Python.h not found using swig and Anaconda Python

Question

I'm trying to compile a simple python/C example following this tutorial:

http://www.swig.org/tutorial.html

I'm on MacOS using Anaconda python.

however, when I run

gcc -c example.c example_wrap.c -I/Users/myuser/anaconda/include/

I get:

example_wrap.c:130:11: fatal error: 'Python.h' file not found
# include <Python.h>
          ^

It seems that this problem is reported in a number of questions:

Missing Python.h while trying to compile a C extension module

Missing Python.h and impossible to find

Python.h: No such file or directory

but none seem to provide an answer specific to Anaconda on MacOS

Anyone solved this?

Answer 1

Use the option -I/Users/myuser/anaconda/include/python2.7 in the gcc command. (That's assuming you are using python 2.7. Change the name to match the version of python that you are using.) You can use the command python-config --cflags to get the full set of recommended compilation flags:

$ python-config --cflags
-I/Users/myuser/anaconda/include/python2.7 -I/Users/myuser/anaconda/include/python2.7 -fno-strict-aliasing -I/Users/myuser/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

However, to build the extension module, I recommend using a simple setup script, such as the following setup.py, and let distutils figure out all the compiling and linking options for you.

# setup.py

from distutils.core import setup, Extension


example_module = Extension('_example', sources=['example_wrap.c', 'example.c'])

setup(name='example', ext_modules=[example_module], py_modules=["example"])

Then you can run:

$ swig -python example.i
$ python setup.py build_ext --inplace

(Take a look at the compiler commands that are echoed to the terminal when setup.py is run.)

distutils knows about SWIG, so instead of including example_wrap.c in the list of source files, you can include example.i, and swig will be run automatically by the setup script:

# setup.py

from distutils.core import setup, Extension


example_module = Extension('_example', sources=['example.c', 'example.i'])

setup(name='example', ext_modules=[example_module], py_modules=["example"])

With the above version of setup.py, you can build the extension module with the single command

$ python setup.py build_ext --inplace

Once you've built the extension module, you should be able to use it in python:

>>> import example
>>> example.fact(5)
120

If you'd rather not use the script setup.py, here's a set of commands that worked for me:

$ swig -python example.i
$ gcc -c -I/Users/myuser/anaconda/include/python2.7 example.c example_wrap.c 
$ gcc -bundle -undefined dynamic_lookup -L/Users/myuser/anaconda/lib example.o example_wrap.o -o _example.so

Note: I'm using Mac OS X 10.9.4:

$ gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.3.0
Thread model: posix