Refine python usage

[actyp]

Since currently it is the norm to use virtual environments instead of the system's python environment, this PR adds uv to the project to manage the dependency of the beautify_model.py script.

Given the required changes, uv might seem redundant to use for just a single dependency, but it has the following benefits:

• simplifies a lot the setup of the virtual environment (just uv sync)
• pins the python and dependency versions enabling reproducibility
• enables automatic usage of the correct virtual environment (e.g. the uv run ... in beautify_model.sh

Aside from leveraging uv, this PR cleans up the beautify_model.{sh, py} scripts, updates the github actions to use uv and updates the README.