Hi Egor,
Thanks for the response. I have no issues with compiling the C code, I have a
full compile chain setup on the machine etc. What I was expecting to happen is
that the C code generated by Cython would be included in the tarball and
therefore not need Cython to build from a tarball.
This assumption is mainly based on the error that was printed: "RuntimeError:
Cython >= 0.23 is required to build scikit-image from git checkout" which
indicates (and the fact it's not in the package requirements) Cython should
not be needed to build from PyPI.
I hope that makes it a little clearer,
Thanks again,
Stuart
On Friday, 27 July 2018 12:02:46 BST Egor Panfilov wrote:
> 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@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/d3e736493b16e9455ce8579722d6
> > 44b313814c599d5824d34e448845f746/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/cor
> > e.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/mis
> > c_util.py", line 1034, in add_subpackage
> >
> > caller_level = 2)
> >
> > File
> >
> > "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/mis
> > c_util.py", line 1003, in get_subpackage
> >
> > caller_level = caller_level + 1)
> >
> > File
> >
> > "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/mis
> > c_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/mis
> > c_util.py", line 1034, in add_subpackage
> >
> > caller_level = 2)
> >
> > File
> >
> > "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/mis
> > c_util.py", line 1003, in get_subpackage
> >
> > caller_level = caller_level + 1)
> >
> > File
> >
> > "/opt/miniconda/envs/clean/lib/python3.7/site-packages/numpy/distutils/mis
> > c_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@python.org
> > https://mail.python.org/mailman/listinfo/scikit-image
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