setup.py

#!/usr/bin/env python

from setuptools import setup, find_packages
from distutils.extension import Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
import numpy
import os

MODULE_NAME = "tierpsy"
AUTHOR = 'Avelino Javer'
AUTHOR_EMAIL = 'avelino.javer@imperial.ac.uk'
URL = 'https://github.com/ver228/tierpsy-tracker'
DOWNLOAD_URL = 'https://github.com/ver228/tierpsy-tracker'
DESCRIPTION = "tierpsy: Tierpsy Tracker Multi-Worm Tracker."
exec(open(MODULE_NAME + '/version.py').read())
VERSION = __version__

def _get_ext_modules():
  #build cython files
  # python3 setup.py build_ext --inplace
  path_parts = [MODULE_NAME, 'analysis', 'ske_create', 'segWormPython', 'cython_files']
  cython_path = os.path.join(*path_parts)
  cython_path_e = os.path.join(MODULE_NAME, 'analysis', 'stage_aligment')

  def _add_path(f_list):
  	return [os.path.join(cython_path, x) for x in f_list]

  def _get_mod_path(name):
      return '.'.join(path_parts + [name])

  ext_files = {
  	"circCurvature" : ["circCurvature.pyx", "c_circCurvature.c"],
  	"curvspace" : ["curvspace.pyx", "c_curvspace.c"]
  }

  include_dirs = [numpy.get_include()]
  ext_modules = cythonize(os.path.join(cython_path, "*_cython.pyx"))
  ext_modules += cythonize(os.path.join(cython_path_e, "*.pyx"))
  ext_modules += [Extension(_get_mod_path(name), 
                            sources=_add_path(files), 
                            include_dirs=include_dirs) 
  			   for name, files in ext_files.items()]
  return ext_modules

PKG_DATA = [
  'extras/*',
  'extras/param_files/*',
  'features/tierpsy_features/extras/*',
  'features/open_worm_analysis_toolbox/features/master_eigen_worms_N2.mat',
  'features/open_worm_analysis_toolbox/features/feature_metadata/features_list.csv'
]


#install setup
setup(name = MODULE_NAME,
   version = VERSION,
   description = DESCRIPTION,
   author = AUTHOR,
   author_email = AUTHOR_EMAIL,
   url = URL,
   packages = find_packages(),
   cmdclass = {'build_ext': build_ext},
   ext_modules = _get_ext_modules(),
   include_dirs = [numpy.get_include()],
   package_data = {'tierpsy': PKG_DATA},
   entry_points= {
          'gui_scripts': [
              'tierpsy_gui_simple = tierpsy.gui.HDF5VideoPlayer:tierpsy_gui_simple'
          ],
          'console_scripts': [
              'tierpsy_gui = tierpsy.gui.SelectApp:tierpsy_gui', #windows bug, if I put tierpsy_gui as a gui application I cannot run batch processing since the command line stdout is supressed.
              'tierpsy_process = tierpsy.processing.processMultipleFilesFun:tierpsy_process',
              'tierpsy_tests = tierpsy.tests.run_tests:tierpsy_tests'
          ]
      }
   )