[RTR] Model interface for a wider use of bioptim #581

Ipuch · 2022-11-24T20:39:41Z

All Submissions:

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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?
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New Feature Submissions:

Does your submission pass the tests (if not please explain why this is intended)?
Did you write a proper documentation (docstrings and ReadMe)
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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?

Tackling #507

This change is

codecov · 2022-11-24T20:57:17Z

Codecov Report

Base: 81.27% // Head: 81.60% // Increases project coverage by +0.32% 🎉

Coverage data is based on head (dffe9eb) compared to base (54404fb).
Patch coverage: 90.78% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #581      +/-   ##
==========================================
+ Coverage   81.27%   81.60%   +0.32%     
==========================================
  Files          99      104       +5     
  Lines       11057    11367     +310     
==========================================
+ Hits         8987     9276     +289     
- Misses       2070     2091      +21

Impacted Files	Coverage Δ
bioptim/examples/__main__.py	`0.00% <ø> (ø)`
...act/contact_forces_inequality_constraint_muscle.py	`13.46% <0.00%> (ø)`
...ith_contact/muscle_activations_contacts_tracker.py	`22.44% <0.00%> (ø)`
bioptim/optimization/solution.py	`86.90% <0.00%> (-0.56%)`	⬇️
...tim/examples/getting_started/example_multistart.py	`24.24% <16.66%> (-2.23%)`	⬇️
bioptim/limits/path_conditions.py	`86.52% <46.66%> (+0.03%)`	⬆️
...les/torque_driven_ocp/track_markers_2D_pendulum.py	`53.03% <50.00%> (ø)`
bioptim/examples/custom_model/main.py	`60.00% <60.00%> (ø)`
bioptim/examples/moving_horizon_estimation/mhe.py	`50.87% <66.66%> (ø)`
...getting_started/example_continuity_as_objective.py	`46.75% <70.00%> (-0.69%)`	⬇️
... and 65 more

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relative parent import fixed

I dislike this commit but needed to make it work

…ct_biorbd

Ipuch

Reviewable status: 85 of 102 files reviewed, 26 unresolved discussions (waiting on @pariterre)

bioptim/__init__.py line 176 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

Use a Protocol instead?

obsolete

bioptim/dynamics/dynamics_functions.py line 748 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

Move this to the BioModel (set_excitation(u))

Set Excitation is not possible to move !

bioptim/dynamics/dynamics_functions.py line 785 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

Move this to the BioModel (set_excitation(u))

But this one yes !

bioptim/dynamics/ode_solver.py line 137 at r13 (raw file):

Previously, pariterre (Pariterre) wrote…

Do not keep numpy dependency

ok,

bioptim/examples/custom_model/main.py line 23 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

BioModel

MyModel is fine because it made on the custom model.

bioptim/examples/getting_started/custom_constraint.py line 59 at r2 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

to modify !

Saved by you

bioptim/interfaces/biomodel.py line 84 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

Be more precise

node needed anymore.

bioptim/interfaces/biorbd_model.py line 282 at r13 (raw file):

reshape_fext_to_fcontact
removed.

bioptim/limits/constraints.py line 388 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

This should be done internally

internally done.

bioptim/limits/phase_transition.py line 262 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

Add a new method in BioModel to load a fresh model when needed

nlp_post.model.copy

Done

bioptim/optimization/optimal_control_program.py line 274 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

"bio_model_serialized": [m.serialize() for m in bio_model],
with serialize being a tuple[type, dict]

done

bioptim/optimization/optimal_control_program.py line 547 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

to adjust

done

bioptim/optimization/optimal_control_program.py line 157 at r13 (raw file):

Previously, pariterre (Pariterre) wrote…

Remove the dependency to numpy

Done

bioptim/optimization/receding_horizon_optimization.py line 201 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

To adjust

done

bioptim/optimization/receding_horizon_optimization.py line 367 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

To adjust

done

bioptim/optimization/receding_horizon_optimization.py line 507 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

To adjust

done

bioptim/examples/custom_model/my_model.py line 15 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

No need if it implements a Protocol

done.

bioptim/examples/custom_model/my_model.py line 51 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

TODO

done

Ipuch

Reviewable status: 85 of 102 files reviewed, 26 unresolved discussions (waiting on @pariterre)

bioptim/interfaces/custom_model.py line 8 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

Change this for a set_attr at start of OCP (if not in the class)

Done.

pariterre

Reviewed 1 of 6 files at r16, 9 of 13 files at r17, 1 of 4 files at r18, 1 of 1 files at r19, 3 of 6 files at r20, 2 of 3 files at r21, 3 of 3 files at r22, all commit messages.
Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @Ipuch)

pariterre

Reviewed 2 of 2 files at r23, all commit messages.
Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @Ipuch)

Ipuch

Reviewable status: 94 of 102 files reviewed, 2 unresolved discussions (waiting on @pariterre)

bioptim/examples/custom_model/main.py line 1 at r2 (raw file):

Previously, pariterre (Pariterre) wrote…

Make sure to add in the GUI examples

Done.

bioptim/examples/custom_model/main.py line 8 at r11 (raw file):

Previously, pariterre (Pariterre) wrote…

To verify

Done.

bioptim/limits/constraints.py line 463 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

This should be done internally

Done.

bioptim/limits/penalty.py line 151 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

Move this in the actual interface

Done

bioptim/limits/penalty.py line 606 at r12 (raw file):

Previously, pariterre (Pariterre) wrote…

Not sure is it part of the API

Done

bioptim/optimization/optimal_control_program.py line 261 at r12 (raw file):

Done

Ipuch

Reviewable status: 94 of 102 files reviewed, 2 unresolved discussions (waiting on @pariterre)

pariterre

Reviewed 8 of 8 files at r24, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @Ipuch)

Ipuch · 2022-12-10T00:01:21Z

Should animate be a method of bioModel ?

pariterre · 2022-12-10T02:23:55Z

@Ipuch Could be... Add this to a todo!

Ipuch added 5 commits November 24, 2022 15:38

biorbd model interface

60caf7b

adding the abstract class in ocp

a8884db

blacked

f17eb1d

update types

c52a794

blacked

fcb5404

Ipuch added 24 commits November 24, 2022 18:19

going there, example not working yet

a50c96d

blacked

7613baa

string fix and integrator

9b4bd3d

black

b7a82cc

scoot doc

231f324

moving and splitting files to a dedicated folder

746e653

cleaning quat normalization

0119aa6

scoot

6f10ab7

trying stuff

0a85a5b

restored multiphases and phase mapping

e6aef4a

restored to string

9aafe91

bioviz error

8ef16dc

cleaning main

60c8880

fixing the bug

4190a40

blacked

0cca083

test it

989facb

test and example are working now

2fd36f8

relative parent import fixed

more pythonic function names

a5e909f

only BiorbdModel and pythonic methods

0869e70

fixing nb_muscle_total

75db780

soft_contact_names

72c05e3

implementing some more methods

6199ba6

.marker()

9e7c897

I dislike this commit but needed to make it work

import and more methods to pythonic

dd139f0

Ipuch and others added 8 commits December 9, 2022 16:03

graph and wild copy

8254776

all tests works

b81cfd5

serialize custom example

dc44f2a

towards better external forces

b383fcd

external forces fixed

c746253

Cleaned a bit

a2d7d67

update readme

2cac182

Merge remote-tracking branch 'origin/disconnect_biorbd' into disconne…

338646b

…ct_biorbd

Ipuch commented Dec 9, 2022

View reviewed changes

pariterre and others added 7 commits December 9, 2022 17:45

Fixed call to mx_to_cx

ffb349d

Fixed a parameter call

522d6fd

Moved state_set into BiorbdModel

601e5ce

Moved state_set into BiorbdModel

80f8e87

removed some wild modifs.

47b6f99

Fixed excitation

36771c1

Fixed last call

d873b68

pariterre reviewed Dec 9, 2022

View reviewed changes

Fixed some hints

57dab85

pariterre previously approved these changes Dec 9, 2022

View reviewed changes

black

dffe9eb

Ipuch dismissed pariterre’s stale review via dffe9eb December 9, 2022 23:07

Ipuch commented Dec 9, 2022

View reviewed changes

pariterre approved these changes Dec 9, 2022

View reviewed changes

pariterre merged commit 8c1cd1a into pyomeca:master Dec 10, 2022

Ipuch deleted the disconnect_biorbd branch December 12, 2022 14:32

Ipuch mentioned this pull request Jan 11, 2023

mx_to_cx should be a method of nlp #413

Closed

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[RTR] Model interface for a wider use of bioptim #581

[RTR] Model interface for a wider use of bioptim #581

Ipuch commented Nov 24, 2022 •

edited

codecov bot commented Nov 24, 2022 •

edited

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pariterre commented Dec 10, 2022

[RTR] Model interface for a wider use of bioptim #581

[RTR] Model interface for a wider use of bioptim #581

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Ipuch commented Nov 24, 2022 • edited

All Submissions:

New Feature Submissions:

Changes to Core Features:

codecov bot commented Nov 24, 2022 • edited

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Ipuch commented Dec 10, 2022

pariterre commented Dec 10, 2022

Ipuch commented Nov 24, 2022 •

edited

codecov bot commented Nov 24, 2022 •

edited