removed 0 duration sim logic

biosimulators_copasi/core.py

@@ -191,9 +191,6 @@ def exec_sed_task(task: Task, variables: List[Variable], preprocessed_task: Opti
     # prepare task
     basico.set_task_settings(preprocessed_task.task_type, preprocessed_task.get_simulation_configuration())
 
-    # temporary work around for issue with 0.0 duration tasks
-    basico_task_settings = basico.get_task_settings(basico.T.TIME_COURSE)
-
     # Execute Simulation
     data: pandas.DataFrame
     dh: COPASI.CDataHandler
@@ -229,15 +226,10 @@ def exec_sed_task(task: Task, variables: List[Variable], preprocessed_task: Opti
                     if not first_sub_series.equals(series.iloc[:, i]):
                         raise RuntimeError("Different data sets for same variable")
                 series: pandas.Series = first_sub_series
-
-            if basico_task_settings["problem"]["Duration"] > 0.0:
-                variable_results[variable.id] = numpy.full(copasi_output_length, numpy.nan)
-                for index, value in enumerate(series):
-                    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
-                variable_results[variable.id] = numpy.full(copasi_output_length, value)
+            variable_results[variable.id] = numpy.full(copasi_output_length, numpy.nan)
+            for index, value in enumerate(series):
+                adjusted_value = value if data_target != "Time" else value + offset
+                variable_results[variable.id][index] = adjusted_value
     except Exception as e:
         raise e
 

biosimulators_copasi/data_model.py

@@ -984,6 +984,8 @@ def configure_simulation_settings(self, sim: Union[UniformTimeCourseSimulation,
             self.task_type = basico.T.TIME_COURSE
             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
+            if self._duration_arg <= 0:
+                raise ValueError("A simulation's initial_time can not be equal to or greater than the output end time.")
             self._step_size: float = BasicoInitialization._calc_biosimulators_simulation_step_size(self.sim)
             # What COPASI understands as number of steps and what biosimulators
             # understands as number of steps is different; we must manually calculate
@@ -1044,15 +1046,7 @@ def generate_data_handler(self, output_selection: list[str]):
 
     @staticmethod
     def _calc_biosimulators_simulation_step_size(sim: UniformTimeCourseSimulation) -> int:
-        if sim.output_end_time - sim.output_start_time < 0:
+        if (time_diff := sim.output_end_time - sim.output_start_time) <= 0:
             raise ValueError('Output end time must be greater than the output start time.')
 
-        try:
-            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
-        except ZeroDivisionError:  # sim.output_end_time == sim.output_start_time
-            step_size_arg = sim.number_of_points
-
-        return step_size_arg
+        return time_diff / sim.number_of_steps

tests/test_core.py

@@ -841,6 +841,9 @@ def test_raw_cli(self):
 
     def test_exec_sedml_docs_in_combine_archive_with_cli(self):
         doc, archive_filename = self._build_combine_archive()
+        self._prepare_and_assert_combine_archive_outputs(doc, archive_filename)
+
+    def _prepare_and_assert_combine_archive_outputs(self, doc: sedml_data_model.SedDocument, archive_filename: str):
         out_dir = os.path.join(self.directory_name, 'out')
         env = TestCore._get_combine_archive_exec_env()
 
@@ -867,14 +870,17 @@ def test_exec_sedml_docs_in_combine_archive_with_docker_image(self):
 
         self._assert_combine_archive_outputs(doc, out_dir)
 
-    def _build_combine_archive(self, algorithm=None, orig_model_filename='model.xml', var_targets=None):
+    def _build_combine_archive(self, algorithm: sedml_data_model.Algorithm = None,
+                               orig_model_filename: str = 'model.xml', var_targets: str = None,
+                               initial_time: float = 0., output_start_time: float = 0.1, output_end_time: float = 0.2):
         if var_targets is None:
             var_targets = [None, 'A', 'C', 'DA']
-        doc = self._build_sed_doc(algorithm=algorithm)
+        doc = self._build_sed_doc(algorithm=algorithm, initial_time=initial_time,
+                                  output_start_time=output_start_time, output_end_time=output_end_time)
 
         for data_gen, target in zip(doc.data_generators, var_targets):
             if target is not None:
-                data_gen.variables[0].target = "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='{}']".format(target)
+                data_gen.variables[0].target = f"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='{target}']"
 
         archive_dirname = os.path.join(self.directory_name, 'archive')
         if not os.path.isdir(archive_dirname):
@@ -897,12 +903,13 @@ def _build_combine_archive(self, algorithm=None, orig_model_filename='model.xml'
             ],
         )
         archive_filename = os.path.join(self.directory_name,
-                                        'archive.omex' if algorithm is None else 'archive-{}.omex'.format(algorithm.kisao_id))
+                                        'archive.omex' if algorithm is None else f'archive-{algorithm.kisao_id}.omex')
         CombineArchiveWriter().run(archive, archive_dirname, archive_filename)
 
         return doc, archive_filename
 
-    def _build_sed_doc(self, algorithm=None):
+    def _build_sed_doc(self, algorithm: sedml_data_model.Algorithm = None, initial_time: float = 0.,
+                       output_start_time: float = 0.1, output_end_time: float = 0.2):
         if algorithm is None:
             algorithm = sedml_data_model.Algorithm(
                 kisao_id='KISAO_0000304',
@@ -924,9 +931,9 @@ def _build_sed_doc(self, algorithm=None):
         doc.simulations.append(sedml_data_model.UniformTimeCourseSimulation(
             id='sim_1_time_course',
             algorithm=algorithm,
-            initial_time=0.,
-            output_start_time=0.1,
-            output_end_time=0.2,
+            initial_time=initial_time,
+            output_start_time=output_start_time,
+            output_end_time=output_end_time,
             number_of_points=20,
         ))
         doc.tasks.append(sedml_data_model.Task(