使用C头文件编译Cython错误

Question

So I'm trying to wrap some C code with Cython. I read read applied Cython's tutorials on doing this ( 1 , 2 ), but these tutorials do not say much on how to compile the code once you have wrapped it with Cython, and so I have an error saying it can't find my C code.

First, my cython script ("calcRMSD.pyx"):

import numpy as np
cimport numpy as np

cdef extern from "rsmd.h":
    double rmsd(int n, double* x, double* y)

#rest of the code ommited

The C code I am trying to wrap ("rmsd.h"):

#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>

extern "C" {
  // svd from lapack
  void dgesvd_(char*,char*,int*,int*,double*,int*,double*,double*,int*,double*,
           int*,double*,int*,int*);
}

double rmsd(int n, double* x, double* y)
{
   //code omitted
}

Setup.py

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
import numpy as np


setup(
    ext_modules = cythonize([Extension("calcRMSD", 
                            sources = ["calcRMSD.pyx"],
                            include_dirs = [np.get_include()],
                            libraries = ["dgesvd"]
                            #extra_compile_args = ["-I."],
                            #extra_link_args = ["-L./usr/lib/liblapack.dylib"]
                            )])

) 

My error:

calcRMSD.c:269:10: fatal error: 'rsmd.h' file not found
#include "rsmd.h"

I read this stack overflow thread Using Cython To Link Python To A Shared Library

but following it gives me different errors. If I try to put rmsd.h in sources, it says it doesnt recognize the file type.

How to link custom C (which itself needs special linking options to compile) with Cython?

This looks somewhat promising but im not sure how to use it.

Please help!

Answer 1

First of all it has to find the include file, rsmd.h . You need to add the path where this header can be found to the include_dirs parameter. The error about the missing file should disappear.

Then you will additionally need to include the library you get from compiling that C code. If that's librsmd.a you would add 'rsmd' to the libraries parameter. Additionally you might need a library_dirs parameter that contains the path where that library can be found.