def __init__(self, model_file, gold_standard_file, arguments): self.model_file = model_file self.gold_standard_file = gold_standard_file self.gold_standard = get_gold_standard_timeseries(gold_standard_file) self.solver_config = arguments self.solver = solve_model.get_solver(model_file, arguments) self.cost_function = None
def test_check_biopepa_cvodes(self):
"""Simply check the solving of a biopepa model, using the cvodes
solver, by first converting the biopepa to xml"""
filename = "test_data/mm/mm.biopepa"
arguments = self.arg_parser.parse_args(["--solver", "cvodes"])
arguments.stop_time = 1.0
solver = solve_model.get_solver(filename, arguments)
solver.initialise_solver()
timecourse = solver.solve_model(arguments)
# And now we actually need something to assert
expected_final_time = 1.0
final_time = timecourse.get_final_time()
self.assertEqual(expected_final_time, final_time)
expected_column_names = ["E", "ES", "P", "S" ]
column_names = timecourse.get_column_names()
self.assertEqual(expected_column_names, column_names)
