bioanalyzer-backend/pyproject.toml at main · waldronlab/bioanalyzer-backend · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "bioanalyzer-package"
version = "1.0.0"
description = "A specialized AI-powered tool for analyzing scientific papers for BugSigDB curation readiness"
readme = "README.md"
requires-python = ">=3.8"
license = {text = "MIT"}
authors = [
    {name = "Ouma Ronald", email = "[email protected]"}
]
keywords = ["bioinformatics", "microbiome", "bugsigdb", "curation", "ai", "analysis"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "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",
]
dependencies = [
    # Core dependencies - PyTorch (standard versions)
    # Note: For CPU-only versions, install separately with:
    # pip install --extra-index-url https://download.pytorch.org/whl/cpu torch>=2.1.0+cpu torchvision>=0.16.0+cpu torchaudio>=2.1.0+cpu
    "torch>=2.1.0",
    "torchvision>=0.16.0",
    "torchaudio>=2.1.0",
    # Core ML dependencies
    "transformers>=4.34.0",
    "scikit-learn>=1.3.0",
    "pandas>=2.1.1",
    "numpy>=1.26.0",
    "biopython>=1.81",
    # NLP and LLM dependencies
    "sentencepiece>=0.1.99",
    "accelerate>=0.24.0",
    "datasets>=2.14.0",
    "google-generativeai>=0.7.2",
    "tiktoken>=0.5.0",
    "litellm>=1.50.0",
    # Paper-QA agent integration
    # Note: paper-qa>=5.0.0 requires Python >=3.11
    # For Python <3.11, install paper-qa>=4.9.0,<5.0.0
    "paper-qa>=4.9.0",
    # Web and data retrieval
    "requests>=2.31.0",
    "beautifulsoup4>=4.12.2",
    "lxml>=4.9.0",
    "defusedxml>=0.7.1",
    # Excel file processing
    "openpyxl>=3.1.0",
    "xlrd>=2.0.1",
    # Utilities
    "tqdm>=4.65.0",
    "python-dotenv>=1.0.0",
    "psutil>=5.9.0",
    # WebSocket dependencies
    "fastapi>=0.104.0",
    "uvicorn[standard]>=0.23.2",
    "aiohttp>=3.8.6",
    "websockets>=11.0.3",
    "python-multipart>=0.0.5",
    "aiofiles>=0.7.0",
    "pydantic>=2.4.2",
    "typing-extensions>=3.10.0.2",
    "starlette>=0.31.1",
    "click>=8.0.1",
    "h11>=0.12.0",
    "httptools>=0.3.0",
    "PyYAML>=5.4.1",
    "watchfiles[watchdog]>=1.0.0",
    "wsproto>=1.0.0",
    "tokenizers>=0.14.1",
    "pytz>=2023.3",
    # Vector database (optional - for persistent storage)
    "qdrant-client>=1.7.0",
    # Curator table (sortable/searchable Streamlit UI)
    "streamlit>=1.28.0",
    "pyarrow>=14.0.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "black>=23.0.0",
    "flake8>=6.0.0",
    "mypy>=1.5.0",
]
cli = [
    "click>=8.0.1",
    "rich>=13.0.0",
    "tabulate>=0.9.0",
]
torch-cpu = [
    # PyTorch CPU versions - install separately with: pip install -e ".[torch-cpu]"
    # Note: These require --extra-index-url https://download.pytorch.org/whl/cpu
    # Install with: pip install --extra-index-url https://download.pytorch.org/whl/cpu torch>=2.1.0+cpu torchvision>=0.16.0+cpu torchaudio>=2.1.0+cpu
    # Or use the standard PyTorch versions from PyPI
]

[project.urls]
Homepage = "https://github.com/your-repo/bioanalyzer-backend"
Documentation = "https://github.com/your-repo/bioanalyzer-backend/docs"
Repository = "https://github.com/your-repo/bioanalyzer-backend"
"Bug Reports" = "https://github.com/your-repo/bioanalyzer-backend/issues"

[project.scripts]
bioanalyzer = "scripts.cli:main"
bioanalyzer-cli = "scripts.cli:main"

[tool.setuptools]
packages = {find = {}}
include-package-data = true

[tool.setuptools.package-data]
"*" = ["*.md", "*.txt", "*.yml", "*.yaml"]