old_contents: # -*- coding: utf-8 -*-
  
  ## Copyright 2015 Kevin B Jacobs
  ##
  ## Licensed under the Apache License, Version 2.0 (the "License"); you may
  ## not use this file except in compliance with the License.  You may obtain
  ## a copy of the License at
  ##
  ##        http://www.apache.org/licenses/LICENSE-2.0
  ##
  ## Unless required by applicable law or agreed to in writing, software
  ## distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
  ## WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  See the
  ## License for the specific language governing permissions and limitations
  ## under the License.
  
  import sys
  
  if sys.version_info < (3, 4):
      sys.exit('Sorry, Python 3.4 or newer is required to install and run vgraph')
  
  
  from setuptools import setup, find_packages
  from Cython.Distutils import build_ext
  from distutils.extension import Extension
  
  
  install_requires = ['Cython', 'pysam']
  setup_requires   = ['pytest-runner', 'pysam', 'setuptools_scm==1.15.0', 'setuptools_scm_git_archive==1.0']
  tests_require    = ['pytest', 'coverage']
  
  
  ext_modules = [
      Extension('vgraph.norm',      ['vgraph/norm.pyx']),
      Extension('vgraph.intervals', ['vgraph/intervals.pyx']),
  ]
  
  
  classifiers = """
  Development Status :: 2 - Alpha
  Operating System :: MacOS :: MacOS X
  Operating System :: Microsoft :: Windows :: Windows NT/2000
  Operating System :: OS Independent
  Operating System :: POSIX
  Operating System :: POSIX :: Linux
  Operating System :: Unix
  Programming Language :: Python :: 3.5
  Topic :: Scientific/Engineering
  Topic :: Scientific/Engineering :: Bioinformatics
  """
  
  
  if __name__ == '__main__':
      setup(
          name = 'vgraph',
          description = 'Graph-based variant normalization and comparison tools',
          url = 'https://github.com/bioinformed/vgraph',
          author = 'Kevin Jacobs',
          maintainer = 'Kevin Jacobs',
          author_email = 'jacobs@bioinformed.com',
          maintainer_email = 'jacobs@bioinformed.com',
          license = 'APACHE-2.0',
          classifiers = classifiers.split('\n'),
          use_scm_version=True,
          zip_safe = False,
          tests_require = tests_require,
          packages = find_packages(),
          install_requires = install_requires,
          setup_requires = setup_requires,
          cmdclass = {'build_ext': build_ext},
          ext_modules = ext_modules,
          entry_points={'console_scripts': ['vgraph = vgraph.vgraph:main']},
      )
  
new_contents: # -*- coding: utf-8 -*-
  
  ## Copyright 2015 Kevin B Jacobs
  ##
  ## Licensed under the Apache License, Version 2.0 (the "License"); you may
  ## not use this file except in compliance with the License.  You may obtain
  ## a copy of the License at
  ##
  ##        http://www.apache.org/licenses/LICENSE-2.0
  ##
  ## Unless required by applicable law or agreed to in writing, software
  ## distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
  ## WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  See the
  ## License for the specific language governing permissions and limitations
  ## under the License.
  
  import sys
  
  if sys.version_info < (3, 4):
      sys.exit('Sorry, Python 3.4 or newer is required to install and run vgraph')
  
  
  from setuptools import setup, find_packages
  from Cython.Distutils import build_ext
  from distutils.extension import Extension
  
  
  install_requires = ['pysam']
  setup_requires   = ['pysam', 'setuptools_scm==1.15.0', 'setuptools_scm_git_archive==1.0']
  tests_require    = ['pytest-runner', 'pytest', 'coverage']
  
  
  ext_modules = [
      Extension('vgraph.norm',      ['vgraph/norm.pyx']),
      Extension('vgraph.intervals', ['vgraph/intervals.pyx']),
  ]
  
  
  classifiers = """
  Development Status :: 2 - Alpha
  Operating System :: MacOS :: MacOS X
  Operating System :: Microsoft :: Windows :: Windows NT/2000
  Operating System :: OS Independent
  Operating System :: POSIX
  Operating System :: POSIX :: Linux
  Operating System :: Unix
  Programming Language :: Python :: 3.5
  Topic :: Scientific/Engineering
  Topic :: Scientific/Engineering :: Bioinformatics
  """
  
  
  if __name__ == '__main__':
      setup(
          name = 'vgraph',
          description = 'Graph-based variant normalization and comparison tools',
          url = 'https://github.com/bioinformed/vgraph',
          author = 'Kevin Jacobs',
          maintainer = 'Kevin Jacobs',
          author_email = 'jacobs@bioinformed.com',
          maintainer_email = 'jacobs@bioinformed.com',
          license = 'APACHE-2.0',
          classifiers = classifiers.split('\n'),
          use_scm_version=True,
          zip_safe = False,
          tests_require = tests_require,
          packages = find_packages(),
          install_requires = install_requires,
          setup_requires = setup_requires,
          cmdclass = {'build_ext': build_ext},
          ext_modules = ext_modules,
          entry_points={'console_scripts': ['vgraph = vgraph.vgraph:main']},
      )
  
subject: Remove Cython from install_requires, move pytest-runner to tests_require