Update and fix issues raised by Python QA tools

[guilieb]

• Update pre-commit tools version numbers
• Fix the issues raised by the pre-commit tools (new mypy errors & pyupgrade suggestions).
• Remove un-necessary x permission on some non-source files.
• Add a simple ruffconfiguration in pyproject and add it in the dev group of dependencies.
• Harmonize the location of configuration to pyproject.toml instead of having explicing args in pre-commit-config.yaml.
• Add a GitHub Actions with pre-commit