Force re-cythonization to fix stale .c files breaking downstream builds - #121
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`setup.py` shipped Cython-generated .c/.h files in the sdist, produced at release time with whatever NumPy/Cython happened to be newest. Since the old `Cython.Distutils.build_ext` only re-cythonized when the .pyx was newer than the shipped .c, downstream builders (e.g. bioconda) compiled that stale .c as-is against their own, often older, NumPy headers, causing "implicit declaration" errors for `PyDataType_*` functions, see: bioconda/bioconda-recipes#68558 Replace this with an explicit `cythonize(ext_modules, force=True)` call in `setup.py`, so every real build always regenerates C sources fresh against whatever NumPy/Cython is actually installed. NumPy and Cython are both already hard build-time requirements (`build-system.requires` in `pyproject.toml`), so drop the now-pointless `ImportError` fallback and merge their imports. With sources always regenerated, there's no need to ship the generated .c/.h files in the sdist either: trim `MANIFEST.in` to just the .pyx/.pxd sources plus the one genuinely hand-written .c/.h pair (`lib/bx/align/sitemask/find_cpg.*`), and skip building ext_modules for the "sdist" action so setuptools doesn't pull the freshly cythonized files back in as extension sources. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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@mr-c Would this be a problem for Debian? |
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@nsoranzo Not a problem for us, we already delete the ".c" files before building execute_after_dh_auto_clean:
# C files are generated by Cython
find -name "*.pyx" | sed 's/pyx$$/c/' | xargs $(RM)
grep -rli "Generated by Cython" lib/ | xargs -r rm |
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setup.pyshipped Cython-generated .c/.h files in the sdist, produced at release time with whatever NumPy/Cython happened to be newest. Since the oldCython.Distutils.build_extonly re-cythonized when the .pyx was newer than the shipped .c, downstream builders (e.g. bioconda) compiled that stale .c as-is against their own, often older, NumPy headers, causing "implicit declaration" errors forPyDataType_*functions, see:bioconda/bioconda-recipes#68558
Replace this with an explicit
cythonize(ext_modules, force=True)call insetup.py, so every real build always regenerates C sources fresh against whatever NumPy/Cython is actually installed.NumPy and Cython are both already hard build-time requirements (
build-system.requiresinpyproject.toml), so drop the now-pointlessImportErrorfallback and merge their imports.With sources always regenerated, there's no need to ship the generated .c/.h files in the sdist either: trim
MANIFEST.into just the .pyx/.pxd sources plus the one genuinely hand-written .c/.h pair (lib/bx/align/sitemask/find_cpg.*), and skip building ext_modules for the "sdist" action so setuptools doesn't pull the freshly cythonized files back in as extension sources.