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MNT update Cython 3.0.10 to 3.1.2 #31905

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@lorentzenchr lorentzenchr commented Aug 9, 2025

Reference Issues/PRs

This will help #31882 a bit. Similar to #28743.

What does this implement/fix? Explain your changes.

Update minimum Cython from 3.0.10 to 3.1.2.

Any other comments?

Some bugfixes (e.g. fused ctypes) and some nice features that we want to have sooner or later (e.g. Support for freethreading builds of CPython 3.13).

- fixes for fused ctuples
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Can you push a commit with [cd build] to check that the wheels build correctly?

@lorentzenchr lorentzenchr added cython Quick Review For PRs that are quick to review dependencies Pull requests that update a dependency file labels Aug 11, 2025
@adrinjalali
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lock file conflicts, could you please rerender them?

@adrinjalali adrinjalali enabled auto-merge (squash) August 11, 2025 09:48
@lesteve
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lesteve commented Aug 11, 2025

I would wait for #31918 to be merged first and for now there seems to be a OpenML issue that prevents the doc build to be succesful.

Also can you use python build_tools/update_environment_and_lock_files.py --select-build '<some_regex>' to update only the lock-files you care about? I guess these ones from a quick git grep:

❯ git grep -P 'cython.+3\.0' build_tools/**/*lock*
build_tools/azure/pymin_conda_forge_openblas_min_dependencies_linux-64_conda.lock:https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.10-py310hc6cd4ac_0.conda#bd1d71ee240be36f1d85c86177d6964f
build_tools/azure/ubuntu_atlas_lock.txt:cython==3.0.10
build_tools/circle/doc_min_dependencies_linux-64_conda.lock:https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.10-py310hc6cd4ac_0.conda#bd1d71ee240be36f1d85c86177d6964f

When you update all the lock-files, there are more things to check like:

  • push a commit with [doc build] if doc lock-files are touched to make sure the full doc build passes
  • same thing with [scipy-dev] if scipy-dev lock-file is changed
  • label the PR with "CUDA CI" if CUDA CI lock-file is changed
  • maybe more things ...

@lesteve lesteve disabled auto-merge August 11, 2025 09:52
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@StefanieSenger since you've been working on GH actions and CI, maybe you fancy implementing a secure @sklearn-bot please re-render kinda thing like what we had but disabled.

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lesteve commented Aug 11, 2025

I am -0.5 on reviving the "update lock-file bot" attempt (too little functionality for too many security risks) but we can discuss this elsewhere ...

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lesteve commented Aug 11, 2025

Just for completeness you would need a commit with [doc build] to merge this since you are updating the doc lock-files. The CI will likely be red because there are OpenML issues right now ...

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Just for completeness you would need a commit with [doc build] to merge this since you are updating the doc lock-files. The CI will likely be red because there are OpenML issues right now ...

Let's try.

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4 participants