old_contents: #!/usr/bin/env python
  
  # ----------------------------------------------------------------------------
  # Copyright (c) 2015--, microprot development team.
  #
  # Distributed under the terms of the Modified BSD License.
  #
  # The full license is in the file COPYING.txt, distributed with this software.
  # ----------------------------------------------------------------------------
  
  import re
  import ast
  from setuptools import find_packages, setup
  
  
  # version parsing from __init__ pulled from Flask's setup.py
  # https://github.com/mitsuhiko/flask/blob/master/setup.py
  _version_re = re.compile(r'__version__\s+=\s+(.*)')
  
  with open('microprot/__init__.py', 'rb') as f:
      hit = _version_re.search(f.read().decode('utf-8')).group(1)
      version = str(ast.literal_eval(hit))
  
  classifiers = [
      'Development Status :: 2 - Pre-Alpha',
      'License :: OSI Approved :: BSD License',
      'Environment :: Console',
      'Topic :: Software Development :: Libraries :: Application Frameworks',
      'Topic :: Scientific/Engineering',
      'Topic :: Scientific/Engineering :: Bio-Informatics',
      'Programming Language :: Python',
      'Programming Language :: Python :: 3',
      'Programming Language :: Python :: 3.3',
      'Programming Language :: Python :: 3.4',
      'Operating System :: Unix',
      'Operating System :: POSIX',
      'Operating System :: MacOS :: MacOS X',
      'Operating System :: Microsoft :: Windows']
  
  
  description = 'MICROPROT: annotation pipeline for microbial (meta)proteomes'
  with open('README.md') as f:
      long_description = f.read()
  
  keywords = 'protein annotation structure',
  
  setup(name='microprot',
        version=version,
        license='BSD',
        description=description,
        long_description=long_description,
        keywords=keywords,
        classifiers=classifiers,
        author="microprot development team",
        author_email="tkosciolek@ucsd.edu",
        maintainer="microprot development team",
        maintainer_email="tkosciolek@ucsd.edu",
        url='http://microbio.me/microprot',
        test_suite='nose.collector',
        packages=find_packages(),
        install_requires=[
            'click >= 6',
            'scikit-bio >= 0.4.0',
            'burrito >= 0.9'
        ],
        extras_require={'test': ["nose", "pep8", "flake8"],
                        'coverage': ["coverage"]})
  
new_contents: #!/usr/bin/env python
  
  # ----------------------------------------------------------------------------
  # Copyright (c) 2016--, microprot development team.
  #
  # Distributed under the terms of the Modified BSD License.
  #
  # The full license is in the file COPYING.txt, distributed with this software.
  # ----------------------------------------------------------------------------
  
  import re
  import ast
  from setuptools import find_packages, setup
  
  
  # version parsing from __init__ pulled from Flask's setup.py
  # https://github.com/mitsuhiko/flask/blob/master/setup.py
  _version_re = re.compile(r'__version__\s+=\s+(.*)')
  
  with open('microprot/__init__.py', 'rb') as f:
      hit = _version_re.search(f.read().decode('utf-8')).group(1)
      version = str(ast.literal_eval(hit))
  
  classifiers = [
      'Development Status :: 1 - Pre-Alpha',
      'License :: OSI Approved :: BSD License',
      'Environment :: Console',
      'Topic :: Software Development :: Libraries :: Application Frameworks',
      'Topic :: Scientific/Engineering',
      'Topic :: Scientific/Engineering :: Bio-Informatics',
      'Programming Language :: Python',
      'Programming Language :: Python :: 3',
      'Programming Language :: Python :: 3.3',
      'Programming Language :: Python :: 3.4',
      'Operating System :: Unix',
      'Operating System :: POSIX',
      'Operating System :: MacOS :: MacOS X',
      'Operating System :: Microsoft :: Windows']
  
  
  description = 'MICROPROT: annotation pipeline for microbial (meta)proteomes'
  with open('README.md') as f:
      long_description = f.read()
  
  keywords = 'proteins residue-residue contact predictions protein families',
  
  setup(name='microprot',
        version=version,
        license='BSD',
        description=description,
        long_description=long_description,
        keywords=keywords,
        classifiers=classifiers,
        author="microprot development team",
        author_email="tkosciolek@ucsd.edu",
        maintainer="microprot development team",
        maintainer_email="tkosciolek@ucsd.edu",
        url='http://microbio.me/microprot',
        test_suite='nose.collector',
        packages=find_packages(),
        install_requires=[
            'click >= 6',
            'scikit-bio >= 0.4.0',
        ],
        extras_require={'test': ["nose", "pep8", "flake8"],
                        'coverage': ["coverage"]})
  
subject: Update setup.py