old_contents: #!/usr/bin/env python
  # coding=utf-8
  
  import sys
  import distribute_setup
  distribute_setup.use_setuptools()
  
  from setuptools import setup, find_packages
  
  version_string = '0.1.0'
  
  
  # Defaults for py2app / cx_Freeze
  default_build_options=dict(
      packages=['wheezy.template'],
      )
  
  
  setup(
  
      name='metapath',
      version=version_string,
      author='Martin Fitzpatrick',
      author_email='martin.fitzpatrick@gmail.com',
      url='https://github.com/mfitzp/gpml2svg',
      download_url='http://github.com/mfitzp/gpml2svg',
      description='Render GPML pathway markup to SVG from the commandline/Python.',
      long_description='GPML2SVG is a command line and Python API for the conversion of pathways marked up \
          using GPML to SVG. The command-line interface is currently basic. Simply call the script with the name of the \
          GPML file to convert. The resulting SVG will be saved using the same name, with the \
          extension change to .svg. The resulting SVG is marked up with object identifiers, \
          and links to relevant databases. The python interface offers a single function call to which you can optionally provide \
          colouring information (for data visualisation) and links for custom XRefs. \
          The sofware is in development as an extension to MetaPath.',
      packages = find_packages(),
      include_package_data = True,
      package_data = {
          '': ['*.txt', '*.rst', '*.md', '.svg'],
      },
      exclude_package_data = { '': ['README.txt'] },
  
      entry_points = {
          'console_scripts': [
              'gpml2svg = gpml2svg.gpml2svg:main',
          ],
      },
  
      install_requires = ['wheezy.template>=0.1.135'],
  
      keywords='bioinformatics metabolomics signalling pathways research analysis science',
      license='GPL',
      classifiers=['Development Status :: 4 - Beta',
                 'Natural Language :: English',
                 'Operating System :: OS Independent',
                 'Programming Language :: Python :: 2',
                 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
                 'Topic :: Scientific/Engineering :: Bio-Informatics',
                 'Topic :: Education',
                 'Intended Audience :: Science/Research',
                 'Intended Audience :: Education',
                ],
  
      executables=executables,
  
      )
new_contents: #!/usr/bin/env python
  # coding=utf-8
  
  import sys
  import distribute_setup
  distribute_setup.use_setuptools()
  
  from setuptools import setup, find_packages
  
  version_string = '0.1.0'
  
  
  # Defaults for py2app / cx_Freeze
  default_build_options=dict(
      packages=['wheezy.template'],
      )
  
  
  setup(
  
      name='gpml2svg',
      version=version_string,
      author='Martin Fitzpatrick',
      author_email='martin.fitzpatrick@gmail.com',
      url='https://github.com/mfitzp/gpml2svg',
      download_url='http://github.com/mfitzp/gpml2svg',
      description='Render GPML pathway markup to SVG from the commandline/Python.',
      long_description='GPML2SVG is a command line and Python API for the conversion of pathways marked up \
          using GPML to SVG. The command-line interface is currently basic. Simply call the script with the name of the \
          GPML file to convert. The resulting SVG will be saved using the same name, with the \
          extension change to .svg. The resulting SVG is marked up with object identifiers, \
          and links to relevant databases. The python interface offers a single function call to which you can optionally provide \
          colouring information (for data visualisation) and links for custom XRefs. \
          The sofware is in development as an extension to MetaPath.',
      packages = find_packages(),
      include_package_data = True,
      package_data = {
          '': ['*.txt', '*.rst', '*.md', '.svg'],
      },
      exclude_package_data = { '': ['README.txt'] },
  
      entry_points = {
          'console_scripts': [
              'gpml2svg = gpml2svg.gpml2svg:main',
          ],
      },
  
      install_requires = ['wheezy.template>=0.1.135'],
  
      keywords='bioinformatics metabolomics signalling pathways research analysis science',
      license='GPL',
      classifiers=['Development Status :: 4 - Beta',
                 'Natural Language :: English',
                 'Operating System :: OS Independent',
                 'Programming Language :: Python :: 2',
                 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
                 'Topic :: Scientific/Engineering :: Bio-Informatics',
                 'Topic :: Education',
                 'Intended Audience :: Science/Research',
                 'Intended Audience :: Education',
                ],
  
      )
subject: Fix setup.py for upload to PyPi