Feature #511 lists in command line single config overrides (#2815)

* exclude metplus/scripts dir from PyCharm project to prevent incorrect duplicate code warnings with files that are sym linked

* to expand on #2772, updating instructions to include note to set tmp directory for apptainer to prevent issues pulling large images that require a lot of temp space

* per #511, add unit test for expected behavior to support comma-separated lists in a command line single config override that should fail until fix is made

* add a test to ensure that the -c argument is properly ignored since it is can be used in old use cases that were created when the argument was required

* per #511, add support for command line single config overrides to include values that are lists. Simplify logic to parse arguments to strip out -c/--config/-config arguments and skip check/error if argument is invalid because it is already handled in the metplus_config setup step that parses the arguments

* added unit test to ensure that an invalid command line argument causes the appropriate failure from run_metplus.py

docs/Users_Guide/getting_started.rst

@@ -463,10 +463,22 @@ METplus in Apptainer
 Apptainer (formerly Singularity) can also be used to run METplus.
 Images can be pulled from DockerHub using Apptainer commands.
 
-If running on the NCAR Casper cluster, be sure to first load the Apptainer module via::
+If running on the NCAR Casper cluster,
+be sure to first load the Apptainer module via::
 
     module load apptainer
 
+It is recommended to set the **APPTAINER_TMPDIR** environment variable to a
+directory where the user has write permissions to prevent issues with temporary
+files exceeding the size of the /tmp directory.
+See the
+`Apptainer documentation <https://apptainer.org/docs/user/1.0/build_env.html#temporary-folders>`_
+for more information.
+
+Example::
+
+    export APPTAINER_TMP_DIR=/d1/${USER}/apptainer_tmp
+
 Navigate to a working directory and pull an image from DockerHub, e.g.::
 
     apptainer pull docker://dtcenter/metplus:5.1-latest

internal/tests/pytests/run_metplus/test_run_metplus.py

@@ -20,6 +20,12 @@
 NEW_OUTPUT_BASE = os.path.join(TEST_OUTPUT_DIR, 'run_metplus')
 OUTPUT_BASE_OVERRIDE = f"config.OUTPUT_BASE={NEW_OUTPUT_BASE}"
 
+# test that a list of values specified in a command line config override
+# will no longer cause an error in the run. The list can be specified without
+# quotes if no spaces are present or with quotes if spaces are present
+LIST_CONFIG_OVERRIDE_1 = 'config.LEAD_SEQ=3H,6H'
+LIST_CONFIG_OVERRIDE_2 = 'config.LEAD_SEQ="3H, 6H"'
+
 @pytest.mark.run_metplus
 def test_run_metplus_exists():
     """! Check that run_metplus.py script exists """
@@ -31,6 +37,10 @@ def test_run_metplus_exists():
         ([RUN_METPLUS], 2),
         ([RUN_METPLUS, EXAMPLE_CONF], 2),
         ([RUN_METPLUS, EXAMPLE_CONF, MINIMUM_CONF, OUTPUT_BASE_OVERRIDE], 0),
+        ([RUN_METPLUS, '-c', EXAMPLE_CONF, MINIMUM_CONF, OUTPUT_BASE_OVERRIDE], 0),
+        ([RUN_METPLUS, EXAMPLE_CONF, MINIMUM_CONF, LIST_CONFIG_OVERRIDE_1], 0),
+        ([RUN_METPLUS, EXAMPLE_CONF, MINIMUM_CONF, LIST_CONFIG_OVERRIDE_2], 0),
+        ([RUN_METPLUS, EXAMPLE_CONF, MINIMUM_CONF, '--fake-arg'], 1),
     ]
 )
 @pytest.mark.run_metplus

ush/run_metplus.py

@@ -78,24 +78,9 @@ def get_config_inputs_from_command_line():
     if any(arg in sys.argv for arg in help_args):
         usage()
 
-    # pull out command line arguments
-    config_inputs = []
-    for arg in sys.argv[1:]:
-        if arg.startswith('-'):
-            # ignore -c and --config since they are now optional
-            if arg == '-c' or arg == '--config' or arg == '-config':
-                continue
-
-            # error/exit if an argument that is not supported was used
-            print('ERROR: Invalid argument: %s.' % arg)
-            usage()
-
-        # split up comma separated lists into individual items
-        # and add each to list of arguments
-        # NOTE: to support lists in a config variable override,
-        # this logic will have to be enhanced
-        # i.e. config.PROCESS_LIST=PCPCombine,GridStat
-        config_inputs.extend(arg.split(','))
+    # pull out command line arguments, removing deprecated config arguments
+    config_args = ('-c', '--config', '-config')
+    config_inputs = [arg for arg in sys.argv[1:] if arg not in config_args]
 
     # if no valid config_inputs were found, print usage and exit
     if not config_inputs: