feat: test_entry_size; bound_checking biorbd_model

[Infa60]

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 2 of 2 files at r1, all commit messages.
Reviewable status: all files reviewed, 9 unresolved discussions (waiting on @Infa60)

---

bioptim/models/biorbd/biorbd_model.py line 107 at r1 (raw file):

    def check_q_size(self, q):
        if q.shape[0] > self.nb_q:
            raise ValueError(f"Length of q is too big. Expected size: {self.nb_q}, but got: {q.shape[0]}")

is too large?
Is not the right size? (what happens if too small... it does not seem to raise)

---

bioptim/models/biorbd/biorbd_model.py line 634 at r1 (raw file):

    @staticmethod
    def animate(
        solution: Any, show_now: bool = True, tracked_markers: list[np.ndarray, ...] = None, **kwargs: Any

If you cannot import "SolutionData" then do not write anything. It is not "Any" type

---

bioptim/models/biorbd/biorbd_model.py line 643 at r1 (raw file):

        check_version(bioviz, "2.0.0", "2.4.0")

        states = solution.states

This will not work... as states does not return "q" by itself

---

tests/shard1/test_entry_size.py line 1 at r1 (raw file):

import pytest

Please rename the file for test_biorbd_model_size.py

---

tests/shard1/test_entry_size.py line 5 at r1 (raw file):

from casadi import MX

BIORBD_MODEL_PATH = "/home/lim/Documents/Bioptim/bioptim/bioptim/examples/muscle_driven_with_contact/models/2segments_4dof_2contacts_1muscle.bioMod"

This does not make sense

---

tests/shard1/test_entry_size.py line 193 at r1 (raw file):

# # q and qdot valid but tau_activations not valid
#     with pytest.raises(ValueError, match="Length of tau is too big"):
#         model.torque(tau_activations_too_large, q_valid, qdot_valid)

Why is this commented?

---

tests/shard1/test_entry_size.py line 315 at r1 (raw file):

# # muscle not valid
#     with pytest.raises(ValueError, match="Length of muscle is too big"):
#         model.muscle_activation_dot(muscle_too_large)

Why is this commented?

---

tests/shard1/test_entry_size.py line 358 at r1 (raw file):

# # q and qdot valid but qddot not valid
#     with pytest.raises(ValueError, match="Length of qddot is too big"):
#         model.muscle_joint_torque(muscle_too_large, q_valid, qdot_valid)

Why is this commented?

---

tests/shard1/test_entry_size.py line 427 at r1 (raw file):

# # q valid but qdot not valid
#     with pytest.raises(ValueError, match="Length of qdot is too big"):
#         model.tau_max(q_valid, qdot_too_large)

Why is this commented?

[codecov]

Codecov Report

Attention: 4 lines in your changes are missing coverage. Please review.

Comparison is base (ae901fd) 78.12% compared to head (4e90df7) 78.22%.
Report is 1 commits behind head on master.

Files	Patch %	Lines
bioptim/models/biorbd/biorbd_model.py	95.95%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #832      +/-   ##
==========================================
+ Coverage   78.12%   78.22%   +0.10%     
==========================================
  Files         140      140              
  Lines       16100    16189      +89     
==========================================
+ Hits        12578    12664      +86     
- Misses       3522     3525       +3     

Flag	Coverage Δ
unittests	78.22% <96.07%> (+0.10%)	⬆️

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

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[EveCharbie]

@pariterre there is a problem with black could we merge anyway? Worst case scenario, my next PR will resolve the black issue.

[pariterre]

Reviewed 3 of 3 files at r3, all commit messages.
Reviewable status: all files reviewed, 2 unresolved discussions (waiting on @Infa60)

---

bioptim/models/biorbd/biorbd_model.py line 107 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

is too large?
Is not the right size? (what happens if too small... it does not seem to raise)

change > for ==

---

bioptim/models/biorbd/biorbd_model.py line 151 at r3 (raw file):

        if muscle_size > self.nb_muscles:
            raise ValueError(f"Length of muscle is too big. Expected size: {self.nb_muscles}, but got: {muscle_size}")

The ">" should be a "=="

[pariterre]

Reviewed 2 of 2 files at r4, 5 of 5 files at r5, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @Infa60)

[pariterre]

@mickaelbegon @Infa60 @EveCharbie
This example seems to have been modified by both of you. Which is the (see the conflict). Which version is the expected one?

[EveCharbie]

It was not purposely changed by Infa60, his modifications are due to the merging problem we talked about.
Between my changes and mickaelbegon's changes, mickaelbegon should be kept (I will reintroduce root_torque_dynamics elsewhere).