[RTM] sol.graphs crashes if Meyer term in objective

[lsechoir]

All Submissions:

• Have you followed the guidelines in our Contributing document [docs/contribution.md]?
• [x ] Have you checked to ensure there aren't other open [Pull Requests] for the same update/change?
• [x ] Have you opened/linked the issue related to your pull request? [Release 2.2.2] sol.graphs crashes if mayer term in objective #478
• 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, 9 unresolved discussions (waiting on @lsechoir)

---

bioptim/examples/getting_started/example_multiphase.py line 66 at r1 (raw file):

    # Add objective functions
    objective_functions = ObjectiveList()
    # objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_CONTROL, key="tau", weight=100, phase=0)

Don't forget to reintroduce

Code quote:

    # objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_CONTROL, key="tau", weight=100, phase=0)
    # objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_CONTROL, key="tau", weight=100, phase=1)
    # objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_CONTROL, key="tau", weight=100, phase=2)

---

bioptim/gui/plot.py line 388 at r1 (raw file):

                    ]
                    # for nlp_tp in self.ocp.nlp :
                    #     print(f'nlp_tp is {nlp_tp} and nlp_tp.plot is {nlp_tp.plot}')

Don't forget to remove

Code quote:

                    # for nlp_tp in self.ocp.nlp :
                    #     print(f'nlp_tp is {nlp_tp} and nlp_tp.plot is {nlp_tp.plot}')
                    #     print(f' new plot_func is {self.plot_func[variable]}')

---

bioptim/gui/plot.py line 421 at r1 (raw file):

                    plot_type = self.plot_func[variable][i].type
                  #  if _ in [8 9 12 13] :
                   #     plot_type = PlotType.INTEGRATED

Don't forget to remove

Code quote:

                  #  if _ in [8 9 12 13] :
                   #     plot_type = PlotType.INTEGRATED

---

bioptim/gui/plot.py line 599 at r1 (raw file):

        -------

        """

I assume this will become relevent

Code quote:

    @staticmethod
    def save():
        """

        Returns
        -------

        """

---

bioptim/gui/plot.py line 664 at r1 (raw file):

            for key in self.variable_sizes[i]:
                # print(f' key is {key}')

Don't forget to remove

Code quote:

    # print(f' key is {key}')

---

bioptim/gui/plot.py line 728 at r1 (raw file):

                        #if self.plot_func[key][i].parameters:
                        print(f' key is {key} and phase is {i}')
                        print(self.plot_func[key][i].parameters)

Don't forget to remove

Code quote:

                    print('plot type point ')
                    for i_var in range(self.variable_sizes[i][key]):
                        #if self.plot_func[key][i].parameters:
                        print(f' key is {key} and phase is {i}')
                        print(self.plot_func[key][i].parameters)

---

bioptim/gui/plot.py line 925 at r1 (raw file):

        #for i, plot in enumerate(self.plots):
          #  plot.plt.savefig("/home/mickaelbegon/Documents/Stage_Lisa/AnthropoImpactOnTech/Solutions_vrille_et_demi/,
          #           dpi=500)

Don't forget to remove

Code quote:

        #for i, plot in enumerate(self.plots):
          #  plot.plt.savefig("/home/mickaelbegon/Documents/Stage_Lisa/AnthropoImpactOnTech/Solutions_vrille_et_demi/,
          #           dpi=500)

---

bioptim/limits/penalty_option.py line 585 at r1 (raw file):

                    self.target_plot_name,
                    plot_function,
                    penalty = self,

Replace this for :
penalty = self if plot_type == PlotType.POINT else None
Then you can remove the outer "if"

Suggestion:

penalty = self, 

---

bioptim/optimization/solution.py line 1288 at r1 (raw file):

        show_now: bool = True,
        shooting_type: Shooting = Shooting.MULTIPLE,
        save_path: str = None,

save_figure_path?

Don't forget to add it in Parameters docstring

Code quote:

save_path

[pariterre]

Reviewed 6 of 6 files at r2, all commit messages.
Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @lsechoir)

---

bioptim/gui/plot.py line 599 at r1 (raw file):

Previously, pariterre (Pariterre) wrote…

I assume this will become relevent

Please remove

[codecov]

Codecov Report

Patch coverage: 90.28% and project coverage change: -0.11 ⚠️

Comparison is base (ae6c337) 81.90% compared to head (1f9a849) 81.79%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #644      +/-   ##
==========================================
- Coverage   81.90%   81.79%   -0.11%     
==========================================
  Files         109      112       +3     
  Lines       12133    12558     +425     
==========================================
+ Hits         9937    10272     +335     
- Misses       2196     2286      +90     

Impacted Files	Coverage Δ
...tim/examples/getting_started/example_multiphase.py	87.71% <0.00%> (-1.57%)	⬇️
...act/contact_forces_inequality_constraint_muscle.py	13.46% <0.00%> (ø)
...ith_contact/muscle_activations_contacts_tracker.py	22.44% <0.00%> (ø)
...es/muscle_driven_ocp/muscle_activations_tracker.py	76.14% <50.00%> (ø)
bioptim/limits/phase_transition.py	92.22% <50.00%> (ø)
.../torque_driven_ocp/pendulum_with_passive_torque.py	65.71% <60.00%> (ø)
...es/torque_driven_ocp/example_multi_biorbd_model.py	72.72% <72.72%> (ø)
...amples/torque_driven_ocp/ocp_mass_with_ligament.py	75.75% <75.75%> (ø)
bioptim/limits/penalty.py	89.81% <80.00%> (-1.61%)	⬇️
...ples/torque_driven_ocp/torque_activation_driven.py	81.81% <81.81%> (ø)
... and 20 more

... and 13 files with indirect coverage changes

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

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

[pariterre]

Reviewed 1 of 1 files at r3, all commit messages.
Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @lsechoir)