[RTM] Sample data control

[Kev1CO]

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?
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New Feature Submissions:

1. Does your submission pass the tests (if not please explain why this is intended)?
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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?

---

This change is 

[Kev1CO]

This pull request is to allow the execution in Bioptim of Pontryagin : optimal sampled-data control

[pariterre]

Reviewed 5 of 10 files at r3, 9 of 9 files at r5, all commit messages.
Reviewable status: all files reviewed, 12 unresolved discussions (waiting on @Kev1CO)

---

bioptim/dynamics/integrator.py line 76 at r5 (raw file):

            self.u_sym = ode["p_scaled"]
        else:
            self.u_sym = []

Please use ternary operator for these trivial tests
e.g. self.u_sym = ode["p_scaled"] if "p_scale" in ode.keys() else []

Also unless it makes sense to do so, prefer None to []

Code quote:

        if "p_scale" in ode.keys():
            self.u_sym = ode["p_scaled"]
        else:
            self.u_sym = []

---

bioptim/dynamics/ode_solver.py line 128 at r5 (raw file):

            "defects_type": DefectType.NOT_APPLICABLE,
        }
        if nlp.controls.shape != 0:

Try to avoid "not" operator when possible in if statements, unless it avoids the else completely. It is far more easier to understand if something is ..., then ... otherwise ..., than to understand if something is not ..., then ... otherwise ....

Code quote:

 if nlp.controls.shape != 0:

---

bioptim/dynamics/ode_solver.py line 146 at r5 (raw file):

                "x_scaled": nlp.states["scaled"].cx,
                "ode": nlp.dynamics_func,
                "implicit_ode": nlp.implicit_dynamics_func,

Providing different data structure is generally bad practise as it leads to having to test if some key exists.
A better practise is to make sure it is a valid structure, but filled with None for the non-sensical one.

Code quote:

        else:
            ode = {
                "x_unscaled": nlp.states.cx,
                "x_scaled": nlp.states["scaled"].cx,
                "ode": nlp.dynamics_func,
                "implicit_ode": nlp.implicit_dynamics_func,
            }

---

bioptim/dynamics/ode_solver.py line 155 at r5 (raw file):

                dynamics_out.append(nlp.ode_solver.rk_integrator(ode, ode_opt))
            return dynamics_out
        elif isinstance(ode["ode"], list):

This elif does not oppose if len(nlp.external_forcesin any meaningful way. both can be true and therefore your piece of code will never be run.

Also do not test for instance unless you are trying to differentiate inherited elements. Use a flag instead.

Code quote:

elif isinstance(ode["ode"], list):

---

bioptim/interfaces/solve_ivp_interface.py line 350 at r5 (raw file):

    for s, func in enumerate(dynamics_func):
        u_slice = slice(s, s + 1) if control_type == ControlType.CONSTANT else slice(s, s + 2)
        u_controls = [] if not u else u[:, u_slice]

if u, instead of not u. Also, u should be a None, not an empty list. So if u is None is a better option

Code quote:

[] if not u else u[:, u_slice]

---

bioptim/limits/penalty.py line 676 at r5 (raw file):

            penalty.expand = all_pn.nlp.dynamics_type.expand

Please add a raise here (just prior to that line) that raises a NotImplementedYet if len(penalty.node_idx) > 1
(PS I know you are not the one who wrote that piece of code)

Code quote:

node_idx = penalty.node_idx[0] if len(penalty.node_idx) == 1 else 0

---

bioptim/limits/penalty_option.py line 427 at r5 (raw file):

        param_cx = nlp.cx(nlp.parameters.cx)
        if isinstance(nlp.controls.cx, list):

Do not test for instance unless it makes sense. If you used a None, then test for None

In other word, avoid encoding the information that something means something else because it is empty.

Code quote:

isinstance(nlp.controls.cx, list)

---

bioptim/optimization/optimal_control_program.py line 513 at r5 (raw file):

            self.nlp[i].initialize(self.cx)
            ConfigureProblem.initialize(self, self.nlp[i])
        for i in range(self.n_phases):

Why do you need two for loops for that?
please add a comment in the second to quickly explain why

Code quote:

 for i in range(self.n_phases):

---

bioptim/optimization/optimization_variable.py line 483 at r5 (raw file):

        """

        return self._cx[:, 0] if self.shape != 0 else []

This should be CX() and not a list OR a None

Also do not test negative when there is an else

Code quote:

[]

---

bioptim/optimization/optimization_variable.py line 491 at r5 (raw file):

        """

        return self._cx_end[:, 0] if self.shape != 0 else []

This should be CX() and not a list OR a None

Also do not test negative when there is an else

Code quote:

 if self.shape != 0 else []

---

bioptim/optimization/optimization_vector.py line 312 at r5 (raw file):

        p_idx = 0

        if self.n_all_u != 0:

Are you sure that this loop does not already do what you want? I feel that if data are empty, then the loop will just be skipped anyway (as dimensions will be 0). It seems redundant and unnecessarily complex...

Code quote:

if self.n_all_u != 0:

---

bioptim/optimization/solution.py line 1017 at r5 (raw file):

            param_scaling = nlp.parameters.scaling
            x0 = self._get_first_frame_states(out, shooting_type, phase=p)
            u = np.array([]) if nlp.controls.shape == 0 else self._controls["unscaled"][controls_phase_idx]["all"]

I feel this should be a None... but maybe it causes problem

Code quote:

 np.array([])

[Kev1CO]

Reviewable status: 4 of 16 files reviewed, 12 unresolved discussions (waiting on @pariterre)

---

bioptim/dynamics/integrator.py line 76 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Please use ternary operator for these trivial tests
e.g. self.u_sym = ode["p_scaled"] if "p_scale" in ode.keys() else []

Also unless it makes sense to do so, prefer None to []

Done.
Not able to put None as the program needs a list, even empty

---

bioptim/dynamics/ode_solver.py line 128 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Try to avoid "not" operator when possible in if statements, unless it avoids the else completely. It is far more easier to understand if something is ..., then ... otherwise ..., than to understand if something is not ..., then ... otherwise ....

Done.

---

bioptim/dynamics/ode_solver.py line 146 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Providing different data structure is generally bad practise as it leads to having to test if some key exists.
A better practise is to make sure it is a valid structure, but filled with None for the non-sensical one.

Done.

---

bioptim/dynamics/ode_solver.py line 155 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

This elif does not oppose if len(nlp.external_forcesin any meaningful way. both can be true and therefore your piece of code will never be run.

Also do not test for instance unless you are trying to differentiate inherited elements. Use a flag instead.

Ode is either a function or a list of function with our case, this is the reason why we used a isinstance condition to verify our problem
not sure to understant the use of flag instead of isinstance

---

bioptim/interfaces/solve_ivp_interface.py line 350 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

if u, instead of not u. Also, u should be a None, not an empty list. So if u is None is a better option

Done.
Not able to put None as the program needs a list, even empty

---

bioptim/limits/penalty.py line 676 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Please add a raise here (just prior to that line) that raises a NotImplementedYet if len(penalty.node_idx) > 1
(PS I know you are not the one who wrote that piece of code)

Done.

---

bioptim/limits/penalty_option.py line 427 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Do not test for instance unless it makes sense. If you used a None, then test for None

In other word, avoid encoding the information that something means something else because it is empty.

Test is mendatory, cannot use none as the solver needs a list

---

bioptim/optimization/optimal_control_program.py line 513 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Why do you need two for loops for that?
please add a comment in the second to quickly explain why

Forgotten modification for tests
Done.

---

bioptim/optimization/optimization_variable.py line 483 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

This should be CX() and not a list OR a None

Also do not test negative when there is an else

Can't

---

bioptim/optimization/optimization_variable.py line 491 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

This should be CX() and not a list OR a None

Also do not test negative when there is an else

Can't

---

bioptim/optimization/optimization_vector.py line 312 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

Are you sure that this loop does not already do what you want? I feel that if data are empty, then the loop will just be skipped anyway (as dimensions will be 0). It seems redundant and unnecessarily complex...

No this flag is necessary otherwise it will go trought and try to slice a empty control vector

---

bioptim/optimization/solution.py line 1017 at r5 (raw file):

Previously, pariterre (Pariterre) wrote…

I feel this should be a None... but maybe it causes problem

Yes it does if not np.array([])

[pariterre]

Reviewed 3 of 12 files at r6, 3 of 9 files at r7, 5 of 7 files at r8, all commit messages.
Reviewable status: 14 of 16 files reviewed, 15 unresolved discussions (waiting on @Kev1CO)

---

bioptim/dynamics/integrator.py line 73 at r8 (raw file):

        self.cx = ode_opt["cx"]
        self.x_sym = ode["x_scaled"]
        self.u_sym = ode["p_scaled"] if "p_scale" in ode.keys() else []

This should be useless

Code quote:

 if "p_scale" in ode.keys() else

---

bioptim/dynamics/integrator.py line 300 at r8 (raw file):

        """

        return x_prev + h * self.fun(x_prev, self.get_u(u, t), p)  # [:, self.idx]

Why did you remove "[:, idx]"?

Code quote:

# [:, self.idx]

---

bioptim/dynamics/ode_solver.py line 128 at r8 (raw file):

            "defects_type": DefectType.NOT_APPLICABLE,
        }
        if nlp.controls.shape == 0:

This if should be be element, so we are sure we have the same dict

Code quote:

if nlp.controls.shape == 0:

---

bioptim/dynamics/ode_solver.py line 133 at r8 (raw file):

                "x_scaled": nlp.states["scaled"].cx,
                "p_unscaled": None,
                "p_scaled": None,

p_scaled: None if nlp.controls.shape == 0 else nlp.controls["scaled"]

Change to MX()

Code quote:

"p_scaled": None,

---

bioptim/dynamics/ode_solver.py line 333 at r8 (raw file):

            if len(nlp.external_forces) == 0:
                return [nlp.ode_solver.rk_integrator(ode, ode_opt)]
            else:

No need for else (as it already returns)

Code quote:

else:

[Ipuch]

Reviewed 3 of 12 files at r6, 1 of 9 files at r7, 3 of 7 files at r8, all commit messages.
Reviewable status: 15 of 16 files reviewed, 15 unresolved discussions (waiting on @Kev1CO and @pariterre)

---

bioptim/dynamics/ode_solver.py line 155 at r5 (raw file):

Previously, Kev1CO wrote…

Ode is either a function or a list of function with our case, this is the reason why we used a isinstance condition to verify our problem
not sure to understant the use of flag instead of isinstance

We need a more META way to treat this information.
Instead of sending list of dynamics we need to have a MX of size n x n_shooting nodes as we have for external forces. So there will be only one if case.

---

bioptim/limits/penalty_option.py line 427 at r5 (raw file):

Previously, Kev1CO wrote…

Test is mendatory, cannot use none as the solver needs a list

We need a need feature, global flag to test this:
"ControlType.NONE"

---

bioptim/optimization/optimization_variable.py line 483 at r5 (raw file):

Previously, Kev1CO wrote…

Can't

Let's try again together.

---

bioptim/optimization/optimization_variable.py line 491 at r5 (raw file):

Let's try again together.

---

bioptim/optimization/optimization_vector.py line 312 at r5 (raw file):

Previously, Kev1CO wrote…

No this flag is necessary otherwise it will go trought and try to slice a empty control vector

ControlType.NONE

---

bioptim/optimization/solution.py line 1017 at r5 (raw file):

Previously, Kev1CO wrote…

Yes it does if not np.array([])

ControlType.None

Code quote:

nlp.controls.shape == 0

[Kev1CO]

Reviewable status: 15 of 16 files reviewed, 15 unresolved discussions (waiting on @pariterre)

---

bioptim/dynamics/integrator.py line 73 at r8 (raw file):

if "p_scale" in ode.keys() else
When there is no control, there is no "p_scale" in the ode
That is why we keep it

---

bioptim/dynamics/integrator.py line 300 at r8 (raw file):

Previously, pariterre (Pariterre) wrote…

Why did you remove "[:, idx]"?

Cannot remember, works well with it anyway
Done.

---

bioptim/dynamics/ode_solver.py line 128 at r8 (raw file):

Previously, pariterre (Pariterre) wrote…

This if should be be element, so we are sure we have the same dict

Done.

---

bioptim/dynamics/ode_solver.py line 133 at r8 (raw file):

Previously, pariterre (Pariterre) wrote…

p_scaled: None if nlp.controls.shape == 0 else nlp.controls["scaled"]

Change to MX()

Done.

---

bioptim/dynamics/ode_solver.py line 333 at r8 (raw file):

Previously, pariterre (Pariterre) wrote…

No need for else (as it already returns)

Done.

Code quote:

                dynamics_out = []
                for idx in range(len(nlp.external_forces)):
                    ode_opt["idx"] = idx

[Ipuch]

Reviewable status: 13 of 16 files reviewed, 15 unresolved discussions (waiting on @pariterre)

---

bioptim/dynamics/ode_solver.py line 155 at r5 (raw file):

len(nlp.external_forces)
up

[Kev1CO]

Reviewable status: 10 of 17 files reviewed, 15 unresolved discussions (waiting on @Ipuch, @Kev1CO, and @pariterre)

---

bioptim/optimization/optimization_vector.py line 312 at r5 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

ControlType.NONE

DONE.

---

bioptim/optimization/solution.py line 1017 at r5 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

ControlType.None

DONE.

[pariterre]

Reviewed 1 of 7 files at r8, 1 of 5 files at r10, 6 of 6 files at r11, all commit messages.
Reviewable status: all files reviewed, 12 unresolved discussions (waiting on @Kev1CO)

---

bioptim/dynamics/integrator.py line 73 at r8 (raw file):

Previously, Kev1CO wrote…

if "p_scale" in ode.keys() else
When there is no control, there is no "p_scale" in the ode
That is why we keep it

self.u_sym = [] if ode_opt["control_type"] is ControlType.NONE else ode["p_scaled"]

---

bioptim/dynamics/integrator.py line 122 at r11 (raw file):

            return u[:, 0] + (u[:, 1] - u[:, 0]) * dt_norm
        elif self.control_type == ControlType.NONE:
            return np.ndarray([])

either:
np.ndarray(0) or np.array(())

Code quote:

np.ndarray([])

---

bioptim/dynamics/ode_solver.py line 132 at r11 (raw file):

            "x_unscaled": nlp.states.cx,
            "x_scaled": nlp.states["scaled"].cx,
            "p_unscaled": MX() if nlp.controls.shape == 0 else nlp.controls.cx

change this for ControlType

Code quote:

nlp.controls.shape

---

bioptim/dynamics/ode_solver.py line 135 at r11 (raw file):

            if nlp.control_type == ControlType.CONSTANT
            else horzcat(nlp.controls.cx, nlp.controls.cx_end),
            "p_scaled": MX() if nlp.controls.shape == 0 else nlp.controls["scaled"].cx

Use ControlType

Code quote:

nlp.controls.shape

---

bioptim/limits/penalty.py line 670 at r11 (raw file):

                u = horzcat(nlp.controls.cx, nlp.controls.cx_end)
            elif nlp.control_type == ControlType.NONE:
                u = []

This should be a CX...

Code quote:

[]

---

bioptim/optimization/optimization_vector.py line 453 at r11 (raw file):

            # For controls
            if nlp.use_controls_from_phase_idx == nlp.phase_idx:
                if nlp.control_type == ControlType.CONSTANT or nlp.control_type == ControlType.NONE:

nlp.control_type in (ControlType.CONSTANT, ControlType.NONE)

Code quote:

nlp.control_type == ControlType.CONSTANT or nlp.control_type == ControlType.NONE

---

bioptim/optimization/optimization_vector.py line 508 at r11 (raw file):

            if nlp.use_controls_from_phase_idx == nlp.phase_idx:
                if nlp.control_type == ControlType.CONSTANT or nlp.control_type == ControlType.NONE:

nlp.control_type in (ControlType.CONSTANT, ControlType.NONE)

Code quote:

nlp.control_type == ControlType.CONSTANT or nlp.control_type == ControlType.NONE

---

bioptim/optimization/optimization_vector.py line 544 at r11 (raw file):

            # For controls
            if nlp.use_controls_from_phase_idx == nlp.phase_idx:
                if nlp.control_type == ControlType.CONSTANT or nlp.control_type == ControlType.NONE:

Suggestion:

`nlp.control_type in (ControlType.CONSTANT, ControlType.NONE)`

---

bioptim/optimization/solution.py line 1276 at r11 (raw file):

                        axis=1,
                    )
            elif nlp.control_type == ControlType.LINEAR_CONTINUOUS or nlp.control_type == ControlType.NONE:

remove this

Code quote:

 nlp.control_type == ControlType.LINEAR_CONTINUOUS or nlp.control_type == ControlType.NONE

[codecov]

Codecov Report

Patch coverage: 94.54% and project coverage change: +0.01 🎉

Comparison is base (249e163) 81.54% compared to head (386be40) 81.56%.

❗ Current head 386be40 differs from pull request most recent head 07fc240. Consider uploading reports for the commit 07fc240 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #628      +/-   ##
==========================================
+ Coverage   81.54%   81.56%   +0.01%     
==========================================
  Files         110      110              
  Lines       12341    12359      +18     
==========================================
+ Hits        10064    10080      +16     
- Misses       2277     2279       +2     

Impacted Files	Coverage Δ
bioptim/gui/check_conditioning.py	85.53% <0.00%> (ø)
bioptim/limits/penalty.py	91.11% <66.66%> (-0.31%)	⬇️
bioptim/optimization/optimization_variable.py	87.63% <92.85%> (+0.13%)	⬆️
bioptim/dynamics/integrator.py	95.67% <100.00%> (+0.05%)	⬆️
bioptim/dynamics/ode_solver.py	89.07% <100.00%> (-0.19%)	⬇️
bioptim/interfaces/solve_ivp_interface.py	96.80% <100.00%> (+0.03%)	⬆️
bioptim/optimization/non_linear_program.py	90.57% <100.00%> (+0.20%)	⬆️
bioptim/optimization/optimization_vector.py	95.73% <100.00%> (+0.01%)	⬆️
bioptim/optimization/solution.py	83.65% <100.00%> (ø)

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[Kev1CO]

Reviewable status: 9 of 19 files reviewed, 12 unresolved discussions (waiting on @pariterre)

---

bioptim/dynamics/ode_solver.py line 155 at r5 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

len(nlp.external_forces)
up

done.

[Ipuch]

Reviewed 2 of 4 files at r12, 1 of 2 files at r13, 1 of 5 files at r14, 6 of 6 files at r15, all commit messages.
Reviewable status: all files reviewed, 15 unresolved discussions (waiting on @Kev1CO and @pariterre)

---

bioptim/dynamics/ode_solver.py line 135 at r11 (raw file):

Previously, Kev1CO wrote…

Done.

nlp.controls.cx if nlp.control_type in (ControlType.CONSTANT, ...) else ...

---

bioptim/dynamics/ode_solver.py line 135 at r15 (raw file):

            if nlp.control_type == ControlType.NONE
            else nlp.controls.cx
            if nlp.control_type == ControlType.CONSTANT

nlp.controls.cx if nlp.control_type in (ControlType.CONSTANT, ...) else ...

---

bioptim/optimization/optimization_variable.py line 602 at r15 (raw file):

    def _set_casadi_symbolic_callable(self, casadi_symbolic_callable: Callable = None):
        if casadi_symbolic_callable is None:
            raise ValueError()

if casadi_symbolic_callable is None and not isinstance(..., Callable):

"This entry should be either casadi.MX or casadi.SX"

---

bioptim/optimization/optimization_vector.py line 312 at r15 (raw file):

        p_idx = 0

        if self.ocp.nlp[0].control_type != ControlType.NONE:

self.ocp.nlp[0].control_type in (CONSTANT and LINEAR_CONTINUOUS...)

Code quote:

self.ocp.nlp[0].control_type

[Kev1CO]

Reviewable status: 19 of 20 files reviewed, 15 unresolved discussions (waiting on @Ipuch and @pariterre)

---

bioptim/optimization/optimization_variable.py line 602 at r15 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

if casadi_symbolic_callable is None and not isinstance(..., Callable):

"This entry should be either casadi.MX or casadi.SX"

Done.

---

bioptim/optimization/optimization_vector.py line 312 at r15 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

self.ocp.nlp[0].control_type in (CONSTANT and LINEAR_CONTINUOUS...)

Done.

[Kev1CO]

Reviewable status: 16 of 20 files reviewed, 15 unresolved discussions (waiting on @Ipuch and @pariterre)

---

bioptim/dynamics/ode_solver.py line 135 at r11 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

nlp.controls.cx if nlp.control_type in (ControlType.CONSTANT, ...) else ...

Done.

---

bioptim/dynamics/ode_solver.py line 135 at r15 (raw file):

Previously, Ipuch (Pierre Puchaud) wrote…

nlp.controls.cx if nlp.control_type in (ControlType.CONSTANT, ...) else ...

Done.

---

bioptim/limits/penalty.py line 670 at r11 (raw file):

Previously, pariterre (Pariterre) wrote…

This should be a CX...

Done.

[pariterre]

Reviewed 3 of 4 files at r17, 7 of 7 files at r18, 1 of 1 files at r19, 2 of 2 files at r20, 1 of 1 files at r21, all commit messages.
Reviewable status: all files reviewed, 10 unresolved discussions (waiting on @Ipuch and @Kev1CO)

---

bioptim/optimization/optimization_variable.py line 3 at r20 (raw file):

import numpy as np
from casadi import MX, SX, vertcat
from typing import Callable

Typing is a built-in package. It should therefore appear first followed by a white space

Code quote:

from typing import Callable

---

bioptim/optimization/optimization_variable.py line 324 at r20 (raw file):

    mx_reduced: MX
        The reduced MX to the size of _cx
    _casadi_symbolic_callable: Callable

change the name to cx_constructor

Code quote:

_casadi_symbolic_callable

---

bioptim/optimization/optimization_variable.py line 578 at r20 (raw file):

class OptimizationVariableContainer:
    def __init__(self, variable_scaled=None, variables_unscaled=None, casadi_symbolic_callable: Callable = None):

Update this name

Code quote:

casadi_symbolic_callable

[Ipuch]

Reviewed 2 of 4 files at r17, 7 of 7 files at r18, 1 of 1 files at r19, 2 of 2 files at r20, all commit messages.
Reviewable status: all files reviewed, 7 unresolved discussions (waiting on @Kev1CO and @pariterre)

[Kev1CO]

Reviewable status: 17 of 20 files reviewed, 7 unresolved discussions (waiting on @Ipuch and @pariterre)

---

bioptim/optimization/optimization_variable.py line 3 at r20 (raw file):

Previously, pariterre (Pariterre) wrote…

Typing is a built-in package. It should therefore appear first followed by a white space

Done.

---

bioptim/optimization/optimization_variable.py line 324 at r20 (raw file):

Previously, pariterre (Pariterre) wrote…

change the name to cx_constructor

Done.

---

bioptim/optimization/optimization_variable.py line 578 at r20 (raw file):

Previously, pariterre (Pariterre) wrote…

Update this name

Done.

[Kev1CO]

@pariterre RTM

[pariterre]

Reviewed 2 of 3 files at r22, 1 of 1 files at r23, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @Kev1CO)