Run notebook examples in CI

[Saityi]

Issue

Our notebook examples easily go out of date, and it's hard to notice when it happens without a regular CI checking them

Fix

Convert notebook examples to Julia code and run them

Fix errors CI exposed:

• Graph was removed from visualization.jl, but was used by examples, especially older ones
• ClOUD -> CLOUD
• Graph -> GraphCL
• Remove Pkg.activate('../../../') in a causal loop example
• Fix a causal loop example to use vectors instead of tuples

Notes

Includes commits from #131 and verifies removing GraphViz did not break any examples. @KevinDCarlson

Also addresses https://github.com/AlgebraicJulia/StockFlow.jl/issues/113#issuecomment-1861809454

Misc

• Removed ipynb-checkpoints and add a more generalised pattern to exclude them
• Ignore vim & emacs temporary files
• Clean up a couple complaints from Aqua.jl around non-existent exports
• Renamed full_fledged_schema_examples/CaulsalLoopDiagrams to full_fledged_schema_examples/CausalLoopDiagrams

These tests can be run locally by running the helper script, validate-notebook-examples.sh, which does what the workflow does:

$ validate-notebook-examples.sh
Starting to run notebooks ...
Checking: ["./jlexamples/full_fledged_schema_examples.COVID_full_model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.Pertussis Model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.SEIR_full_model_measles_chickenpox.ipynb.jl", "./jlexamples/full_fledged_schema_examples.SIR_example_function_structure_test_compostion_and_stratification.ipynb.jl", "./jlexamples/full_fledged_schema_examples.composed open population SIRV model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.convert_from_SEIR_stockFlowDiagram.ipynb.jl", "./jlexamples/full_fledged_schema_examples.create_a_causalLoopDiagram.ipynb.jl", "./jlexamples/full_fledged_schema_examples.curable sexually transmitted diseases model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.diabetes model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.diabetes_diagnose.ipynb.jl", "./jlexamples/full_fledged_schema_examples.sex_transmission_SIS.ipynb.jl", "./jlexamples/full_fledged_schema_examples_new.COVID_full_model.ipynb.jl", "./jlexamples/
OK: Any["./jlexamples/full_fledged_schema_examples.COVID_full_model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.Pertussis Model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.SEIR_full_model_measles_chickenpox.ipynb.jl", "./jlexamples/full_fledged_schema_examples.SIR_example_function_structure_test_compostion_and_stratification.ipynb.jl", "./jlexamples/full_fledged_schema_examples.composed open population SIRV model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.convert_from_SEIR_stockFlowDiagram.ipynb.jl", "./jlexamples/full_fledged_schema_examples.create_a_causalLoopDiagram.ipynb.jl", "./jlexamples/full_fledged_schema_examples.curable sexually transmitted diseases model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.diabetes model.ipynb.jl", "./jlexamples/full_fledged_schema_examples.diabetes_diagnose.ipynb.jl", "./jlexamples/full_fledged_schema_examples.sex_transmission_SIS.ipynb.jl", "./jlexamples/full_fledged_schema_examples_new.COVID_full_model.ipynb.jl", "./jlexamples/ful

TODO

• In line with the comment in https://github.com/AlgebraicJulia/StockFlow.jl/pull/128#pullrequestreview-2236662771 we should consider renaming functions like Graph and what our 'display' API looks like going into a full initial 1.0
• Speed up notebook regression tests (e.g., parallelism in the test runner or performance improvements in the library).
  • I tried a simple speed up using the Threads.@threads on the for loop in the test runner, but was getting strange errors: Reason: LoadError: package StockFlow did not define the expected module StockFlow, check for typos in package module name

[KevinDCarlson]

Just a remark that the “official” way to accomplish what you’re doing here is with Literate.jl, which will generate Documenter files, notebooks, and scripts from the same markdown source, if you find that shell script inconvenient to maintain at some point.