"""
MuLGIT: Multi-layer Genotype Integration Transformer
=====================================================

Causal deep learning-powered cross-layer multi-omics harmonization and 
integration framework following the central dogma of biology for deciphering 
molecular interplays underlying exceptional longevity.

Installation
------------
    pip install -e .

Usage
-----
    python -m mulgit.pipeline --mode quick_test
    python -m mulgit.pipeline --mode train --data synthetic --epochs 50
"""

from setuptools import setup, find_packages

setup(
    name="mulgit",
    version="0.1.0",
    description="Multi-layer Genotype Integration Transformer for Exceptional Longevity",
    author="MuLGIT Team",
    packages=find_packages(),
    python_requires=">=3.10",
    install_requires=[
        "torch>=2.0.0",
        "transformers>=4.40.0",
        "datasets>=2.14.0",
        "trackio>=0.1.0",
        "numpy>=1.24.0",
        "pandas>=2.0.0",
        "scikit-learn>=1.3.0",
    ],
    extras_require={
        "dev": [
            "pytest>=7.0",
            "black>=23.0",
            "isort>=5.12",
        ],
        "huggingface": [
            "huggingface_hub>=0.20.0",
            "peft>=0.7.0",
        ],
    },
    classifiers=[
        "Development Status :: 3 - Alpha",
        "Intended Audience :: Science/Research",
        "Topic :: Scientific/Engineering :: Artificial Intelligence",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.10",
    ],
)