Bump ruff from 0.5.5 to 0.16.3 - #889

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/cache@v4, actions/checkout@v4, actions/setup-python@v5. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/