return 1
-
-    @staticmethod
-    def _mock_revparse_commit(ref, dirname):
-        _ = ref
-        return (TestValidRef._shell_true, '97ebc0e0deadc0de')
-
-    @staticmethod
-    def _mock_revparse_commit_false(ref, dirname):
-        _ = ref
-        return (TestValidRef._shell_false, '97ebc0e0deadc0de')
-
-    def test_tag_not_tag_branch_commit(self):
-        """Verify a non-tag returns false
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_false
-        self._repo._tag = 'something'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_tag_not_tag(self):
-        """Verify a non-tag, untracked remote returns false
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_true
-        self._repo._git_lsremote_branch = self._shell_true
-        self._repo._git_revparse_commit = self._mock_revparse_commit_false
-        self._repo._tag = 'tag1'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_tag_indeterminant(self):
-        """Verify an indeterminant tag/branch returns false
-        """
-        self._repo._git_showref_tag = self._shell_true
-        self._repo._git_showref_branch = self._shell_true
-        self._repo._git_lsremote_branch = self._shell_true
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = 'something'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_tag_is_unique(self):
-        """Verify a unique tag match returns true
-        """
-        self._repo._git_showref_tag = self._shell_true
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = 'tag1'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertTrue(received)
-
-    def test_tag_is_not_hash(self):
-        """Verify a commit hash is not classified as a tag
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = '97ebc0e0'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_hash_is_commit(self):
-        """Verify a commit hash is not classified as a tag
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = '97ebc0e0'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-
-class TestValidRef(unittest.TestCase):
-    """Test logic verifying that a reference is a valid tag, branch or sha1
-
-    """
-
-    def setUp(self):
-        """Setup reusable git repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG: 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'tmp',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    @staticmethod
-    def _shell_true(url, remote=None):
-        _ = url
-        _ = remote
-        return 0
-
-    @staticmethod
-    def _shell_false(url, remote=None):
-        _ = url
-        _ = remote
-        return 1
-
-    @staticmethod
-    def _mock_revparse_commit_false(ref, dirname):
-        _ = ref
-        return (TestValidRef._shell_false, '')
-
-    @staticmethod
-    def _mock_revparse_commit_true(ref, dirname):
-        _ = ref
-        _ = dirname
-        return (TestValidRef._shell_true, '')
-
-    def test_valid_ref_is_invalid(self):
-        """Verify an invalid reference raises an exception
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_false
-        self._repo._tag = 'invalid_ref'
-        with self.assertRaises(RuntimeError):
-            self._repo._check_for_valid_ref(self._repo._tag,
-                                            remote_name=None,
-                                            dirname=os.getcwd())
-
-    def test_valid_tag(self):
-        """Verify a valid tag return true
-        """
-        self._repo._git_showref_tag = self._shell_true
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_true
-        self._repo._tag = 'tag1'
-        received = self._repo._check_for_valid_ref(self._repo._tag,
-                                                   remote_name=None,
-                                                   dirname=os.getcwd())
-        self.assertTrue(received)
-
-    def test_valid_branch(self):
-        """Verify a valid tag return true
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_true
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_true
-        self._repo._tag = 'tag1'
-        received = self._repo._check_for_valid_ref(self._repo._tag,
-                                                   remote_name=None,
-                                                   dirname=os.getcwd())
-        self.assertTrue(received)
-
-    def test_valid_hash(self):
-        """Verify a valid hash return true
-        """
-        def _mock_revparse_commit_true(ref, dirname):
-            _ = ref
-            return (0, '56cc0b539426eb26810af9e')
-
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = _mock_revparse_commit_true
-        self._repo._hash = '56cc0b5394'
-        received = self._repo._check_for_valid_ref(self._repo._hash,
-                                                   remote_name=None,
-                                                   dirname=os.getcwd())
-        self.assertTrue(received)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_repository_svn.py b/manage_externals/test/test_unit_repository_svn.py
deleted file mode 100755
index d9309df7f6..0000000000
--- a/manage_externals/test/test_unit_repository_svn.py
+++ /dev/null
@@ -1,501 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import unittest
-
-from manic.repository_svn import SvnRepository
-from manic.externals_status import ExternalStatus
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.global_constants import EMPTY_STR
-
-# pylint: disable=W0212
-
-SVN_INFO_MOSART = """Path: components/mosart
-Working Copy Root Path: /Users/andreb/projects/ncar/git-conversion/clm-dev-experimental/components/mosart
-URL: https://svn-ccsm-models.cgd.ucar.edu/mosart/trunk_tags/mosart1_0_26
-Relative URL: ^/mosart/trunk_tags/mosart1_0_26
-Repository Root: https://svn-ccsm-models.cgd.ucar.edu
-Repository UUID: fe37f545-8307-0410-aea5-b40df96820b5
-Revision: 86711
-Node Kind: directory
-Schedule: normal
-Last Changed Author: erik
-Last Changed Rev: 86031
-Last Changed Date: 2017-07-07 12:28:10 -0600 (Fri, 07 Jul 2017)
-"""
-SVN_INFO_CISM = """
-Path: components/cism
-Working Copy Root Path: /Users/andreb/projects/ncar/git-conversion/clm-dev-experimental/components/cism
-URL: https://svn-ccsm-models.cgd.ucar.edu/glc/trunk_tags/cism2_1_37
-Relative URL: ^/glc/trunk_tags/cism2_1_37
-Repository Root: https://svn-ccsm-models.cgd.ucar.edu
-Repository UUID: fe37f545-8307-0410-aea5-b40df96820b5
-Revision: 86711
-Node Kind: directory
-Schedule: normal
-Last Changed Author: sacks
-Last Changed Rev: 85704
-Last Changed Date: 2017-06-15 05:59:28 -0600 (Thu, 15 Jun 2017)
-"""
-
-
-class TestSvnRepositoryCheckURL(unittest.TestCase):
-    """Verify that the svn_check_url function is working as expected.
-    """
-
-    def setUp(self):
-        """Setup reusable svn repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'svn',
-                 ExternalsDescription.REPO_URL:
-                     'https://svn-ccsm-models.cgd.ucar.edu',
-                 ExternalsDescription.TAG:
-                     'mosart/trunk_tags/mosart1_0_26',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: '',
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = SvnRepository('test', repo)
-
-    def test_check_url_same(self):
-        """Test that we correctly identify that the correct URL.
-        """
-        svn_output = SVN_INFO_MOSART
-        expected_url = self._repo.url()
-        result, current_version = \
-            self._repo._check_url(svn_output, expected_url)
-        self.assertEqual(result, ExternalStatus.STATUS_OK)
-        self.assertEqual(current_version, 'mosart/trunk_tags/mosart1_0_26')
-
-    def test_check_url_different(self):
-        """Test that we correctly reject an incorrect URL.
-        """
-        svn_output = SVN_INFO_CISM
-        expected_url = self._repo.url()
-        result, current_version = \
-            self._repo._check_url(svn_output, expected_url)
-        self.assertEqual(result, ExternalStatus.MODEL_MODIFIED)
-        self.assertEqual(current_version, 'glc/trunk_tags/cism2_1_37')
-
-    def test_check_url_none(self):
-        """Test that we can handle an empty string for output, e.g. not an svn
-        repo.
-
-        """
-        svn_output = EMPTY_STR
-        expected_url = self._repo.url()
-        result, current_version = \
-            self._repo._check_url(svn_output, expected_url)
-        self.assertEqual(result, ExternalStatus.UNKNOWN)
-        self.assertEqual(current_version, '')
-
-
-class TestSvnRepositoryCheckSync(unittest.TestCase):
-    """Test whether the SvnRepository svn_check_sync functionality is
-    correct.
-
-    """
-
-    def setUp(self):
-        """Setup reusable svn repository object
-        """
-        self._name = "component"
-        rdata = {ExternalsDescription.PROTOCOL: 'svn',
-                 ExternalsDescription.REPO_URL:
-                     'https://svn-ccsm-models.cgd.ucar.edu/',
-                 ExternalsDescription.TAG:
-                     'mosart/trunk_tags/mosart1_0_26',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = SvnRepository('test', repo)
-
-    @staticmethod
-    def _svn_info_empty(*_):
-        """Return an empty info string. Simulates svn info failing.
-        """
-        return ''
-
-    @staticmethod
-    def _svn_info_synced(*_):
-        """Return an info sting that is synced with the setUp data
-        """
-        return SVN_INFO_MOSART
-
-    @staticmethod
-    def _svn_info_modified(*_):
-        """Return and info string that is modified from the setUp data
-        """
-        return SVN_INFO_CISM
-
-    def test_repo_dir_not_exist(self):
-        """Test that a directory that doesn't exist returns an error status
-
-        Note: the Repository classes should be prevented from ever
-        working on an empty directory by the _Source object.
-
-        """
-        stat = ExternalStatus()
-        self._repo._check_sync(stat, 'junk')
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_ERROR)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_repo_dir_exist_no_svn_info(self):
-        """Test that an empty info string returns an unknown status
-        """
-        stat = ExternalStatus()
-        # Now we over-ride the _svn_info method on the repo to return
-        # a known value without requiring access to svn.
-        self._repo._svn_info = self._svn_info_empty
-        self._repo._check_sync(stat, '.')
-        self.assertEqual(stat.sync_state, ExternalStatus.UNKNOWN)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_repo_dir_synced(self):
-        """Test that a valid info string that is synced to the repo in the
-        externals description returns an ok status.
-
-        """
-        stat = ExternalStatus()
-        # Now we over-ride the _svn_info method on the repo to return
-        # a known value without requiring access to svn.
-        self._repo._svn_info = self._svn_info_synced
-        self._repo._check_sync(stat, '.')
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_repo_dir_modified(self):
-        """Test that a valid svn info string that is out of sync with the
-        externals description returns a modified status.
-
-        """
-        stat = ExternalStatus()
-        # Now we over-ride the _svn_info method on the repo to return
-        # a known value without requiring access to svn.
-        self._repo._svn_info = self._svn_info_modified
-        self._repo._check_sync(stat, '.')
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-
-class TestSVNStatusXML(unittest.TestCase):
-    """Test parsing of svn status xml output
-    """
-    SVN_STATUS_XML_DIRTY_ALL = '''
-<status>
-<target
-   path=".">
-<entry
-   path="ChangeLog">
-<wc-status
-   item="missing"
-   revision="86711"
-   props="none">
-<commit
-   revision="85703">
-<author>sacks</author>
-<date>2017-06-15T11:59:00.355419Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="README.parallelization">
-<wc-status
-   props="none"
-   item="modified"
-   revision="86711">
-<commit
-   revision="43811">
-<author>sacks</author>
-<date>2013-02-07T16:17:56.412878Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="SVN_EXTERNAL_DIRECTORIES">
-<wc-status
-   item="deleted"
-   revision="86711"
-   props="none">
-<commit
-   revision="84725">
-<author>sacks</author>
-<date>2017-05-01T16:48:27.893741Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="junk.txt">
-<wc-status
-   item="unversioned"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="stuff.txt">
-<wc-status
-   props="none"
-   item="added"
-   revision="-1">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_MISSING = '''
-<status>
-<target
-   path=".">
-<entry
-   path="ChangeLog">
-<wc-status
-   item="missing"
-   revision="86711"
-   props="none">
-<commit
-   revision="85703">
-<author>sacks</author>
-<date>2017-06-15T11:59:00.355419Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_MODIFIED = '''
-<status>
-<target
-   path=".">
-<entry
-   path="README.parallelization">
-<wc-status
-   props="none"
-   item="modified"
-   revision="86711">
-<commit
-   revision="43811">
-<author>sacks</author>
-<date>2013-02-07T16:17:56.412878Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_DELETED = '''
-<status>
-<target
-   path=".">
-<entry
-   path="SVN_EXTERNAL_DIRECTORIES">
-<wc-status
-   item="deleted"
-   revision="86711"
-   props="none">
-<commit
-   revision="84725">
-<author>sacks</author>
-<date>2017-05-01T16:48:27.893741Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_UNVERSION = '''
-<status>
-<target
-   path=".">
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="junk.txt">
-<wc-status
-   item="unversioned"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_ADDED = '''
-<status>
-<target
-   path=".">
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="stuff.txt">
-<wc-status
-   props="none"
-   item="added"
-   revision="-1">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_CLEAN = '''
-<status>
-<target
-   path=".">
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="junk.txt">
-<wc-status
-   item="unversioned"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    def test_xml_status_dirty_missing(self):
-        """Verify that svn status output is consindered dirty when there is a
-        missing file.
-
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_MISSING
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_modified(self):
-        """Verify that svn status output is consindered dirty when there is a
-        modified file.
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_MODIFIED
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_deleted(self):
-        """Verify that svn status output is consindered dirty when there is a
-        deleted file.
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_DELETED
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_unversion(self):
-        """Verify that svn status output ignores unversioned files when making
-        the clean/dirty decision.
-
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_UNVERSION
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertFalse(is_dirty)
-
-    def test_xml_status_dirty_added(self):
-        """Verify that svn status output is consindered dirty when there is a
-        added file.
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_ADDED
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_all(self):
-        """Verify that svn status output is consindered dirty when there are
-        multiple dirty files..
-
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_ALL
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_clean(self):
-        """Verify that svn status output is consindered clean when there are
-        no 'dirty' files. This means accepting untracked and externals.
-
-        """
-        svn_output = self.SVN_STATUS_XML_CLEAN
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertFalse(is_dirty)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_utils.py b/manage_externals/test/test_unit_utils.py
deleted file mode 100644
index 80e1636649..0000000000
--- a/manage_externals/test/test_unit_utils.py
+++ /dev/null
@@ -1,350 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import unittest
-
-from manic.utils import last_n_lines, indent_string
-from manic.utils import str_to_bool, execute_subprocess
-from manic.utils import is_remote_url, split_remote_url, expand_local_url
-
-
-class TestExecuteSubprocess(unittest.TestCase):
-    """Test the application logic of execute_subprocess wrapper
-    """
-
-    def test_exesub_return_stat_err(self):
-        """Test that execute_subprocess returns a status code when caller
-        requests and the executed subprocess fails.
-
-        """
-        cmd = ['false']
-        status = execute_subprocess(cmd, status_to_caller=True)
-        self.assertEqual(status, 1)
-
-    def test_exesub_return_stat_ok(self):
-        """Test that execute_subprocess returns a status code when caller
-        requests and the executed subprocess succeeds.
-
-        """
-        cmd = ['true']
-        status = execute_subprocess(cmd, status_to_caller=True)
-        self.assertEqual(status, 0)
-
-    def test_exesub_except_stat_err(self):
-        """Test that execute_subprocess raises an exception on error when
-        caller doesn't request return code
-
-        """
-        cmd = ['false']
-        with self.assertRaises(RuntimeError):
-            execute_subprocess(cmd, status_to_caller=False)
-
-
-class TestLastNLines(unittest.TestCase):
-    """Test the last_n_lines function.
-
-    """
-
-    def test_last_n_lines_short(self):
-        """With a message with <= n lines, result of last_n_lines should
-        just be the original message.
-
-        """
-        mystr = """three
-line
-string
-"""
-
-        mystr_truncated = last_n_lines(
-            mystr, 3, truncation_message='[truncated]')
-        self.assertEqual(mystr, mystr_truncated)
-
-    def test_last_n_lines_long(self):
-        """With a message with > n lines, result of last_n_lines should
-        be a truncated string.
-
-        """
-        mystr = """a
-big
-five
-line
-string
-"""
-        expected = """[truncated]
-five
-line
-string
-"""
-
-        mystr_truncated = last_n_lines(
-            mystr, 3, truncation_message='[truncated]')
-        self.assertEqual(expected, mystr_truncated)
-
-
-class TestIndentStr(unittest.TestCase):
-    """Test the indent_string function.
-
-    """
-
-    def test_indent_string_singleline(self):
-        """Test the indent_string function with a single-line string
-
-        """
-        mystr = 'foo'
-        result = indent_string(mystr, 4)
-        expected = '    foo'
-        self.assertEqual(expected, result)
-
-    def test_indent_string_multiline(self):
-        """Test the indent_string function with a multi-line string
-
-        """
-        mystr = """hello
-hi
-goodbye
-"""
-        result = indent_string(mystr, 2)
-        expected = """  hello
-  hi
-  goodbye
-"""
-        self.assertEqual(expected, result)
-
-
-class TestStrToBool(unittest.TestCase):
-    """Test the string to boolean conversion routine.
-
-    """
-
-    def test_case_insensitive_true(self):
-        """Verify that case insensitive variants of 'true' returns the True
-        boolean.
-
-        """
-        values = ['true', 'TRUE', 'True', 'tRuE', 't', 'T', ]
-        for value in values:
-            received = str_to_bool(value)
-            self.assertTrue(received)
-
-    def test_case_insensitive_false(self):
-        """Verify that case insensitive variants of 'false' returns the False
-        boolean.
-
-        """
-        values = ['false', 'FALSE', 'False', 'fAlSe', 'f', 'F', ]
-        for value in values:
-            received = str_to_bool(value)
-            self.assertFalse(received)
-
-    def test_invalid_str_error(self):
-        """Verify that a non-true/false string generates a runtime error.
-        """
-        values = ['not_true_or_false', 'A', '1', '0',
-                  'false_is_not_true', 'true_is_not_false']
-        for value in values:
-            with self.assertRaises(RuntimeError):
-                str_to_bool(value)
-
-
-class TestIsRemoteURL(unittest.TestCase):
-    """Crude url checking to determine if a url is local or remote.
-
-    """
-
-    def test_url_remote_git(self):
-        """verify that a remote git url is identified.
-        """
-        url = 'git@somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_remote_ssh(self):
-        """verify that a remote ssh url is identified.
-        """
-        url = 'ssh://user@somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_remote_http(self):
-        """verify that a remote http url is identified.
-        """
-        url = 'http://somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_remote_https(self):
-        """verify that a remote https url is identified.
-        """
-        url = 'https://somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_local_user(self):
-        """verify that a local path with '~/path/to/repo' gets rejected
-
-        """
-        url = '~/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_var_curly(self):
-        """verify that a local path with env var '${HOME}' gets rejected
-        """
-        url = '${HOME}/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_var(self):
-        """verify that a local path with an env var '$HOME' gets rejected
-        """
-        url = '$HOME/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_abs(self):
-        """verify that a local abs path gets rejected
-        """
-        url = '/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_rel(self):
-        """verify that a local relative path gets rejected
-        """
-        url = '../../path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-
-class TestSplitRemoteURL(unittest.TestCase):
-    """Crude url checking to determine if a url is local or remote.
-
-    """
-
-    def test_url_remote_git(self):
-        """verify that a remote git url is identified.
-        """
-        url = 'git@somewhere.com:org/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, "org/repo")
-
-    def test_url_remote_ssh(self):
-        """verify that a remote ssh url is identified.
-        """
-        url = 'ssh://user@somewhere.com/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, 'somewhere.com/path/to/repo')
-
-    def test_url_remote_http(self):
-        """verify that a remote http url is identified.
-        """
-        url = 'http://somewhere.org/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, 'somewhere.org/path/to/repo')
-
-    def test_url_remote_https(self):
-        """verify that a remote http url is identified.
-        """
-        url = 'http://somewhere.gov/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, 'somewhere.gov/path/to/repo')
-
-    def test_url_local_url_unchanged(self):
-        """verify that a local path is unchanged
-
-        """
-        url = '/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, url)
-
-
-class TestExpandLocalURL(unittest.TestCase):
-    """Crude url checking to determine if a url is local or remote.
-
-    Remote should be unmodified.
-
-    Local, should perform user and variable expansion.
-
-    """
-
-    def test_url_local_user1(self):
-        """verify that a local path with '~/path/to/repo' gets expanded to an
-        absolute path.
-
-        NOTE(bja, 2017-11) we can't test for something like:
-        '~user/path/to/repo' because the user has to be in the local
-        machine password directory and we don't know a user name that
-        is valid on every system....?
-
-        """
-        field = 'test'
-        url = '~/path/to/repo'
-        received = expand_local_url(url, field)
-        print(received)
-        self.assertTrue(os.path.isabs(received))
-
-    def test_url_local_expand_curly(self):
-        """verify that a local path with '${HOME}' gets expanded to an absolute path.
-        """
-        field = 'test'
-        url = '${HOME}/path/to/repo'
-        received = expand_local_url(url, field)
-        self.assertTrue(os.path.isabs(received))
-
-    def test_url_local_expand_var(self):
-        """verify that a local path with '$HOME' gets expanded to an absolute path.
-        """
-        field = 'test'
-        url = '$HOME/path/to/repo'
-        received = expand_local_url(url, field)
-        self.assertTrue(os.path.isabs(received))
-
-    def test_url_local_env_missing(self):
-        """verify that a local path with env var that is missing gets left as-is
-
-        """
-        field = 'test'
-        url = '$TMP_VAR/path/to/repo'
-        received = expand_local_url(url, field)
-        print(received)
-        self.assertEqual(received, url)
-
-    def test_url_local_expand_env(self):
-        """verify that a local path with another env var gets expanded to an
-        absolute path.
-
-        """
-        field = 'test'
-        os.environ['TMP_VAR'] = '/some/absolute'
-        url = '$TMP_VAR/path/to/repo'
-        received = expand_local_url(url, field)
-        del os.environ['TMP_VAR']
-        print(received)
-        self.assertTrue(os.path.isabs(received))
-        self.assertEqual(received, '/some/absolute/path/to/repo')
-
-    def test_url_local_normalize_rel(self):
-        """verify that a local path with another env var gets expanded to an
-        absolute path.
-
-        """
-        field = 'test'
-        url = '/this/is/a/long/../path/to/a/repo'
-        received = expand_local_url(url, field)
-        print(received)
-        self.assertEqual(received, '/this/is/a/path/to/a/repo')
-
-
-if __name__ == '__main__':
-    unittest.main()

From b463da08ee3c5d40fe59150ec74db795e12a06e8 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 09:51:50 -0600
Subject: [PATCH 135/161] using clm branch

---
 .gitmodules      | 4 ++--
 bin/git-fleximod | 8 ++++++++
 components/clm   | 2 +-
 3 files changed, 11 insertions(+), 3 deletions(-)
 create mode 100755 bin/git-fleximod

diff --git a/.gitmodules b/.gitmodules
index 4b2a94beb3..37fba58bd5 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -185,8 +185,8 @@ fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
 [submodule "clm"]
 path = components/clm
-url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.2.007
+url = https://github.com/jedwards4b/CTSM
+fxtag = ctsm5.2.007/candidate
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
diff --git a/bin/git-fleximod b/bin/git-fleximod
new file mode 100755
index 0000000000..f69ede1c22
--- /dev/null
+++ b/bin/git-fleximod
@@ -0,0 +1,8 @@
+#!/usr/bin/env python3
+import sys
+import os
+sys.path.insert(0,os.path.abspath(os.path.join(os.path.dirname(__file__),"..",".lib","git-fleximod")))
+from git_fleximod.git_fleximod import main
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/components/clm b/components/clm
index 6aebaad42f..5cdf117265 160000
--- a/components/clm
+++ b/components/clm
@@ -1 +1 @@
-Subproject commit 6aebaad42f1db6d8be2c84205adce60a884cc254
+Subproject commit 5cdf117265bb457ed64af741be0caed593a3a82b

From 585ff448d06721b777663294ec666bdcb22c5178 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 09:55:44 -0600
Subject: [PATCH 136/161] Squashed '.lib/git-fleximod/' content from commit
 94121295

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 94121295e57a1d6e713b8e3ba84261d9e9cfebe6
---
 .github/workflows/pre-commit  |  13 +
 .github/workflows/pytest.yaml |  77 ++++
 .pre-commit-config.yaml       |  18 +
 License                       |  20 +
 README.md                     | 110 ++++++
 doc/Makefile                  |  20 +
 doc/conf.py                   |  26 ++
 doc/index.rst                 |  24 ++
 doc/make.bat                  |  35 ++
 escomp_install                |  25 ++
 git_fleximod/__init__.py      |   0
 git_fleximod/cli.py           | 119 ++++++
 git_fleximod/git_fleximod.py  | 601 +++++++++++++++++++++++++++++
 git_fleximod/gitinterface.py  |  79 ++++
 git_fleximod/gitmodules.py    |  97 +++++
 git_fleximod/lstripreader.py  |  43 +++
 git_fleximod/metoflexi.py     | 236 ++++++++++++
 git_fleximod/utils.py         | 365 ++++++++++++++++++
 poetry.lock                   | 693 ++++++++++++++++++++++++++++++++++
 pyproject.toml                |  41 ++
 tbump.toml                    |  43 +++
 tests/__init__.py             |   3 +
 tests/conftest.py             | 138 +++++++
 tests/test_a_import.py        |   8 +
 tests/test_b_update.py        |  26 ++
 tests/test_c_required.py      |  30 ++
 tests/test_d_complex.py       |  67 ++++
 27 files changed, 2957 insertions(+)
 create mode 100644 .github/workflows/pre-commit
 create mode 100644 .github/workflows/pytest.yaml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 License
 create mode 100644 README.md
 create mode 100644 doc/Makefile
 create mode 100644 doc/conf.py
 create mode 100644 doc/index.rst
 create mode 100644 doc/make.bat
 create mode 100644 escomp_install
 create mode 100644 git_fleximod/__init__.py
 create mode 100644 git_fleximod/cli.py
 create mode 100755 git_fleximod/git_fleximod.py
 create mode 100644 git_fleximod/gitinterface.py
 create mode 100644 git_fleximod/gitmodules.py
 create mode 100644 git_fleximod/lstripreader.py
 create mode 100755 git_fleximod/metoflexi.py
 create mode 100644 git_fleximod/utils.py
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 create mode 100644 tbump.toml
 create mode 100644 tests/__init__.py
 create mode 100644 tests/conftest.py
 create mode 100644 tests/test_a_import.py
 create mode 100644 tests/test_b_update.py
 create mode 100644 tests/test_c_required.py
 create mode 100644 tests/test_d_complex.py

diff --git a/.github/workflows/pre-commit b/.github/workflows/pre-commit
new file mode 100644
index 0000000000..1a6ad0082a
--- /dev/null
+++ b/.github/workflows/pre-commit
@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
new file mode 100644
index 0000000000..0868dd9a33
--- /dev/null
+++ b/.github/workflows/pytest.yaml
@@ -0,0 +1,77 @@
+# Run this job on pushes to `main`, and for pull requests. If you don't specify
+# `branches: [main], then this actions runs _twice_ on pull requests, which is
+# annoying.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
+      # reference the matrixe python version here.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
+      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
+      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
+      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
+      # mildly cleaner by using an environment variable, but I don't really care.
+      - name: cache poetry install
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-1.7.1
+
+      # Install Poetry. You could do this manually, or there are several actions that do this.
+      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
+      # Poetry's default install script, which feels correct. I pin the Poetry version here
+      # because Poetry does occasionally change APIs between versions and I don't want my
+      # actions to break if it does.
+      #
+      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
+      # venv as a `.venv` in your testing directory, which allows the next step to easily
+      # cache it.
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.7.1
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
+      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
+      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
+      - name: cache deps
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+
+      # Install dependencies. `--no-root` means "install all dependencies but not the project
+      # itself", which is what you want to avoid caching _your_ code. The `if` statement
+      # ensures this only runs on a cache miss.
+      - run: poetry install --no-interaction --no-root
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+
+      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
+      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
+      # pyproject.toml and makes that if you add things like console-scripts at some point that
+      # they'll be installed and working.
+      - run: poetry install --no-interaction
+
+      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
+      # so this line is super-simple. But it could be as complex as you need.
+      - run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+          poetry run pytest
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000..2f6089da72
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+exclude: ^utils/.*$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.11.1
+    hooks:
+      - id: pylint
+        args:
+          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/License b/License
new file mode 100644
index 0000000000..2c6fe768c2
--- /dev/null
+++ b/License
@@ -0,0 +1,20 @@
+Copyright 2024 National Center for Atmospheric Sciences (NCAR)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+“Software�), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS�, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000..d1ef632f28
--- /dev/null
+++ b/README.md
@@ -0,0 +1,110 @@
+# git-fleximod
+
+Flexible, Enhanced Submodule Management for Git
+
+## Overview
+
+Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+
+## Installation
+
+#TODO    Install using pip:
+#        pip install git-fleximod
+  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
+
+## Usage
+
+    Basic Usage:
+        git fleximod <command> [options]
+    Available Commands:
+        status: Display the status of submodules.
+        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
+        test: Make sure that fxtags and submodule hashes are consistant,
+              make sure that official urls (as defined by fxDONOTUSEurl) are set
+              make sure that fxtags are defined for all submodules
+    Additional Options:
+        See git fleximod --help for more details.
+
+## Supported .gitmodules Variables
+
+    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxrequired: Mark a submodule's checkout behavior, with allowed values:
+      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
+      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - AlwaysRequired:       Always required (always checked out).
+      - AlwaysOptional:       Always optional (checked out with --optional flag).
+    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
+           changed by users.  Use the url variable to change to a fork if desired.
+
+## Sparse Checkouts
+
+    To enable sparse checkout for a submodule, set the fxsparse variable
+    in the .gitmodules file to the path of a file containing the desired
+    sparse checkout paths. Git-fleximod will automatically configure
+    sparse checkout based on this file when applicable commands are run.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
+    for details on the format of this file.
+
+## Tests
+
+   The git fleximod test action is designed to be used by, for example, github workflows
+   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
+
+## Examples
+
+Here are some common usage examples:
+
+Update all submodules, including optional ones:
+```bash
+  git fleximod update --optional
+```
+
+Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+```bash
+    git fleximod update submodule-name
+```
+Example .gitmodules entry:
+```ini, toml
+    [submodule "cosp2"]
+        path = src/physics/cosp2/src
+        url = https://github.com/CFMIP/COSPv2.0
+        fxsparse = ../.cosp_sparse_checkout
+        fxrequired = AlwaysRequired
+        fxtag = v2.1.4cesm
+```
+Explanation:
+
+This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
+should be checked out into the directory src/physics/cosp2/src
+relative to the .gitmodules directory.  It should be checked out from
+the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+described in the file ../.cosp_sparse_checkout relative to the path
+directory.  It should be checked out anytime this .gitmodules entry is
+read.
+
+Additional example:
+```ini, toml
+    [submodule "cime"]
+        path = cime
+        url = https://github.com/jedwards4b/cime
+        fxrequired = ToplevelRequired
+        fxtag = cime6.0.198_rme01
+```
+
+Explanation:
+
+This entry indicates that the submodule cime should be checked out
+into a directory named cime at tag cime6.0.198_rme01 from the URL
+https://github.com/jedwards4b/cime.  This should only be done if
+the .gitmodules file is at the top level of the repository clone.
+
+## Contributing
+
+We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
+
+## License
+
+Git-fleximod is released under the MIT License.
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000000..d4bb2cbb9e
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000000..423099eec9
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,26 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "git-fleximod"
+author = "Jim Edwards <jedwards@ucar.edu>"
+release = "0.4.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_argparse_cli"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000000..0f9c1a7f7e
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,24 @@
+.. git-fleximod documentation master file, created by
+   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to git-fleximod's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+.. module:: sphinxcontrib.autoprogram
+.. sphinx_argparse_cli::
+   :module: git_fleximod.cli
+   :func: get_parser
+   :prog: git-fleximod
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000000..32bb24529f
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/escomp_install b/escomp_install
new file mode 100644
index 0000000000..ae782e72a4
--- /dev/null
+++ b/escomp_install
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# updates git-fleximod in an ESCOMP model
+# this script should be run from the model root directory, it expects
+# git-fleximod to already be installed with the script in bin
+# and the classes in lib/python/site-packages
+import sys
+import shutil
+import os
+
+from glob import iglob
+
+fleximod_root = sys.argv[1]
+fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
+if os.path.isfile(fleximod_path):
+   with open(fleximod_path,"r") as f:
+        fleximod = f.readlines()
+   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
+        for line in fleximod:
+            f.write(line)
+            if "import argparse" in line:
+               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
+
+   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
+       shutil.copy(file,
+        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/git_fleximod/__init__.py b/git_fleximod/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
new file mode 100644
index 0000000000..1fb959dad0
--- /dev/null
+++ b/git_fleximod/cli.py
@@ -0,0 +1,119 @@
+from pathlib import Path
+import argparse
+
+__version__ = "0.7.4"
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return attempt
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    choices = ["update", "status", "test"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="update",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
+    )
+
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
new file mode 100755
index 0000000000..103cc82a50
--- /dev/null
+++ b/git_fleximod/git_fleximod.py
@@ -0,0 +1,601 @@
+#!/usr/bin/env python
+import sys
+
+MIN_PYTHON = (3, 7)
+if sys.version_info < MIN_PYTHON:
+    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
+
+import os
+import shutil
+import logging
+import textwrap
+from git_fleximod import utils
+from git_fleximod import cli
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from configparser import NoOptionError
+
+# logger variable is global
+logger = None
+
+
+def fxrequired_allowed_values():
+    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
+
+
+def commandline_arguments(args=None):
+    parser = cli.get_parser()
+
+    if args:
+        options = parser.parse_args(args)
+    else:
+        options = parser.parse_args()
+
+    # explicitly listing a component overrides the optional flag
+    if options.optional or options.components:
+        fxrequired = [
+            "ToplevelRequired",
+            "ToplevelOptional",
+            "AlwaysRequired",
+            "AlwaysOptional",
+        ]
+    else:
+        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
+
+    action = options.action
+    if not action:
+        action = "update"
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    if hasattr(options, "version"):
+        exit()
+
+    return (
+        options.path,
+        options.gitmodules,
+        fxrequired,
+        options.components,
+        options.exclude,
+        options.force,
+        action,
+    )
+
+
+def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
+    """
+    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
+    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
+    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
+    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
+    and disk space consuming.
+
+    Parameters:
+    root_dir (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    url (str): The URL of the submodule.
+    path (str): The path to the submodule.
+    sparsefile (str): The sparse file for the submodule.
+    tag (str, optional): The tag to checkout. Defaults to "master".
+
+    Returns:
+    None
+    """
+    logger.info("Called sparse_checkout for {}".format(name))
+    rgit = GitInterface(root_dir, logger)
+    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    if superroot:
+        gitroot = superroot.strip()
+    else:
+        gitroot = root_dir.strip()
+    assert os.path.isdir(os.path.join(gitroot, ".git"))
+    # first create the module directory
+    if not os.path.isdir(os.path.join(root_dir, path)):
+        os.makedirs(os.path.join(root_dir, path))
+
+    # initialize a new git repo and set the sparse checkout flag
+    sprep_repo = os.path.join(root_dir, path)
+    sprepo_git = GitInterface(sprep_repo, logger)
+    if os.path.exists(os.path.join(sprep_repo, ".git")):
+        try:
+            logger.info("Submodule {} found".format(name))
+            chk = sprepo_git.config_get_value("core", "sparseCheckout")
+            if chk == "true":
+                logger.info("Sparse submodule {} already checked out".format(name))
+                return
+        except NoOptionError:
+            logger.debug("Sparse submodule {} not present".format(name))
+        except Exception as e:
+            utils.fatal_error("Unexpected error {} occured.".format(e))
+
+    sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
+    # set the repository remote
+
+    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
+    status = sprepo_git.git_operation("remote", "-v")
+    if url not in status:
+        sprepo_git.git_operation("remote", "add", "origin", url)
+
+    topgit = os.path.join(gitroot, ".git")
+
+    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
+        with open(os.path.join(root_dir, ".git")) as f:
+            gitpath = os.path.relpath(
+                os.path.join(root_dir, f.read().split()[1]),
+                start=os.path.join(root_dir, path),
+            )
+        topgit = os.path.join(gitpath, "modules")
+    else:
+        topgit = os.path.relpath(
+            os.path.join(root_dir, ".git", "modules"),
+            start=os.path.join(root_dir, path),
+        )
+
+    with utils.pushd(sprep_repo):
+        if not os.path.isdir(topgit):
+            os.makedirs(topgit)
+    topgit += os.sep + name
+
+    if os.path.isdir(os.path.join(root_dir, path, ".git")):
+        with utils.pushd(sprep_repo):
+            shutil.move(".git", topgit)
+            with open(".git", "w") as f:
+                f.write("gitdir: " + os.path.relpath(topgit))
+            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
+            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+        if os.path.isfile(gitsparse):
+            logger.warning(
+                "submodule {} is already initialized {}".format(name, topgit)
+            )
+            return
+
+        with utils.pushd(sprep_repo):
+            shutil.copy(sparsefile, gitsparse)
+
+    # Finally checkout the repo
+    sprepo_git.git_operation("fetch", "origin", "--tags")
+    sprepo_git.git_operation("checkout", tag)
+
+    print(f"Successfully checked out {name:>20} at {tag}")
+    rgit.config_set_value(f'submodule "{name}"', "active", "true")
+    rgit.config_set_value(f'submodule "{name}"', "url", url)
+
+
+def single_submodule_checkout(
+    root, name, path, url=None, tag=None, force=False, optional=False
+):
+    """
+    This function checks out a single git submodule.
+
+    Parameters:
+    root (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    path (str): The path to the submodule.
+    url (str, optional): The URL of the submodule. Defaults to None.
+    tag (str, optional): The tag to checkout. Defaults to None.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
+    git = GitInterface(root, logger)
+    repodir = os.path.join(root, path)
+    logger.info("Checkout {} into {}/{}".format(name, root, path))
+    # if url is provided update to the new url
+    tmpurl = None
+    repo_exists = False
+    if os.path.exists(os.path.join(repodir, ".git")):
+        logger.info("Submodule {} already checked out".format(name))
+        repo_exists = True
+    # Look for a .gitmodules file in the newly checkedout repo
+    if not repo_exists and url:
+        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
+        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
+        # opened with a GitModules object we don't need to worry about restoring the file here
+        # it will be done by the GitModules class
+        if url.startswith("git@"):
+            tmpurl = url
+            url = url.replace("git@github.com:", "https://github.com/")
+            git.git_operation("clone", url, path)
+            smgit = GitInterface(repodir, logger)
+            if not tag:
+                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
+            smgit.git_operation("checkout", tag)
+            # Now need to move the .git dir to the submodule location
+            rootdotgit = os.path.join(root, ".git")
+            if os.path.isfile(rootdotgit):
+                with open(rootdotgit) as f:
+                    line = f.readline()
+                    if line.startswith("gitdir: "):
+                        rootdotgit = line[8:].rstrip()
+
+            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
+            if os.path.exists(newpath):
+                shutil.rmtree(os.path.join(repodir, ".git"))
+            else:
+                shutil.move(os.path.join(repodir, ".git"), newpath)
+
+            with open(os.path.join(repodir, ".git"), "w") as f:
+                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
+                
+    if not os.path.exists(repodir):
+        parent = os.path.dirname(repodir)
+        if not os.path.isdir(parent):
+            os.makedirs(parent)
+        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
+
+    if not repo_exists or not tmpurl:
+        git.git_operation("submodule", "update", "--init", "--", path)
+            
+    if os.path.exists(os.path.join(repodir, ".gitmodules")):
+        # recursively handle this checkout
+        print(f"Recursively checking out submodules of {name}")
+        gitmodules = GitModules(logger, confpath=repodir)
+        requiredlist = ["AlwaysRequired"]
+        if optional:
+            requiredlist.append("AlwaysOptional")
+        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
+    if not os.path.exists(os.path.join(repodir, ".git")):
+        utils.fatal_error(
+            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
+        )
+
+    if tmpurl:
+        print(git.git_operation("restore", ".gitmodules"))
+
+    return
+
+
+def submodules_status(gitmodules, root_dir, toplevel=False):
+    testfails = 0
+    localmods = 0
+    needsupdate = 0
+    for name in gitmodules.sections():
+        path = gitmodules.get(name, "path")
+        tag = gitmodules.get(name, "fxtag")
+        required = gitmodules.get(name, "fxrequired")
+        level = required and "Toplevel" in required
+        if not path:
+            utils.fatal_error("No path found in .gitmodules for {}".format(name))
+        newpath = os.path.join(root_dir, path)
+        logger.debug("newpath is {}".format(newpath))
+        if not os.path.exists(os.path.join(newpath, ".git")):
+            rootgit = GitInterface(root_dir, logger)
+            # submodule commands use path, not name
+            url = gitmodules.get(name, "url")
+            url = url.replace("git@github.com:", "https://github.com/")
+            tags = rootgit.git_operation("ls-remote", "--tags", url)
+            atag = None
+            needsupdate += 1
+            if not toplevel and level:
+                continue
+            for htag in tags.split("\n"):
+                if tag and tag in htag:
+                    atag = (htag.split()[1])[10:]
+                    break
+            if tag and tag == atag:
+                print(f"e {name:>20} not checked out, aligned at tag {tag}")
+            elif tag:
+                ahash = rootgit.git_operation(
+                    "submodule", "status", "{}".format(path)
+                ).rstrip()
+                ahash = ahash[1 : len(tag) + 1]
+                if tag == ahash:
+                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
+                else:
+                    print(
+                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
+                    )
+                    testfails += 1
+            else:
+                print(f"e {name:>20} has no fxtag defined in .gitmodules")
+                testfails += 1
+        else:
+            with utils.pushd(newpath):
+                git = GitInterface(newpath, logger)
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                ahash = git.git_operation("status").partition("\n")[0].split()[-1]
+                if tag and atag == tag:
+                    print(f"  {name:>20} at tag {tag}")
+                elif tag and ahash[: len(tag)] == tag:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif atag == ahash:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif tag:
+                    print(
+                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
+                    )
+                    testfails += 1
+                    needsupdate += 1
+                else:
+                    print(
+                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
+                    )
+                    testfails += 1
+
+                status = git.git_operation("status", "--ignore-submodules")
+                if "nothing to commit" not in status:
+                    localmods = localmods + 1
+                    print("M" + textwrap.indent(status, "                      "))
+
+    return testfails, localmods, needsupdate
+
+
+def submodules_update(gitmodules, root_dir, requiredlist, force):
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+
+    if localmods and not force:
+        local_mods_output()
+        return
+    if needsupdate == 0:
+        return
+
+    for name in gitmodules.sections():
+        fxtag = gitmodules.get(name, "fxtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        logger.info(
+            "name={} path={} url={} fxtag={} requiredlist={}".format(
+                name, os.path.join(root_dir, path), url, fxtag, requiredlist
+            )
+        )
+        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+        fxrequired = gitmodules.get(name, "fxrequired")
+        assert fxrequired in fxrequired_allowed_values()
+        rgit = GitInterface(root_dir, logger)
+        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+
+        fxsparse = gitmodules.get(name, "fxsparse")
+
+        if (
+            fxrequired
+            and (superroot and "Toplevel" in fxrequired)
+            or fxrequired not in requiredlist
+        ):
+            if "ToplevelOptional" == fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
+            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+        else:
+            logger.info(
+                "Calling submodule_checkout({},{},{},{})".format(
+                    root_dir, name, path, url
+                )
+            )
+
+            single_submodule_checkout(
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional=("AlwaysOptional" in requiredlist),
+            )
+
+        if os.path.exists(os.path.join(path, ".git")):
+            submoddir = os.path.join(root_dir, path)
+            with utils.pushd(submoddir):
+                git = GitInterface(submoddir, logger)
+                # first make sure the url is correct
+                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
+                newremote = "origin"
+                if upstream != url:
+                    # TODO - this needs to be a unique name
+                    remotes = git.git_operation("remote", "-v")
+                    if url in remotes:
+                        for line in remotes:
+                            if url in line and "fetch" in line:
+                                newremote = line.split()[0]
+                                break
+                    else:
+                        i = 0
+                        while newremote in remotes:
+                            i = i + 1
+                            newremote = f"newremote.{i:02d}"
+                        git.git_operation("remote", "add", newremote, url)
+
+                tags = git.git_operation("tag", "-l")
+                if fxtag and fxtag not in tags:
+                    git.git_operation("fetch", newremote, "--tags")
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                if fxtag and fxtag != atag:
+                    try:
+                        git.git_operation("checkout", fxtag)
+                        print(f"{name:>20} updated to {fxtag}")
+                    except Exception as error:
+                        print(error)
+                elif not fxtag:
+                    print(f"No fxtag found for submodule {name:>20}")
+                else:
+                    print(f"{name:>20} up to date.")
+
+
+def local_mods_output():
+    text = """\
+    The submodules labeled with 'M' above are not in a clean state.
+    The following are options for how to proceed:
+    (1) Go into each submodule which is not in a clean state and issue a 'git status'
+        Either revert or commit your changes so that the submodule is in a clean state.
+    (2) use the --force option to git-fleximod
+    (3) you can name the particular submodules to update using the git-fleximod command line
+    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
+        then rerun git-fleximod update.
+"""
+    print(text)
+
+
+# checkout is done by update if required so this function may be depricated
+def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
+    """
+    This function checks out all git submodules based on the provided parameters.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+    requiredlist (list): The list of required modules.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
+    print("")
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    if localmods and not force:
+        local_mods_output()
+        return
+    if not needsupdate:
+        return
+    for name in gitmodules.sections():
+        fxrequired = gitmodules.get(name, "fxrequired")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        fxtag = gitmodules.get(name, "fxtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        if fxrequired and fxrequired not in requiredlist:
+            if "Optional" in fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
+            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+        else:
+            logger.debug(
+                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
+            )
+            single_submodule_checkout(
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional="AlwaysOptional" in requiredlist,
+            )
+
+
+def submodules_test(gitmodules, root_dir):
+    """
+    This function tests the git submodules based on the provided parameters.
+
+    It first checks that fxtags are present and in sync with submodule hashes.
+    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
+    and that sparse checkout files exist.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+
+    Returns:
+    int: The number of test failures.
+    """
+    # First check that fxtags are present and in sync with submodule hashes
+    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    print("")
+    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
+    # and that sparse checkout files exist
+    for name in gitmodules.sections():
+        url = gitmodules.get(name, "url")
+        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        path = gitmodules.get(name, "path")
+        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
+        url = url[:-4] if url.endswith(".git") else url
+        if not fxurl or url.lower() != fxurl.lower():
+            print(f"{name:>20} url {url} not in sync with required {fxurl}")
+            testfails += 1
+        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
+            print(f"{name:>20} sparse checkout file {fxsparse} not found")
+            testfails += 1
+    return testfails + localmods + needsupdate
+
+
+def main():
+    (
+        root_dir,
+        file_name,
+        fxrequired,
+        includelist,
+        excludelist,
+        force,
+        action,
+    ) = commandline_arguments()
+    # Get a logger for the package
+    global logger
+    logger = logging.getLogger(__name__)
+
+    logger.info("action is {}".format(action))
+
+    if not os.path.isfile(os.path.join(root_dir, file_name)):
+        file_path = utils.find_upwards(root_dir, file_name)
+
+        if file_path is None:
+            utils.fatal_error(
+                "No {} found in {} or any of it's parents".format(file_name, root_dir)
+            )
+
+        root_dir = os.path.dirname(file_path)
+    logger.info(
+        "root_dir is {} includelist={} excludelist={}".format(
+            root_dir, includelist, excludelist
+        )
+    )
+    gitmodules = GitModules(
+        logger,
+        confpath=root_dir,
+        conffile=file_name,
+        includelist=includelist,
+        excludelist=excludelist,
+    )
+    if not gitmodules.sections():
+        sys.exit("No submodule components found")
+    retval = 0
+    if action == "update":
+        submodules_update(gitmodules, root_dir, fxrequired, force)
+    elif action == "status":
+        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        if tfails + lmods + updates > 0:
+            print(
+                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
+            )
+            if lmods > 0:
+                local_mods_output()
+    elif action == "test":
+        retval = submodules_test(gitmodules, root_dir)
+    else:
+        utils.fatal_error(f"unrecognized action request {action}")
+    return retval
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
new file mode 100644
index 0000000000..93ae38ecde
--- /dev/null
+++ b/git_fleximod/gitinterface.py
@@ -0,0 +1,79 @@
+import os
+import sys
+from . import utils
+from pathlib import Path
+
+class GitInterface:
+    def __init__(self, repo_path, logger):
+        logger.debug("Initialize GitInterface for {}".format(repo_path))
+        if isinstance(repo_path, str):
+            self.repo_path = Path(repo_path).resolve()
+        elif isinstance(repo_path, Path):
+            self.repo_path = repo_path.resolve()
+        else:
+            raise TypeError("repo_path must be a str or Path object")
+        self.logger = logger
+        try:
+            import git
+
+            self._use_module = True
+            try:
+                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
+            except git.exc.InvalidGitRepositoryError:
+                self.git = git
+                self._init_git_repo()
+            msg = "Using GitPython interface to git"
+        except ImportError:
+            self._use_module = False
+            if not (self.repo_path / ".git").exists():
+                self._init_git_repo()
+            msg = "Using shell interface to git"
+        self.logger.info(msg)
+
+    def _git_command(self, operation, *args):
+        self.logger.info(operation)
+        if self._use_module and operation != "submodule":
+            try:
+                return getattr(self.repo.git, operation)(*args)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return ["git", "-C", str(self.repo_path), operation] + list(args)
+
+    def _init_git_repo(self):
+        if self._use_module:
+            self.repo = self.git.Repo.init(str(self.repo_path))
+        else:
+            command = ("git", "-C", str(self.repo_path), "init")
+            utils.execute_subprocess(command)
+
+    # pylint: disable=unused-argument
+    def git_operation(self, operation, *args, **kwargs):
+        command = self._git_command(operation, *args)
+        self.logger.info(command)
+        if isinstance(command, list):
+            try:
+                return utils.execute_subprocess(command, output_to_caller=True)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return command
+
+    def config_get_value(self, section, name):
+        if self._use_module:
+            config = self.repo.config_reader()
+            return config.get_value(section, name)
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
+            output = utils.execute_subprocess(cmd, output_to_caller=True)
+            return output.strip()
+
+    def config_set_value(self, section, name, value):
+        if self._use_module:
+            with self.repo.config_writer() as writer:
+                writer.set_value(section, name, value)
+            writer.release()  # Ensure changes are saved
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
+            self.logger.info(cmd)
+            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
new file mode 100644
index 0000000000..68c82d066f
--- /dev/null
+++ b/git_fleximod/gitmodules.py
@@ -0,0 +1,97 @@
+import shutil
+from pathlib import Path
+from configparser import RawConfigParser, ConfigParser
+from .lstripreader import LstripReader
+
+
+class GitModules(RawConfigParser):
+    def __init__(
+        self,
+        logger,
+        confpath=Path.cwd(),
+        conffile=".gitmodules",
+        includelist=None,
+        excludelist=None,
+    ):
+        """
+        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
+        conffile: Name of the configuration file (defaults to .gitmodules).
+        includelist: Optional list of submodules to include.
+        excludelist: Optional list of submodules to exclude.
+        """
+        self.logger = logger
+        self.logger.debug(
+            "Creating a GitModules object {} {} {} {}".format(
+                confpath, conffile, includelist, excludelist
+            )
+        )
+        super().__init__()
+        self.conf_file = (Path(confpath) / Path(conffile))
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
+        self.includelist = includelist
+        self.excludelist = excludelist
+        self.isdirty = False
+        
+    def reload(self):
+        self.clear()
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
+
+        
+    def set(self, name, option, value):
+        """
+        Sets a configuration value for a specific submodule:
+        Ensures the appropriate section exists for the submodule.
+        Calls the parent class's set method to store the value.
+        """
+        self.isdirty = True
+        self.logger.debug("set called {} {} {}".format(name, option, value))
+        section = f'submodule "{name}"'
+        if not self.has_section(section):
+            self.add_section(section)
+        super().set(section, option, str(value))
+
+    # pylint: disable=redefined-builtin, arguments-differ
+    def get(self, name, option, raw=False, vars=None, fallback=None):
+        """
+        Retrieves a configuration value for a specific submodule:
+        Uses the parent class's get method to access the value.
+        Handles potential errors if the section or option doesn't exist.
+        """
+        self.logger.debug("get called {} {}".format(name, option))
+        section = f'submodule "{name}"'
+        try:
+            return ConfigParser.get(
+                self, section, option, raw=raw, vars=vars, fallback=fallback
+            )
+        except ConfigParser.NoOptionError:
+            return None
+
+    def save(self):
+        if self.isdirty:
+            self.logger.info("Writing {}".format(self.conf_file))
+            with open(self.conf_file, "w") as fd:
+                self.write(fd)
+        self.isdirty = False
+        
+    def __del__(self):
+        self.save()
+
+    def sections(self):
+        """Strip the submodule part out of section and just use the name"""
+        self.logger.debug("calling GitModules sections iterator")
+        names = []
+        for section in ConfigParser.sections(self):
+            name = section[11:-1]
+            if self.includelist and name not in self.includelist:
+                continue
+            if self.excludelist and name in self.excludelist:
+                continue
+            names.append(name)
+        return names
+
+    def items(self, name, raw=False, vars=None):
+        self.logger.debug("calling GitModules items for {}".format(name))
+        section = f'submodule "{name}"'
+        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/git_fleximod/lstripreader.py b/git_fleximod/lstripreader.py
new file mode 100644
index 0000000000..01d5580ee8
--- /dev/null
+++ b/git_fleximod/lstripreader.py
@@ -0,0 +1,43 @@
+class LstripReader(object):
+    "LstripReader formats .gitmodules files to be acceptable for configparser"
+
+    def __init__(self, filename):
+        with open(filename, "r") as infile:
+            lines = infile.readlines()
+        self._lines = list()
+        self._num_lines = len(lines)
+        self._index = 0
+        for line in lines:
+            self._lines.append(line.lstrip())
+
+    def readlines(self):
+        """Return all the lines from this object's file"""
+        return self._lines
+
+    def readline(self, size=-1):
+        """Format and return the next line or raise StopIteration"""
+        try:
+            line = self.next()
+        except StopIteration:
+            line = ""
+
+        if (size > 0) and (len(line) < size):
+            return line[0:size]
+
+        return line
+
+    def __iter__(self):
+        """Begin an iteration"""
+        self._index = 0
+        return self
+
+    def next(self):
+        """Return the next line or raise StopIteration"""
+        if self._index >= self._num_lines:
+            raise StopIteration
+
+        self._index = self._index + 1
+        return self._lines[self._index - 1]
+
+    def __next__(self):
+        return self.next()
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
new file mode 100755
index 0000000000..cc347db2dd
--- /dev/null
+++ b/git_fleximod/metoflexi.py
@@ -0,0 +1,236 @@
+#!/usr/bin/env python
+from configparser import ConfigParser
+import sys
+import shutil
+from pathlib import Path
+import argparse
+import logging
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from git_fleximod import utils
+
+logger = None
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return d
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument('-e', '--externals', nargs='?',
+                        default='Externals.cfg',
+                        help='The externals description filename. '
+                        'Default: %(default)s.')
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
+
+def commandline_arguments(args=None):
+    parser = get_parser()
+
+    options = parser.parse_args(args)
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    return(
+        options.path,
+        options.gitmodules,
+        options.externals
+        )
+
+class ExternalRepoTranslator:
+    """
+    Translates external repositories configured in an INI-style externals file.
+    """
+
+    def __init__(self, rootpath, gitmodules, externals):
+        self.rootpath = rootpath
+        if gitmodules:
+            self.gitmodules = GitModules(logger, confpath=rootpath)
+        self.externals = (rootpath / Path(externals)).resolve()
+        print(f"Translating {self.externals}")
+        self.git = GitInterface(rootpath, logger)
+        
+#    def __del__(self):
+#        if (self.rootpath / "save.gitignore"):
+            
+
+    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+        """
+        Translates a single repository based on configuration details.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            tag (str): The tag to use for the external repository.
+            url (str): The URL of the external repository.
+            path (str): The relative path within the main repository for the external repository.
+            efile (str): The external file or file containing submodules.
+            hash_ (str): The commit hash to checkout (if applicable).
+            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
+            protocol (str): The protocol to use (e.g., 'git', 'http').
+        """
+        assert protocol != "svn", "SVN protocol is not currently supported"
+        print(f"Translating repository {section}")
+        if efile:
+            file_path = Path(path) / Path(efile)
+            newroot = (self.rootpath / file_path).parent.resolve()
+            if not newroot.exists():
+                newroot.mkdir(parents=True)
+            logger.info("Newroot is {}".format(newroot))
+            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
+            newt.translate_repo()
+        if protocol == "externals_only":
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+        else:
+            newpath = (self.rootpath / Path(path))
+            if newpath.exists():
+                shutil.rmtree(newpath)
+                logger.info("Creating directory {}".format(newpath))
+            newpath.mkdir(parents=True)
+            if tag:
+                logger.info("cloning {}".format(section))
+                try:
+                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                except:
+                    self.git.git_operation("clone", url, path)
+                    with utils.pushd(newpath):
+                        ngit = GitInterface(newpath, logger)
+                        ngit.git_operation("checkout", tag)
+            if hash_:
+                self.git.git_operation("clone", url, path)
+                git = GitInterface(newpath, logger)
+                git.git_operation("fetch", "origin")
+                git.git_operation("checkout", hash_)
+            if sparse:
+                print("setting as sparse submodule {}".format(section))
+                sparsefile = (newpath / Path(sparse))
+                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                print(f"sparsefile {sparsefile} newfile {newfile}")
+                shutil.copy(sparsefile, newfile)
+        
+            logger.info("adding submodule {}".format(section))        
+            self.gitmodules.save()
+            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
+            self.git.git_operation("submodule","absorbgitdirs")
+            self.gitmodules.reload()
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+    
+        
+    def translate_repo(self):
+        """
+        Translates external repositories defined within an external file.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            external_file (str): The path to the external file containing repository definitions.
+        """
+        econfig = ConfigParser()
+        econfig.read((self.rootpath / Path(self.externals)))
+
+        for section in econfig.sections():
+            if section == "externals_description":
+                logger.info("skipping section {}".format(section))
+                return
+            logger.info("Translating section {}".format(section))
+            tag = econfig.get(section, "tag", raw=False, fallback=None)
+            url = econfig.get(section, "repo_url", raw=False, fallback=None)
+            path = econfig.get(section, "local_path", raw=False, fallback=None)
+            efile = econfig.get(section, "externals", raw=False, fallback=None)
+            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
+            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
+            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
+
+            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
+
+
+
+def _main():
+    rootpath, gitmodules, externals = commandline_arguments()
+    global logger
+    logger = logging.getLogger(__name__)
+    with utils.pushd(rootpath):
+        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
+        logger.info("Translating {}".format(rootpath))
+        t.translate_repo()
+
+        
+if __name__ == "__main__":
+    sys.exit(_main())
diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py
new file mode 100644
index 0000000000..7cc1de38cc
--- /dev/null
+++ b/git_fleximod/utils.py
@@ -0,0 +1,365 @@
+#!/usr/bin/env python3
+"""
+Common public utilities for manic package
+
+"""
+
+import logging
+import os
+import subprocess
+import sys
+from threading import Timer
+from pathlib import Path
+
+LOCAL_PATH_INDICATOR = "."
+# ---------------------------------------------------------------------
+#
+# functions to massage text for output and other useful utilities
+#
+# ---------------------------------------------------------------------
+from contextlib import contextmanager
+
+
+@contextmanager
+def pushd(new_dir):
+    """context for chdir. usage: with pushd(new_dir)"""
+    previous_dir = os.getcwd()
+    os.chdir(new_dir)
+    try:
+        yield
+    finally:
+        os.chdir(previous_dir)
+
+
+def log_process_output(output):
+    """Log each line of process output at debug level so it can be
+    filtered if necessary. By default, output is a single string, and
+    logging.debug(output) will only put log info heading on the first
+    line. This makes it hard to filter with grep.
+
+    """
+    output = output.split("\n")
+    for line in output:
+        logging.debug(line)
+
+
+def printlog(msg, **kwargs):
+    """Wrapper script around print to ensure that everything printed to
+    the screen also gets logged.
+
+    """
+    logging.info(msg)
+    if kwargs:
+        print(msg, **kwargs)
+    else:
+        print(msg)
+    sys.stdout.flush()
+
+
+def find_upwards(root_dir, filename):
+    """Find a file in root dir or any of it's parents"""
+    d = Path(root_dir)
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.exists():
+            return attempt
+        d = d.parent
+    return None
+
+
+def last_n_lines(the_string, n_lines, truncation_message=None):
+    """Returns the last n lines of the given string
+
+    Args:
+        the_string: str
+        n_lines: int
+        truncation_message: str, optional
+
+    Returns a string containing the last n lines of the_string
+
+    If truncation_message is provided, the returned string begins with
+    the given message if and only if the string is greater than n lines
+    to begin with.
+    """
+
+    lines = the_string.splitlines(True)
+    if len(lines) <= n_lines:
+        return_val = the_string
+    else:
+        lines_subset = lines[-n_lines:]
+        str_truncated = "".join(lines_subset)
+        if truncation_message:
+            str_truncated = truncation_message + "\n" + str_truncated
+        return_val = str_truncated
+
+    return return_val
+
+
+def indent_string(the_string, indent_level):
+    """Indents the given string by a given number of spaces
+
+    Args:
+       the_string: str
+       indent_level: int
+
+    Returns a new string that is the same as the_string, except that
+    each line is indented by 'indent_level' spaces.
+
+    In python3, this can be done with textwrap.indent.
+    """
+
+    lines = the_string.splitlines(True)
+    padding = " " * indent_level
+    lines_indented = [padding + line for line in lines]
+    return "".join(lines_indented)
+
+
+# ---------------------------------------------------------------------
+#
+# error handling
+#
+# ---------------------------------------------------------------------
+
+
+def fatal_error(message):
+    """
+    Error output function
+    """
+    logging.error(message)
+    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
+
+
+# ---------------------------------------------------------------------
+#
+# Data conversion / manipulation
+#
+# ---------------------------------------------------------------------
+def str_to_bool(bool_str):
+    """Convert a sting representation of as boolean into a true boolean.
+
+    Conversion should be case insensitive.
+    """
+    value = None
+    str_lower = bool_str.lower()
+    if str_lower in ("true", "t"):
+        value = True
+    elif str_lower in ("false", "f"):
+        value = False
+    if value is None:
+        msg = (
+            'ERROR: invalid boolean string value "{0}". '
+            'Must be "true" or "false"'.format(bool_str)
+        )
+        fatal_error(msg)
+    return value
+
+
+REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
+
+
+def is_remote_url(url):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    """
+    remote_url = False
+    for prefix in REMOTE_PREFIXES:
+        if url.startswith(prefix):
+            remote_url = True
+    return remote_url
+
+
+def split_remote_url(url):
+    """check if the user provided a local file path or a
+    remote. If remote, try to strip off protocol info.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        return url
+
+    for prefix in REMOTE_PREFIXES:
+        url = url.replace(prefix, "")
+
+    if "@" in url:
+        url = url.split("@")[1]
+
+    if ":" in url:
+        url = url.split(":")[1]
+
+    return url
+
+
+def expand_local_url(url, field):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
+    represent local copy only, don't work with the remotes.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        if url.strip() == LOCAL_PATH_INDICATOR:
+            pass
+        else:
+            url = os.path.expandvars(url)
+            url = os.path.expanduser(url)
+            if not os.path.isabs(url):
+                msg = (
+                    'WARNING: Externals description for "{0}" contains a '
+                    "url that is not remote and does not expand to an "
+                    "absolute path. Version control operations may "
+                    "fail.\n\nurl={1}".format(field, url)
+                )
+                printlog(msg)
+            else:
+                url = os.path.normpath(url)
+    return url
+
+
+# ---------------------------------------------------------------------
+#
+# subprocess
+#
+# ---------------------------------------------------------------------
+
+# Give the user a helpful message if we detect that a command seems to
+# be hanging.
+_HANGING_SEC = 300
+
+
+def _hanging_msg(working_directory, command):
+    print(
+        """
+
+Command '{command}'
+from directory {working_directory}
+has taken {hanging_sec} seconds. It may be hanging.
+
+The command will continue to run, but you may want to abort
+manage_externals with ^C and investigate. A possible cause of hangs is
+when svn or git require authentication to access a private
+repository. On some systems, svn and git requests for authentication
+information will not be displayed to the user. In this case, the program
+will appear to hang. Ensure you can run svn and git manually and access
+all repositories without entering your authentication information.
+
+""".format(
+            command=command,
+            working_directory=working_directory,
+            hanging_sec=_HANGING_SEC,
+        )
+    )
+
+
+def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
+    """Wrapper around subprocess.check_output to handle common
+    exceptions.
+
+    check_output runs a command with arguments and waits
+    for it to complete.
+
+    check_output raises an exception on a nonzero return code.  if
+    status_to_caller is true, execute_subprocess returns the subprocess
+    return code, otherwise execute_subprocess treats non-zero return
+    status as an error and raises an exception.
+
+    """
+    cwd = os.getcwd()
+    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
+    logging.info(msg)
+    commands_str = " ".join(str(element) for element in commands)
+    logging.info(commands_str)
+    return_to_caller = status_to_caller or output_to_caller
+    status = -1
+    output = ""
+    hanging_timer = Timer(
+        _HANGING_SEC,
+        _hanging_msg,
+        kwargs={"working_directory": cwd, "command": commands_str},
+    )
+    hanging_timer.start()
+    try:
+        output = subprocess.check_output(
+            commands, stderr=subprocess.STDOUT, universal_newlines=True
+        )
+        log_process_output(output)
+        status = 0
+    except OSError as error:
+        msg = failed_command_msg(
+            "Command execution failed. Does the executable exist?", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except ValueError as error:
+        msg = failed_command_msg(
+            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except subprocess.CalledProcessError as error:
+        # Only report the error if we are NOT returning to the
+        # caller. If we are returning to the caller, then it may be a
+        # simple status check. If returning, it is the callers
+        # responsibility determine if an error occurred and handle it
+        # appropriately.
+        if not return_to_caller:
+            msg_context = (
+                "Process did not run successfully; "
+                "returned status {0}".format(error.returncode)
+            )
+            msg = failed_command_msg(msg_context, commands, output=error.output)
+            logging.error(error)
+            logging.error(msg)
+            log_process_output(error.output)
+            fatal_error(msg)
+        status = error.returncode
+    finally:
+        hanging_timer.cancel()
+
+    if status_to_caller and output_to_caller:
+        ret_value = (status, output)
+    elif status_to_caller:
+        ret_value = status
+    elif output_to_caller:
+        ret_value = output
+    else:
+        ret_value = None
+
+    return ret_value
+
+
+def failed_command_msg(msg_context, command, output=None):
+    """Template for consistent error messages from subprocess calls.
+
+    If 'output' is given, it should provide the output from the failed
+    command
+    """
+
+    if output:
+        output_truncated = last_n_lines(
+            output, 20, truncation_message="[... Output truncated for brevity ...]"
+        )
+        errmsg = (
+            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
+        )
+    else:
+        errmsg = ""
+
+    command_str = " ".join(command)
+    errmsg += """In directory
+    {cwd}
+{context}:
+    {command}
+""".format(
+        cwd=os.getcwd(), context=msg_context, command=command_str
+    )
+
+    if output:
+        errmsg += "See above for output from failed command.\n"
+
+    return errmsg
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000000..b59ed3942c
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,693 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.dependencies]
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.2.2"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
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+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
+files = [
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+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.1"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
+    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["html5lib", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+
+[package.extras]
+test = ["flake8", "mypy", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-qthelp"
+version = "1.0.3"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.5"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.2.0"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
+    {file = "urllib3-2.2.0.tar.gz", hash = "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "wheel"
+version = "0.42.0"
+description = "A built-package format for Python"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "wheel-0.42.0-py3-none-any.whl", hash = "sha256:177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d"},
+    {file = "wheel-0.42.0.tar.gz", hash = "sha256:c45be39f7882c9d34243236f2d63cbd58039e360f85d0913425fbd7ceea617a8"},
+]
+
+[package.extras]
+test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
+
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.8"
+content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000..2484552e4f
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,41 @@
+[tool.poetry]
+name = "git-fleximod"
+version = "0.7.4"
+description = "Extended support for git-submodule and git-sparse-checkout"
+authors = ["Jim Edwards <jedwards@ucar.edu>"]
+maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/jedwards4b/git-fleximod"
+keywords = ["git", "submodule", "sparse-checkout"]
+packages = [
+{ include = "git_fleximod"},
+{ include = "doc"},
+]
+
+[tool.poetry.scripts]
+git-fleximod = "git_fleximod.git_fleximod:main"
+me2flexi = "git_fleximod.metoflexi:_main"
+fsspec = "fsspec.fuse:main"
+
+[tool.poetry.dependencies]
+python = "^3.8"
+GitPython = "^3.1.0"
+sphinx = "^5.0.0"
+fsspec = "^2023.12.2"
+wheel = "^0.42.0"
+pytest = "^8.0.0"
+pyfakefs = "^5.3.5"
+
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
+
+[tool.pytest.ini_options]
+markers = [
+        "skip_after_first: only run on first iteration"
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
diff --git a/tbump.toml b/tbump.toml
new file mode 100644
index 0000000000..d4b8eaee11
--- /dev/null
+++ b/tbump.toml
@@ -0,0 +1,43 @@
+# Uncomment this if your project is hosted on GitHub:
+github_url = "https://github.com/jedwards4b/git-fleximod/"
+
+[version]
+current = "0.7.4"
+
+# Example of a semver regexp.
+# Make sure this matches current_version before
+# using tbump
+regex = '''
+  (?P<major>\d+)
+  \.
+  (?P<minor>\d+)
+  \.
+  (?P<patch>\d+)
+  '''
+
+[git]
+message_template = "Bump to {new_version}"
+tag_template = "v{new_version}"
+
+# For each file to patch, add a [[file]] config
+# section containing the path of the file, relative to the
+# tbump.toml location.
+[[file]]
+src = "git_fleximod/cli.py"
+
+[[file]]
+src = "pyproject.toml"
+
+# You can specify a list of commands to
+# run after the files have been patched
+# and before the git commit is made
+
+#  [[before_commit]]
+#  name = "check changelog"
+#  cmd = "grep -q {new_version} Changelog.rst"
+
+# Or run some commands after the git tag and the branch
+# have been pushed:
+#  [[after_push]]
+#  name = "publish"
+#  cmd = "./publish.sh"
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000000..4d4c66c78e
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1,3 @@
+import sys, os
+
+sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000000..942a0efb97
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,138 @@
+import pytest 
+from git_fleximod.gitinterface import GitInterface
+import os
+import subprocess
+import logging
+from pathlib import Path
+
+@pytest.fixture(scope='session')
+def logger():
+    logging.basicConfig(
+        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+    )
+    logger = logging.getLogger(__name__)
+    return logger
+
+all_repos=[
+    {"subrepo_path": "modules/test",
+     "submodule_name": "test_submodule",
+     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_submodule at tag MPIserial_2.4.0",
+     "status3" : "test_submodule at tag MPIserial_2.4.0",
+     "status4" : "test_submodule at tag MPIserial_2.4.0",
+     "gitmodules_content" : """
+    [submodule "test_submodule"]
+    path = modules/test
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelRequired
+"""},
+    {"subrepo_path": "modules/test_optional",
+     "submodule_name": "test_optional",
+     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_optional at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
+     "status4" : "test_optional at tag MPIserial_2.4.0",
+     "gitmodules_content": """
+     [submodule "test_optional"]
+    path = modules/test_optional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelOptional
+"""},
+    {"subrepo_path": "modules/test_alwaysoptional",
+     "submodule_name": "test_alwaysoptional",
+     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+     "status2" : "test_alwaysoptional at hash e5cf35c",
+     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
+     "status4" : "test_alwaysoptional at hash e5cf35c",
+     "gitmodules_content": """
+    [submodule "test_alwaysoptional"]
+    path = modules/test_alwaysoptional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = e5cf35c
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysOptional
+"""},    
+    {"subrepo_path": "modules/test_sparse",
+     "submodule_name": "test_sparse",
+     "status1" : "test_sparse at tag MPIserial_2.5.0",
+     "status2" : "test_sparse at tag MPIserial_2.5.0",
+     "status3" : "test_sparse at tag MPIserial_2.5.0",
+     "status4" : "test_sparse at tag MPIserial_2.5.0",
+     "gitmodules_content": """
+    [submodule "test_sparse"]
+    path = modules/test_sparse
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.5.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysRequired
+    fxsparse = ../.sparse_file_list
+"""},
+]
+@pytest.fixture(params=all_repos)
+
+def shared_repos(request):
+    return request.param
+
+@pytest.fixture
+def get_all_repos():
+    return all_repos
+
+def write_sparse_checkout_file(fp):
+    sparse_content = """m4
+"""
+    fp.write_text(sparse_content)
+
+@pytest.fixture
+def test_repo(shared_repos, tmp_path, logger):
+    subrepo_path = shared_repos["subrepo_path"]
+    submodule_name = shared_repos["submodule_name"]
+    test_dir = tmp_path / "testrepo"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    assert test_dir.joinpath(".git").is_dir()
+    (test_dir / "modules").mkdir()
+    if "sparse" in submodule_name:
+        (test_dir / subrepo_path).mkdir()
+        # Add the sparse checkout file
+        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
+        gitp.git_operation("add","modules/.sparse_file_list")
+    else:
+        gitp = GitInterface(str(test_dir), logger)
+        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        assert test_dir.joinpath(".gitmodules").is_file()
+        gitp.git_operation("add",subrepo_path)
+    gitp.git_operation("commit","-a","-m","\"add submod\"")
+    test_dir2 = tmp_path / "testrepo2"
+    gitp.git_operation("clone",test_dir,test_dir2)
+    return test_dir2    
+
+
+@pytest.fixture
+def complex_repo(tmp_path, logger):
+    test_dir = tmp_path / "testcomplex"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation("fetch", "origin", "main")
+    gitp.git_operation("checkout", "main")
+    return test_dir
+    
+@pytest.fixture
+def git_fleximod():
+    def _run_fleximod(path, args, input=None):
+        cmd = ["git", "fleximod"] + args.split()
+        result = subprocess.run(cmd, cwd=path, input=input, 
+                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
+                                text=True)
+        if result.returncode:
+            print(result.stdout)
+            print(result.stderr)
+        return result
+    return _run_fleximod
+
diff --git a/tests/test_a_import.py b/tests/test_a_import.py
new file mode 100644
index 0000000000..d5ca878de5
--- /dev/null
+++ b/tests/test_a_import.py
@@ -0,0 +1,8 @@
+# pylint: disable=unused-import
+from git_fleximod import cli
+from git_fleximod import utils
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+
+def test_import():
+    print("here")
diff --git a/tests/test_b_update.py b/tests/test_b_update.py
new file mode 100644
index 0000000000..159f1cfae0
--- /dev/null
+++ b/tests/test_b_update.py
@@ -0,0 +1,26 @@
+import pytest
+from pathlib import Path
+                
+def test_basic_checkout(git_fleximod, test_repo, shared_repos):
+    # Prepare a simple .gitmodules
+    gm = shared_repos['gitmodules_content']
+    file_path = (test_repo / ".gitmodules")
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+
+    file_path.write_text(gm)
+    
+    # Run the command
+    result = git_fleximod(test_repo, f"update {repo_name}")
+
+    # Assertions
+    assert result.returncode == 0 
+    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    if "sparse" in repo_name:
+        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
+        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
+    
+    status = git_fleximod(test_repo, f"status {repo_name}")
+        
+    assert shared_repos["status2"] in status.stdout
+        
diff --git a/tests/test_c_required.py b/tests/test_c_required.py
new file mode 100644
index 0000000000..89ab8d294d
--- /dev/null
+++ b/tests/test_c_required.py
@@ -0,0 +1,30 @@
+import pytest
+from pathlib import Path
+                
+def test_required(git_fleximod, test_repo, shared_repos):
+    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    repo_name = shared_repos["submodule_name"]
+    if file_path.exists():
+        with file_path.open("r") as f:
+            gitmodules_content = f.read()
+            # add the entry if it does not exist
+            if repo_name not in gitmodules_content:
+                file_path.write_text(gitmodules_content+gm)
+            # or if it is incomplete
+            elif gm not in gitmodules_content:
+                file_path.write_text(gm)
+    else:
+        file_path.write_text(gm)
+    result = git_fleximod(test_repo, "update")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status3"] in status.stdout
+    status = git_fleximod(test_repo, f"update --optional")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
+    status = git_fleximod(test_repo, f"update {repo_name}")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
new file mode 100644
index 0000000000..fdce516274
--- /dev/null
+++ b/tests/test_d_complex.py
@@ -0,0 +1,67 @@
+import pytest
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_complex_checkout(git_fleximod, complex_repo, logger):
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+    
+    # This should checkout and update test_submodule and complex_sub
+    result = git_fleximod(complex_repo, "update")    
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex")
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+    # update a single optional submodule
+
+    result = git_fleximod(complex_repo, "update ToplevelOptional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+
+
+    # Finally update optional
+    result = git_fleximod(complex_repo, "update --optional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
+    
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex" )
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+

From 9c46501e49265ec9b4049a502399b46c659ee197 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 15:09:36 -0600
Subject: [PATCH 137/161] update hemco external

---
 .gitmodules          | 2 +-
 components/mizuRoute | 2 +-
 src/dynamics/fv3     | 2 +-
 src/hemco            | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 37fba58bd5..de0d660878 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -57,7 +57,7 @@
 [submodule "hemco"]
 	path = src/hemco
 	url = https://github.com/ESCOMP/HEMCO_CESM.git
-        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm 
+        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm_rme01
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
 
diff --git a/components/mizuRoute b/components/mizuRoute
index 81c720c7ee..c55bd1ab74 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit 81c720c7ee51f9c69f2934f696078c42f4493565
+Subproject commit c55bd1ab746734ea77a00606dde895ab034edf1a
diff --git a/src/dynamics/fv3 b/src/dynamics/fv3
index 38b889fcff..e838751297 160000
--- a/src/dynamics/fv3
+++ b/src/dynamics/fv3
@@ -1 +1 @@
-Subproject commit 38b889fcfff1e316ef5b4d4d02ecc47c801b8669
+Subproject commit e838751297b31845d0456b3a2d99fceff4ef5c60
diff --git a/src/hemco b/src/hemco
index 83127485c1..3a6d999ab0 160000
--- a/src/hemco
+++ b/src/hemco
@@ -1 +1 @@
-Subproject commit 83127485c149846ba79d5472ae131acd7bda0544
+Subproject commit 3a6d999ab0dbee9f03ab6b9a13dd3b6d9670eb54

From 4aa073c3482ad30b6952834ccc5eb99778f88c09 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 09:56:18 -0600
Subject: [PATCH 138/161] update find_root_dir to work with git worktree

---
 git_fleximod/cli.py          | 24 +++++++++++++++++-------
 git_fleximod/git_fleximod.py | 10 +++++++---
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 1fb959dad0..3eb90870dc 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,17 +1,27 @@
 from pathlib import Path
 import argparse
+from git_fleximod import utils
 
 __version__ = "0.7.4"
 
-def find_root_dir(filename=".git"):
+def find_root_dir(filename=".gitmodules"):
+    """ finds the highest directory in tree
+    which contains a file called filename """
     d = Path.cwd()
     root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return attempt
-        d = d.parent
-    return None
+    dirlist = []
+    dl = d
+    while dl != root:
+        dirlist.append(dl)
+        dl = dl.parent
+    dirlist.append(root)
+    dirlist.reverse()
+
+    for dl in dirlist:
+        attempt = dl / filename
+        if attempt.is_file():
+            return dl
+    utils.fatal_error("No .gitmodules found in directory tree")
 
 
 def get_parser():
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 103cc82a50..f080513a52 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -312,7 +312,11 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                ahash = git.git_operation("status").partition("\n")[0].split()[-1]
+                part =  git.git_operation("status").partition("\n")[0]
+                # fake hash to initialize
+                ahash = "xxxx"
+                if part:
+                    ahash = part.split()[-1]
                 if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
                 elif tag and ahash[: len(tag)] == tag:
@@ -554,8 +558,8 @@ def main():
     global logger
     logger = logging.getLogger(__name__)
 
-    logger.info("action is {}".format(action))
-
+    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
+    
     if not os.path.isfile(os.path.join(root_dir, file_name)):
         file_path = utils.find_upwards(root_dir, file_name)
 

From 1fddaac99d83852380738c44ca33f615898123ca Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:09:31 -0600
Subject: [PATCH 139/161] return str not Path

---
 License             | 2 +-
 README.md           | 2 --
 git_fleximod/cli.py | 2 +-
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/License b/License
index 2c6fe768c2..88bc22515e 100644
--- a/License
+++ b/License
@@ -1,4 +1,4 @@
-Copyright 2024 National Center for Atmospheric Sciences (NCAR)
+Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
diff --git a/README.md b/README.md
index d1ef632f28..53917da400 100644
--- a/README.md
+++ b/README.md
@@ -8,8 +8,6 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
 
 ## Installation
 
-#TODO    Install using pip:
-#        pip install git-fleximod
   If you choose to locate git-fleximod in your path you can access it via command: git fleximod
 
 ## Usage
diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 3eb90870dc..d24d07c59c 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -20,7 +20,7 @@ def find_root_dir(filename=".gitmodules"):
     for dl in dirlist:
         attempt = dl / filename
         if attempt.is_file():
-            return dl
+            return str(dl)
     utils.fatal_error("No .gitmodules found in directory tree")
 
 

From a354b0528228ac89ce103b3b42b2a203fe495ba5 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:14:11 -0600
Subject: [PATCH 140/161] Bump to 0.7.5

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index d24d07c59c..4c3fb1a8f9 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.4"
+__version__ = "0.7.5"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
diff --git a/pyproject.toml b/pyproject.toml
index 2484552e4f..ac1684ea0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.4"
+version = "0.7.5"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index d4b8eaee11..e644fc4d24 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.4"
+current = "0.7.5"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From e9b20b57db64c0854dd0dcbff5618f44bbe2d589 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:25:10 -0600
Subject: [PATCH 141/161] Squashed '.lib/git-fleximod/' changes from
 94121295..a354b052

a354b052 Bump to 0.7.5
71273de6 Merge pull request #37 from ESMCI/fix/git_workflow
1fddaac9 return str not Path
4aa073c3 update find_root_dir to work with git worktree

git-subtree-dir: .lib/git-fleximod
git-subtree-split: a354b0528228ac89ce103b3b42b2a203fe495ba5
---
 License                      |  2 +-
 README.md                    |  2 --
 git_fleximod/cli.py          | 26 ++++++++++++++++++--------
 git_fleximod/git_fleximod.py | 10 +++++++---
 pyproject.toml               |  2 +-
 tbump.toml                   |  2 +-
 6 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/License b/License
index 2c6fe768c2..88bc22515e 100644
--- a/License
+++ b/License
@@ -1,4 +1,4 @@
-Copyright 2024 National Center for Atmospheric Sciences (NCAR)
+Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
diff --git a/README.md b/README.md
index d1ef632f28..53917da400 100644
--- a/README.md
+++ b/README.md
@@ -8,8 +8,6 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
 
 ## Installation
 
-#TODO    Install using pip:
-#        pip install git-fleximod
   If you choose to locate git-fleximod in your path you can access it via command: git fleximod
 
 ## Usage
diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 1fb959dad0..4c3fb1a8f9 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,17 +1,27 @@
 from pathlib import Path
 import argparse
+from git_fleximod import utils
 
-__version__ = "0.7.4"
+__version__ = "0.7.5"
 
-def find_root_dir(filename=".git"):
+def find_root_dir(filename=".gitmodules"):
+    """ finds the highest directory in tree
+    which contains a file called filename """
     d = Path.cwd()
     root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return attempt
-        d = d.parent
-    return None
+    dirlist = []
+    dl = d
+    while dl != root:
+        dirlist.append(dl)
+        dl = dl.parent
+    dirlist.append(root)
+    dirlist.reverse()
+
+    for dl in dirlist:
+        attempt = dl / filename
+        if attempt.is_file():
+            return str(dl)
+    utils.fatal_error("No .gitmodules found in directory tree")
 
 
 def get_parser():
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 103cc82a50..f080513a52 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -312,7 +312,11 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                ahash = git.git_operation("status").partition("\n")[0].split()[-1]
+                part =  git.git_operation("status").partition("\n")[0]
+                # fake hash to initialize
+                ahash = "xxxx"
+                if part:
+                    ahash = part.split()[-1]
                 if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
                 elif tag and ahash[: len(tag)] == tag:
@@ -554,8 +558,8 @@ def main():
     global logger
     logger = logging.getLogger(__name__)
 
-    logger.info("action is {}".format(action))
-
+    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
+    
     if not os.path.isfile(os.path.join(root_dir, file_name)):
         file_path = utils.find_upwards(root_dir, file_name)
 
diff --git a/pyproject.toml b/pyproject.toml
index 2484552e4f..ac1684ea0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.4"
+version = "0.7.5"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index d4b8eaee11..e644fc4d24 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.4"
+current = "0.7.5"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 0da3e6394140b520ef973d1b8f786187c6a751b2 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:29:20 -0600
Subject: [PATCH 142/161] update fv3 interface

---
 .gitmodules      | 2 +-
 src/dynamics/fv3 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 37fba58bd5..51710c0156 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -44,7 +44,7 @@
 	path = src/dynamics/fv3
 	url = https://github.com/ESCOMP/CAM_FV3_interface.git
         fxrequired = AlwaysRequired
-        fxtag = fv3int_022824
+        fxtag = fv3int_053124
 	fxDONOTUSEurl = https://github.com/ESCOMP/CAM_FV3_interface.git
         
 [submodule "geoschem"]
diff --git a/src/dynamics/fv3 b/src/dynamics/fv3
index 38b889fcff..df3550b0f6 160000
--- a/src/dynamics/fv3
+++ b/src/dynamics/fv3
@@ -1 +1 @@
-Subproject commit 38b889fcfff1e316ef5b4d4d02ecc47c801b8669
+Subproject commit df3550b0f6a835778f32ccc8c6291942e0413f62

From 6f1f86b428082e31da2bc6f6f50593a1c160052a Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:31:50 -0600
Subject: [PATCH 143/161] update externals

---
 components/mizuRoute | 2 +-
 src/hemco            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/components/mizuRoute b/components/mizuRoute
index c55bd1ab74..81c720c7ee 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit c55bd1ab746734ea77a00606dde895ab034edf1a
+Subproject commit 81c720c7ee51f9c69f2934f696078c42f4493565
diff --git a/src/hemco b/src/hemco
index 3a6d999ab0..83127485c1 160000
--- a/src/hemco
+++ b/src/hemco
@@ -1 +1 @@
-Subproject commit 3a6d999ab0dbee9f03ab6b9a13dd3b6d9670eb54
+Subproject commit 83127485c149846ba79d5472ae131acd7bda0544

From 87a14836dfbaf467c1595b34fadcad3de9a590d9 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:33:50 -0600
Subject: [PATCH 144/161] update ctsm external

---
 components/clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/clm b/components/clm
index 5cdf117265..a7f62dab98 160000
--- a/components/clm
+++ b/components/clm
@@ -1 +1 @@
-Subproject commit 5cdf117265bb457ed64af741be0caed593a3a82b
+Subproject commit a7f62dab9830cf0fc6246ce75afff3a3412f1aab

From 00b7b38174360d20b9c2bdeeb8d09f1ac0656fca Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Sat, 1 Jun 2024 11:41:49 -0600
Subject: [PATCH 145/161] some fixes when modifying url

---
 git_fleximod/git_fleximod.py | 49 ++++++++++++++++++++----------------
 git_fleximod/gitmodules.py   |  2 +-
 2 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index f080513a52..a003c0da8c 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -263,6 +263,21 @@ def single_submodule_checkout(
 
     return
 
+def add_remote(git, url):
+    remotes = git.git_operation("remote", "-v")
+    newremote = "newremote.00"
+    if url in remotes:
+        for line in remotes:
+            if url in line and "fetch" in line:
+                newremote = line.split()[0]
+                break
+    else:
+        i = 0
+        while "newremote" in remotes:
+            i = i + 1
+            newremote = f"newremote.{i:02d}"
+        git.git_operation("remote", "add", newremote, url)
+    return newremote
 
 def submodules_status(gitmodules, root_dir, toplevel=False):
     testfails = 0
@@ -271,6 +286,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
+        url = gitmodules.get(name, "url")
         required = gitmodules.get(name, "fxrequired")
         level = required and "Toplevel" in required
         if not path:
@@ -280,7 +296,6 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
         if not os.path.exists(os.path.join(newpath, ".git")):
             rootgit = GitInterface(root_dir, logger)
             # submodule commands use path, not name
-            url = gitmodules.get(name, "url")
             url = url.replace("git@github.com:", "https://github.com/")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
@@ -312,11 +327,11 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                part =  git.git_operation("status").partition("\n")[0]
-                # fake hash to initialize
-                ahash = "xxxx"
-                if part:
-                    ahash = part.split()[-1]
+                ahash =  git.git_operation("rev-list", "HEAD").partition("\n")[0]
+                rurl = git.git_operation("ls-remote","--get-url").rstrip()
+                if rurl != url:
+                    remote = add_remote(git, url)
+                    git.git_operation("fetch", remote)
                 if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
                 elif tag and ahash[: len(tag)] == tag:
@@ -335,7 +350,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                     )
                     testfails += 1
 
-                status = git.git_operation("status", "--ignore-submodules")
+                status = git.git_operation("status", "--ignore-submodules", "-uno")
                 if "nothing to commit" not in status:
                     localmods = localmods + 1
                     print("M" + textwrap.indent(status, "                      "))
@@ -357,11 +372,11 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         logger.info(
-            "name={} path={} url={} fxtag={} requiredlist={}".format(
+            "name={} path={} url={} fxtag={} requiredlist={} ".format(
                 name, os.path.join(root_dir, path), url, fxtag, requiredlist
             )
         )
-        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+
         fxrequired = gitmodules.get(name, "fxrequired")
         assert fxrequired in fxrequired_allowed_values()
         rgit = GitInterface(root_dir, logger)
@@ -409,19 +424,7 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 upstream = git.git_operation("ls-remote", "--get-url").rstrip()
                 newremote = "origin"
                 if upstream != url:
-                    # TODO - this needs to be a unique name
-                    remotes = git.git_operation("remote", "-v")
-                    if url in remotes:
-                        for line in remotes:
-                            if url in line and "fetch" in line:
-                                newremote = line.split()[0]
-                                break
-                    else:
-                        i = 0
-                        while newremote in remotes:
-                            i = i + 1
-                            newremote = f"newremote.{i:02d}"
-                        git.git_operation("remote", "add", newremote, url)
+                    add_remote(git, url)
 
                 tags = git.git_operation("tag", "-l")
                 if fxtag and fxtag not in tags:
@@ -439,6 +442,8 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                     print(f"{name:>20} up to date.")
 
 
+
+
 def local_mods_output():
     text = """\
     The submodules labeled with 'M' above are not in a clean state.
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
index 68c82d066f..7e4e05394a 100644
--- a/git_fleximod/gitmodules.py
+++ b/git_fleximod/gitmodules.py
@@ -59,7 +59,7 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
         Uses the parent class's get method to access the value.
         Handles potential errors if the section or option doesn't exist.
         """
-        self.logger.debug("get called {} {}".format(name, option))
+        self.logger.debug("git get called {} {}".format(name, option))
         section = f'submodule "{name}"'
         try:
             return ConfigParser.get(

From a34070be02d10071b544be3839f6c9ed79662665 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Sat, 1 Jun 2024 11:46:24 -0600
Subject: [PATCH 146/161] Bump to 0.7.6

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 4c3fb1a8f9..7d09abd83b 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.5"
+__version__ = "0.7.6"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
diff --git a/pyproject.toml b/pyproject.toml
index ac1684ea0f..3c70c6c9c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.5"
+version = "0.7.6"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index e644fc4d24..3854682df4 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.5"
+current = "0.7.6"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 5ceadc9e923b337e206e03d73a35b040d908e75a Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Sat, 1 Jun 2024 12:01:40 -0600
Subject: [PATCH 147/161] remove git-fleximod

---
 .../git-fleximod/.github/workflows/pre-commit |  13 -
 .../.github/workflows/pytest.yaml             |  77 --
 .lib/git-fleximod/.pre-commit-config.yaml     |  18 -
 .lib/git-fleximod/License                     |  20 -
 .lib/git-fleximod/README.md                   | 108 ---
 .lib/git-fleximod/doc/Makefile                |  20 -
 .lib/git-fleximod/doc/conf.py                 |  26 -
 .lib/git-fleximod/doc/index.rst               |  24 -
 .lib/git-fleximod/doc/make.bat                |  35 -
 .lib/git-fleximod/escomp_install              |  25 -
 .lib/git-fleximod/git_fleximod/__init__.py    |   0
 .lib/git-fleximod/git_fleximod/cli.py         | 129 ----
 .../git-fleximod/git_fleximod/git_fleximod.py | 605 ---------------
 .../git-fleximod/git_fleximod/gitinterface.py |  79 --
 .lib/git-fleximod/git_fleximod/gitmodules.py  |  97 ---
 .../git-fleximod/git_fleximod/lstripreader.py |  43 --
 .lib/git-fleximod/git_fleximod/metoflexi.py   | 236 ------
 .lib/git-fleximod/git_fleximod/utils.py       | 365 ---------
 .lib/git-fleximod/poetry.lock                 | 693 ------------------
 .lib/git-fleximod/pyproject.toml              |  41 --
 .lib/git-fleximod/tbump.toml                  |  43 --
 .lib/git-fleximod/tests/__init__.py           |   3 -
 .lib/git-fleximod/tests/conftest.py           | 138 ----
 .lib/git-fleximod/tests/test_a_import.py      |   8 -
 .lib/git-fleximod/tests/test_b_update.py      |  26 -
 .lib/git-fleximod/tests/test_c_required.py    |  30 -
 .lib/git-fleximod/tests/test_d_complex.py     |  67 --
 27 files changed, 2969 deletions(-)
 delete mode 100644 .lib/git-fleximod/.github/workflows/pre-commit
 delete mode 100644 .lib/git-fleximod/.github/workflows/pytest.yaml
 delete mode 100644 .lib/git-fleximod/.pre-commit-config.yaml
 delete mode 100644 .lib/git-fleximod/License
 delete mode 100644 .lib/git-fleximod/README.md
 delete mode 100644 .lib/git-fleximod/doc/Makefile
 delete mode 100644 .lib/git-fleximod/doc/conf.py
 delete mode 100644 .lib/git-fleximod/doc/index.rst
 delete mode 100644 .lib/git-fleximod/doc/make.bat
 delete mode 100644 .lib/git-fleximod/escomp_install
 delete mode 100644 .lib/git-fleximod/git_fleximod/__init__.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/cli.py
 delete mode 100755 .lib/git-fleximod/git_fleximod/git_fleximod.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/gitinterface.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/gitmodules.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/lstripreader.py
 delete mode 100755 .lib/git-fleximod/git_fleximod/metoflexi.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/utils.py
 delete mode 100644 .lib/git-fleximod/poetry.lock
 delete mode 100644 .lib/git-fleximod/pyproject.toml
 delete mode 100644 .lib/git-fleximod/tbump.toml
 delete mode 100644 .lib/git-fleximod/tests/__init__.py
 delete mode 100644 .lib/git-fleximod/tests/conftest.py
 delete mode 100644 .lib/git-fleximod/tests/test_a_import.py
 delete mode 100644 .lib/git-fleximod/tests/test_b_update.py
 delete mode 100644 .lib/git-fleximod/tests/test_c_required.py
 delete mode 100644 .lib/git-fleximod/tests/test_d_complex.py

diff --git a/.lib/git-fleximod/.github/workflows/pre-commit b/.lib/git-fleximod/.github/workflows/pre-commit
deleted file mode 100644
index 1a6ad0082a..0000000000
--- a/.lib/git-fleximod/.github/workflows/pre-commit
+++ /dev/null
@@ -1,13 +0,0 @@
-name: pre-commit
-on:
-  pull_request:
-  push:
-    branches: [main]
-
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/action@v3.0.0
diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml
deleted file mode 100644
index 0868dd9a33..0000000000
--- a/.lib/git-fleximod/.github/workflows/pytest.yaml
+++ /dev/null
@@ -1,77 +0,0 @@
-# Run this job on pushes to `main`, and for pull requests. If you don't specify
-# `branches: [main], then this actions runs _twice_ on pull requests, which is
-# annoying.
-
-on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
-      # reference the matrixe python version here.
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-
-      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
-      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
-      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
-      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
-      # mildly cleaner by using an environment variable, but I don't really care.
-      - name: cache poetry install
-        uses: actions/cache@v4
-        with:
-          path: ~/.local
-          key: poetry-1.7.1
-
-      # Install Poetry. You could do this manually, or there are several actions that do this.
-      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
-      # Poetry's default install script, which feels correct. I pin the Poetry version here
-      # because Poetry does occasionally change APIs between versions and I don't want my
-      # actions to break if it does.
-      #
-      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
-      # venv as a `.venv` in your testing directory, which allows the next step to easily
-      # cache it.
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.7.1
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
-      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
-      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v4
-        with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-
-      # Install dependencies. `--no-root` means "install all dependencies but not the project
-      # itself", which is what you want to avoid caching _your_ code. The `if` statement
-      # ensures this only runs on a cache miss.
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-
-      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
-      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
-      # pyproject.toml and makes that if you add things like console-scripts at some point that
-      # they'll be installed and working.
-      - run: poetry install --no-interaction
-
-      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
-      # so this line is super-simple. But it could be as complex as you need.
-      - run: |
-          git config --global user.name "${GITHUB_ACTOR}"
-          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          poetry run pytest
-
diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml
deleted file mode 100644
index 2f6089da72..0000000000
--- a/.lib/git-fleximod/.pre-commit-config.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-exclude: ^utils/.*$
-
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
-    hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/pylint
-    rev: v2.11.1
-    hooks:
-      - id: pylint
-        args:
-          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/.lib/git-fleximod/License b/.lib/git-fleximod/License
deleted file mode 100644
index 88bc22515e..0000000000
--- a/.lib/git-fleximod/License
+++ /dev/null
@@ -1,20 +0,0 @@
-Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-“Software�), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED “AS IS�, WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/.lib/git-fleximod/README.md b/.lib/git-fleximod/README.md
deleted file mode 100644
index 53917da400..0000000000
--- a/.lib/git-fleximod/README.md
+++ /dev/null
@@ -1,108 +0,0 @@
-# git-fleximod
-
-Flexible, Enhanced Submodule Management for Git
-
-## Overview
-
-Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
-
-## Installation
-
-  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
-
-## Usage
-
-    Basic Usage:
-        git fleximod <command> [options]
-    Available Commands:
-        status: Display the status of submodules.
-        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
-        test: Make sure that fxtags and submodule hashes are consistant,
-              make sure that official urls (as defined by fxDONOTUSEurl) are set
-              make sure that fxtags are defined for all submodules
-    Additional Options:
-        See git fleximod --help for more details.
-
-## Supported .gitmodules Variables
-
-    fxtag: Specify a specific tag or branch to checkout for a submodule.
-    fxrequired: Mark a submodule's checkout behavior, with allowed values:
-      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
-      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
-      - AlwaysRequired:       Always required (always checked out).
-      - AlwaysOptional:       Always optional (checked out with --optional flag).
-    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
-    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
-           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
-           changed by users.  Use the url variable to change to a fork if desired.
-
-## Sparse Checkouts
-
-    To enable sparse checkout for a submodule, set the fxsparse variable
-    in the .gitmodules file to the path of a file containing the desired
-    sparse checkout paths. Git-fleximod will automatically configure
-    sparse checkout based on this file when applicable commands are run.
-    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
-    for details on the format of this file.
-
-## Tests
-
-   The git fleximod test action is designed to be used by, for example, github workflows
-   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
-
-## Examples
-
-Here are some common usage examples:
-
-Update all submodules, including optional ones:
-```bash
-  git fleximod update --optional
-```
-
-Updating a specific submodule to the fxtag indicated in .gitmodules:
-
-```bash
-    git fleximod update submodule-name
-```
-Example .gitmodules entry:
-```ini, toml
-    [submodule "cosp2"]
-        path = src/physics/cosp2/src
-        url = https://github.com/CFMIP/COSPv2.0
-        fxsparse = ../.cosp_sparse_checkout
-        fxrequired = AlwaysRequired
-        fxtag = v2.1.4cesm
-```
-Explanation:
-
-This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
-should be checked out into the directory src/physics/cosp2/src
-relative to the .gitmodules directory.  It should be checked out from
-the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
-described in the file ../.cosp_sparse_checkout relative to the path
-directory.  It should be checked out anytime this .gitmodules entry is
-read.
-
-Additional example:
-```ini, toml
-    [submodule "cime"]
-        path = cime
-        url = https://github.com/jedwards4b/cime
-        fxrequired = ToplevelRequired
-        fxtag = cime6.0.198_rme01
-```
-
-Explanation:
-
-This entry indicates that the submodule cime should be checked out
-into a directory named cime at tag cime6.0.198_rme01 from the URL
-https://github.com/jedwards4b/cime.  This should only be done if
-the .gitmodules file is at the top level of the repository clone.
-
-## Contributing
-
-We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
-
-## License
-
-Git-fleximod is released under the MIT License.
diff --git a/.lib/git-fleximod/doc/Makefile b/.lib/git-fleximod/doc/Makefile
deleted file mode 100644
index d4bb2cbb9e..0000000000
--- a/.lib/git-fleximod/doc/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/.lib/git-fleximod/doc/conf.py b/.lib/git-fleximod/doc/conf.py
deleted file mode 100644
index 423099eec9..0000000000
--- a/.lib/git-fleximod/doc/conf.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = "git-fleximod"
-author = "Jim Edwards <jedwards@ucar.edu>"
-release = "0.4.0"
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-extensions = ["sphinx_argparse_cli"]
-
-templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = "alabaster"
-html_static_path = ["_static"]
diff --git a/.lib/git-fleximod/doc/index.rst b/.lib/git-fleximod/doc/index.rst
deleted file mode 100644
index 0f9c1a7f7e..0000000000
--- a/.lib/git-fleximod/doc/index.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-.. git-fleximod documentation master file, created by
-   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to git-fleximod's documentation!
-========================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-.. module:: sphinxcontrib.autoprogram
-.. sphinx_argparse_cli::
-   :module: git_fleximod.cli
-   :func: get_parser
-   :prog: git-fleximod
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/.lib/git-fleximod/doc/make.bat b/.lib/git-fleximod/doc/make.bat
deleted file mode 100644
index 32bb24529f..0000000000
--- a/.lib/git-fleximod/doc/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/.lib/git-fleximod/escomp_install b/.lib/git-fleximod/escomp_install
deleted file mode 100644
index ae782e72a4..0000000000
--- a/.lib/git-fleximod/escomp_install
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python
-# updates git-fleximod in an ESCOMP model
-# this script should be run from the model root directory, it expects
-# git-fleximod to already be installed with the script in bin
-# and the classes in lib/python/site-packages
-import sys
-import shutil
-import os
-
-from glob import iglob
-
-fleximod_root = sys.argv[1]
-fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
-if os.path.isfile(fleximod_path):
-   with open(fleximod_path,"r") as f:
-        fleximod = f.readlines()
-   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
-        for line in fleximod:
-            f.write(line)
-            if "import argparse" in line:
-               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
-
-   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
-       shutil.copy(file,
-        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/.lib/git-fleximod/git_fleximod/__init__.py b/.lib/git-fleximod/git_fleximod/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
deleted file mode 100644
index 4c3fb1a8f9..0000000000
--- a/.lib/git-fleximod/git_fleximod/cli.py
+++ /dev/null
@@ -1,129 +0,0 @@
-from pathlib import Path
-import argparse
-from git_fleximod import utils
-
-__version__ = "0.7.5"
-
-def find_root_dir(filename=".gitmodules"):
-    """ finds the highest directory in tree
-    which contains a file called filename """
-    d = Path.cwd()
-    root = Path(d.root)
-    dirlist = []
-    dl = d
-    while dl != root:
-        dirlist.append(dl)
-        dl = dl.parent
-    dirlist.append(root)
-    dirlist.reverse()
-
-    for dl in dirlist:
-        attempt = dl / filename
-        if attempt.is_file():
-            return str(dl)
-    utils.fatal_error("No .gitmodules found in directory tree")
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    #
-    # user options
-    #
-    choices = ["update", "status", "test"]
-    parser.add_argument(
-        "action",
-        choices=choices,
-        default="update",
-        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
-    )
-
-    parser.add_argument(
-        "components",
-        nargs="*",
-        help="Specific component(s) to checkout. By default, "
-        "all required submodules are checked out.",
-    )
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-
-    parser.add_argument(
-        "-x",
-        "--exclude",
-        nargs="*",
-        help="Component(s) listed in the gitmodules file which should be ignored.",
-    )
-    parser.add_argument(
-        "-f",
-        "--force",
-        action="store_true",
-        default=False,
-        help="Override cautions and update or checkout over locally modified repository.",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--optional",
-        action="store_true",
-        default=False,
-        help="By default only the required submodules "
-        "are checked out. This flag will also checkout the "
-        "optional submodules relative to the toplevel directory.",
-    )
-
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-
-    parser.add_argument(
-        "-V",
-        "--version",
-        action="version",
-        version=f"%(prog)s {__version__}",
-        help="Print version and exit.",
-    )
-
-    #
-    # developer options
-    #
-    parser.add_argument(
-        "--backtrace",
-        action="store_true",
-        help="DEVELOPER: show exception backtraces as extra " "debugging output",
-    )
-
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
deleted file mode 100755
index f080513a52..0000000000
--- a/.lib/git-fleximod/git_fleximod/git_fleximod.py
+++ /dev/null
@@ -1,605 +0,0 @@
-#!/usr/bin/env python
-import sys
-
-MIN_PYTHON = (3, 7)
-if sys.version_info < MIN_PYTHON:
-    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
-
-import os
-import shutil
-import logging
-import textwrap
-from git_fleximod import utils
-from git_fleximod import cli
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-from configparser import NoOptionError
-
-# logger variable is global
-logger = None
-
-
-def fxrequired_allowed_values():
-    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
-
-
-def commandline_arguments(args=None):
-    parser = cli.get_parser()
-
-    if args:
-        options = parser.parse_args(args)
-    else:
-        options = parser.parse_args()
-
-    # explicitly listing a component overrides the optional flag
-    if options.optional or options.components:
-        fxrequired = [
-            "ToplevelRequired",
-            "ToplevelOptional",
-            "AlwaysRequired",
-            "AlwaysOptional",
-        ]
-    else:
-        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
-
-    action = options.action
-    if not action:
-        action = "update"
-    handlers = [logging.StreamHandler()]
-
-    if options.debug:
-        try:
-            open("fleximod.log", "w")
-        except PermissionError:
-            sys.exit("ABORT: Could not write file fleximod.log")
-        level = logging.DEBUG
-        handlers.append(logging.FileHandler("fleximod.log"))
-    elif options.verbose:
-        level = logging.INFO
-    else:
-        level = logging.WARNING
-    # Configure the root logger
-    logging.basicConfig(
-        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
-    )
-
-    if hasattr(options, "version"):
-        exit()
-
-    return (
-        options.path,
-        options.gitmodules,
-        fxrequired,
-        options.components,
-        options.exclude,
-        options.force,
-        action,
-    )
-
-
-def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
-    """
-    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
-    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
-    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
-    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
-    and disk space consuming.
-
-    Parameters:
-    root_dir (str): The root directory for the git operation.
-    name (str): The name of the submodule.
-    url (str): The URL of the submodule.
-    path (str): The path to the submodule.
-    sparsefile (str): The sparse file for the submodule.
-    tag (str, optional): The tag to checkout. Defaults to "master".
-
-    Returns:
-    None
-    """
-    logger.info("Called sparse_checkout for {}".format(name))
-    rgit = GitInterface(root_dir, logger)
-    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-    if superroot:
-        gitroot = superroot.strip()
-    else:
-        gitroot = root_dir.strip()
-    assert os.path.isdir(os.path.join(gitroot, ".git"))
-    # first create the module directory
-    if not os.path.isdir(os.path.join(root_dir, path)):
-        os.makedirs(os.path.join(root_dir, path))
-
-    # initialize a new git repo and set the sparse checkout flag
-    sprep_repo = os.path.join(root_dir, path)
-    sprepo_git = GitInterface(sprep_repo, logger)
-    if os.path.exists(os.path.join(sprep_repo, ".git")):
-        try:
-            logger.info("Submodule {} found".format(name))
-            chk = sprepo_git.config_get_value("core", "sparseCheckout")
-            if chk == "true":
-                logger.info("Sparse submodule {} already checked out".format(name))
-                return
-        except NoOptionError:
-            logger.debug("Sparse submodule {} not present".format(name))
-        except Exception as e:
-            utils.fatal_error("Unexpected error {} occured.".format(e))
-
-    sprepo_git.config_set_value("core", "sparseCheckout", "true")
-
-    # set the repository remote
-
-    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
-    status = sprepo_git.git_operation("remote", "-v")
-    if url not in status:
-        sprepo_git.git_operation("remote", "add", "origin", url)
-
-    topgit = os.path.join(gitroot, ".git")
-
-    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
-        with open(os.path.join(root_dir, ".git")) as f:
-            gitpath = os.path.relpath(
-                os.path.join(root_dir, f.read().split()[1]),
-                start=os.path.join(root_dir, path),
-            )
-        topgit = os.path.join(gitpath, "modules")
-    else:
-        topgit = os.path.relpath(
-            os.path.join(root_dir, ".git", "modules"),
-            start=os.path.join(root_dir, path),
-        )
-
-    with utils.pushd(sprep_repo):
-        if not os.path.isdir(topgit):
-            os.makedirs(topgit)
-    topgit += os.sep + name
-
-    if os.path.isdir(os.path.join(root_dir, path, ".git")):
-        with utils.pushd(sprep_repo):
-            shutil.move(".git", topgit)
-            with open(".git", "w") as f:
-                f.write("gitdir: " + os.path.relpath(topgit))
-            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
-            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
-        if os.path.isfile(gitsparse):
-            logger.warning(
-                "submodule {} is already initialized {}".format(name, topgit)
-            )
-            return
-
-        with utils.pushd(sprep_repo):
-            shutil.copy(sparsefile, gitsparse)
-
-    # Finally checkout the repo
-    sprepo_git.git_operation("fetch", "origin", "--tags")
-    sprepo_git.git_operation("checkout", tag)
-
-    print(f"Successfully checked out {name:>20} at {tag}")
-    rgit.config_set_value(f'submodule "{name}"', "active", "true")
-    rgit.config_set_value(f'submodule "{name}"', "url", url)
-
-
-def single_submodule_checkout(
-    root, name, path, url=None, tag=None, force=False, optional=False
-):
-    """
-    This function checks out a single git submodule.
-
-    Parameters:
-    root (str): The root directory for the git operation.
-    name (str): The name of the submodule.
-    path (str): The path to the submodule.
-    url (str, optional): The URL of the submodule. Defaults to None.
-    tag (str, optional): The tag to checkout. Defaults to None.
-    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
-    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
-
-    Returns:
-    None
-    """
-    # function implementation...
-    git = GitInterface(root, logger)
-    repodir = os.path.join(root, path)
-    logger.info("Checkout {} into {}/{}".format(name, root, path))
-    # if url is provided update to the new url
-    tmpurl = None
-    repo_exists = False
-    if os.path.exists(os.path.join(repodir, ".git")):
-        logger.info("Submodule {} already checked out".format(name))
-        repo_exists = True
-    # Look for a .gitmodules file in the newly checkedout repo
-    if not repo_exists and url:
-        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
-        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
-        # opened with a GitModules object we don't need to worry about restoring the file here
-        # it will be done by the GitModules class
-        if url.startswith("git@"):
-            tmpurl = url
-            url = url.replace("git@github.com:", "https://github.com/")
-            git.git_operation("clone", url, path)
-            smgit = GitInterface(repodir, logger)
-            if not tag:
-                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
-            smgit.git_operation("checkout", tag)
-            # Now need to move the .git dir to the submodule location
-            rootdotgit = os.path.join(root, ".git")
-            if os.path.isfile(rootdotgit):
-                with open(rootdotgit) as f:
-                    line = f.readline()
-                    if line.startswith("gitdir: "):
-                        rootdotgit = line[8:].rstrip()
-
-            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
-            if os.path.exists(newpath):
-                shutil.rmtree(os.path.join(repodir, ".git"))
-            else:
-                shutil.move(os.path.join(repodir, ".git"), newpath)
-
-            with open(os.path.join(repodir, ".git"), "w") as f:
-                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
-                
-    if not os.path.exists(repodir):
-        parent = os.path.dirname(repodir)
-        if not os.path.isdir(parent):
-            os.makedirs(parent)
-        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
-
-    if not repo_exists or not tmpurl:
-        git.git_operation("submodule", "update", "--init", "--", path)
-            
-    if os.path.exists(os.path.join(repodir, ".gitmodules")):
-        # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name}")
-        gitmodules = GitModules(logger, confpath=repodir)
-        requiredlist = ["AlwaysRequired"]
-        if optional:
-            requiredlist.append("AlwaysOptional")
-        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
-    if not os.path.exists(os.path.join(repodir, ".git")):
-        utils.fatal_error(
-            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
-        )
-
-    if tmpurl:
-        print(git.git_operation("restore", ".gitmodules"))
-
-    return
-
-
-def submodules_status(gitmodules, root_dir, toplevel=False):
-    testfails = 0
-    localmods = 0
-    needsupdate = 0
-    for name in gitmodules.sections():
-        path = gitmodules.get(name, "path")
-        tag = gitmodules.get(name, "fxtag")
-        required = gitmodules.get(name, "fxrequired")
-        level = required and "Toplevel" in required
-        if not path:
-            utils.fatal_error("No path found in .gitmodules for {}".format(name))
-        newpath = os.path.join(root_dir, path)
-        logger.debug("newpath is {}".format(newpath))
-        if not os.path.exists(os.path.join(newpath, ".git")):
-            rootgit = GitInterface(root_dir, logger)
-            # submodule commands use path, not name
-            url = gitmodules.get(name, "url")
-            url = url.replace("git@github.com:", "https://github.com/")
-            tags = rootgit.git_operation("ls-remote", "--tags", url)
-            atag = None
-            needsupdate += 1
-            if not toplevel and level:
-                continue
-            for htag in tags.split("\n"):
-                if tag and tag in htag:
-                    atag = (htag.split()[1])[10:]
-                    break
-            if tag and tag == atag:
-                print(f"e {name:>20} not checked out, aligned at tag {tag}")
-            elif tag:
-                ahash = rootgit.git_operation(
-                    "submodule", "status", "{}".format(path)
-                ).rstrip()
-                ahash = ahash[1 : len(tag) + 1]
-                if tag == ahash:
-                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
-                else:
-                    print(
-                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
-                    )
-                    testfails += 1
-            else:
-                print(f"e {name:>20} has no fxtag defined in .gitmodules")
-                testfails += 1
-        else:
-            with utils.pushd(newpath):
-                git = GitInterface(newpath, logger)
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                part =  git.git_operation("status").partition("\n")[0]
-                # fake hash to initialize
-                ahash = "xxxx"
-                if part:
-                    ahash = part.split()[-1]
-                if tag and atag == tag:
-                    print(f"  {name:>20} at tag {tag}")
-                elif tag and ahash[: len(tag)] == tag:
-                    print(f"  {name:>20} at hash {ahash}")
-                elif atag == ahash:
-                    print(f"  {name:>20} at hash {ahash}")
-                elif tag:
-                    print(
-                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
-                    )
-                    testfails += 1
-                    needsupdate += 1
-                else:
-                    print(
-                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
-                    )
-                    testfails += 1
-
-                status = git.git_operation("status", "--ignore-submodules")
-                if "nothing to commit" not in status:
-                    localmods = localmods + 1
-                    print("M" + textwrap.indent(status, "                      "))
-
-    return testfails, localmods, needsupdate
-
-
-def submodules_update(gitmodules, root_dir, requiredlist, force):
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-
-    if localmods and not force:
-        local_mods_output()
-        return
-    if needsupdate == 0:
-        return
-
-    for name in gitmodules.sections():
-        fxtag = gitmodules.get(name, "fxtag")
-        path = gitmodules.get(name, "path")
-        url = gitmodules.get(name, "url")
-        logger.info(
-            "name={} path={} url={} fxtag={} requiredlist={}".format(
-                name, os.path.join(root_dir, path), url, fxtag, requiredlist
-            )
-        )
-        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
-        fxrequired = gitmodules.get(name, "fxrequired")
-        assert fxrequired in fxrequired_allowed_values()
-        rgit = GitInterface(root_dir, logger)
-        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-
-        fxsparse = gitmodules.get(name, "fxsparse")
-
-        if (
-            fxrequired
-            and (superroot and "Toplevel" in fxrequired)
-            or fxrequired not in requiredlist
-        ):
-            if "ToplevelOptional" == fxrequired:
-                print("Skipping optional component {}".format(name))
-            continue
-        if fxsparse:
-            logger.debug(
-                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                    root_dir, name, url, path, fxsparse, fxtag
-                )
-            )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
-        else:
-            logger.info(
-                "Calling submodule_checkout({},{},{},{})".format(
-                    root_dir, name, path, url
-                )
-            )
-
-            single_submodule_checkout(
-                root_dir,
-                name,
-                path,
-                url=url,
-                tag=fxtag,
-                force=force,
-                optional=("AlwaysOptional" in requiredlist),
-            )
-
-        if os.path.exists(os.path.join(path, ".git")):
-            submoddir = os.path.join(root_dir, path)
-            with utils.pushd(submoddir):
-                git = GitInterface(submoddir, logger)
-                # first make sure the url is correct
-                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
-                newremote = "origin"
-                if upstream != url:
-                    # TODO - this needs to be a unique name
-                    remotes = git.git_operation("remote", "-v")
-                    if url in remotes:
-                        for line in remotes:
-                            if url in line and "fetch" in line:
-                                newremote = line.split()[0]
-                                break
-                    else:
-                        i = 0
-                        while newremote in remotes:
-                            i = i + 1
-                            newremote = f"newremote.{i:02d}"
-                        git.git_operation("remote", "add", newremote, url)
-
-                tags = git.git_operation("tag", "-l")
-                if fxtag and fxtag not in tags:
-                    git.git_operation("fetch", newremote, "--tags")
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                if fxtag and fxtag != atag:
-                    try:
-                        git.git_operation("checkout", fxtag)
-                        print(f"{name:>20} updated to {fxtag}")
-                    except Exception as error:
-                        print(error)
-                elif not fxtag:
-                    print(f"No fxtag found for submodule {name:>20}")
-                else:
-                    print(f"{name:>20} up to date.")
-
-
-def local_mods_output():
-    text = """\
-    The submodules labeled with 'M' above are not in a clean state.
-    The following are options for how to proceed:
-    (1) Go into each submodule which is not in a clean state and issue a 'git status'
-        Either revert or commit your changes so that the submodule is in a clean state.
-    (2) use the --force option to git-fleximod
-    (3) you can name the particular submodules to update using the git-fleximod command line
-    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
-        then rerun git-fleximod update.
-"""
-    print(text)
-
-
-# checkout is done by update if required so this function may be depricated
-def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
-    """
-    This function checks out all git submodules based on the provided parameters.
-
-    Parameters:
-    gitmodules (ConfigParser): The gitmodules configuration.
-    root_dir (str): The root directory for the git operation.
-    requiredlist (list): The list of required modules.
-    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
-
-    Returns:
-    None
-    """
-    # function implementation...
-    print("")
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-    if localmods and not force:
-        local_mods_output()
-        return
-    if not needsupdate:
-        return
-    for name in gitmodules.sections():
-        fxrequired = gitmodules.get(name, "fxrequired")
-        fxsparse = gitmodules.get(name, "fxsparse")
-        fxtag = gitmodules.get(name, "fxtag")
-        path = gitmodules.get(name, "path")
-        url = gitmodules.get(name, "url")
-        if fxrequired and fxrequired not in requiredlist:
-            if "Optional" in fxrequired:
-                print("Skipping optional component {}".format(name))
-            continue
-
-        if fxsparse:
-            logger.debug(
-                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                    root_dir, name, url, path, fxsparse, fxtag
-                )
-            )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
-        else:
-            logger.debug(
-                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
-            )
-            single_submodule_checkout(
-                root_dir,
-                name,
-                path,
-                url=url,
-                tag=fxtag,
-                force=force,
-                optional="AlwaysOptional" in requiredlist,
-            )
-
-
-def submodules_test(gitmodules, root_dir):
-    """
-    This function tests the git submodules based on the provided parameters.
-
-    It first checks that fxtags are present and in sync with submodule hashes.
-    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
-    and that sparse checkout files exist.
-
-    Parameters:
-    gitmodules (ConfigParser): The gitmodules configuration.
-    root_dir (str): The root directory for the git operation.
-
-    Returns:
-    int: The number of test failures.
-    """
-    # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-    print("")
-    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
-    # and that sparse checkout files exist
-    for name in gitmodules.sections():
-        url = gitmodules.get(name, "url")
-        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
-        fxsparse = gitmodules.get(name, "fxsparse")
-        path = gitmodules.get(name, "path")
-        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
-        url = url[:-4] if url.endswith(".git") else url
-        if not fxurl or url.lower() != fxurl.lower():
-            print(f"{name:>20} url {url} not in sync with required {fxurl}")
-            testfails += 1
-        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
-            print(f"{name:>20} sparse checkout file {fxsparse} not found")
-            testfails += 1
-    return testfails + localmods + needsupdate
-
-
-def main():
-    (
-        root_dir,
-        file_name,
-        fxrequired,
-        includelist,
-        excludelist,
-        force,
-        action,
-    ) = commandline_arguments()
-    # Get a logger for the package
-    global logger
-    logger = logging.getLogger(__name__)
-
-    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
-    
-    if not os.path.isfile(os.path.join(root_dir, file_name)):
-        file_path = utils.find_upwards(root_dir, file_name)
-
-        if file_path is None:
-            utils.fatal_error(
-                "No {} found in {} or any of it's parents".format(file_name, root_dir)
-            )
-
-        root_dir = os.path.dirname(file_path)
-    logger.info(
-        "root_dir is {} includelist={} excludelist={}".format(
-            root_dir, includelist, excludelist
-        )
-    )
-    gitmodules = GitModules(
-        logger,
-        confpath=root_dir,
-        conffile=file_name,
-        includelist=includelist,
-        excludelist=excludelist,
-    )
-    if not gitmodules.sections():
-        sys.exit("No submodule components found")
-    retval = 0
-    if action == "update":
-        submodules_update(gitmodules, root_dir, fxrequired, force)
-    elif action == "status":
-        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
-        if tfails + lmods + updates > 0:
-            print(
-                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
-            )
-            if lmods > 0:
-                local_mods_output()
-    elif action == "test":
-        retval = submodules_test(gitmodules, root_dir)
-    else:
-        utils.fatal_error(f"unrecognized action request {action}")
-    return retval
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
deleted file mode 100644
index 93ae38ecde..0000000000
--- a/.lib/git-fleximod/git_fleximod/gitinterface.py
+++ /dev/null
@@ -1,79 +0,0 @@
-import os
-import sys
-from . import utils
-from pathlib import Path
-
-class GitInterface:
-    def __init__(self, repo_path, logger):
-        logger.debug("Initialize GitInterface for {}".format(repo_path))
-        if isinstance(repo_path, str):
-            self.repo_path = Path(repo_path).resolve()
-        elif isinstance(repo_path, Path):
-            self.repo_path = repo_path.resolve()
-        else:
-            raise TypeError("repo_path must be a str or Path object")
-        self.logger = logger
-        try:
-            import git
-
-            self._use_module = True
-            try:
-                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
-            except git.exc.InvalidGitRepositoryError:
-                self.git = git
-                self._init_git_repo()
-            msg = "Using GitPython interface to git"
-        except ImportError:
-            self._use_module = False
-            if not (self.repo_path / ".git").exists():
-                self._init_git_repo()
-            msg = "Using shell interface to git"
-        self.logger.info(msg)
-
-    def _git_command(self, operation, *args):
-        self.logger.info(operation)
-        if self._use_module and operation != "submodule":
-            try:
-                return getattr(self.repo.git, operation)(*args)
-            except Exception as e:
-                sys.exit(e)
-        else:
-            return ["git", "-C", str(self.repo_path), operation] + list(args)
-
-    def _init_git_repo(self):
-        if self._use_module:
-            self.repo = self.git.Repo.init(str(self.repo_path))
-        else:
-            command = ("git", "-C", str(self.repo_path), "init")
-            utils.execute_subprocess(command)
-
-    # pylint: disable=unused-argument
-    def git_operation(self, operation, *args, **kwargs):
-        command = self._git_command(operation, *args)
-        self.logger.info(command)
-        if isinstance(command, list):
-            try:
-                return utils.execute_subprocess(command, output_to_caller=True)
-            except Exception as e:
-                sys.exit(e)
-        else:
-            return command
-
-    def config_get_value(self, section, name):
-        if self._use_module:
-            config = self.repo.config_reader()
-            return config.get_value(section, name)
-        else:
-            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
-            output = utils.execute_subprocess(cmd, output_to_caller=True)
-            return output.strip()
-
-    def config_set_value(self, section, name, value):
-        if self._use_module:
-            with self.repo.config_writer() as writer:
-                writer.set_value(section, name, value)
-            writer.release()  # Ensure changes are saved
-        else:
-            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
-            self.logger.info(cmd)
-            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py
deleted file mode 100644
index 68c82d066f..0000000000
--- a/.lib/git-fleximod/git_fleximod/gitmodules.py
+++ /dev/null
@@ -1,97 +0,0 @@
-import shutil
-from pathlib import Path
-from configparser import RawConfigParser, ConfigParser
-from .lstripreader import LstripReader
-
-
-class GitModules(RawConfigParser):
-    def __init__(
-        self,
-        logger,
-        confpath=Path.cwd(),
-        conffile=".gitmodules",
-        includelist=None,
-        excludelist=None,
-    ):
-        """
-        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
-        conffile: Name of the configuration file (defaults to .gitmodules).
-        includelist: Optional list of submodules to include.
-        excludelist: Optional list of submodules to exclude.
-        """
-        self.logger = logger
-        self.logger.debug(
-            "Creating a GitModules object {} {} {} {}".format(
-                confpath, conffile, includelist, excludelist
-            )
-        )
-        super().__init__()
-        self.conf_file = (Path(confpath) / Path(conffile))
-        if self.conf_file.exists():
-            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
-        self.includelist = includelist
-        self.excludelist = excludelist
-        self.isdirty = False
-        
-    def reload(self):
-        self.clear()
-        if self.conf_file.exists():
-            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
-
-        
-    def set(self, name, option, value):
-        """
-        Sets a configuration value for a specific submodule:
-        Ensures the appropriate section exists for the submodule.
-        Calls the parent class's set method to store the value.
-        """
-        self.isdirty = True
-        self.logger.debug("set called {} {} {}".format(name, option, value))
-        section = f'submodule "{name}"'
-        if not self.has_section(section):
-            self.add_section(section)
-        super().set(section, option, str(value))
-
-    # pylint: disable=redefined-builtin, arguments-differ
-    def get(self, name, option, raw=False, vars=None, fallback=None):
-        """
-        Retrieves a configuration value for a specific submodule:
-        Uses the parent class's get method to access the value.
-        Handles potential errors if the section or option doesn't exist.
-        """
-        self.logger.debug("get called {} {}".format(name, option))
-        section = f'submodule "{name}"'
-        try:
-            return ConfigParser.get(
-                self, section, option, raw=raw, vars=vars, fallback=fallback
-            )
-        except ConfigParser.NoOptionError:
-            return None
-
-    def save(self):
-        if self.isdirty:
-            self.logger.info("Writing {}".format(self.conf_file))
-            with open(self.conf_file, "w") as fd:
-                self.write(fd)
-        self.isdirty = False
-        
-    def __del__(self):
-        self.save()
-
-    def sections(self):
-        """Strip the submodule part out of section and just use the name"""
-        self.logger.debug("calling GitModules sections iterator")
-        names = []
-        for section in ConfigParser.sections(self):
-            name = section[11:-1]
-            if self.includelist and name not in self.includelist:
-                continue
-            if self.excludelist and name in self.excludelist:
-                continue
-            names.append(name)
-        return names
-
-    def items(self, name, raw=False, vars=None):
-        self.logger.debug("calling GitModules items for {}".format(name))
-        section = f'submodule "{name}"'
-        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/.lib/git-fleximod/git_fleximod/lstripreader.py b/.lib/git-fleximod/git_fleximod/lstripreader.py
deleted file mode 100644
index 01d5580ee8..0000000000
--- a/.lib/git-fleximod/git_fleximod/lstripreader.py
+++ /dev/null
@@ -1,43 +0,0 @@
-class LstripReader(object):
-    "LstripReader formats .gitmodules files to be acceptable for configparser"
-
-    def __init__(self, filename):
-        with open(filename, "r") as infile:
-            lines = infile.readlines()
-        self._lines = list()
-        self._num_lines = len(lines)
-        self._index = 0
-        for line in lines:
-            self._lines.append(line.lstrip())
-
-    def readlines(self):
-        """Return all the lines from this object's file"""
-        return self._lines
-
-    def readline(self, size=-1):
-        """Format and return the next line or raise StopIteration"""
-        try:
-            line = self.next()
-        except StopIteration:
-            line = ""
-
-        if (size > 0) and (len(line) < size):
-            return line[0:size]
-
-        return line
-
-    def __iter__(self):
-        """Begin an iteration"""
-        self._index = 0
-        return self
-
-    def next(self):
-        """Return the next line or raise StopIteration"""
-        if self._index >= self._num_lines:
-            raise StopIteration
-
-        self._index = self._index + 1
-        return self._lines[self._index - 1]
-
-    def __next__(self):
-        return self.next()
diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py
deleted file mode 100755
index cc347db2dd..0000000000
--- a/.lib/git-fleximod/git_fleximod/metoflexi.py
+++ /dev/null
@@ -1,236 +0,0 @@
-#!/usr/bin/env python
-from configparser import ConfigParser
-import sys
-import shutil
-from pathlib import Path
-import argparse
-import logging
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-from git_fleximod import utils
-
-logger = None
-
-def find_root_dir(filename=".git"):
-    d = Path.cwd()
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return d
-        d = d.parent
-    return None
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
-
-def commandline_arguments(args=None):
-    parser = get_parser()
-
-    options = parser.parse_args(args)
-    handlers = [logging.StreamHandler()]
-
-    if options.debug:
-        try:
-            open("fleximod.log", "w")
-        except PermissionError:
-            sys.exit("ABORT: Could not write file fleximod.log")
-        level = logging.DEBUG
-        handlers.append(logging.FileHandler("fleximod.log"))
-    elif options.verbose:
-        level = logging.INFO
-    else:
-        level = logging.WARNING
-    # Configure the root logger
-    logging.basicConfig(
-        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
-    )
-
-    return(
-        options.path,
-        options.gitmodules,
-        options.externals
-        )
-
-class ExternalRepoTranslator:
-    """
-    Translates external repositories configured in an INI-style externals file.
-    """
-
-    def __init__(self, rootpath, gitmodules, externals):
-        self.rootpath = rootpath
-        if gitmodules:
-            self.gitmodules = GitModules(logger, confpath=rootpath)
-        self.externals = (rootpath / Path(externals)).resolve()
-        print(f"Translating {self.externals}")
-        self.git = GitInterface(rootpath, logger)
-        
-#    def __del__(self):
-#        if (self.rootpath / "save.gitignore"):
-            
-
-    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
-        """
-        Translates a single repository based on configuration details.
-
-        Args:
-            rootpath (str): Root path of the main repository.
-            gitmodules (str): Path to the .gitmodules file.
-            tag (str): The tag to use for the external repository.
-            url (str): The URL of the external repository.
-            path (str): The relative path within the main repository for the external repository.
-            efile (str): The external file or file containing submodules.
-            hash_ (str): The commit hash to checkout (if applicable).
-            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
-            protocol (str): The protocol to use (e.g., 'git', 'http').
-        """
-        assert protocol != "svn", "SVN protocol is not currently supported"
-        print(f"Translating repository {section}")
-        if efile:
-            file_path = Path(path) / Path(efile)
-            newroot = (self.rootpath / file_path).parent.resolve()
-            if not newroot.exists():
-                newroot.mkdir(parents=True)
-            logger.info("Newroot is {}".format(newroot))
-            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
-            newt.translate_repo()
-        if protocol == "externals_only":
-            if tag:
-                self.gitmodules.set(section, "fxtag", tag)
-            if hash_:
-                self.gitmodules.set(section, "fxtag", hash_)
-            
-            self.gitmodules.set(section, "fxDONOTUSEurl", url)
-            if sparse:
-                self.gitmodules.set(section, "fxsparse", sparse)
-            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-        else:
-            newpath = (self.rootpath / Path(path))
-            if newpath.exists():
-                shutil.rmtree(newpath)
-                logger.info("Creating directory {}".format(newpath))
-            newpath.mkdir(parents=True)
-            if tag:
-                logger.info("cloning {}".format(section))
-                try:
-                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
-                except:
-                    self.git.git_operation("clone", url, path)
-                    with utils.pushd(newpath):
-                        ngit = GitInterface(newpath, logger)
-                        ngit.git_operation("checkout", tag)
-            if hash_:
-                self.git.git_operation("clone", url, path)
-                git = GitInterface(newpath, logger)
-                git.git_operation("fetch", "origin")
-                git.git_operation("checkout", hash_)
-            if sparse:
-                print("setting as sparse submodule {}".format(section))
-                sparsefile = (newpath / Path(sparse))
-                newfile = (newpath / ".git" / "info" / "sparse-checkout")
-                print(f"sparsefile {sparsefile} newfile {newfile}")
-                shutil.copy(sparsefile, newfile)
-        
-            logger.info("adding submodule {}".format(section))        
-            self.gitmodules.save()
-            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
-            self.git.git_operation("submodule","absorbgitdirs")
-            self.gitmodules.reload()
-            if tag:
-                self.gitmodules.set(section, "fxtag", tag)
-            if hash_:
-                self.gitmodules.set(section, "fxtag", hash_)
-            
-            self.gitmodules.set(section, "fxDONOTUSEurl", url)
-            if sparse:
-                self.gitmodules.set(section, "fxsparse", sparse)
-            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-    
-        
-    def translate_repo(self):
-        """
-        Translates external repositories defined within an external file.
-
-        Args:
-            rootpath (str): Root path of the main repository.
-            gitmodules (str): Path to the .gitmodules file.
-            external_file (str): The path to the external file containing repository definitions.
-        """
-        econfig = ConfigParser()
-        econfig.read((self.rootpath / Path(self.externals)))
-
-        for section in econfig.sections():
-            if section == "externals_description":
-                logger.info("skipping section {}".format(section))
-                return
-            logger.info("Translating section {}".format(section))
-            tag = econfig.get(section, "tag", raw=False, fallback=None)
-            url = econfig.get(section, "repo_url", raw=False, fallback=None)
-            path = econfig.get(section, "local_path", raw=False, fallback=None)
-            efile = econfig.get(section, "externals", raw=False, fallback=None)
-            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
-            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
-            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
-
-            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
-
-
-
-def _main():
-    rootpath, gitmodules, externals = commandline_arguments()
-    global logger
-    logger = logging.getLogger(__name__)
-    with utils.pushd(rootpath):
-        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
-        logger.info("Translating {}".format(rootpath))
-        t.translate_repo()
-
-        
-if __name__ == "__main__":
-    sys.exit(_main())
diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
deleted file mode 100644
index 7cc1de38cc..0000000000
--- a/.lib/git-fleximod/git_fleximod/utils.py
+++ /dev/null
@@ -1,365 +0,0 @@
-#!/usr/bin/env python3
-"""
-Common public utilities for manic package
-
-"""
-
-import logging
-import os
-import subprocess
-import sys
-from threading import Timer
-from pathlib import Path
-
-LOCAL_PATH_INDICATOR = "."
-# ---------------------------------------------------------------------
-#
-# functions to massage text for output and other useful utilities
-#
-# ---------------------------------------------------------------------
-from contextlib import contextmanager
-
-
-@contextmanager
-def pushd(new_dir):
-    """context for chdir. usage: with pushd(new_dir)"""
-    previous_dir = os.getcwd()
-    os.chdir(new_dir)
-    try:
-        yield
-    finally:
-        os.chdir(previous_dir)
-
-
-def log_process_output(output):
-    """Log each line of process output at debug level so it can be
-    filtered if necessary. By default, output is a single string, and
-    logging.debug(output) will only put log info heading on the first
-    line. This makes it hard to filter with grep.
-
-    """
-    output = output.split("\n")
-    for line in output:
-        logging.debug(line)
-
-
-def printlog(msg, **kwargs):
-    """Wrapper script around print to ensure that everything printed to
-    the screen also gets logged.
-
-    """
-    logging.info(msg)
-    if kwargs:
-        print(msg, **kwargs)
-    else:
-        print(msg)
-    sys.stdout.flush()
-
-
-def find_upwards(root_dir, filename):
-    """Find a file in root dir or any of it's parents"""
-    d = Path(root_dir)
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.exists():
-            return attempt
-        d = d.parent
-    return None
-
-
-def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
-    """
-
-    lines = the_string.splitlines(True)
-    if len(lines) <= n_lines:
-        return_val = the_string
-    else:
-        lines_subset = lines[-n_lines:]
-        str_truncated = "".join(lines_subset)
-        if truncation_message:
-            str_truncated = truncation_message + "\n" + str_truncated
-        return_val = str_truncated
-
-    return return_val
-
-
-def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
-    """
-
-    lines = the_string.splitlines(True)
-    padding = " " * indent_level
-    lines_indented = [padding + line for line in lines]
-    return "".join(lines_indented)
-
-
-# ---------------------------------------------------------------------
-#
-# error handling
-#
-# ---------------------------------------------------------------------
-
-
-def fatal_error(message):
-    """
-    Error output function
-    """
-    logging.error(message)
-    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
-
-
-# ---------------------------------------------------------------------
-#
-# Data conversion / manipulation
-#
-# ---------------------------------------------------------------------
-def str_to_bool(bool_str):
-    """Convert a sting representation of as boolean into a true boolean.
-
-    Conversion should be case insensitive.
-    """
-    value = None
-    str_lower = bool_str.lower()
-    if str_lower in ("true", "t"):
-        value = True
-    elif str_lower in ("false", "f"):
-        value = False
-    if value is None:
-        msg = (
-            'ERROR: invalid boolean string value "{0}". '
-            'Must be "true" or "false"'.format(bool_str)
-        )
-        fatal_error(msg)
-    return value
-
-
-REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
-
-
-def is_remote_url(url):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    """
-    remote_url = False
-    for prefix in REMOTE_PREFIXES:
-        if url.startswith(prefix):
-            remote_url = True
-    return remote_url
-
-
-def split_remote_url(url):
-    """check if the user provided a local file path or a
-    remote. If remote, try to strip off protocol info.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        return url
-
-    for prefix in REMOTE_PREFIXES:
-        url = url.replace(prefix, "")
-
-    if "@" in url:
-        url = url.split("@")[1]
-
-    if ":" in url:
-        url = url.split(":")[1]
-
-    return url
-
-
-def expand_local_url(url, field):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
-    represent local copy only, don't work with the remotes.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        if url.strip() == LOCAL_PATH_INDICATOR:
-            pass
-        else:
-            url = os.path.expandvars(url)
-            url = os.path.expanduser(url)
-            if not os.path.isabs(url):
-                msg = (
-                    'WARNING: Externals description for "{0}" contains a '
-                    "url that is not remote and does not expand to an "
-                    "absolute path. Version control operations may "
-                    "fail.\n\nurl={1}".format(field, url)
-                )
-                printlog(msg)
-            else:
-                url = os.path.normpath(url)
-    return url
-
-
-# ---------------------------------------------------------------------
-#
-# subprocess
-#
-# ---------------------------------------------------------------------
-
-# Give the user a helpful message if we detect that a command seems to
-# be hanging.
-_HANGING_SEC = 300
-
-
-def _hanging_msg(working_directory, command):
-    print(
-        """
-
-Command '{command}'
-from directory {working_directory}
-has taken {hanging_sec} seconds. It may be hanging.
-
-The command will continue to run, but you may want to abort
-manage_externals with ^C and investigate. A possible cause of hangs is
-when svn or git require authentication to access a private
-repository. On some systems, svn and git requests for authentication
-information will not be displayed to the user. In this case, the program
-will appear to hang. Ensure you can run svn and git manually and access
-all repositories without entering your authentication information.
-
-""".format(
-            command=command,
-            working_directory=working_directory,
-            hanging_sec=_HANGING_SEC,
-        )
-    )
-
-
-def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
-    """Wrapper around subprocess.check_output to handle common
-    exceptions.
-
-    check_output runs a command with arguments and waits
-    for it to complete.
-
-    check_output raises an exception on a nonzero return code.  if
-    status_to_caller is true, execute_subprocess returns the subprocess
-    return code, otherwise execute_subprocess treats non-zero return
-    status as an error and raises an exception.
-
-    """
-    cwd = os.getcwd()
-    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
-    logging.info(msg)
-    commands_str = " ".join(str(element) for element in commands)
-    logging.info(commands_str)
-    return_to_caller = status_to_caller or output_to_caller
-    status = -1
-    output = ""
-    hanging_timer = Timer(
-        _HANGING_SEC,
-        _hanging_msg,
-        kwargs={"working_directory": cwd, "command": commands_str},
-    )
-    hanging_timer.start()
-    try:
-        output = subprocess.check_output(
-            commands, stderr=subprocess.STDOUT, universal_newlines=True
-        )
-        log_process_output(output)
-        status = 0
-    except OSError as error:
-        msg = failed_command_msg(
-            "Command execution failed. Does the executable exist?", commands
-        )
-        logging.error(error)
-        fatal_error(msg)
-    except ValueError as error:
-        msg = failed_command_msg(
-            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
-        )
-        logging.error(error)
-        fatal_error(msg)
-    except subprocess.CalledProcessError as error:
-        # Only report the error if we are NOT returning to the
-        # caller. If we are returning to the caller, then it may be a
-        # simple status check. If returning, it is the callers
-        # responsibility determine if an error occurred and handle it
-        # appropriately.
-        if not return_to_caller:
-            msg_context = (
-                "Process did not run successfully; "
-                "returned status {0}".format(error.returncode)
-            )
-            msg = failed_command_msg(msg_context, commands, output=error.output)
-            logging.error(error)
-            logging.error(msg)
-            log_process_output(error.output)
-            fatal_error(msg)
-        status = error.returncode
-    finally:
-        hanging_timer.cancel()
-
-    if status_to_caller and output_to_caller:
-        ret_value = (status, output)
-    elif status_to_caller:
-        ret_value = status
-    elif output_to_caller:
-        ret_value = output
-    else:
-        ret_value = None
-
-    return ret_value
-
-
-def failed_command_msg(msg_context, command, output=None):
-    """Template for consistent error messages from subprocess calls.
-
-    If 'output' is given, it should provide the output from the failed
-    command
-    """
-
-    if output:
-        output_truncated = last_n_lines(
-            output, 20, truncation_message="[... Output truncated for brevity ...]"
-        )
-        errmsg = (
-            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
-        )
-    else:
-        errmsg = ""
-
-    command_str = " ".join(command)
-    errmsg += """In directory
-    {cwd}
-{context}:
-    {command}
-""".format(
-        cwd=os.getcwd(), context=msg_context, command=command_str
-    )
-
-    if output:
-        errmsg += "See above for output from failed command.\n"
-
-    return errmsg
diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock
deleted file mode 100644
index b59ed3942c..0000000000
--- a/.lib/git-fleximod/poetry.lock
+++ /dev/null
@@ -1,693 +0,0 @@
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-
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-[package.dependencies]
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-
-[package.extras]
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-
-[[package]]
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-version = "2024.2.2"
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-zstd = ["zstandard (>=0.18.0)"]
-
-[[package]]
-name = "wheel"
-version = "0.42.0"
-description = "A built-package format for Python"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "wheel-0.42.0-py3-none-any.whl", hash = "sha256:177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d"},
-    {file = "wheel-0.42.0.tar.gz", hash = "sha256:c45be39f7882c9d34243236f2d63cbd58039e360f85d0913425fbd7ceea617a8"},
-]
-
-[package.extras]
-test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
-
-[[package]]
-name = "zipp"
-version = "3.17.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
-
-[metadata]
-lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
deleted file mode 100644
index ac1684ea0f..0000000000
--- a/.lib/git-fleximod/pyproject.toml
+++ /dev/null
@@ -1,41 +0,0 @@
-[tool.poetry]
-name = "git-fleximod"
-version = "0.7.5"
-description = "Extended support for git-submodule and git-sparse-checkout"
-authors = ["Jim Edwards <jedwards@ucar.edu>"]
-maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
-license = "MIT"
-readme = "README.md"
-homepage = "https://github.com/jedwards4b/git-fleximod"
-keywords = ["git", "submodule", "sparse-checkout"]
-packages = [
-{ include = "git_fleximod"},
-{ include = "doc"},
-]
-
-[tool.poetry.scripts]
-git-fleximod = "git_fleximod.git_fleximod:main"
-me2flexi = "git_fleximod.metoflexi:_main"
-fsspec = "fsspec.fuse:main"
-
-[tool.poetry.dependencies]
-python = "^3.8"
-GitPython = "^3.1.0"
-sphinx = "^5.0.0"
-fsspec = "^2023.12.2"
-wheel = "^0.42.0"
-pytest = "^8.0.0"
-pyfakefs = "^5.3.5"
-
-[tool.poetry.urls]
-"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
-
-[tool.pytest.ini_options]
-markers = [
-        "skip_after_first: only run on first iteration"
-]
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
deleted file mode 100644
index e644fc4d24..0000000000
--- a/.lib/git-fleximod/tbump.toml
+++ /dev/null
@@ -1,43 +0,0 @@
-# Uncomment this if your project is hosted on GitHub:
-github_url = "https://github.com/jedwards4b/git-fleximod/"
-
-[version]
-current = "0.7.5"
-
-# Example of a semver regexp.
-# Make sure this matches current_version before
-# using tbump
-regex = '''
-  (?P<major>\d+)
-  \.
-  (?P<minor>\d+)
-  \.
-  (?P<patch>\d+)
-  '''
-
-[git]
-message_template = "Bump to {new_version}"
-tag_template = "v{new_version}"
-
-# For each file to patch, add a [[file]] config
-# section containing the path of the file, relative to the
-# tbump.toml location.
-[[file]]
-src = "git_fleximod/cli.py"
-
-[[file]]
-src = "pyproject.toml"
-
-# You can specify a list of commands to
-# run after the files have been patched
-# and before the git commit is made
-
-#  [[before_commit]]
-#  name = "check changelog"
-#  cmd = "grep -q {new_version} Changelog.rst"
-
-# Or run some commands after the git tag and the branch
-# have been pushed:
-#  [[after_push]]
-#  name = "publish"
-#  cmd = "./publish.sh"
diff --git a/.lib/git-fleximod/tests/__init__.py b/.lib/git-fleximod/tests/__init__.py
deleted file mode 100644
index 4d4c66c78e..0000000000
--- a/.lib/git-fleximod/tests/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-import sys, os
-
-sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py
deleted file mode 100644
index 942a0efb97..0000000000
--- a/.lib/git-fleximod/tests/conftest.py
+++ /dev/null
@@ -1,138 +0,0 @@
-import pytest 
-from git_fleximod.gitinterface import GitInterface
-import os
-import subprocess
-import logging
-from pathlib import Path
-
-@pytest.fixture(scope='session')
-def logger():
-    logging.basicConfig(
-        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
-    )
-    logger = logging.getLogger(__name__)
-    return logger
-
-all_repos=[
-    {"subrepo_path": "modules/test",
-     "submodule_name": "test_submodule",
-     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_submodule at tag MPIserial_2.4.0",
-     "status3" : "test_submodule at tag MPIserial_2.4.0",
-     "status4" : "test_submodule at tag MPIserial_2.4.0",
-     "gitmodules_content" : """
-    [submodule "test_submodule"]
-    path = modules/test
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.4.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelRequired
-"""},
-    {"subrepo_path": "modules/test_optional",
-     "submodule_name": "test_optional",
-     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
-     "status4" : "test_optional at tag MPIserial_2.4.0",
-     "gitmodules_content": """
-     [submodule "test_optional"]
-    path = modules/test_optional
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.4.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelOptional
-"""},
-    {"subrepo_path": "modules/test_alwaysoptional",
-     "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
-     "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
-     "status4" : "test_alwaysoptional at hash e5cf35c",
-     "gitmodules_content": """
-    [submodule "test_alwaysoptional"]
-    path = modules/test_alwaysoptional
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = e5cf35c
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = AlwaysOptional
-"""},    
-    {"subrepo_path": "modules/test_sparse",
-     "submodule_name": "test_sparse",
-     "status1" : "test_sparse at tag MPIserial_2.5.0",
-     "status2" : "test_sparse at tag MPIserial_2.5.0",
-     "status3" : "test_sparse at tag MPIserial_2.5.0",
-     "status4" : "test_sparse at tag MPIserial_2.5.0",
-     "gitmodules_content": """
-    [submodule "test_sparse"]
-    path = modules/test_sparse
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.5.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = AlwaysRequired
-    fxsparse = ../.sparse_file_list
-"""},
-]
-@pytest.fixture(params=all_repos)
-
-def shared_repos(request):
-    return request.param
-
-@pytest.fixture
-def get_all_repos():
-    return all_repos
-
-def write_sparse_checkout_file(fp):
-    sparse_content = """m4
-"""
-    fp.write_text(sparse_content)
-
-@pytest.fixture
-def test_repo(shared_repos, tmp_path, logger):
-    subrepo_path = shared_repos["subrepo_path"]
-    submodule_name = shared_repos["submodule_name"]
-    test_dir = tmp_path / "testrepo"
-    test_dir.mkdir()
-    str_path = str(test_dir)
-    gitp = GitInterface(str_path, logger)
-    assert test_dir.joinpath(".git").is_dir()
-    (test_dir / "modules").mkdir()
-    if "sparse" in submodule_name:
-        (test_dir / subrepo_path).mkdir()
-        # Add the sparse checkout file
-        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
-        gitp.git_operation("add","modules/.sparse_file_list")
-    else:
-        gitp = GitInterface(str(test_dir), logger)
-        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
-        assert test_dir.joinpath(".gitmodules").is_file()
-        gitp.git_operation("add",subrepo_path)
-    gitp.git_operation("commit","-a","-m","\"add submod\"")
-    test_dir2 = tmp_path / "testrepo2"
-    gitp.git_operation("clone",test_dir,test_dir2)
-    return test_dir2    
-
-
-@pytest.fixture
-def complex_repo(tmp_path, logger):
-    test_dir = tmp_path / "testcomplex"
-    test_dir.mkdir()
-    str_path = str(test_dir)
-    gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
-    gitp.git_operation("fetch", "origin", "main")
-    gitp.git_operation("checkout", "main")
-    return test_dir
-    
-@pytest.fixture
-def git_fleximod():
-    def _run_fleximod(path, args, input=None):
-        cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=path, input=input, 
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
-                                text=True)
-        if result.returncode:
-            print(result.stdout)
-            print(result.stderr)
-        return result
-    return _run_fleximod
-
diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py
deleted file mode 100644
index d5ca878de5..0000000000
--- a/.lib/git-fleximod/tests/test_a_import.py
+++ /dev/null
@@ -1,8 +0,0 @@
-# pylint: disable=unused-import
-from git_fleximod import cli
-from git_fleximod import utils
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-
-def test_import():
-    print("here")
diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py
deleted file mode 100644
index 159f1cfae0..0000000000
--- a/.lib/git-fleximod/tests/test_b_update.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import pytest
-from pathlib import Path
-                
-def test_basic_checkout(git_fleximod, test_repo, shared_repos):
-    # Prepare a simple .gitmodules
-    gm = shared_repos['gitmodules_content']
-    file_path = (test_repo / ".gitmodules")
-    repo_name = shared_repos["submodule_name"]
-    repo_path = shared_repos["subrepo_path"]
-
-    file_path.write_text(gm)
-    
-    # Run the command
-    result = git_fleximod(test_repo, f"update {repo_name}")
-
-    # Assertions
-    assert result.returncode == 0 
-    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
-    if "sparse" in repo_name:
-        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
-        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
-    
-    status = git_fleximod(test_repo, f"status {repo_name}")
-        
-    assert shared_repos["status2"] in status.stdout
-        
diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py
deleted file mode 100644
index 89ab8d294d..0000000000
--- a/.lib/git-fleximod/tests/test_c_required.py
+++ /dev/null
@@ -1,30 +0,0 @@
-import pytest
-from pathlib import Path
-                
-def test_required(git_fleximod, test_repo, shared_repos):
-    file_path = (test_repo / ".gitmodules")
-    gm = shared_repos["gitmodules_content"]
-    repo_name = shared_repos["submodule_name"]
-    if file_path.exists():
-        with file_path.open("r") as f:
-            gitmodules_content = f.read()
-            # add the entry if it does not exist
-            if repo_name not in gitmodules_content:
-                file_path.write_text(gitmodules_content+gm)
-            # or if it is incomplete
-            elif gm not in gitmodules_content:
-                file_path.write_text(gm)
-    else:
-        file_path.write_text(gm)
-    result = git_fleximod(test_repo, "update")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status3"] in status.stdout
-    status = git_fleximod(test_repo, f"update --optional")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
-    status = git_fleximod(test_repo, f"update {repo_name}")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py
deleted file mode 100644
index fdce516274..0000000000
--- a/.lib/git-fleximod/tests/test_d_complex.py
+++ /dev/null
@@ -1,67 +0,0 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
-
-def test_complex_checkout(git_fleximod, complex_repo, logger):
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
-    
-    # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_repo, "update")    
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
-    # update a single optional submodule
-
-    result = git_fleximod(complex_repo, "update ToplevelOptional")
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
-
-
-    # Finally update optional
-    result = git_fleximod(complex_repo, "update --optional")
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
-

From 253ba00e6d2747d5dc9bd0ba043b8df58c55ec00 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Sat, 1 Jun 2024 14:59:33 -0600
Subject: [PATCH 148/161] update externals

---
 .gitmodules    | 4 ++--
 components/clm | 2 +-
 src/hemco      | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 2299a58c9d..62364e0354 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -185,8 +185,8 @@ fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
 [submodule "clm"]
 path = components/clm
-url = https://github.com/jedwards4b/CTSM
-fxtag = ctsm5.2.007/candidate
+url = https://github.com/ESCOMP/CTSM
+fxtag = ctsm5.2.007
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
diff --git a/components/clm b/components/clm
index a7f62dab98..a9433779f0 160000
--- a/components/clm
+++ b/components/clm
@@ -1 +1 @@
-Subproject commit a7f62dab9830cf0fc6246ce75afff3a3412f1aab
+Subproject commit a9433779f0ae499d60ad118d2ec331628f0eaaa8
diff --git a/src/hemco b/src/hemco
index 83127485c1..3a6d999ab0 160000
--- a/src/hemco
+++ b/src/hemco
@@ -1 +1 @@
-Subproject commit 83127485c149846ba79d5472ae131acd7bda0544
+Subproject commit 3a6d999ab0dbee9f03ab6b9a13dd3b6d9670eb54

From 2c96bae4d59c6b7048448a266942a154a37dcaa3 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 3 Jun 2024 07:36:17 -0600
Subject: [PATCH 149/161] update hemco tag

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index 62364e0354..cffb557ee8 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -57,7 +57,7 @@
 [submodule "hemco"]
 	path = src/hemco
 	url = https://github.com/ESCOMP/HEMCO_CESM.git
-        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm_rme01
+        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm_rme
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
 

From 4ae9171f03b1da9cb0be7c90707b2be92cf1363d Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Mon, 3 Jun 2024 13:40:31 -0600
Subject: [PATCH 150/161] Update README.md with directions about git-fleximod

---
 README.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/README.md b/README.md
index e03fb36018..d03fd2f311 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,18 @@
 
 ## NOTE: This is **unsupported** development code and is subject to the [CESM developer's agreement](http://www.cgd.ucar.edu/cseg/development-code.html).
 
+-----------
+
+To checkout externals:
+    bin/git-fleximod update
+
+The externals are stored in:
+    .gitmodules
+
+.gitmodules can be modified.  Then run "bin/git-fleximod update" to get the updated externals
+
+------------
+
 ### CAM Documentation - https://ncar.github.io/CAM/doc/build/html/index.html
 
 ### CAM6 namelist settings - http://www.cesm.ucar.edu/models/cesm2/settings/current/cam_nml.html

From 9473a8137c37bd6a5ea487bc139c8a25d808abc0 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Mon, 3 Jun 2024 14:06:24 -0600
Subject: [PATCH 151/161] Add details to README.md and add script for
 manage_externals/checkout_externals

---
 README.md                           | 2 ++
 manage_externals/checkout_externals | 3 +++
 2 files changed, 5 insertions(+)
 create mode 100755 manage_externals/checkout_externals

diff --git a/README.md b/README.md
index d03fd2f311..a6aa6fee8c 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,8 @@ The externals are stored in:
 
 .gitmodules can be modified.  Then run "bin/git-fleximod update" to get the updated externals
 
+Details about git-fleximod and the variables in the .gitmodules file can be found at:  .lib/git-fleximod/README.md
+
 ------------
 
 ### CAM Documentation - https://ncar.github.io/CAM/doc/build/html/index.html
diff --git a/manage_externals/checkout_externals b/manage_externals/checkout_externals
new file mode 100755
index 0000000000..ac6b718ee0
--- /dev/null
+++ b/manage_externals/checkout_externals
@@ -0,0 +1,3 @@
+echo "Error:  manage_externals/checkout_externals is no longer supported"
+echo "        It has been replaced by bin/git-fleximod"
+echo "        Please refer to the README.md file in the home directory of a CAM checkout for more information"

From 87708b631dac23ff9f586fd7e6bc4f7c3bf6f66a Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Mon, 3 Jun 2024 15:12:26 -0600
Subject: [PATCH 152/161] Update TGIT test to check for .gitmodules

---
 test/system/TGIT.sh | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/test/system/TGIT.sh b/test/system/TGIT.sh
index db04179217..e6d6557030 100755
--- a/test/system/TGIT.sh
+++ b/test/system/TGIT.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Test for bad git repo
-# Ensures that the top-level CAM directory 
+# Ensures that the top-level CAM directory
 # has ".git" directory and ".gitignore" file,
 # and no other git files or directories.
 
@@ -9,7 +9,7 @@
 # 2: Missing ".git" directory
 # 3: Missing ".gitignore" file
 # 4: Missing ".github" directory
-# 5: More than three ".git*" files or directories
+# 5: Missing ".gitmodules" file
 # 6: Error from running an external command
 
 # Utility to check return code.
@@ -66,7 +66,7 @@ The ".gitignore" file is missing from the CAM git repo.  Was this repo cloned, c
 modified incorrectly?  If so then copy the .gitignore file from a standard CAM git repo.
 EOF
         rc=3
-    fi   
+    fi
 
     # Check for ".github" directory:
     if [ ! -d "${cam_top_dir}/.github" ]; then
@@ -77,15 +77,11 @@ EOF
         rc=4
     fi
 
-    # Check if there are more ".git*" files or directories than just ".git", ".gitignore",
-    # and ".github":
-    git_file_num=$(find "${cam_top_dir}" -maxdepth 1 -name '.git*' | wc -l)
-
-    check_code "$?" "Problem running 'find' command for multi-git file check."
-
-    if [ "${git_file_num}" -gt 3 ]; then
+    # Check for ".github" directory:
+    if [ ! -f "${cam_top_dir}/.gitmodules" ]; then
         cat <<EOF
-More than three ".git*" files or sub-directories present in this CAM git repo.
+The ".gitmodules" directory is missing from the CAM git repo.  Was this repo cloned, copied, or
+modified incorrectly?  If so then copy the .gitmodules directory from a standard CAM git repo.
 EOF
         rc=5
     fi
@@ -94,7 +90,7 @@ fi # git-repo check
 
 # If all tests pass, let user know:
 if [ "$rc" -eq 0 ]; then
-    echo "No problems found in the git repostiory ($cam_top_dir)."
+    echo "No problems found in the git repository ($cam_top_dir)."
 fi
 
 # Exit script with final error value:

From 27fa5108184d32e8ea884e5943df3bbdd6073d9b Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Wed, 5 Jun 2024 09:11:47 -0600
Subject: [PATCH 153/161] Update chem_proc tag with one with .gitignore in it

---
 .gitmodules | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index cffb557ee8..77e9c2fc56 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -2,7 +2,7 @@
 	path = chem_proc
 	url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
         fxrequired = AlwaysRequired
-        fxtag = chem_proc5_0_05
+        fxtag = chem_proc5_0_06
 	fxDONOTUSEurl = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
 
 [submodule "carma"]
@@ -46,7 +46,7 @@
         fxrequired = AlwaysRequired
         fxtag = fv3int_053124
 	fxDONOTUSEurl = https://github.com/ESCOMP/CAM_FV3_interface.git
-        
+
 [submodule "geoschem"]
 	path = src/chemistry/geoschem/geoschem_src
 	url = https://github.com/geoschem/geos-chem.git
@@ -95,7 +95,7 @@
 	path = src/physics/clubb
 	url = https://github.com/larson-group/clubb_release
         fxrequired = AlwaysRequired
-        fxsparse = ../.clubb_sparse_checkout 
+        fxsparse = ../.clubb_sparse_checkout
         fxtag = clubb_4ncar_20231115_5406350
         fxDONOTUSEurl = https://github.com/larson-group/clubb_release
 
@@ -126,7 +126,7 @@ url = https://github.com/ESCOMP/mizuRoute
 fxtag = cesm-coupling.n02_v2.1.2
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
-        
+
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git

From c304487aff29425777e08fc5e009320b50282149 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 5 Jun 2024 11:36:26 -0600
Subject: [PATCH 154/161] update complex test

---
 git_fleximod/cli.py          | 2 +-
 git_fleximod/git_fleximod.py | 8 +++++---
 tests/test_d_complex.py      | 8 ++++----
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 7d09abd83b..d4498b84f9 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -21,7 +21,7 @@ def find_root_dir(filename=".gitmodules"):
         attempt = dl / filename
         if attempt.is_file():
             return str(dl)
-    utils.fatal_error("No .gitmodules found in directory tree")
+    return None
 
 
 def get_parser():
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index a003c0da8c..48a9b69f65 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -565,10 +565,12 @@ def main():
 
     logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
     
-    if not os.path.isfile(os.path.join(root_dir, file_name)):
-        file_path = utils.find_upwards(root_dir, file_name)
+    if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)):
+        if root_dir:
+            file_path = utils.find_upwards(root_dir, file_name)
 
-        if file_path is None:
+        if root_dir is None or file_path is None:
+            root_dir = "."
             utils.fatal_error(
                 "No {} found in {} or any of it's parents".format(file_name, root_dir)
             )
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
index fdce516274..62889f2cba 100644
--- a/tests/test_d_complex.py
+++ b/tests/test_d_complex.py
@@ -7,7 +7,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
     assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
     
     # This should checkout and update test_submodule and complex_sub
@@ -18,7 +18,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
 
     # now check the complex_sub
     root = (complex_repo / "modules" / "complex")
@@ -39,7 +39,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
     assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
 
 
@@ -51,7 +51,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
     assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
     
     # now check the complex_sub

From 8ca8b13358f476c9df671de8a260f97f0972f9d7 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Wed, 5 Jun 2024 12:16:20 -0600
Subject: [PATCH 155/161] update chem_proc external

---
 chem_proc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/chem_proc b/chem_proc
index ed4ba1b27e..f923081508 160000
--- a/chem_proc
+++ b/chem_proc
@@ -1 +1 @@
-Subproject commit ed4ba1b27e40c8d5af6657ec49a3e3cc8e6f8b5f
+Subproject commit f923081508f4264e61fcef2753a9898e55d1598e

From d95f5d61ba381fbef6274eae5547e08d09e1a10d Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 5 Jun 2024 14:08:19 -0600
Subject: [PATCH 156/161] fix status issue

---
 git_fleximod/git_fleximod.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 48a9b69f65..a847c9fc6b 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -298,15 +298,22 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             # submodule commands use path, not name
             url = url.replace("git@github.com:", "https://github.com/")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
+            ahash = rootgit.git_operation("submodule","status",newpath).split()[0][1:]
+            hhash = None
             atag = None
             needsupdate += 1
             if not toplevel and level:
                 continue
             for htag in tags.split("\n"):
-                if tag and tag in htag:
+                if htag.endswith('^{}'):
+                    htag = htag[:-3]
+                if not atag and ahash in htag:
                     atag = (htag.split()[1])[10:]
+                if not hhash and htag.endswith(tag):
+                    hhash = htag.split()[0]
+                if hhash and atag:
                     break
-            if tag and tag == atag:
+            if tag and (ahash == hhash or atag == tag):
                 print(f"e {name:>20} not checked out, aligned at tag {tag}")
             elif tag:
                 ahash = rootgit.git_operation(

From 0593149d3c106509daa1fbb235fe5b747e26c9a5 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 5 Jun 2024 14:17:46 -0600
Subject: [PATCH 157/161] one more improvement

---
 git_fleximod/git_fleximod.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index a847c9fc6b..b0a5a33070 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -309,7 +309,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                     htag = htag[:-3]
                 if not atag and ahash in htag:
                     atag = (htag.split()[1])[10:]
-                if not hhash and htag.endswith(tag):
+                if tag and not hhash and htag.endswith(tag):
                     hhash = htag.split()[0]
                 if hhash and atag:
                     break

From 3ff935b835d1793e0840f00230e323efc52fba76 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 5 Jun 2024 14:47:54 -0600
Subject: [PATCH 158/161] update tests

---
 git_fleximod/git_fleximod.py | 7 +++++--
 tests/conftest.py            | 4 ++--
 tests/test_d_complex.py      | 5 ++---
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index b0a5a33070..ca5f90622d 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -298,7 +298,10 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             # submodule commands use path, not name
             url = url.replace("git@github.com:", "https://github.com/")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
-            ahash = rootgit.git_operation("submodule","status",newpath).split()[0][1:]
+            result = rootgit.git_operation("submodule","status",newpath).split()
+            ahash = None
+            if result:
+                ahash = result[0][1:]
             hhash = None
             atag = None
             needsupdate += 1
@@ -307,7 +310,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             for htag in tags.split("\n"):
                 if htag.endswith('^{}'):
                     htag = htag[:-3]
-                if not atag and ahash in htag:
+                if ahash and not atag and ahash in htag:
                     atag = (htag.split()[1])[10:]
                 if tag and not hhash and htag.endswith(tag):
                     hhash = htag.split()[0]
diff --git a/tests/conftest.py b/tests/conftest.py
index 942a0efb97..1cc008eb1d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -32,7 +32,7 @@ def logger():
      "submodule_name": "test_optional",
      "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0",
      "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
      [submodule "test_optional"]
@@ -46,7 +46,7 @@ def logger():
      "submodule_name": "test_alwaysoptional",
      "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
      "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
+     "status3" : "out of sync at tag None, expected tag is e5cf35c",
      "status4" : "test_alwaysoptional at hash e5cf35c",
      "gitmodules_content": """
     [submodule "test_alwaysoptional"]
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
index 62889f2cba..edde7d816d 100644
--- a/tests/test_d_complex.py
+++ b/tests/test_d_complex.py
@@ -8,7 +8,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
     assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
     
     # This should checkout and update test_submodule and complex_sub
     result = git_fleximod(complex_repo, "update")    
@@ -40,8 +40,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
     assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
-
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
 
     # Finally update optional
     result = git_fleximod(complex_repo, "update --optional")

From 87640adf43cdd3c30acd258185f128e638cb41ac Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 6 Jun 2024 13:29:04 -0600
Subject: [PATCH 159/161] Bump to 0.7.7

---
 git_fleximod/cli.py | 2 +-
 pyproject.toml      | 2 +-
 tbump.toml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index d4498b84f9..bc099fcbc0 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.6"
+__version__ = "0.7.7"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
diff --git a/pyproject.toml b/pyproject.toml
index 3c70c6c9c7..a316914bf5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.6"
+version = "0.7.7"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 3854682df4..c22637ccda 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.6"
+current = "0.7.7"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 74cfa9d7db42c6356505ac98dfc45817a473f92b Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Fri, 7 Jun 2024 12:06:23 -0600
Subject: [PATCH 160/161] update ChangeLog for cam6_3_162

---
 doc/ChangeLog | 130 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 130 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 3a5c46527d..9e627f133c 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,6 +1,136 @@
 
 ===============================================================
 
+Tag name: cam6_3_162
+Originator(s): cacraig, jedwards, nusbaume
+Date: June 7, 2024
+One-line Summary: Remove manage externals
+Github PR URL: https://github.com/ESCOMP/CAM/pull/1052
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+  - Removes manage_externals/checkout_externals and replaces with git-fleximod (no GitHub issue)
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist: N/A
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by: cacraigucar
+
+List all files eliminated:
+D       Externals.cfg
+D       Externals_CAM.cfg
+D       manage_externals
+          - Removed manage_externals functionality
+
+List all files added and what they do:
+A       .gitmodules
+A       .lib/git-fleximod
+          - Add git-fleximod functionality
+
+A       bin/git-fleximod
+          - The actual git-fleximod executable
+
+A       ccs_config
+A       chem_proc
+A       cime
+A       components/cdeps
+A       components/cice
+A       components/cism
+A       components/clm
+A       components/cmeps
+A       components/mizuRoute
+A       components/mosart
+A       components/rtm
+A       libraries/FMS
+A       libraries/mct
+A       libraries/parallelio
+A       share
+A       src/atmos_phys
+A       src/chemistry/geoschem/geoschem_src
+A       src/dynamics/fv3
+A       src/dynamics/mpas/dycore
+A       src/hemco
+A       src/physics/ali_arms
+A       src/physics/carma/base
+A       src/physics/clubb
+A       src/physics/cosp2/src
+A       src/physics/pumas
+A       src/physics/pumas-frozen
+A       src/physics/rrtmgp/data
+A       src/physics/rrtmgp/ext
+          - Added external directories as required by git-submodule, which git-fleximod is built upon
+
+List all existing files that have been modified, and describe the changes:
+
+M       .gitignore
+          - Removed unneeded gitignore lines
+
+M       README.md
+          - Updated README to reflect new git-fleximod
+
+M       manage_externals/checkout_externals
+          - Script which tells folks where to find git-fleximod (when they were used to running manage_externals)
+
+M       test/system/TGIT.sh
+          - modified test to include a check for require .gitmodules file
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+Most tests had the following namelist failures:
+  -----
+Comparison failed between '/glade/derecho/scratch/cacraig/aux_cam_20240606135848/SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s_nochem.GC.aux_cam_20240606135848/CaseDocs/nuopc.runconfig' with '/glade/campaign/cesm/community/amwg/cam_baselines/cam6_3_161/SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s_nochem/CaseDocs/nuopc.runconfig'
+DRIVER_attributes->PELAYOUT_attributes->ALLCOMP_attributes:
+ocn2glc_levels as key not in /glade/derecho/scratch/cacraig/aux_cam_20240606135848/SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s_nochem.GC.aux_cam_20240606135848/CaseDocs/nuopc.runconfig
+  -----
+
+derecho/intel/aux_cam:
+
+  SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+  ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+       - pre-existing failure due to HEMCO not having reproducible results
+
+  ERP_Lh12.f19_f19_mg17.FW4madSD.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+    FAIL ERP_Lh12.f19_f19_mg17.FW4madSD.derecho_intel.cam-outfrq3h BASELINE /glade/campaign/cesm/community/amwg/cam_baselines/cam6_3_161: ERROR BFAIL some baseline files were missing
+       - This test did not run in previous tag due to CTSM tag failure.  Is now running, but no baseline to compare against
+
+  ERP_Ln9.ne30_ne30_mg17.FCnudged.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+    FAIL ERP_Ln9.ne30_ne30_mg17.FCnudged.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD failed to initialize
+  SMS_D_Ln9.ne16_ne16_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: PEND) details:
+    PEND SMS_D_Ln9.ne16_ne16_mg17.FX2000.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD
+  SMS_D_Ln9_P1280x1.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.FHIST.derecho_intel.cam-outfrq9s (Overall: PEND) details:
+    PEND SMS_D_Ln9_P1280x1.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.FHIST.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD
+  SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: PEND) details:
+    PEND SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s SHAREDLIB_BUILD
+       - These transient grids are no longer supported by CTSM - will update tests in future PR
+
+  SMS_D_Ln9.T42_T42.FSCAM.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+    FAIL SMS_D_Ln9.T42_T42.FSCAM.derecho_intel.cam-outfrq9s RUN time=43
+       - Bug in med.F90 - Will go away when CICE external is updated post git-fleximod
+
+  SMS_Lm13.f10_f10_mg37.F2000climo.derecho_intel.cam-outfrq1m (Overall: DIFF) details:
+    FAIL SMS_Lm13.f10_f10_mg37.F2000climo.derecho_intel.cam-outfrq1m BASELINE
+/glade/campaign/cesm/community/amwg/cam_baselines/cam6_3_161: FIELDLIST field lists differ (otherwise bit-for-bit)
+       - cice history file has attributes that changed with this run
+
+izumi/nag/aux_cam:
+  DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+     - pre-existing failure
+
+izumi/gnu/aux_cam:
+  SMS_P48x1_D_Ln9.f19_f19_mg17.FW4madSD.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+      FAIL SMS_P48x1_D_Ln9.f19_f19_mg17.FW4madSD.izumi_gnu.cam-outfrq9s BASELINE /fs/cgd/csm/models/atm/cam/pretag_bl/cam6_3_161_gnu: ERROR BFAIL some baseline files were missing
+     - This test did not run in previous tag due to CTSM tag failure.  Is now running, but no baseline to compare against
+
+===============================================================
+===============================================================
+
 Tag name: cam6_3_161
 Originator(s): cacraig
 Date: May 16, 2024

From d1e19d4ef7d72b34cdf20c834147abc7690d6ff4 Mon Sep 17 00:00:00 2001
From: "G. Dylan Dickerson" <gdicker@ucar.edu>
Date: Tue, 20 Aug 2024 17:14:12 -0600
Subject: [PATCH 161/161] Keep v7.3 MPAS-A for EarthWorks

This is to ensure there's no conflicts with other MPAS components (esp.
in the framework) and to allow for easier integration when MPAS-A
OpenACC is added again.
---
 .gitmodules              | 2 +-
 src/dynamics/mpas/dycore | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 77e9c2fc56..a0cb5ea697 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -80,7 +80,7 @@
 	url = https://github.com/MPAS-Dev/MPAS-Model.git
         fxrequired = AlwaysRequired
         fxsparse = ../.mpas_sparse_checkout
-        fxtag = b8c33daa
+        fxtag = ff76a231
 	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 
 [submodule "cosp2"]
diff --git a/src/dynamics/mpas/dycore b/src/dynamics/mpas/dycore
index b8c33daa4b..ff76a231dd 160000
--- a/src/dynamics/mpas/dycore
+++ b/src/dynamics/mpas/dycore
@@ -1 +1 @@
-Subproject commit b8c33daa4b124f116b0ba1b1386968c4c15b42e4
+Subproject commit ff76a231ddf6bfd3bdb878afb02821c70ba1a856