Merge pull request #16 from biosimulators/fix-initial-vs-output-diff

Fix situation when the output start time is different from the initia…

biosimulators_tellurium/_version.py

@@ -1 +1 @@
-__version__ = '0.1.37'
+__version__ = '0.1.38'

biosimulators_tellurium/core.py

@@ -263,20 +263,14 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
 
  # simulate
  if isinstance(sim, UniformTimeCourseSimulation):
- number_of_points = (sim.output_end_time - sim.initial_time) / \
- (sim.output_end_time - sim.output_start_time) * sim.number_of_steps + 1
- if abs(number_of_points % 1) > 1e-8:
- msg = (
- 'The number of simulation points `{}` must be an integer:'
- '\n Initial time: {}'
- '\n Output start time: {}'
- '\n Output end time: {}'
- '\n Number of points: {}'
- ).format(number_of_points, sim.initial_time, sim.output_start_time, sim.output_start_time, sim.number_of_points)
- raise NotImplementedError(msg)
-
- number_of_points = round(number_of_points)
- results = numpy.array(road_runner.simulate(sim.initial_time, sim.output_end_time, number_of_points).tolist()).transpose()
+ if sim.initial_time < sim.output_start_time:
+ number_of_presim_points = (sim.output_end_time - sim.initial_time) / \
+ (sim.output_end_time - sim.output_start_time) * sim.number_of_steps + 1
+
+ number_of_presim_points = round(number_of_presim_points) - sim.number_of_steps
+ road_runner.simulate(sim.initial_time, sim.output_start_time, number_of_presim_points)
+
+ results = numpy.array(road_runner.simulate(sim.output_start_time, sim.output_end_time, sim.number_of_steps+1).tolist()).transpose()
  else:
  road_runner.steadyState()
  results = road_runner.getSteadyStateValues()

tests/test_core_main.py

@@ -436,12 +436,6 @@ def test_exec_sed_task_error_handling_with_biosimulators(self):
  with self.assertRaisesRegex(ValueError, 'targets are not supported'):
  variable_results, log = core.exec_sed_task(task, variables_2, simulator_config=simulator_config)
 
- task_2 = copy.deepcopy(task)
- task_2.simulation.output_start_time = 1.5
- simulator_config.sedml_interpreter = SedmlInterpreter.biosimulators
- with self.assertRaises(NotImplementedError):
- variable_results, log = core.exec_sed_task(task_2, variables, simulator_config=simulator_config)
-
  def test_exec_sed_task_with_preprocesssed_task(self):
  # configure simulation
  task = sedml_data_model.Task(