Re: [scikit-image] Installing from pypi tarball without cython
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
Hi Stuart, I created a PR to address this issue here: https://github.com/scikit-image/scikit-image/pull/3295 Hope this helps, Matt On Fri, Jul 27, 2018 at 7:24 AM Stuart Mumford <stuart@cadair.com> wrote:
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
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",
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",
On Friday, 27 July 2018 12:02:46 BST Egor Panfilov wrote: line 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
_______________________________________________ scikit-image mailing list scikit-image@python.org https://mail.python.org/mailman/listinfo/scikit-image
participants (2)
-
Matthew McCormick -
Stuart Mumford