old_contents: # from distutils.core import setup
  from setuptools import setup
  import os
  with open('requirements.txt') as f:
      required = f.read().splitlines()
  from Cython.Build import cythonize
  
  setup(
      name='bigsi',
      version='0.2',
      packages=[
          'bigsi',
          'bigsi.cmds',
          'bigsi.utils',
          'bigsi.graph',
          'bigsi.sketch',
          'bigsi.tasks',
          'bigsi.storage',
          'bigsi.matrix',
          'bigsi.scoring',
          'bigsi.variants',
          'bigsi.storage.graph',
      ],
      keywords='DBG coloured de bruijn graphs sequence search signture files signature index bitsliced',
      license='MIT',
      url='http://github.com/phelimb/bigsi',
      description='BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data',
      author='Phelim Bradley',
      author_email='wave@phel.im',
      install_requires=required[4:],
      entry_points={
          'console_scripts': [
              'bigsi = bigsi.__main__:main',
          ]},
      classifiers=[
          # How mature is this project? Common values are
          #   3 - Alpha
          #   4 - Beta
          #   5 - Production/Stable
          'Development Status :: 3 - Alpha',
  
          # Pick your license as you wish (should match "license" above)
          'License :: OSI Approved :: MIT License',
  
          # Specify the Python versions you support here. In particular, ensure
          # that you indicate whether you support Python 2, Python 3 or both.
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.2',
          'Programming Language :: Python :: 3.3',
          'Programming Language :: Python :: 3.4',
          'Programming Language :: Python :: 3.5',
          'Programming Language :: Python :: 3.6',
      ]
  )
  
new_contents: # from distutils.core import setup
  from setuptools import setup
  import os
  
  with open("requirements.txt") as f:
      required = f.read().splitlines()
  from Cython.Build import cythonize
  
  setup(
      name="bigsi",
      version="0.2",
      packages=[
          "bigsi",
          "bigsi.cmds",
          "bigsi.utils",
          "bigsi.graph",
          "bigsi.storage",
          "bigsi.matrix",
          "bigsi.scoring",
          "bigsi.storage.graph",
      ],
      keywords="DBG coloured de bruijn graphs sequence search signture files signature index bitsliced",
      license="MIT",
      url="http://github.com/phelimb/bigsi",
      description="BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data",
      author="Phelim Bradley",
      author_email="wave@phel.im",
      install_requires=required[4:],
      entry_points={"console_scripts": ["bigsi = bigsi.__main__:main"]},
      classifiers=[
          # How mature is this project? Common values are
          #   3 - Alpha
          #   4 - Beta
          #   5 - Production/Stable
          "Development Status :: 3 - Alpha",
          # Pick your license as you wish (should match "license" above)
          "License :: OSI Approved :: MIT License",
          # Specify the Python versions you support here. In particular, ensure
          # that you indicate whether you support Python 2, Python 3 or both.
          "Programming Language :: Python :: 3",
          "Programming Language :: Python :: 3.2",
          "Programming Language :: Python :: 3.3",
          "Programming Language :: Python :: 3.4",
          "Programming Language :: Python :: 3.5",
          "Programming Language :: Python :: 3.6",
      ],
  )
  
subject: Update setup.py packages