openvax / topiary / 24372918168

88%

master: 90%

Build Type

Pull #121

github

Committed by iskandr

Commit Message

Address PR #121 review: filter ordering, source_type vocabulary, CHANGELOG

- Extract _build_antigen_rows from predict_from_antigens so the legacy
  variant path can rebase peptide_offset before filter/sort evaluates.
  Filter expressions referencing peptide_offset now see absolute
  protein coordinates on both paths.
- Simplify source_type classifier: table-driven mapping aligned with
  docs/antigens.md vocabulary (PrematureStop → variant:stop_gain,
  multi-residue Substitution → variant:indel), free-form
  variant:<classname_lowered> fallback for unlisted effect types so
  new varcode effects remain representable without a code change.
- Vectorize peptide_offset rebasing via Series.map on the fragment_id →
  annotation lookups; mutation_interval still uses apply for the
  result_type="expand" tuple return.
- Bump version to 5.3.0 and add CHANGELOG entry covering the refactor
  and the new fragment-derived columns on the variant path.
- Add regression tests: PrematureStop source_type, multi-residue
  Substitution → indel, unknown effect class fallback, and
  gene_expression_dict / transcript_expression_dict propagation
  through the refactored path.

Pull Request Pull Request #121: Refactor predict_from_variants onto AntigenFragment (PR B)

Coverage Stats

79 of 82 new or added lines in 3 files covered. (96.34%)

8 existing lines in 2 files now uncovered.

3011 of 3417 relevant lines covered (88.12%)

2.64 hits per line