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
  
  readme_filename = os.path.join(os.path.dirname(__file__), 'README.md')
  with open(readme_filename, 'r') as f:
    readme = f.read()
  
  try:
    import pypandoc
    readme = pypandoc.convert(readme, to='rst', format='md')
  except:
    #print "Conversion of long_description from markdown to reStructuredText failed, skipping..."
    pass
  
  
  from setuptools import setup
  
  if __name__ == '__main__':
      setup(
          name='epitopes',
          version="0.2",
          description="Python interface to IEDB and other immune epitope data",
          author="Alex Rubinsteyn",
          author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",
          url="https://github.com/hammerlab/epitope",
          license="http://www.opensource.org/licenses/BSD-3-Clause",
          classifiers=[
              'Development Status :: 3 - Alpha',
              'Environment :: Console',
              'Operating System :: OS Independent',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache License',
              'Programming Language :: Python',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
               ],
          requires=[
              'numpy(>=1.7)',
              'pandas(>=0.13.1)',
              'scikit.learn(>=0.14.1)',
              'appdirs',
              'progressbar',
              'biopython',
          ],
          long_description=readme,
          packages=['epitopes'],
          package_data = { 'epitopes' : ['data/*csv'] },
          include_package_data = True
      )
  
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
  
  readme_filename = os.path.join(os.path.dirname(__file__), 'README.md')
  with open(readme_filename, 'r') as f:
    readme = f.read()
  
  try:
    import pypandoc
    readme = pypandoc.convert(readme, to='rst', format='md')
  except:
    #print "Conversion of long_description from markdown to reStructuredText failed, skipping..."
    pass
  
  
  from setuptools import setup
  
  if __name__ == '__main__':
      setup(
          name='epitopes',
          version="0.2",
          description="Python interface to IEDB and other immune epitope data",
          author="Alex Rubinsteyn",
          author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",
          url="https://github.com/hammerlab/epitopes",
  	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',
               ],
          requires=[
              'numpy(>=1.7)',
              'pandas(>=0.13.1)',
              'scikit.learn(>=0.14.1)',
              'appdirs',
              'progressbar',
              'biopython',
          ],
          long_description=readme,
          packages=['epitopes'],
          package_data = { 'epitopes' : ['data/*csv'] },
          include_package_data = True
      )
  
subject: fix setup