As the first rule of optimization is to measure performance before starting any optimization work, one should have made profile of the pure Python code before starting any Cythonization. However, in the next optimization cycle one should profile also the Cython code.
By default, Cython code does not show up in the measurements of cProfile. One can, however, enable profiling either for the whole module or for individual functions. In order to enable profiling for the whole function, simply include a global directive at the top of a file:
# cython: profile=True
import numpy as np
def myfunc():
...In order to enable profiling for a single function, one can include the cython decorator before a function definition:
cimport cython
@cython.profile(True)
def my_func():
...As profiling adds always some overhead, small functions that are called very frequently can mess up the profile. In these cases one can use the decorator for disabling profiling for some functions (if profiling is enabled for the whole module).
# cython: profile=True
cimport cython
@cython.profile(False)
def my_func_not_to_profile():
...