saev/pyproject.toml at main · Imageomics/saev · GitHub

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[project]
name = "saev"
version = "0.1.0"
description = "Sparse autoencoders for vision transformers in PyTorch"
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
    "adjusttext>=1.3.0",
    "altair>=5.4.1",
    "beartype>=0.19.0",
    "datasets>=3.0.1",
    "duckdb>=1.3.2",
    "einops>=0.8.0",
    "glasbey>=0.3.0",
    "h5py>=3.15.1",
    "invoke>=2.2.0",
    "jaxtyping>=0.3.2",
    "marimo[mcp]>=0.20.2",
    "matplotlib>=3.9.2",
    "numpy>=2.3.2",
    "open-clip-torch>=2.28.0",
    "orjson>=3.11.2",
    "pillow>=10.4.0",
    "polars>=1.36.0",
    "psutil>=6.1.0",
    "scikit-learn>=1.7.0",
    "scipy>=1.16.1",
    "submitit>=1.5.4",
    "torch>=2.9.0",
    "tqdm>=4.66.5",
    "tyro>=0.8.12",
    "viztracer>=1.0.4",
    "wandb==0.22.0",
]

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

[project.urls]
Homepage = "https://imageomics.github.io/saev"
Issues = "https://github.com/Imageomics/saev/issues"

[tool.ruff]
extend-exclude = ["tests/sweeps"]

[tool.ruff.lint]
select = ["E", "F", "I"]
ignore = ["F722", "E402", "E501"]

[tool.uv]
package = true
default-groups = "all"

[tool.uv.workspace]
members = [
    "contrib/trait_discovery",
    "contrib/birdsong",
    "contrib/mimics",
]

[tool.coverage.run]
patch = ["subprocess"]

[dependency-groups]
dev = [
    "coverage-badge>=1.1.2",
    "gradio>=3.36.1",
    "hypothesis[codemods]>=6.119.0",
    "hypothesis-torch>=0.8.4",
    "huggingface-hub>=0.26.5",
    "mkdocs-material>=9.6.20",
    "mkdocstrings[python]>=0.30.1",
    "mkdocs-gen-files>=0.5.0",
    "mkdocs-literate-nav>=0.6.2",
    "pytest>=8.3.3",
    "pytest-xdist>=3.6.1",
    "pytest-cov>=6.1.1",
    "pytest-json-report>=1.5.0",
    "pytest-timeout>=2.2.0",
    "vl-convert-python>=1.8.0",
    # https://github.com/mkdocs/mkdocs/issues/4032
    "click==8.2.1",
    "transformers>=4.57.3",
]

[tool.pytest.ini_options]
timeout = 300
timeout_method = "thread"
addopts = "-m 'not integration'"
filterwarnings = [
    "ignore:Can't initialize NVML:UserWarning"
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests (deselect with '-m \"not integration\"')",
]

[tool.marimo.runtime]
watcher_on_save = "autorun"