Update develop-ref after dtcenter/MET#2561 and #2208 (#2213)

Co-authored-by: johnhg <johnhg@ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@ucar.edu> Co-authored-by: cristianastan2 <cstan@gmu.edu> Co-authored-by: John Halley Gotway <johnhg@ucar.edu> Co-authored-by: bikegeek <minnawin@ucar.edu> Co-authored-by: Lisa Goodrich <lisag@ucar.edu> Co-authored-by: Julie Prestopnik <jpresto@seneca.rap.ucar.edu> Co-authored-by: George McCabe <23407799+georgemccabe@users.noreply.github.com> Co-authored-by: Hank Fisher <fisherh@ucar.edu> Co-authored-by: Dan Adriaansen <dadriaan@ucar.edu> Co-authored-by: jprestop <jpresto@ucar.edu> Co-authored-by: Tracy Hertneky <hertneky@seneca.rap.ucar.edu> Co-authored-by: Giovanni Rosa <giovanni.rosa@unimol.it> Co-authored-by: j-opatz <59586397+j-opatz@users.noreply.github.com> Co-authored-by: Mrinal Biswas <biswas@seneca.rap.ucar.edu> Co-authored-by: bikegeek <3753118+bikegeek@users.noreply.github.com> Co-authored-by: j-opatz <jopatz@ucar.edu> Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> Co-authored-by: lisagoodrich <33230218+lisagoodrich@users.noreply.github.com> Co-authored-by: metplus-bot <97135045+metplus-bot@users.noreply.github.com> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Giovanni Rosa <g.rosa1@studenti.unimol.it> Co-authored-by: mrinalbiswas <biswas@ucar.edu> Co-authored-by: Christina Kalb <kalb@ucar.edu> fix Contributor's Guide GitHub Workflow page (#1774) fix release (#1790) fix GitHub Actions warnings (#1864) fix #1884 develop PCPCombine {custom} in subtract method (#1887) fix #1939 develop - failure reading obs when zipped file also exists (#1941) Closes #1986 fix develop Fix broken documentation links (#2004) fix #2026 develop StatAnalysis looping (#2028) fix priority of obs_window config variables so that wrapper-specific version is preferred over generic OBS_WINDOW_BEGIN/END (#2062) fix #2070 var list numeric order (#2072) fix #2087 develop docs_pdf (#2091) fix #2096/#2098 develop - fix skip if output exists and do not error if no commands were run (#2099) Fix for Dockerfile smell DL4000 (#2112) fix #2082 develop regrid.convert/censor_thresh/censor_val (#2140) fix #2082 main_v5.0 regrid.convert/censor_thresh/censor_val (#2101) fix #2137 develop PointStat -obs_valid_beg/end (#2141) fix failured introduced by urllib3 (see urllib3/urllib3#2168) fix #2161 develop PCPCombine additional field arguments in -subtract mode (#2162) fix #2168 develop - StatAnalysis time shift (#2169) fix releases. (#2183) fix #2189 develop - spaces in complex thresholds (#2191) fix #2179 develop TCPairs fix -diag argument (#2187) fixes (#2200)
dtcenter · Jun 13, 2023 · 06ba88e · 06ba88e
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diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
@@ -11,7 +11,7 @@
   },
   {
     "category": "air_quality_and_comp",
-    "index_list": "0-6",
+    "index_list": "0",
     "run": false
   },
   {
@@ -20,48 +20,13 @@
     "run": false
   },
   {
-    "category": "short_range",
-    "index_list": "0",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "1",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "2-6",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "7",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "8",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "9",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "10-12",
-    "run": false
-  },
-  {
-    "category": "short_range",
-    "index_list": "13",
+    "category": "data_assimilation",
+    "index_list": "0-1",
     "run": false
   },
   {
-    "category": "data_assimilation",
-    "index_list": "0-1",
+    "category": "land_surface",
+    "index_list": "0",
     "run": false
   },
   {
@@ -172,7 +137,7 @@
   {
     "category": "s2s",
     "index_list": "3",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
@@ -214,6 +179,46 @@
     "index_list": "4",
     "run": false
   },
+  {
+    "category": "short_range",
+    "index_list": "0",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "1",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "2-6",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "7",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "8",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "9",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "10-12",
+    "run": false
+  },
+  {
+    "category": "short_range",
+    "index_list": "13",
+    "run": false
+  },
   {
     "category": "space_weather",
     "index_list": "0-1",
@@ -233,10 +238,5 @@
     "category": "unstructured_grids",
     "index_list": "0",
     "run": false
-  },
-  {
-    "category": "land_surface",
-    "index_list": "0",
-    "run": false
   }
 ]
diff --git a/...pt_obsPrecip_obsOnly_CrossSpectraPlot.png → ...erScript_fcstS2S_obsERAI_CrossSpectra.png b/...pt_obsPrecip_obsOnly_CrossSpectraPlot.png → ...erScript_fcstS2S_obsERAI_CrossSpectra.png
diff --git a/...ipt_obsPrecip_obsOnly_CrossSpectraPlot.py → ...serScript_fcstS2S_obsERAI_CrossSpectra.py b/...ipt_obsPrecip_obsOnly_CrossSpectraPlot.py → ...serScript_fcstS2S_obsERAI_CrossSpectra.py
@@ -1,46 +1,48 @@
 """
-UserScript: Make a Cross Spectra plot 
+UserScript: Compue Cross Spectra and make a plot 
 ========================================================================
 
 model_applications/
 s2s/
-UserScript_obsPrecip_obsOnly_CrossSpectraPlot.py
+UserScript_fcstS2S_obsERAI_CrossSpectra.py
 
 """
 
 #################################################################################
 # Scientific Objective
 # --------------------
 #
-# This use case calls the METplotpy space time plot to create a sample cross 
-# spectra diagram
-# using sample data created by METcalcpy cross spectra functions
+# This use case calls the METcalcpy cross spectra function and then the METplotpy 
+# space time plot to compute cross-spectra and create a sample cross spectra 
+# diagram using sample data.
 #
 # The space time plot and cross spectra calculations were created by Maria Gehne 
-# at the 
-# Physical Sciences Labratory in NOAA 
+# at the Physical Sciences Labratory in NOAA. 
 
 #################################################################################
 # Datasets
 # --------
 #
+#  * Forecast dataset: UFS Prototype 7
+#  * Observation dataset: ERAI
+#
 
 ##############################################################################
 # METplus Components
 # ------------------
 #
-# This use case runs the UserScript wrapper tool to run a user provided script,
-# in this case, cross_spectra_plot.py.
+# This use case runs the UserScript wrapper tool to run a user provided script, 
+# in this case, cross_spectra.py and cross_spectra_plot.py.
 #
 
 ##############################################################################
 # METplus Workflow
 # ----------------
 #
-# This use case does not loop but plots the entire time period of data
-# 
-# UserScript
-#
+# This use case computes spectra and plots for the entire time period of data. 
+# The use case loops over two processes, computing and plotting the 
+# cross-spectra. The user is able to edit the process list to turn off the 
+# computation part if only plotting is desired, or vice versa.
 #
 
 ##############################################################################
@@ -49,10 +51,10 @@
 #
 # 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_obsPrecip_obsOnly_CrossSpectraPlot.conf
+# with the -c option, i.e. -c parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
 #
 
 #############################################################################
@@ -76,7 +78,7 @@
 # This use case uses a Python script to perform plotting
 #
 # .. highlight:: python
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot/cross_spectra_plot.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/cross_spectra_plot.py
 #
 
 ##############################################################################
@@ -85,14 +87,14 @@
 #
 # This use case can be run two ways:
 #
-# 1) Passing in UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf, 
+# 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_obsPrecip_obsOnly_CrossSpectraPlot.conf -c /path/to/user_system.conf
+#        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_obsPrecip_obsOnly_CrossSpectraPlot.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_obsPrecip_obsOnly_CrossSpectraPlot.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:
 #
@@ -143,4 +145,4 @@
 #
 #
 #
-# sphinx_gallery_thumbnail_path = '_static/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.png'
+# sphinx_gallery_thumbnail_path = '_static/s2s-UserScript_fcstS2S_obsERAI_CrossSpectra.png'
diff --git a/internal/tests/use_cases/all_use_cases.txt b/internal/tests/use_cases/all_use_cases.txt
@@ -65,12 +65,12 @@ Category: met_tool_wrapper
 
 Category: air_quality_and_comp
 0::EnsembleStat_fcstICAP_obsMODIS_aod::model_applications/air_quality_and_comp/EnsembleStat_fcstICAP_obsMODIS_aod.conf
-1::GridStat_fcstMPAS_obsSATCORPS_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstMPAS_obsSATCORPS_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
-2::GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp::model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf:: pandac_env, py_embed
-3::GridStat_fcstMPAS_obsMERRA2_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstMPAS_obsMERRA2_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
-4::GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
-5::GridStat_fcstMPAS_obsERA5_cloudBaseHgt::model_applications/air_quality_and_comp/GridStat_fcstMPAS_obsERA5_cloudBaseHgt.conf:: pandac_env, py_embed
-6::GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
+#X::GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp::model_applications/air_quality_and_comp/GridStat_fcstGFS_obsSATCORPS_cloudTopPressAndTemp.conf:: pandac_env, py_embed
+#X::GridStat_fcstMPAS_obsSATCORPS_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstMPAS_obsSATCORPS_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
+#X::GridStat_fcstMPAS_obsMERRA2_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstMPAS_obsMERRA2_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
+#X::GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstGFS_obsMERRA2_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
+#X::GridStat_fcstMPAS_obsERA5_cloudBaseHgt::model_applications/air_quality_and_comp/GridStat_fcstMPAS_obsERA5_cloudBaseHgt.conf:: pandac_env, py_embed
+#X::GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac::model_applications/air_quality_and_comp/GridStat_fcstGFS_obsERA5_lowAndTotalCloudFrac.conf:: pandac_env, py_embed
 
 
 Category: climate
@@ -129,7 +129,7 @@ Category: s2s
 0::GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast:: model_applications/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf:: netcdf4_env
 1::TCGen_fcstGFSO_obsBDECKS_GDF_TDF:: model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.conf:: metplotpy_env,cartopy,metplus
 2::UserScript_obsPrecip_obsOnly_Hovmoeller:: model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.conf:: metplotpy_env,cartopy
-3:: UserScript_obsPrecip_obsOnly_CrossSpectraPlot:: model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf:: spacetime_env
+3:: UserScript_fcstS2S_obsERAI_CrossSpectra:: model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf:: spacetime_env
 4:: UserScript_obsERA_obsOnly_Stratosphere:: model_applications/s2s/UserScript_obsERA_obsOnly_Stratosphere.conf:: metplotpy_env,metdataio
 5::SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool:: model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf:: netcdf4_env
 6::GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile:: model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.conf:: netcdf4_env

diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
@@ -346,7 +346,7 @@ def run_at_time(self, input_dict):
 
                 if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
                     self.logger.debug('Skipping run time')
-                    return
+                    continue
 
                 self.run_at_time_loop_string(time_info)
 

diff --git a/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf b/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
@@ -0,0 +1,45 @@
+[config]
+
+PROCESS_LIST = UserScript(comp_spectra), UserScript(plot_spectra)
+
+# Note: time looping is not used in this use case
+LOOP_BY = REALTIME
+VALID_TIME_FMT = %Y
+VALID_BEG = 2014
+
+USER_SCRIPT_RUNTIME_FREQ = RUN_ONCE
+
+[user_env_vars]
+# Make output base avabilable to the script
+COMP_SPECTRA_SCRIPT_OUTPUT_DIR = {OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output
+
+# YAML configuration file for the cross spectra calculation
+COMP_SPECTRA_YAML_CONFIG_NAME = {METPLUS_BASE}/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/spectra_comp.yaml
+
+# Input files for the cross spectra calculation
+COMP_SPECTRA_INPUT_FILE_NAMES = {INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/precip.erai.sfc.1p0.2x.2014-2016.nc,{INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/prate_avg_ufs_p7_2014040100.nc,{INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/u850_ufs_p7_2014040100.nc,{INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/u200_ufs_p7_2014040100.nc
+
+PLOT_SPECTRA_INPUT_FILE_NAMES = {OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output/SpaceTimeSpectra_ufs_p7_P_D850_symm_4spd.nc,{OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output/SpaceTimeSpectra_ufs_p7_P_D200_symm_4spd.nc,{OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output/SpaceTimeSpectra_ufs_p7_P_D200_symm_4spd.nc
+
+PLOT_SPECTRA_YAML_CONFIG_NAME = {METPLUS_BASE}/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/spectra_plot.yaml
+
+PLOT_SPECTRA_OUTPUT_DIR = {OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/plots/
+
+
+[comp_spectra]
+# Settings for computing the cross-spectra
+USER_SCRIPT_COMMAND = python {METCALCPY_BASE}/metcalcpy/contributed/spacetime/cross_spectra.py
+
+LOG_FILE = "cross_spectra.log"
+LOG_LEVEL = "DEBUG"
+
+METCALCPY_BASE = {METPLUS_BASE}/../METcalcpy
+
+
+[plot_spectra]
+# settings for plotting the cross-spectra
+
+USER_SCRIPT_COMMAND = python {METPLUS_BASE}/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/cross_spectra_plot.py
+
+LOG_FILE = "cross_spectra_plot.log"
+LOG_LEVEL = "INFO"