[scikit-image] Installing from pypi tarball without cython

[Egor Panfilov]

Hi Stuart,

I don't think what you are experiencing is an issue. Several components
(i.e. functions) of `scikit-image` are implemented in Cython, and require
it in order to be build and linked with Python API. "Binary" distributions
of `scikit-image` (including the PyPi .whl-files) ship such components
pre-built, so the requirements for running `scikit-image` and building it
are different. You can take a look at the requirements for different
usecases (building package, executing package, building gallery, etc) in
our repository in
https://github.com/scikit-image/scikit-image/tree/master/requirements .
If you are only interested in installing `scikit-image`, I'd you recommend
you to use the provided pre-built distributions available for the most
popular architectures and operating systems:
    pip install --no-cache-dir scikit-image

Regards,
Egor

On Fri, 27 Jul 2018 at 13:28, Stuart Mumford <stuart at cadair.com> wrote:

> Hello,
>
>
>
> I have just run into an error while trying to install scikit-image from
> the pip tarball on linux (as part of the SunPy test infrastructure). It
> seems that the PyPI tarball needs Cython to be installed:
>
>
>
>  pip install --no-binary=:all: --no-cache-dir scikit-image
> Collecting scikit-image
>  Downloading
> https://files.pythonhosted.org/packages/fc/20/d3e736493b16e9455ce8579722d644b313814c599d5824d34e448845f746/scikit-image-0.14.0.tar.gz
> (27.0MB)
>    100% |████████████████████████████████| 27.0MB 5.9MB/s
>    Complete output from command python setup.py egg_info:
>    Partial import of skimage during the build process.
>    Traceback (most recent call last):
>      File "/tmp/pip-install-ypyllick/scikit-image/skimage/_build.py", line
> 30, in cython
>        from Cython import __version__
>    ModuleNotFoundError: No module named 'Cython'
>
>    During handling of the above exception, another exception occurred:
>
>    Traceback (most recent call last):
>      File "<string>", line 1, in <module>
>      File "/tmp/pip-install-ypyllick/scikit-image/setup.py", line 149, in
> <module>
>        **extra
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/core.py",
> line 135, in setup
>        config = configuration()
>      File "/tmp/pip-install-ypyllick/scikit-image/setup.py", line 70, in
> configuration
>        config.add_subpackage('skimage')
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/misc_util.py",
> line 1034, in add_subpackage
>        caller_level = 2)
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/misc_util.py",
> line 1003, in get_subpackage
>        caller_level = caller_level + 1)
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/misc_util.py",
> line 940, in _get_configuration_from_setup_py
>        config = setup_module.configuration(*args)
>      File "skimage/setup.py", line 14, in configuration
>        config.add_subpackage('feature')
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/misc_util.py",
> line 1034, in add_subpackage
>        caller_level = 2)
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/misc_util.py",
> line 1003, in get_subpackage
>        caller_level = caller_level + 1)
>      File
> "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/misc_util.py",
> line 940, in _get_configuration_from_setup_py
>        config = setup_module.configuration(*args)
>      File "skimage/feature/setup.py", line 22, in configuration
>        cython(['_haar.pyx'], working_path=base_path)
>      File "/tmp/pip-install-ypyllick/scikit-image/skimage/_build.py", line
> 42, in cython
>        % CYTHON_VERSION)
>    RuntimeError: Cython >= 0.23 is required to build scikit-image from git
> checkout
>    Cython >= 0.23 not found; falling back to pre-built geometry.c
>    Cython >= 0.23 not found; falling back to pre-built transform.c
>    Cython >= 0.23 not found; falling back to pre-built interpolation.c
>    Cython >= 0.23 not found; falling back to pre-built _draw.c
>    Cython >= 0.23 not found; falling back to pre-built corner_cy.c
>    Cython >= 0.23 not found; falling back to pre-built censure_cy.c
>    Cython >= 0.23 not found; falling back to pre-built orb_cy.c
>    Cython >= 0.23 not found; falling back to pre-built brief_cy.c
>    Cython >= 0.23 not found; falling back to pre-built _texture.c
>    Cython >= 0.23 not found; falling back to pre-built _hessian_det_appx.c
>    Cython >= 0.23 not found; falling back to pre-built _hoghistogram.c
>
>    ----------------------------------------
> Command "python setup.py egg_info" failed with error code 1 in
> /tmp/pip-install-ypyllick/scikit-image/
>
> I don't know if this is a bug in the tarball / setup machinery or if it's
> some silly mistake I am making.
>
>
>
> Thanks for any help,
>
> Stuart
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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