More refined fixes thanks to Jim Schaff

biosimulators_copasi/core.py

@@ -209,7 +209,7 @@ def exec_sed_task(task: Task, variables: List[Variable], preprocessed_task: Opti
     preprocessed_task.basico_data_model.removeInterface(dh)
 
     # Process output 'data'
-    actual_output_length, _ = data.shape
+    copasi_output_length, _ = data.shape
     variable_results = VariableResults()
     offset = preprocessed_task.init_time_offset
 
@@ -220,8 +220,7 @@ def exec_sed_task(task: Task, variables: List[Variable], preprocessed_task: Opti
             try:
                 series = data.loc[:, data_target]
             except KeyError as e:
-                msg = "Unable to find output. Most likely a bug regarding BASICO and DisplayNames with nested braces."
-                raise RuntimeError(msg, e)
+                raise RuntimeError("Unable to find output", e)
             # Check for duplicates (yes, that can happen)
             if isinstance(series, pandas.DataFrame):
                 _, num_cols = series.shape
@@ -232,13 +231,13 @@ def exec_sed_task(task: Task, variables: List[Variable], preprocessed_task: Opti
                 series: pandas.Series = first_sub_series
 
             if basico_task_settings["problem"]["Duration"] > 0.0:
-                variable_results[variable.id] = numpy.full(actual_output_length, numpy.nan)
+                variable_results[variable.id] = numpy.full(copasi_output_length, numpy.nan)
                 for index, value in enumerate(series):
-                    variable_results[variable.id][index] = value if data_target != "Time" else value + offset
+                    adjusted_value = value if data_target != "Time" else value + offset
+                    variable_results[variable.id][index] = adjusted_value
             else:
                 value = series.get(0) if data_target != "Time" else series.get(0) + offset
-                sedml_utc_sim: Simulation = task.simulation
-                variable_results[variable.id] = numpy.full(sedml_utc_sim.number_of_steps + 1, value)
+                variable_results[variable.id] = numpy.full(copasi_output_length, value)
     except Exception as e:
         raise e
 

biosimulators_copasi/data_model.py

@@ -985,14 +985,14 @@ def configure_simulation_settings(self, sim: Union[UniformTimeCourseSimulation,
             self.init_time_offset: float = self.sim.initial_time
             self._duration_arg: float = self.sim.output_end_time - self.init_time_offset  # COPASI is kept in the dark
             self._step_size: float = BasicoInitialization._calc_simulation_step_size(self.sim)
-            self.number_of_steps = self._duration_arg / self._step_size
-            if int(self.number_of_steps) != self.number_of_steps:
+            self.number_of_steps = sim.number_of_steps
+            if int(round(self.number_of_steps)) != self.number_of_steps:
                 difference = self.number_of_steps - int(round(self.number_of_steps))
                 decimal_off = difference / int(round(self.number_of_steps))
                 if abs(decimal_off) > pow(10, -6):
                     raise NotImplementedError("Number of steps must be an integer number of time points, "
                                               f"not '{self.number_of_steps}'")
-                self.number_of_steps = int(self.number_of_steps)
+                self.number_of_steps = int(round(self.number_of_steps))
             self._length_of_output: int = (
                 int((self.sim.output_end_time - self.sim.output_start_time) / self._step_size))
             self._length_of_output += 1
@@ -1004,7 +1004,6 @@ def get_simulation_configuration(self) -> dict:
         problem = {
             "AutomaticStepSize": False,
             "StepNumber": self.number_of_steps,
-            "StepSize": self._step_size,
             "Duration": self._duration_arg,
             "OutputStartTime": self.sim.output_start_time - self.init_time_offset
         }
@@ -1048,7 +1047,7 @@ def _calc_simulation_step_size(sim: UniformTimeCourseSimulation) -> int:
             time_diff = sim.output_end_time - sim.output_start_time
             if time_diff == 0:
                 raise ZeroDivisionError  # We want to have exactly 1 step, and that's what our except block does
-            step_size_arg = time_diff / sim.number_of_steps
+            step_size_arg = (sim.output_end_time - sim.initial_time) / sim.number_of_steps
         except ZeroDivisionError:  # sim.output_end_time == sim.output_start_time
             step_size_arg = sim.number_of_points