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topiary.self_proteome imports from Bio.Align.substitution_matrices for BLOSUM62 scoring (added in v5.9.0), but biopython was never declared as a dependency — CI on any PR that triggers the self_proteome tests fails with ModuleNotFoundError: No module named 'Bio'.
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Closing — alternative approach coming (biopython should not be a dep). |
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coverage: 88.402%. remained the same — fix-biopython-dependency into master |
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Summary
`topiary.self_proteome` imports `from Bio.Align.substitution_matrices import load` for BLOSUM62 scoring (added in v5.9.0, #138), but `biopython` was never added to `requirements.txt`. As a result, `pip install -e .` in CI does not pull it in, and any PR that exercises the `test_self_proteome.py` suite fails with:
```
FAILED tests/test_self_proteome.py::TestNearest::test_exact_match_distance_zero - ModuleNotFoundError: No module named 'Bio'
... (17 failures)
```
This is blocking CI on PRs #141, #142, #143, #144.
Change
Add `biopython>=1.80` to `requirements.txt`. The 1.80 floor matches the `substitution_matrices` API surface and is conservative — any modern install will satisfy it.
No version bump; this is a declared-dependency correction, not a behavior change.
Test plan