ruff.toml

# Ruff Linter Configuration
# Phenotype Standard - Python linter rules
# https://docs.astral.sh/ruff/settings/

# Target Python 3.10 minimum
target-version = "py310"

# Line length (should match .editorconfig)
line-length = 100

# Vendored upstream trees (see AGENTS.md / ARCHITECTURE.md) are retained as
# read-only reference material and are not linted or formatted by CI.
# Top-level extend-exclude (not [lint] per-file-ignores) so that both
# `ruff check` and `ruff format` skip them.
extend-exclude = [
    "codex-rs",
    "codex-cli",
    # Ruff 0.16+ also formats Python code fences inside Markdown, which
    # churns research/consolidated docs on every formatter upgrade. Scope
    # the formatter to Python source files only.
    "*.md",
]

# Enable rule sections
[lint]
# pyflakes + pycodestyle
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # pyflakes
]
# Additional rules
extend-select = [
    "I",      # isort (import sorting)
    "N",      # pep8-naming
    "UP",     # pyupgrade
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "SIM",    # flake8-simplify
    "RUF",    # Ruff-specific rules
]

# Ignore specific rules
ignore = [
    "E501",   # line too long (handled by formatter)
    "B008",   # do not perform function calls in argument defaults
    "SIM102", # Use a single if statement instead of nested if
]

# Fixable rules (auto-fix on format)
fixable = ["ALL"]
unfixable = []

# Exclude patterns
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".pytest_cache",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]

# Per-file ignores
[lint.per-file-ignores]
"__init__.py" = ["F401", "I001"]  # Allow unused imports in __init__
"tests/**/*.py" = ["S101", "B011"]  # Allow assert in tests, allow deliberate bugs