Question

I have a problem importing the vector class to cython using

from libcpp.vector cimport vector

when I add this and try to compile the pyx file I get

python setup.py build_ext --inplace
running build_ext
skipping 'kmc_cy.c' Cython extension (up-to-date)
building 'kmc_cy' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fPIC -I/usr/include/python2.7 -c kmc_cy.c -o build/temp.linux-x86_64-2.7/kmc_cy.o
kmc_cy.c:254:18: fatal error: vector: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

Here is my setup.py

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
import sys
sys.path.append("/usr/lib64/python2.7/site-packages/Cython/Includes/libcpp")

ext_modules = [Extension("kmc_cy", ["kmc_cy.pyx"])]

setup(
  name = 'kmc_cy',
  cmdclass = {'build_ext': build_ext},
  ext_modules = ext_modules,
)

Cheers

Answer 1

As std::vector is C++ code, you need to set the correct language:

  ext_modules = [Extension("kmc_cy", ["kmc_cy.pyx"],language='c++')]

Then g++ should be used instead of gcc and the file name should end with .cpp or .cc.
See this answer for more details.