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Date: Sun, 21 Jun 2020 11:31:37 -0700
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Subject: Re: What's the official state of Python module scipy in Cygwin?
To: Marco Atzeri <marco DOT atzeri AT gmail DOT com>
From: My Name via Cygwin <cygwin AT cygwin DOT com>
Reply-To: My Name <mname989 AT gmail DOT com>
Cc: The Cygwin Mailing List <cygwin AT cygwin DOT com>
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(M.A., I've figured out how to reply to the Cygwin Mailing List on these.
If you'd like me to remove your name from the list of addressees in my
future emails, please let me know? I have not found comprehensive docs for
this mailing-list software, so I'm clueless.)

I was delighted when Numpy first showed up as an official Cygwin Package
and am using Numpy in Python 3.7 in Cygwin now. I've realized that the
latest Cygwin versions of Python (now 3.8) are often incomplete, but that's
no problem for me. I'm also able to use Sympy in Cygwin by installing Sympy
via Pip in python3.7 in Cygwin.

Scipy includes functions outside Numpy and Sympy that would be useful to me
at least, and I regularly rely on JupyterLab; so for those, I've been
resorting to Windows 10 versions of Python3.

I should have clarified in my original post in this thread, when I did
happen to have success installing full Scipy in Cygwin, it was with this
command:

$ python3.7 -m pip install scipy

When I did have that success installing Scipy in Cygwin, I later realized
that whether Cygwin package gcc-fortran was installed locally made a
difference. Without gcc-fortran installed locally, the pip command would
fail to install Scipy. When I run that pip command now, I don't comprehend
the output, but I recognize that the Scipy installation has failed, even
though I do have Cygwin's gcc-fortran installed:

==================================
$ python3.7 -m pip install scipy
Collecting scipy
  Downloading scipy-1.5.0.tar.gz (25.6 MB)
     |████████████████████████████████| 25.6 MB 11.8 MB/s
  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/python3.7
/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py
prepare_metadata_for_build_wheel /tmp/tmpc3ao3jht
         cwd: /tmp/pip-install-593dlngp/scipy
    Complete output (137 lines):
    lapack_opt_info:
    lapack_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib',
'/usr/lib/']
      NOT AVAILABLE

    openblas_lapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/usr/local/lib', '/usr/lib',
'/usr/lib/']
      NOT AVAILABLE

    openblas_clapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib',
'/usr/lib/']
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib/
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib/
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib/
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    lapack_info:
    customize UnixCCompiler
      libraries lapack not found in ['/usr/local/lib', '/usr/lib',
'/usr/lib/']
      NOT AVAILABLE

    lapack_src_info:
      NOT AVAILABLE

      NOT AVAILABLE

    setup.py:462: UserWarning: Unrecognized setuptools command ('dist_info
--egg-base /tmp/pip-modern-metadata-ib3nkeed'), proceeding with generating
Cython sources and expanding templates
      ' '.join(sys.argv[1:])))
    Running from SciPy source directory.

/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624:
UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      self.calc_info()

/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624:
UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      self.calc_info()

/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624:
UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      self.calc_info()
    Traceback (most recent call last):
      File
"/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line
280, in <module>
        main()
      File
"/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line
263, in main
        json_out['return_val'] = hook(**hook_input['kwargs'])
      File
"/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line
133, in prepare_metadata_for_build_wheel
        return hook(metadata_directory, config_settings)
      File
"/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/setuptools/build_meta.py",
line 157, in prepare_metadata_for_build_wheel
        self.run_setup()
      File
"/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/setuptools/build_meta.py",
line 249, in run_setup
        self).run_setup(setup_script=setup_script)
      File
"/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/setuptools/build_meta.py",
line 142, in run_setup
        exec(compile(code, __file__, 'exec'), locals())
      File "setup.py", line 583, in <module>
        setup_package()
      File "setup.py", line 579, in setup_package
        setup(**metadata)
      File
"/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/core.py",
line 135, in setup
        config = configuration()
      File "setup.py", line 477, in configuration
        raise NotFoundError(msg)
    numpy.distutils.system_info.NotFoundError: No lapack/blas resources
found.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.7
/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py
prepare_metadata_for_build_wheel /tmp/tmpc3ao3jht Check the logs for full
command output.

$
==================================

Going by an old memory of mine, I recall that parts of Scipy rely on BLAS,
https://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms, and I read
somewhere that that dependency adds to the difficulty of porting Scipy to
new platforms.

On Sun, Jun 21, 2020 at 10:52 AM Marco Atzeri via Cygwin <cygwin AT cygwin DOT com>
wrote:

> On 21.06.2020 15:03, My Name via Cygwin wrote:
> > IIRC, at one point I was able to use scipy in Cygwin, after a period of
> > failed attempts. I believe that having installed gcc-fortran might have
> > been part of the solution I stumbled upon.
> >
> > But now I'm back to being unable to install scipy in Cygwin. Is it
> > supported officially? Or unsupported but sometimes possible?
> >
> > Thank you.
> > --
>
>
> partially supported ?
>
> pythonXX-numpy is available, except the 3.8 version for the
> time being as all the 3.8 packages are under deployment.
>
> All the rest is not, as no one has spent time to package them.
>
> What is the problem and on which package ?
>
> Regards
> Marco
>
>
>
> --
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