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Update setting of environment variables for MET config files to add support for all to METPLUS_ vars #768

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georgemccabe opened this issue Jan 21, 2021 · 33 comments · Fixed by #792, #810, #837 or #886
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component: code cleanup Code cleanup and maintenance issue component: logging METplus: Configuration priority: blocker Blocker reporting: DTC NCAR Base NCAR Base DTC Project reporting: DTC NOAA BASE NOAA Office of Atmospheric Research DTC Project requestor: METplus Team METplus Development Team type: enhancement Improve something that it is currently doing
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@georgemccabe
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georgemccabe commented Jan 21, 2021

We are moving towards a new format of setting environment variables that are read by the wrapped MET config files.

  • All environment variables set that are used in the wrapped files should start with METPLUS_, i.e. METPLUS_MODEL. These variables should either contain an empty string (if not used so the default value will be used) or set to a string that contains the MET config variable name, an equals sign, the value, and a semi-colon at the end, i.e.

METPLUS_MODEL = model = "WRF";
or
METPLUS_MODEL = ""

  • We should continue to support the old naming of environment variables for a few releases so that users' wrapped MET config files that use the old naming do not need to be updated immediately upon switching to v4.0.0.

  • We should keep track of the list of METPLUS_ variables that are used for each wrapper and output a warning log message if any of them are not currently being utilized in the user's wrapped MET config file so that they are aware that they can update their file to add additional capability.

  • We should add a "MET Configuration" section to the Python Wrappers page in the User's Guide to describe how each environment variable corresponds to the METplus configuration variables. Currently there are a couple examples that have this information. Here is one: https://dtcenter.github.io/METplus/latest/Users_Guide/wrappers.html#tc-rmw-met-conf

  • Once the information about the env vars set for the MET config files are in the Python Wrappers section, we should remove that content from each use case documentation file and instead provide a link to the appropriate section in the Python Wrappers section so that this information does not need to be updated in multiple places.

Describe the Enhancement

Engineering: Modifications to each wrapper should be made to

  • support the new env vars (METPLUS_)
  • Ensure old env vars are still set properly
  • Add warnings if any METPLUS_ variable is not utilized in the MET config file used

Documentation:

  • Add information on how each METPLUS_ variable is set for each wrapper in the Python Wrappers section
  • Update use case docs to link to the appropriate section in Python Wrappers instead of repeating info about MET config variables

Time Estimate

~5 days

Sub-Issues

Consider breaking the enhancement down into sub-issues.

  • Engineering Changes
  • Documentation Updates

Relevant Deadlines

4.0.0

Funding Source

2790541 (no longer valid)
Now split between 2702691, 2788881, 2799991

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@georgemccabe georgemccabe added type: enhancement Improve something that it is currently doing component: use case configuration priority: blocker Blocker component: logging component: code cleanup Code cleanup and maintenance issue requestor: METplus Team METplus Development Team labels Jan 21, 2021
@georgemccabe georgemccabe added this to the METplus-4.0 milestone Jan 21, 2021
@georgemccabe georgemccabe added this to To do in METplus-4.0.0-beta4 (3/2/21) via automation Jan 21, 2021
@georgemccabe georgemccabe self-assigned this Jan 21, 2021
@georgemccabe georgemccabe added the alert: NEED ACCOUNT KEY Need to assign an account key to this issue label Jan 21, 2021
@TaraJensen TaraJensen removed the alert: NEED ACCOUNT KEY Need to assign an account key to this issue label Jan 21, 2021
@DanielAdriaansen DanielAdriaansen added alert: NEED ACCOUNT KEY Need to assign an account key to this issue and removed alert: NEED ACCOUNT KEY Need to assign an account key to this issue labels Jan 26, 2021
@georgemccabe georgemccabe moved this from To do to In progress in METplus-4.0.0-beta4 (3/2/21) Feb 3, 2021
@georgemccabe
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Dan and I are working on branch feature_768_met_config
I have finished implementing support for all new METPLUS_ environment variables in the following wrappers:

ASCII2NC
EnsembleStat
GridStat
MODE
MTD
PointStat

Changes made to these wrappers are easy to replicate in the other wrappers. Some variables have already been supported in the other wrappers with changes to be consistent across wrappers.

Still need to finish:

GridDiag
PB2NC
SeriesAnalysis
STATAnalysis
TCGen
TCPairs
TCRMW
TCStat

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georgemccabe commented Feb 4, 2021

Finished:
GridDiag
PB2NC
SeriesAnalysis
STATAnalysis
TCGen
TCRMW

To go:
TCPairs
TCStat

Still need to test changes against previous version to ensure output is the same and update docs

@georgemccabe
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All wrappers have now implemented the new method for setting environment variables.

@georgemccabe georgemccabe linked a pull request Feb 4, 2021 that will close this issue
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@georgemccabe
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@DanielAdriaansen I added a check for unused environment variables in the wrapped MET config files. Any item that is in the wrappers WRAPPER_ENV_VAR_KEYS list that is not found in the wrapped MET config file will produce a warning:

(command_builder.py:146) WARNING: Environment variable ${METPLUS_FCST_FIELD} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_OBS_FIELD} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_MESSAGE_TYPE} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_CLIMO_MEAN_FILE} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_CLIMO_STDEV_FILE} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_OBS_WINDOW_DICT} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_MASK_GRID} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_MASK_POLY} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_MASK_SID} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped
(command_builder.py:146) WARNING: Environment variable ${METPLUS_OUTPUT_PREFIX} is not utilized in MET config file: /d1/personal/mccabe/METplus/parm/met_config/PointStatConfig_wrapped

This should make it easier for you to see what has not yet been updated in the files in parm/met_config. Keep in mind that if I have forgotten to add a variable name to the wrapper's list, then it will not show up here.

@georgemccabe
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The diff output from running develop and this branch can be found on kiowa here:

/d1/personal/mccabe/diff-output/diff.log

The differences in the CyclonePlotter text file are due to the wrapper writing the output in a different order each run, which will be resolved with this PR: #797

The differences in the TCStat output have been resolved in a config change on the feature branch feature_768_met_config

@georgemccabe georgemccabe linked a pull request Feb 18, 2021 that will close this issue
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DanielAdriaansen commented Feb 18, 2021

All met_tool_wrapper GridStat use cases were tested with the new wrapped GridStat config file and no differences between the output of each use case using the wrapped GridStat config file from this branch and the wrapped GridStat config file from the develop branch were noted. Documentation for the met_tool_wrapper GridStat use cases has been updated. Next up will be testing model_applications GridStat use cases:

GridStat_fcstCESM_obsGFS_ConusTemp.py
GridStat_fcstHRRR_obsPracPerfect_SurrogateSevereProb.py
GridStat_fcstHRRR_obsPracPerfect_SurrogateSevere.py
GridStat_MODE_fcstIMS_obsNCEP_sea_ice.py
GridStat_fcstGFS_obsGFS_climoNCEP_MultiField.py
GridStat_fcstGFS_obsGFS_Sfc_MultiField.py
GridStat_fcstGFS_obsCCPA_GRIB.py
GridStat_fcstHREFmean_obsStgIV_Gempak.py
GridStat_fcstHREFmean_obsStgIV_NetCDF.py
GridStat_fcstHRRR-TLE_obsStgIV_GRIB.py
GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.py
GridStat_fcstGloTEC_obsGloTEC_vx7.py

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DanielAdriaansen commented Feb 19, 2021

All of the GridStat model_applications use cases have been updated in two places:

  1. Each METplus conf file was switched to use the GridStatConfig_wrapped MET config file
  2. Each METplus docs Python/RST file was updated so the literalinclude is including the GridStatConfig_wrappped MET config file
  3. Each METplus conf file for the use case was switched from using CONFIG_DIR to PARM_BASE/met_config (for GRID_STAT_MET_CONFIG only)

No testing was done on these changes locally. I will be moving to the next wrapper now.

A checklist of sorts based on my experience with GridStat:

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DanielAdriaansen commented Feb 19, 2021

Checklist for each wrapper:

  • GridStat
  • EnsembleStat
  • ASCII2NC
  • GridDiag
  • MODE
  • MTD
  • PB2NC
  • PointStat
  • SeriesAnalysis
  • StatAnalysis
  • TcGen
  • TcPairs
  • TcRMW
  • TcStat

@TaraJensen TaraJensen added the reporting: DTC NOAA BASE NOAA Office of Atmospheric Research DTC Project label Mar 3, 2021
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PointStat is complete. Automation is running now. Here are the modified use cases:

met_tool_wrapper/PointStat/PointStat.conf
met_tool_wrapper/PointStat/PointStat_once_per_field.conf
model_applications/medium_range/PointStat_fcstGFS_obsGDAS_UpperAir_MultiField_PrepBufr.conf
model_applications/medium_range/PointStat_fcstGFS_obsNAM_Sfc_MultiField_PrepBufr.conf
model_applications/tc_and_extra_tc/UserScript_ASCII2NC_PointStat_fcstHAFS_obsFRD_NetCDFci_overrides.conf

Docs build.

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DanielAdriaansen commented Mar 3, 2021

Moving to StatAnalysis:

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DanielAdriaansen commented Mar 4, 2021

StatAnalysis is complete. All use cases appear to be passing automation. Here are the modified use cases:

met_tool_wrapper/StatAnalysis/StatAnalysis.conf
met_tool_wrapper/StatAnalysis/StatAnalysis_python_embedding.conf
model_applications/data_assimilation/StatAnalysis_fcstHAFS_obsPrepBufr_JEDI_IODA_interface.conf

Docs build- some issues with items not in conf glossary. Will resolve later.

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DanielAdriaansen commented Mar 4, 2021

Moving to SeriesAnalysis:

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SeriesAnalysis is complete. Automation has not run yet. Here are the modified use cases:

met_tool_wrapper/SeriesAnalysis/SeriesAnalysis.conf
met_tool_wrapper/SeriesAnalysis/SeriesAnalysis_python_embedding.conf
model_applications/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf

Note that it appears all SeriesAnalysis use cases were already using the _wrapped MET config file, and that file already contained all the new METPLUS_* items supported by series_analysis_wrapper so theoretically these changes are only for documentation and all use cases should still run.

Docs build- some issues with items not in conf glossary. Will resolve later.

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DanielAdriaansen commented Mar 4, 2021

Moving to TcGen:

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TCGen is complete. Automation has not run yet. Here are the modified use cases:

met_tool_wrapper/TCGen/TCGen.conf

Note that it appears all TCGen use cases were already using the _wrapped MET config file, and that file already contained all the new METPLUS_* items supported by tc_gen_wrapper so theoretically these changes are only for documentation and all use cases should still run.

Docs build- some issues with items not in conf glossary. Will resolve later.

NOTE- these changes align with METv9.1 When #801 is complete this section will need to be updated appropriately.

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DanielAdriaansen commented Mar 4, 2021

Moving to TcPairs:

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TCPairs is complete. Automation has not run yet. Here are the modified use cases:

met_tool_wrapper/TCPairs/TCPairs_extra_tropical.py
met_tool_wrapper/TCPairs/TCPairs_tropical.py
model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.py
model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_RPlotting.py

Docs build- some issues with items not in conf glossary. Will resolve later.

The use cases using TCPairs should be monitored because the _wrapped MET config file was changed for these use cases.

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DanielAdriaansen commented Mar 4, 2021

Moving to TcRMW:

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georgemccabe commented Mar 4, 2021

While doing this work, I learned that the values for fcst_raw_plot.color_table and the equivalent obs color table were incorrect in the parm/met_config/MODEConfig_wrapped file (differs from share/met/config version). This will result in differences in ps output.
I have seen this a couple cases but there may be more. Once we get a full list of use cases that are affected, we can rerun them with the old value to confirm that no differences arise to ensure that the changes are expected.

Use cases that should have no differences if the color scale is changed back to the wrong default (may not be a complete list):

  • met_tool_wrapper/MODE/MODE.conf
  • model_applications/convection_allowing_models/MODE_fcstHRRR_obsMRMS_Hail_GRIB2.conf
  • model_applications/convection_allowing_models/MODE_fcstFV3_obsGOES_BrightnessTemp.conf

The following run includes overriding the color scale to the old value for these 3 cases. If no differences occur in result, then we can safely assume that the output of these 3 use cases will differ and that is expected:
https://github.com/dtcenter/METplus/actions/runs/625210865
We will need to update the develop-ref branch from develop after these changes are merged in.

georgemccabe added a commit that referenced this issue Mar 8, 2021
…nges from #768 available to be able to do the same for MODE config, but I added the overrides that will be needed when that is available
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georgemccabe commented Mar 9, 2021

Update: The following are output in the difference output that are expected changes:

Caused by incorrect default color table in default wrapped MET config:

met_tool_wrapper

Text diff
A:/data/truth/MODE/mode/2005080712/mode_WRF_RH_vs_WRF_RH_P500_120000L_20050807_120000V_000000A.ps
B:/data/output/MODE/mode/2005080712/mode_WRF_RH_vs_WRF_RH_P500_120000L_20050807_120000V_000000A.ps

convection_allowing_models:0-5

Text diff
A:/data/truth/MODE_fcstHRRR_obsMRMS_Hail_GRIB2/hailtest/mode_270000L_20190529_030000V_010000A.ps
B:/data/output/MODE_fcstHRRR_obsMRMS_Hail_GRIB2/hailtest/mode_270000L_20190529_030000V_010000A.ps
Text diff
A:/data/truth/MODE_fcstHRRR_obsMRMS_Hail_GRIB2/hailtest/mode_260000L_20190529_020000V_010000A.ps
B:/data/output/MODE_fcstHRRR_obsMRMS_Hail_GRIB2/hailtest/mode_260000L_20190529_020000V_010000A.ps

convection_allowing_models:6+

Text diff
A:/data/truth/MODE_fcstFV3_obsGOES_BrightnessTemp/convection_allowing_models/brightness_temperature/mode_FV3_core_lsm1_020000L_20190521_020000V_NAA.ps
B:/data/output/MODE_fcstFV3_obsGOES_BrightnessTemp/convection_allowing_models/brightness_temperature/mode_FV3_core_lsm1_020000L_20190521_020000V_NAA.ps

New output from new use cases (PointStat_python_embedding and MODE_python_embedding) that are not found in truth data set

met_tool_wrapper

file not found (new output)
A:
B:/data/output/PointStat_python_embedding/metplus_final.conf
file not found (new output)
A:
B:/data/output/PointStat_python_embedding/point_stat_py_embed/point_stat_000000L_20200906_060000V.stat
file not found (new output)
A:
B:/data/output/MODE_python_emedding/metplus_final.conf
file not found (new output)
A:
B:/data/output/MODE_python_emedding/met_tool_wrapper/MODE_python_embedding/2005080712/mode_FCST_vs_OBS_120000L_20050807_120000V_120000A_obj.nc
file not found (new output)
A:
B:/data/output/MODE_python_emedding/met_tool_wrapper/MODE_python_embedding/2005080712/mode_FCST_vs_OBS_120000L_20050807_120000V_120000A_cts.txt
file not found (new output)
A:
B:/data/output/MODE_python_emedding/met_tool_wrapper/MODE_python_embedding/2005080712/mode_FCST_vs_OBS_120000L_20050807_120000V_120000A_obj.txt
file not found (new output)
A:
B:/data/output/MODE_python_emedding/met_tool_wrapper/MODE_python_embedding/2005080712/mode_FCST_vs_OBS_120000L_20050807_120000V_120000A.ps

Extra masking fields were generated mistakenly

We need @lindsayrblank to confirm that the extra fields are not needed, but I believe this to be the case.
The settings for this use case had an empty string set for the mask.grid, i.e.:

mask = {
   grid = [ "" ];
  poly = [ ${VERIF_MASK} ];
}

This should actually be set to:

grid = [];

because we want to only use the poly values to determine the grid. All of the downstream output from MODE is identical to the truth data, which implies that the extra mask output fields are not being used in the use case.

COMPARING GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V.stat
file_A: /data/truth/GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V.stat
file_B: /data/output/GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V.stat

Comparing text files
Comparing stat file
ERROR: Different number of lines in /data/output/GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V.stat
File_A: 18
File_B: 9
ERROR: File differs: /data/output/GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V.stat

COMPARING GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V_pairs.nc
file_A: /data/truth/GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V_pairs.nc
file_B: /data/output/GridStat_MODE_fcstIMS_obsNCEP_sea_ice/model_applications/cryosphere/sea_ice/GridStat/20190201/grid_stat/grid_stat_IMS_ICEC_vs_NCEP_ICEC_Z0_000000L_20190201_220000V_pairs.nc

Comparing NetCDF
ERROR: Field list differs between files
File_A: ['DIFF_ICEC_Z0_ICEC_Z0_', 'DIFF_ICEC_Z0_ICEC_Z0_data_mask', 'FCST_ICEC_Z0_', 'FCST_ICEC_Z0__eq1.0_NBRHD_25', 'FCST_ICEC_Z0__eq1.0_NBRHD_49', 'FCST_ICEC_Z0__eq1.0_NBRHD_81', 'FCST_ICEC_Z0__eq1.0_NBRHD_9', 'FCST_ICEC_Z0_data_mask', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_25', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_49', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_81', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_9', 'OBS_ICEC_Z0_', 'OBS_ICEC_Z0__ge0.40_NBRHD_25', 'OBS_ICEC_Z0__ge0.40_NBRHD_49', 'OBS_ICEC_Z0__ge0.40_NBRHD_81', 'OBS_ICEC_Z0__ge0.40_NBRHD_9', 'OBS_ICEC_Z0_data_mask', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_25', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_49', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_81', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_9', 'lat', 'lon']
File_B:['DIFF_ICEC_Z0_ICEC_Z0_data_mask', 'FCST_ICEC_Z0_data_mask', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_25', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_49', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_81', 'FCST_ICEC_Z0_data_mask_eq1.0_NBRHD_9', 'OBS_ICEC_Z0_data_mask', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_25', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_49', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_81', 'OBS_ICEC_Z0_data_mask_ge0.40_NBRHD_9', 'lat', 'lon']
Using File_A fields.
ERROR: Field DIFF_ICEC_Z0_ICEC_Z0_ not found

No output lines in truth data

precipitation

Text diff
A:/data/truth/GridStat_fcstGFS_obsCCPA_GRIB/model_applications/precipitation/GridStat_fcstGFS_obsCCPA_GRIB/met_out/GFS/precip/201706130000/grid_stat/grid_stat_GFS_APCP_vs_ANLYS_APCP_A24_240000L_20170613_000000V.stat
B:/data/output/GridStat_fcstGFS_obsCCPA_GRIB/model_applications/precipitation/GridStat_fcstGFS_obsCCPA_GRIB/met_out/GFS/precip/201706130000/grid_stat/grid_stat_GFS_APCP_vs_ANLYS_APCP_A24_240000L_20170613_000000V.stat

Threshold values were removed from this use case, which caused there to be no output lines. 5 threshold values were added back and the use case now produces output.

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Full logs of the differences tests can be viewed here (for ~90 days):
https://github.com/dtcenter/METplus/actions/runs/633804009

@georgemccabe georgemccabe linked a pull request Mar 9, 2021 that will close this issue
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METplus-4.0.0-beta5 (5/3/21) automation moved this from To do to Done Mar 11, 2021
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We should also update the docs about adding a new use case to note that a MET conf file is no longer needed- the _wrapped file should be used.

https://dtcenter.github.io/METplus/latest/Contributors_Guide/add_use_case.html

@georgemccabe georgemccabe linked a pull request Apr 15, 2021 that will close this issue
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@georgemccabe georgemccabe changed the title Environment variables for MET config files - Add support for all to METPLUS_ vars Update setting of environment variables for MET config files to add support for all to METPLUS_ vars Apr 27, 2021
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