old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from setuptools import setup, find_packages
  
  with open('README.rst') as readme_file:
      readme = readme_file.read()
  
  with open('HISTORY.rst') as history_file:
      history = history_file.read()
  
  requirements = [
      "numpy>=1.0",
      "torch>=0.4",
      "matplotlib>=2.0",
      "scikit-learn>=0.18",
      "scipy>=1.0",
      "h5py>=2.8",
      "pandas>=0.2",
      "loompy>=2.0"
  ]
  
  setup_requirements = ['pytest-runner', ]
  
  test_requirements = ['pytest', ]
  
  author = 'Romain Lopez, Jeffrey Regier, Maxime Langevin, Edouard Mehlman, Yining Liu'
  
  setup(
      author=author,
      author_email='romain_lopez@berkeley.edu',
      classifiers=[
          'Development Status :: 4 - Beta',
          'Intended Audience :: Science/Research',
          'License :: OSI Approved :: MIT License',
          'Natural Language :: English',
          'Programming Language :: Python :: 3.6',
          'Operating System :: MacOS :: MacOS X',
          'Operating System :: Microsoft :: Windows',
          'Operating System :: POSIX :: Linux',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
      ],
      description="Single-cell Variational Inference",
      install_requires=requirements,
      license="MIT license",
      long_description=readme + '\n\n' + history,
      include_package_data=True,
      keywords='scvi',
      name='scvi',
      packages=find_packages(),
      setup_requires=setup_requirements,
      test_suite='tests',
      tests_require=test_requirements,
      url='https://github.com/YosefLab/scVI',
      version='0.1.2',
      zip_safe=False,
  )
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from setuptools import setup, find_packages
  
  with open('README.rst') as readme_file:
      readme = readme_file.read()
  
  with open('HISTORY.rst') as history_file:
      history = history_file.read()
  
  requirements = [
      "numpy>=1.0",
      "torch>=0.4",
      "matplotlib>=2.0",
      "scikit-learn>=0.18",
      "scipy>=1.0",
      "h5py>=2.8",
      "pandas>=0.2",
      "loompy>=2.0",
      "tqdm >= 4"
  ]
  
  setup_requirements = ['pytest-runner', ]
  
  test_requirements = ['pytest', ]
  
  author = 'Romain Lopez, Jeffrey Regier, Maxime Langevin, Edouard Mehlman, Yining Liu'
  
  setup(
      author=author,
      author_email='romain_lopez@berkeley.edu',
      classifiers=[
          'Development Status :: 4 - Beta',
          'Intended Audience :: Science/Research',
          'License :: OSI Approved :: MIT License',
          'Natural Language :: English',
          'Programming Language :: Python :: 3.6',
          'Operating System :: MacOS :: MacOS X',
          'Operating System :: Microsoft :: Windows',
          'Operating System :: POSIX :: Linux',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
      ],
      description="Single-cell Variational Inference",
      install_requires=requirements,
      license="MIT license",
      long_description=readme + '\n\n' + history,
      include_package_data=True,
      keywords='scvi',
      name='scvi',
      packages=find_packages(),
      setup_requires=setup_requirements,
      test_suite='tests',
      tests_require=test_requirements,
      url='https://github.com/YosefLab/scVI',
      version='0.1.2',
      zip_safe=False,
  )
  
subject: add tqdm to dependencies (#53)