examples: refactors

[Ipuch]

Following

• [RTR] Walking example #991
• Issue installing Acados #993

With @EveCharbie, we were thinking about the following step to make the examples more clear to new users. This is really critical that someone tried to install bioptim and failed because she went into the first folder 'acados' and failed because it's complicated to install. We should guide more the users to their insterests.

1. GUI presented in the readme Added information about the GUI examples in the ReadMe #1001 and Added GUI to launch.json #1003
2. Re-organize models in a common folder instead of duplicating them among all the subfolders with their geometries [RTM] Moving examples #1023
3. Add Opensim models as a submodules to lighten the bioptim folder
4. Categorize examples into three categories :

• toy examples [RTM] Moving examples #1023
• biomech examples
• and feature examples.

[pariterre]

Great points

Maybe we should also put more forward the GUI that allows to run all these examples?

[pariterre]

@EveCharbie
I made you change the name of the "biomechanics-model". After discussing with @Ipuch , having a proper model repo would be an additionnal (and useless) burden on us. He proposed to actually only fork the folder and never think about it again (as opposed to what we discussed last time where I thought the goal would be to populate the repo with plenty of models).

So the suggestion would be to revert back the name of the repo, then add a submodule in bioptim following this structure

To discuss together next time

[CdrSonan]

When trying to run the examples by using the command
python -m bioptim.examples
and then selecting a script requiring a model in the GUI, I get the following error:
RuntimeError: File /opt/miniconda3/envs/bioptim/lib/python3.13/site-packages/bioptim/examples/models/cube.bioMod could not be open
Looking at the folder structure, the models folder is not present, only the getting_started and toy_examples folders are.
I am using the latest version of the Conda package (3.3.1), so presumably something is going wrong with packaging right now.

[pariterre]

Hi @CdrSonan !
Thanks for reporting! That is probably due to a previous move of the examples that was done last month. I will fix this soon and let you know!

[pariterre]

The PR #1033 should solve this issue, when it is merged and pushed (probably version 3.4.0), it should work.
Until then, if you are able to install bioptim via the source, you can clone the bioptim folder from my fork (https://github.com/pariterre/pyomeca) and install it using pip install .

Thanks again for reporting

[CdrSonan]

Thank you very much!

[pariterre]

@CdrSonan The update is done :)