pyproject.toml

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

[dependency-groups]
dev = ["sentinel[dev]"]
test = ["sentinel[test]"]

[project]
authors = [
  {email = "j.euko@instadeep.com", name = "Joao Paulo Euko"},
  {email = "t.d.barrett91@gmail.com", name = "Tom Barrett"},
  {email = "t.makkink@instadeep.com", name = "Thomas Makkink"}
]
dependencies = [
  "fastapi",
  "fpdf>=1.7.2",
  "hydra-core>=1.3.2",
  "langchain",
  "langchain-community",
  "langchain-google-genai",
  "langchain-ollama",
  "langchain-openai",
  "markdown2>=2.5.3",
  "matplotlib>=3.10.3",
  "openpyxl>=3.1.0",
  "python-dotenv",
  "pyyaml",
  "reportlab>=4.0.0"
]
description = "LLM-based Cancer Risk Assessment Assistant"
name = "sentinel"
readme = "README.md"
requires-python = ">=3.12"
version = "0.1.0"

[project.optional-dependencies]
dev = [
  "ipywidgets",
  "jupyterlab",
  "plotly",
  "pre-commit",
  "pyright",
  "pyright>=1.1.405",
  "seaborn",
  "uvicorn"
]
test = [
  "pytest-cov>=4.0.0",
  "pytest-mock>=3.15.1",
  "pytest>=7.0.0"
]

[tool.ruff]
line-length = 88
target-version = "py312"

[tool.ruff.format]
indent-style = "space"
line-ending = "auto"
quote-style = "double"
skip-magic-trailing-comma = false

[tool.ruff.lint]
ignore = [
  "ARG001", # unused function argument (test fixtures)
  "ARG002", # unused method argument (pydantic callbacks)
  "B008", # do not perform function calls in argument defaults
  "B904", # raise from err (requires manual review)
  "C408", # unnecessary dict call (plotly API requires dict())
  "C901", # too complex
  "E501", # line too long, handled by formatter
  "F841", # unused variable (sometimes needed for future use)
  "RUF002", # ambiguous hyphen (requires manual review)
  "RUF012", # ClassVar annotations (requires manual review)
  "SIM102", # nested if statements (sometimes clearer)
  "SIM108", # ternary operator (sometimes if-else is clearer)
  "TCH" # type-checking rules (often can't be auto-fixed)
]
select = [
  "ARG", # flake8-unused-arguments
  "B", # flake8-bugbear
  "C4", # flake8-comprehensions
  "E", # pycodestyle errors
  "F", # pyflakes
  "I", # isort
  "Q", # flake8-quotes
  "RUF", # ruff-specific rules
  "SIM", # flake8-simplify
  "TCH", # flake8-type-checking
  "UP", # pyupgrade
  "W" # pycodestyle warnings
]

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

[tool.ruff.lint.pydocstyle]
# Use Google-style docstrings.
convention = "google"

[tool.ruff.lint.pylint]
allow-magic-value-types = ["int", "str"]

[tool.setuptools.packages.find]
include = ["sentinel*"]
where = ["src"]

[tool.uv]
default-groups = ["dev", "test"] # By default, install all dependencies.