Adam TODO before deferring some TODO items to another PR:

• ensure branch is stable
• bring in library conflict -- should be a single change from radiation force extrapolation

@kmruehl this PR is ready for review. I was able to get the few top-level mask initialization functions moved to .m files, but not the rest. I believe all of the applications cases run. The regression tests fail but I don't know their most recent status.

I was not able to update documentation yet to reflect the removal of the nonhydro body

Thanks @akeeste I'm making a few revisions to the library:

• updating all library files to 2020b
• naming all libraries so that they are alphabetically grouped, e.g., lib_body_drag and lib_body_hydro, instead of lib_drag_body and lib_hydro_body
• resolving the linking between the main library and the bodies library

Okay, after discussion between @akeeste and @kmruehl, this PR has changed scope significantly and now does the following:

• removes the nonhydro body and replaces it with the drag body
  • The flag body.nonHydro can take values of 0, 1, 2, but now values of 1 and 2 both result in a drag body for backwards compatibility
  • bodyClass pre-processing, initializeWecSim and the docs are updated appropriately
• removes the WEC-Sim GUI from all library files due to the maintenance burden
  • documentation on this is removed
  • the runFromSimTest.m is still presented but heavily simplified
  • the RM3FromSimulink example is removed. It was actually a WEC-Sim GUI example and demonstrating the ability to run from Simulink does not require a separate example case. It will work with any case

The body types are no longer split into multiple files because it does not add value and increases burden on the user

@akeeste is this ready for review?

I'm still having issues with the Simulink Library rendering. I'm running MATLAB 2024a. Maybe someone else on the team can check to see if they're having the same issue?

I'm still having issues with the Simulink Library rendering. I'm running MATLAB 2024a. Maybe someone else on the team can check to see if they're having the same issue?

I am actually having this issue on this PR, main and dev, so it must be an issue on my end. Furthermore, @jtgrasb confirmed that he does not have this issue viewing the library. I'm going to reinstall MATLAB, and upgrade to 2025a.

@kmruehl Yes this is ready for review.

I'm not sure what's causing the library appearance issue. On R2024b PTO-Sim renders fine but not the rest. I agree that maybe it's a MATLAB version problem

@akeeste that's the same for me with 2024a. PTO-Sim renders properly, but nothing else does.

Everything renders properly for me on 2025a and @jtgrasb confirmed that 2023b renders properly, so it must be an issue with the 2024a and 2024b distributions. I don't think it's worth debugging because the library blocks still work, they just don't render in the library. I'm just mentioning it in this thread for future awareness.

@akeeste I made some very minor updates towards the requested changes. Let's chat about how to get these revisions done and merging the PR. Thanks!

Also, why are the tests failing?

Thanks @kmruehl I'll make the requested changes. I don't know why the tests are failing. They have not run consistently for a while and the regression were only recently fixed

It looks like the tests are not running to completion, I'll look into that too

I'm not sure why there tests are having issues that they weren't before, but I also fixed that. They were failing on the 2nd regression test because the RM3 simulink file from the previous one was still open, leading to conflicts with open models on the path. I force close all simulink models after each regression test

Tests finally passing. Merged

Thanks @akeeste