setup.py

import setuptools
import re

def readme():
    with open("README.rst", 'r') as f:
        return f.read()

# version-handling code stolen from: https://stackoverflow.com/questions/
    #458550/standard-way-to-embed-version-into-python-package
VERSIONFILE="geonomics/version.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE, verstrline, re.M)
if mo:
    verstr = mo.group(1)
else:
    raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))

setuptools.setup(
    name='geonomics',
    # version num.: MAJOR.MINOR.PATCH
    version=verstr,
    author='Drew Ellison Hart',
    author_email='drew.ellison.hart@gmail.com',
    description='A package for landscape genomic simulation',
    long_description=readme(),
    long_description_content_type='text/x-rst',
    url='https://github.com/drewhart/geonomics',
    # include the download URL, from the latest release on Github
    download_url=('https://github.com/drewhart/geonomics/archive/'
                  '%s.tar.gz') % verstr,
    include_package_data=True,
    # packages=setuptools.find_packages(),
    packages=['geonomics',
              'geonomics.sim',
              'geonomics.utils',
              'geonomics.structs',
              'geonomics.ops',
              'geonomics.help',
              'geonomics.demos'],
    classifiers=[
        'Programming Language :: Python :: 3',
        'License :: OSI Approved :: MIT License',
        'Operating System :: OS Independent',
        'Intended Audience :: Science/Research',
        'Intended Audience :: Education',
        'Natural Language :: English',
        'Topic :: Scientific/Engineering :: Bio-Informatics'
    ],
    keywords=('landscape genomics genetics ecology evolution simulation model '
              'environmental model agent-based'),
    project_urls={
        'Documentation': ('https://htmlpreview.github.io/?https://github.com/'
                          'drewhart/geonomics/blob/master/doc/built/doc.html'),
        'Methods Paper': 'https://doi.org/10.1093/molbev/msab175',
        'Source': 'https://github.com/drewhart/geonomics',
    },
#    install_requires=['numpy', 'matplotlib>=3.0.0', 'pandas>=0.23.4', 'geopandas',
#                      'scipy>=1.3.1', 'scikit-learn', 'statsmodels>=0.9.0',
#                      'shapely', 'bitarray', 'rasterio',
#                      'msprime>=0.7.4', 'tskit>=0.2.3'],
    extras_require={'simulation on neutral landscape models': ['nlmpy'],
                   '3d plots for Yosemite demo': ['pykrige']},
    python_requires='>=3.6',
    package_data={'demos': ['geonomics/demos/*']},
)