8000 setuptools >= 61 package discovery issue with python setup.py clean · Issue #23423 · scikit-learn/scikit-learn · GitHub
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lesteve opened this issue May 19, 2022 Discussed in #23413 · 1 comment · Fixed by #23426
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setuptools >= 61 package discovery issue with python setup.py clean #23423

lesteve opened this issue May 19, 2022 Discussed in #23413 · 1 comment · Fixed by #23426
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@lesteve
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lesteve commented May 19, 2022 •
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Originally reported in #23413

This seems to be a change in setuptools 61 about package discovery ... probably a related issue is pypa/setuptools#3197

mamba create -n test -c conda-forge python=3.9 numpy scipy cython -y
conda activate test
python setup.py clean

error: Multiple top-level packages discovered in a flat-layout: ['prof', 'sklearn', 'maint_tools', 'build_tools', 'asv_benchmarks', 'cache_directory'].

To avoid accidental inclusion of unwanted files or directories,
setuptools will not proceed with this build.

If you are trying to create a single distribution with multiple packages
on purpose, you should not rely on automatic discovery.
Instead, consider the following options:

1. set up custom discovery (`find` directive with `include` or `exclude`)
2. use a `src-layout`
3. explicitly set `py_modules` or `packages` with a list of names

To find more information, look for "package discovery" on setuptools docs.

Weirdly enough the other setup.py commands seems to work OK e.g. python setup.py develop or python setup.py install ...
@lesteve lesteve added the Bug label May 19, 2022
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lesteve commented May 19, 2022 •
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Maybe we should follow numpy and not support python setup.py clean: https://github.com/numpy/numpy/blob/ad1096884e82a8176e7b5125d168ceeca77c3bf7/setup.py#L367-L373. They have done this 7 years ago apparently.

We can change make clean to do git clean -Xdf (remove only ignored files so amongst other things compiled files and leave unversioned files alone) as suggested by the numpy error message.

@thomasjpfan thomasjpfan mentioned this issue May 19, 2022
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MNT Quick fix for setup.py clean thomasjpfan/scikit-learn
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