SEAL/pyproject.toml at main · mahmoodlab/SEAL · GitHub

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[project]
name = "seal"
version = "0.0.1"
description = "Vision-omics model for histology and spatial transcriptomics inference"
requires-python = ">=3.11,<3.12"
dependencies = [
    "numpy==1.24.4",
    "pandas==2.0.0",
    "torch==2.1.2",
    "torchaudio==2.1.2",
    "torchvision==0.16.2",
    "torchtext==0.16.2",
    "timm==1.0.9",
    "xgboost==2.1.1",
    "transformers==4.48.0",
    "albumentations==2.0.5",
    "accelerate==0.33.0",
    "matplotlib==3.8.2",
    "wandb==0.19.9",
    "tifffile==2023.12.9",
    "scikit-learn==1.4.0",
    "conch @ git+https://github.com/Mahmoodlab/CONCH.git",
    "hest @ git+https://github.com/mahmoodlab/HEST.git@2c777630b1e8a74db6b36ef05582de3bd52ccb61",
    "scanpy==1.10.3",
    "scikit-image==0.22.0",
    "openslide-bin==4.0.0.6",
    "cudf-cu12==24.8.* ; sys_platform == 'linux'",
    "cucim-cu12==24.8.* ; sys_platform == 'linux'",
    "cuml-cu12==24.8.* ; sys_platform == 'linux'",
    "cupy-cuda12x ; sys_platform == 'linux'",
    "loguru==0.7.3",
    "scib==1.1.5",
    "ipython==8.18.1",
    "line-profiler==4.2.0",
    "requests-cache==1.2.1",
    "pybiomart==0.2.0",
    "jupyter>=1.1.1",
    "peft>=0.17.1",
    "huggingface-hub<1.0.0",
]

[project.optional-dependencies]
cross-platform = [
    "threadpoolctl>=3.1.0",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.uv]
# Add NVIDIA PyPI index for CUDA packages
index-url = "https://pypi.org/simple"
extra-index-url = ["https://pypi.nvidia.com"]
# Allow pre-releases for CUDA packages
prerelease = "allow"
# Use unsafe-best-match to check all indexes for best version
index-strategy = "unsafe-best-match"

[tool.uv.sources]
# Git dependencies
conch = { git = "https://github.com/Mahmoodlab/CONCH.git" }
hest = { git = "https://github.com/mahmoodlab/HEST.git", rev = "2c777630b1e8a74db6b36ef05582de3bd52ccb61" }

[tool.hatch.metadata]
allow-direct-references = true