old_contents: #!/usr/bin/env python
  
  import sys, os
  from glob import glob
  
  # Install setuptools if it isn't available:
  try:
      import setuptools
  except ImportError:
      from distribute_setup import use_setuptools
      use_setuptools()
  
  from distutils.command.install import INSTALL_SCHEMES
  from distutils.command.install_headers import install_headers
  from setuptools import find_packages
  from setuptools import setup
  
  NAME =               'neurokernel'
  VERSION =            '0.01'
  AUTHOR =             'Lev Givon'
  AUTHOR_EMAIL =       'lev@columbia.edu'
  URL =                'http://github.com/bionet/neurokernel/'
  DESCRIPTION =        'An open architecture for Drosophila brain emulation'
  LONG_DESCRIPTION =   DESCRIPTION
  DOWNLOAD_URL =       URL
  LICENSE =            'BSD'
  CLASSIFIERS = [
      'Development Status :: 3 - Alpha',
      'Intended Audience :: Developers',
      'Intended Audience :: Science/Research',
      'License :: OSI Approved :: BSD License',
      'Operating System :: OS Independent',
      'Programming Language :: Python',
      'Topic :: Scientific/Engineering',
      'Topic :: Software Development']
  NAMESPACE_PACKAGES = ['neurokernel']
  PACKAGES =           find_packages()
  
  if __name__ == "__main__":
      if os.path.exists('MANIFEST'): 
          os.remove('MANIFEST')
  
      # This enables the installation of neurokernel/__init__.py as a data
      # file:
      for scheme in INSTALL_SCHEMES.values():
          scheme['data'] = scheme['purelib']
  
      setup(
          name = NAME,
          version = VERSION,
          author = AUTHOR,
          author_email = AUTHOR_EMAIL,
          license = LICENSE,
          classifiers = CLASSIFIERS,
          description = DESCRIPTION,
          long_description = LONG_DESCRIPTION,
          url = URL,
          namespace_packages = NAMESPACE_PACKAGES,
          packages = PACKAGES,
  
          # Force installation of __init__.py in namespace package:
          data_files = [('neurokernel', ['neurokernel/__init__.py'])],
          include_package_data = True,
          install_requires = [
              'bidict',
              'la',
              'msgpack_numpy',
              'networkx',
              'numpy',
              'pycuda >= 2012.1',
              'pyzmq',
              'scipy',
              'twiggy'],
          )
  
new_contents: #!/usr/bin/env python
  
  import sys, os
  from glob import glob
  
  # Install setuptools if it isn't available:
  try:
      import setuptools
  except ImportError:
      from distribute_setup import use_setuptools
      use_setuptools()
  
  from distutils.command.install import INSTALL_SCHEMES
  from distutils.command.install_headers import install_headers
  from setuptools import find_packages
  from setuptools import setup
  
  NAME =               'neurokernel'
  VERSION =            '0.01'
  AUTHOR =             'Lev Givon'
  AUTHOR_EMAIL =       'lev@columbia.edu'
  URL =                'http://github.com/bionet/neurokernel/'
  DESCRIPTION =        'An open architecture for Drosophila brain emulation'
  LONG_DESCRIPTION =   DESCRIPTION
  DOWNLOAD_URL =       URL
  LICENSE =            'BSD'
  CLASSIFIERS = [
      'Development Status :: 3 - Alpha',
      'Intended Audience :: Developers',
      'Intended Audience :: Science/Research',
      'License :: OSI Approved :: BSD License',
      'Operating System :: OS Independent',
      'Programming Language :: Python',
      'Topic :: Scientific/Engineering',
      'Topic :: Software Development']
  NAMESPACE_PACKAGES = ['neurokernel']
  PACKAGES =           find_packages()
  
  if __name__ == "__main__":
      if os.path.exists('MANIFEST'): 
          os.remove('MANIFEST')
  
      # This enables the installation of neurokernel/__init__.py as a data
      # file:
      for scheme in INSTALL_SCHEMES.values():
          scheme['data'] = scheme['purelib']
  
      setup(
          name = NAME,
          version = VERSION,
          author = AUTHOR,
          author_email = AUTHOR_EMAIL,
          license = LICENSE,
          classifiers = CLASSIFIERS,
          description = DESCRIPTION,
          long_description = LONG_DESCRIPTION,
          url = URL,
          namespace_packages = NAMESPACE_PACKAGES,
          packages = PACKAGES,
  
          # Force installation of __init__.py in namespace package:
          data_files = [('neurokernel', ['neurokernel/__init__.py'])],
          include_package_data = True,
          install_requires = [
              'bidict',
              'bottleneck',
              'la',
              'msgpack_numpy',
              'networkx',
              'numpy',
              'pycuda >= 2012.1',
              'pyzmq',
              'scipy',
              'twiggy'],
          )
  
subject: Add bottleneck to install requirements.