old_contents: from setuptools import setup
  from pathlib    import Path
  
  base_dir     = Path(__file__).parent.resolve()
  version_file = base_dir / "augur/__version__.py"
  
  # Eval the version file to get __version__; avoids importing our own package
  with version_file.open() as f:
      exec(f.read())
  
  setup(
          name = "nextstrain-augur",
          version = __version__,
          author = "nextstrain developers",
          author_email = "trevor@bedford.io, richard.neher@unibas.ch",
          description = ("Pipelines for real-time phylogenetic analysis"),
          license = "MIT",
          keywords = "nextstrain, molecular epidemiology",
          url = "https://github.com/nextstrain/augur",
          packages=['augur'],
          package_data={'augur': ['data/*']},
          python_requires = '>=3.4',
          install_requires = [
              "bcbio-gff >=0.6.4, ==0.6.*",
              "biopython >=1.69, ==1.*",
              "boto >=2.38, ==2.*",
              "cvxopt >=1.1.8, ==1.1.*",
              "ipdb >=0.10.1",
              "jsonschema ==3.0.0a1",
              "matplotlib >=2.0, ==2.*",
              "pandas >=0.17.1",
              "phylo-treetime >=0.4.1, ==0.4.*",
              "seaborn >=0.6.0, ==0.6.*",
              "snakemake >=5.1.5, ==5.*"
          ],
          extras_require={
              'dev': [
                  "pylint >=1.7.6, ==1.7.*",
                  "pytest >=3.2.1, ==3.*",
              ]
          },
          classifiers=[
              "Development Status :: 3 - Alpha",
              "Topic :: Science",
              "License :: OSI Approved :: MIT License",
  
              # Python 3 only; pathlib is >=3.4
              "Programming Language :: Python :: 3",
              "Programming Language :: Python :: 3.4",
              "Programming Language :: Python :: 3.5",
              "Programming Language :: Python :: 3.6",
              ],
          scripts=['bin/augur']
          )
  
new_contents: from setuptools import setup
  from pathlib    import Path
  
  base_dir     = Path(__file__).parent.resolve()
  version_file = base_dir / "augur/__version__.py"
  
  # Eval the version file to get __version__; avoids importing our own package
  with version_file.open() as f:
      exec(f.read())
  
  setup(
          name = "nextstrain-augur",
          version = __version__,
          author = "nextstrain developers",
          author_email = "trevor@bedford.io, richard.neher@unibas.ch",
          description = ("Pipelines for real-time phylogenetic analysis"),
          license = "MIT",
          keywords = "nextstrain, molecular epidemiology",
          url = "https://github.com/nextstrain/augur",
          packages=['augur'],
          package_data={'augur': ['data/*']},
          python_requires = '>=3.4',
          install_requires = [
              "bcbio-gff >=0.6.4, ==0.6.*",
              "biopython >=1.69, ==1.*",
              "boto >=2.38, ==2.*",
              "cvxopt >=1.1.8, ==1.1.*",
              "ipdb >=0.10.1",
              "jsonschema ==3.0.0a1",
              "matplotlib >=2.0, ==2.*",
              "pandas >=0.17.1",
              "phylo-treetime >=0.4.1, ==0.4.*",
              "seaborn >=0.6.0, ==0.6.*",
              "snakemake >=5.1.5, ==5.*"
          ],
          extras_require={
              'dev': [
                  "pylint >=1.7.6, ==1.7.*",
                  "pytest >=3.2.1, ==3.*",
              ]
          },
          classifiers=[
              "Development Status :: 3 - Alpha",
              "Topic :: Scientific/Engineering :: Bio-Informatics",
              "License :: OSI Approved :: MIT License",
  
              # Python 3 only; pathlib is >=3.4
              "Programming Language :: Python :: 3",
              "Programming Language :: Python :: 3.4",
              "Programming Language :: Python :: 3.5",
              "Programming Language :: Python :: 3.6",
              ],
          scripts=['bin/augur']
          )
  
subject: Use an allowed Topic classifier