Moving opensim-moco into opensim-core

opensim-org / opensim-core

SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

https://opensim.stanford.edu

Apache License 2.0

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Moving opensim-moco into opensim-core #2559

Closed chrisdembia closed 3 years ago

chrisdembia commented 5 years ago

The opensim-moco contains a lot of code that belongs better in opensim-core. Here's a list:

[x] ModelProcessor #2712
[x] TableProcessor #2713
[x] analyze() #2718
[x] visualize() #2717
[x] DeGrooteFregly2016Muscle #2714
[x] ModelFactory #2715
[x] Stopwatch
[x] Catch2 testing framework #2716
[x] format()
[x] SmoothSphereHalfspaceForce
[x] ActivationCoordinateActuator
[x] requiring numpy for python bindings.
[x] Combine Moco's doxygen with opensim-core's.
[ ] What to do with build_on_* scripts?
[x] Should opensim-models still be a submodule?
[ ] Merge CHANGELOG and README?
[x] Update opensim-cmd to support running .omoco files.

@nickbianco feel free to add to this list.

Proposal in Google Doc: https://docs.google.com/document/d/10SiVJGqMJxiXtiDdI4Ozpxf5HTKHaixX_ynymYuJwk4/edit?usp=sharing

aymanhab commented 4 years ago

Moving DeGroote muscle to opensim-core is high priority so that users don't have to juggle muscle models to use/visualize results from Moco in GUI. What is involved @chrisdembia @nickbianco ?

jenhicks commented 4 years ago

@chrisdembia Is this issue up-to-date? I think one key task we talked about was formulating a plan/rough timeline for integration. Let us know how we can help. I chatted with Scott a couple weeks ago and he agreed that the integration sounded like a good plan (in terms of how we spend development resources/time). @aymanhab

chrisdembia commented 4 years ago

I've started working on requiring NumPy for the Python bindings.

chrisdembia commented 4 years ago

I created a branch in this repo moco into which I've merged the opensim-moco repository. I roughly followed these steps to perform the merge: https://stackoverflow.com/questions/1425892/how-do-you-merge-two-git-repositories

The merge had the conflicts listed below; I attempted to merge these files but more work must still be done here.

warning: Cannot merge binary files: .github/.deploy_myosin_sourceforge_rsa.enc (HEAD vs. moco/master) dependencies/CMakeLists.txt cmake/CMakeLists.txt README.md CONTRIBUTING.md CMakeLists.txt CHANGELOG.md .travis.yml .gitignore .github/workflows/continuous_integration.yml .github/PULL_REQUEST_TEMPLATE.md .github/.deploy_myosin_sourceforge_rsa.enc .gitattributes .clang-format

chrisdembia commented 4 years ago

I've encountered an issue with Moco and doxygen. I created a doxygen but report: https://github.com/doxygen/doxygen/issues/7873