pyproject.toml

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

[project]
name = "oncomind"
version = "0.1.0"
description = "LLM-powered cancer variant actionability assessment with validation"
readme = "README.md"
requires-python = ">=3.11"
license = {text = "MIT"}
authors = [
    {name = "Tumor Board Team"}
]
dependencies = [
    "httpx>=0.27.0",
    "litellm>=1.30.0",
    "pandas>=2.0.0",
    "pydantic>=2.6.0",
    "pydantic-settings>=2.1.0",
    "typer>=0.9.0",
    "python-dotenv>=1.0.0",
    "streamlit>=1.31.0",
    "tenacity>=8.2.0",
    "scipy>=1.11.0",
    "openpyxl>=3.1.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0",
    "pytest-asyncio>=0.23.0",
    "pytest-cov>=4.1.0",
    "ruff>=0.2.0",
    "mypy>=1.8.0",
]

[project.scripts]
mind = "oncomind.cli:app"

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

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

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long (handled by formatter)
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
ignore_missing_imports = true

[tool.pytest.ini_options]
asyncio_mode = "auto"
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--strict-markers",
    "--strict-config",
    "-ra",
]

[tool.coverage.run]
source = ["src"]
branch = true

[tool.coverage.report]
precision = 2
show_missing = true
skip_covered = false