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Add Python 3.14 support - #11

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CarlKCarlK wants to merge 15 commits into
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py314
Open

Add Python 3.14 support#11
CarlKCarlK wants to merge 15 commits into
masterfrom
py314

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@CarlKCarlK

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Summary

  • Add Python 3.14 support
  • Update dependency markers and migrate packaging to uv_build
  • Modernize and expand CI and installed-artifact testing
  • Repair tutorial sample-data retrieval
  • Update and execute the maintained notebooks
  • Add a Trusted Publishing release workflow
  • Prepare version 0.5.15

Validation

  • 725 canonical tests pass locally
  • Optional BGEN tests pass
  • Tutorial and paper notebooks were executed and reviewed
  • GitHub CI covers Python 3.10 through 3.14 across supported platforms

- Updated Jupyter notebooks (paper.ipynb, tutorial.ipynb) to use example_file_synth for synthetic data retrieval.
- Modified pyproject.toml and pysnptools.pyproj to include synth.hashdown.json in the package.
- Enhanced bed.py and pairs.py to utilize example_file_synth for synthetic BED file access.
- Introduced example_file_synth function in _example_file.py for synthetic file retrieval.
- Updated pysnptools.hashdown.json to remove references to unavailable tutorial files.
- Added synth.hashdown.json to manage synthetic data file hashes.
- Revised PYTHON_3_14_SUPPORT_SPEC.md to reflect changes in tutorial data handling and hashdown integrity.
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