old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  import io
  import os
  import re
  
  from setuptools import setup, find_packages
  
  
  PKG_NAME = 'bioframe'
  README_PATH = 'README.md'
  
  
  classifiers = """\
      Development Status :: 4 - Beta
      Operating System :: OS Independent
      Programming Language :: Python
      Programming Language :: Python :: 2
      Programming Language :: Python :: 2.7
      Programming Language :: Python :: 3
      Programming Language :: Python :: 3.3
      Programming Language :: Python :: 3.4
      Programming Language :: Python :: 3.5
      Programming Language :: Python :: 3.6
  """
  
  
  def _read(*parts, **kwargs):
      filepath = os.path.join(os.path.dirname(__file__), *parts)
      encoding = kwargs.pop('encoding', 'utf-8')
      with io.open(filepath, encoding=encoding) as fh:
          text = fh.read()
      return text
  
  
  def get_version():
      version = re.search(
          r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
          _read('{}.py'.format(PKG_NAME)),
          re.MULTILINE).group(1)
      return version
  
  
  def get_long_description():
      descr = _read(README_PATH)
      try:
          import pypandoc
          descr = pypandoc.convert_text(descr, to='rst', format='md')
      except (IOError, ImportError):
          pass
      return descr
  
  
  install_requires = [
      'six', 
      'numpy>=1.9', 
      'pandas>=0.17',
  ]
  
  
  # tests_require = [
  #     'nose',
  #     'mock'
  # ]
  
  
  # extras_require = {
  #     'docs': [
  #         'Sphinx>=1.1', 
  #         'numpydoc>=0.5'
  #     ]
  # }
  
  
  setup(
      name=PKG_NAME,
      author='Nezar Abdennur',
      author_email='nezar@mit.edu',
      version=get_version(),
      license='MIT',
      description='Pandas utilities for tab-delimited and other genomic files',
      long_description=get_long_description(),
      #url='',
      keywords=[],
      py_modules=[PKG_NAME],
      zip_safe=False,
      classifiers=[s.strip() for s in classifiers.split('\n') if s],
      install_requires=install_requires,
      # tests_require=tests_require,
      # extras_require=extras_require,
      # entry_points={
      # }
  )
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  import io
  import os
  import re
  
  from setuptools import setup, find_packages
  
  
  PKG_NAME = 'bioframe'
  README_PATH = 'README.md'
  
  
  classifiers = """\
      Development Status :: 3 - Alpha
      Operating System :: OS Independent
      Programming Language :: Python
      Programming Language :: Python :: 2
      Programming Language :: Python :: 2.7
      Programming Language :: Python :: 3
      Programming Language :: Python :: 3.3
      Programming Language :: Python :: 3.4
      Programming Language :: Python :: 3.5
      Programming Language :: Python :: 3.6
  """
  
  
  def _read(*parts, **kwargs):
      filepath = os.path.join(os.path.dirname(__file__), *parts)
      encoding = kwargs.pop('encoding', 'utf-8')
      with io.open(filepath, encoding=encoding) as fh:
          text = fh.read()
      return text
  
  
  def get_version():
      version = re.search(
          r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
          _read('{}.py'.format(PKG_NAME)),
          re.MULTILINE).group(1)
      return version
  
  
  def get_long_description():
      descr = _read(README_PATH)
      try:
          import pypandoc
          descr = pypandoc.convert_text(descr, to='rst', format='md')
      except (IOError, ImportError):
          pass
      return descr
  
  
  install_requires = [
      'six', 
      'numpy>=1.9', 
      'pandas>=0.17',
      'pysam',
      'pyfaidx',
      'pypairix',
  ]
  
  
  # tests_require = [
  #     'nose',
  #     'mock'
  # ]
  
  
  # extras_require = {
  #     'docs': [
  #         'Sphinx>=1.1', 
  #         'numpydoc>=0.5'
  #     ]
  # }
  
  
  setup(
      name=PKG_NAME,
      author='Nezar Abdennur',
      author_email='nezar@mit.edu',
      version=get_version(),
      license='MIT',
      description='Pandas utilities for tab-delimited and other genomic files',
      long_description=get_long_description(),
      #url='',
      keywords=['pandas', 'bioinformatics'],
      py_modules=[PKG_NAME],
      zip_safe=False,
      classifiers=[s.strip() for s in classifiers.split('\n') if s],
      install_requires=install_requires,
      # tests_require=tests_require,
      # extras_require=extras_require,
      # entry_points={
      # }
  )
  
subject: Update setup.py