setup.py

from setuptools import setup, Extension, find_packages
import numpy
from Cython.Build import cythonize

import glob

setup(
    name="reat",
    version="0.6.1",
    packages=find_packages(".", exclude=["tests"]),
    url="https://github.com/ei-corebioinformatics/reat",
    classifiers=[
        "Development Status :: 4 - Beta",
        "Topic :: Scientific Engineering :: Bio/Informatics",
        "License :: OSI Approved :: MIT License",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
    ],
    license="MIT",
    author="Luis Yanes, Gemy Kaithakottil",
    author_email="luis.yanes@earlham.ac.uk, gemy.kaithakottil@earlham.ac.uk",
    description="Robust Eukaryotic Annotation Toolkit",
    zip_safe=False,
    keywords="gene annotation WDL pipeline workflow cromwell transcriptome homology",
    ext_modules=cythonize(
        [
            Extension(
                "annotation.lib.cy_utils.contrast",
                include_dirs=[numpy.get_include()],
                sources=["annotation/lib/cy_utils/contrast.pyx"],
            ),
        ],
        compiler_directives={"language_level": "3"},
    ),
    scripts=[script for script in glob.glob("annotation/scripts/*")],
    install_requires=[
        "parasail~=1.2.4",
        "2passtools @ git+https://github.com/bartongroup/2passtools.git#d4378d0",
    ],
    extras_require={"docs": ["sphinx", "sphinx_rtd_theme",]},
    package_data={
        "validation": ["transcriptome.schema.json", "homology.schema.json"],
        "annotation": [
            "transcriptome_module/*.wdl",
            "transcriptome_module/*/**/*.wdl",
            "transcriptome_module/*/**/**/*.wdl",
            "homology_module/*.wdl",
            "prediction_module/*",
        ],
        "annotation.lib.cy_utils": ["annotation/lib/cy_utils/contrast.pxd"],
    },
    entry_points={"console_scripts": ["reat=annotation.__main__:main"]},
)