pip install cythonize failure (Trac #1878)

[scipy-gitbot]

Original ticket http://projects.scipy.org/scipy/ticket/1878 on 2013-03-28 by trac user akrimkevich, assigned to @cournape.

When installing scipy using 'pip install -e git+git://github.com/scipy/scipy.git#egg=scipy-dev', the cythonize.py script fails because it attempts to execute the 'cython' program, which it appears is not a byproduct of the install of cython 0.18. Please see attached output.
[[BR]][[BR]]
$ python --version[[BR]]
Python 2.7.3[[BR]][[BR]]
$ python -c "import Cython; print Cython.version"[[BR]]
0.18[[BR]][[BR]]
$ uname -prsv[[BR]]
Darwin 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 i386[[BR]]

An executable cython.py is, however, placed in site-packages. Wrapping it in a script like the following allowed a successful install.

/bin/bash

python /usr/local/lib/python2.7/site-packages/cython.py $@

[scipy-gitbot]

Attachment added by trac user akrimkevich on 2013-03-28: output.txt

[scipy-gitbot]

Title changed from scipy to pip install cythonize failure by @pv on 2013-03-28

[scipy-gitbot]

@rgommers wrote on 2013-04-01

How did you install Cython? I haven't seen this on Linux yet.

On Windows this does happen, we probably need something like this (snippet copied from scikit-image):

            try:
                subprocess.call(['cython', '-o', c_file, pyxfile])
            except WindowsError:
                # On Windows cython.exe may be missing if Cython was installed
                # via distutils. Run the cython.py script instead.
                subprocess.call(
                    [sys.executable,
                     os.path.join(os.path.dirname(sys.executable),
                                  'Scripts', 'cython.py'),
                     '-o', c_file, pyxfile],
                    shell=True)

[scipy-gitbot]

trac user akrimkevich wrote on 2013-04-03

I used 'pip install cython'. Both python and pip were obtained from homebrew.

Replying to [comment:2 rgommers]:

How did you install Cython? I haven't seen this on Linux yet.

On Windows this does happen, we probably need something like this (snippet copied from scikit-image):
{{{
try:
subprocess.call(['cython', '-o', c_file, pyxfile])
except WindowsError:
# On Windows cython.exe may be missing if Cython was installed
# via distutils. Run the cython.py script instead.
subprocess.call(
[sys.executable,
os.path.join(os.path.dirname(sys.executable),
'Scripts', 'cython.py'),
'-o', c_file, pyxfile],
shell=True)
}}}

[scipy-gitbot]

@rgommers wrote on 2013-04-03

OK, Cython has this in its setup.py:

if 'setuptools' in sys.modules:
    setuptools_extra_args['zip_safe'] = False
    setuptools_extra_args['entry_points'] = {
        'console_scripts': [
            'cython = Cython.Compiler.Main:setuptools_main',
        ]
    }
    scripts = []
else:
    if os.name == "posix":
        scripts = ["bin/cython"]
    else:
        scripts = ["cython.py"]

Sigh. With pip it should install the cython executable though, not sure why that didn't happen for you.

[rgommers]

Probably fixed by gh-2449.