CythonGSL 0.2.1alpha

Cython declarations for the Gnu Scientific Library.

Introduction

Date:

May 13, 2012

Version:

0.2.1alpha

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

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 http://gnuwin32.sourceforge.net/packages/gsl.htm)

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