parPE
v0.4.4
Contents:
About parPE
FAQ
Usage
parPE API
parPE
Docs
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
author (conf attribute)
(setup attribute)
author_email (setup attribute)
autoescape (parpe.loadleveler attribute)
B
breathe_default_project (conf attribute)
breathe_projects (conf attribute)
built-in function
conf.setup()
extractMultiStartParameters.extractMultiStartResults()
extractMultiStartParameters.main()
extractMultiStartParameters.printUsage()
final_parameters_to_tsv.final_parameters_to_df()
final_parameters_to_tsv.main()
final_parameters_to_tsv.parse_cli_args()
mergeResultFiles.copyRecursive()
mergeResultFiles.main()
mergeResultFiles.mergeFiles()
mergeResultFiles.printUsage()
optimizationOptions.convertValue()
optimizationOptions.getOptionsObject()
optimizationOptions.printAttributes()
optimizationOptions.printOptions()
optimizationOptions.printUsage()
optimizationOptions.setOption()
optimizationOptions.unsetOption()
parpe.dataprovider.DataProvider.__init__()
parpe.dataprovider.DataProvider.apply_model_settings()
parpe.dataprovider.DataProvider.apply_solver_settings()
parpe.dataprovider.DataProvider.get_expdata_for_condition()
parpe.dataprovider.DataProvider.get_opt_sim_mapping()
parpe.dataprovider.DataProvider.get_starting_points()
parpe.dataprovider.DataProvider.num_simulations()
parpe.hdf5.write_float_array()
parpe.hdf5.write_int_array()
parpe.hdf5.write_string_array()
parpe.hdf5_pe_input.HDF5DataGenerator.__init__()
parpe.hdf5_pe_input.HDF5DataGenerator.create_fixed_parameter_dataset_and_write_attributes()
parpe.hdf5_pe_input.HDF5DataGenerator.generate_file()
parpe.hdf5_pe_input.HDF5DataGenerator.get_index_mapping_for_par()
parpe.hdf5_pe_input.HDF5DataGenerator.handle_offset_parameter()
parpe.hdf5_pe_input.HDF5DataGenerator.write_measurements()
parpe.hdf5_pe_input.main()
parpe.hdf5_pe_input.parse_cli_args()
parpe.hdf5_pe_input.requires_preequilibration()
parpe.hdf5_pe_input.write_optimization_options()
parpe.hdf5_pe_input.write_parameter_map()
parpe.hierarchical_optimization.get_analytical_parameter_table()
parpe.hierarchical_optimization.get_candidates_for_hierarchical()
parpe.hierarchical_optimization.parameter_is_offset_parameter()
parpe.hierarchical_optimization.parameter_is_scaling_parameter()
parpe.loadleveler.create_job_file()
parpe.misc.compare_optimization_results_to_true_parameters()
parpe.misc.concatenateStarts()
parpe.misc.get_amici_model()
parpe.misc.get_global_name_for_local_parameter()
parpe.misc.getConditionNames()
parpe.misc.getCorrTable()
parpe.misc.getCorrTableLegacy()
parpe.misc.getCostTrajectories()
parpe.misc.getCostTrajectory2()
parpe.misc.getCostTrajectoryFromSummary()
parpe.misc.getFinalCostFromSummary()
parpe.misc.readSimulationsFromFile()
parpe.misc.readSimulationsFromFileLegacy()
parpe.misc.simulation_to_df()
parpe.misc.unique_ordered()
parpe.petab.get_noise_placeholders_by_observable()
parpe.petab.get_observable_placeholders_by_observable()
parpe.petab.get_parameter_override_id_to_placeholder_id()
parpe.plotting.correlation_coefficient()
parpe.plotting.flatten_filter_nan()
parpe.plotting.plotCorrelation()
parpe.plotting.plotCorrelationBox()
parpe.plotting.plotCorrelationBoxMulti()
parpe.plotting.plotCorrelationDensity()
parpe.plotting.plotCorrelationOld()
parpe.plotting.plotCorrelations()
parpe.plotting.plotCorrelationsByObsDensity()
parpe.plotting.plotCostTrajectory()
parpe.plotting.plotDoseResponseCategorical()
parpe.plotting.plotDoseResponseLogDose()
parpe.plotting.plotTrajectoryFit()
parpe.plotting.plotTrajectoryFits()
parpe.plotting.plotWaterfall()
parpe.plotting.square_plot_equal_ranges()
selectStartingPoints.backupStartsIfNotExists()
selectStartingPoints.getOptionsObject()
selectStartingPoints.parse_selection()
selectStartingPoints.printStarts()
selectStartingPoints.printUsage()
selectStartingPoints.setStarts()
selectStartingPoints.updateOptions()
C
check (conf attribute)
chinese (conf attribute)
compression (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
condition_id_to_index (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
condition_ids (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
condition_map (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
conf.setup()
built-in function
context (conf attribute)
copyright (conf attribute)
cwd (conf attribute)
D
description (setup attribute)
doc_dir (conf attribute)
E
ENTRY_POINTS (setup attribute)
entry_points (setup attribute)
env (parpe.loadleveler attribute)
exclude_patterns (conf attribute)
exhale_args (conf attribute)
extensions (conf attribute)
extractMultiStartParameters.extractMultiStartResults()
built-in function
extractMultiStartParameters.main()
built-in function
extractMultiStartParameters.printUsage()
built-in function
F
f (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
filename (optimizationOptions attribute)
(parpe.dataprovider.DataProvider attribute)
(selectStartingPoints attribute)
final_parameters_to_tsv.final_parameters_to_df()
built-in function
final_parameters_to_tsv.main()
built-in function
final_parameters_to_tsv.parse_cli_args()
built-in function
G
github_doc_root (conf attribute)
H
highlight_language (conf attribute)
html_context (conf attribute)
html_logo (conf attribute)
html_static_path (conf attribute)
html_style (conf attribute)
html_theme (conf attribute)
html_theme_options (conf attribute)
html_theme_path (conf attribute)
I
install_requires (setup attribute)
int (parpe.hdf5_pe_input attribute)
J
japanese (conf attribute)
L
language_user (conf attribute)
latex_elements (conf attribute)
latex_elements_rtd (conf attribute)
latex_elements_user (conf attribute)
latex_engine (conf attribute)
latex_engine_user (conf attribute)
latex_use_xindy (conf attribute)
loader (parpe.loadleveler attribute)
M
mergeResultFiles.copyRecursive()
built-in function
mergeResultFiles.main()
built-in function
mergeResultFiles.mergeFiles()
built-in function
mergeResultFiles.printUsage()
built-in function
N
name (setup attribute)
nk (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
num_condition_vectors (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
ny (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
O
observable_ids (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
on_rtd (conf attribute)
optimization_parameter_name_to_index (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
optimizationOptions.convertValue()
built-in function
optimizationOptions.getOptionsObject()
built-in function
optimizationOptions.printAttributes()
built-in function
optimizationOptions.printOptions()
built-in function
optimizationOptions.printUsage()
built-in function
optimizationOptions.setOption()
built-in function
optimizationOptions.unsetOption()
built-in function
P
packages (setup attribute)
parameter_mapping (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
parpe.dataprovider.DataProvider (built-in class)
parpe.dataprovider.DataProvider.__init__()
built-in function
parpe.dataprovider.DataProvider.apply_model_settings()
built-in function
parpe.dataprovider.DataProvider.apply_solver_settings()
built-in function
parpe.dataprovider.DataProvider.get_expdata_for_condition()
built-in function
parpe.dataprovider.DataProvider.get_opt_sim_mapping()
built-in function
parpe.dataprovider.DataProvider.get_starting_points()
built-in function
parpe.dataprovider.DataProvider.num_simulations()
built-in function
parpe.hdf5.write_float_array()
built-in function
parpe.hdf5.write_int_array()
built-in function
parpe.hdf5.write_string_array()
built-in function
parpe.hdf5_pe_input.HDF5DataGenerator (built-in class)
parpe.hdf5_pe_input.HDF5DataGenerator.__init__()
built-in function
parpe.hdf5_pe_input.HDF5DataGenerator.create_fixed_parameter_dataset_and_write_attributes()
built-in function
parpe.hdf5_pe_input.HDF5DataGenerator.generate_file()
built-in function
parpe.hdf5_pe_input.HDF5DataGenerator.get_index_mapping_for_par()
built-in function
parpe.hdf5_pe_input.HDF5DataGenerator.handle_offset_parameter()
built-in function
parpe.hdf5_pe_input.HDF5DataGenerator.write_measurements()
built-in function
parpe.hdf5_pe_input.main()
built-in function
parpe.hdf5_pe_input.parse_cli_args()
built-in function
parpe.hdf5_pe_input.requires_preequilibration()
built-in function
parpe.hdf5_pe_input.write_optimization_options()
built-in function
parpe.hdf5_pe_input.write_parameter_map()
built-in function
parpe.hierarchical_optimization.get_analytical_parameter_table()
built-in function
parpe.hierarchical_optimization.get_candidates_for_hierarchical()
built-in function
parpe.hierarchical_optimization.parameter_is_offset_parameter()
built-in function
parpe.hierarchical_optimization.parameter_is_scaling_parameter()
built-in function
parpe.loadleveler.create_job_file()
built-in function
parpe.misc.compare_optimization_results_to_true_parameters()
built-in function
parpe.misc.concatenateStarts()
built-in function
parpe.misc.get_amici_model()
built-in function
parpe.misc.get_global_name_for_local_parameter()
built-in function
parpe.misc.getConditionNames()
built-in function
parpe.misc.getCorrTable()
built-in function
parpe.misc.getCorrTableLegacy()
built-in function
parpe.misc.getCostTrajectories()
built-in function
parpe.misc.getCostTrajectory2()
built-in function
parpe.misc.getCostTrajectoryFromSummary()
built-in function
parpe.misc.getFinalCostFromSummary()
built-in function
parpe.misc.ParameterEstimationResultFile (built-in class)
parpe.misc.ParameterEstimationSummaryFile (built-in class)
parpe.misc.readSimulationsFromFile()
built-in function
parpe.misc.readSimulationsFromFileLegacy()
built-in function
parpe.misc.simulation_to_df()
built-in function
parpe.misc.unique_ordered()
built-in function
parpe.petab.get_noise_placeholders_by_observable()
built-in function
parpe.petab.get_observable_placeholders_by_observable()
built-in function
parpe.petab.get_parameter_override_id_to_placeholder_id()
built-in function
parpe.plotting.correlation_coefficient()
built-in function
parpe.plotting.flatten_filter_nan()
built-in function
parpe.plotting.plotCorrelation()
built-in function
parpe.plotting.plotCorrelationBox()
built-in function
parpe.plotting.plotCorrelationBoxMulti()
built-in function
parpe.plotting.plotCorrelationDensity()
built-in function
parpe.plotting.plotCorrelationOld()
built-in function
parpe.plotting.plotCorrelations()
built-in function
parpe.plotting.plotCorrelationsByObsDensity()
built-in function
parpe.plotting.plotCostTrajectory()
built-in function
parpe.plotting.plotDoseResponseCategorical()
built-in function
parpe.plotting.plotDoseResponseLogDose()
built-in function
parpe.plotting.plotTrajectoryFit()
built-in function
parpe.plotting.plotTrajectoryFits()
built-in function
parpe.plotting.plotWaterfall()
built-in function
parpe.plotting.square_plot_equal_ranges()
built-in function
parpe::act (C++ member)
parpe::almostEqual (C++ function)
parpe::applyChainRule (C++ function)
parpe::applyOptimalOffset (C++ function)
parpe::applyOptimalScaling (C++ function)
parpe::calcf (C++ function)
parpe::calcg (C++ function)
parpe::checkGradientForAnalyticalParameters (C++ function)
parpe::closeHDF5File (C++ function)
parpe::column_vector (C++ type)
parpe::computeAnalyticalOffsets (C++ function)
parpe::computeAnalyticalScalings (C++ function)
parpe::computeAnalyticalSigmas (C++ function)
parpe::constr (C++ function)
parpe::createDirectoryIfNotExists (C++ function)
parpe::dblOpts (C++ member)
parpe::dlibColumnVectorFromDoubleArray (C++ function)
parpe::error (C++ function)
parpe::fileExists (C++ function)
parpe::fillArrayRandomDoubleIndividualInterval (C++ function)
parpe::fillArrayRandomDoubleSameInterval (C++ function)
parpe::fillFilteredParams (C++ function)
parpe::finalizeMpiIfNeeded (C++ function)
parpe::fsqpGetLock (C++ function)
parpe::FsqpProblem (C++ class)
parpe::FsqpProblem::bigbnd (C++ member)
parpe::FsqpProblem::bl (C++ member)
parpe::FsqpProblem::bu (C++ member)
parpe::FsqpProblem::eps (C++ member)
parpe::FsqpProblem::epseqn (C++ member)
parpe::FsqpProblem::f (C++ member)
parpe::FsqpProblem::FsqpProblem (C++ function)
parpe::FsqpProblem::g (C++ member)
parpe::FsqpProblem::gradientDummy (C++ member)
parpe::FsqpProblem::gradob (C++ function)
parpe::FsqpProblem::inform (C++ member)
parpe::FsqpProblem::iprint (C++ member)
parpe::FsqpProblem::iw (C++ member)
parpe::FsqpProblem::iwsize (C++ member)
parpe::FsqpProblem::miter (C++ member)
parpe::FsqpProblem::mode (C++ member)
parpe::FsqpProblem::neq (C++ member)
parpe::FsqpProblem::neqn (C++ member)
parpe::FsqpProblem::nf (C++ member)
parpe::FsqpProblem::nineq (C++ member)
parpe::FsqpProblem::nineqn (C++ member)
parpe::FsqpProblem::nparam (C++ member)
parpe::FsqpProblem::nwsize (C++ member)
parpe::FsqpProblem::obj (C++ function)
parpe::FsqpProblem::optimize (C++ function)
parpe::FsqpProblem::problem (C++ member)
parpe::FsqpProblem::reporter (C++ member)
parpe::FsqpProblem::udelta (C++ member)
parpe::FsqpProblem::w (C++ member)
parpe::FsqpProblem::x (C++ member)
parpe::fsqpReleaseLock (C++ function)
parpe::general_matrix (C++ type)
parpe::getBacktrace (C++ function)
parpe::getCeresOptions (C++ function)
parpe::getDefaultOffsetParameter (C++ function)
parpe::getDefaultScalingFactor (C++ function)
parpe::getFinalParameters (C++ function)
parpe::getFunctionEvaluationWithMinimalCost (C++ function)
parpe::getLocalOptimum (C++ function)
parpe::getLocalOptimumThreadWrapper (C++ function)
parpe::getModelOutputsAndSigmas (C++ function)
parpe::getMpiActive (C++ function)
parpe::getMpiCommSize (C++ function)
parpe::getMpiRank (C++ function)
parpe::getNumStarts (C++ function)
parpe::getNwff (C++ function)
parpe::getNwgrf (C++ function)
parpe::getOuterParameters (C++ function)
parpe::getParameterTrajectory (C++ function)
parpe::getProblemFromFj (C++ function)
parpe::getProblemFromGradFj (C++ function)
parpe::getScalarProduct (C++ function)
parpe::getVectorDifference (C++ function)
parpe::getVectorNorm (C++ function)
parpe::gradcn (C++ function)
parpe::gradob (C++ function)
parpe::hdf5AttributeExists (C++ function)
parpe::hdf5CreateExtendableDouble2DArray (C++ function)
parpe::hdf5CreateExtendableDouble3DArray (C++ function)
parpe::hdf5CreateExtendableInt2DArray (C++ function)
parpe::hdf5CreateExtendableString1DArray (C++ function)
parpe::hdf5CreateGroup (C++ function)
parpe::hdf5CreateOrExtendAndWriteToDouble2DArray (C++ function)
parpe::hdf5CreateOrExtendAndWriteToDouble3DArray (C++ function)
parpe::hdf5CreateOrExtendAndWriteToInt2DArray (C++ function)
parpe::hdf5CreateOrExtendAndWriteToString1DArray (C++ function)
parpe::hdf5ErrorStackWalker_cb (C++ function)
parpe::hdf5Extend2ndDimensionAndWriteToDouble2DArray (C++ function)
parpe::hdf5Extend2ndDimensionAndWriteToInt2DArray (C++ function)
parpe::hdf5Extend3rdDimensionAndWriteToDouble3DArray (C++ function)
parpe::hdf5ExtendAndWriteToString1DArray (C++ function)
parpe::hdf5Get3DDoubleHyperslab (C++ function)
parpe::hdf5GetDatasetDimensions (C++ function)
parpe::hdf5MutexGetLock (C++ function)
parpe::hdf5OpenForAppending (C++ function)
parpe::hdf5OpenForReading (C++ function)
parpe::hdf5Read1DIntegerHyperslab (C++ function)
parpe::hdf5Read1dStringDataset (C++ function)
parpe::hdf5Read2DDoubleHyperslab (C++ function)
parpe::hdf5Read2DIntegerHyperslab (C++ function)
parpe::hdf5Read3DDoubleHyperslab (C++ function)
parpe::hdf5Write1dStringDataset (C++ function)
parpe::hdf5WriteStringAttribute (C++ function)
parpe::informExitStatus (C++ enum)
parpe::informExitStatus::bigbndExceeded (C++ enumerator)
parpe::informExitStatus::converged (C++ enumerator)
parpe::informExitStatus::equivalentIterates (C++ enumerator)
parpe::informExitStatus::failureInconsistentInput (C++ enumerator)
parpe::informExitStatus::failureQPSolverD0 (C++ enumerator)
parpe::informExitStatus::failureQPSolverD1 (C++ enumerator)
parpe::informExitStatus::infeasibleStartingPointByLinearContraints (C++ enumerator)
parpe::informExitStatus::infeasibleStartingPointByNonLinearContraints (C++ enumerator)
parpe::informExitStatus::lineSearchStepTooSmall (C++ enumerator)
parpe::informExitStatus::maxIterationsReached (C++ enumerator)
parpe::initHDF5Mutex (C++ function)
parpe::intOpts (C++ member)
parpe::ipOptGetLock (C++ function)
parpe::ipOptReleaseLock (C++ function)
parpe::iprintPrintLevel (C++ enum)
parpe::iprintPrintLevel::eachIteration (C++ enumerator)
parpe::iprintPrintLevel::eachIterationDetailed (C++ enumerator)
parpe::iprintPrintLevel::firstLast (C++ enumerator)
parpe::iprintPrintLevel::nothing (C++ enumerator)
parpe::loglevelShortStr (C++ member)
parpe::logProcessStats (C++ function)
parpe::messageHandler (C++ function)
parpe::minimumLogLevel (C++ member)
parpe::mkpath (C++ function)
parpe::mkpathConstChar (C++ function)
parpe::mutexFsqp (C++ member)
parpe::mutexFsqpType (C++ type)
parpe::mutexHdf (C++ member)
parpe::MyCeresFirstOrderFunction (C++ class)
parpe::MyCeresFirstOrderFunction::Evaluate (C++ function)
parpe::MyCeresFirstOrderFunction::MyCeresFirstOrderFunction (C++ function)
parpe::MyCeresFirstOrderFunction::NumParameters (C++ function)
parpe::MyIterationCallback (C++ class)
parpe::MyIterationCallback::MyIterationCallback (C++ function)
parpe::MyIterationCallback::operator() (C++ function)
parpe::obj (C++ function)
parpe::oldact (C++ member)
parpe::operator== (C++ function)
parpe::optimizationOptionsFromAttribute (C++ function)
parpe::optimizerFactory (C++ function)
parpe::patch::to_string (C++ function)
parpe::printAvailableOptimizers (C++ function)
parpe::printBacktrace (C++ function)
parpe::printDebugInfoAndWait (C++ function)
parpe::printfToString (C++ function)
parpe::printlogmessage (C++ function)
parpe::printMPIInfo (C++ function)
parpe::printSimulationResult (C++ function)
parpe::randDouble (C++ function)
parpe::runAlongTrajectory (C++ function)
parpe::runAndLogSimulation (C++ function)
parpe::runFinalParameters (C++ function)
parpe::runInParallelAndWaitForFinish (C++ function)
parpe::runMinibatchOptimization (C++ function)
parpe::runNominalParameters (C++ function)
parpe::runSimulationTasks (C++ function)
parpe::runSimulator (C++ function)
parpe::saveSimulation (C++ function)
parpe::saveTotalCpuTime (C++ function)
parpe::setCeresOption (C++ function)
parpe::setIpOptOption (C++ function)
parpe::setIpOptOptions (C++ function)
parpe::setMinibatchOption (C++ function)
parpe::setToms611Option (C++ function)
parpe::signalHandler (C++ function)
parpe::spliceParameters (C++ function)
parpe::strFormatCurrentLocaltime (C++ function)
parpe::strOpts (C++ member)
parpe::sumslUserData (C++ struct)
parpe::sumslUserData::parametersMax (C++ member)
parpe::sumslUserData::parametersMin (C++ member)
parpe::sumslUserData::problem (C++ member)
parpe::sumslUserData::reporter (C++ member)
parpe::swap (C++ function)
parpe::toms611intOptionsIndices (C++ enum)
parpe::toms611intOptionsIndices::inith (C++ enumerator)
parpe::toms611intOptionsIndices::mxfcal (C++ enumerator)
parpe::toms611intOptionsIndices::mxiter (C++ enumerator)
parpe::toms611intOptionsIndices::outlev (C++ enumerator)
parpe::toms611intOptionsIndices::solprt (C++ enumerator)
parpe::toms611intOptionsIndices::x0prt (C++ enumerator)
parpe::toms611realOptionsIndices (C++ enum)
parpe::toms611realOptionsIndices::afctol (C++ enumerator)
parpe::toms611realOptionsIndices::bias (C++ enumerator)
parpe::toms611realOptionsIndices::dinit (C++ enumerator)
parpe::toms611realOptionsIndices::lmax0 (C++ enumerator)
parpe::toms611realOptionsIndices::lmaxs (C++ enumerator)
parpe::toms611realOptionsIndices::rfctol (C++ enumerator)
parpe::toms611realOptionsIndices::sctol (C++ enumerator)
parpe::toms611realOptionsIndices::tuner1 (C++ enumerator)
parpe::toms611realOptionsIndices::xctol (C++ enumerator)
parpe::toms611realOptionsIndices::xftol (C++ enumerator)
parpe::warning (C++ function)
parpe_dir (conf attribute)
problem_parameter_ids (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
project (conf attribute)
project_language (conf attribute)
R
release (conf attribute)
replacements (conf attribute)
S
selection (selectStartingPoints attribute)
selectStartingPoints.backupStartsIfNotExists()
built-in function
selectStartingPoints.getOptionsObject()
built-in function
selectStartingPoints.parse_selection()
built-in function
selectStartingPoints.printStarts()
built-in function
selectStartingPoints.printUsage()
built-in function
selectStartingPoints.setStarts()
built-in function
selectStartingPoints.updateOptions()
built-in function
source_suffix (conf attribute)
startingPointBackupPath (selectStartingPoints attribute)
startingPointPath (selectStartingPoints attribute)
SUFFIX (conf attribute)
T
templates_path (conf attribute)
theme (conf attribute)
U
unique_timepoints (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
url (setup attribute)
using_rtd_theme (conf attribute)
V
verbose (parpe.hdf5_pe_input.HDF5DataGenerator attribute)
version (setup attribute)
W
websupport2_base_url (conf attribute)
websupport2_static_url (conf attribute)
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v: v0.4.4
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