setup.py

import os
import sys
from setuptools import setup, find_packages

install_requires = [
    "numpy>=1.16.0",
    "scipy>=1.1.0",
    "scikit-learn>=0.20.0",
    "future",
    "tasklogger>=1.0",
    "graphtools>=1.5.3",
    "scprep>=0.11.1",
    "Deprecated",
    "s_gd2>=1.8.1",
]

test_requires = ["nose2", "anndata", "coverage", "coveralls", "nose"]

doc_requires = ["sphinx", "sphinxcontrib-napoleon"]

version_py = os.path.join(os.path.dirname(__file__), "phate", "version.py")
version = open(version_py).read().strip().split("=")[-1].replace('"', "").strip()

if sys.version_info[:2] < (3, 5):
    raise RuntimeError("Python version >=3.5 required.")
elif sys.version_info[:2] < (3, 6):
    install_requires += ["matplotlib>=3.0,<3.1"]
else:
    install_requires += ["matplotlib>=3.0"]

readme = open("README.md").read()

setup(
    name="phate",
    version=version,
    description="PHATE",
    author="Daniel Burkhardt, Krishnaswamy Lab, Yale University",
    author_email="daniel.burkhardt@yale.edu",
    packages=find_packages(),
    license="GNU General Public License Version 2",
    install_requires=install_requires,
    extras_require={"test": test_requires, "doc": doc_requires},
    test_suite="nose2.collector.collector",
    long_description=readme,
    long_description_content_type="text/markdown",
    url="https://github.com/KrishnaswamyLab/PHATE",
    download_url="https://github.com/KrishnaswamyLab/PHATE/archive/v{}.tar.gz".format(
        version
    ),
    keywords=[
        "visualization",
        "big-data",
        "dimensionality-reduction",
        "embedding",
        "manifold-learning",
        "computational-biology",
    ],
    classifiers=[
        "Development Status :: 5 - Production/Stable",
        "Environment :: Console",
        "Framework :: Jupyter",
        "Intended Audience :: Developers",
        "Intended Audience :: Science/Research",
        "Natural Language :: English",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: Microsoft :: Windows",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: 3.7",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Visualization",
    ],
)

# get location of setup.py
setup_dir = os.path.dirname(os.path.realpath(__file__))