old_contents: #!/usr/bin/env python
  
  # ----------------------------------------------------------------------------
  # Copyright (c) 2013--, scikit-bio development team.
  #
  # Distributed under the terms of the Modified BSD License.
  #
  # The full license is in the file COPYING.txt, distributed with this software.
  # ----------------------------------------------------------------------------
  
  __version__ = '0.0.0-dev'
  
  import os
  from setuptools import find_packages, setup
  from distutils.command.build_py import build_py
  
  classes = """
      Development Status :: 1 - Planning
      License :: OSI Approved :: BSD License
      Topic :: Software Development :: Libraries
      Topic :: Scientific/Engineering
      Topic :: Scientific/Engineering :: Bio-Informatics
      Programming Language :: Python
      Programming Language :: Python :: 2.7
      Operating System :: Unix
      Operating System :: POSIX
      Operating System :: MacOS :: MacOS X
  """
  classifiers = [s.strip() for s in classes.split('\n') if s]
  
  long_description = """The scikit-bio project"""
  
  # If readthedocs.org is building the project, we're not able to build the
  # required numpy/scipy versions on their machines (nor do we want to, as that
  # would take a long time). To build the docs, we don't need the latest versions
  # of these dependencies anyways, so we use whatever is in their system's
  # site-packages to make scikit-bio importable. See doc/rtd-requirements.txt for
  # dependencies that RTD must install in order to build our docs.
  #
  # Code to check whether RTD is building our project is taken from
  # http://read-the-docs.readthedocs.org/en/latest/faq.html
  on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
  if on_rtd:
      install_requires = []
  else:
      install_requires = ['numpy >= 1.5.1', 'matplotlib >= 1.1.0',
                          'scipy >= 0.13.0']
  
  
  # add the tests & data to be able to do skbio.tests() from a(n) (I)Python shell
  tests = []
  for root, _, fnames in os.walk('skbio'):
      try:
          root = root.split('/', 1)[1]
      except IndexError:
          # nothing to gather at the root directory of skbio
          continue
      else:
          for fname in fnames:
              fp = os.path.join(root, fname)
              # the filepath has to be either test data or a test suite
              if any([e in fp for e in ['/data/', '/tests/', '/test/']]):
                  tests.append(os.path.join(root, fname))
  
  setup(name='scikit-bio',
        cmdclass={'build_py': build_py},
        version=__version__,
        license='BSD',
        description='scikit-bio',
        long_description=long_description,
        author="scikit-bio development team",
        author_email="gregcaporaso@gmail.com",
        maintainer="scikit-bio development team",
        maintainer_email="gregcaporaso@gmail.com",
        url='https://github.com/biocore/scikit-bio',
        packages=find_packages(),
        install_requires=install_requires,
        extras_require={'test': ["nose >= 0.10.1", "pep8"],
                        'doc': ["Sphinx >= 1.2.2", "sphinx-bootstrap-theme"]},
        classifiers=classifiers,
        package_data={'skbio':tests})
  
new_contents: #!/usr/bin/env python
  
  # ----------------------------------------------------------------------------
  # Copyright (c) 2013--, scikit-bio development team.
  #
  # Distributed under the terms of the Modified BSD License.
  #
  # The full license is in the file COPYING.txt, distributed with this software.
  # ----------------------------------------------------------------------------
  
  __version__ = '0.0.0-dev'
  
  import os
  from setuptools import find_packages, setup
  from distutils.command.build_py import build_py
  
  classes = """
      Development Status :: 1 - Planning
      License :: OSI Approved :: BSD License
      Topic :: Software Development :: Libraries
      Topic :: Scientific/Engineering
      Topic :: Scientific/Engineering :: Bio-Informatics
      Programming Language :: Python
      Programming Language :: Python :: 2.7
      Operating System :: Unix
      Operating System :: POSIX
      Operating System :: MacOS :: MacOS X
  """
  classifiers = [s.strip() for s in classes.split('\n') if s]
  
  long_description = """The scikit-bio project"""
  
  # If readthedocs.org is building the project, we're not able to build the
  # required numpy/scipy versions on their machines (nor do we want to, as that
  # would take a long time). To build the docs, we don't need the latest versions
  # of these dependencies anyways, so we use whatever is in their system's
  # site-packages to make scikit-bio importable. See doc/rtd-requirements.txt for
  # dependencies that RTD must install in order to build our docs.
  #
  # Code to check whether RTD is building our project is taken from
  # http://read-the-docs.readthedocs.org/en/latest/faq.html
  on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
  if on_rtd:
      install_requires = []
  else:
      install_requires = ['numpy >= 1.5.1', 'matplotlib >= 1.1.0',
                          'scipy >= 0.13.0']
  
  setup(name='scikit-bio',
        cmdclass={'build_py': build_py},
        version=__version__,
        license='BSD',
        description='scikit-bio',
        long_description=long_description,
        author="scikit-bio development team",
        author_email="gregcaporaso@gmail.com",
        maintainer="scikit-bio development team",
        maintainer_email="gregcaporaso@gmail.com",
        url='https://github.com/biocore/scikit-bio',
        packages=find_packages(),
        install_requires=install_requires,
        extras_require={'test': ["nose >= 0.10.1", "pep8"],
                        'doc': ["Sphinx >= 1.2.2", "sphinx-bootstrap-theme"]},
        classifiers=classifiers,
        package_data={'skbio': ['maths/stats/ordination/test/data/*']})
  
subject: Remove retrieval of tests and data …