ValueError: ndarray is not C-contiguous in cython

Question

I have written the following function in cython to estimate the log-likelihood

@cython.boundscheck(False)
@cython.wraparound(False)
def li         


        

Answer 1

Just before you get the error, try printing the flags attribute of the numpy array(s) you're passing to likelihood. You'll probably see something like:

In [2]: foo.flags
Out[2]: 
  C_CONTIGUOUS : False
  F_CONTIGUOUS : True
  OWNDATA : True
  WRITEABLE : True
  ALIGNED : True
  UPDATEIFCOPY : False

Note where it says C_CONTIGUOUS : False, because that's the issue. To fix it, simply convert it to C-order:

In [6]: foo = foo.copy(order='C')

In [7]: foo.flags
Out[7]: 
  C_CONTIGUOUS : True
  F_CONTIGUOUS : False
  OWNDATA : True
  WRITEABLE : True
  ALIGNED : True
  UPDATEIFCOPY : False