openvax / topiary / 24487813152

88%

master: 90%

Pull #135

github

Address review feedback on PR #135

- Document tie-breaking semantics in SelfProteome.nearest docstring:
  when multiple reference peptides share the minimum Hamming distance,
  the first in internal array order wins.  Deterministic but
  implementation-dependent; the full tied set becomes available via
  the self_nearest_candidates column in part B.
- Add TestEnsemblHappyPath with a mocked pyensembl genome covering
  (a) CTA filtering actually drops proteins from the excluded genes
  and (b) from_ensembl's nearest lookup returns real gene/transcript
  provenance end-to-end (not just error paths).
- Add TestTieBreaking pinning the documented tie-breaking rule so a
  future refactor can't silently change which reference wins when
  multiple candidates are equidistant.

3 new tests (24 total for self_proteome, up from 21; full suite 1135
pass from 1132).  Lint clean.

179 of 203 new or added lines in 3 files covered. (88.18%)

3603 of 4085 relevant lines covered (88.2%)

2.65 hits per line