old_contents: #!/usr/bin/env python
  #
  # -----------------------------------------------------------------------------
  # Copyright (c) 2016 The Regents of the University of California
  #
  # This file is part of kevlar (http://github.com/standage/kevlar) and is
  # licensed under the MIT license: see LICENSE.
  # -----------------------------------------------------------------------------
  
  from setuptools import setup, Extension
  import versioneer
  
  
  align = Extension(
      'kevlar.alignment',
      sources=[
          'kevlar/alignment.c', 'third-party/ksw2/ksw2_extz.c', 'src/align.c'
      ],
      include_dirs=['inc/', 'third-party/ksw2/'],
      language='c',
  )
  
  
  setup(name='biokevlar',
        version=versioneer.get_version(),
        cmdclass=versioneer.get_cmdclass(),
        description=('Reference-free variant discovery scalable to large '
                     'eukaryotic genomes'),
        url='https://github.com/dib-lab/kevlar',
        author='Daniel Standage',
        author_email='daniel.standage@gmail.com',
        license='MIT',
        packages=['kevlar', 'kevlar.cli', 'kevlar.tests'],
        package_data={
            'kevlar': ['kevlar/tests/data/*', 'kevlar/tests/data/*/*']
        },
        include_package_data=True,
        ext_modules=[align],
        setup_requires=['pysam', 'networkx', 'pandas'],
        install_requires=['pysam', 'networkx', 'pandas'],
        entry_points={
            'console_scripts': ['kevlar = kevlar.__main__:main']
        },
        classifiers=[
            'Development Status :: 4 - Beta',
            'Environment :: Console',
            'License :: OSI Approved :: MIT License',
            'Programming Language :: Python :: 3.5',
            'Programming Language :: Python :: 3.6',
            'Topic :: Scientific/Engineering :: Bio-Informatics'
        ],
        zip_safe=True)
  
new_contents: #!/usr/bin/env python
  #
  # -----------------------------------------------------------------------------
  # Copyright (c) 2016 The Regents of the University of California
  #
  # This file is part of kevlar (http://github.com/standage/kevlar) and is
  # licensed under the MIT license: see LICENSE.
  # -----------------------------------------------------------------------------
  
  from setuptools import setup, Extension
  import versioneer
  
  
  align = Extension(
      'kevlar.alignment',
      sources=[
          'kevlar/alignment.c', 'third-party/ksw2/ksw2_extz.c', 'src/align.c'
      ],
      include_dirs=['inc/', 'third-party/ksw2/'],
      language='c',
  )
  
  
  setup(name='biokevlar',
        version=versioneer.get_version(),
        cmdclass=versioneer.get_cmdclass(),
        description=('Reference-free variant discovery scalable to large '
                     'eukaryotic genomes'),
        url='https://github.com/dib-lab/kevlar',
        author='Daniel Standage',
        author_email='daniel.standage@gmail.com',
        license='MIT',
        packages=['kevlar', 'kevlar.cli', 'kevlar.tests'],
        package_data={
            'kevlar': ['kevlar/tests/data/*', 'kevlar/tests/data/*/*']
        },
        include_package_data=True,
        ext_modules=[align],
        setup_requires=['pysam', 'networkx', 'pandas', 'cython'],
        install_requires=['pysam', 'networkx', 'pandas'],
        entry_points={
            'console_scripts': ['kevlar = kevlar.__main__:main']
        },
        classifiers=[
            'Development Status :: 4 - Beta',
            'Environment :: Console',
            'License :: OSI Approved :: MIT License',
            'Programming Language :: Python :: 3.5',
            'Programming Language :: Python :: 3.6',
            'Topic :: Scientific/Engineering :: Bio-Informatics'
        ],
        zip_safe=True)
  
subject: Troubleshoot ReadTheDocs builds