How should I structure a Python package that contains Cython code

I've done this myself now, in a Python package simplerandom (BitBucket repo - EDIT: now github) (I don't expect this to be a popular package, but it was a good chance to learn Cython).

This method relies on the fact that building a .pyx file with Cython.Distutils.build_ext (at least with Cython version 0.14) always seems to create a .c file in the same directory as the source .pyx file.

Here is a cut-down version of setup.py which I hope shows the essentials:

from distutils.core import setup
from distutils.extension import Extension

try:
    from Cython.Distutils import build_ext
except ImportError:
    use_cython = False
else:
    use_cython = True

cmdclass = {}
ext_modules = []

if use_cython:
    ext_modules += [
        Extension("mypackage.mycythonmodule", ["cython/mycythonmodule.pyx"]),
    ]
    cmdclass.update({'build_ext': build_ext})
else:
    ext_modules += [
        Extension("mypackage.mycythonmodule", ["cython/mycythonmodule.c"]),
    ]

setup(
    name='mypackage',
    ...
    cmdclass=cmdclass,
    ext_modules=ext_modules,
    ...
)

I also edited MANIFEST.in to ensure that mycythonmodule.c is included in a source distribution (a source distribution that is created with python setup.py sdist):

...
recursive-include cython *
...

I don't commit mycythonmodule.c to version control 'trunk' (or 'default' for Mercurial). When I make a release, I need to remember to do a python setup.py build_ext first, to ensure that mycythonmodule.c is present and up-to-date for the source code distribution. I also make a release branch, and commit the C file into the branch. That way I have a historical record of the C file that was distributed with that release.

Adding to Craig McQueen's answer: see below for how to override the sdist command to have Cython automatically compile your source files before creating a source distribution.

That way your run no risk of accidentally distributing outdated C sources. It also helps in the case where you have limited control over the distribution process e.g. when automatically creating distributions from continuous integration etc.

from distutils.command.sdist import sdist as _sdist

...

class sdist(_sdist):
    def run(self):
        # Make sure the compiled Cython files in the distribution are up-to-date
        from Cython.Build import cythonize
        cythonize(['cython/mycythonmodule.pyx'])
        _sdist.run(self)
cmdclass['sdist'] = sdist

http://docs.cython.org/en/latest/src/userguide/source_files_and_compilation.html#distributing-cython-modules

It is strongly recommended that you distribute the generated .c files as well as your Cython sources, so that users can install your module without needing to have Cython available.

It is also recommended that Cython compilation not be enabled by default in the version you distribute. Even if the user has Cython installed, he probably doesn’t want to use it just to install your module. Also, the version he has may not be the same one you used, and may not compile your sources correctly.

This simply means that the setup.py file that you ship with will just be a normal distutils file on the generated .c files, for the basic example we would have instead:

from distutils.core import setup
from distutils.extension import Extension
 
setup(
    ext_modules = [Extension("example", ["example.c"])]
)

The easiest is to include both but just use the c-file? Including the .pyx file is nice, but it's not needed once you have the .c file anyway. People who want to recompile the .pyx can install Pyrex and do it manually.

Otherwise you need to have a custom build_ext command for distutils that builds the C file first. Cython already includes one. http://docs.cython.org/src/userguide/source_files_and_compilation.html

What that documentation doesn't do is say how to make this conditional, but

try:
     from Cython.distutils import build_ext
except ImportError:
     from distutils.command import build_ext

Should handle it.

Including (Cython) generated .c files are pretty weird. Especially when we include that in git. I'd prefer to use setuptools_cython. When Cython is not available, it will build an egg which has built-in Cython environment, and then build your code using the egg.

A possible example: https://github.com/douban/greenify/blob/master/setup.py

Update(2017-01-05):

Since setuptools 18.0, there's no need to use setuptools_cython. Here is an example to build Cython project from scratch without setuptools_cython.