Source Files and Compilation

Note

See Compilation reference section for more details

Cython source file names consist of the name of the module followed by a .pyx extension, for example a module called primes would have a source file named primes.pyx.

Once you have written your .pyx file, there are a couple of ways of turning it into an extension module. One way is to compile it manually with the Cython compiler, e.g.:

$ cython primes.pyx

This will produce a file called primes.c, which then needs to be compiled with the C compiler using whatever options are appropriate on your platform for generating an extension module. For these options look at the official Python documentation.

The other, and probably better, way is to use the distutils extension provided with Cython. The benefit of this method is that it will give the platform specific compilation options, acting like a stripped down autotools.

Basic setup.py

The distutils extension provided with Cython allows you to pass .pyx files directly to the Extension constructor in your setup file.

If you have a single Cython file that you want to turn into a compiled extension, say with filename example.pyx the associated setup.py would be:

from distutils.core import setup
from Cython.Build import cythonize

setup(
    ext_modules = cythonize("example.pyx")
)

To understand the setup.py more fully look at the official distutils documentation. To compile the extension for use in the current directory use:

$ python setup.py build_ext --inplace

Multiple Cython Files in a Package

To automatically compile multiple Cython files without listing all of them explicitly, you can use glob patterns:

setup(
    ext_modules = cythonize("package/*.pyx")
)

You can also use glob patterns in Extension objects if you pass them through cythonize():

extensions = [Extension("*", ["*.pyx"])]

setup(
    ext_modules = cythonize(extensions)
)

Pyximport

Cython is a compiler. Therefore it is natural that people tend to go through an edit/compile/test cycle with Cython modules. pyximport simplifies this process by executing the “compile” step at need during import. For instance, if you write a Cython module called foo.pyx, with Pyximport you can import it in a regular Python module like this:

import pyximport; pyximport.install()
import foo

Doing so will result in the compilation of foo.pyx (with appropriate exceptions if it has an error in it).

If you would always like to import Cython files without building them specially, you can also add the first line above to your sitecustomize.py. That will install the hook every time you run Python. Then you can use Cython modules just with simple import statements, even like this:

$ python -c "import foo"

Note that it is not recommended to let pyximport build code on end user side as it hooks into their import system. The best way to cater for end users is to provide pre-built binary packages in the wheel packaging format.

Dependency Handling

Since pyximport does not use cythonize() internally, it currently requires a different setup for dependencies. It is possible to declare that your module depends on multiple files, (likely .h and .pxd files). If your Cython module is named foo and thus has the filename foo.pyx then you should create another file in the same directory called foo.pyxdep. The modname.pyxdep file can be a list of filenames or “globs” (like *.pxd or include/*.h). Each filename or glob must be on a separate line. Pyximport will check the file date for each of those files before deciding whether to rebuild the module. In order to keep track of the fact that the dependency has been handled, Pyximport updates the modification time of your ”.pyx” source file. Future versions may do something more sophisticated like informing distutils of the dependencies directly.

Limitations

Pyximport does not give you any control over how your Cython file is compiled. Usually the defaults are fine. You might run into problems if you wanted to write your program in half-C, half-Cython and build them into a single library.

Pyximport does not hide the Distutils/GCC warnings and errors generated by the import process. Arguably this will give you better feedback if something went wrong and why. And if nothing went wrong it will give you the warm fuzzy feeling that pyximport really did rebuild your module as it was supposed to.

Basic module reloading support is available with the option reload_support=True. Note that this will generate a new module filename for each build and thus end up loading multiple shared libraries into memory over time. CPython does not support reloading shared libraries as such.

Pyximport puts both your .c file and the platform-specific binary into a separate build directory, usually $HOME/.pyxblx/. To copy it back into the package hierarchy (usually next to the source file) for manual reuse, you can pass the option inplace=True.