chore: update pre-commit hooks

[pre-commit-ci[bot]]

updates:

• github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0
• github.com/psf/black: 24.3.0 → 24.4.2
• github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.5.0
• github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.1
• github.com/codespell-project/codespell: v2.2.6 → v2.3.0
• github.com/snakemake/snakefmt: v0.10.0 → v0.10.2