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Wrap-up task list for the CZI Biomechanics project #25508
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I just noticed that the state variables in the muscles are not functions of time, they seem to be simple symbols. We rely heavily on differentiating constants from time varying variables in mechanics by using |
I suggest that we get all the stuff into non-public |
@brocksam I've completed my parts of the two tutorial pages (I think). Once you add the remaining two parts it should be ready to merge. I can open a PR for making _biomechanics public, but were all the docstrings and unit tests completed? I wasn't sure the status. |
I'll add my remaining two parts to the tutorial pages tomorrow to complete that PR. You're correct that we still need some docstrings and tests. I'll hopefully get the vital ones done tomorrow too and then I'll open the PR to make the module public. I'll also open issue for the remaining "nice to haves". |
I've opened #25744 which will encapsulate the majority of the outstanding things in this list. Following the merging of #25744, we can open a PR to make the biomechanics module public. Then following that we will be able to fix the Sphinx errors related to the "missing" biomechanics module in #25525. That should then complete the biomechanics portion of our CZI work. |
Ok, sounds good. Let me know when you are ready for review or if you need help on it. |
General
Merge in remaining functionality
cos(alpha_opt)
in rigid tendon musculotendon dynamicsFiberForceVelocityInverseDeGroote2016
in fiber state elastic tendon musculotendon dynamics.WrappingPathway
insympy.physics.mechanics
#25400ObstacleSetPathway
insympy.physics.mechanics
#25424mechanics._geometry
->mechanics.geometry
(publicizing: Makephysics.mechanics.wrapping_geometry
public #25510)mechanics._pathway
->mechanics.pathway
(publicizing: Makephysics.mechanics.pathway
public. #25511)mechanics._actuator
->mechanics.actuator
Make _actuator.py public. #25518sympy.physics._biomechanics
#25441sympy.physics._biomechanics
#25509sympy.physics._biomechanics
#25516sympy.physics._biomechanics
#25519sympy.physics._biomechanics
#25530sympy.physics._biomechanics
#25539sympy.physics._biomechanics
#25742sympy.physics._biomechanics.curve
#25549sympy.physics._biomechanics
#25743_NamedMixin
mixin class for adding error-checkedname
attribute to classes #25540sympy.physics._biomechanics
#25548sympy.physics._biomechanics
#25553sympy.physics._biomechanics
#25567mechanics.actuator
/mechanics.tests.test_actuator
mechanics.pathway
/mechanics.tests.test_pathway
mechanics.wrapping_geometry
/mechanics.tests.test_wrapping_geometry
biomechanics.curves
/biomechanics.tests.test_curves
sympy.physics.biomechanics
public #25772physics.biomechanics
. Created a new module that acts to extend physics.mechanics with biomechanical modelling functionality.physics.biomechanics
. Implemented musculotendon characteristic curves for tendon and muscle fiber force-length and force-velocity relationships based on De Groote et al., 2016.MusculotendonBase
class #25787Other
To-do requests
These should all be opened as issues if they don't get completely by 31/08/2023.
sympy.physics._biomechanics
#25744__str__
to biomechanical modeling components.PathwayBase
classes.subs
kwargs onto_loads
methods.rhs
method onMusculotendonDeGroote2016
to return simplified RHS equations.MusculotendonBase
class betweenForceActuator
andMusculotendonDeGroote2016
as most musculotendon implementation will be generic to any musculotendon.MusculotendonDeGroote2016
for linking to the...DeGroote2016
musculotendon curves, e.g.MusculotendonDeGroote2016.curves.tendon_force_length = TendonForceLengthDeGroote2016
withMusculotendonDeGroote2016.tendon_force_length
pointing to the musculotendon dynamics-specific instance.Unit test coverage
Docstrings
Create examples in documentation
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