[RTR] Holonomic muscle model

[p-shg]

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2. Did you write a proper documentation (docstrings and ReadMe)
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Working on Muscle driven dynamics for models with holonomic constraints
@pariterre the arm26_pendulum_swingup_Muscle_algebraic.py file reproduces the plotting error I told you about

---

This change is 

[Ipuch]

@Ipuch reviewed 18 of 18 files at r1, all commit messages.
Reviewable status: all files reviewed, 5 unresolved discussions (waiting on @p-shg)

---

bioptim/examples/holonomic_constraints/arm26_pendulum_swingup_Muscle_algebraic.py line 1 at r1 (raw file):

"""

"muscle_algebraic.py"

---

bioptim/examples/holonomic_constraints/four_bar.py line 1 at r1 (raw file):

"""

add the test somewhere.

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bioptim/examples/holonomic_constraints/custom_dynamics.py line 166 at r1 (raw file):

class HolonomicMusclesDynamics(HolonomicTorqueDynamics):

put everything in custom_dynamics_muscle.py, copy paste or import from the other file.

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bioptim/examples/holonomic_constraints/arm26_pendulum_swingup.py line 1 at r1 (raw file):

"""

Not necessary

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bioptim/examples/holonomic_constraints/arm26_pendulum_swingup_Muscle.py line 1 at r1 (raw file):

"""

name of the file "_muscle.py"

[Ipuch]

@Ipuch partially reviewed 26 files and all commit messages, and resolved 5 discussions.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @p-shg).

[codecov]

Codecov Report

❌ Patch coverage is 73.01370% with 394 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.15%. Comparing base (476d88d) to head (e0f5ee5).
⚠️ Report is 753 commits behind head on master.

Files with missing lines	Patch %	Lines
...ples/feature_examples/custom_constraint_weights.py	17.18%	53 Missing ⚠️
bioptim/interfaces/fratrop_options.py	71.00%	29 Missing ⚠️
...es/holonomic_constraints/arm26_pendulum_swingup.py	62.96%	20 Missing ⚠️
...es/toy_examples/holonomic_constraints/three_bar.py	13.33%	13 Missing ⚠️
bioptim/models/viewer_pyorerun.py	0.00%	13 Missing ⚠️
...nomic_constraints/arm26_pendulum_swingup_muscle.py	76.00%	12 Missing ⚠️
...traints/arm26_pendulum_swingup_muscle_algebraic.py	78.94%	12 Missing ⚠️
bioptim/interfaces/interface_utils.py	90.08%	12 Missing ⚠️
...mples/toy_examples/holonomic_constraints/common.py	33.33%	8 Missing ⚠️
...s/holonomic_constraints/two_pendulums_algebraic.py	36.36%	7 Missing ⚠️
... and 86 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1024      +/-   ##
==========================================
- Coverage   78.62%   77.15%   -1.47%     
==========================================
  Files         159      193      +34     
  Lines       18608    21019    +2411     
==========================================
+ Hits        14631    16218    +1587     
- Misses       3977     4801     +824     

Flag	Coverage Δ
unittests	77.15% <73.01%> (-1.47%)	⬇️

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