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pybedtools: Add version 0.12.1 - #3009

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luhenry merged 1 commit into
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pybedtools
Oct 16, 2026
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luhenry merged 1 commit into
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pybedtools

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@luhenry luhenry commented Oct 13, 2026 •

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Compiles pybedtools' Cython extensions (cbedtools, featurefuncs), which wrap ~640 lines of BEDTools' own legacy C++ (BED/GFF file-type sniffing, gzip streaming) linked against system zlib/libstdc++; the actual bedtools command-line toolkit stays an external runtime dependency invoked via subprocess, never vendored or compiled here. Upstream publishes no riscv64 wheel.

Mirrors the build-wheels job of upstream's main.yml.

Differs from upstream

  • One manylinux_riscv64 image instead of x86_64/aarch64/macOS - no Windows job existed to drop (upstream already skips *-win*).
  • Added a CIBW_TEST_COMMAND - upstream's wheel job runs no tests at all; this one imports the compiled extension and builds an Interval.

Matrix: cp312/cp313/cp314 - numpy floors at cp312, and pandas (a runtime dep) has no cp314t wheel on the registry.

Testing

  • upstream's wheel-build job runs no tests; added a minimal import + Interval construction against numpy/pysam from the registry.

License: OK

Built locally on cp311 (x86_64): cythonize + wheel build succeed, install + the smoke import/Interval check pass.

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luhenry marked this pull request as draft October 13, 2026 09:25
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@luhenry
luhenry marked this pull request as ready for review October 16, 2026 00:25
@luhenry
luhenry merged commit 62f75c5 into main Oct 16, 2026
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@luhenry
luhenry deleted the pybedtools branch October 16, 2026 00:25
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