old_contents: #!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  import os
  import subprocess
  import sys
  
  # Version check prior to non-stdlib imports
  if sys.version_info < (3, 5):
      sys.stderr.write(
          "ERROR: mapDamage requires Python v3.5 or above, but "
          "Python v%i.%i was used\n" % sys.version_info[:2]
      )
      sys.exit(1)
  
  
  from setuptools import setup, Extension
  from setuptools.command.build_py import build_py as SetuptoolsBuildPy
  
  
  class GitVersionBuild(SetuptoolsBuildPy):
      def run(self):
          if os.path.exists(".git"):
              try:
                  version = subprocess.check_output(
                      ("git", "describe", "--always", "--tags", "--dirty")
                  )
              except (subprocess.CalledProcessError, OSError) as error:
                  raise SystemExit("Could not determine mapDamage version: %s" % (error,))
  
              with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
                  handle.write("#!/usr/bin/env python\n")
                  handle.write("__version__ = %r\n" % (version.decode("utf-8").strip(),))
  
          super().run()
  
  
  setup(
      cmdclass={"build_py": GitVersionBuild},
      name="mapdamage",
      version="2.2.0",
      author="Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson",
      packages=["mapdamage"],
      package_data={"mapdamage": ["r/*.r", "r/stats/*.r", "tests/*"]},
      entry_points={"console_scripts": ["mapDamage=mapdamage.main:entry_point"]},
      url="https://github.com/ginolhac/mapDamage",
      license="LICENSE.txt",
      description="mapDamage tracks and quantify DNA damage pattern among ancient DNA sequencing reads generated byi Next-Generation Sequencing platforms",
      long_description=open("README.md").read(),
      python_requires=">=3.5",
      install_requires=["coloredlogs", "pysam"],
      ext_modules=[
          Extension(
              "mapdamage.seqtk", sources=["mapdamage/seqtk/seqtk.c"], libraries=["z"],
          )
      ],
  )
  
new_contents: #!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  import os
  import subprocess
  import sys
  
  # Version check prior to non-stdlib imports
  if sys.version_info < (3, 5):
      sys.stderr.write(
          "ERROR: mapDamage requires Python v3.5 or above, but "
          "Python v%i.%i was used\n" % sys.version_info[:2]
      )
      sys.exit(1)
  
  
  from setuptools import setup, Extension
  from setuptools.command.build_py import build_py as SetuptoolsBuildPy
  
  
  class GitVersionBuild(SetuptoolsBuildPy):
      def run(self):
          if os.path.exists(".git"):
              try:
                  version = subprocess.check_output(
                      ("git", "describe", "--always", "--tags", "--dirty")
                  )
              except (subprocess.CalledProcessError, OSError) as error:
                  raise SystemExit("Could not determine mapDamage version: %s" % (error,))
  
              with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
                  handle.write("#!/usr/bin/env python\n")
                  handle.write("__version__ = %r\n" % (version.decode("utf-8").strip(),))
  
          super().run()
  
  
  setup(
      cmdclass={"build_py": GitVersionBuild},
      name="mapdamage",
      version="2.2.1",
      author="Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson",
      packages=["mapdamage"],
      package_data={"mapdamage": ["r/*.r", "r/stats/*.r", "tests/*"]},
      entry_points={"console_scripts": ["mapDamage=mapdamage.main:entry_point"]},
      url="https://github.com/ginolhac/mapDamage",
      license="LICENSE.txt",
      description="mapDamage tracks and quantify DNA damage pattern among ancient DNA sequencing reads generated byi Next-Generation Sequencing platforms",
      long_description=open("README.md").read(),
      python_requires=">=3.5",
      install_requires=["coloredlogs", "pysam"],
      ext_modules=[
          Extension(
              "mapdamage.seqtk", sources=["mapdamage/seqtk/seqtk.c"], libraries=["z"],
          )
      ],
  )
  
subject: update version