Update develop-ref after #1361

.github/parm/use_case_groups.json

@@ -61,7 +61,7 @@
   },
   {
     "category": "marine_and_cryosphere",
-    "index_list": "3",
+    "index_list": "3-4",
     "run": false
   },
   {

ci/docker/docker_data/Dockerfile

@@ -17,7 +17,8 @@ RUN if [ "x${MOUNTPT}" == "x" ]; then \
       exit 1; \
     fi
 
-ENV CASE_DIR=/data/input/METplus_Data
+ARG DATA_DIR=/data/input/METplus_Data
+ENV CASE_DIR=${DATA_DIR}
 RUN mkdir -p ${CASE_DIR}
 
 RUN for URL in `echo ${TARFILE_URL} | tr "," " "`; do \

docs/Users_Guide/glossary.rst

@@ -8723,3 +8723,39 @@ METplus Configuration Glossary
      case and the values differ between them.
 
      | *Used by:* All
+
+   GEN_ENS_PROD_ENS_MEMBER_IDS
+     Specify the value for 'ens_member_ids' in the MET configuration file for GenEnsProd.
+
+     | *Used by:* GenEnsProd
+
+   GEN_ENS_PROD_CONTROL_ID
+     Specify the value for 'control_id' in the MET configuration file for GenEnsProd.
+
+     | *Used by:* GenEnsProd
+
+   ENSEMBLE_STAT_ENS_MEMBER_IDS
+     Specify the value for 'ens_member_ids' in the MET configuration file for EnsembleStat.
+
+     | *Used by:* EnsembleStat
+
+   ENSEMBLE_STAT_CONTROL_ID
+     Specify the value for 'control_id' in the MET configuration file for EnsembleStat.
+
+     | *Used by:* EnsembleStat
+
+   ENSEMBLE_STAT_CTRL_INPUT_DIR
+     Input directory for optional control file to use with EnsembleStat.
+     See also :term:`ENSEMBLE_STAT_CTRL_INPUT_TEMPLATE`.
+
+     | *Used by:*  EnsembleStat
+
+   ENSEMBLE_STAT_CTRL_INPUT_TEMPLATE
+     Template used to specify an optional control filename for EnsembleStat.
+     Note that if a control member file is found in the ensemble file list,
+     it will automatically be removed by the wrapper to prevent an error in the
+     MET tool. This may require adjusting the value for
+     :term:`ENSEMBLE_STAT_N_MEMBERS` and/or
+     :term:`ENSEMBLE_STAT_ENS_VLD_THRESH`.
+
+     | *Used by:*  EnsembleStat

docs/Users_Guide/release-notes.rst

@@ -38,6 +38,30 @@ When applicable, release notes are followed by the GitHub issue number which
 describes the bugfix, enhancement, or new feature:
 https://github.com/dtcenter/METplus/issues
 
+
+METplus Version 4.1.0-beta5 Release Notes (2022-01-14)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+* Enhancements:
+
+  * **Add support for setting control members in EnsembleStat and GenEnsProd** (`#1236 <https://github.com/dtcenter/METplus/issues/1236>`_)
+  * **Enhance SeriesAnalysis wrapper to allow different field info values for each file in a list** (`#1166 <https://github.com/dtcenter/METplus/issues/1166>`_)
+  * Add support for setting INIT_LIST and VALID_LIST for irregular time intervals (`#1286 <https://github.com/dtcenter/METplus/issues/1286>`_)
+  * Support setting the OMP_NUM_THREADS environment variable (`#1320 <https://github.com/dtcenter/METplus/issues/1320>`_)
+  * Enhance ExtractTiles using MTD input to properly match times (`#1285 <https://github.com/dtcenter/METplus/issues/1285>`_)
+  * Add support for commonly changed MET config variables part 2 (`#896 <https://github.com/dtcenter/METplus/issues/896>`_)
+  * Prevent wildcard character from being used in output file path (`#1291 <https://github.com/dtcenter/METplus/issues/1291>`_)
+
+* New Use Cases:
+
+  * Satellite verification of sea surface salinity: SMOS vs RTOFS output (`#1116 <https://github.com/dtcenter/METplus/issues/1116>`_)
+
+* Internal:
+
+  * **Create guidance for memory-intensive use cases, introduce Python memory profiler** (`#1183 <https://github.com/dtcenter/METplus/issues/1183>`_)
+  * **Identify code throughout METplus components that are common utilities** (`#799 <https://github.com/dtcenter/METplus/issues/799>`_)
+  * **Add definitions to the Release Guide for the stages of the release cycle** (`#934 <https://github.com/dtcenter/METplus/issues/934>`_)
+
 METplus Version 4.1.0-beta4 Release Notes (2021-11-16)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

docs/Users_Guide/wrappers.rst

@@ -183,6 +183,8 @@ METplus Configuration
 | :term:`OBS_ENSEMBLE_STAT_GRID_INPUT_TEMPLATE`
 | :term:`FCST_ENSEMBLE_STAT_INPUT_TEMPLATE`
 | :term:`ENSEMBLE_STAT_OUTPUT_TEMPLATE`
+| :term:`ENSEMBLE_STAT_CTRL_INPUT_DIR`
+| :term:`ENSEMBLE_STAT_CTRL_INPUT_TEMPLATE`
 | :term:`LOG_ENSEMBLE_STAT_VERBOSITY`
 | :term:`FCST_ENSEMBLE_STAT_INPUT_DATATYPE`
 | :term:`OBS_ENSEMBLE_STAT_INPUT_POINT_DATATYPE`
@@ -277,6 +279,8 @@ METplus Configuration
 | :term:`ENSEMBLE_STAT_OBS_QUALITY_INC`
 | :term:`ENSEMBLE_STAT_OBS_QUALITY_EXC`
 | :term:`ENSEMBLE_STAT_MET_CONFIG_OVERRIDES`
+| :term:`ENSEMBLE_STAT_ENS_MEMBER_IDS`
+| :term:`ENSEMBLE_STAT_CONTROL_ID`
 | :term:`ENSEMBLE_STAT_VERIFICATION_MASK_TEMPLATE` (optional)
 | :term:`ENS_VAR<n>_NAME` (optional)
 | :term:`ENS_VAR<n>_LEVELS` (optional)
@@ -853,6 +857,28 @@ see :ref:`How METplus controls MET config file settings<metplus-control-met>`.
    * - :term:`ENSEMBLE_STAT_OBS_QUALITY_EXC`
      - obs_quality_exc
 
+**${METPLUS_ENS_MEMBER_IDS}**
+
+.. list-table::
+   :widths: 5 5
+   :header-rows: 0
+
+   * - METplus Config(s)
+     - MET Config File
+   * - :term:`ENSEMBLE_STAT_ENS_MEMBER_IDS`
+     - ens_member_ids
+
+**${METPLUS_CONTROL_ID}**
+
+.. list-table::
+   :widths: 5 5
+   :header-rows: 0
+
+   * - METplus Config(s)
+     - MET Config File
+   * - :term:`ENSEMBLE_STAT_CONTROL_ID`
+     - control_id
+
 **${METPLUS_MET_CONFIG_OVERRIDES}**
 
 .. list-table::
@@ -1049,6 +1075,8 @@ METplus Configuration
 | :term:`GEN_ENS_PROD_ENSEMBLE_FLAG_NMEP`
 | :term:`GEN_ENS_PROD_ENSEMBLE_FLAG_CLIMO`
 | :term:`GEN_ENS_PROD_ENSEMBLE_FLAG_CLIMO_CDF`
+| :term:`GEN_ENS_PROD_ENS_MEMBER_IDS`
+| :term:`GEN_ENS_PROD_CONTROL_ID`
 | :term:`GEN_ENS_PROD_MET_CONFIG_OVERRIDES`
 
 .. _gen-ens-prod-met-conf:
@@ -1339,6 +1367,28 @@ see :ref:`How METplus controls MET config file settings<metplus-control-met>`.
    * - :term:`GEN_ENS_PROD_ENSEMBLE_FLAG_CLIMO_CDF`
      - ensemble_flag.climo_cdf
 
+**${METPLUS_ENS_MEMBER_IDS}**
+
+.. list-table::
+   :widths: 5 5
+   :header-rows: 0
+
+   * - METplus Config(s)
+     - MET Config File
+   * - :term:`GEN_ENS_PROD_ENS_MEMBER_IDS`
+     - ens_member_ids
+
+**${METPLUS_CONTROL_ID}**
+
+.. list-table::
+   :widths: 5 5
+   :header-rows: 0
+
+   * - METplus Config(s)
+     - MET Config File
+   * - :term:`GEN_ENS_PROD_CONTROL_ID`
+     - control_id
+
 **${METPLUS_MET_CONFIG_OVERRIDES}**
 
 .. list-table::

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
 

internal_tests/pytests/ensemble_stat/test_ensemble_stat_wrapper.py

@@ -547,6 +547,12 @@ def test_handle_climo_file_variables(metplus_config, config_overrides,
         ({'ENSEMBLE_STAT_OBS_QUALITY_EXC': '5,6,7', },
          {'METPLUS_OBS_QUALITY_EXC': 'obs_quality_exc = ["5", "6", "7"];'}),
 
+        ({'ENSEMBLE_STAT_ENS_MEMBER_IDS': '1,2,3,4', },
+         {'METPLUS_ENS_MEMBER_IDS': 'ens_member_ids = ["1", "2", "3", "4"];'}),
+
+        ({'ENSEMBLE_STAT_CONTROL_ID': '0', },
+         {'METPLUS_CONTROL_ID': 'control_id = "0";'}),
+
     ]
 )
 def test_ensemble_stat_single_field(metplus_config, config_overrides,

internal_tests/pytests/gen_ens_prod/test_gen_ens_prod_wrapper.py

@@ -343,6 +343,11 @@ def set_minimum_config_settings(config):
              )
          }),
 
+        ({'GEN_ENS_PROD_ENS_MEMBER_IDS': '1,2,3,4', },
+         {'METPLUS_ENS_MEMBER_IDS': 'ens_member_ids = ["1", "2", "3", "4"];'}),
+
+        ({'GEN_ENS_PROD_CONTROL_ID': '0', },
+         {'METPLUS_CONTROL_ID': 'control_id = "0";'}),
     ]
 )
 def test_gen_ens_prod_single_field(metplus_config, config_overrides,

internal_tests/use_cases/all_use_cases.txt

@@ -90,6 +90,7 @@ Category: marine_and_cryosphere
 1::PlotDataPlane_obsHYCOM_coordTripolar::model_applications/marine_and_cryosphere/PlotDataPlane_obsHYCOM_coordTripolar.conf:: xesmf_env, py_embed
 2::GridStat_fcstRTOFS_obsOSTIA_iceCover::model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsOSTIA_iceCover.conf:: icecover_env, py_embed
 3::GridStat_fcstRTOFS_obsSMOS_climWOA_sss::model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMOS_climWOA_sss.conf:: icecover_env, py_embed
+4::GridStat_fcstRTOFS_obsSMAP_climWOA_sss::model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsSMAP_climWOA_sss.conf:: icecover_env, py_embed
 #X::GridStat_fcstRTOFS_obsGHRSST_climWOA_sst::model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst.conf, model_applications/marine_and_cryosphere/GridStat_fcstRTOFS_obsGHRSST_climWOA_sst/ci_overrides.conf:: icecover_env, py_embed
 
 

metplus/VERSION

@@ -1 +1 @@
-4.1.0-beta5-dev
+4.1.0-beta6-dev