old_contents: # Copyright 2017 Google Inc.  All Rights Reserved.
  #
  # 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.
  
  """Beam pipelines for processing variants based on VCF files."""
  
  import setuptools
  
  REQUIRED_PACKAGES = [
      'cython>=0.28.1',
      'apache-beam[gcp]',
      # Note that adding 'google-api-python-client>=1.6' causes some dependency
      # mismatch issues. This is fatal if using 'setup.py install', but works on
      # 'pip install .' as it ignores conflicting versions. See Issue #71.
      'google-api-python-client>=1.6',
      'intervaltree>=2.1.0,<2.2.0',
      'pyvcf<0.7.0',
      'google-nucleus==0.2.0',
      # Nucleus needs uptodate protocol buffer compiler (protoc).
      'protobuf>=3.6.1',
      'mmh3<2.6',
      'google-cloud-storage',
      'pyfarmhash'
  ]
  
  REQUIRED_SETUP_PACKAGES = [
      'nose>=1.0',
  ]
  
  setuptools.setup(
      name='gcp_variant_transforms',
      version='0.8.1',
      description=('Tool for transforming and processing VCF files in a '
                   'scalable manner based on Apache Beam'),
      author='Google',
      license='Apache 2.0',
  
      # See https://pypi.python.org/pypi?%3Aaction=list_classifiers for the list
      # of values.
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Developers',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Information Analysis',
          'Topic :: System :: Distributed Computing',
          'License :: OSI Approved :: Apache Software License',
          'Programming Language :: Python :: 2',
          'Programming Language :: Python :: 2.7',
      ],
  
      setup_requires=REQUIRED_SETUP_PACKAGES,
      install_requires=REQUIRED_PACKAGES,
      test_suite='nose.collector',
      packages=setuptools.find_packages(),
      package_data={
          'gcp_variant_transforms': ['gcp_variant_transforms/testing/testdata/*']
      },
  )
  
new_contents: # Copyright 2017 Google Inc.  All Rights Reserved.
  #
  # 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.
  
  """Beam pipelines for processing variants based on VCF files."""
  
  import setuptools
  
  REQUIRED_PACKAGES = [
      'cython>=0.28.1',
      'apache-beam[gcp]',
      # Note that adding 'google-api-python-client>=1.6' causes some dependency
      # mismatch issues. This is fatal if using 'setup.py install', but works on
      # 'pip install .' as it ignores conflicting versions. See Issue #71.
      'google-api-python-client>=1.6',
      'intervaltree>=2.1.0,<2.2.0',
      'pyvcf<0.7.0',
      'google-nucleus==0.2.0',
      # Nucleus needs uptodate protocol buffer compiler (protoc).
      'protobuf>=3.6.1',
      'mmh3<2.6',
      # Refer to issue #528
      'google-cloud-storage<1.23.0',
      'pyfarmhash'
  ]
  
  REQUIRED_SETUP_PACKAGES = [
      'nose>=1.0',
  ]
  
  setuptools.setup(
      name='gcp_variant_transforms',
      version='0.8.1',
      description=('Tool for transforming and processing VCF files in a '
                   'scalable manner based on Apache Beam'),
      author='Google',
      license='Apache 2.0',
  
      # See https://pypi.python.org/pypi?%3Aaction=list_classifiers for the list
      # of values.
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Developers',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Information Analysis',
          'Topic :: System :: Distributed Computing',
          'License :: OSI Approved :: Apache Software License',
          'Programming Language :: Python :: 2',
          'Programming Language :: Python :: 2.7',
      ],
  
      setup_requires=REQUIRED_SETUP_PACKAGES,
      install_requires=REQUIRED_PACKAGES,
      test_suite='nose.collector',
      packages=setuptools.find_packages(),
      package_data={
          'gcp_variant_transforms': ['gcp_variant_transforms/testing/testdata/*']
      },
  )
  
subject: Resolve google-resumable-media package conflict (#529)