chore: update pre-commit hooks

[pre-commit-ci[bot]]

updates:

• github.com/psf/black: 23.12.1 → 24.3.0
• github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.3.4
• github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0
• github.com/kynan/nbstripout: 0.6.1 → 0.7.1
• github.com/shellcheck-py/shellcheck-py: v0.9.0.6 → v0.10.0.1
• github.com/snakemake/snakefmt: v0.8.5 → v0.10.0