How to do line profiling in cython

Line Profiling in Cython

Setup

1. pip install line_profiler
2. In the cython file itself, add these directives:

   # cython: linetrace=True
   # distutils: define_macros=CYTHON_TRACE_NOGIL=1

3. In the cython file, add the @cython.binding(True) decorator to the function you want to line profile. For example,

   @cython.binding(True)
   def flow_accumulation_d8(
         flow_dir_raster_path_band, target_flow_accum_raster_path,
         weight_raster_path_band=None, custom_decay_factor=None

4. In setup.py, add define_macros=[('CYTHON_TRACE', '1')] to the appropriate Extension().
5. Write a python script to invoke the line profiler. For example:

   # doit.py
   
   import line_profiler
   import pygeoprocessing.routing
   
   def doit():
       profile = line_profiler.LineProfiler(
            pygeoprocessing.routing.flow_accumulation_d8)
       profile.runcall(
            pygeoprocessing.routing.flow_accumulation_d8,
            (flow_dir_path, 1), target_flow_accum_path,
            custom_decay_factor=0.5)
       profile.print_stats()

Execution

1. Recompile and install pygeoprocessing
2. Execute your python script like so: kernprof -l doit.py .
3. View the line profiling results printed to stdout.