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MAINT: build Python 3.14 wheels; fix to_anndata for anndata 0.13 - #1005
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#1004 upgraded cibuildwheel to a version that supports 3.14, but the build selector in pyproject.toml still listed cp39-cp313, so no cp314 wheels were produced. Add cp314-* to the selector. Also note the in1d -> isin fix (#1003) in the ChangeLog. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
anndata 0.13.0 removed the dtype argument to AnnData(), so Table.to_anndata() raised TypeError. Cast the matrix before constructing the AnnData object instead. This also removes the FutureWarning older anndata versions emitted for dtype=. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Prep for 2.1.18. This PR has two commits.
1. Build cp314 wheels
#1004 upgraded cibuildwheel to v3.4.1, but
[tool.cibuildwheel] buildinpyproject.tomlstill listedcp39–cp313. As a result, no cp314 wheels were built. 2.1.17 on PyPI has none, and a release cut from current master wouldn't have any either.This commit adds
cp314-*to the build selector.cibuildwheel==3.4.1 --print-build-identifiersnow listscp314on all five targets: manylinux x86_64/aarch64, macOS x86_64/arm64, and win_amd64. Free-threadedcp314tbuilds stay excluded.2. Fix
Table.to_anndatafor anndata >= 0.13anndata 0.13.0 (July 2026) removed the
dtypeargument toAnnData(). With it,to_anndata()raisesTypeError. Master last passed CI on June 1, before that release. CI for this PR was the first run to pick up anndata 0.13.4, and it failedtest_to_anndata_{dense,sparse,metadata}.This commit casts the matrix before constructing the
AnnDataobject. Verified:dtype=FutureWarning that older anndata emitted is gone.Note: the
to_anndatadocstring example's repr gains alayers: None (.X)line under anndata 0.13. CI doesn't run doctests, so it isn't changed here.Why a 2.1.18 release rather than adding wheels to 2.1.17
2.1.17 calls
np.in1d, which NumPy 2.4 removed (#1003). Built from the 2.1.17 tag on Python 3.14 with NumPy 2.5.3, the test suite fails 5 tests in the HDF5 ID-subsetting paths (from_hdf5(ids=...),biom subset-table). cibuildwheel's test step would reject those wheels. Master already has the fix from #1000.Release notes
manylinux_2_28image, but auditwheel still tags the Linux wheelsmanylinux_2_5(x86_64) andmanylinux2014(aarch64), so they remain installable on older glibc.🤖 Generated with Claude Code