Fix seas val (#307)

* Fix error in seasonal metrics calculator adapter when an empty time series is used * Update changes * Update CI * update env * Update setup.cfg * Update meta packag * Fix docs * Update meta packag * Fix C ext * Update CI * Update CI * Update CI * Rebuild .c ext * Update changelog
TUW-GEO · Jun 15, 2024 · 97d7a46 · 97d7a46
1 parent 0e3cbb0
commit 97d7a46
Show file tree

Hide file tree

Showing 23 changed files with 91,037 additions and 66,661 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,26 +16,28 @@ jobs:
   build:
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10' ]
+        # as we build C extension for users to download, we want to include as many python versions
+        # and OS versions as possible (especially windows to create .whl packages,
+        # see step "Create wheel and dist package")
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: ["ubuntu-latest", "windows-latest"]
-        ymlfile: ["environment.yml"]
-    name: Py${{ matrix.python-version }}@${{ matrix.os }}🐍
+    name: py${{ matrix.python-version }} @ ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: true # does not work with self-hosted testdata
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: "latest"
-          channel-priority: flexible
-          python-version: ${{ matrix.python-version }}
-          environment-file: ${{ matrix.ymlfile }}
-          activate-environment: pytesmo # todo: must match with name in environment.yml
-          auto-activate-base: false
+           miniconda-version: "latest"
+           auto-update-conda: true
+           python-version: ${{ matrix.python-version }}
+           environment-file: environment.yml
+           activate-environment: pytesmo # todo: must match with name in environment.yml
+           mamba-version: "*"
+           auto-activate-base: false
       - name: Print Infos
         shell: bash -l {0}
         run: |
@@ -45,16 +47,13 @@ jobs:
           pip list
           which pip
           which python
+          gcc -v
       - name: Export Environment
         shell: bash -l {0}
         run: |
           mkdir -p .artifacts
-          # Here we could exclude pinned environments (not used):
-          if [ ${{ matrix.ymlfile }} == "environment.yml" ]
-          then
-              filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
-              conda env export --no-builds | grep -v "prefix" > .artifacts/$filename
-          fi
+          filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
+          conda env export --no-builds | grep -v "prefix" > .artifacts/$filename
       - name: Install package and test
         shell: bash -l {0}
         run: |
@@ -84,9 +83,9 @@ jobs:
           fi
           ls .artifacts/dist
       - name: Upload Artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: Artifacts
+          name: Artifacts-${{ matrix.python-version }}-${{ matrix.os }}
           path: .artifacts/*
   coveralls:
     name: Submit Coveralls 👚
@@ -112,7 +111,11 @@ jobs:
           echo "GITHUB_REF = $GITHUB_REF"
           echo "GITHUB_REPOSITORY = $GITHUB_REPOSITORY"
       - name: Download Artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
+        with:
+          path: Artifacts
+          pattern: Artifacts-*
+          merge-multiple: true
       - name: Display downloaded files
         run: ls -aR
       - name: Upload to PyPI

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
--   repo: https://gitlab.com/pycqa/flake8
+-   repo: https://github.com/PyCQA/flake8
     rev: 3.7.9
     hooks:
     -   id: flake8

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,9 @@ Changelog
 
 Unreleased changes in master
 ============================
+- Fixed an issue with the intra-annual metrics adapter when an empty time series is passed (PR `#307 <https://github.com/TUW-GEO/pytesmo/pull/307>`_)
+- Metapackage updated (pyscaffold 4.5) (PR `#307 <https://github.com/TUW-GEO/pytesmo/pull/307>`_)
+- C modules were outdated and could not be compiled, therefore rebuilt (PR `#307 <https://github.com/TUW-GEO/pytesmo/pull/307>`_)
 
 Version 0.16.0, 2023-09-12
 ==========================

diff --git a/docs/Makefile b/docs/Makefile
@@ -11,7 +11,7 @@ AUTODOCDIR    = api
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
-$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
+$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/")
 endif
 
 .PHONY: help clean Makefile

diff --git a/docs/conf.py b/docs/conf.py
@@ -9,11 +9,9 @@
 
 import os
 import sys
-import inspect
 import shutil
 import subprocess
 
-
 # Create kernel for notebooks
 on_rtd = "READTHEDOCS" in os.environ and os.environ["READTHEDOCS"]
 if on_rtd:
@@ -46,19 +44,17 @@
 
 # -- Path setup --------------------------------------------------------------
 
-__location__ = os.path.join(
-    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
-)
+__location__ = os.path.dirname(__file__)
 
 # 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.
-# sys.path.insert(0, os.path.join(__location__, "../src"))
+sys.path.insert(0, os.path.join(__location__, "../src"))
 
 # -- Run sphinx-apidoc -------------------------------------------------------
 # This hack is necessary since RTD does not issue `sphinx-apidoc` before running
 # `sphinx-build -b html . _build/html`. See Issue:
-# https://github.com/rtfd/readthedocs.org/issues/1139
+# https://github.com/readthedocs/readthedocs.org/issues/1139
 # DON'T FORGET: Check the box "Install your project inside a virtualenv using
 # setup.py install" in the RTD Advanced Settings.
 # Additionally it helps us to avoid running apidoc manually
@@ -78,13 +74,7 @@
 try:
     import sphinx
 
-    cmd_line_template = (
-        "sphinx-apidoc --implicit-namespaces"
-        " -Me -d 3 -f -o {outputdir} {moduledir}"
-    )
-    cmd_line = cmd_line_template.format(
-        outputdir=output_dir, moduledir=module_dir
-    )
+    cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}"
 
     args = cmd_line.split(" ")
     if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
@@ -113,7 +103,7 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
-    "nbsphinx",
+    "nbsphinx"
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -130,16 +120,25 @@
 
 # General information about the project.
 project = "pytesmo"
-copyright = "2021, TU Wien"
+copyright = "2024, TU Wien"
 
 # 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 = ""  # Is set by calling `setup.py docs`
-# The full version, including alpha/beta/rc tags.
-release = ""  # Is set by calling `setup.py docs`
+# version: The short X.Y version.
+# release: The full version, including alpha/beta/rc tags.
+# If you don’t need the separation provided between version and release,
+# just set them both to the same value.
+try:
+    from pytesmo import __version__ as version
+except ImportError:
+    version = ""
+
+if not version or version.lower() == "unknown":
+    version = os.getenv("READTHEDOCS_VERSION", "unknown")  # automatically set by RTD
+
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -178,14 +177,16 @@
 # If true, keep warnings as "system message" paragraphs in the built documents.
 # keep_warnings = False
 
+# If this is True, todo emits a warning for each TODO entries. The default is False.
+todo_emit_warnings = 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 = "sphinx_rtd_theme"
 
-
 # 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.
@@ -198,12 +199,7 @@
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-try:
-    from pytesmo import __version__ as version
-except ImportError:
-    pass
-else:
-    release = version
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None
@@ -307,12 +303,15 @@
 # -- External mapping --------------------------------------------------------
 python_version = ".".join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
-    "sphinx": ("http://www.sphinx-doc.org/en/stable", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master", None),
     "python": ("https://docs.python.org/" + python_version, None),
     "matplotlib": ("https://matplotlib.org", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "setuptools": ("https://setuptools.pypa.io/en/stable/", None),
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
+
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -0,0 +1 @@
+.. include:: ../DEVELOPERS_GUIDE.md