old_contents: import os
  import re
  import ast
  from setuptools import setup, find_packages
  from setuptools.command.build_ext import build_ext as _build_ext
  
  package_name = "ipype"
  
  
  # version parsing from __init__ pulled from scikit-bio
  # https://github.com/biocore/scikit-bio/blob/master/setup.py
  # which is itself based off Flask's setup.py https://github.com/mitsuhiko/flask/blob/master/setup.py
  _version_re = re.compile(r'__version__\s+=\s+(.*)')
  
  
  
  with open('ipype/__init__.py', 'rb') as f:
      hit = _version_re.search(f.read().decode('utf-8')).group(1)
      version = str(ast.literal_eval(hit))
  
  
  here = os.path.abspath(os.path.dirname(__file__))
  
  README = open(os.path.join(here, 'README.md')).read()
  CHANGES = open(os.path.join(here, 'CHANGES.md')).read()
  
  try:
      import pypandoc
      long_description = pypandoc.convert(README + '\n\n' +  CHANGES, 'rst', format='md')
  except ImportError:
      long_description= README + '\n\n' + CHANGES
  
  
  setup_requires = [
      ]
  
  
  install_requires = []
  with open(os.path.join(here, 'requirements.txt') as req:
      for line in req:
  	install_requires.append(line)
  
      
  
  setup(name=package_name,
        version=version,
        license='BSD',
        description="Run self-documenting Jupyter notebook pipelines.",
        long_description=long_description,
        classifiers=[
          "Programming Language :: Python",
          "License :: OSI Approved :: BSD License",
          "Topic :: Scientific/Engineering :: Bio-Informatics",
          ],
        cmdclass={'build_ext': build_ext_numpy},
        author='Ahmed Bassiouni',
        author_email='ahmedbassi@gmail.com',
        maintainer="Ahmed Bassiouni",
        maintainer_email="ahmedbassi@gmail.com",
        url='https://github.com/bassio/ipype',
        download_url = 'https://github.com/bassio/ipype/tarball/' + version,
        keywords='bioinformatics',
        packages=find_packages(),
        include_package_data=True,
        zip_safe=False,
        test_suite='ipype.tests',
        install_requires=install_requires,
        setup_requires=setup_requires,
        entry_points="""\
        """,
        )
  
new_contents: import os
  import re
  import ast
  from setuptools import setup, find_packages
  from setuptools.command.build_ext import build_ext as _build_ext
  
  package_name = "ipype"
  
  
  # version parsing from __init__ pulled from scikit-bio
  # https://github.com/biocore/scikit-bio/blob/master/setup.py
  # which is itself based off Flask's setup.py https://github.com/mitsuhiko/flask/blob/master/setup.py
  _version_re = re.compile(r'__version__\s+=\s+(.*)')
  
  
  
  with open('ipype/__init__.py', 'rb') as f:
      hit = _version_re.search(f.read().decode('utf-8')).group(1)
      version = str(ast.literal_eval(hit))
  
  
  here = os.path.abspath(os.path.dirname(__file__))
  
  README = open(os.path.join(here, 'README.md')).read()
  CHANGES = open(os.path.join(here, 'CHANGES.md')).read()
  
  try:
      import pypandoc
      long_description = pypandoc.convert(README + '\n\n' +  CHANGES, 'rst', format='md')
  except ImportError:
      long_description= README + '\n\n' + CHANGES
  
  
  setup_requires = [
      ]
  
  
  install_requires = []
  with open(os.path.join(here, 'requirements.txt')) as req:
      for line in req:
  	install_requires.append(line)
  
      
  
  setup(name=package_name,
        version=version,
        license='BSD',
        description="Run self-documenting Jupyter notebook pipelines.",
        long_description=long_description,
        classifiers=[
          "Programming Language :: Python",
          "License :: OSI Approved :: BSD License",
          "Topic :: Scientific/Engineering :: Bio-Informatics",
          ],
        cmdclass={'build_ext': build_ext_numpy},
        author='Ahmed Bassiouni',
        author_email='ahmedbassi@gmail.com',
        maintainer="Ahmed Bassiouni",
        maintainer_email="ahmedbassi@gmail.com",
        url='https://github.com/bassio/ipype',
        download_url = 'https://github.com/bassio/ipype/tarball/' + version,
        keywords='bioinformatics',
        packages=find_packages(),
        include_package_data=True,
        zip_safe=False,
        test_suite='ipype.tests',
        install_requires=install_requires,
        setup_requires=setup_requires,
        entry_points="""\
        """,
        )
  
subject: fix missing parens in setup.py