updating medium_range and pbl directories

docs/use_cases/model_applications/medium_range/.#MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py

@@ -0,0 +1 @@
+lisag@petrichor.93684

docs/use_cases/model_applications/medium_range/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.py

@@ -66,8 +66,8 @@
 # ---------------------
 #
 # 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/medium_range/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/medium_range/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/medium_range/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.conf
@@ -99,30 +99,12 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
-#
-# 1) Passing in GridStat_fcstGEFS_obsCADB_BinaryObsPOE.conf then a user-specific system configuration file::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/medium_range/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.conf /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstGEFS_obsCADB_BinaryObsPOE::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.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/medium_range/GridStat_fcstGEFS_obsCADB_BinaryObsPOE.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.py

@@ -64,8 +64,8 @@
 # ---------------------
 #
 # 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/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.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 GridStat_fcstGFS_obsGFS_Sfc_MultiField.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstGFS_obsGFS_Sfc_MultiField.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.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/medium_range/GridStat_fcstGFS_obsGFS_Sfc_MultiField.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.py

@@ -71,8 +71,8 @@
 # ---------------------
 #
 # 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/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.conf
@@ -106,31 +106,12 @@
 # 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_fcstGFS_obsGFS_climoNCEP_MultiField.conf then a user-specific system configuration file::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.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/medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.conf /path/to/user_system.conf
 #
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output
@@ -142,10 +123,10 @@
 #
 # 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 gather_by_date/stat_analysis/grid2grid/anom (relative to **OUTPUT_BASE**)
-# and will contain the following files:
+# and will contain the following files::
 #
-# * 00Z/GFS/GFS_20170613.stat
-# * 06Z/GFS/GFS_20170613.stat
+#   * 00Z/GFS/GFS_20170613.stat
+#   * 06Z/GFS/GFS_20170613.stat
 
 ##############################################################################
 # Keywords

docs/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py

@@ -5,7 +5,6 @@
 model_applicaitons/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
 
 """
-
 ##############################################################################
 # .. contents::
 #   :depth: 1
@@ -118,36 +117,17 @@
 # Running METplus
 # ---------------
 #
-# This use case can be run two ways:
-#
-# 1) Passing in MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf, then a user-specific system configuration file::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
-#        /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf::
-#
-#        run_metplus.py /path/to/METplus/parm/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.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
+# 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/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf /path/to/user_system.conf
+
 #  If the 'convert' executable is not in the user's path, specify the full
 #  path to the executable here
 #
 # * **CONVERT = /usr/bin/convert**
 #
-# 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
-#   CONVERT = /path/to/convert
-#
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.py

@@ -62,8 +62,8 @@
 # ---------------------
 #
 # 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/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf
@@ -98,30 +98,12 @@
 # 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_obsGDAS_UpperAir_MultiField_PrepBufr.conf then a user-specific system configuration file::
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf /path/to/user_system.conf
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.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.
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.py

@@ -65,8 +65,8 @@
 # ---------------------
 #
 # 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/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf
@@ -101,30 +101,12 @@
 # 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_obsNAM_Sfc_MultiField_PrepBufr.conf then a user-specific system configuration file::
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf /path/to/user_system.conf
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.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.
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output

docs/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.py

@@ -111,8 +111,8 @@
 # ---------------------
 #
 # 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/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf
+# then it loads any configuration files passed to METplus via the command line,
+# i.e. parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf
 #
 # .. highlight:: bash
 # .. literalinclude:: ../../../../parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf
@@ -154,23 +154,17 @@
 # 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 TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf then a user-specific system configuration file::
+#   run_metplus.py /path/to/METplus/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf /path/to/user_system.conf
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf -c /path/to/user_system.conf
-#
-# 2) Modifying the configurations in parm/metplus_config, then passing in TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.conf::
-#
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByInit.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:
+# 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
@@ -200,9 +194,8 @@
 #   CONVERT = /path/to/convert
 #
 # **NOTE:** The INPUT_BASE, OUTPUT_BASE, and MET_INSTALL_DIR must be located under the [dir] section, while the RM, CUT, TR, NCAP2, CONVERT, and NCDUMP must be located under the [exe] section.
-
-
-
+#
+# See :ref:`running-metplus` for more information.
 
 ##############################################################################
 # Expected Output