Support for python3.9 on macOS (non Homebrew version)

[mayankmetha]

Collecting matplotlib
Using cached matplotlib-3.3.2.tar.gz (37.9 MB)
ERROR: Command errored out with exit status 1:
command: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setup.py'"'"'; file='"'"'/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr
cwd: /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/
Complete output (63 lines):
WARNING: The wheel package is not available.

Edit setup.cfg to change the build options; suppress output with --quiet.

BUILDING MATPLOTLIB
  matplotlib: yes [3.3.2]
      python: yes [3.9.0 (v3.9.0:9cf6752276, Oct  5 2020, 11:29:23)  [Clang 6.0
                  (clang-600.0.57)]]
    platform: yes [darwin]
 sample_data: yes [installing]
       tests: no  [skipping due to configuration]
      macosx: yes [installing]

running egg_info
creating /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info
writing /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info/PKG-INFO
writing dependency_links to /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info/dependency_links.txt
writing namespace_packages to /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info/namespace_packages.txt
writing requirements to /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info/requires.txt
writing top-level names to /private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info/top_level.txt
writing manifest file '/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-pip-egg-info-aq680rqr/matplotlib.egg-info/SOURCES.txt'
init_dgelsd failed init
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setup.py", line 242, in <module>
    setup(  # Finally, pass this all along to distutils to do the heavy lifting.
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/setuptools/__init__.py", line 165, in setup
    return distutils.core.setup(**attrs)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 297, in run
    self.find_sources()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 304, in find_sources
    mm.run()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 535, in run
    self.add_defaults()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 571, in add_defaults
    sdist.add_defaults(self)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/sdist.py", line 228, in add_defaults
    self._add_defaults_ext()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/sdist.py", line 311, in _add_defaults_ext
    build_ext = self.get_finalized_command('build_ext')
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 299, in get_finalized_command
    cmd_obj.ensure_finalized()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 107, in ensure_finalized
    self.finalize_options()
  File "/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setup.py", line 88, in finalize_options
    self.distribution.ext_modules[:] = [
  File "/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setup.py", line 91, in <listcomp>
    for ext in package.get_extensions()
  File "/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setupext.py", line 345, in get_extensions
    add_numpy_flags(ext)
  File "/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/setupext.py", line 469, in add_numpy_flags
    import numpy as np
  File "/private/var/folders/_b/73g4h5qs7qv51ctyl5tby0040000gn/T/pip-install-p_zq0z2f/matplotlib/.eggs/numpy-1.19.2-py3.9-macosx-10.9-x86_64.egg/numpy/__init__.py", line 286, in <module>
    raise RuntimeError(msg)
RuntimeError: Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.
RankWarning: Polyfit may be poorly conditioned

----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

[jklymak]

It seems your numpy is not compatible with 3.9 either? Can you import numpy?

[mayankmetha]

Yes I'm able to download numpy 1.18 and 1.19, but it builds from source. BTW numpy works well for me on python 3.9.

[jklymak]

That error is coming up when you import numpy, so its confusing that the install fails but you are able to use numpy.

[mayankmetha]

Same here, this is weird error issue actually.

[dopplershift]

What command are you running to install matplotlib (e.g. pip install matplotlib)? How are you testing that you can import numpy?

[mayankmetha]

To install matplotlib I used pip install matplotlib. For numpy I installed it using pip and then on my python script ran:
import numpy as np
print(np.arange(10))

[dopplershift]

So I assume you run that script with python myscript.py. Can you try to install matplotlib with python -m pip install matplotlib?

[mayankmetha]

So I assume you run that script with python myscript.py. Can you try to install matplotlib with python -m pip install matplotlib?

Same error!

[jklymak]

Using conda, I can install py3.9 and numpy from conda-forge. matplotlib fails from conda with an unreasonable dependency, but pip install matplotlib works fine.

@mayankmetha Perhaps more info about how you installed python would help, but its still not clear how numpy is working fine during your tests, but failing on matplotlib's install. I would uninstall numpy and matplotlib, and then re-install.

[dopplershift]

This looks identical to numpy/numpy#17550. Most importantly:

There are not yet binary wheels for Python 3.9, consequently the source is built and linked to your local Mac Accelerate library which is known to be buggy.

So I don't think there's anything for us to do here.