openvax / topiary / 24374071502

88%

master: 90%

Build Type

Pull #121

github

Committed by iskandr

Commit Message

Tighten predictor internals and refresh docs

Code:
- Fold contains_mutant_residues into overlaps_target with a single
  vectorized .where() — drops one redundant df.apply per fragment scan
  and makes the "variant-only narrowing" explicit.
- Extract _finalize_rows (filter + sort + only_novel + reset_index)
  and share it between predict_from_antigens and
  predict_from_mutation_effects. Removes the duplicated three-step tail.

Docs:
- docs/antigens.md — replace variant:silent with the full
  variant:stop_gain/stop_loss/start_loss/exon_loss/alternate_start
  vocabulary; note the substitution-compatible restriction on
  wt_peptide; drop the "Varcode refactor follow-up" bullet (now
  shipped); note read_lens is already available.
- docs/api.md — add predict_from_antigens to the prediction-methods
  table; mark predict_from_variants as building fragments internally.
- docs/quickstart.md — update the variant-pipeline column list and
  add a fragments example for non-variant origins.
- docs/index.md — mention the universal antigen abstraction in the
  feature list and link to antigens.md.
- README.md — split the column enumeration into "fragment-derived"
  (shared between predict_from_antigens and variant methods) and
  "variant-only" rows, so both paths are accurately documented.
- mkdocs.yml — add Antigen Fragments and Expression Semantics to
  the nav; they were orphaned.

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.

3004 of 3409 relevant lines covered (88.12%)

2.64 hits per line