refactor: use linters in the env, fix mypy warns, improve makefiles

[mdevolde]

refactor: use linters in the env, fix mypy warns, improve makefiles

Why the pull request was made

Actually, ruff and mypy are executed outside of the venv, causing some false alerts. It was necessary to patch that to have working linters/type checkers. They are now well implemented in the makefiles, and so, the makefiles are used anywhere we need to use linters/type checkers, or even run tests (so, we have one place to edit the way we run our checks/tests).

Summary of changes

• Added a group in pyproject.toml with ruff and mypy
• In makefiles, using uv run instead of uvx to run tools in our env
• In makefiles, adding some targets
• In CI and in docs, using our makefiles instead of mentionning some "uv run" commands
• Fix some mypy warns

Screenshots (if appropriate):

Not applicable.

How has this been tested?

Applied local tests, tested all makefiles targets (on debian 13/windows 11).

Resources

Not applicable.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update (changes to documentation only)
• Refactor / code style update (non-breaking change that improves code structure or readability)
• Tests / CI improvement (adding or updating tests or CI configuration only)
• Other (please describe):

Checklist

• Followed the project's contributing guidelines.
• Updated any relevant tests.
• Updated any relevant documentation.
• Added comments to your code where necessary.
• Formatted your code, run the linters, checked types and tests.