old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from setuptools import setup, find_packages
  
  requirements = [
      "kipoi>=0.5.5",
      # "genomelake",
      "pyfaidx",
      "numpy",
      "pandas",
      "tqdm",
      # "colorlog",
      # "related>=0.6.0",
      # sometimes required
      # "h5py",
      "gffutils",
      "kipoi-utils>=0.1.1",
      "kipoi-conda>=0.1.0"
  ]
  
  test_requirements = [
      "bumpversion",
      "wheel",
      "epc",
      "jedi",
      "pytest>=3.3.1",
      "pytest-xdist",  # running tests in parallel
      "pytest-pep8",  # see https://github.com/kipoi/kipoi/issues/91
      "pytest-cov",
      "coveralls",
      "scikit-learn",
      "cython",
      "cyvcf2",
      "pyranges",
      # "genomelake",
      "keras",
      "tensorflow",
      "pybedtools"
  ]
  
  setup(
      name='kipoiseq',
      version='0.3.1',
      description="kipoiseq: sequence-based data-laoders for Kipoi",
      author="Kipoi team",
      author_email='avsec@in.tum.de',
      url='https://github.com/kipoi/kipoiseq',
      long_description="kipoiseq: sequence-based data-laoders for Kipoi",
      packages=find_packages(),
      install_requires=requirements,
      extras_require={
          "develop": test_requirements,
      },
      license="MIT license",
      zip_safe=False,
      keywords=["model zoo", "deep learning",
                "computational biology", "bioinformatics", "genomics"],
      test_suite='tests',
      include_package_data=False,
      tests_require=test_requirements
  )
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  from setuptools import setup, find_packages
  
  requirements = [
      "kipoi>=0.5.5",
      # "genomelake",
      "pyfaidx",
      "numpy",
      "pandas",
      "tqdm",
      # "colorlog",
      # "related>=0.6.0",
      # sometimes required
      # "h5py",
      "gffutils",
      "kipoi-utils>=0.1.1",
      "kipoi-conda>=0.1.0"
  ]
  
  test_requirements = [
      "bumpversion",
      "wheel",
      "epc",
      "jedi",
      "pytest>=3.3.1",
      "pytest-xdist",  # running tests in parallel
      "pytest-pep8",  # see https://github.com/kipoi/kipoi/issues/91
      "pytest-cov",
      "coveralls",
      "scikit-learn",
      "cython",
      "cyvcf2",
      "pyranges<=0.0.70",
      # "genomelake",
      "keras",
      "tensorflow",
      "pybedtools"
  ]
  
  setup(
      name='kipoiseq',
      version='0.3.1',
      description="kipoiseq: sequence-based data-laoders for Kipoi",
      author="Kipoi team",
      author_email='avsec@in.tum.de',
      url='https://github.com/kipoi/kipoiseq',
      long_description="kipoiseq: sequence-based data-laoders for Kipoi",
      packages=find_packages(),
      install_requires=requirements,
      extras_require={
          "develop": test_requirements,
      },
      license="MIT license",
      zip_safe=False,
      keywords=["model zoo", "deep learning",
                "computational biology", "bioinformatics", "genomics"],
      test_suite='tests',
      include_package_data=False,
      tests_require=test_requirements
  )
  
subject: add pyranges <= 0.0.70 to setup.py, since 0.0.71 changes from 1-indexed to 0-indexed gtf reader