Building Cython code¶
Cython code must, unlike Python, be compiled. This happens in two stages:
.pyfile is compiled by Cython to a
.cfile, containing the code of a Python extension module.
.cfile is compiled by a C compiler to a
.pydon Windows) which can be
import-ed directly into a Python session. setuptools takes care of this part. Although Cython can call them for you in certain cases.
To understand fully the Cython + setuptools build process, one may want to read more about distributing Python modules.
There are several ways to build Cython code:
Write a setuptools
setup.py. This is the normal and recommended way.
cythonizecommand-line utility. This is a good approach for compiling a single Cython source file directly to an extension. A source file can be built “in place” (so that the extension module is created next to the source file, ready to be imported) with
cythonize -i filename.pyx.
Use Pyximport, importing Cython
.pyxfiles as if they were
.pyfiles (using setuptools to compile and build in the background). This method is easier than writing a
setup.py, but is not very flexible. So you’ll need to write a
setup.pyif, for example, you need certain compilations options.
cythoncommand-line utility manually to produce the
.cfile from the
.pyxfile, then manually compiling the
.cfile into a shared object library or DLL suitable for import from Python. (These manual steps are mostly for debugging and experimentation.)
Use the [Jupyter] notebook or the [Sage] notebook, both of which allow Cython code inline. This is the easiest way to get started writing Cython code and running it.
Currently, using setuptools is the most common way Cython files are built and distributed. The other methods are described in more detail in the Source Files and Compilation section of the reference manual.
Building a Cython module using setuptools¶
Imagine a simple “hello world” script in a file
def say_hello_to(name): print("Hello %s!" % name)
The following could be a corresponding
from setuptools import setup from Cython.Build import cythonize setup( name='Hello world app', ext_modules=cythonize("hello.pyx"), zip_safe=False, )
To build, run
python setup.py build_ext --inplace. Then simply
start a Python session and do
from hello import say_hello_to and
use the imported function as you see fit.
One caveat: the default action when running
python setup.py install is to
create a zipped
egg file which will not work with
files when you try to use them from a dependent package. To prevent this,
zip_safe=False in the arguments to
Using the Jupyter notebook¶
Cython can be used conveniently and interactively from a web browser through the Jupyter notebook. To install Jupyter notebook, e.g. into a virtualenv, use pip:
(venv)$ pip install jupyter (venv)$ jupyter notebook
To enable support for Cython compilation, install Cython as described in the installation guide
and load the
Cython extension from within the Jupyter notebook:
Then, prefix a cell with the
%%cython marker to compile it
%%cython a: cython.int = 0 for i in range(10): a += i print(a)
%%cython cdef int a = 0 for i in range(10): a += i print(a)
You can show Cython’s code analysis by passing the
%%cython --annotate ...
For more information about the arguments of the
%%cython magic, see
Compiling with a Jupyter Notebook.