openvax / topiary / 24513783283

88%

master: 90%

Pull #138

github

Address review: version string, module docstring, indel docs, combined test

- reference_version property: +scope- → +include- to match the
  renamed parameter.
- Module docstring rewritten: "Scopes" → "Include modes", added
  distance metrics and indels sections, updated deferred-features
  list to reflect what's now shipped vs queued.
- nearest() docstring: added explicit note that indel matching
  returns the first hit found (not the best), and that the upcoming
  self_nearest_candidates structured column will expose the full set.
- New test: test_indel_beats_distant_blosum_match verifies that a
  1-deletion at edit_distance=1 wins over a ≥2-sub same-length match
  even when metric="blosum62", and that blosum_distance is None for
  the indel row (can't score across different lengths positionally).
- Fixed version-string assertion in test_reference_version_embeds_*
  and test_from_ensembl_indexes_proteins_and_filters_cta.

39 self_proteome tests (up from 38), 1180 total, lint clean.

109 of 112 new or added lines in 1 file covered. (97.32%)

3689 of 4173 relevant lines covered (88.4%)

2.65 hits per line