Improve testability of pdb_deposition.py - #84
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Refactoring: - substitute_tokens(): pure function for all $Token replacement, pulled out of the inline block in process_input() - merge_mmcifgen_into_structure(): extracts the for-item loop that applied the mmcif-gen template block onto a per-crystal CIF block - run() gains mmcifgen_runner= parameter (default run_mmcifgen) so tests can substitute a stub without running the full external tool Tests (31 total, all passing): - tests/test_pdb_deposition.py: unit tests for substitute_tokens, read_fragalysis_csv, read_cmpd_codes; CIF-level tests for merge_mmcifgen_into_structure using in-memory gemmi objects - tests/test_validate_structure_cif_doc.py: extended with in-memory CIF fixtures covering missing categories, R-factor range checks, unsubstituted placeholders, and software ordinal validation Closes #83 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
substitute_tokens()— a pure function handling all$CompoundCode,$CrystalName,$PoseID, and$ExternalCodeNreplacement, replacing the inline block previously buried insideprocess_input()merge_mmcifgen_into_structure()— pulls the loop that applied the mmcif-gen template block onto a per-crystal CIF block into its own testable functionmmcifgen_runner=run_mmcifgenparameter torun()so tests can inject a stub without invoking the real external toolCloses #83
Test plan
pytest tests/test_pdb_deposition.py -v— 20 new tests (unit + CIF-level)pytest tests/test_validate_structure_cif_doc.py -v— 11 tests (3 existing + 8 new)pytest— full suite stays green🤖 Generated with Claude Code