old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from setuptools import setup, find_packages
  import sys
  
  # add back later
  if sys.version_info[0] != 3:
      # sys.exit("Only Python 3 is supported")
      print("WARNING: Only Python 3 is supported")
  
  with open('README.md') as readme_file:
      readme = readme_file.read()
  
  requirements = [
      "numpy",
      "pandas",
      "scipy",
      "scikit-learn>=0.18",
      "matplotlib",
      # "tensorflow", # - not per-se required
      # "glmnet",
      "keras>=2.0.4",
      'hyperopt',
      'descartes',
      'shapely',
      'gtfparse>=1.0.7'
  ]
  
  test_requirements = [
      "pytest",
  ]
  
  setup(
      name='concise',
      version='0.6.6',
      description="CONCISE (COnvolutional Neural for CIS-regulatory Elements)",
      long_description=readme,
      author="Žiga Avsec",
      author_email='avsec@in.tum.de',
      url='https://github.com/gagneurlab/concise',
      packages=find_packages(),
      package_data={'concise.resources': ['attract_metadata.txt', 'attract_pwm.txt',
                                          'encode_motifs.txt.gz',
                                          'HOCOMOCOv10_pcms_HUMAN_mono.txt'],
                    'concise.resources.RNAplfold': ["H_RNAplfold", "I_RNAplfold", "M_RNAplfold", "E_RNAplfold"]},
      include_package_data=True,
      setup_requires=['numpy'],
      install_requires=requirements,
      # dependency_links=dependency_links,
      license="MIT license",
      zip_safe=False,
      keywords=["computational biology", "bioinformatics", "genomics",
                "deep learning", "tensorflow", ],
      extras_require={
          'tensorflow': ['tensorflow>=1.0'],
          'tensorflow with gpu': ['tensorflow-gpu>=1.0']},
      classifiers=[
          # classifiers
          # default
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Artificial Intelligence',
          'Development Status :: 2 - Pre-Alpha',
          'Intended Audience :: Developers',
          'License :: OSI Approved :: MIT License',
          'Natural Language :: English',
          'Programming Language :: Python :: 3.4',
          'Programming Language :: Python :: 3.5',
      ],
      test_suite='tests',
      tests_require=test_requirements
  )
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from setuptools import setup, find_packages
  import sys
  
  # add back later
  if sys.version_info[0] != 3:
      # sys.exit("Only Python 3 is supported")
      print("WARNING: Only Python 3 is supported")
  
  # with open('README.md') as readme_file:
  #     readme = readme_file.read()
  
  requirements = [
      "numpy",
      "pandas",
      "scipy",
      "scikit-learn>=0.18",
      "matplotlib",
      # "tensorflow", # - not per-se required
      # "glmnet",
      "keras>=2.0.4",
      'hyperopt',
      'descartes',
      'shapely',
      'gtfparse>=1.0.7'
  ]
  
  test_requirements = [
      "pytest",
  ]
  
  setup(
      name='concise',
      version='0.6.6',
      description="CONCISE (COnvolutional Neural for CIS-regulatory Elements)",
      # long_description=readme,
      author="Žiga Avsec",
      author_email='avsec@in.tum.de',
      url='https://github.com/gagneurlab/concise',
      packages=find_packages(),
      package_data={'concise.resources': ['attract_metadata.txt', 'attract_pwm.txt',
                                          'encode_motifs.txt.gz',
                                          'HOCOMOCOv10_pcms_HUMAN_mono.txt'],
                    'concise.resources.RNAplfold': ["H_RNAplfold", "I_RNAplfold", "M_RNAplfold", "E_RNAplfold"]},
      include_package_data=True,
      setup_requires=['numpy'],
      install_requires=requirements,
      # dependency_links=dependency_links,
      license="MIT license",
      zip_safe=False,
      keywords=["computational biology", "bioinformatics", "genomics",
                "deep learning", "tensorflow", ],
      extras_require={
          'tensorflow': ['tensorflow>=1.0'],
          'tensorflow with gpu': ['tensorflow-gpu>=1.0']},
      classifiers=[
          # classifiers
          # default
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Artificial Intelligence',
          'Development Status :: 2 - Pre-Alpha',
          'Intended Audience :: Developers',
          'License :: OSI Approved :: MIT License',
          'Natural Language :: English',
          'Programming Language :: Python :: 3.4',
          'Programming Language :: Python :: 3.5',
      ],
      test_suite='tests',
      tests_require=test_requirements
  )
  
subject: fix the readme