old_contents: # -*- coding: utf-8 -*-
  """Perses: Tools for expanded-ensemble simulations with OpenMM
  """
  
  from __future__ import print_function, absolute_import
  
  DOCLINES = __doc__.split("\n")
  
  import os
  import sys
  import glob
  import traceback
  import numpy as np
  from os.path import join as pjoin
  from os.path import relpath
  from setuptools import setup, Extension, find_packages
  try:
      sys.dont_write_bytecode = True
      sys.path.insert(0, '.')
      from basesetup import write_version_py, CompilerDetection, check_dependencies
  finally:
      sys.dont_write_bytecode = False
  
  
  if '--debug' in sys.argv:
      sys.argv.remove('--debug')
      DEBUG = True
  else:
      DEBUG = False
  
  #Useful function
  def find_package_data(data_root, package_root):
      files = []
      for root, dirnames, filenames in os.walk(data_root):
          for fn in filenames:
              files.append(relpath(pjoin(root, fn), package_root))
      return files
  
  
  # #########################
  VERSION = '0.1'
  ISRELEASED = False
  __version__ = VERSION
  # #########################
  
  CLASSIFIERS = """\
  Intended Audience :: Science/Research
  Intended Audience :: Developers
  License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
  Programming Language :: C++
  Programming Language :: Python
  Development Status :: 4 - Beta
  Topic :: Software Development
  Topic :: Scientific/Engineering
  Operating System :: POSIX
  Operating System :: Unix
  Operating System :: MacOS
  Programming Language :: Python :: 2
  Programming Language :: Python :: 2.6
  Programming Language :: Python :: 2.7
  Programming Language :: Python :: 3
  Programming Language :: Python :: 3.3
  Programming Language :: Python :: 3.4
  """
  
  extensions = []
  
  setup(name='perses',
        author='Patrick Grinaway',
        author_email='patrick.grinaway@choderalab.org',
        description=DOCLINES[0],
        long_description="\n".join(DOCLINES[2:]),
        version=__version__,
        url='https://github.com/choderalab/perses',
        platforms=['Linux', 'Mac OS-X', 'Unix'],
        classifiers=CLASSIFIERS.splitlines(),
        packages=['perses', 'perses.samplers', 'perses.rjmc', 'perses.annihilation', 'perses.bias', 'perses.tests'],
        #package_data={'perses' : find_package_data('perses','examples') + find_package_data('perses','data')}, # I don't think this works
        package_data={'perses' : find_package_data('examples', 'perses') + find_package_data('perses/data', 'perses')}, # I think this is fixed
        zip_safe=False,
        ext_modules=extensions,
        install_requires=[
          'openmm >=7.0',
          'numpy',
          'scipy',
          'numexpr',
          'openmoltools',
          'alchemy >=1.1.3',
          'numexpr',
          ],
        )
  
new_contents: # -*- coding: utf-8 -*-
  """Perses: Tools for expanded-ensemble simulations with OpenMM
  """
  
  from __future__ import print_function, absolute_import
  
  DOCLINES = __doc__.split("\n")
  
  import os
  import sys
  import glob
  import traceback
  import numpy as np
  from os.path import join as pjoin
  from os.path import relpath
  from setuptools import setup, Extension, find_packages
  try:
      sys.dont_write_bytecode = True
      sys.path.insert(0, '.')
      from basesetup import write_version_py, CompilerDetection, check_dependencies
  finally:
      sys.dont_write_bytecode = False
  
  
  if '--debug' in sys.argv:
      sys.argv.remove('--debug')
      DEBUG = True
  else:
      DEBUG = False
  
  #Useful function
  def find_package_data(data_root, package_root):
      files = []
      for root, dirnames, filenames in os.walk(data_root):
          for fn in filenames:
              files.append(relpath(pjoin(root, fn), package_root))
      return files
  
  
  # #########################
  VERSION = '0.1'
  ISRELEASED = False
  __version__ = VERSION
  # #########################
  
  CLASSIFIERS = """\
  Intended Audience :: Science/Research
  Intended Audience :: Developers
  License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
  Programming Language :: C++
  Programming Language :: Python
  Development Status :: 4 - Beta
  Topic :: Software Development
  Topic :: Scientific/Engineering
  Operating System :: POSIX
  Operating System :: Unix
  Operating System :: MacOS
  Programming Language :: Python :: 2
  Programming Language :: Python :: 2.6
  Programming Language :: Python :: 2.7
  Programming Language :: Python :: 3
  Programming Language :: Python :: 3.3
  Programming Language :: Python :: 3.4
  """
  
  extensions = []
  
  setup(name='perses',
        author='Patrick Grinaway',
        author_email='patrick.grinaway@choderalab.org',
        description=DOCLINES[0],
        long_description="\n".join(DOCLINES[2:]),
        version=__version__,
        url='https://github.com/choderalab/perses',
        platforms=['Linux', 'Mac OS-X', 'Unix'],
        classifiers=CLASSIFIERS.splitlines(),
        packages=['perses', 'perses.samplers', 'perses.rjmc', 'perses.annihilation', 'perses.bias', 'perses.tests'],
        #package_data={'perses' : find_package_data('perses','examples') + find_package_data('perses','data')}, # I don't think this works
        package_data={'perses' : find_package_data('examples', 'perses') + find_package_data('perses/data', 'perses')}, # I think this is fixed
        zip_safe=False,
        ext_modules=extensions,
        install_requires=[
          'openmm >=7.0',
          'numpy',
          'scipy',
          'numexpr',
          'openmoltools',
          'alchemy >=1.1.3',
          'numexpr',
          'numba'
          ],
        )
  
subject: add dependency to setup.py