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