# Copyright (c) 2016 The Python Packaging Authority (PyPA)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
# of the Software, and to permit persons to whom the Software is furnished to do
# so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

"""A setuptools based setup module.

See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject

"""

# To use a consistent encoding
from codecs import open
from glob import glob
from os.path import abspath, basename, dirname, join, splitext

from setuptools import find_packages, setup

import versioneer

here = abspath(dirname(__file__))

# Get the long description from the README file
with open(join(here, "README.md"), encoding="utf-8") as f:
    long_description = f.read()

setup(
    name="lineage",
    version=versioneer.get_version(),
    cmdclass=versioneer.get_cmdclass(),
    description="tools for analyzing and exploring genetic relationships",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://github.com/apriha/lineage",
    author="Andrew Riha",
    author_email="apriha@gmail.com",
    license="MIT",
    packages=find_packages("src"),
    package_dir={"": "src"},
    py_modules=[splitext(basename(path))[0] for path in glob("src/*.py")],
    classifiers=[
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Developers",
        "Intended Audience :: End Users/Desktop",
        "Intended Audience :: Healthcare Industry",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Natural Language :: English",
        "Operating System :: OS Independent",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Programming Language :: Python :: 3.12",
        "Programming Language :: Python :: 3.13",
        "Programming Language :: Python :: 3.14",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Information Analysis",
        "Topic :: Scientific/Engineering :: Visualization",
        "Topic :: Utilities",
    ],
    project_urls={
        "Documentation": "https://lineage.readthedocs.io",
        "Changelog": "https://github.com/apriha/lineage/releases",
        "Issue Tracker": "https://github.com/apriha/lineage/issues",
    },
    keywords="dna genes genetics genealogy snps chromosomes genotype "
    "bioinformatics ancestry",
    install_requires=["numpy", "pandas", "matplotlib", "atomicwrites", "snps"],
    python_requires=">=3.9",
    platforms=["any"],
)
