Fix notebook code formatting

[davidorme]

Describe the bug

We want the Python code in notebooks to get auto-formatted.

At the moment, we're using jupytext --pipe black as a pre-commit hook, which does the job but is not configured quite correctly. The way it works is a bit complex:

mwouts/jupytext#1267

The main issue is that the piping process causes code-cell language info to be removed and that breaks pygments lexing in VSCode. In order to retain that, we need to the notebooks to include language-info notebook metadata, which jupyter adds but is not retained in the minimal filtered Myst notebook metadata when it passes through jupytext.

It is possible that in the future we might be able to use ruff to do this job but at present only the .ipynb format for notebooks is supported by ruff-format and it's a pain to have to convert all our '.mdfiles to.ipynband then back again (usingjupytext`) just to format the Python.

astral-sh/ruff#8800 (comment)

So:

1. Add retaining the language_info notebook metadata to the project settings.
2. Add that language_info metadata to the files (at the moment this is manual or open and save in jupyter after step 1)
3. Add {code-cell} ipython3 to code cells.