pie/pyproject.toml at main · ArcInstitute/pie · GitHub

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[project]
name = "arc-pie"
version = "1.0.1"
description = "PIE: predicting transcriptional responses to perturbations from biological knowledge sources"
readme = "README.md"
requires-python = ">=3.12,<3.13"
license = "CC-BY-NC-SA-4.0"
authors = [{ name = "Rishi Verma", email = "rishi.verma@arcinstitute.org" }]
keywords = ["single-cell", "perturbation", "gene-expression", "perceiver", "biology"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "anndata>=0.13.2,<0.14",
    "filelock>=4.0.6,<5",
    "h5py>=3.16.0,<4",
    "huggingface-hub>=1.21.0,<2",
    "hydra-core>=1.3.3,<1.4",
    "lightning>=2.6.5,<2.7",
    "numpy>=2.4.6,<3",
    "omegaconf>=2.3.1,<2.4",
    "pandas>=3.0.3,<4",
    "pyarrow>=24.0.0,<25",
    "pydantic>=2.13.4,<3",
    "safetensors>=0.8.0,<0.9",
    "scipy>=1.18.0,<2",
    "torch>=2.10.0,<2.11",
    "tqdm>=4.68.3,<5",
    "wandb>=0.28.0,<0.29",
]

[project.urls]
Homepage = "https://github.com/ArcInstitute/pie"
Repository = "https://github.com/ArcInstitute/pie"
Issues = "https://github.com/ArcInstitute/pie/issues"
"Data and models" = "https://huggingface.co/collections/arcinstitute/pie"

[project.optional-dependencies]
# `all` installs every extra below
all = ["arc-pie[process,sources]"]
process = ["gpudge[fast]>=0.9.1,<0.10"]
sources = [
    "openai>=2.44.0,<3",
    "rdkit>=2026.3.6,<2027",
    "requests>=2.34.2,<3",
    "tiktoken>=0.13.0,<0.14",
    "transformers>=5.12.1,<6",
]

[dependency-groups]
dev = [
    "mypy==2.1.0",
    "pytest==9.1.1",
    "ruff==0.15.20",
]

[build-system]
requires = ["hatchling==1.27.0"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/pie"]

[tool.uv]
override-dependencies = ["torch==2.10.0"]

[tool.uv.sources]
torch = [{ index = "pytorch-cu128", marker = "sys_platform == 'linux'" }]

[[tool.uv.index]]
name = "pytorch-cu128"
url = "https://download.pytorch.org/whl/cu128"
explicit = true

[tool.ruff]
line-length = 100
target-version = "py312"
src = ["src", "tests"]

[tool.ruff.lint]
select = ["E", "F", "W", "I", "B", "UP", "SIM", "RUF"]

[tool.ruff.lint.isort]
known-first-party = ["pie"]

[tool.mypy]
python_version = "3.12"
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["."]
addopts = "--import-mode=importlib"

[project.scripts]
pie = "pie.cli:main"
pie-process = "pie.cli:process_alias"
pie-prep = "pie.cli:prep_alias"
pie-sources = "pie.cli:sources_alias"
pie-train = "pie.cli:train_alias"
pie-eval = "pie.cli:eval_alias"
pie-infer = "pie.cli:infer_alias"