old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from __future__ import print_function, absolute_import
  
  from setuptools import setup, find_packages
  import os
  
  import pbxplore
  
  here = os.path.abspath(os.path.dirname(__file__))
  
  with open(os.path.join(here, 'README.md')) as f:
      readme = f.read()
  
  
  extras = {
      'analysis': ['weblogo', 'matplotlib'],
      'trajectories': ['MDAnalysis>=0.11'],
      'all': ['weblogo', 'matplotlib', 'MDAnalysis>=0.11']
  }
  
  setup(
  
      name='pbxplore',
      version=pbxplore.__version__,
  
      description="PBxplore is a suite of tools dedicated to Protein Block analysis.",
      long_description=readme,
  
      url='https://github.com/pierrepo/PBxplore',
  
      # Author details
      author='Pierre Poulain',
      author_email='pierre.poulain@cupnet.net',
  
      license='MIT',
  
      classifiers=[
          'Development Status :: 4 - Beta',
  
          # Indicate who your project is intended for
          'Intended Audience :: Science/Research',
          'Intended Audience :: Developers',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Chemistry',
          'Topic :: Scientific/Engineering :: Physics',
  
          'License :: OSI Approved :: MIT License',
  
          'Programming Language :: Python :: 2',
          'Programming Language :: Python :: 2.6',
          'Programming Language :: Python :: 2.7',
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.2',
          'Programming Language :: Python :: 3.3',
          'Programming Language :: Python :: 3.4',
      ],
  
      install_requires=['numpy'],
      tests_require=['nose', 'coverage'],
      # List additional groups of dependencies here
      # To install, use
      # $ pip install -e .[analysis]
      extras_require=extras,
  
      packages=find_packages(exclude=['test']),
      include_package_data=True,
  
      entry_points={
          'console_scripts': [
              'PBassign = pbxplore.scripts.PBassign:pbassign_cli',
              'PBclust  = pbxplore.scripts.PBclust:pbclust_cli',
              'PBcount  = pbxplore.scripts.PBcount:pbcount_cli',
              'PBstat   = pbxplore.scripts.PBstat:pbstat_cli',
          ],
      },
  
  )
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from __future__ import print_function, absolute_import
  
  from setuptools import setup, find_packages
  import os
  
  
  here = os.path.abspath(os.path.dirname(__file__))
  
  with open(os.path.join(here, 'README.md')) as f:
      readme = f.read()
  
  
  ################
  # Version Number
  # Keep it sync with the pbxplore.__version__ in __init__.py
  VERSION = "1.1"
  ################
  
  # Extras requirements for optional dependencies
  extras = {
      'analysis': ['weblogo', 'matplotlib'],
      'trajectories': ['MDAnalysis>=0.11'],
      'all': ['weblogo', 'matplotlib', 'MDAnalysis>=0.11']
  }
  
  setup(
  
      name='pbxplore',
      version=VERSION,
  
      description="PBxplore is a suite of tools dedicated to Protein Block analysis.",
      long_description=readme,
  
      url='https://github.com/pierrepo/PBxplore',
  
      # Author details
      author='Pierre Poulain',
      author_email='pierre.poulain@cupnet.net',
  
      license='MIT',
  
      classifiers=[
          'Development Status :: 4 - Beta',
  
          # Indicate who your project is intended for
          'Intended Audience :: Science/Research',
          'Intended Audience :: Developers',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Chemistry',
          'Topic :: Scientific/Engineering :: Physics',
  
          'License :: OSI Approved :: MIT License',
  
          'Programming Language :: Python :: 2',
          'Programming Language :: Python :: 2.6',
          'Programming Language :: Python :: 2.7',
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.2',
          'Programming Language :: Python :: 3.3',
          'Programming Language :: Python :: 3.4',
      ],
  
      install_requires=['numpy'],
      tests_require=['nose', 'coverage'],
      # List additional groups of dependencies here
      # To install, use
      # $ pip install -e .[analysis]
      extras_require=extras,
  
      packages=find_packages(exclude=['test']),
      include_package_data=True,
  
      entry_points={
          'console_scripts': [
              'PBassign = pbxplore.scripts.PBassign:pbassign_cli',
              'PBclust  = pbxplore.scripts.PBclust:pbclust_cli',
              'PBcount  = pbxplore.scripts.PBcount:pbcount_cli',
              'PBstat   = pbxplore.scripts.PBstat:pbstat_cli',
          ],
      },
  
  )
  
subject: Remove the pbxplore import inside the setup.py. The import caused an import of numpy which can not be yet installed which caused on error. Due to this remove, Version in setup.py have to be sync with the pbxplore.__version__