[codex] Add tests for biopython utilities#1
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Summary
Adds a lightweight pytest suite for the pure helper functions in
protdbench/tools/biopython_utils.py.The tests cover sequence validation notes, interface residue formatting, CA clash detection, hotspot residue detection, target RMSD, and secondary-structure percentage arithmetic. They use small synthetic PDB fixtures so they run without GPUs or external structure-prediction tools.
This PR also adds
pytest.iniandrequirements-dev.txtfor the CPU-only test dependencies. It intentionally does not add a GitHub Actions workflow, leaving CI wiring to the maintainers.Validation
python3 -m pytest -ragit diff --check upstream/main...HEAD