old_contents: # Try using setuptools first, if it's installed
  try:
      from setuptools import setup
  except:
      from distutils.core import setup
  
  from distutils.extension import Extension
  
  
  # Define extensions
  extension1 = Extension('epistasis.decomposition', ["epistasis/decomposition.c"])
  
  # define all packages for distribution
  packages = [
      'epistasis',
      'epistasis.models',
      'epistasis.models.linear',
      'epistasis.models.nonlinear',
      'epistasis.plotting',
      'epistasis.simulate',
  ]
  
  setup(name='epistasis',
        version='0.1.2',
        description='High Order Epistasis Models/Regressions for Genotype-Phenotype Maps',
        author='Zach Sailer',
        author_email='zachsailer@gmail.com',
        url='https://github.com/harmslab/epistasis',
        packages=packages,
        classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Science/Research',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.2',
          'Programming Language :: Python :: 3.3',
          'Programming Language :: Python :: 3.4',
        ],
        ext_modules=[extension1],
        zip_safe=False)
  
new_contents: # Try using setuptools first, if it's installed
  try:
      from setuptools import setup
  except:
      from distutils.core import setup
  
  from distutils.extension import Extension
  
  
  # Define extensions
  extension1 = Extension('epistasis.decomposition', ["epistasis/decomposition.c"])
  
  # define all packages for distribution
  packages = [
      'epistasis',
      'epistasis.models',
      'epistasis.models.linear',
      'epistasis.models.nonlinear',
      'epistasis.models.transformations',
      'epistasis.plot',
      'epistasis.simulate',
  ]
  
  setup(name='epistasis',
        version='0.1.2',
        description='High Order Epistasis Models/Regressions for Genotype-Phenotype Maps',
        author='Zach Sailer',
        author_email='zachsailer@gmail.com',
        url='https://github.com/harmslab/epistasis',
        packages=packages,
        classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Science/Research',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.2',
          'Programming Language :: Python :: 3.3',
          'Programming Language :: Python :: 3.4',
        ],
        ext_modules=[extension1],
        zip_safe=False)
  
subject: update setup.py to new modules