First bigbio release of msgf+#14

Merged

ypriverol merged 517 commits into

May 23, 2026

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Commits on May 6, 2026

chore(workspace): drop placeholder output crate; engine::output is canonical (Track A1)
ypriverol
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refactor(engine): consolidate tiny_param test fixtures into engine::testutil (Track A2)
ypriverol
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refactor(engine): narrow public re-exports to common domain types (Track A3)
ypriverol
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refactor(engine): extract output::row_context shared by pin/tsv writers (Track A4)
ypriverol
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refactor(workspace): rename cli crate → msgf-cli; lib renamed msgf_diff → msgf_cli (Track A5)
ypriverol
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fix(engine): score_psm uses node_score per split (Phase 6 GF scale) (Track B1)
ypriverol
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fix(engine): candidate_gen expands terminal mods (NTerm, CTerm, Protein_*) (Track B2)
ypriverol
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fix(engine): per-charge ScoredSpectrum cache for charge-missing spectra (Track B3)
ypriverol
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fix(engine): per-PSM protein-terminal flags into GF construction (Track B4)
ypriverol
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fix(engine): N-terminal Met cleavage candidate variants (Track B5)
ypriverol
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refactor(workspace): split engine — extract model crate (Phase 1/5)
ypriverol
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refactor(workspace): split engine — extract scoring crate (Phase 2/5)
ypriverol
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refactor(workspace): split engine — extract search crate (Phase 3/5)
ypriverol
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refactor(workspace): split engine — reactivate output crate (Phase 4/5)
ypriverol
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