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luhenry
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luhenry
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October 14, 2026 11:34
The cp312 job segfaulted in tree/tests/test_me.py::test_bme_real, in skbio/tree/_me.py's _bme calling _bal_avgdist_nest, whose prange asks for schedule="dynamic". That compiles to libgomp's GOMP_loop_nonmonotonic_dynamic_* path, which faults on the riscv64 runners (#617). Patch the two dynamic pranges in skbio/tree/_c_me.pyx to schedule="static"; no other extension uses a non-static schedule. The cp310 and cp311 jobs failed installing the wheel's runtime dependencies: h5py and biom-format have riscv64 wheels for cp312+ only, in our registry and on PyPI, and our scipy for them stops at 1.15.2, so pip fell back to a scipy sdist and stopped on missing OpenBLAS. Drop both interpreters until those dependencies are published for them. The extensions build with -fopenmp, so auditwheel vendors the image's libgomp into scikit_bio.libs/. Add the gpl_sources job for gcc and pass its artifact to publish.
All three build legs (cp312/cp313/cp314) failed identically: the wheel itself built fine, but installing it pulled in scikit-bio's unpinned pandas>=1.5.0 runtime dependency, which pip resolved to PyPI's newest release (3.1.0). Our registry only hosts pandas up to 3.0.6 for these interpreters, so pip fell back to the 3.1.0 sdist, which fails to build on riscv64: pandas' SIMD moments code calls xsimd::load_unaligned/ reduce_add/broadcast, none of which exist in xsimd's generic/scalar riscv64 arch. CIBW_TEST_ENVIRONMENT: PIP_PREFER_BINARY=1 (test-phase only, mirroring gotcha 354) makes pip prefer our registry's older wheel-backed pandas over the newer sdist-only one.
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scikit-bio0.7.3Compiles 7 Cython extensions (tree, ordination, distance, alignment, metadata, diversity). Upstream publishes no riscv64 wheel.
Mirrors upstream's
wheels.yml.Differs from upstream
Testing
python -m skbio.test)License: OK
Built on cp311 (local x86_64 rehearsal); 7/7 extensions present,
import skbioand version check pass.