new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  import io
  import os
  import re
  
  import numpy
  
  from setuptools import setup, find_packages
  from setuptools.extension import Extension
  from Cython.Build import cythonize
  
  classifiers = """\
      Development Status :: 4 - Beta
      Operating System :: OS Independent
      Programming Language :: Python
      Programming Language :: Python :: 3
      Programming Language :: Python :: 3.3
      Programming Language :: Python :: 3.4
      Programming Language :: Python :: 3.5
  """
  
  
  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('pairsamtools', '__init__.py'),
          re.MULTILINE).group(1)
      return version
  
  
  def get_long_description():
      return _read('README.md')
  
  
  install_requires = [
      'numpy>=1.10', 
      'cython>=0.25', 
      'click>=6.6', 
  ]
  
  
  extensions = [
      Extension(
          "pairsamtools._dedup", ["pairsamtools/_dedup.pyx"],
      ),
  ]
  
  packages = find_packages()
  setup(
      name='pairsamtools',
      author='Mirny Lab',
      author_email='espresso@mit.edu',
      version=get_version(),
      license='BSD3',
      description='CLI tools to process mapped Hi-C data',
      long_description=get_long_description(),
      keywords=['genomics', 'bioinformatics', 'Hi-C', 'contact'],
      url='https://github.com/mirnylab/pairsamtools',
      packages=find_packages(),
      ext_modules = cythonize(extensions),
      zip_safe=False,
      classifiers=[s.strip() for s in classifiers.split('\n') if s],
      install_requires=install_requires,
      entry_points={
          'console_scripts': [
               'pairsamtools = pairsamtools:cli',
          ]
      },
      include_dirs=[numpy.get_include()]
  )
  
subject: add setup.py