pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "clinlp"
version = "0.9.1"
description = "Performant and production-ready NLP pipelines for clinical text written in Dutch"
readme = "README.md"
authors = [ {name = "UMCU DIT Analytics", email="analytics@umcutrecht.nl"} ]
requires-python = ">=3.10"
dependencies = [
    "intervaltree ~= 3.1",
    "makefun ~= 1.15",
    "numpy ~= 2.0",
    "pandas ~= 2.2",
    "pydantic ~= 2.6",
    "spacy ~= 3.8",
]

[project.optional-dependencies]
metrics = [
    "nervaluate == 0.1.8",
    "scikit-learn ~= 1.5",
]
transformers = [
    "transformers[torch] ~= 4.30",
]

[tool.uv]
dev-dependencies = [
    "emoji ~= 2.12",
    "furo ~= 2024.5",
    "myst-parser ~= 4.0",
    "pytest ~= 8.2",
    "pytest-cov ~= 5.0",
    "pytest-xdist>=3.6.1",
    "ruff ~= 0.4",
    "sphinx ~= 8.1",
    "sphinx-new-tab-link ~= 0.4",
    "toml ~= 0.10",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "--cov=clinlp --cov-fail-under=85"

[tool.ruff]
src = ["src"]

[tool.ruff.lint]
select = [
    "F", "E", "W", "C90", "I", "N", "D", "UP", "ANN", "S",
    "BLE", "FBT", "B", "C4", "EM", "PIE", "T20",
    "PT", "RSE", "RET", "SIM", "ARG", "PTH", "ERA",
    "TRY", "PERF", "RUF"
]
ignore = [
    "ANN002", "ANN003", "ANN101", "ANN102"
]

[tool.ruff.lint.per-file-ignores]
"docs/*" = ["D"]
"tests/*" = ["D", "S", "ANN"]
"scripts/*" = ["D", "T20"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"