"""
Setup script for EvoMotif.
"""

from setuptools import setup, find_packages
from pathlib import Path

# Read long description from README
this_directory = Path(__file__).parent
long_description = (this_directory / "README.md").read_text()

setup(
    name="evomotif",
    version="0.1.0",
    author="Taha",
    author_email="taha@example.com",
    description="Evolution-driven framework for discovering novel protein motifs",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://github.com/yourusername/EvoMotif",
    packages=find_packages(),
    classifiers=[
        "Development Status :: 3 - Alpha",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    python_requires=">=3.8",
    install_requires=[
        "biopython>=1.79",
        "numpy>=1.21.0",
        "scipy>=1.7.0",
        "pandas>=1.3.0",
        "matplotlib>=3.4.0",
        "seaborn>=0.11.0",
        "scikit-learn>=1.0.0",
        "statsmodels>=0.13.0",
        "ete3>=3.1.2",
        "py3Dmol>=1.8.0",
        "requests>=2.26.0",
    ],
    extras_require={
        "dev": [
            "pytest>=7.0.0",
            "pytest-cov>=3.0.0",
            "pytest-mock>=3.6.0",
            "black>=22.0.0",
            "flake8>=4.0.0",
            "mypy>=0.950",
            "isort>=5.10.0",
            "sphinx>=4.5.0",
            "sphinx-rtd-theme>=1.0.0",
            "myst-parser>=0.18.0",
        ]
    },
    entry_points={
        "console_scripts": [
            "evomotif=evomotif.cli:main",
        ],
    },
)
