[RTR] CX for each node

[AnaisFarr]

TODO BEFORE MERGING:

• Launch big OCPs on bioptim main and this branch to compare the effect of the PR on memory.

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 4 of 4 files at r1, all commit messages.
Reviewable status: all files reviewed, 5 unresolved discussions (waiting on @AnaisFarr)

---

bioptim/examples/getting_started/robust_pendulum.py line 127 at r1 (raw file):

    ### New
    multinode_constraints = MultinodeConstraintList()

BinodeConstraint...

Code quote:

MultinodeConstraintList

---

bioptim/limits/multinode_constraint.py line 139 at r1 (raw file):

class AllnodeConstraint(Constraint):

AllNodeConstraint

---

bioptim/limits/multinode_constraint.py line 316 at r1 (raw file):

class AllnodeConstraintList(UniquePerPhaseOptionList):

AllNode...

Code quote:

AllnodeConstraintList

---

bioptim/limits/multinode_constraint.py line 355 at r1 (raw file):

        raise NotImplementedError("Printing of AllConstraintList is not ready yet")

    def prepare_allnode_constraints(self, ocp) -> list:

all_node

Code quote:

allnode

---

bioptim/optimization/optimization_variable.py line 407 at r1 (raw file):

        self.elements.append(value)

# Surement a modifier

This will create a bug in your tests because of the indentation

[codecov]

Codecov Report

Patch coverage: 77.37% and project coverage change: -0.47 ⚠️

Comparison is base (1f9a849) 81.79% compared to head (2cc7f29) 81.33%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #630      +/-   ##
==========================================
- Coverage   81.79%   81.33%   -0.47%     
==========================================
  Files         112      112              
  Lines       12558    12676     +118     
==========================================
+ Hits        10272    10310      +38     
- Misses       2286     2366      +80     

Impacted Files	Coverage Δ
bioptim/gui/graph.py	95.18% <ø> (ø)
bioptim/limits/penalty_node.py	35.08% <0.00%> (ø)
...imal_control/double_pendulum_torque_driven_IOCP.py	37.06% <37.06%> (ø)
bioptim/gui/check_conditioning.py	85.53% <50.00%> (ø)
bioptim/limits/multinode_constraint.py	69.91% <56.52%> (-21.28%)	⬇️
bioptim/limits/penalty_option.py	85.85% <59.45%> (-4.26%)	⬇️
bioptim/limits/objective_functions.py	89.23% <65.51%> (+0.17%)	⬆️
...tim/examples/getting_started/example_multistart.py	81.13% <70.83%> (ø)
bioptim/optimization/multi_start.py	79.59% <72.22%> (ø)
bioptim/limits/constraints.py	81.71% <78.78%> (-1.68%)	⬇️
... and 37 more

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[pariterre]

Reviewed 23 of 23 files at r3, all commit messages.
Reviewable status: all files reviewed, 10 unresolved discussions (waiting on @AnaisFarr)

---

bioptim/limits/multinode_constraint.py line 368 at r3 (raw file):

                raise RuntimeError("Phase index of the allnode_constraint need to be positive")

            if mnc.weight: # ajouter un check, sinon mettre 1

Please write comments in english and/or do not commit non relevent comments

Code quote:

# ajouter un check, sinon mettre 1

---

bioptim/limits/multinode_constraint.py line 369 at r3 (raw file):

            if mnc.weight: # ajouter un check, sinon mettre 1
                mnc.base = ObjectiveFunction.LagrangeFunction # a elever

same

Code quote:

# a elever

---

bioptim/limits/penalty_option.py line 701 at r3 (raw file):

            # all_pn = []
            # # Make sure the penalty behave like a AllNodeConstraint, even though it may be an Objective or Constraint

Add TODO: clear this if not necessary anymore

Code quote:

            # all_pn = []
            # # Make sure the penalty behave like a AllNodeConstraint, even though it may be an Objective or Constraint
            # # self.transition = True
            # self.dt = 1
            # if not self.states_mapping:
            #     self.states_mapping = BiMapping(range(nlp.states.shape), range(nlp.states.shape))
            # nlp = ocp.nlp[self.phase_idx]
            #
            # all_pn.append()
            #
            # penalty_function = self.type(self, all_pn, **self.params)
            # self.set_penalty(penalty_function, all_pn)

---

bioptim/limits/phase_transition.py line 6 at r3 (raw file):

from casadi import vertcat, MX

from .multinode_constraint import BinodeConstraint, BinodeConstraintFunctions # AllNodeConstraint, AllNodeConstraintFunctions

Remove the comments if not necessary anymore

---

bioptim/optimization/optimization_variable.py line 321 at r3 (raw file):

                "OptimizationVariable must have been created by OptimizationVariableList to have a cx. "
            )
        return self.parent_list.cx_all[self.index, :]  #[self.index, :]

Remove that

Code quote:

#[self.index, :]

---

bioptim/optimization/optimization_variable.py line 366 at r3 (raw file):

        self._cx: MX | SX | np.ndarray = np.array([])
        self._cx_end: MX | SX | np.ndarray = np.array([])
        #self._cx_all: list = []

Remove that

---

bioptim/optimization/optimization_variable.py line 525 at r3 (raw file):

        """

        return self._cx_all

If this is already a property, make _cx_all public and remove the current property

Code quote:

self._cx_all

---

bioptim/examples/getting_started/example_binode_constraints.py line 209 at r3 (raw file):

    # sol.graphs()
    # --- Show results --- #
    #sol.animate()

Add a todo to restore that (or at least do not push these modification)

Code quote:

    # sol.graphs()
    # --- Show results --- #
    #sol.animate()

[pariterre]

Reviewed 11 of 11 files at r4, all commit messages.
Reviewable status: all files reviewed, 19 unresolved discussions (waiting on @AnaisFarr)

---

bioptim/dynamics/ode_solver.py line 77 at r4 (raw file):

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

Add a TODO: verify if it is solved

Code quote:

raise NotImplementedError("n_threads > 1 with external_forces is not implemented yet")

---

bioptim/dynamics/ode_solver.py line 79 at r4 (raw file):

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

This can be removed

Code quote:

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

---

bioptim/dynamics/ode_solver.py line 105 at r4 (raw file):

        self.defects_type = DefectType.NOT_APPLICABLE

    def integrator(self, ocp, nlp, node_index) -> list:

Don't forget to add this to other Solvers

Code quote:

, node_index

---

bioptim/dynamics/ode_solver.py line 158 at r4 (raw file):

        #     return dynamics_out
        # else:
        #     return [nlp.ode_solver.rk_integrator(ode, ode_opt)]

Do not forget to reintroduce with external forces

Code quote:

        # if len(nlp.external_forces) != 0:
        #     dynamics_out = []
        #     for idx in range(len(nlp.external_forces)):
        #         ode_opt["idx"] = idx
        #         dynamics_out.append(nlp.ode_solver.rk_integrator(ode, ode_opt))
        #     return dynamics_out
        # else:
        #     return [nlp.ode_solver.rk_integrator(ode, ode_opt)]

---

bioptim/dynamics/ode_solver.py line 300 at r4 (raw file):

            ode = {
                "x_unscaled": [nlp.states.cx[0]] + nlp.states.cx_intermediates_list,

index_node

Code quote:

[0]

---

bioptim/dynamics/ode_solver.py line 300 at r4 (raw file):

            ode = {
                "x_unscaled": [nlp.states.cx[0]] + nlp.states.cx_intermediates_list,

index_node also

Code quote:

cx_intermediates_list,

---

bioptim/examples/getting_started/example_multiphase.py line 31 at r4 (raw file):

def minimize_difference(all_pn: PenaltyNode):
    return all_pn[0].nlp.controls.cx[-1] - all_pn[1].nlp.controls.cx[0]

node_index= all_pn.node_index
all_pn[0].nlp.controls[node_index].cx_end

Code quote:

all_pn[0].nlp.controls.cx[-1]

---

bioptim/limits/multinode_constraint.py line 192 at r3 (raw file):

        if "force_allnode" in params:
            # This is a hack to circumvent the apparatus that moves the functions to a custom function
            # It is necessary for PhaseTransition

keep this unless it is now the vanilla way to do it

Code quote:

            # This is a hack to circumvent the apparatus that moves the functions to a custom function
            # It is necessary for PhaseTransition

---

bioptim/limits/multinode_constraint.py line 375 at r4 (raw file):

            if not mnc.weight: # ajouter un check, sinon mettre 1
                mnc.base = 1

verify what it is for

Code quote:

mnc.base = 1

---

bioptim/limits/penalty.py line 666 at r4 (raw file):

            nlp = all_pn.nlp
            if nlp.control_type == ControlType.CONSTANT:
                u = nlp.controls.cx[0]

0 should be node_index
nlp.controls[node_index].cx
nlp.controls[node_index].cx_end

Code quote:

 nlp.controls.cx[0]

---

bioptim/limits/phase_transition.py line 287 at r4 (raw file):

                    nlp_pre.states[key].mapping.to_second.map(nlp_pre.states[key].cx[-1]),
                )
                cx_start = vertcat(cx[0], nlp_post.states[key].mapping.to_second.map(nlp_post.states[key].cx[0]))

rewrite when ready

Code quote:

                    cx[-1],
                    nlp_pre.states[key].mapping.to_second.map(nlp_pre.states[key].cx[-1]),
                )
                cx_start = vertcat(cx[0], nlp_post.states[key].mapping.to_second.map(nlp_post.states[key].cx[0]))

[pariterre]

Reviewed 29 of 29 files at r10, all commit messages.
Reviewable status: all files reviewed, 10 unresolved discussions (waiting on @AnaisFarr)

---

bioptim/dynamics/ode_solver.py line 40 at r10 (raw file):

        self.is_direct_shooting = False

    def integrator(self, ocp, nlp, node_index=None) -> list:

Adde a TODO to remove that None

Code quote:

, node_index=None

---

tests/test_controltype_none.py line 126 at r9 (raw file):

        nlp.dynamics_func = Function(
            "ForwardDyn",
            [nlp.states[0]["scaled"].mx_reduced, nlp.controls[0]["scaled"].mx_reduced, nlp.parameters.mx],  # TODO: [0] to [node_index]

This TODO should be kept

Code quote:

 # TODO: [0] to [node_index]

---

tests/test_global_getting_started.py line 1281 at r10 (raw file):

    TestUtils.save_and_load(sol, ocp, True)

    # TODO: Restore that

I comment so I can see it later

Code quote:

 # TODO: Restore that

[pariterre]

Reviewed all commit messages.
Reviewable status: 7 of 63 files reviewed, 10 unresolved discussions (waiting on @AnaisFarr)