fm-pm-evaluator/pyproject.toml at 4da34d39fdadbbc28019da9b552a4656e515c59c · lagillenwater/fm-pm-evaluator · GitHub

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[project]
name = "fmharness"
version = "0.1.0.dev0"
description = "Foundation-model evaluation harness for patient-derived tumor organoid drug response"
authors = [{ name = "Lucas Gillenwater", email = "lucas.gillenwater@cuanschutz.edu" }]
license = { text = "BSD-2-Clause-Patent" }
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "pydantic>=2.7",
    "pydantic-settings>=2.2",
    "numpy>=1.26",
    "pandas>=2.2",
    "pyarrow>=15.0",
    "anndata>=0.10",
    "scanpy>=1.10",
    "scikit-learn>=1.5",
    "scipy>=1.13",
    "joblib>=1.4",
    "typer>=0.12",
    "pydeseq2>=0.4",
    "openpyxl>=3.1",
]

[project.optional-dependencies]
ml = [
    "torch>=2.2",
    "transformers>=4.40",
]
stack = [
    "arc-stack @ git+https://github.com/ArcInstitute/stack.git",
]
dev = [
    "pytest>=8.0",
    "pytest-cov>=5.0",
    "hypothesis>=6.100",
    "ruff>=0.4",
    "pyright>=1.1.360",
    "pre-commit>=3.7",
]

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

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

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

[tool.uv]
package = true

[tool.ruff]
line-length = 100
target-version = "py311"
src = ["src", "tests"]

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

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["E501"]

[tool.pyright]
pythonVersion = "3.11"
typeCheckingMode = "strict"
include = ["src", "tests"]
strictListInference = true
strictDictionaryInference = true
strictSetInference = true

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-ra -q"