Building Cython code

Cython code must, unlike Python, be compiled. This happens in two stages:

• A .pyx or .py file is compiled by Cython to a .c file, containing the code of a Python extension module.

• The .c file is compiled by a C compiler to a .so file (or .pyd on 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.

• Run the cythonize command-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 .pyx files as if they were .py files (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.py if, for example, you need certain compilations options.

• Run the cython command-line utility manually to produce the .c file from the .pyx file, then manually compiling the .c file 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 hello.pyx:

def say_hello_to(name):
    print("Hello %s!" % name)

The following could be a corresponding setup.py script:

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 cimport for pxd files when you try to use them from a dependent package. To prevent this, include zip_safe=False in the arguments to setup().

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:

%load_ext Cython

Then, prefix a cell with the %%cython marker to compile it

Pure PythonCython

%%cython

a: cython.int = 0
for i in range(10):
    a += i
print(a)

You can show Cython’s code analysis by passing the --annotate option:

%%cython --annotate
...

For more information about the arguments of the %%cython magic, see Compiling with a Jupyter Notebook.

Using the Sage notebook

For users of the Sage math distribution, the Sage notebook allows transparently editing and compiling Cython code simply by typing %cython at the top of a cell and evaluate it. Variables and functions defined in a Cython cell imported into the running session.

Jupyter

https://jupyter.org/