old_contents: # -*- coding: utf-8 -*-
  
  import numpy
  from setuptools import setup, find_packages, Extension
  
  
  with open('README.rst') as f:
      readme = f.read()
  
  with open('LICENSE') as f:
      lic = f.read()
  
  with open('requirements.txt') as f:
      required = f.read().splitlines()
  
  
  # Obtain the numpy include directory.  This logic works across numpy versions.
  try:
      numpy_include = numpy.get_include()
  except AttributeError:
      numpy_include = numpy.get_numpy_include()
  
  correlation_module = Extension('sga.toolbox._c_impl', 
          sources=['sga/toolbox/src/c_impl.i', 'sga/toolbox/src/correlation.c', 'sga/toolbox/src/table_norm.c', 'sga/toolbox/src/safe.c'],
          include_dirs = [numpy_include],
          swig_opts=['-threads', '-modern', '-outdir', 'sga/toolbox/'],
          libraries = ['gsl', 'gslcblas','m'],
          extra_compile_args = ["-O3"],
      )
  
  console_scripts = [
      'sga-similarity=sga.similarity:main',
      'sga-safe=sga.safe:main'
  ]
  
  setup(
      name='sga',
      version='0.1.0',
      description='SGA Utilities',
      install_requires=required,
      long_description=readme,
      author='Matej Usaj',
      author_email='usaj.m@utoronto.ca',
      url='https://github.com/usajusaj/sga_utils',
      license=lic,
      ext_modules = [correlation_module],
      packages=find_packages(exclude=('tests', 'docs')),
      entry_points = {
          'console_scripts': console_scripts,
      }
  )
  
  
new_contents: # -*- coding: utf-8 -*-
  
  import numpy
  from setuptools import setup, find_packages, Extension
  
  
  with open('README.rst') as f:
      readme = f.read()
  
  with open('LICENSE') as f:
      lic = f.read()
  
  with open('requirements.txt') as f:
      required = f.read().splitlines()
  
  
  # Obtain the numpy include directory.  This logic works across numpy versions.
  try:
      numpy_include = numpy.get_include()
  except AttributeError:
      numpy_include = numpy.get_numpy_include()
  
  correlation_module = Extension('sga.toolbox._c_impl', 
          sources=['sga/toolbox/src/c_impl.i', 'sga/toolbox/src/correlation.c', 'sga/toolbox/src/table_norm.c', 'sga/toolbox/src/safe.c'],
          include_dirs = [numpy_include],
          swig_opts=['-threads', '-modern', '-outdir', 'sga/toolbox/'],
          libraries = ['gsl', 'gslcblas','m'],
          extra_compile_args = ["-O3"],
      )
  
  console_scripts = [
      'sga-similarity=sga.similarity:main',
      'sga-safe=sga.safe:main'
  ]
  
  setup(
      name='sga',
      version='0.1.0',
      description='SGA Utilities',
      install_requires=required,
      long_description=readme,
      author='Matej Usaj',
      author_email='usaj.m@utoronto.ca',
      url='https://github.com/usajusaj/sga_utils',
      license=lic,
      ext_modules = [correlation_module],
      py_modules=['sga.toolbox.c_impl'],
      packages=find_packages(exclude=('tests', 'docs')),
      entry_points = {
          'console_scripts': console_scripts,
      }
  )
  
  
subject: Install missing swig generated file