Add residual torque to TORQUE_ACTIVATIONS_DRIVEN function

[AnaisFarr]

All Submissions:

• Have you followed the guidelines in our Contributing document [docs/contribution.md]?
• Have you checked to ensure there aren't other open [Pull Requests] for the same update/change?
• Have you opened/linked the issue related to your pull request?
• Have you used the tag [WIP] for on-going changes, and removed it when the pull request was ready?
• When ready to merge, have you sent a comment pinging @pariterre in it?

New Feature Submissions:

1. Does your submission pass the tests (if not please explain why this is intended)?
2. Did you write a proper documentation (docstrings and ReadMe)
3. Have you linted your code locally prior to submission (using the command: black . -l120 --exclude "external/*")?

Changes to Core Features:

• Have you added an explanation of what your changes do and why you'd like us to include them?
• Have you written new examples for your core changes, as applicable?
• Have you written new tests for your core changes, as applicable?

---

This change is 

[pariterre]

Reviewed 19 of 19 files at r1, all commit messages.
Reviewable status: all files reviewed, 4 unresolved discussions (waiting on @AnaisFarr)

---

bioptim/dynamics/configure_problem.py line 1233 at r1 (raw file):

        name = "residual_tau"
        name_residual_tau = ConfigureProblem._get_kinematics_based_names(nlp, name)
        ConfigureProblem._adjust_mapping(name, ["qdot", "taudot"], nlp)  ### @pariterre???

I agree

Code quote:

### @pariterre???

---

bioptim/dynamics/dynamics_functions.py line 270 at r1 (raw file):

            tau_residual = DynamicsFunctions.get(nlp.controls["residual_tau"], controls)
        tau = nlp.model.torque(tau_activation, q, qdot)
        tau = tau + tau_residual if with_residual_torque else tau

Please add the ():
(tau + tau_residual) if with_residual_torque else tau

Code quote:

tau + tau_residual if with_residual_torque else tau

---

bioptim/dynamics/dynamics_functions.py line 271 at r1 (raw file):

        tau = nlp.model.torque(tau_activation, q, qdot)
        tau = tau + tau_residual if with_residual_torque else tau
        tau = tau + nlp.model.passive_joint_torque(q, qdot) if with_passive_torque else tau

Add the () here too, just to make sure

---

bioptim/examples/torque_driven_ocp/residual_torque_actuator.py line 2 at r1 (raw file):

"""
This is an example of the use of torque actuator using a model of 2 segments and 2 degrees of freedom

torque_activation_driven.py ?

[pariterre]

Please black with -l120 (and not the default -l80)

Reviewable status: all files reviewed, 4 unresolved discussions (waiting on @AnaisFarr)

[pariterre]

Reviewed 14 of 14 files at r2, all commit messages.
Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @AnaisFarr)

---

bioptim/examples/torque_driven_ocp/residual_torque_actuator.py line 2 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

torque_activation_driven.py ?

Please change this file name

---

bioptim/examples/torque_driven_ocp/residual_torque_actuator.py line 121 at r2 (raw file):

    sol.print_cost()
    print(sol.states)
    print(sol.controls)

Do not add these prints

Code quote:

    print(sol.states)
    print(sol.controls)

[codecov]

Codecov Report

Patch coverage: 84.37% and project coverage change: +0.01 🎉

Comparison is base (91ace20) 81.67% compared to head (55da867) 81.69%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #623      +/-   ##
==========================================
+ Coverage   81.67%   81.69%   +0.01%     
==========================================
  Files         106      107       +1     
  Lines       11805    11849      +44     
==========================================
+ Hits         9642     9680      +38     
- Misses       2163     2169       +6     

Impacted Files	Coverage Δ
...act/contact_forces_inequality_constraint_muscle.py	13.46% <0.00%> (ø)
...ith_contact/muscle_activations_contacts_tracker.py	22.44% <0.00%> (ø)
...es/muscle_driven_ocp/muscle_activations_tracker.py	76.14% <50.00%> (ø)
...ples/torque_driven_ocp/torque_activation_driven.py	81.81% <81.81%> (ø)
bioptim/dynamics/configure_problem.py	91.15% <100.00%> (+0.17%)	⬆️
bioptim/dynamics/dynamics_functions.py	94.38% <100.00%> (+0.06%)	⬆️
bioptim/examples/acados/static_arm.py	42.85% <100.00%> (ø)
...ioptim/examples/fatigue/static_arm_with_fatigue.py	67.85% <100.00%> (ø)
...xamples/getting_started/example_external_forces.py	87.87% <100.00%> (ø)
...es/muscle_driven_ocp/muscle_excitations_tracker.py	73.63% <100.00%> (ø)
... and 3 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

[AnaisFarr]

Ready to merge @pariterre

[pariterre]

Reviewed 5 of 5 files at r3, 1 of 1 files at r4, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @EveCharbie)

[pariterre]

Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @EveCharbie)