Compiling cython with gcc: No such file or directory from #include "ios"

Question

Given a file docprep.pyx as simple as

from spacy.structs cimport TokenC

print("loading")

And trying to cythonize it via

cythonize -3 -i docprep.pyx

I get the following error message

docprep.c:613:10: fatal error: ios: No such file or directory
 #include "ios"
          ^~~~~
compilation terminated

As you can tell from the paths, this system has an Anaconda installation with Python 3.7. numpy, spacy and cython are all installed through conda.

Answer 1

<ios> is a c++-header. The error message shows that you try to compile a C++-code as C-code.

Per default, Cython will produce a file with extension *.c, which will be interpreted as C-code by the compiler later on.

Cython can also produce a file with the right file-extension for c++, i.e. *.cpp. And there are multiple ways to trigger this behavior:

• adding # distutils: language = c++ at the beginning of the pyx-file.
• adding language="c++" to the Extension definition in the setup.py-file.
• call cython with option --cplus.
• in IPython, calling %%cython magic with -+, i.e. %%cython -+.
• for alternatives when building with pyximport, see this SO-question.

Actually, for cythonize there is no command line option to trigger c++-generation, thus the first options looks like the best way to go:

# distutils: language = c++

from spacy.structs cimport TokenC
print("loading") 

---

The problem is that spacy/structs.pxd uses c++-constructs, for example vectors or anything else cimported from libcpp:

...
from libcpp.vector cimport vector
...

and thus also c++-libraries/headers are needed for the build.

Answer 2

In my case, it worked using @mountrix tip, just add the language="c++" to your setup.py, an example:

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


extensions = [
    Extension("processing_module", sources=["processing_module.pyx"], include_dirs=[numpy.get_include()], extra_compile_args=["-O3"], language="c++")
]

setup(
    name="processing_module",
    ext_modules = cythonize(extensions),
)