[uwtools_integration] A handful of housekeeping items (#269)

Includes:

* A change in the Rocoto YAMLS to use && to link commands together.
* Added documentation to the default_config.yaml.
* Updates to machine YAMLs so we might expect the same behavior on all machines.
* An update for the latest uwtools UPP config (using control_file task).
* Linted and applied black to the whole scripts directory (ignoring a couple of out-of-scope files with pylint disable tags)
* Turned on GH actions for this branch to keep our files linted.
* Removed files and default variables that are no longer used.

.github/workflows/python_tests.yaml

@@ -4,6 +4,7 @@ on:
     branches:
       - develop
       - 'release/*'
+      - uwtools_integration
   pull_request:
     branches:
       - develop
@@ -43,6 +44,7 @@ jobs:
           pylint ush/generate_FV3LAM_wflow.py
           pylint ush/set_fv3nml*.py
           pylint ush/update_input_nml.py
+          pylint scripts/*.py
 
       - name: Run python unittests
         run: |

parm/wflow/coldstart.yaml

@@ -104,7 +104,7 @@ metatask_run_ensemble:
     <<: *default_task
     command: 
       cyclestr:
-        value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} ; &SCRIPTSdir;/chgres_cube.py
+        value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} && &SCRIPTSdir;/chgres_cube.py
           -c &GLOBAL_VAR_DEFNS_FP;
           --cycle @Y-@m-@dT@H:@M:@S
           --key-path task_make_ics
@@ -155,7 +155,7 @@ metatask_run_ensemble:
     <<: *default_task
     command: 
       cyclestr:
-        value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} ; &SCRIPTSdir;/chgres_cube.py
+        value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} && &SCRIPTSdir;/chgres_cube.py
           -c &GLOBAL_VAR_DEFNS_FP;
           --cycle @Y-@m-@dT@H:@M:@S
           --key-path task_make_lbcs

parm/wflow/post.yaml

@@ -12,7 +12,7 @@ metatask_run_ens_post:
         maxtries: '2'
       command:
         cyclestr:
-          value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE  }} ; &SCRIPTSdir;/upp.py
+          value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE  }} && &SCRIPTSdir;/upp.py
             -c &GLOBAL_VAR_DEFNS_FP;
             --cycle @Y-@m-@dT@H:@M:@S
             --leadtime #fhr#:00:00

parm/wflow/prep.yaml

@@ -28,7 +28,7 @@ task_make_grid:
 
 task_make_orog:
   <<: *default_task
-  command: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} ; &SCRIPTSdir;/make_orog.py
+  command: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} && &SCRIPTSdir;/make_orog.py
     -c &GLOBAL_VAR_DEFNS_FP;
     --key-path task_make_orog'
   join:
@@ -52,7 +52,7 @@ task_make_orog:
 
 task_make_sfc_climo:
   <<: *default_task
-  command: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }}; &SCRIPTSdir;/make_sfc_climo.py
+  command: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} && &SCRIPTSdir;/make_sfc_climo.py
     -c &GLOBAL_VAR_DEFNS_FP;
     --key-path task_make_sfc_climo'
   join:

scripts/exregional_integration_test.py

@@ -1,56 +1,61 @@
 #!/usr/bin/env python3
 
-################################################################################
-####  Python Script Documentation Block
-#
-# Script name:       	exregional_integration_test.py
-# Script description:  	Ensures the correct number of netcdf files are generated
-# 			for each experiment
-#
-# Author:  Eddie Snyder 	Org: NOAA EPIC		Date: 2024-02-05
-#
-# Instructions:		1. Pass the appropriate info for the required arguments:
-#                              --fcst_dir=/path/to/forecast/files
-#                              --fcst_len=<forecast length as Int>
-#                       2. Run script with arguments
-#
-# Notes/future work:    - Currently SRW App only accepts netcdf as the UFS WM 
-#                         output file format. If that changes, then additional
-#                         logic is needed to address the other file formats.
-#                       - SRW App doesn't have a variable that updates the 
-#                         forecast increment. The UFS WM does with the 
-#                         output_fh variable, which can be found in the 
-#                         model_configure file. If it becomes available with 
-#                         the SRW App, then logic is needed to account for the 
-#                         forecast increment variable.
-#
-################################################################################
+"""
+Python Script Documentation Block
+
+ Script name:       	exregional_integration_test.py
+ Script description:  	Ensures the correct number of netcdf files are generated
+ 			for each experiment
+
+ Author:  Eddie Snyder 	Org: NOAA EPIC		Date: 2024-02-05
+
+ Instructions:		1. Pass the appropriate info for the required arguments:
+                              --fcst_dir=/path/to/forecast/files
+                              --fcst_len=<forecast length as Int>
+                       2. Run script with arguments
+
+ Notes/future work:    - Currently SRW App only accepts netcdf as the UFS WM
+                         output file format. If that changes, then additional
+                         logic is needed to address the other file formats.
+                       - SRW App doesn't have a variable that updates the
+                         forecast increment. The UFS WM does with the
+                         output_fh variable, which can be found in the
+                         model_configure file. If it becomes available with
+                         the SRW App, then logic is needed to account for the
+                         forecast increment variable.
+
+"""
 
 # -------------Import modules --------------------------#
-import os
-import sys
-import logging
 import argparse
+import logging
+import sys
 import unittest
+from pathlib import Path
 
 # --------------Define some functions ------------------#
 
 
 class TestExptFiles(unittest.TestCase):
-    fcst_dir = ''
-    filename_list = ''
+    """
+    Set up the test for expected output files.
+    """
+
+    fcst_dir = ""
+    filename_list = ""
 
     def test_fcst_files(self):
-
+        """
+        Test that expected files exist.
+        """
         for filename in self.filename_list:
-            filename_fp = "{0}/{1}".format(self.fcst_dir, filename)
+            filename_fp = self.fcst_dir / filename
+            logging.info(f"Checking existence of: {str(filename_fp)}")
+            err_msg = f"Missing file: {str(filename_fp)}"
+            self.assertTrue(filename_fp.exists(), err_msg)
 
-            logging.info("Checking existence of: {0}".format(filename_fp))
-            err_msg = "Missing file: {0}".format(filename_fp)
-            self.assertTrue(os.path.exists(filename_fp), err_msg)
 
 def setup_logging(debug=False):
-
     """Calls initialization functions for logging package, and sets the
     user-defined level for logging in the script."""
 
@@ -71,11 +76,13 @@ def setup_logging(debug=False):
         "--fcst_dir",
         help="Directory to forecast files.",
         required=True,
+        type=Path,
     )
     parser.add_argument(
         "--fcst_len",
         help="Forecast length.",
         required=True,
+        type=int,
     )
     parser.add_argument(
         "--fcst_inc",
@@ -89,46 +96,39 @@ def setup_logging(debug=False):
         help="Print debug messages.",
         required=False,
     )
-    parser.add_argument('unittest_args', nargs='*')
+    parser.add_argument("unittest_args", nargs="*")
     args = parser.parse_args()
     sys.argv[1:] = args.unittest_args
-
-    fcst_dir = str(args.fcst_dir) 
-    fcst_len = int(args.fcst_len)
-    fcst_inc = int(args.fcst_inc)
 
     # Start logger
     setup_logging()
 
     # Check if model_configure exists
-    model_configure_fp = "{0}/model_configure".format(fcst_dir)
+    MODEL_CONFIGURE_FP = args.fcst_dir / "model_configure"
 
-    if not os.path.isfile(model_configure_fp):
-        logging.error("Experiments model_configure file is missing! Exiting!")
+    if not MODEL_CONFIGURE_FP.is_file():
+        logging.error("Experiment's model_configure file is missing! Exiting!")
         sys.exit(1)
 
     # Loop through model_configure file to find the netcdf base names
-    f = open(model_configure_fp, 'r')
-
-    for line in f:
-        if line.startswith("filename_base"):
-            filename_base_1 = line.split("'")[1]
-            filename_base_2 = line.split("'")[3]
-            break
-    f.close()
+    with open(MODEL_CONFIGURE_FP, "r", encoding="utf-8") as f:
+        for line in f:
+            if line.startswith("filename_base"):
+                filename_base_1 = line.split("'")[1]
+                filename_base_2 = line.split("'")[3]
+                break
 
     # Create list of expected filenames from the experiment
-    fcst_len = fcst_len + 1
     filename_list = []
 
-    for x in range(0, fcst_len, fcst_inc):
+    for x in range(0, args.fcst_len + 1, args.fcst_inc):
         fhour = str(x).zfill(3)
-        filename_1 = "{0}f{1}.nc".format(filename_base_1, fhour)
-        filename_2 = "{0}f{1}.nc".format(filename_base_2, fhour)
+        filename_1 = f"{filename_base_1}f{fhour}.nc"
+        filename_2 = f"{filename_base_2}f{fhour}.nc"
         filename_list.append(filename_1)
         filename_list.append(filename_2)
 
-    # Call unittest class 
-    TestExptFiles.fcst_dir = fcst_dir
+    # Call unittest class
+    TestExptFiles.fcst_dir = args.fcst_dir
     TestExptFiles.filename_list = filename_list
     unittest.main()