old_contents: #!/usr/bin/env python
  # -*- coding: UTF-8 -*-
  
  from setuptools import setup
  from glob import glob
  
  
  classifiers = [
      'Development Status :: 4 - Beta',
      'Intended Audience :: Science/Research',
      'License :: OSI Approved :: BSD License',
      'Programming Language :: Python',
      'Programming Language :: Python :: 2',
      'Programming Language :: Python :: 3',
      'Topic :: Scientific/Engineering :: Bio-Informatics',
      ]
  
  requirements = ['wget'] + [x.strip() for x in
                             open('requirements.txt').readlines()]
  
  exec(open("goatools/version.py").read())
  setup(
      name="goatools",
      version=__version__,
      author='Haibao Tang',
      author_email='tanghaibao@gmail.com',
      packages=['goatools'],
      scripts=glob('scripts/*.py'),
      license='BSD',
      classifiers=classifiers,
      url='http://github.com/tanghaibao/goatools',
      description="Python scripts to find enrichment of GO terms",
      long_description=open("README.rst").read(),
      install_requires=requirements
      )
  
new_contents: #!/usr/bin/env python
  # -*- coding: UTF-8 -*-
  
  from setuptools import setup
  from glob import glob
  
  
  classifiers = [
      'Development Status :: 4 - Beta',
      'Intended Audience :: Science/Research',
      'License :: OSI Approved :: BSD License',
      'Programming Language :: Python',
      'Programming Language :: Python :: 2',
      'Programming Language :: Python :: 3',
      'Topic :: Scientific/Engineering :: Bio-Informatics',
      ]
  
  requirements = ['wget'] + [x.strip() for x in
                             open('requirements.txt').readlines()]
  
  exec(open("goatools/version.py").read())
  setup(
      name="goatools",
      version=__version__,
      author='Haibao Tang',
      author_email='tanghaibao@gmail.com',
      packages=['goatools'],
      scripts=glob('scripts/*.py'),
      license='BSD',
      classifiers=classifiers,
      url='http://github.com/tanghaibao/goatools',
      description="Python scripts to find enrichment of GO terms",
      long_description=open("README.md").read(),
      install_requires=requirements
      )
  
subject: modify setup.py to include md rather than rst