Feature #2188 move PANDA-C cases to clouds category and fix automated…

… tests (#2237) Co-authored-by: j-opatz <[email protected]>
dtcenter · Jul 6, 2023 · 594f583 · 594f583
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diff --git a/.github/jobs/get_use_case_commands.py b/.github/jobs/get_use_case_commands.py
@@ -164,14 +164,24 @@ def main(categories, subset_list, work_dir=None,
             for use_case in use_case_by_requirement.use_cases:
                 # add parm/use_cases path to config args if they are conf files
                 config_args = []
+                ci_overrides = None
                 for config_arg in use_case.config_args:
                     if config_arg.endswith('.conf'):
                         config_arg = os.path.join(work_dir, 'parm',
-                                                  'use_cases',
-                                                  config_arg)
+                                                  'use_cases', config_arg)
+
+                        # look for CI overrides conf file
+                        override_path = os.path.join(config_arg[0:-5],
+                                                     'ci_overrides.conf')
+                        if os.path.exists(override_path):
+                            ci_overrides = override_path
 
                     config_args.append(config_arg)
 
+                # add CI overrides config file if running in docker
+                if ci_overrides and host_name == 'docker':
+                    config_args.append(ci_overrides)
+
                 output_base = os.path.join(output_top_dir,
                                            group_name.split('-')[0],
                                            use_case.name)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
@@ -19,6 +19,36 @@
     "index_list": "0-1",
     "run": false
   },
+  {
+    "category": "clouds",
+    "index_list": "0",
+    "run": false
+  },
+  {
+    "category": "clouds",
+    "index_list": "1",
+    "run": false
+  },
+  {
+    "category": "clouds",
+    "index_list": "2",
+    "run": false
+  },
+  {
+    "category": "clouds",
+    "index_list": "3",
+    "run": false
+  },
+  {
+    "category": "clouds",
+    "index_list": "4",
+    "run": false
+  },
+  {
+    "category": "clouds",
+    "index_list": "5",
+    "run": false
+  },
   {
     "category": "data_assimilation",
     "index_list": "0-1",

diff --git a/docs/Contributors_Guide/add_use_case.rst b/docs/Contributors_Guide/add_use_case.rst
@@ -44,6 +44,7 @@ one of the following:
 
 * air_quality_and_comp
 * climate
+* clouds
 * data_assimilation
 * extremes
 * land_surface
@@ -835,6 +836,43 @@ new job for the new use case. See the :ref:`cg-ci-subset_category` section
 and the multiple medium_range jobs for an example.
 
 
+Overriding configuration for automated tests
+--------------------------------------------
+
+The automated tests have limited resources available to run the use cases.
+Use cases can be adjusted to reduce file size, run time length,
+memory usage, etc. but may still exceed the limits provided by GitHub Actions.
+We also want to avoid losing scientific significance of a use case to allow
+it to run in the automated testing environment.
+
+An additional METplus configuration file can be provided with a use case to
+override certain configuration settings for the automated testing of the case.
+This allows the use case configuration file to contain a useful example that
+can be run on other environments while still allowing a subset of the use case
+to be included in the automated use case tests.
+
+If needed, create a file named **ci_overrides.conf** in the use case directory,
+e.g. parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac/ci_overrides.conf.
+This configuration file will automatically be read **after** the use case
+configuration file when run in the automated testing environment.
+
+For example, if a use case processes many thresholds::
+
+    [config]
+    ...
+    FCST_VAR1_THRESH = gt0, lt10.0, ge10.0, ge20.0, ge30.0, ge40.0, ge50.0, ge60.0, ge70.0, ge80.0, ge90.0
+    ...
+    OBS_VAR1_THRESH = gt0, lt10.0, ge10.0, ge20.0, ge30.0, ge40.0, ge50.0, ge60.0, ge70.0, ge80.0, ge90.0
+    ...
+
+then one can override these variables so that fewer threshold values are
+processed in the automated tests. In **ci_overrides.conf**, set::
+
+    [config]
+    FCST_VAR1_THRESH = gt0, lt10.0
+    OBS_VAR1_THRESH = gt0, lt10.0
+
+
 .. _exceeded-Github-Actions:
 
 Use Cases That Exceed Memory Allocations of Github Actions
@@ -853,7 +891,7 @@ steps were unsuccessful in lowering memory usage, please take the following step
   Change the number in front of the new use case to an 'X', preceded 
   by the ‘#’ character::
 
-	#X::GridStat_fcstRTOFS_obsGHRSST_climWOA_sst::model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf, model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst/ci_overrides.conf:: icecover_env, py_embed
+	#X::GridStat_fcstRTOFS_obsGHRSST_climWOA_sst::model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf:: icecover_env, py_embed
 
 - In the *.github/parm/use_case_groups.json* file, remove the entry that 
   was added during the :ref:`add_new_category_to_test_runs` 

diff --git a/docs/Users_Guide/quicksearch.rst b/docs/Users_Guide/quicksearch.rst
@@ -74,6 +74,7 @@ Use Cases by Application:
 
    | `Air Quality and Composition <../search.html?q=AirQualityAndCompAppUseCase&check_keywords=yes&area=default>`_
    | `Climate <../search.html?q=ClimateAppUseCase&check_keywords=yes&area=default>`_
+   | `Clouds <../search.html?q=CloudsAppUseCase&check_keywords=yes&area=default>`_
    | `Short Range <../search.html?q=ShortRangeAppUseCase&check_keywords=yes&area=default>`_
    | `Data Assimilation  <../search.html?q=DataAssimilationAppUseCase&check_keywords=yes&area=default>`_
    | `Ensemble  <../search.html?q=EnsembleAppUseCase&check_keywords=yes&area=default>`_
@@ -91,6 +92,7 @@ Use Cases by Application:
 
    | **Air Quality and Composition**: *AirQualityAndCompAppUseCase*
    | **Climate**: *ClimateAppUseCase*
+   | **Clouds**: *CloudsAppUseCase*
    | **Short Range**: *ShortRangeAppUseCase*
    | **Data Assimilation**: *DataAssimilationAppUseCase*
    | **Ensemble**: *EnsembleAppUseCase*

diff --git a/...t_fcstGFS_obsERA5_lowAndTotalCloudFrac.py → ...t_fcstGFS_obsERA5_lowAndTotalCloudFrac.py b/...t_fcstGFS_obsERA5_lowAndTotalCloudFrac.py → ...t_fcstGFS_obsERA5_lowAndTotalCloudFrac.py
@@ -2,7 +2,7 @@
 GridStat: Cloud Fractions with Neighborhood and Probabilities
 =============================================================
 
-model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf
+model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf
 
 """
 ##############################################################################
@@ -57,10 +57,10 @@
 #
 # METplus first loads the default configuration file found in parm/metplus_config,
 # then it loads any configuration files passed to METplus via the command line:
-# parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf
+# parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf
 
 ##############################################################################
 # MET Configuration
@@ -84,10 +84,10 @@
 # ----------------
 #
 # This use case utilizes 1 Python script to read and process the observation fields.
-# parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac/read_input_data.py
+# parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac/read_input_data.py
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac/read_input_data.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac/read_input_data.py
 
 ##############################################################################
 # Running METplus
@@ -96,7 +96,7 @@
 # Pass the use case configuration file to the run_metplus.py script
 # along with any user-specific system configuration files if desired::
 #
-#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf /path/to/user_system.conf
+#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf /path/to/user_system.conf
 #
 # See :ref:`running-metplus` for more information.
 
@@ -109,7 +109,7 @@
 #   INFO: METplus has successfully finished running.
 #
 # Refer to the value set for **OUTPUT_BASE** to find where the output data was generated.
-# Output for this use case will be found in model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac
+# Output for this use case will be found in model_applications/clouds/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac
 # (relative to **OUTPUT_BASE**)
 # and will contain the following files:
 #
@@ -129,10 +129,10 @@
 #
 #   * GridStatToolUseCase
 #   * NetCDFFileUseCase
-#   * AirQualityAndCompAppUseCase
+#   * CloudsAppUseCase
 #   * PythonEmbeddingFileUseCase
 #
 #   Navigate to the :ref:`quick-search` page to discover other similar use cases.
 #
-# sphinx_gallery_thumbnail_path = '_static/air_quality_and_comp-GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.png'
+# sphinx_gallery_thumbnail_path = '_static/clouds-GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.png'
 #
diff --git a/...fcstGFS_obsMERRA2_lowAndTotalCloudFrac.py → ...fcstGFS_obsMERRA2_lowAndTotalCloudFrac.py b/...fcstGFS_obsMERRA2_lowAndTotalCloudFrac.py → ...fcstGFS_obsMERRA2_lowAndTotalCloudFrac.py
@@ -2,7 +2,7 @@
 GridStat: Cloud Fractions with Neighborhood and Probabilities
 =============================================================
 
-model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf
+model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf
 
 """
 ##############################################################################
@@ -57,10 +57,10 @@
 #
 # METplus first loads the default configuration file found in parm/metplus_config,
 # then it loads any configuration files passed to METplus via the command line:
-# parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf
+# parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf
 
 ##############################################################################
 # MET Configuration
@@ -85,10 +85,10 @@
 #
 # This use case utilizes 1 Python script to read and process both forecast and
 # observation fields.
-# parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac/read_input_data.py
+# parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac/read_input_data.py
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac/read_input_data.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac/read_input_data.py
 
 ##############################################################################
 # Running METplus
@@ -97,7 +97,7 @@
 # Pass the use case configuration file to the run_metplus.py script
 # along with any user-specific system configuration files if desired::
 #
-#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf /path/to/user_system.conf
+#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf /path/to/user_system.conf
 #
 # See :ref:`running-metplus` for more information.
 
@@ -110,7 +110,7 @@
 #   INFO: METplus has successfully finished running.
 #
 # Refer to the value set for **OUTPUT_BASE** to find where the output data was generated.
-# Output for this use case will be found in model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac
+# Output for this use case will be found in model_applications/clouds/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac
 # (relative to **OUTPUT_BASE**)
 # and will contain the following files:
 #
@@ -129,10 +129,10 @@
 #
 #   * GridStatToolUseCase
 #   * NetCDFFileUseCase
-#   * AirQualityAndCompAppUseCase
+#   * CloudsAppUseCase
 #   * PythonEmbeddingFileUseCase
 #
 #   Navigate to the :ref:`quick-search` page to discover other similar use cases.
 #
-# sphinx_gallery_thumbnail_path = '_static/air_quality_and_comp-GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.png'
+# sphinx_gallery_thumbnail_path = '_static/clouds-GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.png'
 #
diff --git a/...stGFS_obsSATCORPS_cloudTopPressAndTemp.py → ...stGFS_obsSATCORPS_cloudTopPressAndTemp.py b/...stGFS_obsSATCORPS_cloudTopPressAndTemp.py → ...stGFS_obsSATCORPS_cloudTopPressAndTemp.py
@@ -2,7 +2,7 @@
 GridStat: Cloud Pressure and Temperature Heights
 ================================================
 
-model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf
+model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf
 
 """
 ##############################################################################
@@ -57,10 +57,10 @@
 #
 # METplus first loads the default configuration file found in parm/metplus_config,
 # then it loads any configuration files passed to METplus via the command line:
-# parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf
+# parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf
 
 ##############################################################################
 # MET Configuration
@@ -84,10 +84,10 @@
 # ----------------
 #
 # This use case utilizes 1 Python script to read and process the observation fields.
-# parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp/read_input_data.py
+# parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp/read_input_data.py
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp/read_input_data.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp/read_input_data.py
 
 ##############################################################################
 # Running METplus
@@ -96,7 +96,7 @@
 # Pass the use case configuration file to the run_metplus.py script
 # along with any user-specific system configuration files if desired::
 #
-#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf /path/to/user_system.conf
+#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf /path/to/user_system.conf
 #
 # See :ref:`running-metplus` for more information.
 
@@ -109,7 +109,7 @@
 #   INFO: METplus has successfully finished running.
 #
 # Refer to the value set for **OUTPUT_BASE** to find where the output data was generated.
-# Output for this use case will be found in model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp
+# Output for this use case will be found in model_applications/clouds/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp
 # (relative to **OUTPUT_BASE**)
 # and will contain the following files:
 #
@@ -128,10 +128,10 @@
 #
 #   * GridStatToolUseCase
 #   * NetCDFFileUseCase
-#   * AirQualityAndCompAppUseCase
+#   * CloudsAppUseCase
 #   * PythonEmbeddingFileUseCase
 #
 #   Navigate to the :ref:`quick-search` page to discover other similar use cases.
 #
-# sphinx_gallery_thumbnail_path = '_static/air_quality_and_comp-GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.png'
+# sphinx_gallery_thumbnail_path = '_static/clouds-GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.png'
 #