[RTR] StochastiOCP merge

[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?

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This change is 

[EveCharbie]

@pariterre think we could merge?

[codecov]

Codecov Report

Patch coverage: 79.75% and project coverage change: -0.31 ⚠️

Comparison is base (fe6bb40) 81.75% compared to head (377de7b) 81.44%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #715      +/-   ##
==========================================
- Coverage   81.75%   81.44%   -0.31%     
==========================================
  Files         124      129       +5     
  Lines       14059    15466    +1407     
==========================================
+ Hits        11494    12597    +1103     
- Misses       2565     2869     +304     

Impacted Files	Coverage Δ
...les/custom_model/custom_package/custom_dynamics.py	100.00% <ø> (ø)
...ioptim/examples/getting_started/custom_dynamics.py	88.88% <ø> (ø)
...es/muscle_driven_ocp/muscle_activations_tracker.py	76.99% <ø> (ø)
...es/muscle_driven_ocp/muscle_excitations_tracker.py	74.13% <ø> (ø)
bioptim/interfaces/biomodel.py	81.00% <ø> (ø)
...ptimization/variational_optimal_control_program.py	86.70% <ø> (ø)
bioptim/limits/penalty.py	88.56% <50.00%> (-0.73%)	⬇️
bioptim/limits/multinode_penalty.py	76.11% <51.42%> (-5.21%)	⬇️
bioptim/gui/check_conditioning.py	80.72% <52.63%> (-2.94%)	⬇️
bioptim/gui/plot.py	71.53% <55.55%> (-1.22%)	⬇️
... and 30 more

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[pariterre]

Only two minors comment and we are good to go!

Reviewed 33 of 33 files at r3, all commit messages.
Reviewable status: all files reviewed, 4 unresolved discussions (waiting on @EveCharbie)

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OCP_equation.png line 0 at r3 (raw file):
Is this useful/mandatory? If so, could it be replaced by a <100kB file?

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bioptim/examples/stochastic_optimal_control/arm_reaching_muscle_driven.py line 53 at r3 (raw file):

    nlp: NonLinearProgram,
    motor_noise,
    sensory_noise,

I love those names!

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bioptim/examples/stochastic_optimal_control/LeuvenArmModel.py line 5 at r3 (raw file):

"""

from typing import Callable

Quick change can you name the file as snake_case_file?

[EveCharbie]

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

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OCP_equation.png line at r3 (raw file):

Previously, pariterre (Pariterre) wrote…

Is this useful/mandatory? If so, could it be replaced by a <100kB file?

OK

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bioptim/examples/stochastic_optimal_control/arm_reaching_muscle_driven.py line 53 at r3 (raw file):

Previously, pariterre (Pariterre) wrote…

I love those names!

Done.

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bioptim/examples/stochastic_optimal_control/LeuvenArmModel.py line 5 at r3 (raw file):

Previously, pariterre (Pariterre) wrote…

Quick change can you name the file as snake_case_file?

Done.

[EveCharbie]

@pariterre Should be good now

[pariterre]

Reviewed 6 of 6 files at r4, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @EveCharbie)