feat(speclib): Skyline transition list CSV support + speclib_build_cli bundle#55

Merged

jspaezp merged 24 commits intomainfrom

feat/skyline-speclib

Apr 16, 2026

Commits on Apr 16, 2026

feat(timsseek): add DigestSlice::as_str() for zero-alloc access
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feat(timsseek): add SerSpeclibElement constructors + SpeclibWriter for msgpack.zst
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feat: scaffold speclib_build_cli crate
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feat(speclib_build): CLI, config, mods, dedup, decoys
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feat(speclib_build): Koina HTTP client + model registry + request/response adapter
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feat(speclib_build): entry builder — Koina predictions to SerSpeclibElement
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feat(speclib_build): pipeline orchestration — digest→dedup→expand→predict→write
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feat(speclib_build): integration tests, lib.rs, Taskfile recipes
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fix(speclib_build): strip mods for Koina, convert annotation format
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chore: update speclib build references from Python CLI to Rust CLI
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feat(speclib_build): add --request-delay-ms for Koina rate limiting
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fix(speclib_build): better Koina response error reporting with body preview
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fix(speclib_build): skip peptides with non-standard AAs (U/B/J/Z/X), warn affected proteins
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feat(bench): add --koina-url flag for local/custom Koina server
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fix(taskfile): reuse koina container to avoid re-downloading models
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fix(bench): add request delay for public Koina rate limiting
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fix(speclib_build): use modified sequence for precursor mz + Koina input
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feat(speclib_build): add Prosit_2023_intensity_timsTOF, make it default
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fix: default RT tolerance to Unrestricted for iRT library compatibility
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feat(speclib): add Skyline transition list CSV parser
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chore: remove Python speclib_builder, superseded by Rust speclib_build_cli
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chore: drop jupyter and ipykernel from workspace
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ci(release): publish speclib_build binary
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chore: bump version to 0.28.0
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