4.2.0-alpha.3

What's Changed

• Replace C/Cython with ms2rescore-rs by @RalfG in #260
• Update DeepLC and IM2Deep integration for their v4/v2 API rewrites by @RalfG in #261
• Merge correlate_preloaded into correlate with auto-detection of PSM spectrum property by @RalfG in #262
• Refactor/cleanup python internals by @RalfG in #263
• Cherry-pick fixes from fix/predict-library (PR #248) by @RalfG in #264

Full Changelog: v4.2.0-alpha.2...4.2.0-alpha.3

v4.2.0-alpha.2

Full Changelog: v4.2.0-alpha.1...v4.2.0-alpha.2

v4.2.0-alpha.1

Full Changelog: v4.2.0-alpha.0...v4.2.0-alpha.1

v4.2.0-alpha.0

Full Changelog: v4.1.2...v4.2.0-alpha.0

v4.1.2

Fixed

• Prefer (faster) Genesis for model downloads, with a fall back to Zenodo
• CI: Update build runners for macOS (see actions/runner-images#13046)
• Fix logging for spectral library prediction (by @paretje in #257)

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Full Changelog: v4.1.1...v4.1.2

v4.1.1

Fixed

• ⬆️ Fix support for sqlalchemy v2, keeping backwards compatibility with v1.4 (#249, fixes #250)
• 📝 Fix typo of max_length in search_space documentation (#245 by @paretje)
• 👷 In CI workflows, don't build dependencies like pyarrow from source. This can result in failed build workflows.

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Full Changelog: v4.1.0...v4.1.1

v4.1.0

Added

• ✨ Support for Thermo raw (requiring dotnet runtime) and gzipped spectrum files, through mobiusklein/mzdata (#226, by @paretje)
• ✨ New Python API usage mode correlate-single to correlate to a single ObservedSpectrum object with predictions (#232)
• ✨ Added support for Python 3.12 and 3.13, Numpy v2, and newer Pandas and XGBoost versions (#228)
• ✅ CI: Add integration test for predict-single (#228)

Changed

• ⚠️ Ion mobility is now returned instead of collisional cross section when IM2Deep is used through the add_ion_mobility option (#236, by rodvrees)
• 🏗️ Model files are now downloaded from Zenodo instead of Genesis (#225, by paretje, fixes #229)
• 📝 Docs: Updated README to include correlate-single; moved webserver API docs from old Wiki (#239)

Removed

• 🐍 Removed support for Python 3.8 (EOL) and for musllinux distributions (#228, #237)
• 🗑️ Removed old conversion scripts, mostly implemented in psm_utils (#239)
• 🗑️ Removed old train script, to be replaced with page in docs (#239)

v4.0.0

Fully refactored and drastically more user-friendly version of MS²PIP:

• More modular Python API
• One consolidated command-line interface with subcommands
• Support for all file formats readable by psm_utils
• Support for MGF, mzML, and Bruker raw spectrum files
• Support for ProForma 2.0 peptide notation (no modification configuration required anymore)
• Support for multiple peptides/PSMs per spectrum
• Detailed documentation on ms2pip.readthedocs.io
• ...

v3.13.0

Added

• New timsTOF 2024 model added (now alias for timsTOF) by @ArthurDeclercq in #211

Full Changelog: v3.12.0...v3.13.0

v3.12.0

What's Changed

• Add code and figures for 2023 NAR manuscript @ArthurDeclercq in #196 and #197
• Backport timsTOF model from 4.0 dev release to 3.12 release by @RalfG in #206

Full Changelog: v3.11.0...v3.12.0