old_contents: import os
  from distutils.extension import Extension
  from setuptools import setup
  
  failed_imports = []
  
  try:
      from Cython.Build import cythonize
  except ImportError:
      failed_imports.append('cython')
  
  try:
      import numpy
  except ImportError:
      failed_imports.append('numpy')
  
  if len(failed_imports) > 0:
      raise ImportError('{} need to be installed before GAMtools can be '
                        'compiled. Try installing them with "pip '
                        'install {}" before installing GAMtools.'.format(
                            ' and '.join(failed_imports),
                            ' '.join(failed_imports)))
  
  # 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 ...
  def read(fname):
      return open(os.path.join(os.path.dirname(__file__), fname)).read()
  
  setup(
      name = "gamtools",
      version = "0.0.1",
      author = "Rob Beagrie",
      author_email = "rob@beagrie.com",
      description = ("A package containing some utilities for analyzing GAM data."),
      license = "BSD",
      packages=['gamtools'],
      install_requires=['numpy', 'scipy', 'doit', 'pandas', 'wrapit', 'pytest'],
      include_dirs=[numpy.get_include()],
      ext_modules = [Extension('gamtools.cosegregation_internal',
                              ["gamtools/cosegregation_internal.c"])],
      entry_points = {
                      # TODO: make new EIYBrowse filetypes using IO functions in gamtools.matrix
                      #'EIYBrowse.filetypes': [
                      #    'gam_segmentation_file = gamtools.segmentation:GamSegmentationFile',
                      #],
                      'console_scripts': [
                          'gamtools = gamtools.main:main',
                          'create_empty_bedgraph = gamtools.utils:empty_bedgraph_from_cmdline',
                      ]
                     },
      long_description=read('README'),
      classifiers=[
          "Development Status :: 3 - Alpha",
          "Topic :: Utilities",
          "License :: OSI Approved :: BSD License",
      ],
  )
  
new_contents: import os
  from distutils.extension import Extension
  from setuptools import setup
  
  failed_imports = []
  
  try:
      from Cython.Build import cythonize
  except ImportError:
      failed_imports.append('cython')
  
  try:
      import numpy
  except ImportError:
      failed_imports.append('numpy')
  
  if len(failed_imports) > 0:
      raise ImportError('{} need to be installed before GAMtools can be '
                        'compiled. Try installing them with "pip '
                        'install {}" before installing GAMtools.'.format(
                            ' and '.join(failed_imports),
                            ' '.join(failed_imports)))
  
  # 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 ...
  def read(fname):
      return open(os.path.join(os.path.dirname(__file__), fname)).read()
  
  setup(
      name = "gamtools",
      version = "1.0.0-alpha.1",
      author = "Rob Beagrie",
      author_email = "rob@beagrie.com",
      description = ("A package containing some utilities for analyzing GAM data."),
      license = "BSD",
      packages=['gamtools'],
      install_requires=['numpy', 'scipy', 'doit', 'pandas', 'wrapit', 'pytest'],
      include_dirs=[numpy.get_include()],
      ext_modules = [Extension('gamtools.cosegregation_internal',
                              ["gamtools/cosegregation_internal.c"])],
      entry_points = {
                      # TODO: make new EIYBrowse filetypes using IO functions in gamtools.matrix
                      #'EIYBrowse.filetypes': [
                      #    'gam_segmentation_file = gamtools.segmentation:GamSegmentationFile',
                      #],
                      'console_scripts': [
                          'gamtools = gamtools.main:main',
                          'create_empty_bedgraph = gamtools.utils:empty_bedgraph_from_cmdline',
                      ]
                     },
      long_description=read('README'),
      classifiers=[
          "Development Status :: 3 - Alpha",
          "Topic :: Utilities",
          "License :: OSI Approved :: BSD License",
      ],
  )
  
subject: Bump version number