Ms2rescore

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev2...v3.1.0-dev3

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev1...v3.1.0-dev2

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.0.3...v3.1.0-dev1

Added

- Allow user to pass `model_dir` to MS²PIP in feature generator (fixes 134)

Changed

- Missing precursor information (retention time and ion mobility) is now parsed in Rust using [mzdata](https://github.com/mobiusklein/mzdata) and [timsrust](https://github.com/MannLabs/timsrust), adding the new [ms2rescore-rs](https://github.com/compomics/ms2rescore-rs) package. This change also adds support for Bruker TDF and miniTDF raw files for this feature.
- Use single quotes instead of back ticks when logging strings for improved Rich formatting.
- Reactivate tests in CI.

Fixed

- Fix writing of FlashLFQ output file with Mokapot when PSM List `run` fields are empty.
- Write partial report when confidence before could not be calculated (e.g., when no PSMs identified before rescoring)

---

Windows installer Includes changes from upstream tools:

- psm_utils: https://github.com/compomics/psm_utils/compare/v0.7.3...v0.8.2
- MS²PIP: https://github.com/compomics/ms2pip/compare/v4.0.0-dev8...v4.0.0-dev10

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.0.2...v3.0.3

Fixed

- Remove PSMs with invalid amino acids to avoid errors in feature generators (126 )

Fixed

- Don't use unsupported icon on Linux systems (fixes 118)

Changed

- Improved exception handling and logging for report generation
- Update deeplc_retrainer version
- Pin Numpy version for Python 3.11 (incompatibility between pyGAM, sklearn, and tensorflow)


**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.0.0...v3.0.1