new_contents: """
  Modified from the OpenPathSampling setup.py
  """
  #from distutils.sysconfig import get_config_var
  from distutils.core import setup, Extension
  from setuptools import setup, Extension
  import numpy
  import glob
  import os
  import subprocess
  
  ##########################
  VERSION = "0.1.0"
  ISRELEASED = False
  __version__ = VERSION
  ##########################
  
  ################################################################################
  # Writing version control information to the module
  ################################################################################
  
  def git_version():
      # Return the git revision as a string
      # copied from numpy setup.py
      def _minimal_ext_cmd(cmd):
          # construct minimal environment
          env = {}
          for k in ['SYSTEMROOT', 'PATH']:
              v = os.environ.get(k)
              if v is not None:
                  env[k] = v
          # LANGUAGE is used on win32
          env['LANGUAGE'] = 'C'
          env['LANG'] = 'C'
          env['LC_ALL'] = 'C'
          out = subprocess.Popen(
              cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
          return out
  
      try:
          out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
          GIT_REVISION = out.strip().decode('ascii')
      except OSError:
          GIT_REVISION = 'Unknown'
  
      return GIT_REVISION
  
  
  def write_version_py(filename='annotated_trajectories/version.py'):
      cnt = """
  # This file is automatically generated by setup.py
  short_version = '%(version)s'
  version = '%(version)s'
  full_version = '%(full_version)s'
  git_revision = '%(git_revision)s'
  release = %(isrelease)s
  
  if not release:
      version = full_version
  """
      # Adding the git rev number needs to be done inside write_version_py(),
      # otherwise the import of numpy.version messes up the build under Python 3.
      FULLVERSION = VERSION
      if os.path.exists('.git'):
          GIT_REVISION = git_version()
      else:
          GIT_REVISION = 'Unknown'
  
      if not ISRELEASED:
          FULLVERSION += '.dev-' + GIT_REVISION[:7]
  
      a = open(filename, 'w')
      try:
          a.write(cnt % {'version': VERSION,
                         'full_version': FULLVERSION,
                         'git_revision': GIT_REVISION,
                         'isrelease': str(ISRELEASED)})
      finally:
          a.close()
  
  ################################################################################
  # Installation
  ################################################################################
  
  write_version_py()
  
  def buildKeywordDictionary():
      from distutils.core import Extension
      setupKeywords = {}
      setupKeywords["name"]              = "annotated_trajectories"
      setupKeywords["version"]           = "0.1.0-alpha"
      setupKeywords["author"]            = "David W.H. Swenson"
      setupKeywords["author_email"]      = "dwhs@hyperblazer.net"
      setupKeywords["license"]           = "LGPL 2.1 or greater"
      setupKeywords["download_url"]      = \
              "http://github.com/dwhswenson/annotated_trajectories"
      setupKeywords["packages"]          = ['annotated_trajectories', 
                                            'annotated_trajectories.tests']
      setupKeywords["package_dir"]       = {
          'annotated_trajectories' : 'annotated_trajectories',
          'annotated_trajectories.tests' : 'annotated_trajectories/tests'
      }
      setupKeywords["data_files"]        = []
      setupKeywords["ext_modules"]       = []
      setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
      setupKeywords["description"]       = \
          "Add state annotations for OpenPathSampling trajectories"
      setupKeywords["requires"]          = ["openpathsampling", "nose"]
      setupKeywords["long_description"]  = """
      State annotations for OpenPathSampling trajectories. Trajectories can be
      "annotated" by labeling a range of frame numbers with a given string
      (e.g., the name of the state the system is in). Then a specific
      implementation of that state (as an OPS volume) can be associated with
      each string, and the state definition can be validated (check for false
      positives) using the AnnotatedTrajectory object.
      """
      outputString=""
      firstTab     = 40
      secondTab    = 60
      for key in sorted( setupKeywords.iterkeys() ):
           value         = setupKeywords[key]
           outputString += key.rjust(firstTab) + str( value ).rjust(secondTab) + "\n"
      
      print("%s" % outputString)
  
      #get_config_var(None)  # this line is necessary to fix the imports Mac OS X
      return setupKeywords
      
  
  def main():
      setupKeywords = buildKeywordDictionary()
      setup(**setupKeywords)
  
  if __name__ == '__main__':
      main()
  
  
  
subject: Add setup.py