old_contents: #!/usr/bin/env python
  
  from setuptools import setup
  from os import path
  
  with open(path.join(path.abspath(path.dirname(__file__)), 'README.md')) as f:
      README = f.read()
  
  setup(
      name='biseqt',
      version='0.0.1',
      description='Biseqt is a biological sequence analysis tool',
      long_description=README,
      url='https://github.com/amirkdv/biseqt',
      author='Amir Kadivar',
      author_email='amir@amirkdv.ca',
      license='BSD',
      packages=['biseqt'],
      # NOTE numpy has some weirdness with setuptools (cf. open issue
      # https://github.com/numpy/numpy/issues/2434). We need it because it's a
      # dependency of scipy but has to be installed either manually before our
      # setup.py or as part of setup_requires (cf.
      # https://github.com/numpy/numpy/issues/2434#issuecomment-65252402)
      # However, it is still much faster to install numpy separately via pip
      # because the following way wants to compile all the fortran and C/C++ code.
      setup_requires=[ # these are the packages that must be installed or
          'numpy',
      ],
      install_requires=[
          'scipy',
          'matplotlib',
          'pysqlite',     # for kmer handling with sqlite3
          'termcolor',    # for colored text output
          'cffi',         # for the C component
          'python-igraph',# for bindings to igraph
          'cairocffi',    # for igraph plots
      ],
      extras_require={
          'docs': [
              'sphinx',
              'pycparser', # used to generate C component docs index
              'sphinx_rtd_theme',
              'sphinxcontrib-wiki',
              'breathe',
              'mock', # only used on rtfd.org to mock packages with binary dependencies
          ],
          'tests': [
              'flake8',
              'pytest',
              'tox'
          ]
      }
  )
  
new_contents: #!/usr/bin/env python
  
  from setuptools import setup
  from os import path
  
  with open(path.join(path.abspath(path.dirname(__file__)), 'README.md')) as f:
      README = f.read()
  
  setup(
      name='biseqt',
      version='0.0.1',
      description='Biseqt is a biological sequence analysis tool',
      long_description=README,
      url='https://github.com/amirkdv/biseqt',
      author='Amir Kadivar',
      author_email='amir@amirkdv.ca',
      license='BSD',
      packages=['biseqt'],
      # NOTE numpy has some weirdness with setuptools; cf. open issue:
      #   https://github.com/numpy/numpy/issues/2434
      #
      # We need it because it's a dependency of scipy but has to be installed
      # either manually before our setup.py or declared as setup_requires, cf.
      #   https://github.com/numpy/numpy/issues/2434#issuecomment-65252402.
      #
      # However, it is still much faster to install numpy separately via pip
      # because installing by setup_requires wants to compile all the fortran and
      # C/C++ code.
      setup_requires=[
          'numpy',        # for setup.py to work at all
      ],
      install_requires=[
          'scipy',
          'matplotlib',
          'pysqlite',     # for kmer handling with sqlite3
          'termcolor',    # for colored text output
          'cffi',         # for the C component
          'python-igraph',# for bindings to igraph
          'cairocffi',    # for igraph plots
      ],
      extras_require={
          'docs': [
              'sphinx',
              'pycparser', # for generating C component docs index, cf. cdocs.py
              'alabaster', # our theme
              'sphinxcontrib-wiki', # for breaking down doc pages to sections
              'breathe',   # for doxygen integration
              'mock',      # for rtfd.org to skip installing system dependencies
          ],
          'tests': [
              'mock',
              'flake8',
              'pytest',
              'tox'
          ]
      }
  )
  
subject: update package dependencies