can't compile on alpine `x86_64` - Cython crashes with Pythran installed

Please describe your issue.

I’m trying to build the wheel on alpine 3.14 x86_64 and it fails with the following error:

Collecting scipy
  Using cached scipy-1.7.1.tar.gz (36.1 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... error
    ERROR: Command errored out with exit status -11:
     command: /usr/bin/python3 /usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmp2uftwhqd
         cwd: /tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026
    Complete output (59 lines):
    setup.py:490: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-uabymhkz'), proceeding with generating Cython sources and expanding templates
      warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
    Running from SciPy source directory.
    Running scipy/special/_generate_pyx.py
    Running scipy/stats/_generate_pyx.py
    Running scipy/linalg/_generate_pyx.py
    Processing scipy/signal/_spectral.pyx
    Processing scipy/signal/_upfirdn_apply.pyx
    Processing scipy/signal/_peak_finding_utils.pyx
    Processing scipy/signal/_max_len_seq_inner.pyx
    Processing scipy/signal/_sosfilt.pyx
    Processing scipy/cluster/_optimal_leaf_ordering.pyx
    Traceback (most recent call last):
    Processing scipy/cluster/_vq.pyx
      File "/tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026/tools/cythonize.py", line 324, in <module>
        main()
      File "/tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026/tools/cythonize.py", line 320, in main
        find_process_files(root_dir)
      File "/tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026/tools/cythonize.py", line 309, in find_process_files
        for result in pool.imap_unordered(lambda args: process(*args), jobs):
      File "/usr/lib/python3.9/multiprocessing/pool.py", line 870, in next
        raise value
      File "/usr/lib/python3.9/multiprocessing/pool.py", line 125, in worker
        result = (True, func(*args, **kwds))
      File "/tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026/tools/cythonize.py", line 309, in <lambda>
        for result in pool.imap_unordered(lambda args: process(*args), jobs):
      File "/tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026/tools/cythonize.py", line 243, in process
        processor_function(fromfile, tofile, cwd=path)
      File "/tmp/pip-install-2i8zjvju/scipy_b9b335f22566436a952efcb76e4e4026/tools/cythonize.py", line 108, in process_pyx
        raise Exception('Cython failed')
    Exception: Cython failed
    Cythonizing sources
    Traceback (most recent call last):
      File "setup.py", line 356, in generate_cython
        import pip
    ModuleNotFoundError: No module named 'pip'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 349, in <module>
        main()
      File "/usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 331, in main
        json_out['return_val'] = hook(**hook_input['kwargs'])
      File "/usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 151, in prepare_metadata_for_build_wheel
        return hook(metadata_directory, config_settings)
      File "/tmp/pip-build-env-yv3cbv9y/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 166, in prepare_metadata_for_build_wheel
        self.run_setup()
      File "/tmp/pip-build-env-yv3cbv9y/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 258, in run_setup
        super(_BuildMetaLegacyBackend,
      File "/tmp/pip-build-env-yv3cbv9y/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 150, in run_setup
        exec(compile(code, __file__, 'exec'), locals())
      File "setup.py", line 629, in <module>
        setup_package()
      File "setup.py", line 613, in setup_package
        generate_cython()
      File "setup.py", line 365, in generate_cython
        raise RuntimeError("Running cythonize failed!")
    RuntimeError: Running cythonize failed!
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/47/33/a24aec22b7be7fdb10ec117a95e1e4099890d8bbc6646902f443fc7719d1/scipy-1.7.1.tar.gz#sha256=6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764 (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10). Command errored out with exit status -11: /usr/bin/python3 /usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmp2uftwhqd Check the logs for full command output.

I have all the dependencies installed, including blas-dev, lapack-dev and openblas-dev. Pip and cython are installed and are the latest versions.

Interestingly, the same steps taken on alpine 3.14 on armhf, with the same version packages builds successfully (Did not have to specifically install cython there).

Thanks

[ilayn]

On windows. Something I encountered that is related to the tempita issue. Somehow existence of pythran is enough to trigger the issue and without it everything works. I will create some time later to dig deeper.

[rgommers]

@ilayn on Alpine, or on some other platform?