Installing Cython

Many scientific Python distributions, such as Anaconda [Anaconda], Enthought Canopy [Canopy], and Sage [Sage], bundle Cython and no setup is needed. Note however that if your distribution ships a version of Cython which is too old you can still use the instructions below to update Cython.

Unlike most Python software, Cython requires a C compiler to be present on the system. The details of getting a C compiler varies according to the system used:

  • Linux The GNU C Compiler (gcc) is usually present, or easily available through the package system. On Ubuntu or Debian, for instance, it is part of the build-essential package. Next to a C compiler, Cython requires the Python header files. On Ubuntu or Debian, the command sudo apt-get install build-essential python3-dev will fetch everything you need.

  • Mac OS X To retrieve gcc, one option is to install Apple’s XCode, which can be retrieved from the Mac OS X’s install DVDs or from https://developer.apple.com/.

  • Windows The CPython project recommends building extension modules (including Cython modules) with the same compiler that Python was built with. This is usually a specific version of Microsoft Visual C/C++ (MSVC) - see https://wiki.python.org/moin/WindowsCompilers. MSVC is the only compiler that Cython is currently tested with on Windows. If you’re having difficulty making setuptools detect MSVC then PyMSVC aims to solve this.

    A possible alternative is the open source MinGW (a Windows distribution of gcc). See the appendix for instructions for setting up MinGW manually. Enthought Canopy and Python(x,y) bundle MinGW, but some of the configuration steps in the appendix might still be necessary.

The simplest way of installing Cython is by using pip:

pip install Cython

On platforms that are covered by one of the binary wheel packages provided on PyPI, this will install an accelerated wheel which contains some Cython compiled modules. Other platforms will use pure Python wheels that install quickly but run somewhat slower, which is still well adapted for one-time builds e.g. in CI build servers.

For installations on systems where Cython is executed a lot, it is worth checking that the installation uses a binary module, or otherwise to build a binary wheel locally.

The newest Cython release can always be downloaded from https://cython.org/. Unpack the tarball or zip file, enter the directory, and then run:

pip install .

For one-time installations from a Cython source checkout, it is substantially faster than a full binary build to just install the uncompiled (slower) version of Cython with something like

NO_CYTHON_COMPILE=true  pip install .
Anaconda

https://docs.anaconda.com/anaconda/

Canopy

https://www.enthought.com/product/canopy/

Sage
  1. Stein et al., Sage Mathematics Software, https://www.sagemath.org/