from setuptools import setup, find_packages

with open("README.md", "r", encoding="utf-8") as fh:
    long_description = fh.read()

setup(
    name="nb-transformer",
    version="1.0.0",
    author="Valentine Svensson",
    author_email="valentine.svensson@gmail.com",
    description="Fast Negative Binomial GLM parameter estimation using transformers - a DESeq2 replacement",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://huggingface.co/valsv/nb-transformer",
    packages=find_packages(),
    classifiers=[
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Science/Research",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Artificial Intelligence",
        "License :: OSI Approved :: MIT License",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
    ],
    python_requires=">=3.8",
    install_requires=[
        "torch>=1.10.0",
        "pytorch-lightning>=1.8.0",
        "numpy>=1.21.0",
        "scipy>=1.7.0",
        "tensorboard>=2.8.0",
    ],
    extras_require={
        "dev": [
            "pytest>=6.2.0",
            "flake8>=4.0.0",
            "black>=21.0.0",
            "mypy>=0.910",
        ],
        "analysis": [
            "pandas>=1.3.0",
            "pyarrow>=5.0.0",
            "matplotlib>=3.4.0",
            "scikit-learn>=1.0.0",
            "statsmodels>=0.13.0",
        ],
    },
    entry_points={
        "console_scripts": [
            "train-nb-transformer=nb_transformer.train:main",
        ],
    },
)