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Changelog

All notable changes to this project will be documented in this file. The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

[0.5.0] - 2026-07-13

First stable 0.5.0 release. No functional changes since 0.5.0-beta.1.

0.5.0-beta.1 - 2026-06-18

Added

  • annotate_ms2_spectra: annotate MS2 spectra with theoretical fragment ions (tolerance in Da or ppm, configurable fragmentation model and mass mode)
  • score_ms2_spectra: compute per-ion-series MS2 scoring features (matched ions, longest sequence, explained intensity) with optional hyperscore
  • ms2pip_compute_features: compute 139 MS2PIP XGBoost feature vectors per cleavage site from ProForma peptide strings
  • ms2pip_compute_theoretical_mz: compute theoretical fragment m/z arrays (numpy float32) for arbitrary ion types and charges
  • ms2pip_extract_targets: extract per-ion-type observed intensity arrays from annotated spectra for model training
  • AnnotatedMS2Spectrum and FragmentAnnotation types with pickle support
  • Codebase restructured into types/, io/, scoring/, and ms2pip/ modules
  • ARM64 wheel builds for Windows and macOS

0.4.3 - 2025-09-30

Fixed

  • Crash on empty spectra (contributed by @di-hardt)

Changed

  • Updated mzdata to 0.59.2

0.4.2 - 2025-04-01

Changed

  • Updated mzdata to 0.48.3

0.4.1 - 2025-01-15

Fixed

  • Thermo RAW files without pre-centroided peaks now read correctly (vendor centroiding is now requested explicitly)

Changed

  • Updated timsrust to 0.4

0.4.0-1 - 2024-11-20

Changed

  • Added Python 3.13 wheel builds

0.4.0 - 2024-10-24

Added

  • Thermo RAW file support via mzdata
  • is_supported_file_type utility function

Changed

  • Dropped x86 Linux wheel builds
  • Updated mzdata

0.3.0 - 2024-07-17

Changed

  • Updated timsrust to 0.3.0

0.2.1 - 2024-07-01

Added

  • Tests for get_ms2_spectra

Changed

  • Updated mzdata to 0.20.0

0.2.0 - 2024-04-08

Added

  • get_ms2_spectra: read MS2 spectra from spectrum files

0.1.0 - 2024-04-05

Added

  • Initial release: get_precursor_info for mzML, MGF, and Bruker TDF files