Simplification of the definition of projects to run in GitHub actions

[vincent-noel]

I wrote a simpler version of the GitHub actions, using what's called a matrix: https://docs.github.com/en/actions/using-jobs/using-a-matrix-for-your-jobs

We define the list of projects to run like this:

projects: [
          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample"},
          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines"},
          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project"},
          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Initialisation/mymodel_initialisation.xml"},
          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Cell_Fibre_Mechanics/mymodel_rotating.xml"},
          {project: "template", name: "PhysiCell Template", binary: "project"}
]

Each element needs a project, which is the name used when running make <project>, a name, the filename of the binary file, and the optional path of a config file.
This needs to be set up for all the different runners: macos-12 (x86_64), macos-14 (arm64), linux, windows. But the syntax is exactly the same.

[vincent-noel]

Now I have tests which also compare the first SVG from the output to some reference, stored in tests/cases/output_{project_name}.
Projects are defined like this :

projects: [
   {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
   {project: "heterogeneity-sample", name: "PhysiCell Heterogeneity", binary: "heterogeneity", max_time: 99, config: "config/PhysiCell_settings.xml", output_folder: "output"},
   {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
   {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
]

So basically the same as above, plus a max_time, and an output folder. This will compare all the SVGs generated in the output folder until max_time, to their reference. So a new project needs a new definition here, plus the reference SVGs.

It compiles the project, and then use two scripts based on Randy's work:

• One which modifies the XML definition to use only one core, and limit the simulation time to max_time (beta/test_run_sample.py)
• One which runs the diff tools, and checks the result (beta/test_diff_svg.py)