openvax / topiary / 24376471099

88%

master: 90%

Build Type

Pull #121

github

Committed by iskandr

Commit Message

Rename AntigenFragment → ProteinFragment (no back-compat alias)

The new name describes what the object IS (a slice of some protein —
natural, chimeric, foreign, or designed) rather than what it's FOR
(antigenicity is a prediction outcome, not an inherent property).
Matches Isovar's convention.

Clean break — per the major-version-cleanup preference, no deprecated
alias. v5.3.0 hasn't tagged yet, so this is in-flight with the
AntigenFragment refactor rather than a follow-up.

Renamed:
- AntigenFragment → ProteinFragment
- topiary/antigen.py → topiary/protein_fragment.py
- topiary/io_antigen.py → topiary/io_protein_fragment.py
- tests/test_antigen.py → tests/test_protein_fragment.py
- tests/test_predict_from_antigens.py → tests/test_predict_from_fragments.py
- docs/antigens.md → docs/fragments.md
- TopiaryPredictor.predict_from_antigens → predict_from_fragments
- TopiaryPredictor._build_antigen_rows → _build_fragment_rows
- read_antigens / write_antigens / iter_antigens →
  read_fragments / write_fragments / iter_fragments

All cross-references updated: mkdocs.yml nav, CHANGELOG 5.3.0 entry,
README, docs, error messages, __str__ output, test error-message
expectations. CHANGELOG 5.2.0 entry left as historical record (that
release really did ship with AntigenFragment).

962 tests passing, lint clean.

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

Coverage Stats

94 of 98 new or added lines in 4 files covered. (95.92%)

5 existing lines in 1 file now uncovered.

3004 of 3409 relevant lines covered (88.12%)

2.64 hits per line