old_contents: #!/usr/bin/env python3
  
  import os
  import io
  import re
  import numpy
  from setuptools import setup, find_packages, Extension
  
  
  def read(*names, **kwargs):
      with io.open(
              os.path.join(os.path.dirname(__file__), *names),
              encoding=kwargs.get("encoding", "utf8")) as fp:
          return fp.read()
  
  
  # Get the version form the init file
  def find_version(*file_paths):
      version_file = read(*file_paths)
      version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                                version_file, re.M)
      if version_match:
          return version_match.group(1)
      raise RuntimeError("Unable to find version string.")
  
  
  # Add the README as the long description
  root = os.path.abspath(os.path.dirname(__file__))
  with open(os.path.join(root, 'README.md'), encoding='utf-8') as f:
      long_description = f.read()
  
  setup(
      name='camoco-cob',
      version=find_version('cob', '__init__.py'),
      packages=find_packages(),
      scripts=['cob/cli/cob'],
      ext_modules=[],
      package_data={'': ['*.cyx']},
      install_requires=['flask>=1.0.2', 'gunicorn>=19.9.0', 'camoco==0.6.2'],
      include_package_data=True,
      python_requires='>=3',
      author='Rob Schaefer, Joe Jeffers',
      author_email='schae234@gmail.com',
      description='The Co-Expression Network Browser',
      long_description=long_description,
      long_description_content_type='text/markdown',
      license="MIT",
      url='https://github.com/LinkageIO/cob')
  
new_contents: #!/usr/bin/env python3
  
  import os
  import io
  import re
  import numpy
  from setuptools import setup, find_packages, Extension
  
  
  def read(*names, **kwargs):
      with io.open(
              os.path.join(os.path.dirname(__file__), *names),
              encoding=kwargs.get("encoding", "utf8")) as fp:
          return fp.read()
  
  
  # Get the version form the init file
  def find_version(*file_paths):
      version_file = read(*file_paths)
      version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                                version_file, re.M)
      if version_match:
          return version_match.group(1)
      raise RuntimeError("Unable to find version string.")
  
  
  # Add the README as the long description
  root = os.path.abspath(os.path.dirname(__file__))
  with open(os.path.join(root, 'README.md'), encoding='utf-8') as f:
      long_description = f.read()
  
  setup(
      name='camoco-cob',
      version=find_version('cob', '__init__.py'),
      packages=find_packages(),
      scripts=['cob/cli/cob'],
      ext_modules=[],
      package_data={'': ['*.cyx']},
      setup_requires = [
          # Setuptools 18.0 properly handles Cython extensions.
          'setuptools>=18.0',
          #'numpy==1.14.5',
          'cython',  
      ],
      install_requires=[
          'flask>=1.0.2', 
          'gunicorn>=19.9.0', 
          'camoco==0.6.2'
      ],
      extras_require={
          'docs' : [
              'ipython>=6.5.0',
              'matplotlib>=2.2.3',
              'numpydoc',
              'sphinx_materialdesign_theme',
              'sphinxcontrib-programoutput'
          ]
      },
      include_package_data=True,
      python_requires='>=3',
      author='Rob Schaefer, Joe Jeffers',
      author_email='schae234@gmail.com',
      description='The Co-Expression Network Browser',
      long_description=long_description,
      long_description_content_type='text/markdown',
      license="MIT",
      url='https://github.com/LinkageIO/cob'
  )
  
subject: update deps for building docs