Sorry but I am also seeing this happening with Cython 0.23.4 so I doubt that the Cython version is the problem. (test) ✔ ~ pip list cycler (0.10.0) Cython (0.23.4) dask (0.8.0) decorator (4.0.9) matplotlib (1.5.1) networkx (1.11) numpy (1.10.4) Pillow (3.1.1) pip (8.1.0) pyparsing (2.1.0) python-dateutil (2.5.0) pytz (2015.7) scipy (0.17.0) setuptools (20.2.2) six (1.10.0) toolz (0.7.4) wheel (0.29.0) (test) ✔ ~ pip install scikit-image Collecting scikit-image Using cached scikit-image-0.12.0.tar.gz Complete output from command python setup.py egg_info: Partial import of skimage during the build process. Traceback (most recent call last): File "<string>", line 1, in <module> File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/setup.py", line 146, in <module> **extra File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/setup.py", line 69, in configuration config.add_subpackage('skimage') File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 21, in configuration config.add_subpackage('morphology') File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/morphology/setup.py", line 19, in configuration cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/_build.py", line 39, in cython if not _changed(pyxfile): File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/_build.py", line 70, in _changed with open(filename, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/ The problem is that skimage/morphology/setup.py contains: cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) but that file is not in the pypi tar ball. It should presumably try to process the template processed file _skeletonize_3d_cy.pyx? Best Jens On Monday, 7 March 2016 08:43:25 UTC, stefanv wrote:

Hi Jean-Patrick

On 7 March 2016 at 00:06, Jean-Patrick Pommier <jeanpatri...@gmail.com <javascript:>> wrote:

...

'/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_ skeletonize_3d_cy.pyx.in'

scikit-image now requires a newer version of Cython to build. See:

https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5

Best regards Stéfan