Pull request for adding simple command line based tutorial.

[BJackal]

Added two new tutorials for executing Chaste tests with command line arguments through bash scripts.

The first is a very simple Hello World style example which takes in multiple command line arguments and outputs the sum. For now this has been placed in global as it seemed the most appropriate location.

Another example has been added for running a bash script with command line arguments to execute multiple vertex based simulations with the height and width of tissue based on command line parameters. This is a slightly expanded version of the vertex based simulation tutorial.

[mirams]

Sounds as if it will make the test pack fail as well then? We can't really be having that, might need to put heads together on how to do a tutorial a different way...

It should be easy to do an "overwriting defaults" using e.g.

unsigned outp1 = 0;
if CommandLineArguments::Instance()->OptionExists("-opt1")
{
    outp1 = CommandLineArguments::Instance()->GetUnsignedCorrespondingToOption("-opt1");
}

and then we can put in comments saying "Please rerun the executable with arguments to see how the output changes, but note you will have to do this outside the ctest framework".

[BJackal]

I can think of one alternative way. The test could have some default conditions that are ran if command line arguments are not detected. Allowing the tutorial to simply run with those default initial conditions.

[BJackal]

This will similarly be changed for TestCommandLineArgumentsTutorial

[mirams]

A few suggestions, I think I would simplify quite a bit as there's nothing vertexey or cell based about wanting to pass in arguments, and would complicate the tutorial to show off more of the capabilities of the CommandLineArguments class!

[BJackal]

1. Removed the vertex based simulation and its accompanying bash script.
2. Added a secondary test for the TestCommandLineArgumentsTutorial using a vector of doubles as the input.
3. Added a commented section to each test with the required bash script to run them, by default left the simpler test as the pre-existing bash script.
4. Changed int in the first test to unsigned as suggested.
5. The bash script to take in doubles requires awk (or a similar other tool) to allow for doubles to be input as arguments.
6. Added a default case for each test if the correct corresponding command line argument is not detected to prevent the test failing.

Possible further additions I can think of now, it may be best to add some simple testing into the default cases or exceptions/assertions to ensure it is running as expected. Additionally , as the CommandLineArguments has the GetBoolCorrespondingToOption method should a test just showing this also be added ?

[mirams]

A few tweaks @BJackal I think it is getting there, the main one is probably to just get the tutorial to put the bash script in a code block, and give instructions to copy and paste into a bash script in the build folder, then you can remove the script and the need for hardcoded paths I think.

[mirams]

(you can manually run the generate tutorials and website build to see how the generated webpage looks following these instructions: #193 (comment))

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (e26ac25) to head (b3b2fad).
Report is 33 commits behind head on develop.

❗ Current head b3b2fad differs from pull request most recent head 2d19b79

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  Coverage   100.00%   100.00%           
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  Files         1029      1029           
  Lines        51386     51383    -3     
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- Hits         51386     51383    -3     

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[mirams]

Didn't mean to delete branch, we'll do that when ticket is closed!

We'll want to add (manually) an entry to the "Core Functionality" part of the menu page: https://chaste.github.io/docs/user-tutorials/