You can scope the exclude to linting only — ruff has separate [lint] and [format] config sections, and each has its own exclude / extend-exclude. The top-level exclude applies to both, but anything in [lint.exclude] only skips ruff check:

# pyproject.toml
[tool.ruff.lint]
extend-exclude = ["migrations/**"]

# (no exclude under [tool.ruff.format] — these files will still be formatted)

Or in ruff.toml:

[lint]
extend-exclude = ["migrations/**"]

After that:

• ruff check . — skips migrations/, won't fail on autogenerated stuff.
• ruff format . — still formats files in migrations/, including the custom one you wrote.
• ruff format path/to/migrations/0123_my_migration.py — works directly too.

Use extend-exclude rather than exclude if you want to keep the default exclude list (.git, node_modules, etc.); plain exclude replaces the defaults.

Quick way to verify it's set up right:

ruff check --show-settings | grep -A 5 "exclude"
ruff format --show-settings | grep -A 5 "exclude"

You should see migrations/** in the lint settings but not in the format settings.

Refs:

• lint.exclude / format.exclude