Default to Python 3.12, add idxml extra, upgrade DeepLC ≥ 3.1, and fix ignored profile config parameter #237
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…dows installer) - Python versions: Drop support for 3.9 (EOL); evaluate support for 3.12, 3.13, 3.14; move to 3.12 as default for Docker and Windows installer - Upgrade to DeepLC >=3.1 - Attempt to suppress OpenMS data warning
…y the CLI argument was checked.
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Pull Request Overview
This PR updates packaging and environment configurations, focusing on Python version standardization, dependency updates, and bug fixes. The changes enable Python 3.12+ support, update DeepLC dependency constraints, add an optional idxml extra for pyopenms integration, fix a bug in profile config parameter handling, and suppress pyopenms warnings.
- Default Python version updated to 3.12 across CI/CD workflows
- DeepLC dependency constraint relaxed from
<3.1to>=3.1 - New optional
idxmlextra added for pyopenms support with warning suppression
Reviewed Changes
Copilot reviewed 6 out of 7 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| pyproject.toml | Updated DeepLC version constraint and added idxml optional dependency |
| ms2rescore/main.py | Fixed profile parameter to read from config instead of CLI args |
| ms2rescore/init.py | Added warning filter for pyopenms OPENMS_DATA_PATH message |
| Dockerfile | Updated sync command to include all extras |
| .github/workflows/test.yml | Updated Python versions to 3.10-3.14 and added idxml extra to installation |
| .github/workflows/publish.yml | Updated default Python version to 3.12 |
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RalfG
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Added
idxmlextra for pyOpenMS; enabled by default in the Docker image and Windows installer to provide idXML support out of the box.Changed
>= 3.1.Fixed
profileparameter from configuration files — previously, only the CLI argument was honored.