[RTM?] Bug fix in holonomic torque dynamics

[p-shg]

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This fixes a bug in the dynamics of Holonomic Torque Driven
Bug was not covered by tests since example uses RK4 not COLLOCATION
As such, changed the example to collocation
Also commented out a lot of the compute_all_states because it has been unreliable lately and we only need q in this example. This last point should be discussed
@Ipuch

---

This change is 

[Ipuch]

Modify the related test that is failing
add the decorator @pytest.parametrize("ode_solver", [OdeSolver.Rk4, OdeSolver.COLLOCATION])
add a if for the collocation values.

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

---

bioptim/examples/holonomic_constraints/two_pendulums.py line 84 at r1 (raw file):

        # )

    return q  # , qdot, qddot, lambdas

Decomment

Code quote:

        # qdot[:, i] = bio_model.compute_qdot()(q[:, i], states["qdot_u"][:, i]).toarray().squeeze()
        # qddot_u_i = (
        #     bio_model.partitioned_forward_dynamics()(
        #         states["q_u"][:, i], states["qdot_u"][:, i], q_v_init[:, i], tau[:, i]
        #     )
        #     .toarray()
        #     .squeeze()
        # )
        # qddot[:, i] = bio_model.compute_qddot()(q[:, i], qdot[:, i], qddot_u_i).toarray().squeeze()
        # lambdas[:, i] = (
        #     bio_model.compute_the_lagrangian_multipliers()(
        #         states["q_u"][:, i][:, np.newaxis], states["qdot_u"][:, i], q_v_init[:, i], tau[:, i]
        #     )
        #     .toarray()
        #     .squeeze()
        # )

    return q  # , qdot, qddot, lambdas

---

bioptim/examples/holonomic_constraints/two_pendulums.py line 91 at r1 (raw file):

    n_shooting: int = 30,
    final_time: float = 1,
    expand_dynamics: bool = False,

add ode_solvers: odeSolver = OdeSolver.RK4,

Code quote:

expand_dynamics: bool = False,

---

bioptim/examples/holonomic_constraints/two_pendulums.py line 140 at r1 (raw file):

    # Dynamics
    dynamics = DynamicsOptionsList()
    dynamics.add(DynamicsOptions(ode_solver=OdeSolver.COLLOCATION(), expand_dynamics=expand_dynamics))

RK4

[p-shg]

All comments should have been taken into account @Ipuch @pariterre

[pariterre]

@pariterre reviewed 3 of 3 files at r2, all commit messages.
Reviewable status: all files reviewed, 3 unresolved discussions (waiting on @p-shg)

[pariterre]

@p-shg please merge with master and resolve the conflict, then its RTM for me :)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.28%. Comparing base (0b6be62) to head (71dcb2e).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1021      +/-   ##
==========================================
+ Coverage   77.26%   77.28%   +0.02%     
==========================================
  Files         184      184              
  Lines       20339    20339              
==========================================
+ Hits        15714    15720       +6     
+ Misses       4625     4619       -6     

Flag	Coverage Δ
unittests	77.28% <100.00%> (+0.02%)	⬆️

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[p-shg]

I think we're good
Tests related to the new examples are in another PR. Working on it

[pariterre]

@pariterre reviewed 13 of 13 files at r3, all commit messages.
Reviewable status: all files reviewed, 3 unresolved discussions (waiting on @p-shg)

[pariterre]

@p-shg
Can you add tests to these examples, then we can merge both PR associated with the examples

[p-shg]

Tests should be ok on my side
RTM ?

[Ipuch]

handled in #1024