BioReason-Pro/pyproject.toml at main · bowang-lab/BioReason-Pro · GitHub

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[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "bioreason-pro"
version = "0.1.0"
description = "Protein Function Prediction with Multimodal Reasoning"
readme = "README.md"
requires-python = ">=3.11"
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
    "torch>=2.6.0,<2.8.0",
    "torchvision",
    "transformers>=4.51.0,<5.0.0",
    "accelerate",
    "datasets",
    "peft",
    "pytorch_lightning",
    "wandb",
    "trl",
    "vllm>=0.9.0",
    "bitsandbytes",
    "deepspeed",
    # esm>=3.2.1 must be installed separately: pip install esm --no-deps (conflicts with vllm on transformers version)
    "goatools",
    "cafaeval",
    "colorama",
    # flash-attn must be installed separately: pip install flash-attn --no-build-isolation
    "typing-extensions",
    "triton",
    "sentence-transformers",
    "torch_geometric",
    "networkx",
    "obonet",
    "huggingface_hub",
    "safetensors",
    "requests",
    "tqdm",
    "pandas",
]

[project.optional-dependencies]
dev = [
    "pytest",
    "black",
    "isort",
    "mypy",
]

[tool.setuptools]
packages = ["bioreason2"]

[tool.black]
line-length = 88
target-version = ["py311"]

[tool.isort]
profile = "black"
line_length = 88

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true