[RTR]PR changes for ligaments

[AntoineLeroy]

few changes to prepare arrival of ligaments in bioptim

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Changes to Core Features:

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This change is 

[codecov]

Codecov Report

Patch coverage: 83.01% and project coverage change: -0.03 ⚠️

Comparison is base (354ee4e) 81.69% compared to head (702b59f) 81.67%.

❗ Current head 702b59f differs from pull request most recent head 619af4d. Consider uploading reports for the commit 619af4d to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #614      +/-   ##
==========================================
- Coverage   81.69%   81.67%   -0.03%     
==========================================
  Files         107      107              
  Lines       11849    11850       +1     
==========================================
- Hits         9680     9678       -2     
- Misses       2169     2172       +3     

Impacted Files	Coverage Δ
bioptim/limits/constraints.py	82.78% <66.66%> (-0.18%)	⬇️
...amples/torque_driven_ocp/ocp_mass_with_ligament.py	75.75% <75.75%> (ø)
bioptim/dynamics/configure_problem.py	90.97% <100.00%> (-0.18%)	⬇️
bioptim/dynamics/dynamics_functions.py	94.46% <100.00%> (+0.08%)	⬆️
bioptim/interfaces/biomodel.py	100.00% <100.00%> (ø)
bioptim/interfaces/biorbd_model.py	94.79% <100.00%> (+0.03%)	⬆️
bioptim/optimization/optimal_control_program.py	87.13% <100.00%> (ø)
... and 3 more

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[pariterre]

Reviewed 6 of 6 files at r1, 3 of 3 files at r2, 1 of 3 files at r3, 9 of 9 files at r4, all commit messages.
Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @AntoineLeroy)

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tests/test_ligaments.py line 357 at r4 (raw file):

            # initial and final position
            np.testing.assert_almost_equal(q[:, 0], np.array([0.0]))
            np.testing.assert_almost_equal(q[:, -1], np.array([-3.1415927]))

Why these values changed?

Code quote:

3.1415927])

---

bioptim/examples/torque_driven_ocp/ocp_mass_with_ligament.py line 72 at r4 (raw file):

        )
        u_init.add([tau_init] * bio_model.nb_tau)
    else:

please use elif for all of the case and raise a NotImplementedYet if it gets to else

[AntoineLeroy]

Reviewable status: 10 of 11 files reviewed, 2 unresolved discussions (waiting on @pariterre)

---

tests/test_ligaments.py line 357 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

Why these values changed?

because these are the right values for the test to pass

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bioptim/examples/torque_driven_ocp/ocp_mass_with_ligament.py line 72 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

please use elif for all of the case and raise a NotImplementedYet if it gets to else

Done.

[pariterre]

Reviewed 1 of 1 files at r5, all commit messages.
Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @AntoineLeroy)

---

tests/test_ligaments.py line 357 at r4 (raw file):

Previously, AntoineLeroy wrote…

because these are the right values for the test to pass

I understand that these are the current values for the tests to pass, but why did it changed? Making the tests passing is not the goal, the goal is that it returns the right answer. I am asking, what did you change that made these values change and are we sure it is intended

[AntoineLeroy]

Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @pariterre)

---

tests/test_ligaments.py line 357 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

I understand that these are the current values for the tests to pass, but why did it changed? Making the tests passing is not the goal, the goal is that it returns the right answer. I am asking, what did you change that made these values change and are we sure it is intended

This is a test I created specifically for this PR and the change is from RigidBodyDynamics.ODE to RigidBodyDynamics.DAE_FORWARD_DYNAMICS and RigidBodyDynamics.DAE_FINVERSE_DYNAMICS. I just wanted to test the last two.

[pariterre]

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