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Relax Dask, Sphinx and stale dependency pins - #1364
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jeromekelleher merged 2 commits intoOct 27, 2026
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Newer Dask releases no longer accept a lazy scalar as the stop value of da.arange, which Tajimas_D used to build the harmonic sums from the number of sampled chromosomes. Compute the sums with map_blocks instead. The results are unchanged, and Tajimas_D no longer computes the allele counts when it is called, which older Dask did implicitly.
Require Dask >= 2025.2.0, the minimum Xarray 2026.9.0 tests against, and drop the <= 2024.8.0 cap. Remove the Sphinx < 9 cap and the obsolete fsspec and ablog exclusions, and keep pandas < 3.0 for now. Refresh uv.lock, which moves to Dask 2026.8.0, NumPy 2.5, Numba 0.68 and Sphinx 9. Drop the Dask override from the docs workflows and the contributing guide, and install Dask 2025.2.0 in the minimum-version job so the new floor is tested. Replace the obsolete StoreLike nitpick entry with a mapping from the zarr.core.group.StoreLike reference that the newer sphinx-autodoc-typehints generates to zarr.storage.StoreLike, where Zarr documents it, and move the coverage pragma in TruncatedSVD to the branch for Dask releases without svd(full_matrices=...).
Billyzhang1229
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October 26, 2026 23:37
Billyzhang1229
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Dask has been capped at 2024.8.0 since #1248, because later releases made the main build very slow (#1247, tracked in #1267). The Sphinx < 9 and pandas < 3 caps were added in #1339, and the fsspec and ablog exclusions date from 2021 and 2022 (#625, #877).
This PR:
Tajimas_Dwith newer Dask, which no longer accepts a lazy scalar as the stop value ofda.arange. The harmonic sums are now computed withmap_blocks. The results are unchanged, andTajimas_Dno longer computes the allele counts when it is called.uv.lock, which moves to Dask 2026.8.0, NumPy 2.5, Numba 0.68 and Sphinx 9.zarr.core.group.StoreLikereference that sphinx-autodoc-typehints now generates tozarr.storage.StoreLike, where Zarr documents it, soStoreLikelinks to the Zarr docs. This replaces the nitpick entry that Sphinx 8 needed.TruncatedSVDto the branch for Dask releases withoutsvd(full_matrices=...), which the locked Dask no longer runs.With newer Dask,
pairwise_distancestill rebuilds and recompiles its Numba gufuncs on every call, which adds about 2 seconds per call for the correlation metric. Following PR #1365 will fix this and closes #1267, so it would be best to merge the two together.Part of #1267.
Testing: