Replace pylint + autopep8 with ruff for Python linting and formatting

[sbryngelson]

Motivation

We currently use two separate tools for Python code quality:

• autopep8 for formatting (in format_python.sh)
• pylint for linting (in lint.sh, with ~20 disabled rules passed as CLI flags)

Both are slow compared to modern alternatives, and the pylint configuration is scattered across inline CLI flags in bash scripts with no centralized config file. There are also 229 inline # pylint: disable=... comments spread across the toolchain source.

Ruff is a single tool that replaces both, written in Rust, and is 10-100x faster than pylint/autopep8. We already use uv (also from Astral) for dependency installation.

Proposed changes

1. Replace autopep8 with ruff format

• Configure max line length (200) in pyproject.toml under [tool.ruff]
• Update format_python.sh to call ruff format instead of autopep8

2. Replace pylint with ruff check

• Translate the currently-disabled pylint rules to ruff equivalents in pyproject.toml
• Update lint.sh to call ruff check instead of three separate pylint invocations
• Use per-path rule overrides in pyproject.toml for the different configs (toolchain vs examples/benchmarks)

3. Enable ruff check --fix for auto-fixable lint violations

• Ruff can auto-fix many issues (unused imports, import sorting, simple style fixes)
• Integrate this into ./mfc.sh format so fixable lint issues are corrected alongside formatting
• The ./mfc.sh lint step then only reports issues that require manual intervention

4. Remove all 229 inline # pylint: disable= comments

Current breakdown of inline disables:

Count	pylint rule	Ruff disposition
79	import-outside-toplevel	Globally disable — intentional lazy-import pattern
44	too-many-locals	Globally disable — project style
23	too-many-branches	Globally disable — project style
18	too-many-statements	Globally disable — project style
17	too-many-arguments	Globally disable — project style
14	too-many-positional-arguments	Globally disable — project style
14	protected-access	Globally disable — intentional in this codebase
8	too-many-instance-attributes	Globally disable — project style
7	too-many-nested-blocks	Globally disable — project style
7	too-many-boolean-expressions	Globally disable — project style
5	too-many-lines	Globally disable — project style
3	too-many-return-statements	Globally disable — project style
1	too-many-public-methods	Globally disable — project style
1	too-few-public-methods	Globally disable — project style
9	unsubscriptable-object	Globally disable — false positives
5	unused-import	Keep enabled, auto-fix with ruff check --fix
2	unused-argument	Keep enabled, auto-fix (prefix with _)
6	wrong-import-position	Keep enabled, auto-fix with isort rules
2	consider-using-with	Keep enabled, fix manually where appropriate
1	consider-using-enumerate	Keep enabled, auto-fix
1	use-dict-literal	Keep enabled, auto-fix
4	broad-except	Keep enabled — catch-all exceptions should be flagged
10	global-statement	Keep enabled — discourage new globals
3	global-variable-not-assigned	Keep enabled
1	redefined-builtin	Keep enabled
1	not-an-iterable	Keep enabled

Once the ruff config in pyproject.toml globally disables the ~200 project-style suppressions, all 229 inline comments can be removed.

5. Centralize config in toolchain/pyproject.toml

• All rule selection, ignores, and per-path overrides in one place under [tool.ruff]
• Remove inline CLI flag sprawl from lint.sh

6. Update dependencies in pyproject.toml

• Remove autopep8 and pylint
• Add ruff

Benefits

• Single tool instead of two
• 10-100x faster linting and formatting
• Auto-fix for common issues (unused imports, import order, etc.)
• Remove 229 inline # pylint: disable comments
• Centralized configuration in pyproject.toml
• Already in the Astral ecosystem alongside uv