old_contents: import os
  from setuptools import setup
  
  
  def read(fname):
      """
      Utility function to read the README file. Used for the long_description.
      It's nice, because now:
      1) we have a top level README file, and
      2) it's easier to type in the README file than to put a raw string in
      below.
      """
      return open(os.path.join(os.path.dirname(__file__), fname)).read()
  
  
  setup(
      name="proteingraph",
      version="0.2.0",
      author="Eric J. Ma",
      author_email="ericmajinglong@gmail.com",
      description=(
          "A package for making graph representations of protein\
  structures."
      ),
      license="MIT",
      keywords="protein, biochemistry, structural biology, graph theory",
      url="http://github.com/ericmjl/protein-interaction-network/",
      packages=["proteingraph"],
      long_description=read("README.md"),
      classifiers=[
          "Development Status :: 3 - Alpha",
          "Intended Audience :: Science/Research",
          "Topic :: Scientific/Engineering :: Bio-Informatics",
          "Topic :: Scientific/Engineering :: Mathematics",
          "License :: OSI Approved :: MIT License",
          "Programming Language :: Python :: 3",
      ],
      include_package_data=True,
  )
  
new_contents: import os
  from setuptools import setup
  
  
  def read(fname):
      """
      Utility function to read the README file. Used for the long_description.
      It's nice, because now:
      1) we have a top level README file, and
      2) it's easier to type in the README file than to put a raw string in
      below.
      """
      return open(os.path.join(os.path.dirname(__file__), fname)).read()
  
  
  setup(
      name="proteingraph",
      version="0.2.0",
      author="Eric J. Ma",
      author_email="ericmajinglong@gmail.com",
      description=(
          "A package for making graph representations of protein\
  structures."
      ),
      license="MIT",
      keywords="protein, biochemistry, structural biology, graph theory",
      url="http://github.com/ericmjl/protein-interaction-network/",
      packages=["proteingraph"],
      long_description=read("README.md"),
      classifiers=[
          "Development Status :: 3 - Alpha",
          "Intended Audience :: Science/Research",
          "Topic :: Scientific/Engineering :: Bio-Informatics",
          "Topic :: Scientific/Engineering :: Mathematics",
          "License :: OSI Approved :: MIT License",
          "Programming Language :: Python :: 3",
      ],
      include_package_data=True,
      long_description_content_type="text/markdown",
  )
  
subject: set long description content type to markdown