[RTR] adressing node specific dynamics

[Ipuch]

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? ODE integrator is not node specific as expected #621
• 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 6 of 6 files at r1, all commit messages.
Reviewable status: all files reviewed, 4 unresolved discussions (waiting on @Ipuch)

---

bioptim/dynamics/ode_solver.py line 74 at r1 (raw file):

        if len(nlp.dynamics) != 1 and ocp.n_threads != 1:
            raise NotImplementedError("n_threads > 1 with external_forces is not implemented yet")
        # if len(nlp.dynamics) == 1:

This should be kept

Code quote:

        # if len(nlp.dynamics) == 1:
        #     nlp.dynamics = nlp.dynamics * nlp.ns

---

bioptim/examples/getting_started/example_external_forces.py line 78 at r1 (raw file):

    external_forces = [[np.array([[0, 0, 0, 0, 0, -2], [0, 0, 0, 0, 0, 5]]).T for _ in range(n_shooting)]]
    external_forces[0][2] = np.array([[0, 0, 0, 0, 0, -22], [0, 0, 0, 0, 0, 52]]).T
    # external_forces[0][5] = np.array([[0, 0, 500, 0, 0, -2], [0, 0, 500, 0, 0, 5]]).T

Don't forget to clean up

Code quote:

    external_forces[0][2] = np.array([[0, 0, 0, 0, 0, -22], [0, 0, 0, 0, 0, 52]]).T
    # external_forces[0][5] = np.array([[0, 0, 500, 0, 0, -2], [0, 0, 500, 0, 0, 5]]).T
    # external_forces[0][8] = np.array([[0, 0, 500, 0, 0, -2], [0, 0, 500, 0, -1000, 5]]).T
    # external_forces[0][11] = np.array([[0, 0, 500, 0, 0, -2], [0, 0, 500, 0, 0, 5]]).T
    external_forces[0][14] = np.array([[0, 0, 0, 0, 0, 100], [0, 0, 0, 0, 0, -6]]).T
    # external_forces[0][17] = np.array([[0, 0, 500, 0, 0, -2], [0, 0, 500, 0, 0, 5]]).T
    # external_forces[0][20] = np.array([[0, 0, 500, 0, 0, -2], [0, 0, 500, 0, -1000, 5]]).T

---

bioptim/limits/objective_functions.py line 297 at r1 (raw file):

        # Dynamics must be sound within phases
        for nlp in ocp.nlp:
            if len(nlp.dynamics) > 1:

This will always be the case

Code quote:

if len(nlp.dynamics) > 1:

---

bioptim/optimization/solution.py line 1032 at r1 (raw file):

            else:
                dynamics_func = nlp.dynamics * nlp.ns if len(nlp.dynamics) == 1 else nlp.dynamics

This will not be necessary

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.02 🎉

Comparison is base (c3e03b2) 81.67% compared to head (31682be) 81.70%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #624      +/-   ##
==========================================
+ Coverage   81.67%   81.70%   +0.02%     
==========================================
  Files         106      106              
  Lines       11804    11817      +13     
==========================================
+ Hits         9641     9655      +14     
+ Misses       2163     2162       -1     

Impacted Files	Coverage Δ
bioptim/dynamics/ode_solver.py	89.25% <100.00%> (+0.56%)	⬆️
...xamples/getting_started/example_external_forces.py	88.23% <100.00%> (+0.35%)	⬆️
bioptim/limits/constraints.py	83.39% <100.00%> (+0.43%)	⬆️
bioptim/limits/objective_functions.py	88.71% <100.00%> (+0.05%)	⬆️
bioptim/limits/penalty.py	91.41% <100.00%> (+0.03%)	⬆️
bioptim/optimization/solution.py	83.65% <100.00%> (+0.07%)	⬆️

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☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

[Ipuch]

Reviewable status: 1 of 7 files reviewed, 4 unresolved discussions (waiting on @pariterre)

---

bioptim/dynamics/ode_solver.py line 74 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

This should be kept

Done

---

bioptim/examples/getting_started/example_external_forces.py line 78 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

Don't forget to clean up

Done

---

bioptim/limits/objective_functions.py line 297 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

This will always be the case

Done

---

bioptim/optimization/solution.py line 1032 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

This will not be necessary

Done

[Ipuch]

@pariterre PR ready to merge to me.

[Ipuch]

rk8 didn't fail but test_cyclic_nmpc failed this time .

[pariterre]

Reviewed 3 of 5 files at r2, 2 of 3 files at r3, 1 of 1 files at r4, 1 of 1 files at r5, 2 of 2 files at r6, all commit messages.
Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @Ipuch)

---

tests/test_global_getting_started.py line 860 at r6 (raw file):

    f = np.array(sol.cost)
    np.testing.assert_equal(f.shape, (1, 1))
    np.testing.assert_almost_equal(f[0, 0], 7067.851604540213)

Is this expected?

Code quote:

7067.851604540213

[pariterre]

Reviewed 3 of 3 files at r7, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @Ipuch)