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How to use viewvalues method in autotest

Best Python code snippet using autotest_python

test2_dict_interface.py

Source:test2_dict_interface.py

...407        self.assertTrue(operator.lt(oc.viewkeys(), ('a', 'f')))408        self.assertTrue(operator.le(oc.viewkeys(), ('a', 'f')))409        self.assertFalse(operator.gt(oc.viewkeys(), ('a', 'f')))410        self.assertFalse(operator.ge(oc.viewkeys(), ('a', 'f')))411        v = oc.viewvalues() | {1, 9 }412        self.assertEqual(v, {1,2,3,4,5,9})413        self.assertIsInstance(v, set)414        self.assertRaises(TypeError, operator.or_, oc.viewvalues(), (1, 9))415        self.assertRaises(TypeError, operator.or_, (1, 9), oc.viewvalues())416        v = oc.viewvalues() & {1, 9 }417        self.assertEqual(v, {1})418        self.assertIsInstance(v, set)419        self.assertRaises(TypeError, operator.and_, oc.viewvalues(), (1, 9))420        self.assertRaises(TypeError, operator.and_, (1, 9), oc.viewvalues())421        v = oc.viewvalues() ^ {1, 9 }422        self.assertEqual(v, {2, 3, 4, 5, 9})423        self.assertIsInstance(v, set)424        self.assertRaises(TypeError, operator.xor, oc.viewvalues(), (1, 9))425        self.assertRaises(TypeError, operator.xor, (1, 9), oc.viewvalues())426        v = oc.viewvalues() - {1, 9 }427        self.assertEqual(v, {2,3,4,5})428        self.assertIsInstance(v, set)429        self.assertRaises(TypeError, operator.sub, oc.viewvalues(), (1, 9))430        self.assertRaises(TypeError, operator.sub, (1, 9), oc.viewvalues())431        self.assertTrue(operator.lt(oc.viewvalues(), (1, 9)))432        self.assertTrue(operator.le(oc.viewvalues(), (1, 9)))433        self.assertFalse(operator.gt(oc.viewvalues(), (1, 9)))434        self.assertFalse(operator.ge(oc.viewvalues(), (1, 9)))435        v = oc.viewitems() | {('a', 1), ('f', 9) }436        self.assertEqual(v, {('a', 1), ('b', 2), ('c', 3), ('d', 4), ('e', 5), ('f', 9)})437        self.assertIsInstance(v, set)438        self.assertRaises(TypeError, operator.or_, oc.viewitems(), (('a', 1), ('f', 9)))439        self.assertRaises(TypeError, operator.or_, (1, 9), oc.viewitems())440        v = oc.viewitems() & {('a',1), ('f',9)}441        self.assertEqual(v, {('a', 1)})442        self.assertIsInstance(v, set)443        self.assertRaises(TypeError, operator.and_, oc.viewitems(), (('a', 1), ('f', 9)))444        self.assertRaises(TypeError, operator.and_, (('a', 1), ('f', 9)), oc.viewitems())445        v = oc.viewitems() ^ {('a',1), ('f',9)}446        self.assertEqual(v, {('b', 2), ('c', 3), ('d', 4), ('e', 5), ('f', 9)})447        self.assertIsInstance(v, set)448        self.assertRaises(TypeError, operator.xor, oc.viewitems(), (('a', 1), ('f', 9)))...

simulation.py

Source:simulation.py

...133			# initialize random streams134			internal_state.seed = self._seedFromName(state_name)135			internal_state.randomState = np.random.RandomState(seed=internal_state.seed)136			internal_state.initialize(self, sim_data)137		for external_state in six.viewvalues(self.external_states):138			external_state.initialize(self, sim_data, self._timeline)139		for process_name, process in six.viewitems(self.processes):140			# initialize random streams141			process.seed = self._seedFromName(process_name)142			process.randomState = np.random.RandomState(seed=process.seed)143			process.initialize(self, sim_data)144		for listener in six.viewvalues(self.listeners):145			listener.initialize(self, sim_data)146		for hook in six.viewvalues(self.hooks):147			hook.initialize(self, sim_data)148		for internal_state in six.viewvalues(self.internal_states):149			internal_state.allocate()150		for listener in six.viewvalues(self.listeners):151			listener.allocate()152		self._initialConditionsFunction(sim_data)153		self._timeTotal = self.initialTime()154		for hook in six.viewvalues(self.hooks):155			hook.postCalcInitialConditions(self)156		# Make permanent reference to evaluation time listener157		self._eval_time = self.listeners["EvaluationTime"]158		# Perform initial mass calculations159		for state in six.viewvalues(self.internal_states):160			state.calculateMass()161		# Update environment state according to the current time in time series162		for external_state in six.viewvalues(self.external_states):163			external_state.update()164		# Perform initial listener update165		for listener in six.viewvalues(self.listeners):166			listener.initialUpdate()167		# Start logging168		for logger in six.viewvalues(self.loggers):169			logger.initialize(self)170	def _initLoggers(self):171		self.loggers = collections.OrderedDict()172		if self._logToShell:173			self.loggers["Shell"] = wholecell.loggers.shell.Shell(174				self._shellColumnHeaders175				)176		if self._logToDisk:177			self.loggers["Disk"] = wholecell.loggers.disk.Disk(178				self._outputDir,179				self._overwriteExistingFiles,180				self._logToDiskEvery181				)182	# Run simulation183	def run(self):184		"""185		Run the simulation for the time period specified in `self._lengthSec`186		and then clean up.187		"""188		try:189			self.run_incremental(self._lengthSec + self.initialTime())190			if not self._raise_on_time_limit:191				self.cellCycleComplete()192		finally:193			self.finalize()194		if self._raise_on_time_limit and not self._cellCycleComplete:195			raise SimulationException('Simulation time limit reached without cell division')196	def run_incremental(self, run_until):197		"""198		Run the simulation for a given amount of time.199		Args:200		    run_until (float): absolute time to run the simulation until.201		"""202		# Simulate203		while self.time() < run_until and not self._isDead:204			if self.time() > self.initialTime() + self._lengthSec:205				self.cellCycleComplete()206			if self._cellCycleComplete:207				self.finalize()208				break209			self._simulationStep += 1210			self._timeTotal += self._timeStepSec211			self._pre_evolve_state()212			for processes in self._processClasses:213				self._evolveState(processes)214			self._post_evolve_state()215	def run_for(self, run_for):216		self.run_incremental(self.time() + run_for)217	def finalize(self):218		"""219		Clean up any details once the simulation has finished.220		Specifically, this calls `finalize` in all hooks,221		invokes the simulation's `_divideCellFunction` if the222		cell cycle has completed and then shuts down all loggers.223		"""224		if not self._finalized:225			# Run post-simulation hooks226			for hook in six.viewvalues(self.hooks):227				hook.finalize(self)228			# Divide mother into daughter cells229			if self._cellCycleComplete:230				self.daughter_paths = self._divideCellFunction()231			# Finish logging232			for logger in six.viewvalues(self.loggers):233				logger.finalize(self)234			self._finalized = True235	def _pre_evolve_state(self):236		self._adjustTimeStep()237		# Run pre-evolveState hooks238		for hook in six.viewvalues(self.hooks):239			hook.preEvolveState(self)240		# Reset process mass difference arrays241		for state in six.viewvalues(self.internal_states):242			state.reset_process_mass_diffs()243		# Reset values in evaluationTime listener244		self._eval_time.reset_evaluation_times()245	# Calculate temporal evolution246	def _evolveState(self, processes):247		# Update queries248		# TODO: context manager/function calls for this logic?249		for i, state in enumerate(six.viewvalues(self.internal_states)):250			t = monotonic_seconds()251			state.updateQueries()252			self._eval_time.update_queries_times[i] += monotonic_seconds() - t253		# Calculate requests254		for i, process in enumerate(six.viewvalues(self.processes)):255			if process.__class__ in processes:256				t = monotonic_seconds()257				process.calculateRequest()258				self._eval_time.calculate_request_times[i] += monotonic_seconds() - t259		# Partition states among processes260		for i, state in enumerate(six.viewvalues(self.internal_states)):261			t = monotonic_seconds()262			state.partition(processes)263			self._eval_time.partition_times[i] += monotonic_seconds() - t264		# Simulate submodels265		for i, process in enumerate(six.viewvalues(self.processes)):266			if process.__class__ in processes:267				t = monotonic_seconds()268				process.evolveState()269				self._eval_time.evolve_state_times[i] += monotonic_seconds() - t270		# Check that timestep length was short enough271		for process_name, process in six.viewitems(self.processes):272			if process_name in processes and not process.wasTimeStepShortEnough():273				raise Exception("The timestep (%.3f) was too long at step %i, failed on process %s" % (self._timeStepSec, self.simulationStep(), str(process.name())))274		# Merge state275		for i, state in enumerate(six.viewvalues(self.internal_states)):276			t = monotonic_seconds()277			state.merge(processes)278			self._eval_time.merge_times[i] += monotonic_seconds() - t279		# update environment state280		for state in six.viewvalues(self.external_states):281			state.update()282	def _post_evolve_state(self):283		# Calculate mass of all molecules after evolution284		for i, state in enumerate(six.viewvalues(self.internal_states)):285			t = monotonic_seconds()286			state.calculateMass()287			self._eval_time.calculate_mass_times[i] = monotonic_seconds() - t288		# Update listeners289		for i, listener in enumerate(six.viewvalues(self.listeners)):290			t = monotonic_seconds()291			listener.update()292			self._eval_time.update_times[i] = monotonic_seconds() - t293		# Run post-evolveState hooks294		for hook in six.viewvalues(self.hooks):295			hook.postEvolveState(self)296		# Append loggers297		for i, logger in enumerate(six.viewvalues(self.loggers)):298			t = monotonic_seconds()299			logger.append(self)300			# Note: these values are written at the next timestep301			self._eval_time.append_times[i] = monotonic_seconds() - t302	def _seedFromName(self, name):303		return binascii.crc32(name.encode('utf-8'), self._seed) & 0xffffffff304	def initialTime(self):305		return self._initialTime306	# Save to disk307	def tableCreate(self, tableWriter):308		tableWriter.writeAttributes(309			states = list(self.internal_states.keys()),310			processes = list(self.processes.keys())311			)312	def tableAppend(self, tableWriter):313		tableWriter.append(314			time = self.time(),315			timeStepSec = self.timeStepSec()316			)317	def time(self):318		return self._timeTotal319	def simulationStep(self):320		return self._simulationStep321	def timeStepSec(self):322		return self._timeStepSec323	def lengthSec(self):324		return self._lengthSec325	def cellCycleComplete(self):326		self._cellCycleComplete = True327	def get_sim_data(self):328		return self._simData329	def _adjustTimeStep(self):330		# Adjust timestep if needed or at a frequency of updateTimeStepFreq regardless331		validTimeSteps = self._maxTimeStep * np.ones(len(self.processes))332		resetTimeStep = False333		for i, process in enumerate(six.viewvalues(self.processes)):334			if not process.isTimeStepShortEnough(self._timeStepSec, self._timeStepSafetyFraction) or self.simulationStep() % self._updateTimeStepFreq == 0:335				validTimeSteps[i] = self._findTimeStep(0., self._maxTimeStep, process.isTimeStepShortEnough)336				resetTimeStep = True337		if resetTimeStep:338			self._timeStepSec = validTimeSteps.min()339	def _findTimeStep(self, minTimeStep, maxTimeStep, checkerFunction):340		N = 10000341		candidateTimeStep = maxTimeStep342		for i in range(N):343			if checkerFunction(candidateTimeStep, self._timeStepSafetyFraction):344				minTimeStep = candidateTimeStep345				if (maxTimeStep - minTimeStep) / minTimeStep <= 1e-2:346					break347			else:...

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