README.md

cythonRMath

Cython wrapper of the RMath library (based on cythonGSL).

TODO

• See if nogil should be added

Dependencies

The Rmath library must be built and libRmath.so (libRmath.dylib on OSX) must be in a standard directory (e.g. /usr/local/lib), or in a directory on LD_LIBRARY_PATH (DYLD_LIBRARY_PATH on OSX), or in the same directory as your project. Installing R will not suffice (at least on OSX). You need to build libRmath.{so|dylib} for standalone use.

First get a copy of Rmath (e.g. https://github.com/JuliaLang/Rmath) and build it. Then copy the resulting .so (or .dylib on OSX) to either a standard place that your system searches to dynamically link libraries, or add the directory containing libRmath.{so|dylib} to {DY}LD_LIBRARY_PATH, or a cheap solution is to just copy libRmath.{so|dylib} to the directory where you will build your cython code.

Installation:

Run python setup.py install.

Usage

There will be a demo at some point.

Make sure cythonRmath is on your PYTHONPATH

Import cythonRmath into your cython code

In the cython file from which you want to call Rmath functions, import the library:

    from cython_rmath cimport *

You should be able to call Rmath functions from here on out.

Compile your module

Your setup.py should look like (see examples/setup.py):

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

    ext = Extension("your_ext",
                    ["your.pyx"],
                    define_macros=[('MATHLIB_STANDALONE', '1')],
                    include_dirs = [path_to_Rmath/include, ...],
                    library_dirs = [path_to_Rmath/lib, ...],
                    libraries = ['Rmath', 'm', ...]
                   )

    setup(cmdclass = ['build_ext': build_ext},
          ext_modules = [ext])

Note: The libRmath.{so|dylib} may not be in the lib directory (if you use the repository above it will be in the src directory).