Changed

• 📌 Update installer dependency pins (pyopenms 3.5, psm_utils 1.5, ms2rescore-rs 0.4.3, deeplc 3.1.13, im2deep 1.2.0)
• 🔒 Update lock file

Removed

• 🔥 Dropped support for Python 3.10 (required for DeepLC)

Fixed

• 🐛 report: Catch indexerror if no confidently identified PSMs (#243, fixes #231).
• 🐛 report: Fixed empty charts due to mismatching plotly.js version. The version is now determined dynamically preventing future issues (#242)
• 🐛 GUI: Fixed missing log file when running MS²Rescore through the GUI (#242)
• 🐛 GUI: Fix an issue where running DeepLC through the GUI in debug mode resulted in an error due to stdout/stderr being None (#242)
• 🐛 PyInstaller: Fix recent issues with missing dependencies in Windows Installer (#242)
• 📌 PyInstaller: Use dependency groups and uv to pin certain package versions for the Windows installer (#241)
• 📝 docs: Fix typo in default argument of IM2Deep docstring (#241)

The Windows installer also contains changes from these upstream packages

psm_utils (v1.5.1)

Fixed

• 🐛 io.idxml: Fix compatibility with pyOpenMS 3.5+ for PeptideIdentificationList handling (also see OpenMS/OpenMS#8552).
• 🐛 io.percolator: Fix missing ScanNr values when using write_file (fixes #235).
• 🐛 io.percolator: Fix missing style argument when checking whether PercolatorTabWriter supports write_psm.
• 🐛 io.pepxml: Fix robustness of PepXMLReader against missing params in file.

IM2Deep (v1.2.0, v1.1.0)

Fixed

• ⬆️ Remove Numpy version pin; general linting and typing updates (CompOmics/IM2Deep#17, fixes #244)
• 🐛 Fix MS2Rescore compatibility (calibration data typing) (CompOmics/IM2Deep#15)

MS²PIP (v4.1.2, v4.1.1)

Fixed

• 🐛 Prefer (faster) Genesis for model downloads, with a fall back to Zenodo
• ⬆️ Fix support for sqlalchemy v2, keeping backwards compatibility with v1.4 (CompOmics/ms2pip#249, fixes CompOmics/ms2pip#250)
• 📝 Fix typo of max_length in search_space documentation (CompOmics/ms2pip#245)
• 👷 CI: Update build runners for macOS (see actions/runner-images#13046)
• 👷 CI: Don't build dependencies like pyarrow from source. This can result in failed build workflows.

Full Changelog: v3.2.0...v3.2.1

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