black

cocofest/examples/dynamics/reaching_task/make_gaph.py

@@ -64,11 +64,7 @@
 
         else:
             plt.setp(
-                axs[i][j],
-                xticks=[0, 0.5, 1, 1.5],
-                xticklabels=[],
-                yticks=[0, 75, 150, 225],
-                yticklabels=[],
+                axs[i][j], xticks=[0, 0.5, 1, 1.5], xticklabels=[], yticks=[0, 75, 150, 225], yticklabels=[],
             )
 
         if i == 0 and j == 0:
@@ -134,24 +130,14 @@
 
     else:
         plt.setp(
-            axs[2][i],
-            xticks=[0, 0.5, 1, 1.5],
-            xticklabels=[0, 0.5, 1, 1.5],
-            yticks=[-1, 0, 1, 2],
-            yticklabels=[],
+            axs[2][i], xticks=[0, 0.5, 1, 1.5], xticklabels=[0, 0.5, 1, 1.5], yticks=[-1, 0, 1, 2], yticklabels=[],
         )
 
     axs[2][i].plot(
-        data_minimize_force["time"],
-        data_minimize_force["states"]["q"][i],
-        ms=4,
-        linewidth=5.0,
+        data_minimize_force["time"], data_minimize_force["states"]["q"][i], ms=4, linewidth=5.0,
     )
     axs[2][i].plot(
-        data_minimize_fatigue["time"],
-        data_minimize_fatigue["states"]["q"][i],
-        ms=4,
-        linewidth=5.0,
+        data_minimize_fatigue["time"], data_minimize_fatigue["states"]["q"][i], ms=4, linewidth=5.0,
     )
 
 # fatigue across time
@@ -204,19 +190,11 @@
 )
 
 axs[2][2].text(
-    0,
-    1.15,
-    f"{'%'}",
-    transform=axs[2][2].transAxes,
-    ha="left",
-    va="top",
-    fontsize=10,
+    0, 1.15, f"{'%'}", transform=axs[2][2].transAxes, ha="left", va="top", fontsize=10,
 )
 
 plt.setp(
-    axs[2][2],
-    xticks=[0, 0.5, 1, 1.5],
-    xticklabels=[0, 0.5, 1, 1.5],
+    axs[2][2], xticks=[0, 0.5, 1, 1.5], xticklabels=[0, 0.5, 1, 1.5],
 )
 
 # Figure labels

cocofest/examples/getting_started/muscle_model_identification.py

@@ -325,10 +325,7 @@
 pulse_intensity_values = [20, 20, 30, 40, 50, 60, 70, 80, 90, 100]
 fes_parameters = {"model": DingModelIntensityFrequency(), "n_stim": 10, "pulse_intensity": pulse_intensity_values}
 ivp_parameters = {"n_shooting": 10, "final_time": 1, "use_sx": True}
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 result, time = ivp.integrate()
@@ -409,10 +406,7 @@
 
 fes_parameters = {"model": identified_model, "n_stim": 10, "pulse_intensity": pulse_intensity_values}
 ivp_parameters = {"n_shooting": 10, "final_time": 1, "use_sx": True}
-ivp_from_identification = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp_from_identification = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 identified_result, identified_time = ivp_from_identification.integrate()

cocofest/examples/getting_started/pulse_mode_example.py

@@ -18,10 +18,7 @@
 fes_parameters = {"model": DingModelFrequencyWithFatigue(), "n_stim": n_stim, "pulse_mode": "Single"}
 ivp_parameters = {"n_shooting": ns, "final_time": final_time, "use_sx": True}
 
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 result_single, time_single = ivp.integrate()
 force_single = result_single["F"][0]
@@ -37,10 +34,7 @@
 final_time = 1
 fes_parameters = {"model": DingModelFrequencyWithFatigue(), "n_stim": n_stim, "pulse_mode": "Doublet"}
 ivp_parameters = {"n_shooting": ns, "final_time": final_time, "use_sx": True}
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 result_doublet, time_doublet = ivp.integrate()
 force_doublet = result_doublet["F"][0]
@@ -53,10 +47,7 @@
 n_stim = 30
 fes_parameters = {"model": DingModelFrequencyWithFatigue(), "n_stim": n_stim, "pulse_mode": "Triplet"}
 ivp_parameters = {"n_shooting": 10, "final_time": 1, "use_sx": True}
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 result_triplet, time_triplet = ivp.integrate()
 force_triplet = result_triplet["F"][0]

cocofest/examples/identification/ding2003_model_identification.py

@@ -35,10 +35,7 @@
 
 # --- Creating the simulated data to identify on --- #
 # Building the Initial Value Problem
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 result, time = ivp.integrate()
@@ -94,10 +91,7 @@
     "extend_last_phase": extra_phase_time,
     "use_sx": True,
 }
-ivp_from_identification = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp_from_identification = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 identified_result, identified_time = ivp_from_identification.integrate()

cocofest/examples/identification/ding2007_model_identification.py

@@ -35,10 +35,7 @@
 
 # --- Creating the simulated data to identify on --- #
 # Building the Initial Value Problem
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 result, time = ivp.integrate()
@@ -97,10 +94,7 @@
     "extend_last_phase": extra_phase_time,
     "use_sx": True,
 }
-ivp_from_identification = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp_from_identification = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 identified_result, identified_time = ivp_from_identification.integrate()

cocofest/examples/identification/hmed2018_model_identification.py

@@ -35,10 +35,7 @@
 
 # --- Creating the simulated data to identify on --- #
 # Building the Initial Value Problem
-ivp = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 result, time = ivp.integrate()
@@ -99,10 +96,7 @@
     "extend_last_phase": extra_phase_time,
 }
 
-ivp_from_identification = IvpFes(
-    fes_parameters,
-    ivp_parameters,
-)
+ivp_from_identification = IvpFes(fes_parameters, ivp_parameters,)
 
 # Integrating the solution
 identified_result, identified_time = ivp_from_identification.integrate()

cocofest/examples/sensitivity/truncation/sensitivity_analysis.py

@@ -59,10 +59,7 @@
                 "pulse_mode": mode,
             }
             ivp_parameters = {"n_shooting": temp_node_shooting, "final_time": 1, "use_sx": True}
-            ivp = IvpFes(
-                fes_parameters=fes_parameters,
-                ivp_parameters=ivp_parameters,
-            )
+            ivp = IvpFes(fes_parameters=fes_parameters, ivp_parameters=ivp_parameters,)
             ocp_end_time = time.time()
 
             for k in range(repetition):

cocofest/examples/sensitivity/truncation/summation_truncation_graph.py

@@ -150,13 +150,7 @@
     color="black",
 )
 
-cbar1 = fig.colorbar(
-    im1,
-    ax=axs,
-    extend="min",
-    ticks=[1e-12, 1e-10, 1e-8, 1e-6, 1e-4, 1e-2, 1, max_error],
-    cmap=cmap,
-)
+cbar1 = fig.colorbar(im1, ax=axs, extend="min", ticks=[1e-12, 1e-10, 1e-8, 1e-6, 1e-4, 1e-2, 1, max_error], cmap=cmap,)
 cbar1.set_label(label="Force absolute error (N)", size=25, fontname="Times New Roman")
 
 cbar1.ax.set_yticklabels(

cocofest/identification/identification_abstract_class.py

@@ -2,7 +2,6 @@
 
 
 class ParameterIdentification(ABC):
-
     @abstractmethod
     def _set_default_values(self, model):
         """

cocofest/integration/ivp_fes.py

@@ -38,9 +38,7 @@ class IvpFes:
     """
 
     def __init__(
-        self,
-        fes_parameters: dict = None,
-        ivp_parameters: dict = None,
+        self, fes_parameters: dict = None, ivp_parameters: dict = None,
     ):
         """
         Enables the creation of an ivp problem
@@ -92,8 +90,7 @@ def __init__(
         )
 
         parameters_init.add(
-            key="pulse_apparition_time",
-            initial_guess=np.array(self.pulse_apparition_time),
+            key="pulse_apparition_time", initial_guess=np.array(self.pulse_apparition_time),
         )
 
         parameters.add(
@@ -431,9 +428,7 @@ def build_initial_guess_from_ocp(self, ocp):
 
     @classmethod
     def from_frequency_and_final_time(
-        cls,
-        fes_parameters: dict = None,
-        ivp_parameters: dict = None,
+        cls, fes_parameters: dict = None, ivp_parameters: dict = None,
     ):
         """
         Enables the creation of an ivp problem from final time and frequency information instead of the stimulation
@@ -469,16 +464,11 @@ def from_frequency_and_final_time(
                 "The number of stimulation needs to be integer within the final time t, set round down "
                 "to True or set final_time * frequency to make the result an integer."
             )
-        return cls(
-            fes_parameters,
-            ivp_parameters,
-        )
+        return cls(fes_parameters, ivp_parameters,)
 
     @classmethod
     def from_frequency_and_n_stim(
-        cls,
-        fes_parameters: dict = None,
-        ivp_parameters: dict = None,
+        cls, fes_parameters: dict = None, ivp_parameters: dict = None,
     ):
         """
         Enables the creation of an ivp problem from stimulation number and frequency information instead of the final
@@ -502,7 +492,4 @@ def from_frequency_and_n_stim(
             raise ValueError("Frequency must be an int")
 
         ivp_parameters["final_time"] = n_stim / frequency
-        return cls(
-            fes_parameters,
-            ivp_parameters,
-        )
+        return cls(fes_parameters, ivp_parameters,)

cocofest/models/ding2003.py

@@ -30,10 +30,7 @@ class DingModelFrequency(FesModel):
     """
 
     def __init__(
-        self,
-        model_name: str = "ding2003",
-        muscle_name: str = None,
-        sum_stim_truncation: int = None,
+        self, model_name: str = "ding2003", muscle_name: str = None, sum_stim_truncation: int = None,
     ):
         super().__init__()
         self._model_name = model_name

cocofest/models/ding2003_with_fatigue.py

@@ -28,10 +28,7 @@ class DingModelFrequencyWithFatigue(DingModelFrequency):
     """
 
     def __init__(
-        self,
-        model_name: str = "ding2003_with_fatigue",
-        muscle_name: str = None,
-        sum_stim_truncation: int = None,
+        self, model_name: str = "ding2003_with_fatigue", muscle_name: str = None, sum_stim_truncation: int = None,
     ):
         super().__init__(model_name=model_name, muscle_name=muscle_name, sum_stim_truncation=sum_stim_truncation)
         self._with_fatigue = True

cocofest/models/fes_model.py

@@ -5,7 +5,6 @@
 
 
 class FesModel(ABC):
-
     @abstractmethod
     def set_a_rest(self, model, a_rest: MX | float):
         """