Using Cython To Link Python To A Shared Library

Question

I am trying to integrate a third party library written in C with my python application using Cython. I have all of the python code written for a test. I am having trouble finding an example for setting this up.

I have a pyd/pyx file I created manually. The third party has given me a header file (*.h) and a shared library (*.so). As far as I can tell, there are no other dependencies. Can someone provide an example of how to set this up using Cython and disutils?

Thanks

Answer 1

Sure !

(In the following, I assume that you already know how to deal with cimport and the interactions between .pxd and .pyx. If this is not completely the case, just ask and I will develop that part as well)

The sample (grabbed from a C++ project of mine, but a C project would work pretty much the same) :

1. The Distutils setup file :

Assuming that the extension to be created will be called myext and the 3rd party shared library is libexternlib.so (note the lib* prefix, here)...

# setup.py file import sys import os import shutil  from distutils.core import setup from distutils.extension import Extension from Cython.Distutils import build_ext  # clean previous build for root, dirs, files in os.walk(".", topdown=False):     for name in files:         if (name.startswith("myext") and not(name.endswith(".pyx") or name.endswith(".pxd"))):             os.remove(os.path.join(root, name))     for name in dirs:         if (name == "build"):             shutil.rmtree(name)  # build "myext.so" python extension to be added to "PYTHONPATH" afterwards... setup(     cmdclass = {'build_ext': build_ext},     ext_modules = [         Extension("myext",                    sources=["myext.pyx",                            "SomeAdditionalCppClass1.cpp",                            "SomeAdditionalCppClass2.cpp"                        ],                   libraries=["externlib"],          # refers to "libexternlib.so"                   language="c++",                   # remove this if C and not C++                   extra_compile_args=["-fopenmp", "-O3"],                   extra_link_args=["-DSOME_DEFINE_OPT",                                     "-L./some/extra/dependency/dir/"]              )         ] )            

Note : Your external .so file is linked via the libraries option :

libraries=["externlib"]   # Without the 'lib' prefix and the '.so' extension... 

Note : the sources option can be used to get some additional source files compiled.

Important : myext.pxd (do not confound with .pyd - Windows stuff) and myext.pyx should be in the same directory. At compile time the definition file, if it exists, is processed first (more).

2. Then run it as follows :

After having changed directory to the one containing your myext.pxd, your myext.pyx, as well as the above setup.py script :

# setup.sh # Make the "myext" Python Module ("myext.so") CC="gcc"   \ CXX="g++"   \ CFLAGS="-I./some/path/to/includes/ -I../../../DEPENDENCIES/python2.7/inc -I../../../DEPENDENCIES/gsl-1.15"   \ LDFLAGS="-L./some/path/to/externlib/"   \     python setup.py build_ext --inplace 

Where :

• libexternlib.so is assumed to be located at ./some/path/to/externlib/
• yourheader.h is assumed to be located at ./some/path/to/includes/

Note : CFLAGS could also have been setup using the extra_compile_args option :

extra_compile_args=["-I./some/path/to/includes/", "-fopenmp", "-O3"] 

Note : LDFLAGS could also have been setup using the extra_link_args option :

extra_link_args=["-L./some/path/to/externlib/", "-DSOME_DEFINE_OPT", "-L./some/extra/dependency/dir/"] 

Once distutils is done with the build, you get some new files, specially the myext.cpp, myext.h and most importantly, the myext.so.

3. After that, you're good to go :

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:./some/path/to/externlib/ export PYTHONPATH=$PYTHONPATH:./some/path/to/myext/  # Run some script requiring "myext.so" python somescript.py 

Where your freshly created Python extension can be imported by its name :

# somescript.py import myext from myext import PySomeFeature ... 

Note about Optimization : By default -O2 is used for compiling the extension, but this can be overloaded (see above setup where -O3 is specified).

Note about Cython paths : If Cython was installed in a custom directory, you might want to add it to your environment, before all :

PYTHONPATH=$PYTHONPATH:../../../DEPENDENCIES/Cython-0.18 export PYTHONPATH; PATH=$PATH:../../../DEPENDENCIES/Cython-0.18/bin; export PATH; 

Well, hope I covered the main points...