Merge branch 'develop' of https://github.com/dtcenter/METplus into fe…

…ature_1091_extent_cycloneplotter

.github/parm/use_case_groups.json

@@ -39,19 +39,14 @@
     "index_list": "8",
     "run": false
   },
-  {
-    "category": "cryosphere",
-    "index_list": "0",
-    "run": false
-  },
   {
     "category": "data_assimilation",
     "index_list": "0",
     "run": false
   },
   {
-    "category": "marine_and_coastal",
-    "index_list": "0-1",
+    "category": "marine_and_cryosphere",
+    "index_list": "0-2",
     "run": false
   },
   {

docs/Contributors_Guide/add_use_case.rst

@@ -42,13 +42,11 @@ one of the following:
 
 * air_quality_and_comp
 * climate
-* coastal
 * convection_allowing_models
-* cryosphere
 * data_assimilation
 * extremes
 * land_surface
-* marine_and_coastal
+* marine_and_cryosphere
 * medium_range
 * miscellaneous
 * pbl
@@ -437,11 +435,11 @@ Verify that the correct directory structure is found inside the tarfile::
 The output should show that all of the data is found under the
 model_applications/<category>/<use_case> directory. For example::
 
-    model_applications/marine_and_coastal/
-    model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar/
-    model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar/weight_north.nc
-    model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar/rtofs_glo_2ds_n048_daily_diag.nc
-    model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar/weight_south.nc
+    model_applications/marine_and_cryosphere/
+    model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar/
+    model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar/weight_north.nc
+    model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar/rtofs_glo_2ds_n048_daily_diag.nc
+    model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar/weight_south.nc
 
 Copy files to DTC Web Server
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/Contributors_Guide/github_workflow.rst

@@ -344,7 +344,7 @@ Creating a pull request
     `GitHub Actions <https://github.com/dtcenter/METplus/actions>`_ have
     passed.  See "All checks have passed" in the figure below. If the tests
     were not successful or if there are conflicts with the base branch,
-    ask the requestor make changes.
+    ask the requestor to make changes.
 
     .. figure:: figure/checks_pass_no_conflicts.png
 

docs/Release_Guide/met_bugfix.rst

@@ -16,4 +16,5 @@ Create a new vX.Y.Z bugfix release from the main_vX.Y branch.
 .. include:: release_steps/create_release_extra.rst
 .. include:: release_steps/met/attach_release_tarfile.rst
 .. include:: release_steps/met/update_dtc_website.rst
+.. include:: release_steps/met/confirm_zenodo.rst
 .. include:: release_steps/finalize_release_on_github_bugfix.rst

docs/Release_Guide/met_official.rst

@@ -20,4 +20,5 @@ Create a new vX.Y.Z official release from the develop branch.
 .. include:: release_steps/met/update_dtc_website.rst
 .. include:: release_steps/finalize_release_on_github_official.rst
 .. include:: release_steps/update_docs_official.rst
+.. include:: release_steps/met/confirm_zenodo.rst
 .. include:: release_steps/set_beta_deletion_reminder_official.rst

docs/Release_Guide/metplus_official.rst

@@ -23,4 +23,5 @@ Create a new vX.Y.Z official release from the develop branch.
 .. include:: release_steps/metplus/update_version_on_develop.rst
 .. include:: release_steps/update_docs_official.rst
 .. include:: release_steps/metplus/update_web_server_data.rst
+.. include:: release_steps/metplus/update_zenodo.rst
 .. include:: release_steps/set_beta_deletion_reminder_official.rst

docs/Release_Guide/release_steps/met/confirm_zenodo.rst

@@ -0,0 +1,12 @@
+Confirm Updated Zenodo Link
+---------------------------
+
+In the `MET GitHub repository <https://github.com/dtcenter/MET>`_
+scroll down to the README file and check the
+`MET Digital Object Identifier (DOI) <https://doi.org/10.5281/zenodo.5565322>`_
+on Zenodo. The newly released version should be automatically updated on Zenodo and that
+link should automatically update to this latest released version. Confirm
+that the Zenodo link was correctly updated for this latest release.
+
+
+

docs/Release_Guide/release_steps/metplus/update_zenodo.rst

@@ -0,0 +1,12 @@
+Update Zenodo
+-------------
+
+In the `METplus GitHub repository <https://github.com/dtcenter/METplus>`_
+scroll down to the README file and check the
+`METplus Coordinated Release Digital Object Identifier (DOI) <https://doi.org/10.5281/zenodo.5567804>`_
+on Zenodo. Once all METplus components have been released, gather the zip files
+for each METplus component release in the METplus Verification System
+Coordinated Release and upload them to create a new version on Zenodo.
+
+
+

docs/Users_Guide/quicksearch.rst

@@ -67,10 +67,9 @@ 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>`_
    | `Convection Allowing Models <../search.html?q=ConvectionAllowingModelsAppUseCase&check_keywords=yes&area=default>`_
-   | `Cryosphere  <../search.html?q=CryosphereAppUseCase&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>`_
-   | `Marine and Coastal <../search.html?q=MarineAndCoastalAppUseCase&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>`_
    | `Precipitation <../search.html?q=PrecipitationAppUseCase&check_keywords=yes&area=default>`_
    | `Space Weather <../search.html?q=SpaceWeatherAppUseCase&check_keywords=yes&area=default>`_
@@ -82,10 +81,9 @@ Use Cases by Application:
    | **Air Quality and Composition**: *AirQualityAndCompAppUseCase*
    | **Climate**: *ClimateAppUseCase*
    | **Convection Allowing Models**: *ConvectionAllowingModelsAppUseCase*
-   | **Cryosphere**: *CryosphereAppUseCase*
    | **Data Assimilation**: *DataAssimilationAppUseCase*
    | **Ensemble**: *EnsembleAppUseCase*
-   | **Marine and Coastal**: *MarineAndCoastalAppUseCase*
+   | **Marine and Cryosphere**: *MarineAndCryosphereAppUseCase*
    | **Medium Range**: *MediumRangeAppUseCase*
    | **Precipitation**: *PrecipitationAppUseCase*
    | **Space Weather**: *SpaceWeatherAppUseCase*

docs/Users_Guide/release-notes.rst

@@ -107,7 +107,7 @@ METplus Version 4.1.0-beta1 Release Notes (2021-07-21)
 
 * New Use Cases:
 
-  * Marine and Coastal: GridStat_fcstRTOFS_obsOSTIA_iceCover (`#834 <https://github.com/dtcenter/METplus/issues/834>`_)
+  * Marine and Cryosphere: GridStat_fcstRTOFS_obsOSTIA_iceCover (`#834 <https://github.com/dtcenter/METplus/issues/834>`_)
   * met_tool_wrapper: GFDLTracker_TC (`#615 <https://github.com/dtcenter/METplus/issues/615>`_)
   * Seasonal to Subseasonal: UserScript_fcstGFS_obsERA_OMI
   * Seasonal to Subseasonal: UserScript_fcstGFS_obsERA_PhaseDiagram

docs/use_cases/model_applications/cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.py → docs/use_cases/model_applications/marine_and_cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.py

@@ -2,7 +2,7 @@
 Grid-Stat and MODE: Sea Ice Validation   
 ====================================================================================================
 
-model_applications/cryosphere/GridStat_MODE_fcstIMS
+model_applications/marine_and_cryosphere/GridStat_MODE_fcstIMS
 _obsNCEP_sea_ice.conf
 
 """
@@ -65,7 +65,7 @@
 # any configuration files passed to METplus by the command line with the -c option.
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf
 #
 
 ###################################################################################################
@@ -102,10 +102,10 @@
 #
 # 1) Passing in GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf then a user-specific system configuration file::
 #       
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf -c /path/to/user_system.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf -c /path/to/user_system.conf
 #
 # 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf::
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_MODE_fcstIMS_obsNCEP_sea_ice.conf
 #
 # The former method is recommended. Whether you add them to a user-specific configuration file or modify the metplus_config files, the following variables must be set correctly:
 #
@@ -134,8 +134,8 @@
 # A successful run will have the following output files in the location defined by {OUTPUT_BASE}, which
 # is located in the metplus_system.conf configuration file located in /path/to/METplus/parm/metplus_config.
 # This list of files should be found for every time run through METplus. 
-# GridStat output will be in model_applications/cryosphere/sea_ice/GridStat relative to the {OUTPUT_BASE}.
-# MODE output will be in model_applications/cryosphere/sea_ice/MODE relative to the {OUTPUT_BASE}.
+# GridStat output will be in model_applications/marine_and_cryosphere/sea_ice/GridStat relative to the {OUTPUT_BASE}.
+# MODE output will be in model_applications/marine_and_cryosphere/sea_ice/MODE relative to the {OUTPUT_BASE}.
 # Using the output for 20190201 as an example:
 #
 # **GridStat output**:
@@ -176,7 +176,7 @@
 #
 #   * GridStatToolUseCase
 #   * MODEToolUseCase
-#   * CryosphereAppUseCase
+#   * MarineAndCryosphereAppUseCase
 #   * ValidationUseCase
 #   * S2SAppUseCase
 #   * NOAAEMCOrgUseCase
@@ -186,4 +186,4 @@
 #
 #
 #
-# sphinx_gallery_thumbnail_path = '_static/cryosphere_GridStat_MODE_fcstIMS_obsNCEP_Sea_Ice.png'
+# sphinx_gallery_thumbnail_path = '_static/marine_and_cryosphere_GridStat_MODE_fcstIMS_obsNCEP_Sea_Ice.png'

docs/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.py → docs/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.py

@@ -2,7 +2,7 @@
 GridStat: Python Embedding to read and process SST
 ==================================================
 
-model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf
+model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf
 
 """
 ##############################################################################
@@ -74,7 +74,7 @@
 # then it loads any configuration files passed to METplus via the command line.
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf
 
 ##############################################################################
 # MET Configuration
@@ -99,10 +99,10 @@
 #
 # This use case uses one Python script to read forecast, observation, and climatology data
 #
-# parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst/read_rtofs_ghrsst_woa.py
+# parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst/read_rtofs_ghrsst_woa.py
 #
 # .. highlight:: python
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst/read_rtofs_ghrsst_woa.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst/read_rtofs_ghrsst_woa.py
 #
 
 ##############################################################################
@@ -113,11 +113,11 @@
 #
 # 1) Passing in GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf then a user-specific system configuration file::
 #
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf /path/to/user_system.conf
+#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf /path/to/user_system.conf
 #
 # 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf::
 #
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf
+#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf
 #
 # The former method is recommended. Whether you add them to a user-specific configuration file or modify the metplus_config files, the following variables must be set correctly:
 #
@@ -158,11 +158,11 @@
 #
 #   * GridStatToolUseCase
 #   * PythonEmbeddingFileUseCase
-#   * MarineAndCoastalAppUseCase
+#   * MarineAndCryosphereAppUseCase
 #
 #   Navigate to the :ref:`quick-search` page to discover other similar use cases.
 #
 #
 #
-# sphinx_gallery_thumbnail_path = '_static/marine_and_coastal-GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.png'
+# sphinx_gallery_thumbnail_path = '_static/marine_and_cryosphere-GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.png'
 

docs/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover.py → docs/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.py

@@ -2,7 +2,7 @@
 GridStat: Python Embedding to read and process ice cover
 ========================================================
 
-model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
+model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
 
 """
 ##############################################################################
@@ -70,10 +70,10 @@
 #
 # METplus first loads all of the configuration files found in parm/metplus_config,
 # then it loads any configuration files passed to METplus via the command line
-# with the -c option, i.e. -c parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
+# with the -c option, i.e. -c parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
 
 ##############################################################################
 # MET Configuration
@@ -98,10 +98,10 @@
 #
 # This use case uses one Python script to read forecast and observation data
 #
-# parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover/read_ice_data.py
+# parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover/read_ice_data.py
 #
 # .. highlight:: python
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover/read_ice_data.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover/read_ice_data.py
 #
 
 ##############################################################################
@@ -112,11 +112,11 @@
 #
 # 1) Passing in GridStat_fcstRTOFS_obsOSTIA_iceCover.conf then a user-specific system configuration file::
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf -c /path/to/user_system.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf -c /path/to/user_system.conf
 #
 # 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstRTOFS_obsOSTIA_iceCover.conf::
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_coastal/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
 #
 # The former method is recommended. Whether you add them to a user-specific configuration file or modify the metplus_config files, the following variables must be set correctly:
 #
@@ -159,11 +159,11 @@
 #
 #   * GridStatToolUseCase
 #   * PythonEmbeddingFileUseCase
-#   * MarineAndCoastalAppUseCase
+#   * MarineAndCryosphereAppUseCase
 #
 #   Navigate to the :ref:`quick-search` page to discover other similar use cases.
 #
 #
 #
-# sphinx_gallery_thumbnail_path = '_static/marine_and_coastal-GridStat_fcstRTOFS_obsOSTIA_iceCover.png'
+# sphinx_gallery_thumbnail_path = '_static/marine_and_cryosphere-GridStat_fcstRTOFS_obsOSTIA_iceCover.png'
 #

docs/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar.py → docs/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.py

@@ -2,7 +2,7 @@
 PlotDataPlane: Python Embedding of tripolar coordinate file
 ===========================================================
 
-model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar.conf
+model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
 
 """
 ##############################################################################
@@ -68,10 +68,10 @@
 #
 # METplus first loads all of the configuration files found in parm/metplus_config,
 # then it loads any configuration files passed to METplus via the command line
-# with the -c option, i.e. -c parm/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar.conf
+# with the -c option, i.e. -c parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
 
 ##############################################################################
 # MET Configuration
@@ -86,10 +86,10 @@
 #
 # This use case uses one Python script to read input data, passed through two times
 #
-# parm/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar/read_tripolar_grid.py
+# parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar/read_tripolar_grid.py
 #
 # .. highlight:: python
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar/read_tripolar_grid.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar/read_tripolar_grid.py
 #
 
 ##############################################################################
@@ -100,11 +100,11 @@
 #
 # 1) Passing in PlotDataPlane_obsHYCOM_coordTripolar.conf then a user-specific system configuration file::
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar.conf -c /path/to/user_system.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf -c /path/to/user_system.conf
 #
 # 2) Modifying the configurations in parm/metplus_config, then passing in PlotDataPlane_obsHYCOM_coordTripolar.conf::
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_coastal/PlotDataPlane_obsHYCOM_coordTripolar.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
 #
 # The former method is recommended. Whether you add them to a user-specific configuration file or modify the metplus_config files, the following variables must be set correctly:
 #
@@ -146,11 +146,11 @@
 #
 #   * PlotDataPlaneToolUseCase
 #   * PythonEmbeddingFileUseCase
-#   * MarineAndCoastalAppUseCase
+#   * MarineAndCryosphereAppUseCase
 #
 #   Navigate to the :ref:`quick-search` page to discover other similar use cases.
 #
 #
 #
-# sphinx_gallery_thumbnail_path = '_static/marine_and_coastal-PlotDataPlane_obsHYCOM_coordTripolar.png'
+# sphinx_gallery_thumbnail_path = '_static/marine_and_cryosphere-PlotDataPlane_obsHYCOM_coordTripolar.png'
 #