Use pytest.mark.skip for ChemRxiv tests instead of comments

[Copilot]

• Add optional skip_reason field to ReferenceCase dataclass
• Uncomment the ChemRxiv test case and add skip_reason
• Update test_output.py to use pytest.param with pytest.mark.skip for skipped cases
• Update test_from_identifier.py to use pytest.param with pytest.mark.skip for skipped cases
• Validate changes by running tests
• Refactor to reduce code duplication with helper functions
• Fix mypy type error in test_from_identifier.py
• Final review

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[Copilot]

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  • Triggering command: /usr/bin/python python -m pytest tests/test_from_identifier.py -v (dns block)
• export.arxiv.org
  • Triggering command: /usr/bin/python python -m pytest tests/test_from_identifier.py -v (dns block)
• www.ncbi.nlm.nih.gov
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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.59%. Comparing base (4484383) to head (41eb096).
⚠️ Report is 6 commits behind head on skip-chemrxiv.

Additional details and impacted files

@@              Coverage Diff               @@
##           skip-chemrxiv      #86   +/-   ##
==============================================
  Coverage          88.59%   88.59%           
==============================================
  Files                 13       13           
  Lines                526      526           
==============================================
  Hits                 466      466           
  Misses                60       60           

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[njzjz]

pre-commit.ci autofix

[njzjz]

@copilot mypy.....................................................................Failed

• hook id: mypy
• exit code: 1

tests/test_from_identifier.py:27: error: Argument 2 to "_create_test_param" has incompatible type "str | None"; expected "str" [arg-type]
Found 1 error in 1 file (checked 21 source files

[Copilot]

@copilot mypy.....................................................................Failed

• hook id: mypy
• exit code: 1...

Fixed in 41eb096. Changed the identifier parameter type from str to str | None to match the actual types of doi and arxiv fields which are optional.

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• www.ncbi.nlm.nih.gov
  • Triggering command: /usr/bin/python python -m pytest tests/test_from_identifier.py::test_from_identifier -v --tb=short (dns block)

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[Copilot]

Pull request overview

This PR refactors the test suite to use pytest's built-in skip mechanism instead of commenting out problematic test cases. It enables the previously commented ChemRxiv test case and marks it to be skipped with a clear reason.

Changes:

• Added optional skip_reason field to the ReferenceCase dataclass
• Uncommented the ChemRxiv test case and marked it with skip_reason="ChemRxiv API broken"
• Introduced _create_test_param helper functions in both test files to reduce code duplication and properly handle test skipping

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
tests/cases.py	Added skip_reason field to ReferenceCase dataclass and uncommented the ChemRxiv test case with skip reason
tests/test_output.py	Added _create_test_param helper function and updated parametrize decorators to use pytest.param with skip marks
tests/test_from_identifier.py	Added _create_test_param helper function and updated parametrize decorator to use pytest.param with skip marks

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