Update notebook utilities and testing

[mlshapiro]

Closes #18

Looking at the Github Actions doctest run, it may impractical to actually run nb-test in the actions. Lets discuss at the next standup

Changes

Updates notebook plumbing to execute notebooks on validation in Doc / Notebook Tests and ensure outputs are cleaned up.

Note that if there is a cell that won't execute on a generic complete installation of pycontrails, you need to add the tags skip-execution and nbval-skip to that cell. The Cache notebook has an example of this.

You add tags with the Property Inspector (View -> Property Inspector).

Internals

• Executes notebooks when validating outputs (make nb-test). Continues to use nbval-lax.
• Adds convenience Make recipe to execute all notebooks in the docs (make nb-execute)
• Adds new Make recipe to cleanup notebooks (make nb-clean)
• Adds pre-commit hook to check if notebooks are clean.
• Cleans up contributing and develop documentation.
• Re-organizes notebooks in documentation

TODO:

• For a future PR, this will not raise on notebook cells.
• cfgrib won't load in the doctest action because the eccodes is not present. This is unfortunately complicated, so I ignored the GFS notebook.
• The tutorial run-cocip-on-flight requires special meteorology. I ignored the file from nb-test since we haven't staged in this meteorology.
• The turotial specific-humidity-interpolation requires metview, which we don't install on the Action. Ignored for now.

Tests

• [x] QC test passes locally (make test)
• [x] CI tests pass

Reviewer

Select @zebengberg @trdean1

[mlshapiro]

TODO:

• Replace nbval with nbval-lax
• Ensure there are no Warnings.
• Remove metview dependency - put info into notebook.

[trdean1]

• Ensure there are no Warnings.

This warning will come up in my notebook. Should we just remove this warning or maybe not raise it if fuel_flow is provided?

[zebengberg]

• Ensure there are no Warnings.

This warning will come up in my notebook. Should we just remove this warning or maybe not raise it if fuel_flow is provided?

I think it's best to remove this warning. I think it's mostly a historical artifact.

[review-notebook-app[bot]]

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