Introduction

Date

May 13, 2012

Version

0.2.1

Authors

Thomas Wiecki, thomas.wiecki[at]gmail.com

Web site

https://github.com/twiecki/CythonGSL

Copyright

This document has been placed in the public domain.

License

CythonGSL is released under the GPLv3.

Purpose

CythonGSL provides a Cython interface for the GNU Scientific Library (GSL).

Cython is the ideal tool to speed up numerical computations by converting typed Python code to C and generating Python wrappers so that these compiled functions can be called from Python. Scientific programming often requires use of various numerical routines (e.g. numerical integration, optimization). While SciPy provides many of those tools, there is an overhead associated with using these functions within your Cython code. CythonGSL allows you to shave off that last layer by providing Cython declarations for the GSL which allow you to use this high-quality library from within Cython without any Python overhead.

Fork of PyrexGsl by Mario Pernici (http://wwwteor.mi.infn.it/~pernici/pyrexgsl/pyrexgsl.html).

Usage

For a quick demo, see: http://nbviewer.ipython.org/urls/raw.github.com/twiecki/CythonGSL/master/examples/cython_gsl_ipythonnb.ipynb

Import CythonGSL in your pyx file

In your cython file from which you want to call gsl routines, import gsl like this:

from cython_gsl cimport *

From there you should be able to call any gsl function, see http://www.gnu.org/software/gsl/manual/gsl-ref.html for the GSL reference.

For more examples, check out the examples directory.

Compile your module

Here is what your setup.py could look like:

from distutils.core import setup
from Cython.Distutils import Extension
from Cython.Distutils import build_ext
import cython_gsl

setup(
    [...]
    include_dirs = [cython_gsl.get_include()],
    cmdclass = {'build_ext': build_ext},
    ext_modules = [Extension("my_cython_script",
             ["src/my_cython_script.pyx"],
             libraries=cython_gsl.get_libraries(),
             library_dirs=[cython_gsl.get_library_dir()],
             include_dirs=[cython_gsl.get_cython_include_dir()])]
    )

Installation

Dependencies

• Python
• Cython (http://cython.org)
• GSL (for a Windows port see https://code.google.com/p/oscats/downloads/list)

Installing CythonGSL

python setup.py build
python setup.py install

Installing CythonGSL Unittests

python setup_test.py build
python setup_test.py install
nosetest cython_gsl