setup.py

# coding: utf-8
from setuptools import setup, find_packages
from setuptools.extension import Extension
from distutils.extension import Extension
from codecs import open
from os import path
import glob
import sys


here = path.abspath(path.dirname("__file__"))

with open(path.join(here, "DESCRIPTION.md"), encoding="utf-8") as description:
    description = long_description = description.read()

name = "minos"
version = "1.8.0"

if sys.version_info.major != 3:
    raise EnvironmentError(
        """minos is a python module that requires python3, and is not compatible with python2. Also, it is now 2020 and support for 2.x has ceased."""
    )

requirements = [line.rstrip() for line in open("requirements.txt", "rt")]

setup(
    name=name,
    python_requires=">=3.6",
    version=version,
    description=description,
    long_description=long_description,
    author="Christian Schudoma, Gemy Kaithakottil",
    author_email="christian.schudoma@earlham.ac.uk, gemy.kaithakottil@earlham.ac.uk",
    license="MIT",
    classifiers=[
        "Development Status :: 4 - Beta",
        "Topic :: Scientific Engineering :: Bio/Informatics",
        "License :: OSI Approved :: MIT License",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python :: 3.4",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6" "Programming Language :: Python :: 3.7",
    ],
    zip_safe=False,
    keywords="gene annotation",
    packages=find_packages(exclude=["test"]),
    scripts=[script for script in glob.glob("bin/slurm/*_sub")],
    install_requires=requirements,
    entry_points={
        "console_scripts": [
            "minos=minos.__main__:main",
            "generate_metrics=minos.scripts.generate_metrics:main",
            "parse_mikado_gff=minos.scripts.parse_mikado_gff:main",
            "protein_completeness=minos.scripts.protein_completeness:main",
            "collapse_metrics=minos.scripts.collapse_metrics:main",
            "validate_gff3=minos.scripts.validate_gff3:main",
            "create_release_gff3=minos.scripts.create_release_gff:main",
            "sanity_check=minos.scripts.sanity_check:main",
            "parse_mikado_stats=minos.scripts.parse_mikado_stats:main",
            "analyse_busco=minos.scripts.analyse_busco:main",
            "clean_fasta_header=minos.scripts.clean_fasta_header:main",
            "install_cpc2=minos.scripts.install_cpc2:main",
            "generate_final_table=minos.scripts.generate_final_table:main",
        ]
    },
    package_data={
        "minos.zzz": ["*.smk"],
        "minos.etc": ["*.json", "*.yaml", "*.def", "test/*"],
        "minos.dependencies": ["*.sh", "container_defs/*"],
    },
    include_package_data=True,
)