Compiled C/Cython extensions

Python packages can include compiled extensions in a variety of languages, most commonly C and Cython (Cython is a language close to Python that can be automatically translated into C). An extension, once compiled, looks just like a regular Python module/sub-module.

There are a number of reasons why you might want to include compiled extensions including for example to speed up code that is otherwise slow in Python, or because you want to include an existing stable library without having to re-implement it in Python.

Defining extensions in setup.py

To define an extension, we need to create an instance of distutils.core.Extension inside the setup.py file. For a simple case with a single .c file, this would look like:

from distutils.core import Extension
ext = Extension(name='my_package.my_extension',
                sources=['my_package/my_extension.c'])

Here name is the final name the compiled extension will have, which means that if the extension defines a function fast_function it can be imported as:

from my_package.my_extension import fast_function

The sources argument should be set to a list of source files to compile and link together to create the extension, and the filenames should be relative to the setup.py file. If your extension uses the Numpy C API, you should also specify the Numpy include directory using:

ext = Extension(name='my_package.my_extension',
                sources=['my_package/my_extension.c'],
                include_dirs=[numpy.get_include()])

There are a number of other options that can be passed to set for example what other libraries to link to, flags or macros to pass to the compiler, and so on. For more information about these, see the Extension section in the Python documentation.

Once your extension has been defined, you should pass a list of extensions to the ext_modules keyword argument to the setup() function in the setup.py file:

setup(..., ext_modules=[ext])

If you want to build a Cython extension instead of a C extension, specify the .pyx file(s) in the sources argument:

ext = Extension(name='my_package.my_extension',
                sources=['my_package/my_extension.pyx'])

And make sure you also add cython to your pyproject.toml build-time dependencies:

[build-system]
requires = [..., "cython"]
build-backend = 'setuptools.build_meta'

Packages with many extensions

For packages with many extensions, you might want to consider using the extension-helpers package. This package serves two main purposes:

  • For single-file Cython extensions, it will automatically discover and define these extensions.
  • For other extensions, it allows you to define extensions inside setup_package.py files which can be anywhere in your package. These files should contain a single function called get_extensions that returns a list of extensions. The idea is then to make it easier to manage extensions for large packages by placing the setup_package.py files close to the extension code.

To use extension-helpers, first make sure it is included in your pyproject.toml file as a build-time dependency:

[build-system]
requires = [..., "extension-helpers"]
build-backend = 'setuptools.build_meta'

Then adjust your setup.py to include:

from extension_helpers.setup_helpers import get_extensions

setup(..., ext_modules=get_extensions())

Finally, if needed, create setup_package.py files in sub-modules where you have extensions, add a get_extensions() function, and make sure that it returns a list of Extension objects.