Fix notebook code formatting

[davidorme]

Description

This updates markdown notebook metadata to make sure {code-cell} block language info is retained, mostly for syntax colouring within VSCode. See #329 for details but basically our jupytext --pipe black pre-commit step was doing a great job of keeping the python code in notebooks formatted but kept stripping out the cell language information used to set the pygments lexing in VSCode.

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

This is partly fixed on #328 but all the small file changes there are just cluttering that branch with lots of out of scope noise, so the plan is to fix it properly and then declutter #328.

Fixes #329

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist

• Make sure you've run the pre-commit checks: $ pre-commit run -a
• All tests pass: $ poetry run pytest

Further checks

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.70%. Comparing base (1f315ba) to head (6accc05).
Report is 206 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #330      +/-   ##
===========================================
+ Coverage    95.29%   95.70%   +0.41%     
===========================================
  Files           28       34       +6     
  Lines         1720     2469     +749     
===========================================
+ Hits          1639     2363     +724     
- Misses          81      106      +25     

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[j-emberton]

lgtm