[build-system]
requires = ["hatchling>=1.24"]
build-backend = "hatchling.build"

[project]
name = "simurg"
description = "SimurgArray: open research toolkit for Illumina Infinium genotyping BeadChip data"
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.12"
authors = [{ name = "Kemal Yaylali" }]
dynamic = ["version"]
dependencies = [
    "numpy>=1.26",   # all numerics
    "typer>=0.12",   # CLI
    "rich>=13",      # progress / human-readable output
    "pyyaml>=6",     # --config files
    "pyarrow>=15",   # canonical columnar model and Parquet outputs (plan §5)
]

[project.optional-dependencies]
dev = [
    "pytest>=8",
    "pytest-benchmark>=4",
    "hypothesis>=6.100",
    "ruff>=0.6",
    "mypy>=1.11",
    "types-PyYAML",
]

[project.scripts]
simurg = "simurg.cli.main:app"

[tool.hatch.version]
path = "src/simurg/__init__.py"

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

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-q --strict-markers"
markers = [
    "data: needs downloaded datasets under data/ (skipped when absent)",
    "oracle: compares against a reference implementation under refs/ (skipped when absent)",
    "slow: long-running test",
]

[tool.ruff]
line-length = 120
target-version = "py312"
src = ["src", "tests"]

[tool.ruff.lint]
select = ["E", "F", "W", "I", "B", "UP", "N", "SIM", "RUF"]
ignore = ["N802", "N806", "RUF001", "RUF002", "RUF003"]

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

[tool.mypy]
python_version = "3.12"
strict = true
files = ["src/simurg"]
ignore_missing_imports = true