Update develop-ref after dtcenter/MET#2988 (#2722)

dtcenter · Oct 14, 2024 · 8f4460d · 8f4460d
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diff --git a/.coveragerc b/.coveragerc
@@ -3,3 +3,4 @@ relative_files = True
 source = metplus
 omit =
   metplus/wrappers/cyclone_plotter_wrapper.py
+  metplus/produtil/**
diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
@@ -276,6 +276,12 @@
     "disabled": true,
     "run": false
   },
+  {
+    "category": "short_range",
+    "index_list": "15",
+    "disabled": true,
+    "run":false
+  },
   {
     "category": "space_weather",
     "index_list": "0-1",

diff --git a/.github/update_truth_change_log.txt b/.github/update_truth_change_log.txt
@@ -7,3 +7,4 @@
 [20240905_16:45:56 develop] dtcenter/MET#2959 - Correct bugs in SEDI and BAGSS contingency table statistics found in the CTS line type
 [20240910_19:03:38 develop] dtcenter/MET#2967 - Fixes integer overflow bug in the computation of the CTS and NBRCTS ORSS, ORSS_NCL, and ORSS_NCU columns.
 [20240926_16:50:38 develop] #2701 - #2701 added a new use case (SeriesAnalysis_aggr) that produces new output
+[20241014_16:47:58 develop] dtcenter/MET#2988 - dtcenter/MET#2988 -- see issue #2719 for details
diff --git a/docs/Contributors_Guide/add_use_case.rst b/docs/Contributors_Guide/add_use_case.rst
@@ -169,6 +169,7 @@ Use Cases that Exceed GitHub Actions Disk Space
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 - *model_applications/s2s_stratosphere/UserScript_fcstGFS_obsERA_StratospherePolar*
 - *model_applications/s2s_stratosphere/UserScript_fcstGFS_obsERA_StratosphereQBO*
+- *model_applications/short_range/MODEMultivar_fcstRRFS_obsGOES_MRMS_BrightnessTemp_Lightning*
 
 .. _use_case_documentation:
 

diff --git a/docs/Contributors_Guide/documentation.rst b/docs/Contributors_Guide/documentation.rst
@@ -218,7 +218,7 @@ for more information.
 
 **What to bold:**
 
-  * Variables (e.g. **MET_INSTALL_DIR, INPUT_BASE, METCALCPY_HOME**, etc.)
+  * Environment Variables (e.g. **MET_INSTALL_DIR, INPUT_BASE, METCALCPY_HOME**, etc.)
   * Filenames (**line_defaults.yaml, contour_defaults.yaml, defaults.conf**, etc.)
 
 Italics
@@ -395,6 +395,20 @@ resulting in the following displayed text:
 
 See `Overleaf's Guide - Matrices <https://www.overleaf.com/learn/latex/Matrices>`_ for more information.
 
+Literal Include
+---------------
+
+This feature is used often in the Release Guide, but there are other places it could be useful.
+Using a literal include ensures only having to update the documentation in one place.
+It is important to use a relative path (i.e. "../../") to get to the correct 
+directory of the file being referenced in the literal include.  This will keep the 
+file linking to the correct version and branch.  
+
+As an example, refer to the METplus User's Guide.  See this 
+`line <https://github.com/dtcenter/METplus/blob/46f705fc2c1b861e3aa6314d030eb9b4c382d0b3/docs/use_cases/met_tool_wrapper/PointStat/PointStat.py#L55>`_ 
+in the PointStat Wrapper Use Case documentation, which uses RST's :code:`.. literalinclude::` 
+and renders the text of the referenced file in this 
+`section <https://metplus.readthedocs.io/en/develop/generated/met_tool_wrapper/PointStat/PointStat.html#metplus-configuration>`_.
 
 Literal Blocks
 --------------
@@ -425,6 +439,54 @@ and
 `literal blocks <https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#literal-blocks>`_
 for more information.
 
+Substitution References
+-----------------------
+
+Substitution references are replacements in the text as defined in the :code:`rst_epilog` 
+in the **docs/conf.py** file.  For example, instead of hard coding the MET version in 
+the METplus documentation, a variable :code:`met_version` can be set to a value 
+(e.g. 12.0.0) in the **docs/conf.py** file in the following way:
+
+.. code-block:: ini
+
+  met_version = 12.0.0
+
+Then, this variable is used in the :code:`rst_epilog` to set up the substitution, 
+along with other variables.  For example, in the **docs/conf.py** 
+file the following is defined:
+
+.. code-block:: ini
+
+  rst_epilog = f"""
+  .. |copyright|    replace:: {copyright}
+  .. |author_list|  replace:: {author_list}
+  .. |release_date| replace:: {release_date}
+  .. |release_year| replace:: {release_year}
+  .. |release_info| replace:: {release_info}
+  .. |python_version| replace:: {python_version}
+  .. |met_version| replace:: {met_version}
+  """
+
+The value 12.0.0 would then be replaced in the documentation wherever 
+:code:`|met_version|` is used in .rst files.  For example:
+
+.. code-block:: ini
+
+  MET version |met_version| or above 
+
+There are some 
+`reserved substitution variables <https://www.sphinx-doc.org/en/master/usage/restructuredtext/roles.html#substitutions>`_ 
+in Sphinx.  These variables are 
+:code:`|release|`, :code:`|version|`, :code:`|today|`, and 
+:code:`|translation progress|`. Reserved substitution variables do not 
+need to be added to :code:`rst_epilog`, but other variables do.
+
+See 
+`Substitutions <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#substitutions>`_ 
+and 
+`rst_epilog <https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-rst_epilog>`_ 
+for more information.
+
 Line Blocks
 -----------
 
@@ -1413,8 +1475,7 @@ Read the Docs supports multiple versions for each repository. For the METplus
 components, the "latest" version will point to the latest official (stable)
 release. The "develop" or "development" version will point to the most up to
 date development code. There may also be other previous versions of the
-software available in the version selector menu, which is accessible by
-clicking in the bottom left corner of the documentation pages.
+software available in the version selector menu.
 
 Automation rules allow project maintainers to automate actions on new branches
 and tags on repositories.  For the METplus components, documentation is

diff --git a/docs/Users_Guide/glossary.rst b/docs/Users_Guide/glossary.rst
@@ -290,7 +290,12 @@ METplus Configuration Glossary
      | *Used by:* Point2Grid
 
    POINT2GRID_QC_FLAGS
-     Specify the qc flags name that is read by Point2Grid.
+     .. warning:: **DEPRECATED:** Please use :term:`POINT2GRID_GOES_QC_FLAGS`.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_GOES_QC_FLAGS
+     Sets the value for the -goes_qc command line argument for Point2Grid.
 
      | *Used by:* Point2Grid
 
@@ -11624,6 +11629,46 @@ METplus Configuration Glossary
 
      | *Used by:* PointStat
 
+   POINT2GRID_VALID_TIME
+     Specify the value for 'valid_time' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_OBS_WINDOW_BEG
+     Specify the value for 'obs_window.beg' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_OBS_WINDOW_END
+     Specify the value for 'obs_window.end' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_MESSAGE_TYPE
+     Specify the value for 'message_type' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_VAR_NAME_MAP<n>_KEY
+     Specify the value for the nth 'var_name_map.key' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_VAR_NAME_MAP<n>_VAL
+     Specify the value for the nth 'var_name_map.val' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_OBS_QUALITY_INC
+     Specify the value for 'obs_quality_inc' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
+   POINT2GRID_OBS_QUALITY_EXC
+     Specify the value for 'obs_quality_exc' in the MET configuration file for Point2Grid.
+
+     | *Used by:* Point2Grid
+
    MADIS2NC_CUSTOM_LOOP_LIST
     Sets custom string loop list for a specific wrapper. See :term:`CUSTOM_LOOP_LIST`.
 
@@ -11812,105 +11857,39 @@ METplus Configuration Glossary
 
      | *Used by:* MADIS2NC
 
-   MADIS2NC_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for MADIS2NC.
-
-     | *Used by:* MADIS2NC
-
-   ASCII2NC_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for ASCII2NC.
-
-     | *Used by:* ASCII2NC
-
-   ENSEMBLE_STAT_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for EnsembleStat.
-
-     | *Used by:* EnsembleStat
-
-   GEN_ENS_PROD_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for GenEnsProd.
-
-     | *Used by:* GenEnsProd
-
-   GRID_DIAG_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for GridDiag.
-
-     | *Used by:* GridDiag
-
    GRID_STAT_TIME_OFFSET_WARNING
      Specify the value for 'time_offset_warning' in the MET configuration file for GridStat.
 
      | *Used by:* GridStat
 
-   IODA2NC_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for IODA2NC.
-
-     | *Used by:* IODA2NC
-
    MODE_TIME_OFFSET_WARNING
      Specify the value for 'time_offset_warning' in the MET configuration file for MODE.
 
      | *Used by:* MODE
 
-   MTD_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for MTD.
-
-     | *Used by:* MTD
-
-   PB2NC_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for PB2NC.
-
-     | *Used by:* PB2NC
-
-   PLOT_POINT_OBS_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for PlotPointObs.
-
-     | *Used by:* PlotPointObs
-
-   POINT_STAT_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for PointStat.
-
-     | *Used by:* PointStat
-
-   STAT_ANALYSIS_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for StatAnalysis.
-
-     | *Used by:* StatAnalysis
-
    SERIES_ANALYSIS_TIME_OFFSET_WARNING
      Specify the value for 'time_offset_warning' in the MET configuration file for SeriesAnalysis.
 
      | *Used by:* SeriesAnalysis
 
-   TC_DIAG_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for TCDiag.
-
-     | *Used by:* TCDiag
-
-   TC_GEN_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for TCGen.
-
-     | *Used by:* TCGen
-
-   TC_PAIRS_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for TCPairs.
-
-     | *Used by:* TCPairs
-
-   TC_RMW_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for TCRMW.
+   WAVELET_STAT_TIME_OFFSET_WARNING
+     Specify the value for 'time_offset_warning' in the MET configuration file for WaveletStat.
 
-     | *Used by:* TCRMW
+     | *Used by:* WaveletStat
 
-   TC_STAT_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for TCStat.
+   POINT2GRID_MET_CONFIG_OVERRIDES
+     Override any variables in the MET configuration file that are not
+     supported by the wrapper. This should be set to the full variable name
+     and value that you want to override, including the equal sign and the
+     ending semi-colon. The value is directly appended to the end of the
+     wrapped MET config file.
 
-     | *Used by:* TCStat
+     Example:
+     POINT2GRID_MET_CONFIG_OVERRIDES = desc = "override_desc"; model = "override_model";
 
-   WAVELET_STAT_TIME_OFFSET_WARNING
-     Specify the value for 'time_offset_warning' in the MET configuration file for WaveletStat.
+     See :ref:`Overriding Unsupported MET config file settings<met-config-overrides>` for more information
 
-     | *Used by:* WaveletStat
+     | *Used by:*  Point2Grid
 
    ASCII2NC_VALID_BEG
      Specify the value for the command line argument '-valid_beg' for ASCII2NC.

diff --git a/docs/Users_Guide/quicksearch.rst b/docs/Users_Guide/quicksearch.rst
@@ -156,6 +156,7 @@ Use Cases by METplus Feature:
    | `METplotpy <../search.html?q=METplotpyUseCase&check_keywords=yes&area=default>`_
    | `MET_PYTHON_EXE Environment Variable  <../search.html?q=MET_PYTHON_EXEUseCase&check_keywords=yes&area=default>`_
    | `Multiple Conf File Use <../search.html?q=MultiConfUseCase&check_keywords=yes&area=default>`_
+   | `MultivariateMODE <../search.html?q=MvMODEUseCase&check_keywords=yes&area=default>`_
    | `Observation Time Summary <../search.html?q=ObsTimeSummaryUseCase&check_keywords=yes&area=default>`_
    | `Observation Uncertainty <../search.html?q=ObsUncertaintyUseCase&check_keywords=yes&area=default>`_
    | `Python Embedding Ingest <../search.html?q=PyEmbedIngestToolUseCase&check_keywords=yes&area=default>`_
@@ -187,6 +188,7 @@ Use Cases by METplus Feature:
    | **METplotpy**: *METplotpyUseCase*
    | **MET_PYTHON_EXE Environment Variable**: *MET_PYTHON_EXEUseCase*
    | **Multiple Conf File Use**: *MultiConfUseCase*
+   | **MultivariateMODE**: *MvMODEUseCase*
    | **Observation Time Summary**: *ObsTimeSummaryUseCase*
    | **Observation Uncertainty**: *ObsUncertaintyUseCase*
    | **Python Embedding Ingest**: *PyEmbedIngestToolUseCase*