Ms2rescore

Fixed

- 📌 Pin DeepLC version to <3.1, avoiding calibration bug by RalfG in https://github.com/compomics/ms2rescore/pull/198
- 📌 Pin pyOpenMS (upstream dependency for psm_utils) (see openMS/openMS7600) by RalfG in https://github.com/compomics/ms2rescore/pull/199
- 📝 Fix incorrect decoy pattern configuration in documentation example by rodvrees in https://github.com/compomics/ms2rescore/pull/191
- 🐛 Fix UnicodeEncodeError when running IM2Deep (similar to DeepLC issue 188) ArthurDeclercq in https://github.com/compomics/ms2rescore/pull/195

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**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.1.2...v3.1.3

Changed

- 🚸 GUI: Improve user experience with descriptions, open report upon finishing, etc. (175)
- ⬆️ Update dependency versions; drop support for Python 3.8 (required for TensorFlow versions; EOL soon) (189)

Fixed

- 🚨 Fix ruff linting for tutorial notebook (was not checked by previous versions of Ruff) (180)
- 📝 Minor documentation updates: Update overview figure; refer to `ms2rescore.rescore` in Python API tutorial; remove v3.0 warning in readme (181)
- 📝 Fix README URLs to documentation pages (187)
- 🐛 Fix bug where the default TIMS²Rescore configuration items always overwrote user configuration (176)
- 🐛 Fix non-descriptive `IndexError` in Qvality when PEP cannot be calculated (see statisticalbiotechnology/triqler29). To be updated when addressed upstream. (182, fixes 165)
- 🐛 Fix `UnicodeEncodeError` when running DeepLC with transfer learning (188, fixes 183 and 185)

Fixed

- 👷 CI: Add missing ionmob dependency for Windows installer by RalfG in https://github.com/compomics/ms2rescore/pull/163 and https://github.com/compomics/ms2rescore/pull/173
- 🐛 GUI: Correctly parse IM2Deep config in GUI (fixes 172) by ArthurDeclercq in https://github.com/compomics/ms2rescore/pull/172
- 🐛 Limit Percolator processes to 128 (fixes 117) by RalfG in https://github.com/compomics/ms2rescore/pull/169


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Deployment

- 🚀 From this release onward, Docker images will be build and pushed to GHCR (by paretje in https://github.com/compomics/ms2rescore/pull/167)


New Contributors

- paretje made their first contribution in https://github.com/compomics/ms2rescore/pull/167

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.0.2...v3.1.1

Added

- ✨ New `tims2rescore` CLI entrypoint with TIMS-specific configuration defaults
- ✨ [IM2Deep](https://github.com/compomics/im2deep) feature generator for ion mobility
- ✨ Support for Bruker raw (`.d`) and miniTDF formats (was also back-ported to v3.0.3)
- ✨ `psm_id_rt_pattern` and `psm_id_im_pattern`: New options to allow parsing of RT/IM from PSM file spectrum identifiers.
- ✨ `max_psm_rank_input` and `max_psm_rank_output`: New options to control rescoring and reporting of multiple PSMs per spectrum (default 5 and 1)
- ✨ Also store peptide-level q-value and PEPs in the output PSM list, under the `metadata` field.
- ✨ `profile` option to write a cProfile report of the rescoring process (for debugging)
- ✨ Option to pass `train_fdr` to Mokapot (`test_fdr` was already supported as kwarg)
- ⚡ Faster spectrum file reading with `timsrust` and `mzdata` Rust libraries
- 📝 Add TIMS²Rescore docs and citation on README; more detailed docs on formula modifications

Changed

- 👷 CI: Lint with ruff instead of flake8
- ⚡ DeepLC: By default use PSMs initially passing 1% FDR threshold for calibration instead of a fixed number
- 🔊 DeepLC: Throw warning when using `deeplc_retrain` with less than 500 calibration PSMs
- 🔊 Raise exception if missing precursor info (retention time or ion mobility) could not found in both PSM and spectrum files.
- ⬆️ Update (and sort) dependencies in `pyproject.toml`
- 📦 Dockerfile: Use Python 3.11 base image instead of Ubuntu
- 🔧 Config: Change `write_report` default value from `true` to `false`

Fixed

- 🐛 Report: Fix calculation of number of retained peptides in identification overlap chart
- 🐛 DeepLC: Fix issue with conversion to PEPREC (fixes 108, fixes 113)
- 🐛 Fix bug in infer_spectrum_path if path in configuration is None
- 🐛 Fix bug that always set `im_required` to `True`, even if no IM-based feature generators were configured.

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

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev8...v3.1.0-dev9

**Full Changelog**: https://github.com/compomics/ms2rescore/compare/3.1.0-dev7...v3.1.0-dev8