openvax / topiary
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master: 90%

LAST BUILD BRANCH: v5.16.2
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LAST BUILD ON BRANCH pr-b-fragment-refactor
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coverage: 88.127% (+0.1%) from 87.994%
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24409356618 pr-b-fragment-refactor CHANGELOG: spell out the 5.4.0 downstream migration checklist PR #121 consumer feedback flagged that the "breaking rename" section listed what was renamed but didn't give a migration recipe. Add an explicit checklist: old symbol → new symbol for... Pull #121 iskandr github
88.13
24404280509 pr-b-fragment-refactor Add frameshift fragment regression tests — v5.4.0 Pin _fragment_from_effect behavior on varcode FrameShift / FrameShiftTruncation effects, addressing the PR B review concern that inframe=True would drop downstream novel 9-mers under only_novel_ep... Pull #121 iskandr github
88.12
24376471099 pr-b-fragment-refactor 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 ... Pull #121 iskandr github
88.12
24374071502 pr-b-fragment-refactor 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. - Extr... Pull #121 iskandr github
88.12
24372918168 pr-b-fragment-refactor 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 referenc... Pull #121 iskandr github
88.12
24372442691 pr-b-fragment-refactor Refactor predict_from_variants onto AntigenFragment (PR B) predict_from_mutation_effects now builds a list of AntigenFragments from varcode effects and delegates to predict_from_antigens, replacing the parallel per-row metadata loop. The variant ... Pull #121 iskandr github
87.95
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