…r msgpack.zst

Add pub constructors (new()) to PrecursorEntry, ReferenceEG, and SerSpeclibElement
so external crates can construct speclib entries. Make PrecursorEntry pub. Add
SpeclibWriter<W> wrapping zstd::Encoder for streaming msgpack.zst output. Re-export
all four types from data_sources. Two roundtrip tests cover both rmp_serde encode/decode
and the full writer→reader pipeline.

- clap CLI with all args + TOML config merge (CLI > TOML > defaults)
- Proforma mod parser: fixed + variable mod application
- Bloom + bucket HashMap peptide dedup
- REVERSE + EDGE_MUTATE decoy strategies
- Example config at repo root

…ponse adapter

…lement

…dict→write

- lib.rs re-exports for integration test access
- 3 integration tests: digestion+dedup, mod chain, decoy roundtrip
- Taskfile: speclib:build, speclib:local-koina, speclib:stop-koina

- Prosit expects bare AA sequences, strip bracket mods before sending
- Convert Koina annotation format (y1+1) to mzPAF format (y1^1)
- Make strip_mods pub for pipeline use

…review

…warn affected proteins

- Precursor m/z now computed from modified sequence (includes +57 for Cys carbam)
- Koina receives modified sequences with [UNIMOD:N] notation (Prosit handles them)
- to_proforma converts [U:N] → [UNIMOD:N] (rustyms parses [U:N] as element Uranium)
- Isotope distribution also uses modified formula

- Add Prosit_2023_intensity_timsTOF and Prosit_2020_intensity_CID to model registry
- Default fragment model now timsTOF-specific (was HCD)
- Same Triton v2 schema, drop-in compatible

- Tolerance::default() now uses RtTolerance::Unrestricted (was Minutes(5,5))
- Prescore extracts full RT range, calibration maps library→observed RT
- Bench config drops explicit RT tolerance (defaults to unrestricted)
- Users with calibrated libraries can still set "rt": {"minutes": [N, N]} in config

New skyline_io module parses Skyline Peptide Transition List exports
as a spectral library source, mirroring the DIA-NN/Spectronaut pattern
(sniff + group-by-precursor + emit TimsElutionGroup<IonAnnot> plus
SkylinePrecursorExtras). Wires through timsquery's dispatch,
timsquery_viewer's extras view, and timsseek's speclib converter
(reusing convert_diann_to_query_item via a small extras adapter).

Notable behaviors:
- Precursor-isotope rows (Fragment Ion Type == "precursor") are
  skipped; downstream computes the envelope from the sequence.
- `#N/A` Library Intensity values default to 1.0.
- RT/IM columns are absent in Skyline exports; defaults to 0.0
  with a loud warning (use Unrestricted RT tolerance).
- Modifications in `[...]` are stripped for the stripped_peptide
  field; modified_peptide is preserved verbatim.

…d_cli

Drops the Python speclib_builder package and all references (root
pyproject workspace/deps, hatch packages, uv sources, uv.lock).
The Rust speclib_build_cli now owns the digest → dedup → expand →
Koina predict → write pipeline end-to-end.

No notebooks in the repo and no other references to jupyter. Prunes
~100 transitive deps from uv.lock.