updating 3 dirs s2s, space_weather and unstructured_grids

docs/use_cases/model_applications/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.py

@@ -226,32 +226,13 @@
 ##############################################################################
 # Running METplus
 # ---------------
-# This use case can be run two ways:
 #
-# 1) Passing in GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.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.
+# 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/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.py

@@ -67,8 +67,8 @@
 # ---------------------
 #
 # 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
-# i.e. -c parm/use_cases/model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.conf
@@ -88,30 +88,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
-#
-# 1) Passing in GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.conf then a user-specific system configuration file::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.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/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.py

@@ -70,8 +70,8 @@
 # ---------------------
 #
 # 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
-# i.e. -c parm/use_cases/model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf
@@ -93,30 +93,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
-#
-# 1) Passing in SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf then a user-specific system configuration file::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.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/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.py

@@ -171,29 +171,13 @@
 ##############################################################################
 # Running METplus
 # ---------------
-# This use case can be run two ways:
 #
-# 1) Passing in TCGen_fcstGFSO_obsBDECKS_GDF_TDF.conf then a user-specific system configuration file::
+# 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 -c /path/to/METplus/parm/use_cases/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in TCGen_fcstGFSO_obsBDECKS_GDF_TDF.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.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
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.py

@@ -59,8 +59,8 @@
 # ---------------------
 #
 # 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/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
@@ -94,43 +94,12 @@
 # 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 UserScript_fcstS2S_obsERAI_CrossSpectra.conf, 
-# then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in UserScript_fcstS2S_obsERAI_CrossSpectra.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.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
-#
-#  and for the [exe] section, you will need to define the location of NON-MET executables.
-#  If the executable is in the user's path, METplus will find it from the name. 
-#  If the executable is not in the path, specify the full path to the executable here (i.e. RM = /bin/rm)  
-#  The following executables are required for performing series analysis use cases:
-#
-# 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
-#
-#   [exe]
-#   RM = /path/to/rm
-#   CUT = /path/to/cut
-#   TR = /path/to/tr
-#   NCAP2 = /path/to/ncap2
-#   CONVERT = /path/to/convert
-#   NCDUMP = /path/to/ncdump
+#   run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf -c /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.py

@@ -91,46 +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 UserScript_obsPrecip_obsOnly_Hovmoeller.conf, 
-# then a user-specific system configuration file::
-#
-#        run_metplus.py \
-#        /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.conf \
-#        /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in UserScript_obsPrecip_obsOnly_Hovmoeller.conf::
-#
-#        run_metplus.py \
-#        /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.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
-#
-#  and for the [exe] section, you will need to define the location of NON-MET executables.
-#  If the executable is in the user's path, METplus will find it from the name. 
-#  If the executable is not in the path, specify the full path to the executable here (i.e. RM = /bin/rm)  
-#  The following executables are required for performing series analysis use cases:
-#
-# 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
-#
-#   [exe]
-#   RM = /path/to/rm
-#   CUT = /path/to/cut
-#   TR = /path/to/tr
-#   NCAP2 = /path/to/ncap2
-#   CONVERT = /path/to/convert
-#   NCDUMP = /path/to/ncdump
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s_mjo/UserScript_obsCFSR_obsOnly_MJO_ENSO.py

@@ -104,29 +104,12 @@
 # Running METplus
 # ---------------
 #
-# This use case is run in the following 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 UserScript_obsCFSR_obsOnly_MJO_ENSO.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s_mjo/UserScript_obsCFSR_obsOnly_MJO_ENSO.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in UserScript_obsCFSR_obsOnly_MJO_ENSO.py::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s_mjo/UserScript_obsCFSR_obsOnly_MJO_ENSO.conf
-#
-# 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 
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s_mjo/UserScript_obsCFSR_obsOnly_MJO_ENSO.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_PhaseDiagram.py

@@ -103,29 +103,12 @@
 # Running METplus
 # ---------------
 #
-# This use case is run in the following 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 UserScript_obsERA_obsOnly_PhaseDiagram.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_PhaseDiagram.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in UserScript_obsERA_obsOnly_PhaseDiagram.py::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_PhaseDiagram.conf
-#
-# 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 
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/s2s_mjo/UserScript_obsERA_obsOnly_PhaseDiagram.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output