old_contents: # Copyright (c) 2016. 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.
  
  from __future__ import print_function
  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)
  
  readme = ""
  try:
      with open(readme_path, "r") as f:
          readme = f.read()
  except IOError as e:
      print(e)
      print("Failed to open %s" % readme_path)
  
  try:
      import pypandoc
      readme = pypandoc.convert(readme, to="rst", format="md")
  except ImportError as e:
      print(e)
      print("Failed to convert %s to reStructuredText", readme_filename)
      pass
  
  if __name__ == "__main__":
      setup(
          name="cohorts",
          version="0.0.0",
          description="Utilities for analyzing mutations and neoepitopes in patient cohorts",
          author="Tavi Nathanson",
          author_email="tavi {dot} nathanson {at} gmail {dot} com",
          url="https://github.com/tavinathanson/cohorts",
          license="http://www.apache.org/licenses/LICENSE-2.0.html",
          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=[
              "pandas>=0.15",
          ],
          long_description=readme,
          packages=["cohorts"],
      )
  
new_contents: # Copyright (c) 2016. 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.
  
  from __future__ import print_function
  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)
  
  readme = ""
  try:
      with open(readme_path, "r") as f:
          readme = f.read()
  except IOError as e:
      print(e)
      print("Failed to open %s" % readme_path)
  
  try:
      import pypandoc
      readme = pypandoc.convert(readme, to="rst", format="md")
  except ImportError as e:
      print(e)
      print("Failed to convert %s to reStructuredText", readme_filename)
      pass
  
  if __name__ == "__main__":
      setup(
          name="cohorts",
          version="0.0.0",
          description="Utilities for analyzing mutations and neoepitopes in patient cohorts",
          author="Tavi Nathanson",
          author_email="tavi {dot} nathanson {at} gmail {dot} com",
          url="https://github.com/tavinathanson/cohorts",
          license="http://www.apache.org/licenses/LICENSE-2.0.html",
          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=[
              "pandas>=0.15", "topiary>=0.015"
          ],
          long_description=readme,
          packages=["cohorts"],
      )
  
subject: add topiary to the requirements