old_contents: #!/usr/bin/python
  #
  # Copyright (c) 2012 Mikkel Schubert <MSchubert@snm.ku.dk>
  #
  # Permission is hereby granted, free of charge, to any person obtaining a copy
  # of this software and associated documentation files (the "Software"), to deal
  # in the Software without restriction, including without limitation the rights
  # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  # copies of the Software, and to permit persons to whom the Software is
  # furnished to do so, subject to the following conditions:
  #
  # The above copyright notice and this permission notice shall be included in
  # all copies or substantial portions of the Software.
  #
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  # SOFTWARE.
  #
  
  __version_info__ = (1, 1, 1)
  __version__ = 'v%i.%i.%i' % __version_info__
  
  
  def run(command=None):
      """Main entry-point for setuptools"""
      import sys
      import paleomix.main
  
      argv = []
      if command is not None:
          argv.append(command)
      argv.extend(sys.argv[1:])
  
      return paleomix.main.main(argv)
  
  
  def run_bam_pipeline():
      """Legacy entry-point for setuptools"""
      return run("bam_pipeline")
  
  
  def run_gtf_to_bed():
      """Legacy entry-point for setuptools"""
      return run("gtf_to_bed")
  
  
  def run_phylo_pipeline():
      """Legacy entry-point for setuptools"""
      return run("phylo_pipeline")
  
  
  def run_rmdup_collapsed():
      """Legacy entry-point for setuptools"""
      return run("rmdup_collapsed")
  
  
  def run_trim_pipeline():
      """Legacy entry-point for setuptools"""
      return run("trim_pipeline")
  
new_contents: #!/usr/bin/python
  #
  # Copyright (c) 2012 Mikkel Schubert <MSchubert@snm.ku.dk>
  #
  # Permission is hereby granted, free of charge, to any person obtaining a copy
  # of this software and associated documentation files (the "Software"), to deal
  # in the Software without restriction, including without limitation the rights
  # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  # copies of the Software, and to permit persons to whom the Software is
  # furnished to do so, subject to the following conditions:
  #
  # The above copyright notice and this permission notice shall be included in
  # all copies or substantial portions of the Software.
  #
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  # SOFTWARE.
  #
  
  __version_info__ = (1, 2, 0)
  __version__ = 'v%i.%i.%i' % __version_info__
  
  
  def run(command=None):
      """Main entry-point for setuptools"""
      import sys
      import paleomix.main
  
      argv = []
      if command is not None:
          argv.append(command)
      argv.extend(sys.argv[1:])
  
      return paleomix.main.main(argv)
  
  
  def run_bam_pipeline():
      """Legacy entry-point for setuptools"""
      return run("bam_pipeline")
  
  
  def run_gtf_to_bed():
      """Legacy entry-point for setuptools"""
      return run("gtf_to_bed")
  
  
  def run_phylo_pipeline():
      """Legacy entry-point for setuptools"""
      return run("phylo_pipeline")
  
  
  def run_rmdup_collapsed():
      """Legacy entry-point for setuptools"""
      return run("rmdup_collapsed")
  
  
  def run_trim_pipeline():
      """Legacy entry-point for setuptools"""
      return run("trim_pipeline")
  
subject: Bump version number.