Line profiling with cython in jupyter notebook - jupyter-notebook

Question

I'm trying to use liner_profiler library in jupyter notebook with cython function. It is working only halfway. The result I get only consist of first row of the function and no profiling results.
%%cython -a
# cython: linetrace=True
# cython: binding=True
# distutils: define_macros=CYTHON_TRACE_NOGIL=1
import numpy as np
cimport numpy as np
from datetime import datetime
import math
cpdef np.int64_t get_days(np.int64_t year, np.int64_t month):
cdef np.ndarray months=np.array([31,28,31,30,31,30,31,31,30,31,30,31])
if month==2:
if (year%4==0 and year%100!=0) or (year%400==0):
return 29
return months[month-1]
For the profiling result int onlt shows one line of code
Timer unit: 1e-07 s
Total time: 0.0015096 s
File: .ipython\cython\_cython_magic_0154a9feed9bbd6e4f23e57d73acf50f.pyx
Function: get_days at line 15
Line # Hits Time Per Hit % Time Line Contents
==============================================================
15 cpdef np.int64_t get_days(np.int64_t year, np.int64_t month):

Answer 1

This can be seen as a bug in the line_profiler (if it is supposed to support Cython). To get the code of the profiled function, line_profiler reads the pyx-file and tries to extract the code with help of inspect.getblock:
...
# read pyx-file
all_lines = linecache.getlines(filename)
# try to extract body of the function strarting at start_lineno:
sublines = inspect.getblock(all_lines[start_lineno-1:])
...
However, getblock knows nothing about cpdef-function, as python has only def-functions and thus yields wrong function-body (i.e. only the signature).
Workaround:
A simple work around would be to introduce a dummy def-function, which would be a sentinel for the cpdef-function in such a way, that inspect.getblock would yield the whole body of the cpdef-function + body of the the sentinel function, i.e.:
%%cython
...
cpdef np.int64_t get_days(np.int64_t year, np.int64_t month):
...
def get_days_sentinel():
pass
and now the report %lprun -f get_days get_days(2019,3) looks as follows:
Timer unit: 1e-06 s
Total time: 1.7e-05 s
File: XXXX.pyx
Function: get_days at line 10
Line # Hits Time Per Hit % Time Line Contents
==============================================================
10 cpdef np.int64_t get_days(np.int64_t year, np.int64_t month):
11 1 14.0 14.0 82.4 cdef np.ndarray months=np.array([31,28,31,30,31,30,31,31,30,31,30,31])
12 1 1.0 1.0 5.9 if month==2:
13 if (year%4==0 and year%100!=0) or (year%400==0):
14 return 29
15 1 2.0 2.0 11.8 return months[month-1]
16
17 def get_days_sentinel():
18 pass
There are still somewhat ugly trailing lines from the sentinel, but it is probably better as not seeing anything at all.