old_contents: 
  """scLVM - single cell latent variable model
  See:
  https://github.com/PMBio/scLVM
  """
  
  # Always prefer setuptools over distutils
  from setuptools import setup, find_packages
  # To use a consistent encoding
  from codecs import open
  from os import path
  
  here = path.abspath(path.dirname(__file__))
  
  # Get the long description from the relevant file
  with open(path.join(here, 'README'), encoding='utf-8') as f:
      long_description = f.read()
      
  reqs = ['numpy', 'scipy', 'pygp >=1.1.07', 'matplotlib >=1.2','h5py','limix >=0.6.6']
  
  setup(
      name='scLVM',
  
      # Versions should comply with PEP440.  For a discussion on single-sourcing
      # the version across setup.py and the project code, see
      # https://packaging.python.org/en/latest/single_source_version.html
      version='0.1.7',
  
      description='scLVM',
      long_description=long_description,
  
      # The project's main homepage.
      url='https://github.com/PMBio/scLVM',
  
      # Author details
      author='Florian Buettner, F Paolo Casale, Oliver Stegle',
      author_email='scLVM-dev@ebi.ac.uk',
  
      # Choose your license
      license='Apache 2.0',
  
  
      # What does your project relate to?
      keywords=['single-cell RNA-seq, latent variable model',' Variance compoennt modelling'],
  
      # You can just specify the packages manually here if your project is
      # simple. Or you can use find_packages().
      packages=['scLVM', 'scLVM.utils'],#find_packages(),
  
      # List run-time dependencies here.  These will be installed by pip when
      # your project is installed. For an analysis of "install_requires" vs pip's
      # requirements files see:
      # https://packaging.python.org/en/latest/requirements.html
      
      install_requires=reqs,
  
  
      py_modules = ['scLVM.core','scLVM.gp_clvm']
  
  )
  
new_contents: 
  """scLVM - single cell latent variable model
  See:
  https://github.com/PMBio/scLVM
  """
  
  # Always prefer setuptools over distutils
  from setuptools import setup, find_packages
  # To use a consistent encoding
  from codecs import open
  from os import path
  
  here = path.abspath(path.dirname(__file__))
  
  # Get the long description from the relevant file
  with open(path.join(here, 'README.md'), encoding='utf-8') as f:
      long_description = f.read()
      
  reqs = ['numpy', 'scipy', 'pygp >=1.1.07', 'matplotlib >=1.2','h5py','limix >=0.6.6']
  
  setup(
      name='scLVM',
  
      # Versions should comply with PEP440.  For a discussion on single-sourcing
      # the version across setup.py and the project code, see
      # https://packaging.python.org/en/latest/single_source_version.html
      version='0.1.7',
  
      description='scLVM',
      long_description=long_description,
  
      # The project's main homepage.
      url='https://github.com/PMBio/scLVM',
  
      # Author details
      author='Florian Buettner, F Paolo Casale, Oliver Stegle',
      author_email='scLVM-dev@ebi.ac.uk',
  
      # Choose your license
      license='Apache 2.0',
  
  
      # What does your project relate to?
      keywords=['single-cell RNA-seq, latent variable model',' Variance compoennt modelling'],
  
      # You can just specify the packages manually here if your project is
      # simple. Or you can use find_packages().
      packages=['scLVM', 'scLVM.utils'],#find_packages(),
  
      # List run-time dependencies here.  These will be installed by pip when
      # your project is installed. For an analysis of "install_requires" vs pip's
      # requirements files see:
      # https://packaging.python.org/en/latest/requirements.html
      
      install_requires=reqs,
  
  
      py_modules = ['scLVM.core','scLVM.gp_clvm']
  
  )
  
subject: correct README name in setup.py; this prevented instalation - related to #3