Enable coverage monitoring for non-test Python modules

[Copilot]

Python coverage reports were skipped in CI due to missing pytest-cov, and when run locally, only measured test files rather than non-test modules like phlexpy.py, adder.py, reducer.py, etc.

Changes

• Add py-pytest-cov to CI container: Updated ci/spack.yaml to include pytest-cov dependency
• Configure coverage scope: Created test/python/.coveragerc to measure non-test Python modules while excluding test files:

  [run]
  source = .
  omit = test_*.py, **/test_*.py
  
  [report]
  omit = test_*.py, **/test_*.py

• Wire up configuration: Updated CMake files to pass --cov-config=.coveragerc to pytest
• Ignore coverage artifacts: Added .coverage and .pytest_cache to .gitignore

Deployment Note

CI container rebuild required for py-pytest-cov to take effect. Once deployed, coverage workflow will automatically generate and upload Python coverage reports to Codecov.

Original prompt

Please examine recent coverage/codecov workflow logs, and the CMake code in the repository to ascertain whether the test coverage of non-test Python code (such as plugins/python/src/__init__.py) is being monitored as intended, and investigate/resolve if not.

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[greenc-FNAL]

@phlexbot format

[greenc-FNAL]

@phlexbot python-fix

[github-actions]

No automatic markdownlint fixes were necessary.

[github-actions]

No automatic cmake-format fixes were necessary.

[github-actions]

No automatic clang-format fixes were necessary.

[github-actions]

No automatic jsonnetfmt fixes were necessary.

[github-actions]

Automatic ruff fixes pushed (commit 3ca22bb).
⚠️ Note: Some issues may require manual review and fixing.

[Copilot]

Pull request overview

Enables Python coverage collection for non-test modules in test/python by ensuring pytest-cov is available in CI and by standardizing coverage configuration via a checked-in .coveragerc.

Changes:

• Add py-pytest-cov to the CI Spack environment so Python coverage isn’t skipped.
• Introduce test/python/.coveragerc and pass it to pytest via --cov-config to exclude test files from reports.
• Ignore common Python coverage artifacts in test/python/.gitignore.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
ci/spack.yaml	Adds py-pytest-cov to ensure coverage dependencies exist in the CI container.
test/python/.coveragerc	Defines coverage scope/omit rules to focus reporting on non-test modules.
test/python/CMakeLists.txt	Wires --cov-config into the CTest/pytest invocation for Python tests.
Modules/private/CreateCoverageTargets.cmake	Wires --cov-config into the coverage-python custom target.
test/python/.gitignore	Ignores .coverage and .pytest_cache artifacts produced by local test runs.

[greenc-FNAL]

Review the full CodeQL report for details.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

❌ Your project status has failed because the head coverage (74.60%) is below the target coverage (80.00%). You can increase the head coverage or adjust the target coverage.

@@            Coverage Diff             @@
##             main     #304      +/-   ##
==========================================
+ Coverage   74.28%   74.60%   +0.32%     
==========================================
  Files         124      124              
  Lines        2955     2961       +6     
  Branches      513      516       +3     
==========================================
+ Hits         2195     2209      +14     
+ Misses        540      532       -8     
  Partials      220      220              

Flag	Coverage Δ
unittests	74.60% <ø> (+0.32%)	⬆️

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