Migration to joblib + new build system + separate reusable publish workflow #58
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Update Python version requirements and streamline CI workflows Update publish workflow to trigger on version tags Enhance publish workflow with manual trigger and dependency on CI completion Refactor publish workflow to simplify naming and improve tag-based publishing conditions try to fix dispatch fix syntax test without if update workflow
New build system + release actions test
Joblib migration
asiomchen
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This pull request introduces several updates to the parallel processing, GitHub workflows, project configuration, and documentation for the
scikit-molproject.Migration to joblib
Solves #59
multiprocessingwas fully replaced withjobliband separate function inparallel.pyadded to handle the parallel processing, this decreases tests run time on Windows from ~7 minutes to ~1.5 minutesparallelwas replaced withn_jobsto match sklearn APIploting.pywas added for parallel benchmarksFix safe inference on parallel runs
When the safe inference mode is enabled and results are concatenated in case on fully valid/invalid inputs
np.ma.concatenatesimplifies mask to the single boolean, causingfilter_invalid_rowsto fail, additional condition was added to handle thisFix fit check for transformers and SafeInferenceWrapper
Python Support
GitHub Workflows:
.github/workflows/publish.yaml: Added a new workflow to build and publish Python distributions usinguvand sign them with Sigstore. This workflow handles building the distribution, storing artifacts, and creating GitHub releases..github/workflows/pytest.yaml: Renamed fromrun_pytests.yamland updated to include concurrency control, installuv, and use the new publish workflow for tagged commits. [1] [2].github/workflows/welcome.yaml: Added a new workflow to welcome new contributors when they open issues or pull requests.Project Configuration:
pyproject.toml: Migrated the build system to usehatchlingandhatch-vcs, updated project metadata, and added dependencies and optional dependencies for development. [1] [2]Documentation:
CONTRIBUTING.md: Updated the release instructions to reflect the new automated workflow for PyPi releases.README.md: Updated the logo display to use the<picture>element for better support of dark and light modes on PyPi