[RTM after next push] SOCP: Making the noise dependant on the states + controls

[EveCharbie]

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 5 of 36 files at r1, 1 of 7 files at r2, 21 of 34 files at r3, 13 of 13 files at r4, all commit messages.
Reviewable status: all files reviewed, 5 unresolved discussions (waiting on @EveCharbie)

---

bioptim/dynamics/dynamics_functions.py line 645 at r4 (raw file):

        """

        q = nlp.get_var_from_states_or_controls("q", states, controls)

add the capability to send algebraic too

---

bioptim/examples/stochastic_optimal_control/arm_reaching_muscle_driven.py line 711 at r4 (raw file):

        nlp = socp.nlp[0]
        out = stochastic_forward_dynamics(
            None,

None?

---

bioptim/examples/torque_driven_ocp/minimize_maximum_torque_by_extra_parameter.py line 133 at r4 (raw file):

    x_init = InitialGuessList()
    x_init.add(key="q_roots", initial_guess=[0] * n_root, phase=0)
    x_init.add(key="q_jointss", initial_guess=[0] * n_tau, phase=0)

Typo? Remove the capability to declare unused variable?

---

bioptim/models/protocols/biomodel.py line 88 at r4 (raw file):

        return ()

    def biorbd_homogeneous_matrices_in_global(self, q, segment_id, inverse=False) -> tuple:

This should not be in the Protocol

nlp.model: BiorbdModel

---

bioptim/optimization/non_linear_program.py line 521 at r4 (raw file):

        return self.tf / self.ns * node_idx

    def get_var_from_states_or_controls(self, key: str, states: MX.sym, controls: MX.sym) -> MX:

Add the capability to send algebraic

[EveCharbie]

Reviewable status: 36 of 47 files reviewed, 4 unresolved discussions (waiting on @pariterre)

---

bioptim/dynamics/dynamics_functions.py line 645 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

add the capability to send algebraic too

Done.

---

bioptim/examples/stochastic_optimal_control/arm_reaching_muscle_driven.py line 711 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

None?

Done.

---

bioptim/models/protocols/biomodel.py line 88 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

This should not be in the Protocol

nlp.model: BiorbdModel

Done.

---

bioptim/optimization/non_linear_program.py line 521 at r4 (raw file):

Previously, pariterre (Pariterre) wrote…

Add the capability to send algebraic

Done.

[pariterre]

Reviewed 58 of 58 files at r5, all commit messages.
Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @EveCharbie)

---

bioptim/gui/plot.py line 388 at r5 (raw file):

                            )
                            if variable in nlp.plot
                            else 0

Verify that

---

tests/shard5/test_global_stochastic_collocation.py line 384 at r5 (raw file):

    # First collocation state is equal to the states at node
    const = socp.nlp[0].g_internal[1]

constraint

[EveCharbie]

Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @pariterre)

---

bioptim/gui/plot.py line 388 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Verify that

reverted deleted lines

---

tests/shard5/test_global_stochastic_collocation.py line 384 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

constraint

Done.

[pariterre]

Reviewed 2 of 2 files at r6, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @EveCharbie)

[EveCharbie]

@pariterre should be fine

[pariterre]

Reviewed 7 of 7 files at r7, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @EveCharbie)

[codecov]

Codecov Report

Attention: 241 lines in your changes are missing coverage. Please review.

Comparison is base (d2e6dad) 78.90% compared to head (c02d206) 78.39%.
Report is 75 commits behind head on master.

Files	Patch %	Lines
...optimization/stochastic_optimal_control_program.py	8.08%	91 Missing ⚠️
bioptim/dynamics/dynamics_functions.py	70.37%	24 Missing ⚠️
bioptim/dynamics/configure_problem.py	54.16%	22 Missing ⚠️
bioptim/limits/constraints.py	37.93%	18 Missing ⚠️
bioptim/models/biorbd/biorbd_model.py	57.50%	17 Missing ⚠️
bioptim/models/biorbd/stochastic_biorbd_model.py	14.28%	12 Missing ⚠️
bioptim/models/utils.py	64.28%	10 Missing ⚠️
bioptim/limits/penalty_controller.py	66.66%	9 Missing ⚠️
bioptim/models/protocols/stochastic_biomodel.py	25.00%	9 Missing ⚠️
bioptim/optimization/non_linear_program.py	74.07%	7 Missing ⚠️
... and 8 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #809      +/-   ##
==========================================
- Coverage   78.90%   78.39%   -0.51%     
==========================================
  Files         139      140       +1     
  Lines       15721    16081     +360     
==========================================
+ Hits        12404    12607     +203     
- Misses       3317     3474     +157     

Flag	Coverage Δ
unittests	78.39% <60.09%> (-0.51%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

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[pariterre]

Reviewed 1 of 1 files at r9, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @EveCharbie)