import numpy as np
cimport numpy as np
cimport cython
from cython.view cimport array as cvarray
from libc.stdlib cimport malloc, free
from libc.math cimport log, exp
from cython_gsl cimport *
import ctypes
cdef gsl_rng *r = gsl_rng_alloc(gsl_rng_mt19937)


@cython.cdivision(True)
@cython.wraparound(False)
@cython.boundscheck(False)
cdef void generator(double* alpha,int* D, double* m):

     cdef Py_ssize_t i
     for i from 0 <= i < D[0]:
        m[i]=gsl_ran_beta(r, alpha[0], 1)
     return

@cython.cdivision(True)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef void initializer(double* alpha, int* D, int* N, double* m, int** Z ):
     cdef int i, j
     Z = <int **> malloc(N[0] * sizeof(int*))
     for i from 0 <= i < N[0]:
         Z[i] = <int *> malloc(D[0] * sizeof(int))

     generator(&alpha[0], &D[0], &m[0])

     for i from 0 <= i < D[0]:
         for j from 0 <= j < N[0]:
             Z[j][i]= gsl_ran_bernoulli(r, m[i])
             print Z[j][i]
     return

def run(int n, int d, double alpha):
    cdef np.ndarray[double, ndim=1, mode='c'] mu=np.empty((d,), dtype=ctypes.c_double)
    cdef np.ndarray[int, ndim=2, mode='c'] Z=np.zeros((n,d), dtype=ctypes.c_int)
    initializer(&alpha, &d, &n,  &mu[0], &Z[0][0] )

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

ext_modules = [
    Extension(
        "test",
        ["test.pyx"],
        libraries=cython_gsl.get_libraries(),
        library_dirs=[cython_gsl.get_library_dir()],
        include_dirs=[numpy.get_include(), cython_gsl.get_include()])

]
ext_modules = cythonize(ext_modules)

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

def run(int n, int d, double alpha):
    cdef np.ndarray[double, ndim=1, mode='c'] mu=np.empty((d,), dtype=ctypes.c_double)
    cdef np.ndarray[int, ndim=2, mode='c'] Z=np.zeros((n,d), dtype=ctypes.c_int)
    initializer(&alpha, &d, &n,  &mu[0], &Z[0][0] )                                      ^
------------------------------------------------------------

test.pyx:46:39: Cannot take address of Python variable