old_contents: import sys
  import os
  
  # We can't import version.py because only one "version" module can ever be
  # loaded in a Python process, and multiple setup.py scripts may have to run in
  # the same process.
  execfile(os.path.join(os.path.dirname(os.path.realpath(__file__)), "version.py"))
  
  from setuptools import find_packages, setup
  from setuptools.command.test import test as TestCommand
  
  kwargs = dict(
      name='toil-vg',
      version=version,
      description="UC Santa Cruz Computational Genomics Lab's Toil-based VG pipeline",
      author='UCSC Computational Genomics Lab',
      author_email='cgl-toil@googlegroups.com',
      url="https://github.com/BD2KGenomics/toil-vg",
      install_requires=[x + y for x, y in required_versions.iteritems()],
      dependency_links=[],
      # The tests need the optional numpy and scipy dependencies in addition to the actual dependencies
      tests_require=['pytest==2.8.3', 'numpy>=1.9.1,<=1.14.2', 'scipy>=0.14.0,<=1.0.0'],
      package_dir={'': 'src'},
      packages=find_packages('src'),
      entry_points={
          'console_scripts': ['toil-vg = toil_vg.vg_toil:main']}
  )
  
  
  class PyTest(TestCommand):
      user_options = [('pytest-args=', 'a', "Arguments to pass to py.test")]
  
      def initialize_options(self):
          TestCommand.initialize_options(self)
          self.pytest_args = []
  
      def finalize_options(self):
          TestCommand.finalize_options(self)
          self.test_args = []
          self.test_suite = True
  
      def run_tests(self):
          import pytest
          # Sanitize command line arguments to avoid confusing Toil code attempting to parse them
          sys.argv[1:] = []
          errno = pytest.main(self.pytest_args)
          sys.exit(errno)
  
  kwargs['cmdclass'] = {'test': PyTest}
  
  setup(**kwargs)
  
  
  print("\n\n"
        "Thank you for installing the UC Santa Cruz Computuational Genomics Lab VG DNA-seq pipeline! "
        "If you want to run this Toil-based pipeline on a cluster in a cloud, please install Toil "
        "with the appropriate extras. For example, To install AWS/EC2 support for example, run "
        "\n\n"
        "pip install \'toil[aws,mesos]>=3.6.0\'"
        "\n\n"
        "on every EC2 instance. Refer to Toil's documentation at http://toil.readthedocs.io/en/latest/installation.html "
        "for more information.")
  
new_contents: import sys
  import os
  
  # We can't import version.py because only one "version" module can ever be
  # loaded in a Python process, and multiple setup.py scripts may have to run in
  # the same process.
  execfile(os.path.join(os.path.dirname(os.path.realpath(__file__)), "version.py"))
  
  from setuptools import find_packages, setup
  from setuptools.command.test import test as TestCommand
  
  kwargs = dict(
      name='toil-vg',
      version=version,
      description="UC Santa Cruz Computational Genomics Lab's Toil-based VG pipeline",
      author='UCSC Computational Genomics Lab',
      author_email='cgl-toil@googlegroups.com',
      url="https://github.com/BD2KGenomics/toil-vg",
      install_requires=[x + y for x, y in required_versions.iteritems()],
      dependency_links=[],
      # The tests need the optional numpy and scipy dependencies in addition to the actual dependencies
      tests_require=['pytest==2.8.3', 'numpy>=1.9.1', 'scipy>=0.14.0,<=1.0.0'],
      package_dir={'': 'src'},
      packages=find_packages('src'),
      entry_points={
          'console_scripts': ['toil-vg = toil_vg.vg_toil:main']}
  )
  
  
  class PyTest(TestCommand):
      user_options = [('pytest-args=', 'a', "Arguments to pass to py.test")]
  
      def initialize_options(self):
          TestCommand.initialize_options(self)
          self.pytest_args = []
  
      def finalize_options(self):
          TestCommand.finalize_options(self)
          self.test_args = []
          self.test_suite = True
  
      def run_tests(self):
          import pytest
          # Sanitize command line arguments to avoid confusing Toil code attempting to parse them
          sys.argv[1:] = []
          errno = pytest.main(self.pytest_args)
          sys.exit(errno)
  
  kwargs['cmdclass'] = {'test': PyTest}
  
  setup(**kwargs)
  
  
  print("\n\n"
        "Thank you for installing the UC Santa Cruz Computuational Genomics Lab VG DNA-seq pipeline! "
        "If you want to run this Toil-based pipeline on a cluster in a cloud, please install Toil "
        "with the appropriate extras. For example, To install AWS/EC2 support for example, run "
        "\n\n"
        "pip install \'toil[aws,mesos]>=3.6.0\'"
        "\n\n"
        "on every EC2 instance. Refer to Toil's documentation at http://toil.readthedocs.io/en/latest/installation.html "
        "for more information.")
  
subject: remove numpy version cap