old_contents: # Copyright (c) 2014. Mount Sinai School of Medicine
  #
  # 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 os
  
  from setuptools import setup
  
  current_directory = os.path.dirname(__file__)
  readme_filename = 'README.md'
  readme_path = os.path.join(current_directory, readme_filename)
  with open(readme_path, 'r') as f:
      readme = f.read()
  
  try:
      import pypandoc
      readme = pypandoc.convert(readme, to='rst', format='md')
  except:
      print("Failed to convert %s to reStructuredText", readme_filename)
      pass
  
  requirements_path = os.path.join(current_directory, "requirements.txt")
  with open(requirements_path, "r") as f:
      requirements = [
          line.strip()
          for line in f.read().splitlines()
          if line.strip()
      ]
  
  if __name__ == '__main__':
      setup(
          name='pyensembl',
          version="0.5.7",
          description="Python interface to ensembl reference genome metadata",
          author="Alex Rubinsteyn",
          author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",
          url="https://github.com/hammerlab/pyensembl",
          license="http://www.apache.org/licenses/LICENSE-2.0.html",
          entry_points={
            'console_scripts': [
                'pyensembl = pyensembl.shell:run'
            ],
          },
          classifiers=[
              'Development Status :: 3 - Alpha',
              'Environment :: Console',
              'Operating System :: OS Independent',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache Software License',
              'Programming Language :: Python',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
          ],
          install_requires=requirements,
          long_description=readme,
          packages=['pyensembl'],
      )
  
new_contents: # Copyright (c) 2014. Mount Sinai School of Medicine
  #
  # 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 os
  
  from setuptools import setup
  
  current_directory = os.path.dirname(__file__)
  readme_filename = 'README.md'
  readme_path = os.path.join(current_directory, readme_filename)
  with open(readme_path, 'r') as f:
      readme = f.read()
  
  try:
      import pypandoc
      readme = pypandoc.convert(readme, to='rst', format='md')
  except:
      print("Failed to convert %s to reStructuredText", readme_filename)
      pass
  
  requirements_path = os.path.join(current_directory, "requirements.txt")
  with open(requirements_path, "r") as f:
      requirements = [
          line.strip()
          for line in f.read().splitlines()
          if line.strip()
      ]
  
  if __name__ == '__main__':
      setup(
          name='pyensembl',
          version="0.5.8",
          description="Python interface to ensembl reference genome metadata",
          author="Alex Rubinsteyn",
          author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",
          url="https://github.com/hammerlab/pyensembl",
          license="http://www.apache.org/licenses/LICENSE-2.0.html",
          entry_points={
            'console_scripts': [
                'pyensembl = pyensembl.shell:run'
            ],
          },
          classifiers=[
              'Development Status :: 3 - Alpha',
              'Environment :: Console',
              'Operating System :: OS Independent',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache Software License',
              'Programming Language :: Python',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
          ],
          install_requires=requirements,
          long_description=readme,
          packages=['pyensembl'],
          # necessary for Travis if we're parsing setuptools requirements
          # from requirements.txt
          package_data={"pyensembl": [requirements_path]},
          include_package_data=True,
      )
  
subject: include requirements.txt with package, had to increase version number for PyPI update