[RTR] BioBuddy interface

[EveCharbie]

Answering to Issue #62

I have some questions:

1. Why is GlobalJCS(q) called for reach segments independently instead of for all segments at the same time and then using each segment in the matrix (ex: all_gcj[segment_idx, :] ?
2. Where are the tests for the model interfaces (so that I can test that I implemented everything correctly) ?
3. @pariterre is the key word ranges or rangesq or both recognized by biorbd ?

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This change is 

[pariterre]

Why is GlobalJCS(q)

If "False" is sent as update_kinematics, then is does not cost much. That said, getting all at the same time is definitely more elegant

is the key word ranges or rangesq or both recognized by biorbd

Yep

[Ipuch]

@Ipuch reviewed 5 of 5 files at r1, all commit messages.
Reviewable status: all files reviewed, 3 unresolved discussions (waiting on @EveCharbie)

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pyorerun/__init__.py line 23 at r1 (raw file):

    )
except ImportError:
    # BioBuddy is not installed, these classes will not be available

if you want to make a hard dependancy it's okay.

Code quote:

    from .model_interfaces import (
        BiobuddyModel,
        BiobuddyModelNoMesh,
    )
except ImportError:
    # BioBuddy is not installed, these classes will not be available

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examples/biobuddy/models/Wu_Shoulder_Model_kinova_scaled_adjusted_2.bioMod line 1 at r1 (raw file):

version 4

modified this after the paths and the biorbd interface.

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pyorerun/model_interfaces/__init__.py line 15 at r1 (raw file):

    from .biobuddy_model_interface import BiobuddyModelNoMesh, BiobuddyModel
except ImportError:
    # BioBuddy is not installed, these classes will not be available

same comment

Code quote:

try:
    from .osim_model_interface import OsimModelNoMesh, OsimModel
except ImportError:
    # OpenSim is not installed, these classes will not be available
    pass

# Biobuddy
try:
    from .biobuddy_model_interface import BiobuddyModelNoMesh, BiobuddyModel
except ImportError:
    # BioBuddy is not installed, these classes will not be available

[Ipuch]

@EveCharbie I don't remember what was the pb here, do you remember?

[EveCharbie]

@Ipuch The problem was the model duplicate. I just fixed it. Let me know if it's OK for you :)

[Ipuch]

One final requirement for me to merge safely. I need to know to which version of biobuddy we need to stick.

• Can you add a line, to the README for the optional dependency next to Opensim.
• Can you make sure we have a proper version for the example, and thus, specify it in the example docstring.

conda install -c conda-forge biobuddy=XX.XX.X

[EveCharbie]

Made the requested changes, will have to wait tonight to publish the new version on pip

[EveCharbie]

@Ipuch published BioBuddy v0.2.0 to pip :)