Implementation of the STEMMUS_SCOPE BMI, +docs +gprc4bmi

[BSchilperoort]

This is the full implementation of the STEMMUS_SCOPE Basic Model Interface in Python, built upon the Matlab Compiler Runtime (MCR) executable file generated on Snellius.

The communication goes through an open subprocess of STEMMUS_SCOPE running in "interactive" mode (see EcoExtreML/STEMMUS_SCOPE#208). As overhead of MCR starting up is about 5 seconds.

Based on the state that the model wrote to file (the entire workspace), all requires functions including getters and setters can be implemented. With h5py the state file can be modified in-place. This makes the Python overhead per time step <0.10 seconds.

Todo:

• Add time functionality
• Add update_until
• Check if all required grid functions are implemented
• Add set/get value at indices

As a follow up to this PR, the variable list can be extended (see EcoExtreML/STEMMUS_SCOPE#209).

Additionally, the model (with the MCR dependencies) can be packaged in a container. This will allow for:

1. communicating with the container directly from Python (using the BMI of this PR). Done!
2. extending the image of 1. and adding this BMI + grpc4bmi to make the model compatible with systems such as eWaterCycle. Done!

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Update:

The main way of running the BMI is now through docker. Tests with the docker image communication run on CI, allowing us to test the entire BMI interface.
A local option is still available (if you run Linux), which is also required to be able to make a grpc4bmi container.

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[BSchilperoort]

@SarahAlidoost this PR is also ready to review. It should be compatible with the STEMMUS_SCOPE executable in the PR there. Do note that you'll have to mark that file as executable ("allow executing file as program").

[SarahAlidoost]

@BSchilperoort thanks 👍 I was able to run the bmi with local exe but not with docker. please see my comments. One more point, can you please move all bmi and docker to a directory e.g. "bmi"? Another one, if we can pull the image automatically?

[sonarcloud]

Quality Gate failed

Failed conditions

78.2% Coverage on New Code (required ≥ 80%)

See analysis details on SonarCloud

[SarahAlidoost]

@BSchilperoort thanks for the fixes. I was able to run the notebook 🎉 Let's merge this PR 🚀