Feature 2741 running metplus (#2801)

* marine_and_cryosphere directories * fixing underlining * trying to fix warning msg. * trying to fix warning msg. again * Removing space before i.e. * updating medium_range and pbl directories * deleting empty file * removing lots of old text * precipitation files * removing junk file * removing extra # * add return * updating 3 dirs s2s, space_weather and unstructured_grids * updating short_range files * adding tc_and_extra_tc files * removing defunct -c option * Updating Datasets section * Added needed return character before "#Pass" * Added /path/to/user_system.conf to end of run_metplus.py line * Added a comma after "command line" * Updating file path * Added fields for empty Satasets section --------- Co-authored-by: Julie Prestopnik <[email protected]>
dtcenter · Nov 20, 2024 · 2b54612 · 2b54612
1 parent 943d197
commit 2b54612
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diff --git a/...ases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.py b/...ases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.py
@@ -121,30 +121,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
-#
-# 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_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_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:
-#
-# * **INPUT_BASE** - Path to directory where sample data tarballs are unpacked (See Datasets section to obtain tarballs). This is not required to run METplus, but it is required to run the examples in parm/use_cases
-# * **OUTPUT_BASE** - Path where METplus output will be written. This must be in a location where you have write permissions
-# * **MET_INSTALL_DIR** - Path to location where MET is installed locally
-#
-# Example User Configuration File::
-#
-#   [config]
-#   INPUT_BASE = /path/to/sample/input/data
-#   OUTPUT_BASE = /path/to/output/dir
-#   MET_INSTALL_DIR = /path/to/met-X.Y 
+# 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/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

diff --git a/...se_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.py b/...se_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.py
@@ -81,8 +81,8 @@
 # ---------------------
 #
 # 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_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf
@@ -120,31 +120,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
+# Pass the use case configuration file to the run_metplus.py script along 
+# with any user-specific system configuration files if desired::
 #
-# 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_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_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:
-#
-# * **INPUT_BASE** - Path to directory where sample data tarballs are unpacked (See Datasets section to obtain tarballs). This is not required to run METplus, but it is required to run the examples in parm/use_cases
-# * **OUTPUT_BASE** - Path where METplus output will be written. This must be in a location where you have write permissions
-# * **MET_INSTALL_DIR** - Path to location where MET is installed locally
-#
-# Example User Configuration File::
-#
-#   [dir]
-#   INPUT_BASE = /path/to/sample/input/data
-#   OUTPUT_BASE = /path/to/output/dir
-#   MET_INSTALL_DIR = /path/to/met-X.Y 
-#
-# **NOTE:** All of these items must be found under the [dir] section.
+#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

diff --git a/..._cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.py b/..._cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.py
@@ -83,8 +83,8 @@
 # ---------------------
 #
 # 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_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf
@@ -122,31 +122,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
+# Pass the use case configuration file to the run_metplus.py script along 
+# with any user-specific system configuration files if desired::
 #
-# 1) Passing in GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.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:
-#
-# * **INPUT_BASE** - Path to directory where sample data tarballs are unpacked (See Datasets section to obtain tarballs). This is not required to run METplus, but it is required to run the examples in parm/use_cases
-# * **OUTPUT_BASE** - Path where METplus output will be written. This must be in a location where you have write permissions
-# * **MET_INSTALL_DIR** - Path to location where MET is installed locally
-#
-# Example User Configuration File::
-#
-#   [dir]
-#   INPUT_BASE = /path/to/sample/input/data
-#   OUTPUT_BASE = /path/to/output/dir
-#   MET_INSTALL_DIR = /path/to/met-X.Y 
-#
-# **NOTE:** All of these items must be found under the [dir] section.
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

diff --git a/..._cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.py b/..._cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.py
@@ -83,8 +83,8 @@
 # ---------------------
 #
 # 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_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf
@@ -122,31 +122,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
+# Pass the use case configuration file to the run_metplus.py script along 
+# with any user-specific system configuration files if desired::
 #
-# 1) Passing in GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.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:
-#
-# * **INPUT_BASE** - Path to directory where sample data tarballs are unpacked (See Datasets section to obtain tarballs). This is not required to run METplus, but it is required to run the examples in parm/use_cases
-# * **OUTPUT_BASE** - Path where METplus output will be written. This must be in a location where you have write permissions
-# * **MET_INSTALL_DIR** - Path to location where MET is installed locally
-#
-# Example User Configuration File::
-#
-#   [dir]
-#   INPUT_BASE = /path/to/sample/input/data
-#   OUTPUT_BASE = /path/to/output/dir
-#   MET_INSTALL_DIR = /path/to/met-X.Y 
-#
-# **NOTE:** All of these items must be found under the [dir] section.
+#    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

diff --git a/...se_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.py b/...se_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.py
@@ -79,8 +79,8 @@
 # ---------------------
 #
 # 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_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf
@@ -108,31 +108,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
+# Pass the use case configuration file to the run_metplus.py script along 
+# with any user-specific system configuration files if desired::
 #
-# 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_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_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:
-#
-# * **INPUT_BASE** - Path to directory where sample data tarballs are unpacked (See Datasets section to obtain tarballs). This is not required to run METplus, but it is required to run the examples in parm/use_cases
-# * **OUTPUT_BASE** - Path where METplus output will be written. This must be in a location where you have write permissions
-# * **MET_INSTALL_DIR** - Path to location where MET is installed locally
-#
-# Example User Configuration File::
-#
-#   [dir]
-#   INPUT_BASE = /path/to/sample/input/data
-#   OUTPUT_BASE = /path/to/output/dir
-#   MET_INSTALL_DIR = /path/to/met-X.Y 
-#
-# **NOTE:** All of these items must be found under the [dir] section.
+#    run_metplus.py  /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

diff --git a/...ses/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsASCAT_satelliteWinds.py b/...ses/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsASCAT_satelliteWinds.py
@@ -109,7 +109,6 @@
 #    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsASCAT_satelliteWinds.conf /path/to/user_system.conf
 #
 # See :ref:`running-metplus` for more information.
-#
 
 ##############################################################################
 # Expected Output

diff --git a/...odel_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.py b/...odel_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.py
@@ -5,7 +5,6 @@
 model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.conf
 
 """
-
 ##############################################################################
 # .. contents::
 #   :depth: 1
@@ -32,19 +31,24 @@
 # Datasets
 # --------
 #
-# | **Forecast:** GFS forecast data (wind speed and sig. wave hgt)
+# **Forecast:** GFS forecast data (wind speed and sig. wave hgt)
 #
-# | **Observations:** JASON-3 satellite data
+# **Observations:** JASON-3 satellite data
 #
-# | **Location:** All of the input data required for this use case can be found in the met_test sample data tarball. Click here to the METplus releases page and download sample data for the appropriate release: https://github.com/dtcenter/METplus/releases
-# | This tarball should be unpacked into the directory that you will set the value of INPUT_BASE. See `Running METplus`_ section for more information.
+# **Location:** All of the input data required for this use case can be 
+# found in a sample data tarball. Each use case category will have 
+# one or more sample data tarballs. It is only necessary to download 
+# the tarball with the use case’s dataset and not the entire collection 
+# of sample data. Click here to access the METplus releases page and download sample data 
+# for the appropriate release: https://github.com/dtcenter/METplus/releases
+# This tarball should be unpacked into the directory that you will 
+# set the value of INPUT_BASE. See :ref:`running-metplus` section for more information.
 
 ##############################################################################
 # METplus Components
 # ------------------
 #
 # This use case calls Python Embedding during PointStat, which is the only tool used. 
-#
 
 ##############################################################################
 # METplus Workflow
@@ -56,22 +60,21 @@
 # The use case processes the following run time:
 #
 # | **Valid:** 2024-01-02 12Z 12hr lead
-# |
 
 ##############################################################################
 # METplus Configuration
 # ---------------------
 #
 # 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
-# parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.conf
 
 ##############################################################################
 # MET Configuration
-# ---------------------
+# -----------------
 #
 # METplus sets environment variables based on user settings in the METplus configuration file. 
 # See :ref:`How METplus controls MET config file settings<metplus-control-met>` for more details. 
@@ -98,7 +101,6 @@
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry/read_satData.py
 
-
 ##############################################################################
 # Running METplus
 # ---------------
@@ -109,7 +111,6 @@
 #    run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry.conf /path/to/user_system.conf
 #
 # See :ref:`running-metplus` for more information.
-#
 
 ##############################################################################
 # Expected Output
@@ -121,10 +122,10 @@
 #
 # 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/marine_and_cryosphere/PointStat_fcstGFS_obsJASON3_satelliteAltimetry (relative to **OUTPUT_BASE**)
-# and will contain the following files:
+# and will contain the following files::
 #
-# * point_stat_swh_120000L_20240102_120000V.stat
-# * point_stat_wind_120000L_20240102_120000V.stat
+#   * point_stat_swh_120000L_20240102_120000V.stat
+#   * point_stat_wind_120000L_20240102_120000V.stat
 
 ##############################################################################
 # Keywords
@@ -142,4 +143,3 @@
 #
 #
 # sphinx_gallery_thumbnail_path = '_static/marine_and_cryosphere-PointStat_fcstGFS_obsJASON3_satelliteAltimetry.png'
-
diff --git a/...se_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.py b/...se_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.py
@@ -61,8 +61,8 @@
 # ---------------------
 #
 # 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_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.conf
@@ -91,31 +91,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
+# Pass the use case configuration file to the run_metplus.py script along 
+# with any user-specific system configuration files if desired::
 #
-# 1) Passing in PointStat_fcstGFS_obsNDBC_WaveHeight.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in PointStat_fcstGFS_obsNDBC_WaveHeight.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.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:
-#
-# * **INPUT_BASE** - Path to directory where sample data tarballs are unpacked (See Datasets section to obtain tarballs). This is not required to run METplus, but it is required to run the examples in parm/use_cases
-# * **OUTPUT_BASE** - Path where METplus output will be written. This must be in a location where you have write permissions
-# * **MET_INSTALL_DIR** - Path to location where MET is installed locally
-#
-# Example User Configuration File::
-#
-#   [dir]
-#   INPUT_BASE = /path/to/sample/input/data
-#   OUTPUT_BASE = /path/to/output/dir
-#   MET_INSTALL_DIR = /path/to/met-X.Y 
-#
-# **NOTE:** All of these items must be found under the [dir] section.
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/PointStat_fcstGFS_obsNDBC_WaveHeight.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output