old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  """
  .. py:currentmodule:: setup
     :synopsis: Setup script to use with pip for the project pyXraySpectrumFileFormat.
  
  .. moduleauthor:: Hendrix Demers <hendrix.demers@mail.mcgill.ca>
  
  Setup script to use with pip for the project pyXraySpectrumFileFormat.
  """
  
  ###############################################################################
  # Copyright 2015 Hendrix Demers
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  ###############################################################################
  
  # Standard library modules.
  import os.path
  
  # Third party modules.
  from setuptools import setup, find_packages
  
  # Local modules.
  
  # Globals and constants variables.
  with open('README.rst') as readme_file:
      readme = readme_file.read()
  
  with open('HISTORY.rst') as history_file:
      history = history_file.read()
  
  requirements = [
      'numpy',
                          'matplotlib',
                          'scipy',
                          'six'
  ]
  
  test_requirements = [
      'nose', 'coverage'
  ]
  
  readme_file_path = os.path.join(os.path.dirname(__file__), 'README.rst')
  long_description = open(readme_file_path).read() + '\n\n'
  
  setup(name="pySpectrumFileFormat",
      version='0.1',
      url='',
      description="Project to read and write various x-ray spectrum file format.",
  	long_description=readme + '\n\n' + history,
  	author="Hendrix Demers",
  	author_email="hendrix.demers@mail.mcgill.ca",
  	license="Apache License, Version 2.0",
  	classifiers=['Development Status :: 5 - Production/Stable',
  		'Environment :: Console',
  		'Intended Audience :: Developers',
  		'Intended Audience :: Science/Research',
          'License :: OSI Approved :: Apache Software License',
  		'Natural Language :: English',
  		'Programming Language :: Python',
  		'Operating System :: OS Independent',
  		'Topic :: Scientific/Engineering',],
  
      packages=find_packages(),
  #    packages=[
  #        'microanalysis_file_format',
  #    ],
  #    package_dir={'microanalysis_file_format':
  #                 'microanalysis_file_format'},
      install_requires=requirements,
      zip_safe=False,
      keywords='microanalysis_file_format',
  
  	include_package_data=False, # Do not include test data
  
      setup_requires=['nose', 'coverage'],
  
      test_suite='nose.collector',
      tests_require=test_requirements
  
  )
  
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  """
  .. py:currentmodule:: setup
     :synopsis: Setup script to use with pip for the project pyXraySpectrumFileFormat.
  
  .. moduleauthor:: Hendrix Demers <hendrix.demers@mail.mcgill.ca>
  
  Setup script to use with pip for the project pyXraySpectrumFileFormat.
  """
  
  ###############################################################################
  # Copyright 2015 Hendrix Demers
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  ###############################################################################
  
  # Standard library modules.
  import os.path
  
  # Third party modules.
  from setuptools import setup, find_packages
  
  # Local modules.
  
  # Globals and constants variables.
  with open('README.rst') as readme_file:
      readme = readme_file.read()
  
  with open('HISTORY.rst') as history_file:
      history = history_file.read()
  
  requirements = [
      'numpy',
                          'matplotlib',
                          'scipy',
                          'six'
  ]
  
  test_requirements = [
      'nose', 'coverage'
  ]
  
  readme_file_path = os.path.join(os.path.dirname(__file__), 'README.rst')
  long_description = open(readme_file_path).read() + '\n\n'
  
  setup(name="pySpectrumFileFormat",
      version='0.1',
      url='',
      description="Project to read and write various x-ray spectrum file format.",
  	long_description=readme + '\n\n' + history,
  	author="Hendrix Demers",
  	author_email="hendrix.demers@mail.mcgill.ca",
  	license="Apache License, Version 2.0",
  	classifiers=['Development Status :: 5 - Production/Stable',
  		'Environment :: Console',
  		'Intended Audience :: Developers',
  		'Intended Audience :: Science/Research',
          'License :: OSI Approved :: Apache Software License',
  		'Natural Language :: English',
  		'Programming Language :: Python',
  		'Operating System :: OS Independent',
  		'Topic :: Scientific/Engineering',],
  
      packages=find_packages(),
  #    package_dir={'microanalysis_file_format':
  #                 'microanalysis_file_format'},
      install_requires=requirements,
      zip_safe=False,
      keywords='microanalysis_file_format',
  
  	include_package_data=False, # Do not include test data
  
      setup_requires=['nose', 'coverage'],
  
      test_suite='nose.collector',
      tests_require=test_requirements
  
  )
  
  
subject: Correct bug with setup packages option