Feature #3189 and #3194 - pb2nc quality mark thresh and grid_diag mask and output_flag

[georgemccabe]

Pull Request Testing

• Describe testing already performed for these changes:
  

Added unit tests to demonstrate setting new config settings

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

Review code/doc changes, ensure automated tests pass (met_tool_wrapper has a 1 diff file from an unrelated MET PR)

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

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

Note the ioda2nc changes have not yet been made in MET, so setting a threshold value for quality_mark_thresh in ioda2nc will cause a failure in MET until this is implemented

• Will this PR result in changes to the test suite? [No]
  
  If yes, describe the new output and/or changes to the existing output:
  

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

• Please complete this pull request review by 2/3/2026.
  

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.
• Ensure the PR title matches the feature or bugfix branch name.
• Define the PR metadata, as permissions allow.
  Select: Reviewer(s) and Development issue
  Select: Milestone as the version that will include these changes
  Select: Coordinated METplus-X.Y Support project for bugfix releases or METplus-Wrappers-X.Y.Z Development project for official releases
• After submitting the PR, select the ⚙️ icon in the Development section of the right hand sidebar. Search for the issue that this PR will close and select it, if it is not already selected.
• After the PR is approved, merge your changes. If permissions do not allow this, request that the reviewer do the merge.
• Close the linked issue and delete your feature or bugfix branch from GitHub.

[coveralls]

Pull Request Test Coverage Report for Build 21636391197

Details

• 6 of 6 (100.0%) changed or added relevant lines in 3 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.002%) to 92.501%

---

Totals
Change from base Build 21532111836:	0.002%
Covered Lines:	9510
Relevant Lines:	10281

---

💛 - Coveralls

[JohnHalleyGotway]

Recommend removing the .idea directory and files from this PR. Apparently those are artifacts of JetBrains IDE's. You could consider adding .idea to the .gitignore file as well.

[JohnHalleyGotway]

I reviewed the other files changes as well, and they look good to me. Thanks for adding them. I note that there are 0 diffs flagged by GHA after rerunning earlier today.

I'm happy to approve after the .idea files are removed.

[georgemccabe]

@JohnHalleyGotway, I have received mixed messages about best practices for ignorning .idea files. It had previously been suggested to only ignore .idea/workspace.xml and .idea/sonarlint* because the other files can be useful for multiple developers. However, the files that keep changing seem specific to my PyCharm environment and would likely not be useful to others. Previously, the name of the conda env matched the name that we install on various machines, so it made sense to me to use that as the default. However, the formatting appears to change and I'm now leaning towards excluding all .idea files. This would require developers to set up their JetBrains configuration for each new clone, but I think that is OK to avoid confusing/inconsistency in the .idea content.

[JohnHalleyGotway]

Looks great. I approve. Thanks.