Releases · compomics/ms2rescore

02 Oct 08:59

RalfG

v3.1.3

7885db8

v3.1.3 Latest

Latest

Fixed

📌 Pin DeepLC version to <3.1, avoiding calibration bug by @RalfG in #198
📌 Pin pyOpenMS (upstream dependency for psm_utils) (see OpenMS/OpenMS#7600) by @RalfG in #199
📝 Fix incorrect decoy pattern configuration in documentation example by @rodvrees in #191
🐛 Fix UnicodeEncodeError when running IM2Deep (similar to DeepLC issue #188) @ArthurDeclercq in #195

Full Changelog: v3.1.2...v3.1.3

Contributors

RalfG, ArthurDeclercq, and rodvrees

Assets 3

18 Sep 07:16

RalfG

v3.1.2

b1e23f3

v3.1.2

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/triqler#29). To be updated when addressed upstream. (#182, fixes #165)
🐛 Fix UnicodeEncodeError when running DeepLC with transfer learning (#188, fixes #183 and #185)

Assets 3

14 Aug 09:46

RalfG

v3.1.1

4215f8d

v3.1.1

Fixed

👷 CI: Add missing ionmob dependency for Windows installer by @RalfG in #163 and #173
🐛 GUI: Correctly parse IM2Deep config in GUI (fixes #172) by @ArthurDeclercq in #172
🐛 Limit Percolator processes to 128 (fixes #117) by @RalfG in #169

Deployment

🚀 From this release onward, Docker images will be build and pushed to GHCR (by @paretje in #167)

New Contributors

@paretje made their first contribution in #167

Full Changelog: v3.0.2...v3.1.1

Contributors

paretje, RalfG, and ArthurDeclercq

Assets 3

21 Jul 18:54

RalfG

v3.1.0

7ccb280

v3.1.0

Added

✨ New tims2rescore CLI entrypoint with TIMS-specific configuration defaults
✨ 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.

Full Changelog: v3.0.3...v3.1.0

Assets 3