Feature #3218 warn overwrite, #2110 fail if output exists

[georgemccabe]

Change Summary

• Added WARN_IF_DUPLICATE_OUTPUT (when the same output is written within the same METplus run) and wrapper-specific config options -- wrt Create WARNING message for operations that overwrite output files #3218
• Added WARN_IF_OUTPUT_EXISTS (when output already exists on disk) and wrapper-specific config options -- wrt Add config option to fail if output already exists #2110
• Added EXIT_IF_WARN config option to end METplus run immediately when a warning log is encountered (note: issue Enhancement: Support wrapper-specific EXIT_ON_WARN config options #3333 was created for adding support for wrapper-specific options) -- wrt Add config option to fail if output already exists #2110
• Added WARN_IF_ENSEMBLE_IS_MISSING to disable warnings when an ensemble member is not found for GenEnsProd and/or EnsembleStat
• Modified TCStat wrapper to ignore forecast leads to prevent redundant runs of the tool
• Downgraded some warnings to debug messages because they are more informative than needing to raise an alert
• Set EXIT_ON_WARN for all use case tests, requiring that all warnings be resolved or ignored for use cases added to the repository
• Updates some use case config files to prevent unnecessarily warnings/errors
• Added tests to demonstrate behavior of new config variables
• Added documentation to describe how output templates are substituted from different runtime frequency settings, which clarifies confusion discussed in series_analysis in a complex use case #3066
• Updated pillow package version in requirements.txt files to address security vulnerabilities
• (Internal) moved pytest markers from pytest.ini file to pyproject.toml to prevent warnings when tests are run from other directories besides internal/tests/pytests
• (Internal) Enhanced add_met_config_helper.py script to help add config support (documentation, basic use case conf updates, etc.) for all (or multiple) wrappers and for non-MET config variables (skips steps specific to MET tools)

Pull Request Testing

• Describe testing already performed for these changes:
  

Added unit tests to demonstrate expected behavior

• Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:
  

review code changes under metplus directory and unit tests under internal/tests/pytests to confirm correctness. Review use case diffs (see below)

review documentation changes - Are the new configs named well? Should there be a new section in the User's Guide (under Configuration chapter?) to describe warning, config variables to skip certain warnings, and exiting when a warning is encountered? (this could be added in final dev cycle)

• Do these changes include sufficient documentation updates, ensuring that no errors or warnings exist in the build of the documentation? [Yes]

Unless review suggests adding more

• Do these changes include sufficient testing updates? [Yes]

• Will this PR result in changes to the test suite? [Yes]
  
  If yes, describe the new output and/or changes to the existing output:
  

met_tool_wrapper:30-58,68-69

• UserScript_run_once - different number of files found due to init times skipped to prevent warnings
• GenEnsProd - different number of output files used/expected to prevent warnings

medium_range:3-5,10

• medium_range/GridStat_fcstGFS_obsGFS_climoNCEP_MultiField -- more output files that contain field name/level in filename because previously the same file was being overwritten multiple times

• Do these changes introduce new SonarQube findings? [No]
  
  If yes, please describe:

• Please complete this pull request review by 2026/8/18.
  

Pull Request Checklist

See the METplus Workflow for details.

• Add any new Python packages to the METplus Components Python Requirements table.
• For any new datasets, an entry to the METplus Verification Datasets Guide.
• Review the source issue metadata (required labels, projects, and milestone).
• Complete the PR definition above.
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  Select: Reviewer(s) and Development issue
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[coveralls]

Coverage Report for CI Build 33924738465

Coverage increased (+0.1%) to 92.133%

Details

• Coverage increased (+0.1%) from the base build.
• Patch coverage: 5 uncovered changes across 3 files (114 of 119 lines covered, 95.8%).
• 1 coverage regression across 1 file.

Uncovered Changes

File	Changed	Covered	%
metplus/wrappers/command_builder.py	52	50	96.15%
metplus/wrappers/runtime_freq_wrapper.py	7	5	71.43%
metplus/wrappers/point_stat_wrapper.py	1	0	0.0%
Total (17 files)	119	114	95.8%

Coverage Regressions

1 previously-covered line in 1 file lost coverage.

File	Lines Losing Coverage	Coverage
metplus/wrappers/runtime_freq_wrapper.py	1	91.18%

---

Coverage Stats

Relevant Lines:	10639
Covered Lines:	9802
Line Coverage:	92.13%
Coverage Strength:	1.84 hits per line

---

💛 - Coveralls

[JohnHalleyGotway]

I approve of these changes.

There are changes to 84 files, which is a lot to review. Although I realize that many are minor changes in .conf files, adding commented out entries for

{MET_TOOL}_WARN_IF_DUPLICATE_OUTPUT =
{MET_TOOL}_WARN_IF_OUTPUT_EXISTS =

I see that all of the GHA tests passed (other than the expected diffs and linkcheck failures), which is great. Thanks for adding new tests.

I inspected the file diffs flagged by the GHA testing workflow and confirmed that they're the changes you describe.

I see new entries in the docs (https://metplus--3332.org.readthedocs.build/en/3332/Users_Guide/glossary.html) for the new configuration options. You could consider starting a running list of config file changes for METplus-13.0.0 in the METplus Wrappers Upgrade Instructions section... rather than compiling a list prior to METplus-13.0.0 going out the door.

I have not manually replicated all of the situations that trigger these warnings to confirm that it behaves exactly as described. So there's some risk there. Please LMK if you'd rather I do a more in-depth review, and perhaps we could schedule a working meeting to demonstrate each situation.