"""
setup.py - Python package setup for Docking@HOME

Authors: OpenPeer AI, Riemann Computing Inc., Bleunomics, Andrew Magdy Kamal
"""

from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext
import sys
import os

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

# Read requirements
with open("requirements.txt", "r", encoding="utf-8") as fh:
    requirements = [line.strip() for line in fh if line.strip() and not line.startswith("#")]

class CMakeExtension(Extension):
    def __init__(self, name, sourcedir=""):
        Extension.__init__(self, name, sources=[])
        self.sourcedir = os.path.abspath(sourcedir)

class CMakeBuild(build_ext):
    def run(self):
        for ext in self.extensions:
            self.build_extension(ext)

    def build_extension(self, ext):
        # CMake build logic here
        pass

setup(
    name="docking-at-home",
    version="1.0.0",
    author="OpenPeer AI, Riemann Computing Inc., Bleunomics, Andrew Magdy Kamal",
    author_email="contact@docking-at-home.org",
    description="Distributed and Parallel Molecular Docking Platform",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://huggingface.co/OpenPeerAI/DockingAtHOME",
    project_urls={
        "Bug Reports": "https://huggingface.co/OpenPeerAI/DockingAtHOME/discussions",
        "Documentation": "https://huggingface.co/OpenPeerAI/DockingAtHOME",
        "Source": "https://huggingface.co/OpenPeerAI/DockingAtHOME",
        "HuggingFace": "https://huggingface.co/OpenPeerAI/DockingAtHOME",
    },
    packages=find_packages(where="python"),
    package_dir={"": "python"},
    classifiers=[
        "Development Status :: 4 - Beta",
        "Intended Audience :: Science/Research",
        "Topic :: Scientific/Engineering :: Chemistry",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Operating System :: OS Independent",
    ],
    python_requires=">=3.8",
    install_requires=requirements,
    extras_require={
        "dev": [
            "pytest>=7.4.0",
            "pytest-cov>=4.1.0",
            "black>=23.7.0",
            "flake8>=6.1.0",
            "mypy>=1.5.0",
            "sphinx>=7.1.0",
        ],
        "gpu": [
            "cupy>=12.0.0",
        ],
    },
    entry_points={
        "console_scripts": [
            "docking-at-home=docking_at_home.cli:main",
        ],
    },
    include_package_data=True,
    zip_safe=False,
)