Ms2pip

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)

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](https://ms2pip.readthedocs.io)
- ...

**Full Changelog**: https://github.com/compomics/ms2pip/compare/v4.0.0-dev13...v4.0.0-dev14

**Full Changelog**: https://github.com/compomics/ms2pip/compare/v4.0.0-dev12...v4.0.0-dev13

**Full Changelog**: https://github.com/compomics/ms2pip/compare/v4.0.0-dev11...v4.0.0-dev12

**Full Changelog**: https://github.com/compomics/ms2pip/compare/v4.0.0-dev10...v4.0.0-dev11