Failing to install pypmc on macOS - could not cythonize

[MichelDC]

Dear all

I was trying to install pypmc on my Mac (macOS 10.14.5), to use it in EOS, but the installation fails with:

pip3 install --user pypmc Collecting pypmc Using cached https://files.pythonhosted.org/packages/07/d3/86d432f20b2d82109e431c40e536ccac702a2e1cc85d6974c68b4be5d358/pypmc-1.1.2.tar.gz Requirement already satisfied: numpy in /Users/michel/Library/Python/3.7/lib/python/site-packages (from pypmc) (1.17.0) Requirement already satisfied: scipy in /Users/michel/Library/Python/3.7/lib/python/site-packages (from pypmc) (1.3.1) Building wheels for collected packages: pypmc Building wheel for pypmc (setup.py) ... error ERROR: Complete output from command /usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/4w/rfpfxc9d2ndfgz6lv9xtdrjc0000gn/T/pip-install-f1fe16hz/pypmc/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/4w/rfpfxc9d2ndfgz6lv9xtdrjc0000gn/T/pip-wheel-esu5sr7n --python-tag cp37: ERROR: WARNING: Could not cythonize: ModuleNotFoundError("No module named 'Cython'") ...
followed by a long list of errors (I can paste them here if needed).
I did install cython and it is in my PATH

Any help is appreciated, thanks!

[dvandyk]

Sali @MichelDC

could you try to run

pip3 install --user --upgrade cython

and then retry to install pypmc?

[edit: pip -> pip3]

[MichelDC]

That unfortunately results in exactly the same error when trying to install pypmc

[fredRos]

How did you install cython. Via pip?

[MichelDC]

Yes, I did as written above:
pip3 install --user --upgrade cython
I also tried without upgrade, without effect

[fredRos]

Can you try to remove it? The cython dependency should be pulled in automatically during installation of pypmc

[MichelDC]

I removed it, but nothing changed.
I then installed it again, and at least the error is now different, with
ERROR: WARNING: Could not cythonize: ValueError("'pypmc/*/*.pyx' doesn't match any files")

[fredRos]

Can you check what

pip3 --version

says? Perhaps your pip is too old, I remember updating to pip19 that has better ways to define dependencies at build time vs runtime

[fredRos]

An alternative would be to first install cython again, then install an older version of pypmc like

pip3 install pypmc==1.1.2

I didn't add any features in the last release but just fixed the build with newer version of python and cython.

[MichelDC]

I have pip 19.2.3, I updated it today
Unfortunately also trying to install the older version has no effect, the error is exactly the same

[dvandyk]

@MichelDC sorry for coming back to you so late. If you are still interested, please install pypmc-1.1.4. While it is released, it's not on PyPI yet. You need to download the tarball from Github, and then install it manually via pip3 install pypmc-1.1.4.tar.gz. Please let me know if this works for you!

[mingdeyu]

@MichelDC sorry for coming back to you so late. If you are still interested, please install pypmc-1.1.4. While it is released, it's not on PyPI yet. You need to download the tarball from Github, and then install it manually via pip3 install pypmc-1.1.4.tar.gz. Please let me know if this works for you!

@dvandyk had the same issue on my Mac and tried this solution and it works now. Thanks!

[fredRos]

@mingdeyu I just uploaded the tarball and don't have a mac available, could you tell me if the regular installation with

pip3 install pypmc

now works without problems?

[JohannesBuchner]

On Ubuntu Linux, I got the same error as @MichelDC, with up-to-date cython and cython upgraded using pip:

± pip3 install pypmc
Collecting pypmc
  Using cached pypmc-1.1.4.tar.gz (1.0 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 /tmp/tmp8qyxjmxr prepare_metadata_for_build_wheel /tmp/tmp9ht0ozz4
         cwd: /tmp/pip-install-f9rdoeg9/pypmc
    Complete output (26 lines):
    Traceback (most recent call last):
      File "/tmp/tmp8qyxjmxr", line 280, in <module>
        main()
      File "/tmp/tmp8qyxjmxr", line 263, in main
        json_out['return_val'] = hook(**hook_input['kwargs'])
      File "/tmp/tmp8qyxjmxr", line 133, in prepare_metadata_for_build_wheel
        return hook(metadata_directory, config_settings)
      File "/tmp/pip-build-env-n77g5ocv/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 161, in prepare_metadata_for_build_wheel
        self.run_setup()
      File "/tmp/pip-build-env-n77g5ocv/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 253, in run_setup
        super(_BuildMetaLegacyBackend,
      File "/tmp/pip-build-env-n77g5ocv/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 145, in run_setup
        exec(compile(code, __file__, 'exec'), locals())
      File "setup.py", line 91, in <module>
        setup_package()
      File "setup.py", line 85, in setup_package
        setup_args['ext_modules'] = get_extensions()
      File "setup.py", line 37, in get_extensions
        ext_modules = cythonize(extensions, compiler_directives=compiler_directives)
      File "/tmp/pip-build-env-n77g5ocv/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 965, in cythonize
        module_list, module_metadata = create_extension_list(
      File "/tmp/pip-build-env-n77g5ocv/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 815, in create_extension_list
        for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
      File "/tmp/pip-build-env-n77g5ocv/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 114, in nonempty
        raise ValueError(error_msg)
    ValueError: 'pypmc/*/*.pyx' doesn't match any files
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 /tmp/tmp8qyxjmxr prepare_metadata_for_build_wheel /tmp/tmp9ht0ozz4 Check the logs for full command output.

Installing from the github repository works:

pip3 install git+git://github.com/fredRos/pypmc