Undeclared build dependency on cython

Description

pip install scikit-learn --no-binary :all: fails to install scikit because of missing cython build dependency. Once cython is installed manually the above command works and installs scikit-learn.

Steps/Code to Reproduce

pip install scikit-learn --no-binary :all: it’s also the case for python implementations that don’t have scikit-learn wheels available (PyPy3, Python3.8)

Expected Results

scikit-learn installs successfully

Actual Results

  Running setup.py install for scikit-learn ... error
    Complete output from command /home/user/pypy3-venv/bin/pypy3-c -u -c "import setuptools, tokenize;__file__='/var/tmp/pip-install-zf4xear5/scikit-learn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/tmp/pip-record-k9u2qwff/install-record.txt --single-version-externally-managed --compile --install-headers /home/user/pypy3-venv/include/site/python3.6/scikit-learn:
    Partial import of sklearn during the build process.
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/var/tmp/pip-install-zf4xear5/scikit-learn/setup.py", line 290, in <module>
        setup_package()
      File "/var/tmp/pip-install-zf4xear5/scikit-learn/setup.py", line 286, in setup_package
        setup(**metadata)
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/core.py", line 137, in setup
        config = configuration()
      File "/var/tmp/pip-install-zf4xear5/scikit-learn/setup.py", line 174, in configuration
        config.add_subpackage('sklearn')
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/misc_util.py", line 1035, in add_subpackage
        caller_level = 2)
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/misc_util.py", line 1004, in get_subpackage
        caller_level = caller_level + 1)
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/misc_util.py", line 941, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "sklearn/setup.py", line 62, in configuration
        config.add_subpackage('utils')
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/misc_util.py", line 1035, in add_subpackage
        caller_level = 2)
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/misc_util.py", line 1004, in get_subpackage
        caller_level = caller_level + 1)
      File "/home/user/pypy3-venv/site-packages/numpy/distutils/misc_util.py", line 941, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "sklearn/utils/setup.py", line 8, in configuration
        from Cython import Tempita
    ModuleNotFoundError: No module named 'Cython'
    
    ----------------------------------------
Command "/home/user/pypy3-venv/bin/pypy3-c -u -c "import setuptools, tokenize;__file__='/var/tmp/pip-install-zf4xear5/scikit-learn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/tmp/pip-record-k9u2qwff/install-record.txt --single-version-externally-managed --compile --install-headers /home/user/pypy3-venv/include/site/python3.6/scikit-learn" failed with error code 1 in /var/tmp/pip-install-zf4xear5/scikit-learn/

Versions

[jackjansen]

I have the feeling this bug has re-appeared with release scikit-learn 0.24.

As of a few days ago I see CI/CD builds failing for a project that has a deep indirect dependency on scikit-learn, with the ModuleNotFound error reported above. Sorry, I don’t even know which package has the dependency on scikit-learn…

I can tell you the CI/CD machine runs Python 3.6 on Ubuntu 18.04.

[jackjansen]

@adrinjalali no need to reopen. The issue has been solved, see #19068.