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Update notebooks for PySnpTools 1.0 - #19
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- Dist: install pysnptools[bgen]; tutorial and paper: note that the HDF5 readers need pysnptools[hdf5]. - Link to README on main, update the version line, fix a typo. - Re-execute tutorial, paper, and Dist from start to finish on Python 3.14.5 with PySnpTools 1.0.0, bed-reader 1.2.0, FaST-LMM 1.0.0 (local), and QCTool 2.2.5 for Dist's BGEN writing. Dist's outputs are unchanged; tutorial and paper differ only in one p-value at the 7th significant digit and the removal of an old bed-reader RuntimeWarning.
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Update notebooks for PySnpTools 1.0
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Follow-up to #18, before tagging 1.0.0. Notebooks aren't packaged, so this doesn't affect the release artifacts.
Text fixes
pysnptools[bgen](BGEN is now an optional extra).pysnptools[hdf5].maininstead ofmaster, update the version line to 1.0.0, fix a typo.Re-executed from start to finish (RELEASING.md step 7) on Python 3.14.5 with PySnpTools 1.0.0, bed-reader 1.2.0 (PyPI), FaST-LMM 1.0.0 (local annual-update branch, for the tutorial's GWAS example), and QCTool 2.2.5 (for Dist's BGEN writing):
RuntimeWarning: invalid value encountered in cast.Derivation normalization.ipynbis a historical Python 2 note and is unchanged.