benchmark

Run `pre-commit autoupdate`, fix stale pyproject.toml comments (#1712)

* Run `pre-commit autoupdate`, fix stale pyproject.toml comments

* Set `--enable_bzlmod=false` for the moment

Until the newer nanobind tags are pushed to the BCR, it's best to disable
bzlmod for the bindings, because the Python CI breaks due to Bazel 7
enabling bzlmod by default.

* Remove E203 ignore, add linebreaks to semantically group ruff options