Added

• ✨ Release notifications: Update checks for both GUI and CLI, with a popup (GUI) or console notice (CLI); introduce the disable_update_check configuration option.
• ✨ Citations GUI: Add IM2Deep to the citations interface (feature integration).
• 🚸 PSM–spectrum consistency: If observed m/z values are present in the PSM list, always verify that PSMs match the corresponding spectra.
• 🚸 Regex pattern validation: Added validation for PSM and spectrum ID regex patterns with clear error messages when patterns are invalid or don't match expected spectrum IDs.

Changed

• 🔁 FlashLFQ export pathway: Switch to the FlashLFQ writing functionality in psm_utils. This removes the ms2rescore > mokapot > write_flashlfq option and adds a new top-level ms2rescore > write_flashlfq option.
• 🚸 Precursor completeness policy: Do not continue if precursor information (m/z, RT, or IM) is missing for a subset of PSMs; previously, such PSMs were silently removed.
• 🚸 Parsing: Further improve handling of missing LC–IM–MS fields in spectrum files.
• 🔊 Diagnostics: Clearer logging while parsing precursor information—always raise an error if a PSM cannot be found in the spectrum files and include example PSM IDs from both the PSM and spectrum files.
• ⚙️ Allow more unset values in config: Permit null/None for boolean options to explicitly represent an unset state.
• 🐍 Python versions: Drop support for 3.9 (EOL). Test matrix extended to 3.12–3.14 with compatibility verified through 3.12; 3.13 and 3.14 currently fail due to missing third-party dependencies. Default runtime set to Python 3.12 for Docker and the Windows installer.
• ⬆️ Dependencies: DeepLC → >= 3.1; IM2Deep → >= 0.3.1
• 📦 Packaging: Switch to UV for package management and introduce a lockfile to ensure reproducible installations; the version’s single source of truth now resides in pyproject.toml.
• 🐳 Docker: Upgrade base image to python:3.12-slim and use the lockfile to pin dependency versions.
• 📦 Development dependencies: Move dev dependencies into dependency-groups in pyproject.toml.
• 🔇 OpenMS: Attempt to suppress non-actionable OpenMS data warnings to reduce noise.
• 👷 CI: Separate the linting step for faster feedback and update CI action versions.
• 🔧 Tooling: Update pre-commit hook packages.
• ♻️ Code quality: General refactoring of the parse_spectra module; refine and expand type annotations.

Fixed

• 🐛 CLI/Config precedence: Prevent command-line defaults (e.g., False) from overriding True values specified in the configuration file.
• 🐛 Config profile: Respect the profile parameter from configuration files—previously only the CLI argument was honored.
• 🐛 Parsing of missing precursor data: Correct handling of spectrum files with missing precursor information—previously, precursor data were parsed even when not required by the configured feature generators.
• 🐛 XGBoost & CUDA environment: Avoid incompatibility between CUDA_VISIBLE_DEVICES and XGBoost (Windows crash when set to -1) that could lead to a crash without error messages.
• 🐛 NumPy 2 compatibility: Replace Inf/np.Inf usage with inf to maintain compatibility with NumPy 2.0.

Full Changelog: v3.1.5...v3.2.0

Fixed

• 🐛 Fixed compatibility with Numpy 2: Usage of np.inf instead of `np.Inf (PR #224, fixes #219)

What's Changed

• Fix silent crash due to XGBoost-CUDA environment variable incompatibility by @RalfG in #216
• Update pyproject.toml, version bump IM2Deep by @rodvrees in #214
• Add IM2Deep to citations GUI by @rodvrees in #215
• CI: Update action versions by @RalfG in #217

Full Changelog: 3.2.0.dev1...v3.2.0.dev2

What's Changed

• Switch to FlashLFQ output from psm_utils by @RalfG in #186
• Support gzipped spectra files (and Thermo raw!) by @paretje in #184
• Refactor parsing of precursor data from spectrum files by @RalfG in #162

Still planned for 3.2.0, but not yet included

• Spectrum feature generator and Mumble integration (#178)

Full Changelog: v3.1.4...3.2.0.dev1

Fixed

• Update im2deep import after API change in v0.3.1 (#205, fixes #204, by @ArthurDeclercq)

Full Changelog: v3.1.3...v3.1.4

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

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)

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

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