def setUp(self): # Register all views BaseModelViewTestCase.setUp(self) # This could be the manual creation of an instance of the ChromData to # represent. self.model = make_sample_simulation()
def setUp(self): register_all_tree_node_adapters() # Make a study and add all possible chromatography objects to the study # Make a study with 1 experiment self.study = make_sample_study(1) simulation = make_sample_simulation() self.study.simulations.append(simulation)
def test_update_std_run_sim(self): sim = make_sample_simulation(name='Run_1') self.assertIsNone(sim.output) # Contains data from the CADET run: h5file = io_data_path("Sample_Sim_from_Run_1_cadet_simulation_run.h5") with self.assertTraitChanges(sim, "perf_param_data_event", 1): update_simulation_results(sim, h5file) self.assertIsInstance(sim.output, SimulationResults) perf_params = sim.output.performance_data self.assertIsInstance(perf_params, PerformanceData) self.assertIsInstance(perf_params.pool, SolutionWithProduct) num_comp = len(sim.product.product_components) self.assertEqual( len(perf_params.pool.product_component_concentrations), # noqa num_comp) assert_unit_scalar_almost_equal(perf_params.pool_volume, UnitScalar(1.727090, units="CV"), eps=1.e-6) assert_unit_scalar_almost_equal(perf_params.step_yield, UnitScalar(95.814, units='%'), eps=1.e-3) assert_unit_scalar_almost_equal(perf_params.start_collect_time, UnitScalar(200.946, units='minute'), eps=1.e-3) assert_unit_scalar_almost_equal(perf_params.stop_collect_time, UnitScalar(227.9, units='minute'), eps=1.e-3)
def test_add_sim(self): from kromatography.model.tests.sample_data_factories import \ make_sample_simulation study = self.study2 sim = make_sample_simulation() study.simulations.append(sim) self.assertFalse(is_task_blank(self.task2))
def test_change_filename(self): sim = make_sample_simulation() new_fname = str(uuid4()) + FILENAME_SUFFIX with self.assertTraitChanges(sim, "uuid", 1): with self.assertTraitChanges(sim, "cadet_filepath", 1): sim.cadet_filename = new_fname self.assert_cadet_filename_consistent(sim)
def test_change_uuid(self): sim = make_sample_simulation() self.assert_cadet_filename_consistent(sim) new_uuid = uuid4() with self.assertTraitChanges(sim, "cadet_filename", 1): with self.assertTraitChanges(sim, "cadet_filepath", 1): sim.uuid = new_uuid self.assert_cadet_filename_consistent(sim)
def setUp(self): # Manual construction column_type = ColumnType(**COLUMN_TYPE_DATA) resin = Resin(**RESIN_DATA) column = Column(column_type=column_type, resin=resin, **COLUMN_DATA) method = Method(**METHOD_DATA) self.sim_from_scratch = Simulation(name='Sim1', column=column, method=method, output=None) self.sim_from_std_exp = make_sample_simulation()
def test_create_cadet_file(self): from kromatography.model.tests.sample_data_factories import \ make_sample_simulation sim = make_sample_simulation() self.assertFalse(isfile(sim.cadet_filepath)) res = sim.create_cadet_input_file() try: self.assertTrue(isfile(sim.cadet_filepath)) self.assertEqual(res, sim.cadet_filepath) # Asking for it again just returns the filename res2 = sim.create_cadet_input_file() self.assertEqual(res, res2) finally: if isfile(sim.cadet_filepath): os.remove(sim.cadet_filepath)
def setUp(self): self.standard_actions = [ DeleteAction, RenameAction, CopyAction, CutAction ] register_all_tree_node_adapters() # Make a study and add all possible chromatography objects to the study # Make a study with 1 experiment self.study = make_sample_study(1) simulation = make_sample_simulation() self.study.simulations.append(simulation) self.user_ds = make_sample_user_ds(with_bind_trans=True) self.user_ds_entries = self.user_ds.object_catalog.keys() self.user_ds_objects = [ getattr(self.user_ds, key) for key in self.user_ds_entries ] self.study.study_datasource.binding_models.\ append(self.study.simulations[0].binding_model) self.study.study_datasource.transport_models.\ append(self.study.simulations[0].transport_model) in_study_ds = self.study.study_datasource self.in_study_ds_entries = in_study_ds.object_catalog.keys() self.in_study_objects = [ getattr(in_study_ds, key) for key in self.in_study_ds_entries ]
yield run_cadet_simulator, (output_file,), {"use_slurm": use_slurm} if __name__ == "__main__": from traits.api import Any, Button from traitsui.api import View, Item from kromatography.model.tests.sample_data_factories import \ make_sample_simulation, make_sample_simulation_group2 from kromatography.utils.app_utils import initialize_logging from kromatography.model.factories.job_manager import \ create_start_job_manager initialize_logging(verbose=True) sim = make_sample_simulation(name='Run_1') NUM_JOBS = 1 NUM_WORK_ITEMS_PER_JOB = 2 NUM_SIM = NUM_JOBS * NUM_WORK_ITEMS_PER_JOB t0 = time() # runner1 = sim.run() # group = make_sample_simulation_group2(size=2) # runner2 = group.run(wait=True) class SimpleGroupUI(HasStrictTraits): group = Any job_manager = Any button = Button("Run sims") view = View( Item("object.group.run_status"),
def setUp(self): self.source_param = ParameterScanDescription( name="binding_model.sma_nu[2]", low=4, high=6, num_values=10 ) self.sim = make_sample_simulation()
def setUpClass(cls): cls.sim = make_sample_simulation() cls.num_comp = len(cls.sim.product.product_components)
def setUp(self): self.simulation = make_sample_simulation(name='Run_1')
def setUp(self): register_all_tree_node_adapters() self.study = make_sample_study() self.model = make_sample_simulation() self.study.simulations.append(self.model)
editor=InstanceEditor(), style="custom", show_label=False), show_border=True, label="CADET Solver Parameters"), VGroup(Item("discretization_view", editor=InstanceEditor(), style="custom", show_label=False), show_border=True, label="Discretization Parameters"), resizable=True, buttons=OKCancelButtons, ) def _get_solver_view(self): return SolverView(model=self.solver) def _get_discretization_view(self): return DiscretizationView(model=self.discretization) if __name__ == '__main__': # setting up model from kromatography.model.tests.sample_data_factories import \ make_sample_simulation sim = make_sample_simulation() solution_view = SimulationView(model=sim) solution_view.configure_traits()
def setUp(self): self.model = make_sample_simulation() self.klass = Simulation
def _product_changed(self): self.component_name_available = \ self._component_name_available_default() self.component_selected = self._component_selected_default() # Traits initialization methods ------------------------------------------- def _component_selected_default(self): ignore = [] if self.ignore_strip_by_default: ignore.append(STRIP_COMP_NAME) return [ name for name in self.component_name_available if name not in ignore ] def _component_name_available_default(self): if self.product is None: return [] return self.product.product_component_names if __name__ == "__main__": from kromatography.model.tests.sample_data_factories import \ make_sample_simulation prod = make_sample_simulation().product ComponentSelector(product=prod).configure_traits()
def setUpClass(cls): super(TestCreateRunSimulationGroup, cls).setUpClass() cls.sim = make_sample_simulation() cls.sim_class = Simulation
def test_simulation_with_results(self): res_file = io_data_path("Chrom_Example_Run_1_cadet_simulation.h5") model = make_sample_simulation(name='Run_1', result_file=res_file) self.assertIsInstance(model, Simulation)