ruff.toml

# Ruff configuration for OpenSpliceAI.
# Focused on real correctness issues (pyflakes F) + basic errors/warnings; line-length
# (E501) and ambiguous-name (E741, the code uses l/L/W/AR heavily) are intentionally ignored
# to avoid mass churn. Legacy/experimental trees are excluded.
line-length = 120
# Honor `extend-exclude` even for files passed explicitly (e.g. by pre-commit), so excluded
# legacy/standalone files are never linted.
force-exclude = true
# Excludes legacy/experimental trees and standalone (not CLI-wired) scripts:
# temperature_scaling_site_only.py is a dead alternate of temperature_scaling.py;
# gff_to_tsv.py is a standalone annotation converter not imported by the package.
extend-exclude = [
    "openspliceai/scripts", "openspliceai/test", "build", "dist", "examples", "docs", "sandbox",
    "openspliceai/calibrate/temperature_scaling_site_only.py",
    "openspliceai/create_data/gff_to_tsv.py",
]

[lint]
select = ["E", "F", "W"]
# E501 line-length and E741 ambiguous names: pervasive, intentional. W291/W292/W293 whitespace:
# avoided to prevent mass whitespace churn. F403/F405 star-imports: used by design across the
# train_base modules (names resolve at runtime), refactoring them is out of scope.
ignore = ["E501", "E741", "W291", "W292", "W293", "F403", "F405"]

[lint.per-file-ignores]
# predict/utils.py deliberately interleaves small imports with the helpers they support.
"openspliceai/predict/utils.py" = ["E402"]