Update develop-ref after #2206, #2236, #2237 (#2238)

Co-authored-by: johnhg <johnhg@ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@ucar.edu> Co-authored-by: cristianastan2 <cstan@gmu.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: bikegeek <minnawin@ucar.edu> Co-authored-by: Lisa Goodrich <lisag@ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: Hank Fisher <fisherh@ucar.edu> Co-authored-by: Dan Adriaansen <dadriaan@ucar.edu> Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Tracy Hertneky <hertneky@seneca.rap.ucar.edu> Co-authored-by: Giovanni Rosa <giovanni.rosa@unimol.it> Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com> Co-authored-by: Mrinal Biswas <biswas@seneca.rap.ucar.edu> Co-authored-by: j-opatz <jopatz@ucar.edu> Co-authored-by: Daniel Adriaansen <dadriaan@ucar.edu> Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com> Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: metplus-bot <97135045+metplus-bot@users.noreply.github.com> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Giovanni Rosa <g.rosa1@studenti.unimol.it> Co-authored-by: mrinalbiswas <biswas@ucar.edu> Co-authored-by: Christina Kalb <kalb@ucar.edu> Co-authored-by: jason-english <73247785+jason-english@users.noreply.github.com> fix Contributor's Guide GitHub Workflow page (#1774) fix release (#1790) fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200) fix diff tests (#2217) fix automated tests (#2237) fix #2235 rename multivar_itensity to multivar_intensity_flag (#2236)
dtcenter · Jul 6, 2023 · b3f5cf3 · b3f5cf3
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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/jobs/run_difference_tests.sh b/.github/jobs/run_difference_tests.sh
@@ -12,6 +12,7 @@ matrix_categories=$1
 artifact_name=$2
 
 .github/jobs/setup_and_run_diff.py ${matrix_categories} $artifact_name
+ret=$?
 
 if [ "$( ls -A ${RUNNER_WORKSPACE}/diff)" ]; then
   echo "upload_diff=true" >> $GITHUB_OUTPUT
@@ -21,3 +22,4 @@ if [ "$( ls -A ${RUNNER_WORKSPACE}/diff)" ]; then
 fi
 
 echo "upload_diff=false" >> $GITHUB_OUTPUT
+exit $ret
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",
@@ -89,6 +119,11 @@
     "index_list": "9",
     "run": false
   },
+  {
+    "category": "pbl",
+    "index_list": "0",
+    "run": false
+  },
   {
     "category": "precipitation",
     "index_list": "0",
@@ -137,7 +172,7 @@
   {
     "category": "s2s",
     "index_list": "3",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",

diff --git a/.gitignore b/.gitignore
@@ -88,6 +88,8 @@ ENV/
 # pytest cache files
 *.pytest_cache*
 
+.idea
+
 # tilda files generated by emacs
 *~
 

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/glossary.rst b/docs/Users_Guide/glossary.rst
@@ -10661,8 +10661,8 @@ METplus Configuration Glossary
 
      | *Used by:* TCDiag
 
-   MODE_MULTIVAR_INTENSITY
-     Specify the value for 'multivar_intensity' in the MET configuration file for MODE.
+   MODE_MULTIVAR_INTENSITY_FLAG
+     Specify the value for 'multivar_intensity_flag' in the MET configuration file for MODE.
 
      | *Used by:* MODE
 
@@ -10671,8 +10671,8 @@ METplus Configuration Glossary
 
      | *Used by:* MODE
 
-   MODE_FCST_MULTIVAR_UNITS
-     Specify the value for 'fcst.multivar_units' in the MET configuration file for MODE.
+   MODE_FCST_MULTIVAR_LEVEL
+     Specify the value for 'fcst.multivar_level' in the MET configuration file for MODE.
 
      | *Used by:* MODE
 
@@ -10681,7 +10681,7 @@ METplus Configuration Glossary
 
      | *Used by:* MODE
 
-   MODE_OBS_MULTIVAR_UNITS
-     Specify the value for 'obs.multivar_units' in the MET configuration file for MODE.
+   MODE_OBS_MULTIVAR_LEVEL
+     Specify the value for 'obs.multivar_level' in the MET configuration file for MODE.
 
      | *Used by:* MODE
diff --git a/docs/Users_Guide/quicksearch.rst b/docs/Users_Guide/quicksearch.rst
@@ -74,12 +74,14 @@ 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>`_
    | `Land Surface <../search.html?q=LandSurfaceAppUseCase&check_keywords=yes&area=default>`_
    | `Marine and Cryosphere <../search.html?q=MarineAndCryosphereAppUseCase&check_keywords=yes&area=default>`_
    | `Medium Range <../search.html?q=MediumRangeAppUseCase&check_keywords=yes&area=default>`_
+   | `PBL <../search.html?q=PBLAppUseCase&check_keywords=yes&area=default>`_
    | `Precipitation <../search.html?q=PrecipitationAppUseCase&check_keywords=yes&area=default>`_
    | `Space Weather <../search.html?q=SpaceWeatherAppUseCase&check_keywords=yes&area=default>`_
    | `Subseasonal to Seasonal <../search.html?q=S2SAppUseCase&check_keywords=yes&area=default>`_
@@ -91,12 +93,14 @@ Use Cases by Application:
 
    | **Air Quality and Composition**: *AirQualityAndCompAppUseCase*
    | **Climate**: *ClimateAppUseCase*
+   | **Clouds**: *CloudsAppUseCase*
    | **Short Range**: *ShortRangeAppUseCase*
    | **Data Assimilation**: *DataAssimilationAppUseCase*
    | **Ensemble**: *EnsembleAppUseCase*
    | **LandSurface**: *LandSurfaceAppUseCase*
    | **Marine and Cryosphere**: *MarineAndCryosphereAppUseCase*
    | **Medium Range**: *MediumRangeAppUseCase*
+   | **PBL**: *PBLAppUseCase*
    | **Precipitation**: *PrecipitationAppUseCase*
    | **Space Weather**: *SpaceWeatherAppUseCase*
    | **Subseasonal to Seasonal**: *S2SAppUseCase*

diff --git a/docs/Users_Guide/release-notes.rst b/docs/Users_Guide/release-notes.rst
@@ -30,6 +30,14 @@ When applicable, release notes are followed by the
 `GitHub issue <https://github.com/dtcenter/METplus/issues>`__ number which
 describes the bugfix, enhancement, or new feature.
 
+METplus Version 5.1.0-rc2 Release Notes (2023-06-29)
+----------------------------------------------------
+
+  .. dropdown:: Bugfix
+
+     * Fix produtil bug for WCOSS
+       (`#2227 <https://github.com/dtcenter/METplus/issues/2227>`_)
+
 METplus Version 5.1.0-rc1 Release Notes (2023-06-07)
 ----------------------------------------------------
 

diff --git a/docs/Users_Guide/wrappers.rst b/docs/Users_Guide/wrappers.rst
@@ -4055,21 +4055,21 @@ METplus Configuration
 | :term:`FCST_MODE_IS_PROB`
 | :term:`FCST_MODE_PROB_IN_GRIB_PDS`
 | :term:`MODE_MULTIVAR_LOGIC`
-| :term:`MODE_MULTIVAR_INTENSITY`
+| :term:`MODE_MULTIVAR_INTENSITY_FLAG`
 | :term:`FCST_MODE_VAR<n>_NAME`
 | :term:`FCST_MODE_VAR<n>_LEVELS`
 | :term:`FCST_MODE_VAR<n>_THRESH`
 | :term:`FCST_MODE_VAR<n>_OPTIONS`
 | :term:`MODE_FCST_FILE_TYPE`
 | :term:`MODE_FCST_MULTIVAR_NAME`
-| :term:`MODE_FCST_MULTIVAR_UNITS`
+| :term:`MODE_FCST_MULTIVAR_LEVEL`
 | :term:`OBS_MODE_VAR<n>_NAME`
 | :term:`OBS_MODE_VAR<n>_LEVELS`
 | :term:`OBS_MODE_VAR<n>_THRESH`
 | :term:`OBS_MODE_VAR<n>_OPTIONS`
 | :term:`MODE_OBS_FILE_TYPE`
 | :term:`MODE_OBS_MULTIVAR_NAME`
-| :term:`MODE_OBS_MULTIVAR_UNITS`
+| :term:`MODE_OBS_MULTIVAR_LEVEL`
 |
 
 .. warning:: **DEPRECATED:**
@@ -4189,16 +4189,16 @@ see :ref:`How METplus controls MET config file settings<metplus-control-met>`.
    * - :term:`MODE_MULTIVAR_LOGIC`
      - multivar_logic
 
-**${METPLUS_MULTIVAR_INTENSITY}**
+**${METPLUS_MULTIVAR_INTENSITY_FLAG}**
 
 .. list-table::
    :widths: 5 5
    :header-rows: 0
 
    * - METplus Config(s)
      - MET Config File
-   * - :term:`MODE_MULTIVAR_INTENSITY`
-     - multivar_intensity
+   * - :term:`MODE_MULTIVAR_INTENSITY_FLAG`
+     - multivar_intensity_flag
 
 **${METPLUS_FCST_FIELD}**
 
@@ -4285,16 +4285,16 @@ see :ref:`How METplus controls MET config file settings<metplus-control-met>`.
    * - :term:`MODE_FCST_MULTIVAR_NAME`
      - fcst.multivar_name
 
-**${METPLUS_FCST_MULTIVAR_UNITS}**
+**${METPLUS_FCST_MULTIVAR_LEVEL}**
 
 .. list-table::
    :widths: 5 5
    :header-rows: 0
 
    * - METplus Config(s)
      - MET Config File
-   * - :term:`MODE_FCST_MULTIVAR_UNITS`
-     - fcst.multivar_units
+   * - :term:`MODE_FCST_MULTIVAR_LEVEL`
+     - fcst.multivar_level
 
 
 **${METPLUS_OBS_FIELD}**
@@ -4382,16 +4382,16 @@ see :ref:`How METplus controls MET config file settings<metplus-control-met>`.
    * - :term:`MODE_OBS_MULTIVAR_NAME`
      - obs.multivar_name
 
-**${METPLUS_OBS_MULTIVAR_UNITS}**
+**${METPLUS_OBS_MULTIVAR_LEVEL}**
 
 .. list-table::
    :widths: 5 5
    :header-rows: 0
 
    * - METplus Config(s)
      - MET Config File
-   * - :term:`MODE_OBS_MULTIVAR_UNITS`
-     - obs.multivar_units
+   * - :term:`MODE_OBS_MULTIVAR_LEVEL`
+     - obs.multivar_level
 
 **${METPLUS_MASK_POLY}**
 

diff --git a/docs/_static/pbl-PointStat_fcstHRRR_obsAMDAR_PBLH_PyEmbed.png b/docs/_static/pbl-PointStat_fcstHRRR_obsAMDAR_PBLH_PyEmbed.png
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'
 #