Merge pull request #65 from Kev1CO/new_bioptim_ver

moving to new bioptim commit
Kev1CO · Jul 15, 2024 · 2046931 · 2046931
2 parents 30dee6b + ce45bf4
commit 2046931
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Showing 4 changed files with 4 additions and 7 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "external/bioptim"]
-	path = external/bioptim
+    path = external/bioptim
 	url = https://github.com/Kev1CO/bioptim
diff --git a/cocofest/examples/dynamics/reaching_task/reaching_task_pulse_duration_optimization.py b/cocofest/examples/dynamics/reaching_task/reaching_task_pulse_duration_optimization.py
@@ -62,7 +62,8 @@
     fes_muscle_models[i].a_scale = fes_muscle_models[i].a_scale * a_scale_proportion_list[i]
 
 minimum_pulse_duration = DingModelPulseDurationFrequencyWithFatigue().pd0
-pickle_file_list = ["minimize_muscle_fatigue.pkl", "minimize_muscle_force.pkl"]
+# pickle_file_list = ["minimize_muscle_fatigue.pkl", "minimize_muscle_force.pkl"]
+pickle_file_list = ["minimize_muscle_fatigue.pkl"]
 n_stim = 60
 n_shooting = 25
 # Step time of 1ms -> 1sec / (40Hz * 25) = 0.001s

diff --git a/cocofest/optimization/fes_ocp_dynamics.py b/cocofest/optimization/fes_ocp_dynamics.py
@@ -753,10 +753,8 @@ def _set_objective(
                         )
 
         if minimize_muscle_fatigue:
-            # for i in range(n_stim):
             objective_functions.add(
                 CustomObjective.minimize_overall_muscle_fatigue,
-                # custom_type=ObjectiveFcn.Lagrange,
                 custom_type=ObjectiveFcn.Mayer,
                 node=Node.END,
                 quadratic=True,
@@ -769,8 +767,6 @@ def _set_objective(
                 objective_functions.add(
                     CustomObjective.minimize_overall_muscle_force_production,
                     custom_type=ObjectiveFcn.Lagrange,
-                    # custom_type=ObjectiveFcn.Mayer,
-                    # node=Node.ALL,
                     quadratic=True,
                     weight=1,
                     phase=i,

diff --git a/external/bioptim b/external/bioptim
+1 −1		.github/workflows/run_tests_osx_win.yml
+9 −2		README.md
+3 −3		bioptim/dynamics/configure_new_variable.py
+203 −8		bioptim/dynamics/configure_problem.py
+4 −4		bioptim/dynamics/dynamics_functions.py
+1 −1		bioptim/examples/getting_started/example_external_forces.py
+2 −2		bioptim/examples/getting_started/example_multinode_constraints.py
+4 −2		bioptim/examples/holonomic_constraints/two_pendulums.py
+9 −7		bioptim/gui/plot.py
+2 −2		bioptim/interfaces/acados_interface.py
+2 −2		bioptim/limits/constraints.py
+12 −12		bioptim/limits/multinode_penalty.py
+4 −4		bioptim/limits/penalty_helpers.py
+3 −3		bioptim/limits/penalty_option.py
+2 −2		bioptim/limits/phase_transition.py
+6 −1		bioptim/models/biorbd/biorbd_model.py
+21 −0		bioptim/models/biorbd/holonomic_biorbd_model.py
+5 −5		bioptim/models/biorbd/multi_biorbd_model.py
+3 −7		bioptim/models/protocols/biomodel.py
+1 −1		bioptim/models/utils.py
+5 −5		bioptim/optimization/optimization_variable.py
+9 −9		bioptim/optimization/solution/solution.py
+ −		docs/OCP_equation.jpg
+4 −4		environment.yml
+1 −1		external/acados
+18 −26		external/acados_install_linux.sh
+24 −27		external/acados_install_mac.sh
+4 −5		tests/shard1/test__global_plots.py
+42 −41		tests/shard1/test_acados_interface.py
+4 −5		tests/shard1/test_biorbd_model.py
+19 −6		tests/shard1/test_biorbd_model_holonomic.py
+7 −6		tests/shard1/test_biorbd_multi_model.py
+5 −4		tests/shard1/test_bounds_accessor.py
+12 −13		tests/shard1/test_continuity_as_objective.py
+3 −2		tests/shard1/test_continuity_linear_continuous.py
+16 −15		tests/shard1/test_controltype_none.py
+10 −9		tests/shard1/test_custom_model.py
+88 −87		tests/shard1/test_dynamics.py
+31 −36		tests/shard1/test_global_align.py
+156 −155		tests/shard1/test_global_fatigue.py
+8 −7		tests/shard1/test_global_mhe.py
+2 −1		tests/shard1/test_mhe.py
+98 −97		tests/shard2/test_cost_function_integration.py
+11 −10		tests/shard2/test_global_inverse_optimal_control.py
+37 −38		tests/shard2/test_global_minimize_marker_velocity.py
+42 −41		tests/shard2/test_global_muscle_driven_ocp.py
+33 −32		tests/shard2/test_global_muscle_tracking_0_False.py
+33 −32		tests/shard2/test_global_muscle_tracking_0_True.py
+27 −26		tests/shard2/test_global_muscle_tracking_1.py
+71 −70		tests/shard2/test_global_muscle_tracking_2.py
+16 −15		tests/shard2/test_global_nmpc_final.py
+75 −76		tests/shard2/test_global_optimal_time.py
+29 −29		tests/shard2/test_global_optimal_time_mayer_min.py
+10 −9		tests/shard2/test_global_sqp.py
+9 −8		tests/shard3/test_get_time_solution.py
+274 −277		tests/shard3/test_global_getting_started.py
+26 −25		tests/shard3/test_global_symmetrical_torque_driven_ocp.py
+147 −156		tests/shard3/test_global_torque_driven_ocp.py
+37 −38		tests/shard3/test_global_torque_driven_with_contact_ocp.py
+30 −29		tests/shard3/test_initial_condition.py
+21 −20		tests/shard3/test_ligaments.py
+13 −12		tests/shard3/test_mappings.py
+2 −1		tests/shard3/test_multiphase_noised_initial_guess.py
+24 −23		tests/shard3/test_muscle_driven_ocp_implicit.py
+41 −40		tests/shard3/test_passive_torque.py
+102 −101		tests/shard4/test_penalty.py
+19 −20		tests/shard4/test_simulate.py
+12 −11		tests/shard4/test_soft_contacts.py
+151 −150		tests/shard4/test_solution.py
+17 −16		tests/shard4/test_update_bounds_and_init.py
+12 −11		tests/shard4/test_variable_time.py
+19 −18		tests/shard4/test_variational_integrator_examples.py
+38 −37		tests/shard5/test_global_stochastic_collocation.py
+166 −170		tests/shard6/test_global_stochastic_except_collocation.py
+67 −67		tests/shard6/test_time_dependent_ding.py
+114 −113		tests/shard6/test_time_dependent_problems.py
+10 −13		tests/utils.py