In my project, I have a custom Python package that has part of its functionality implemented on Cython. We use it to accelerate some of the slowest parts of our code — the syntax is pretty close to regular Python (it can be absolutely identical except for some imports). Cython compiled with .so libraries can directly access low-level arrays of numpy.
The problem — Cython and numpy packages need to be installed before the
setup.py starts its work.
setup.py look as follows:
import numpy from Cython.Build import cythonize setup( name=..., version=..., ... ext_modules=cythonize([ Extension('package.cython_code1', ['package/cython_code1.pyx']), Extension('package.cython_code1', ['package/cython_code2.pyx']), ]), include_dirs=[numpy.get_include()], )
There several ways to handle Cython and numpy:
Starting from 18.0 release of setuptools (released on 2015-06-23) it is possible to specify Cython in
setup_requires and pass
.pyx modules sources for regular
from setuptools import setup, Extension setup( ... setup_requires=[ # Setuptools 18.0 properly handles Cython extensions. 'setuptools>=18.0', 'cython', ], ext_modules=[ Extension('package.cython_code1', sources=['package/cython_code1.pyx']), Extension('package.cython_code2', sources=['package/cython_code2.pyx']), ], include_dirs=[numpy.get_include()], )
If your installation tool is older and you have put the Cython dependency in
setup_requires, it will not work with ImportError like:
ImportError: No module named Cython.Build
In order to fix this, you can wrap the cythonize function in a dumb closure:
try: from Cython.Build import cythonize except ImportError: # create closure for deferred import def cythonize (*args, ** kwargs ): from Cython.Build import cythonize return cythonize(*args, ** kwargs)
Then, when the
setup_requires argument is processed, Cython will be installed and the installation script will continue. Since Cython is installed at this point, you can successfully import and use cythonize.
Or you can stick to https://github.com/pypa/pip/issues/5761. Here you install cython and numpy using
setuptools.dist before actual setup:
from setuptools import dist dist.Distribution().fetch_build_eggs(['Cython>=0.15.1', 'numpy>=1.10'])
Daily dose of