Cannot build in place on Mac OS X

[mathDR]

So currently both pip install pyhsmm breaks and attempting to manually build via python setup.py build_ext --inplace --with-cython breaks with the same error:

pyhsmm/internals/hmm_messages_interface.cpp:271:10: fatal error: 'numpy/arrayobject.h' file not found

There are other examples of this online (i.e. it is apparently due to cython compiler not finding the numpy header files)

Have you successfully compiled on mac?

[mattjj]

Yeah; actually my main development machine is a mac.

It sounds like there may be a problem with your python setup. Are you able to build other cython code that uses numpy (via cimport numpy)?

Things to check:

• numpy and scipy versions
• locate the arrayobject.h file(s) on your system and compare to the output of np.get_include()

If you're not already using anaconda or miniconda, now might be a good time to give those a shot.

[mattjj]

Here's a small test to see if cython is able to build things:

Put this in foo.pyx:

import numpy as np
cimport numpy as np

def foo(double[:] a, double[:] b):
    return np.dot(a,b)

Put this in setup.py:

from distutils.core import setup
import numpy as np
from Cython.Build import cythonize

setup(ext_modules=cythonize('*.pyx'), include_dirs=[np.get_include()])

I checked that the generated foo.c includes numpy/arrayobject.h and that things build (and run correctly) with python setup.py build_ext --inplace.

[mathDR]

Thanks, yep your example didn't work on my machine. Interesting. I used to be able to compile, but for some reason it doesn't work now. Maybe homebrew did something, but I will close this as it is definitely my environment.

[mathDR]

Just a heads up: if I change from: distutils.core import setup to: from numpy.distutils.core import setup

everything works. This seems super crazy. Apparently with disutils, the default clang couldn't see the numpy header files? Strange...