Merge branch 'develop' into feature_675_ci_doc

.github/parm/use_case_groups.json

@@ -61,7 +61,7 @@
   },
   {
     "category": "marine_and_cryosphere",
-    "index_list": "3",
+    "index_list": "3-4",
     "run": false
   },
   {
@@ -154,6 +154,11 @@
     "index_list": "11",
     "run": false
   },
+  {
+    "category": "s2s",
+    "index_list": "12",
+    "run": false 
+  },
   {
     "category": "space_weather",
     "index_list": "0-1",

ci/docker/docker_env/scripts/metplotpy_env.sh

@@ -10,7 +10,6 @@
 #   matplotlib==3.3.0
 #   scipy==1.5.1
 #   plotly==4.9.0
-#   pingouin==0.3.8
 #   cartopy==0.18.0
 #   eofs==1.3.0
 #   cmocean==2.0
@@ -34,7 +33,6 @@ conda create -y --clone ${BASE_ENV} --name ${ENV_NAME}
 conda install -y --name ${ENV_NAME} -c conda-forge matplotlib==3.3.0
 conda install -y --name ${ENV_NAME} -c conda-forge scipy==1.5.1
 conda install -y --name ${ENV_NAME} -c conda-forge plotly==4.9.0
-conda install -y --name ${ENV_NAME} -c conda-forge pingouin==0.3.8
 conda install -y --name ${ENV_NAME} -c conda-forge cartopy==0.18.0
 conda install -y --name ${ENV_NAME} -c conda-forge eofs==1.3.0
 conda install -y --name ${ENV_NAME} -c conda-forge cmocean==2.0

docs/Release_Guide/release_steps/common/update_dtc_website.rst

@@ -28,14 +28,14 @@ Update DTC Website
     * Add Link: Link text should be "User's Guide" and the URL should be the top
       level directory of the User's Guide hosted on the web. Beta releases can
       use "develop" in the URL, but for official releases, please ensure the
-      link uses the branch name (e.g. main_v4.0) as opposed to the tag name
-      (e.g. v4.0.0).  For example, use
-      "https://metplus.readthedocs.io/en/main_v4.0/Users_Guide/" and NOT
-      "https://metplus.readthedocs.io/en/v4.0.0/Users_Guide/"
+      link uses the branch name (e.g. main_vX.Y) as opposed to the tag name
+      (e.g. vX.Y.Z).  For example, use
+      "https://metplus.readthedocs.io/en/main_vX.Y/Users_Guide/" and NOT
+      "https://metplus.readthedocs.io/en/vX.Y.Z/Users_Guide/"
 
     * Add Link: Link text should be "Existing Builds and Docker" and the URL
       should be the latest Existing Builds page, i.e.
-      https://dtcenter.org/community-code/metplus/metplus-4-0-existing-builds
+      https://dtcenter.org/community-code/metplus/metplus-X-Y-existing-builds
       (If creating a new official release, be sure to add a new *Existing Builds
       and Docker* page, if one was not already created.)
 
@@ -44,8 +44,6 @@ Update DTC Website
 
   * Click on "Create Release".
 
-  * Click on "Save".
-
   * Update the existing releases, as needed.
 
     * For a development release, change any previous *Development*
@@ -58,3 +56,6 @@ Update DTC Website
       releases.
 
   * |otherWebsiteUpdates|
+
+  * Click on "Save".
+

docs/Users_Guide/systemconfiguration.rst

@@ -1116,9 +1116,9 @@ no space between the process name and the parenthesis.
     [my_instance_name]
     GRID_STAT_OUTPUT_DIR = /my/instance/name/output/dir
 
-In this example, the first occurence of GridStat in the PROCESS_LIST does
+In this example, the first occurrence of GridStat in the PROCESS_LIST does
 not have an instance name associated with it, so it will use the value
-/grid/stat/output/dir as the output directory. The second occurence has
+/grid/stat/output/dir as the output directory. The second occurrence has
 an instance name 'my_instance_name' and there is a section header with
 the same name, so this instance will use /my/instance/name/output/dir as
 the output directory.

docs/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.py

@@ -0,0 +1,170 @@
+"""
+GridStat: Python Embedding for sea surface salinity using level 3, 8 day mean obs
+=================================================================================
+
+model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf
+
+"""
+##############################################################################
+# Scientific Objective
+# --------------------
+#
+# This use case utilizes Python embedding to extract several statistics from the sea surface salinity data over the globe, 
+# which was already being done in a closed system. By producing the same output via METplus, this use case
+# provides standardization and reproducible results.
+
+##############################################################################
+# Datasets
+# --------
+#
+# | **Forecast:** RTOFS sss file via Python Embedding script/file
+#
+# | **Observations:** SMAP sss file via Python Embedding script/file
+#
+# | **Sea Ice Masking:** RTOFS ice cover file via Python Embedding script/file
+#
+# | **Climatology:** WOA sss file via Python Embedding script/file
+#
+# | **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.
+#
+# | **Data Source:** JPL's PODAAC and NCEP's FTPPRD data servers
+# |
+
+##############################################################################
+# External Dependencies
+# ---------------------
+#
+# You will need to use a version of Python 3.6+ that has the following packages installed:
+#
+# * scikit-learn
+# * pyresample
+#
+# If the version of Python used to compile MET did not have these libraries at the time of compilation, you will need to add these packages or create a new Python environment with these packages.
+#
+# If this is the case, you will need to set the MET_PYTHON_EXE environment variable to the path of the version of Python you want to use. If you want this version of Python to only apply to this use case, set it in the [user_env_vars] section of a METplus configuration file.:
+#
+#    [user_env_vars]
+#    MET_PYTHON_EXE = /path/to/python/with/required/packages/bin/python
+
+##############################################################################
+# METplus Components
+# ------------------
+#
+# This use case utilizes the METplus GridStat wrapper to generate a
+# command to run the MET tool GridStat with Python Embedding for the specified user hemispheres
+
+##############################################################################
+# METplus Workflow
+# ----------------
+#
+# GridStat is the only tool called in this example. This use case will pass in both the observation, forecast, 
+# and climatology gridded data being pulled from the files via Python Embedding. All of the desired statistics 
+# reside in the CNT line type, so that is the only output requested.
+# It processes the following run time:
+#
+# | **Valid:** 2021-05-02 0Z
+# |
+
+##############################################################################
+# 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
+# with the -c option, i.e. -c 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
+
+##############################################################################
+# 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. 
+#
+# **YOU SHOULD NOT SET ANY OF THESE ENVIRONMENT VARIABLES YOURSELF! THEY WILL BE OVERWRITTEN BY METPLUS WHEN IT CALLS THE MET TOOLS!**
+#
+# If there is a setting in the MET configuration file that is currently not supported by METplus you'd like to control, please refer to:
+# :ref:`Overriding Unsupported MET config file settings<met-config-overrides>`
+#
+# .. note:: See the :ref:`GridStat MET Configuration<grid-stat-met-conf>` section of the User's Guide for more information on the environment variables used in the file below:
+#
+# .. highlight:: bash
+# .. literalinclude:: ../../../../parm/met_config/GridStatConfig_wrapped
+
+##############################################################################
+# Python Embedding
+# ----------------
+#
+# This use case uses one Python script to read forecast and observation data
+#
+# parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss/read_rtofs_smap_woa.py
+#
+# .. highlight:: python
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss/read_rtofs_smap_woa.py
+#
+
+##############################################################################
+# Running METplus
+# ---------------
+#
+# This use case can be run two ways:
+#
+# 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.
+#
+
+##############################################################################
+# Expected Output
+# ---------------
+#
+# A successful run will output the following both to the screen and to the logfile::
+#
+#   INFO: METplus has successfully finished running.
+#
+# Refer to the value set for **OUTPUT_BASE** to find where the output data was generated.
+# Output for thisIce use case will be found in 20210503 (relative to **OUTPUT_BASE**)
+# and will contain the following files:
+#
+# * grid_stat_SSS_000000L_20210502_000000V.stat 
+# * grid_stat_SSS_000000L_20210502_000000V_cnt.txt 
+# * grid_stat_SSS_000000L_20210502_000000V_pairs.nc 
+
+##############################################################################
+# Keywords
+# --------
+#
+# .. note::
+#
+#   * GridStatToolUseCase
+#   * PythonEmbeddingFileUseCase
+#   * MarineAndCryosphereAppUseCase
+#
+#   Navigate to the :ref:`quick-search` page to discover other similar use cases.
+#
+#
+#
+# sphinx_gallery_thumbnail_path = '_static/marine_and_cryosphere-GridStat_fcstRTOFS_obsSMAP_climWOA_sss.png'
+

docs/use_cases/model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.py

@@ -1,6 +1,6 @@
 """
-GridStat: Python Embedding to read and process ice cover
-========================================================
+GridStat: Python Embedding for sea surface salinity using level 3, 1 day composite obs
+======================================================================================
 
 model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf
 

docs/use_cases/model_applications/s2s/UserScript_fcstGFS_obsERA_WeatherRegime.py

@@ -20,7 +20,7 @@
 # clusters.  This helps determine the optimal cluster number by examining the largest 
 # difference between the curve and the straight line.  The EOFs step is optional.  It 
 # computes an empirical orthogonal function analysis.  The K means step uses clustering 
-# to compute the frequency of occurrernce and anomalies for each cluster to give the most 
+# to compute the frequency of occurrence and anomalies for each cluster to give the most 
 # common weather regimes.  Then, the time frequency computes the frequency of each weather
 # regime over a user specified time frame.  Finally, stat_analysis can be run to compute
 # an categorical analysis of the weather regime classification or an anomaly correlation of