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.
  
  from __future__ import print_function
  import os
  
  from setuptools import setup, find_packages
  
  readme_filename = "README.md"
  current_directory = os.path.dirname(__file__)
  readme_path = os.path.join(current_directory, readme_filename)
  
  readme = ""
  try:
      with open(readme_path, 'r') as f:
          readme = f.read()
  except Exception as e:
      print(e)
      print("Failed to open %s" % readme_path)
  
  try:
      import pypandoc
      readme = pypandoc.convert(readme, to='rst', format='md')
  except Exception as e:
      print(e)
      print("Failed to convert %s from Markdown to reStructuredText" % readme_filename)
  
  if __name__ == '__main__':
      setup(
          name='varcode',
          packages=find_packages(),
          version="0.3.19",
          description="Variant annotation in Python",
          long_description=readme,
          url="https://github.com/hammerlab/varcode",
          author="Alex Rubinsteyn",
          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=[
              'numpy>=1.7, <2.0',
              'pandas>=0.15',
              'pyensembl>=0.8.2',
              'biopython>=1.64',
              'pyvcf>=0.6.7',
              'memoized_property>=1.0.2',
              'pysam>=0.8.3',
          ],
      )
  
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.
  
  from __future__ import print_function
  import os
  
  from setuptools import setup, find_packages
  
  readme_filename = "README.md"
  current_directory = os.path.dirname(__file__)
  readme_path = os.path.join(current_directory, readme_filename)
  
  readme = ""
  try:
      with open(readme_path, 'r') as f:
          readme = f.read()
  except Exception as e:
      print(e)
      print("Failed to open %s" % readme_path)
  
  try:
      import pypandoc
      readme = pypandoc.convert(readme, to='rst', format='md')
  except Exception as e:
      print(e)
      print("Failed to convert %s from Markdown to reStructuredText" % readme_filename)
  
  if __name__ == '__main__':
      setup(
          name='varcode',
          packages=find_packages(),
          version="0.4.0",
          description="Variant annotation in Python",
          long_description=readme,
          url="https://github.com/hammerlab/varcode",
          author="Alex Rubinsteyn",
          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=[
              'numpy>=1.7, <2.0',
              'pandas>=0.15',
              'pyensembl>=0.8.2',
              'biopython>=1.64',
              'pyvcf>=0.6.7',
              'memoized_property>=1.0.2',
          ],
      )
  
subject: bump varcode version and remove pysam dependency