1.22.4 BUG: pep517 build fails

Describe the issue:

Looks like with just release 1.22.4 pep517 build fails.

Reproduce the code example:

- Unpacka source tarball https://github.com/numpy/numpy//releases/download/v1.22.4/numpy-1.22.4.tar.gz
- run in source root `/usr/bin/python3 -sBm build -w --no-isolation`

Error message:

+ /usr/bin/python3 -sBm build -w --no-isolation
* Getting dependencies for wheel...
Running from numpy source directory.
running egg_info
running build_src
INFO: build_src
creating numpy.egg-info
writing numpy.egg-info/PKG-INFO
writing dependency_links to numpy.egg-info/dependency_links.txt
writing entry points to numpy.egg-info/entry_points.txt
writing top-level names to numpy.egg-info/top_level.txt
writing manifest file 'numpy.egg-info/SOURCES.txt'
package init file 'numpy/core/include/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/__init__.py' not found (or not a regular file)
package init file 'numpy/core/include/numpy/__init__.py' not found (or not a regular file)
package init file 'numpy/core/include/numpy/libdivide/__init__.py' not found (or not a regular file)
package init file 'numpy/core/include/numpy/random/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/_simd/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/multiarray/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/npymath/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/npysort/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/umath/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/dlpack/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/simd/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/simd/avx2/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/simd/avx512/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/simd/neon/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/simd/sse/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/common/simd/vsx/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/umath/svml/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/umath/svml/linux/__init__.py' not found (or not a regular file)
package init file 'numpy/core/src/umath/svml/linux/avx512/__init__.py' not found (or not a regular file)
package init file 'numpy/core/tests/data/__init__.py' not found (or not a regular file)
package init file 'numpy/core/tests/examples/__init__.py' not found (or not a regular file)
package init file 'numpy/core/tests/examples/cython/__init__.py' not found (or not a regular file)
package init file 'numpy/core/tests/examples/limited_api/__init__.py' not found (or not a regular file)
package init file 'numpy/distutils/checks/__init__.py' not found (or not a regular file)
package init file 'numpy/distutils/mingw/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/src/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/array_from_pyobj/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/assumed_shape/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/common/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/kind/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/mixed/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/module_data/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/parameter/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/regression/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/size/__init__.py' not found (or not a regular file)
package init file 'numpy/f2py/tests/src/string/__init__.py' not found (or not a regular file)
package init file 'numpy/lib/tests/data/__init__.py' not found (or not a regular file)
package init file 'numpy/linalg/lapack_lite/__init__.py' not found (or not a regular file)
package init file 'numpy/random/_examples/__init__.py' not found (or not a regular file)
package init file 'numpy/random/include/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/__init__.py' not found (or not a regular file)
package init file 'numpy/random/_examples/cffi/__init__.py' not found (or not a regular file)
package init file 'numpy/random/_examples/cython/__init__.py' not found (or not a regular file)
package init file 'numpy/random/_examples/numba/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/distributions/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/legacy/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/mt19937/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/pcg64/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/philox/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/sfc64/__init__.py' not found (or not a regular file)
package init file 'numpy/random/src/splitmix64/__init__.py' not found (or not a regular file)
package init file 'numpy/typing/tests/data/__init__.py' not found (or not a regular file)
package init file 'numpy/typing/tests/data/fail/__init__.py' not found (or not a regular file)
package init file 'numpy/typing/tests/data/misc/__init__.py' not found (or not a regular file)
package init file 'numpy/typing/tests/data/pass/__init__.py' not found (or not a regular file)
package init file 'numpy/typing/tests/data/reveal/__init__.py' not found (or not a regular file)
/usr/lib/python3.8/site-packages/setuptools/command/egg_info.py:633: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'.
Please extend command classes from setuptools instead of distutils.
  warnings.warn(
reading manifest file 'numpy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'LICENSES_bundled.txt'
warning: no previously-included files found matching 'azure-*.yml'
no previously-included directories found matching 'doc/build'
no previously-included directories found matching 'doc/source/generated'
no previously-included directories found matching 'benchmarks/env'
no previously-included directories found matching 'benchmarks/results'
no previously-included directories found matching 'benchmarks/html'
no previously-included directories found matching 'benchmarks/numpy'
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*.swp' found anywhere in distribution
warning: no previously-included files matching '*.bak' found anywhere in distribution
warning: no previously-included files matching '*~' found anywhere in distribution
adding license file 'LICENSE.txt'
writing manifest file 'numpy.egg-info/SOURCES.txt'
* Building wheel...
Running from numpy source directory.
Cythonizing sources
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_bounded_integers.pyx.in
Traceback (most recent call last):
  File "/home/tkloczko/rpmbuild/BUILD/numpy-1.22.4/tools/cythonize.py", line 234, in <module>
    main()
  File "/home/tkloczko/rpmbuild/BUILD/numpy-1.22.4/tools/cythonize.py", line 230, in main
    find_process_files(root_dir)
  File "/home/tkloczko/rpmbuild/BUILD/numpy-1.22.4/tools/cythonize.py", line 221, in find_process_files
    process(root_dir, fromfile, tofile, function, hash_db)
  File "/home/tkloczko/rpmbuild/BUILD/numpy-1.22.4/tools/cythonize.py", line 187, in process
    processor_function(fromfile, tofile)
  File "/home/tkloczko/rpmbuild/BUILD/numpy-1.22.4/tools/cythonize.py", line 90, in process_tempita_pyx
    process_pyx(pyxfile, tofile)
  File "/home/tkloczko/rpmbuild/BUILD/numpy-1.22.4/tools/cythonize.py", line 74, in process_pyx
    raise RuntimeError(f'Building {VENDOR} requires Cython >= {required_version}'
RuntimeError: Building NumPy requires Cython >= 0.29.30, found 0.29.25 at /home/tkloczko/.local/lib/python3.8/site-packages/Cython/__init__.py
Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/pep517/in_process/_in_process.py", line 363, in <module>
    main()
  File "/usr/lib/python3.8/site-packages/pep517/in_process/_in_process.py", line 345, in main
    json_out['return_val'] = hook(**hook_input['kwargs'])
  File "/usr/lib/python3.8/site-packages/pep517/in_process/_in_process.py", line 261, in build_wheel
    return _build_backend().build_wheel(wheel_directory, config_settings,
  File "/usr/lib/python3.8/site-packages/setuptools/build_meta.py", line 244, in build_wheel
    return self._build_with_temp_dir(['bdist_wheel'], '.whl',
  File "/usr/lib/python3.8/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir
    self.run_setup()
  File "/usr/lib/python3.8/site-packages/setuptools/build_meta.py", line 281, in run_setup
    super(_BuildMetaLegacyBackend,
  File "/usr/lib/python3.8/site-packages/setuptools/build_meta.py", line 174, in run_setup
    exec(compile(code, __file__, 'exec'), locals())
  File "setup.py", line 458, in <module>
    setup_package()
  File "setup.py", line 440, in setup_package
    generate_cython()
  File "setup.py", line 248, in generate_cython
    raise RuntimeError("Running cythonize failed!")
RuntimeError: Running cythonize failed!

ERROR Backend subproccess exited when trying to invoke build_wheel

NumPy/Python version information:

1.22.4

[seberg]

You have a local install of cython which shadows the system install. Checking rpm -q python-cython --qf "%{VERSION}\n" means nothing much in that scnenario python3 -mcython --version would.

[kloczek]

I must apologize. I’m using multiple LXC zones and I’ve been running build in on of the zone where was older version of the cython and at the same time I’ve been checking cython version in not the same zone. In other words build is perfectly fine.

Successfully built numpy-1.22.4-cp38-cp38-linux_x86_64.whl

Odd only is that build did not fail on checking cython module version and continued to the pint where if failed 🤔