Cython: "fatal error: numpy/arrayobject.h: No such file or directory"

Question

In your setup.py, the Extension should have the argument include_dirs=[numpy.get_include()].

Also, you are missing np.import_array() in your code.

--

Example setup.py:

from distutils.core import setup, Extension
from Cython.Build import cythonize
import numpy

setup(
    ext_modules=[
        Extension("my_module", ["my_module.c"],
                  include_dirs=[numpy.get_include()]),
    ],
)

# Or, if you use cythonize() to make the ext_modules list,
# include_dirs can be passed to setup()

setup(
    ext_modules=cythonize("my_module.pyx"),
    include_dirs=[numpy.get_include()]
)    

For a one-file project like yours, another alternative is to use pyximport. You don't need to create a setup.py ... you don't need to even open a command line if you use IPython ... it's all very convenient. In your case, try running these commands in IPython or in a normal Python script:

import numpy
import pyximport
pyximport.install(setup_args={"script_args":["--compiler=mingw32"],
                              "include_dirs":numpy.get_include()},
                  reload_support=True)

import my_pyx_module

print my_pyx_module.some_function(...)
...

You may need to edit the compiler of course. This makes import and reload work the same for .pyx files as they work for .py files.

Source: http://wiki.cython.org/InstallingOnWindows

The error means that a numpy header file isn't being found during compilation.

Try doing export CFLAGS=-I/usr/lib/python2.7/site-packages/numpy/core/include/, and then compiling. This is a problem with a few different packages. There's a bug filed in ArchLinux for the same issue: https://bugs.archlinux.org/task/22326

Simple answer

A way simpler way is to add the path to your file distutils.cfg. It's path behalf of Windows 7 is by default C:\Python27\Lib\distutils\. You just assert the following contents and it should work out:

[build_ext]
include_dirs= C:\Python27\Lib\site-packages\numpy\core\include

Entire config file

To give you an example how the config file could look like, my entire file reads:

[build]
compiler = mingw32

[build_ext]
include_dirs= C:\Python27\Lib\site-packages\numpy\core\include
compiler = mingw32

It should be able to do it within cythonize() function as mentioned here, but it doesn't work beacuse there is a known issue

If you are too lazy to write setup files and figure out the path for include directories, try cyper. It can compile your Cython code and set include_dirs for Numpy automatically.

Load your code into a string, then simply run cymodule = cyper.inline(code_string), then your function is available as cymodule.sparsemaker instantaneously. Something like this

code = open(your_pyx_file).read()
cymodule = cyper.inline(code)

cymodule.sparsemaker(...)
# do what you want with your function

You can install cyper via pip install cyper.