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I

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"calc_data_generator_results() (in module biosimulators_utils.sedml.utils)": [[24, "biosimulators_utils.sedml.utils.calc_data_generator_results", false]], "calc_data_generators_results() (in module biosimulators_utils.sedml.utils)": [[24, "biosimulators_utils.sedml.utils.calc_data_generators_results", false]], "cannotexportmultidimensionaltablewarning": [[23, "biosimulators_utils.report.warnings.CannotExportMultidimensionalTableWarning", false]], "caption (biosimulators_utils.ref.data_model.pubmedcentralopenaccesgraphic attribute)": [[22, "biosimulators_utils.ref.data_model.PubMedCentralOpenAccesGraphic.caption", false], [22, "id11", false]], "catch_errors() (biosimulators_utils.gh_action.core.githubactionerrorhandling class method)": [[8, "biosimulators_utils.gh_action.core.GitHubActionErrorHandling.catch_errors", false]], "cellml (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, 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"biosimulators_utils.sedml.data_model.Model.changes", false]], "changes (biosimulators_utils.sedml.data_model.repeatedtask attribute)": [[24, "biosimulators_utils.sedml.data_model.RepeatedTask.changes", false]], "circle (biosimulators_utils.sedml.data_model.markerstyletype attribute)": [[24, "biosimulators_utils.sedml.data_model.MarkerStyleType.circle", false]], "citation (class in biosimulators_utils.biosimulations.data_model)": [[6, "biosimulators_utils.biosimulations.data_model.Citation", false]], "citations (biosimulators_utils.biosimulations.data_model.externalreferences attribute)": [[6, "biosimulators_utils.biosimulations.data_model.ExternalReferences.citations", false]], "close_issue() (biosimulators_utils.gh_action.core.githubaction class method)": [[8, "biosimulators_utils.gh_action.core.GitHubAction.close_issue", false]], "code (biosimulators_utils.utils.identifiers_org.identifiersorgcountry attribute)": [[27, 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"biosimulators_utils.sedml.math.compile_math", false]], "computemodelchange (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.ComputeModelChange", false]], "config (class in biosimulators_utils.config)": [[4, "biosimulators_utils.config.Config", false]], "contents (biosimulators_utils.combine.data_model.combinearchive attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchive.contents", false]], "convert_docker_image_to_singularity() (in module biosimulators_utils.image)": [[4, "biosimulators_utils.image.convert_docker_image_to_singularity", false]], "convert_xml_node_to_string() (in module biosimulators_utils.sedml.utils)": [[24, "biosimulators_utils.sedml.utils.convert_xml_node_to_string", false]], "copasiml (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.CopasiML", false]], "copasiml 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"biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource.country", false]], "cpp_header (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.CPP_HEADER", false]], "cpp_header (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.CPP_HEADER", false]], "cpp_source (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.CPP_SOURCE", false]], "cpp_source (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.CPP_SOURCE", false]], "created (biosimulators_utils.biosimulations.data_model.metadata attribute)": [[6, 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(biosimulators_utils.report.data_model.reportformat attribute)": [[23, "biosimulators_utils.report.data_model.ReportFormat.csv", false]], "cubic_bezier_angle() (in module biosimulators_utils.viz.utils)": [[28, "biosimulators_utils.viz.utils.cubic_bezier_angle", false]], "cubic_bezier_point() (in module biosimulators_utils.viz.utils)": [[28, "biosimulators_utils.viz.utils.cubic_bezier_point", false]], "curve (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.Curve", false]], "curves (biosimulators_utils.log.data_model.plot2dlog attribute)": [[11, "biosimulators_utils.log.data_model.Plot2DLog.curves", false]], "curves (biosimulators_utils.sedml.data_model.plot2d attribute)": [[24, "biosimulators_utils.sedml.data_model.Plot2D.curves", false]], "dash (biosimulators_utils.sedml.data_model.linestyletype attribute)": [[24, "biosimulators_utils.sedml.data_model.LineStyleType.dash", false]], "dashdot (biosimulators_utils.sedml.data_model.linestyletype 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"datageneratorresults (class in biosimulators_utils.report.data_model)": [[23, "biosimulators_utils.report.data_model.DataGeneratorResults", false]], "dataset (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.DataSet", false]], "datasetresults (class in biosimulators_utils.report.data_model)": [[23, "biosimulators_utils.report.data_model.DataSetResults", false]], "date (biosimulators_utils.ref.data_model.journalarticle attribute)": [[22, "biosimulators_utils.ref.data_model.JournalArticle.date", false], [22, "id1", false]], "debug (biosimulators_utils.config.config attribute)": [[4, "biosimulators_utils.config.Config.DEBUG", false]], "deprecated (biosimulators_utils.utils.identifiers_org.identifiersorgnamespace attribute)": [[27, "biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace.deprecated", false]], "deprecated (biosimulators_utils.utils.identifiers_org.identifiersorgnamespaceresource attribute)": [[27, 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"sample_id (biosimulators_utils.utils.identifiers_org.identifiersorgnamespaceresource attribute)": [[27, "biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource.sample_id", false]], "sanitize_model() (in module biosimulators_utils.model_lang.xpp.validation)": [[20, "biosimulators_utils.model_lang.xpp.validation.sanitize_model", false]], "save_keys_to_license_file() (biosimulators_utils.licensing.gurobi.gurobilicensemanager method)": [[10, "biosimulators_utils.licensing.gurobi.GurobiLicenseManager.save_keys_to_license_file", false]], "save_plot_data (biosimulators_utils.config.config attribute)": [[4, "biosimulators_utils.config.Config.SAVE_PLOT_DATA", false]], "save_simularium_file() (biosimulators_utils.model_lang.smoldyn.simularium_converter.biosimulatorsdataconverter static method)": [[19, "biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter.save_simularium_file", false]], "sbgn 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attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SED_ML", false]], "sedbase (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.SedBase", false]], "seddocument (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.SedDocument", false]], "seddocumentlog (class in biosimulators_utils.log.data_model)": [[11, "biosimulators_utils.log.data_model.SedDocumentLog", false]], "seddocumentresults (class in biosimulators_utils.report.data_model)": [[23, "biosimulators_utils.report.data_model.SedDocumentResults", false]], "sedidgroupmixin (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.SedIdGroupMixin", false]], "sedmlexecutionerror": [[24, "biosimulators_utils.sedml.exceptions.SedmlExecutionError", false]], "sedmlfeaturenotsupportedwarning": [[24, "biosimulators_utils.sedml.warnings.SedmlFeatureNotSupportedWarning", false]], "sedmlsimulationreader (class in biosimulators_utils.sedml.io)": [[24, "biosimulators_utils.sedml.io.SedmlSimulationReader", false]], "sedmlsimulationwriter (class in biosimulators_utils.sedml.io)": [[24, "biosimulators_utils.sedml.io.SedmlSimulationWriter", false]], "set_model_filepath() (biosimulators_utils.model_lang.smoldyn.simularium_converter.smoldyncombinearchive method)": [[19, "biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynCombineArchive.set_model_filepath", false]], "setvaluecomputemodelchange (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.SetValueComputeModelChange", false]], "shockwave_flash (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.SHOCKWAVE_FLASH", false]], "shockwave_flash (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SHOCKWAVE_FLASH", false]], "simbiology_project (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.SimBiology_Project", false]], "simbiology_project (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SimBiology_Project", false]], "simulation (biosimulators_utils.sedml.data_model.task attribute)": [[24, "biosimulators_utils.sedml.data_model.Task.simulation", false]], "simulation (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.Simulation", false]], "simulations (biosimulators_utils.sedml.data_model.seddocument attribute)": [[24, "biosimulators_utils.sedml.data_model.SedDocument.simulations", false]], "simulator_details (biosimulators_utils.log.data_model.tasklog attribute)": [[11, "biosimulators_utils.log.data_model.TaskLog.simulator_details", false]], "simulatorsubmission (class in biosimulators_utils.simulator_registry.data_model)": [[26, "biosimulators_utils.simulator_registry.data_model.SimulatorSubmission", false]], "size (biosimulators_utils.sedml.data_model.markerstyle attribute)": [[24, "biosimulators_utils.sedml.data_model.MarkerStyle.size", false]], "skip (biosimulators_utils.config.colors attribute)": [[4, "biosimulators_utils.config.Colors.skip", false]], "skip_reason (biosimulators_utils.log.data_model.combinearchivelog attribute)": [[11, "biosimulators_utils.log.data_model.CombineArchiveLog.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.log attribute)": [[11, "biosimulators_utils.log.data_model.Log.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.outputlog attribute)": [[11, "biosimulators_utils.log.data_model.OutputLog.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.plot2dlog attribute)": [[11, "biosimulators_utils.log.data_model.Plot2DLog.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.plot3dlog attribute)": [[11, "biosimulators_utils.log.data_model.Plot3DLog.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.reportlog attribute)": [[11, "biosimulators_utils.log.data_model.ReportLog.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.seddocumentlog attribute)": [[11, "biosimulators_utils.log.data_model.SedDocumentLog.skip_reason", false]], "skip_reason (biosimulators_utils.log.data_model.tasklog attribute)": [[11, "biosimulators_utils.log.data_model.TaskLog.skip_reason", false]], "skipped (biosimulators_utils.config.colors attribute)": [[4, "biosimulators_utils.config.Colors.skipped", false]], "skipped (biosimulators_utils.log.data_model.status attribute)": [[11, "biosimulators_utils.log.data_model.Status.SKIPPED", false]], "sli (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.SLI", false]], "sli (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SLI", false]], "sli (biosimulators_utils.sedml.data_model.modellanguage attribute)": [[24, "biosimulators_utils.sedml.data_model.ModelLanguage.SLI", false]], "sli (biosimulators_utils.sedml.data_model.modellanguageedamid attribute)": [[24, "biosimulators_utils.sedml.data_model.ModelLanguageEdamId.SLI", false]], "sli (biosimulators_utils.sedml.data_model.modellanguagepattern attribute)": [[24, "biosimulators_utils.sedml.data_model.ModelLanguagePattern.SLI", false]], "smoldyn (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.Smoldyn", false]], "smoldyn (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.Smoldyn", false]], "smoldyn (biosimulators_utils.sedml.data_model.modellanguage attribute)": [[24, "biosimulators_utils.sedml.data_model.ModelLanguage.Smoldyn", false]], "smoldyn (biosimulators_utils.sedml.data_model.modellanguageedamid attribute)": [[24, "biosimulators_utils.sedml.data_model.ModelLanguageEdamId.Smoldyn", false]], "smoldyn (biosimulators_utils.sedml.data_model.modellanguagepattern attribute)": [[24, "biosimulators_utils.sedml.data_model.ModelLanguagePattern.Smoldyn", false]], "smoldyncombinearchive (class in biosimulators_utils.model_lang.smoldyn.simularium_converter)": [[19, "biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynCombineArchive", false]], "smoldyndataconverter (class in biosimulators_utils.model_lang.smoldyn.simularium_converter)": [[19, "biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter", false]], "so (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.SO", false]], "so (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SO", false]], "softwareinterface (class in biosimulators_utils.simulator.data_model)": [[25, "biosimulators_utils.simulator.data_model.SoftwareInterface", false]], "solid (biosimulators_utils.sedml.data_model.linestyletype attribute)": [[24, "biosimulators_utils.sedml.data_model.LineStyleType.solid", false]], "source (biosimulators_utils.sedml.data_model.model attribute)": [[24, "biosimulators_utils.sedml.data_model.Model.source", false]], "specifications_patch (biosimulators_utils.simulator_registry.data_model.simulatorsubmission attribute)": [[26, "biosimulators_utils.simulator_registry.data_model.SimulatorSubmission.specifications_patch", false]], "specifications_url (biosimulators_utils.simulator_registry.data_model.simulatorsubmission attribute)": [[26, "biosimulators_utils.simulator_registry.data_model.SimulatorSubmission.specifications_url", false]], "sql (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.SQL", false]], "sql (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SQL", false]], "square (biosimulators_utils.sedml.data_model.markerstyletype attribute)": [[24, "biosimulators_utils.sedml.data_model.MarkerStyleType.square", false]], "standardoutputerrorcapturer (class in biosimulators_utils.log.utils)": [[11, "biosimulators_utils.log.utils.StandardOutputErrorCapturer", false]], "standardoutputerrorcapturerlevel (class in biosimulators_utils.log.data_model)": [[11, "biosimulators_utils.log.data_model.StandardOutputErrorCapturerLevel", false]], "standardoutputnotloggedwarning": [[11, "biosimulators_utils.log.warnings.StandardOutputNotLoggedWarning", false]], "star (biosimulators_utils.sedml.data_model.markerstyletype attribute)": [[24, "biosimulators_utils.sedml.data_model.MarkerStyleType.star", false]], "start (biosimulators_utils.sedml.data_model.uniformrange attribute)": [[24, "biosimulators_utils.sedml.data_model.UniformRange.start", false]], "start() (biosimulators_utils.licensing.core.licensemanager method)": [[10, "biosimulators_utils.licensing.core.LicenseManager.start", false]], "start() (biosimulators_utils.licensing.gurobi.gurobilicensemanager method)": [[10, "biosimulators_utils.licensing.gurobi.GurobiLicenseManager.start", false]], "status (biosimulators_utils.log.data_model.combinearchivelog attribute)": [[11, 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"biosimulators_utils.log.data_model.TaskLog.status", false]], "status (class in biosimulators_utils.log.data_model)": [[11, "biosimulators_utils.log.data_model.Status", false]], "steadystatesimulation (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.SteadyStateSimulation", false]], "step (biosimulators_utils.sedml.data_model.onestepsimulation attribute)": [[24, "biosimulators_utils.sedml.data_model.OneStepSimulation.step", false]], "string (biosimulators_utils.data_model.valuetype attribute)": [[4, "biosimulators_utils.data_model.ValueType.string", false]], "style (biosimulators_utils.sedml.data_model.curve attribute)": [[24, "biosimulators_utils.sedml.data_model.Curve.style", false]], "style (biosimulators_utils.sedml.data_model.surface attribute)": [[24, "biosimulators_utils.sedml.data_model.Surface.style", false]], "style (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.Style", false]], 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false]], "surface (class in biosimulators_utils.sedml.data_model)": [[24, "biosimulators_utils.sedml.data_model.Surface", false]], "surfaces (biosimulators_utils.log.data_model.plot3dlog attribute)": [[11, "biosimulators_utils.log.data_model.Plot3DLog.surfaces", false]], "surfaces (biosimulators_utils.sedml.data_model.plot3d attribute)": [[24, "biosimulators_utils.sedml.data_model.Plot3D.surfaces", false]], "svg (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormat.SVG", false]], "svg (biosimulators_utils.combine.data_model.combinearchivecontentformatpattern attribute)": [[7, "biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern.SVG", false]], "svg (biosimulators_utils.viz.data_model.vizformat attribute)": [[28, "biosimulators_utils.viz.data_model.VizFormat.svg", false]], "svgz (biosimulators_utils.combine.data_model.combinearchivecontentformat attribute)": [[7, 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--- a/docs/source/biosimulators_utils.archive.html +++ b/docs/source/biosimulators_utils.archive.html @@ -8,7 +8,7 @@ - biosimulators_utils.archive package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.archive package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.biosimulations.html b/docs/source/biosimulators_utils.biosimulations.html index 9057c00f..f882ce94 100644 --- a/docs/source/biosimulators_utils.biosimulations.html +++ b/docs/source/biosimulators_utils.biosimulations.html @@ -8,7 +8,7 @@ - biosimulators_utils.biosimulations package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.biosimulations package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.combine.html b/docs/source/biosimulators_utils.combine.html index 7551d304..86346f66 100644 --- a/docs/source/biosimulators_utils.combine.html +++ b/docs/source/biosimulators_utils.combine.html @@ -8,7 +8,7 @@ - biosimulators_utils.combine package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.combine package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.gh_action.html b/docs/source/biosimulators_utils.gh_action.html index eaede5cf..ef8520f5 100644 --- a/docs/source/biosimulators_utils.gh_action.html +++ b/docs/source/biosimulators_utils.gh_action.html @@ -8,7 +8,7 @@ - biosimulators_utils.gh_action package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.gh_action package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.html b/docs/source/biosimulators_utils.html index b1a9e505..80bc9d8f 100644 --- a/docs/source/biosimulators_utils.html +++ b/docs/source/biosimulators_utils.html @@ -8,7 +8,7 @@ - biosimulators_utils package — BioSimulators utils 0.2.0 documentation + biosimulators_utils package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + @@ -1785,6 +1785,7 @@

    Subpackagesget_variables_for_data_generators()

  • get_variables_for_task()
  • get_xml_node_namespace_tag_target()
    • +
  • is_executable_task()
  • is_model_language_encoded_in_xml()
  • remove_algorithm_parameter_changes()
  • remove_model_changes()
    • diff --git a/docs/source/biosimulators_utils.kisao.html b/docs/source/biosimulators_utils.kisao.html index 1d4da702..2b0b4dad 100644 --- a/docs/source/biosimulators_utils.kisao.html +++ b/docs/source/biosimulators_utils.kisao.html @@ -8,7 +8,7 @@ - biosimulators_utils.kisao package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.kisao package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.licensing.html b/docs/source/biosimulators_utils.licensing.html index 4e822b1c..aaccef35 100644 --- a/docs/source/biosimulators_utils.licensing.html +++ b/docs/source/biosimulators_utils.licensing.html @@ -8,7 +8,7 @@ - biosimulators_utils.licensing package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.licensing package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.log.html b/docs/source/biosimulators_utils.log.html index be77e713..7a1a08a6 100644 --- a/docs/source/biosimulators_utils.log.html +++ b/docs/source/biosimulators_utils.log.html @@ -8,7 +8,7 @@ - biosimulators_utils.log package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.log package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.bngl.html b/docs/source/biosimulators_utils.model_lang.bngl.html index cb954650..74e070ed 100644 --- a/docs/source/biosimulators_utils.model_lang.bngl.html +++ b/docs/source/biosimulators_utils.model_lang.bngl.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.bngl package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.bngl package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.cellml.html b/docs/source/biosimulators_utils.model_lang.cellml.html index c06b0136..b19aaa3d 100644 --- a/docs/source/biosimulators_utils.model_lang.cellml.html +++ b/docs/source/biosimulators_utils.model_lang.cellml.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.cellml package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.cellml package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.html b/docs/source/biosimulators_utils.model_lang.html index fa95eb69..825cd5cb 100644 --- a/docs/source/biosimulators_utils.model_lang.html +++ b/docs/source/biosimulators_utils.model_lang.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.lems.html b/docs/source/biosimulators_utils.model_lang.lems.html index 16c8e97f..fe40e905 100644 --- a/docs/source/biosimulators_utils.model_lang.lems.html +++ b/docs/source/biosimulators_utils.model_lang.lems.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.lems package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.lems package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.neuroml.html b/docs/source/biosimulators_utils.model_lang.neuroml.html index 93c61cc7..200eb44a 100644 --- a/docs/source/biosimulators_utils.model_lang.neuroml.html +++ b/docs/source/biosimulators_utils.model_lang.neuroml.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.neuroml package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.neuroml package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.rba.html b/docs/source/biosimulators_utils.model_lang.rba.html index 53ced033..8ec03832 100644 --- a/docs/source/biosimulators_utils.model_lang.rba.html +++ b/docs/source/biosimulators_utils.model_lang.rba.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.rba package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.rba package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.sbml.html b/docs/source/biosimulators_utils.model_lang.sbml.html index 3dbbcfeb..17cb9bf1 100644 --- a/docs/source/biosimulators_utils.model_lang.sbml.html +++ b/docs/source/biosimulators_utils.model_lang.sbml.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.sbml package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.sbml package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.smoldyn.html b/docs/source/biosimulators_utils.model_lang.smoldyn.html index 0e35de25..951e3a9f 100644 --- a/docs/source/biosimulators_utils.model_lang.smoldyn.html +++ b/docs/source/biosimulators_utils.model_lang.smoldyn.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.smoldyn package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.smoldyn package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.model_lang.xpp.html b/docs/source/biosimulators_utils.model_lang.xpp.html index bf301cbe..6ae36b3a 100644 --- a/docs/source/biosimulators_utils.model_lang.xpp.html +++ b/docs/source/biosimulators_utils.model_lang.xpp.html @@ -8,7 +8,7 @@ - biosimulators_utils.model_lang.xpp package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.model_lang.xpp package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.omex_meta.html b/docs/source/biosimulators_utils.omex_meta.html index 0668023a..16ea52f2 100644 --- a/docs/source/biosimulators_utils.omex_meta.html +++ b/docs/source/biosimulators_utils.omex_meta.html @@ -8,7 +8,7 @@ - biosimulators_utils.omex_meta package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.omex_meta package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.ref.html b/docs/source/biosimulators_utils.ref.html index 2f162286..9ee668a8 100644 --- a/docs/source/biosimulators_utils.ref.html +++ b/docs/source/biosimulators_utils.ref.html @@ -8,7 +8,7 @@ - biosimulators_utils.ref package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.ref package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.report.html b/docs/source/biosimulators_utils.report.html index 4062fc2a..4d8df776 100644 --- a/docs/source/biosimulators_utils.report.html +++ b/docs/source/biosimulators_utils.report.html @@ -8,7 +8,7 @@ - biosimulators_utils.report package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.report package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.sedml.html b/docs/source/biosimulators_utils.sedml.html index 38eb451f..f301d3a9 100644 --- a/docs/source/biosimulators_utils.sedml.html +++ b/docs/source/biosimulators_utils.sedml.html @@ -8,7 +8,7 @@ - biosimulators_utils.sedml package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.sedml package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + @@ -402,7 +402,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.AbstractTask(id=None, name=None)[source]#
    +class biosimulators_utils.sedml.data_model.AbstractTask(id: str | None = None, name: str | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    Base class for tasks

    @@ -448,7 +448,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.AddElementModelChange(id=None, name=None, target=None, target_namespaces=None, new_elements=None)[source]#
    +class biosimulators_utils.sedml.data_model.AddElementModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None, new_elements: str | None = None)[source]#

    Bases: ModelChange

    An addition of an element to a model

    @@ -541,7 +541,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Algorithm(kisao_id=None, changes=None)[source]#
    +class biosimulators_utils.sedml.data_model.Algorithm(kisao_id: str | None = None, changes: list[AlgorithmParameterChange] | None = None)[source]#

    Bases: SedBase

    A simulation algorithm

    @@ -601,7 +601,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.AlgorithmParameterChange(kisao_id=None, new_value=None)[source]#
    +class biosimulators_utils.sedml.data_model.AlgorithmParameterChange(kisao_id: str | None = None, new_value: str | None = None)[source]#

    Bases: SedBase

    A changed parameter of an algorithm

    @@ -691,7 +691,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.ComputeModelChange(id=None, name=None, target=None, target_namespaces=None, variables=None, parameters=None, math=None)[source]#
    +class biosimulators_utils.sedml.data_model.ComputeModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None, variables: list[Variable] | None = None, parameters: list[Parameter] | None = None, math: str | None = None)[source]#

    Bases: ModelChange, Calculation

    A replacement of an element of a model

    @@ -806,7 +806,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Curve(id=None, name=None, x_scale=None, y_scale=None, x_data_generator=None, y_data_generator=None, style: Style | None = None)[source]#
    +class biosimulators_utils.sedml.data_model.Curve(id: str | None = None, name: str | None = None, x_scale: AxisScale | None = None, y_scale: AxisScale | None = None, x_data_generator: DataGenerator | None = None, y_data_generator: DataGenerator | None = None, style: Style | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A curve in a 2D plot

    @@ -921,7 +921,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.DataGenerator(id=None, name=None, variables=None, parameters=None, math=None)[source]#
    +class biosimulators_utils.sedml.data_model.DataGenerator(id: str | None = None, name: str | None = None, variables: list[Variable] | None = None, parameters: list[Parameter] | None = None, math: str | None = None)[source]#

    Bases: Calculation, SedIdGroupMixin

    A data generator

    @@ -1017,7 +1017,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.DataSet(id=None, name=None, label=None, data_generator=None)[source]#
    +class biosimulators_utils.sedml.data_model.DataSet(id: str | None = None, name: str | None = None, label: str | None = None, data_generator: DataGenerator | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A data set in a report

    @@ -1148,7 +1148,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.FunctionalRange(id=None, name=None, range=None, variables=None, parameters=None, math=None)[source]#
    +class biosimulators_utils.sedml.data_model.FunctionalRange(id: str | None = None, name: str | None = None, range: Range | None = None, variables: list[Variable] | None = None, parameters: list[Parameter] | None = None, math: str | None = None)[source]#

    Bases: Range, Calculation

    A functional range

    @@ -1537,7 +1537,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Model(id=None, name=None, source=None, language=None, changes=None)[source]#
    +class biosimulators_utils.sedml.data_model.Model(id: str | None = None, name: str | None = None, source: str | None = None, language: str | None = None, changes: list[ModelChange] | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A model

    @@ -1649,7 +1649,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.ModelAttributeChange(id=None, name=None, target=None, target_namespaces=None, new_value=None)[source]#
    +class biosimulators_utils.sedml.data_model.ModelAttributeChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None, new_value: str | None = None)[source]#

    Bases: ModelChange

    A change of an attribute of a model

    @@ -1742,7 +1742,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.ModelChange(id=None, name=None, target=None, target_namespaces=None)[source]#
    +class biosimulators_utils.sedml.data_model.ModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin, TargetGroupMixin

    A change to a model

    @@ -2154,7 +2154,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.OneStepSimulation(id=None, name=None, algorithm=None, step=None)[source]#
    +class biosimulators_utils.sedml.data_model.OneStepSimulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None, step: float | None = None)[source]#

    Bases: Simulation

    A single simulation step

    @@ -2236,7 +2236,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Output(id=None, name=None)[source]#
    +class biosimulators_utils.sedml.data_model.Output(id: str | None = None, name: str | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    An output

    @@ -2282,7 +2282,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Parameter(id=None, name=None, value=None)[source]#
    +class biosimulators_utils.sedml.data_model.Parameter(id: str | None = None, name: str | None = None, value: float | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A parameter involved in a data generator

    @@ -2353,7 +2353,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Plot(id=None, name=None)[source]#
    +class biosimulators_utils.sedml.data_model.Plot(id: str | None = None, name: str | None = None)[source]#

    Bases: Output

    A 2D plot

    @@ -2382,7 +2382,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Plot2D(id=None, name=None, curves=None)[source]#
    +class biosimulators_utils.sedml.data_model.Plot2D(id: str | None = None, name: str | None = None, curves: list[Curve] | None = None)[source]#

    Bases: Plot

    A 2D plot

    @@ -2453,7 +2453,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Plot3D(id=None, name=None, surfaces=None)[source]#
    +class biosimulators_utils.sedml.data_model.Plot3D(id: str | None = None, name: str | None = None, surfaces: list[Surface] | None = None)[source]#

    Bases: Plot

    A 3D plot

    @@ -2524,7 +2524,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Range(id=None, name=None)[source]#
    +class biosimulators_utils.sedml.data_model.Range(id: str | None = None, name: str | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A range

    @@ -2570,7 +2570,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.RemoveElementModelChange(id=None, name=None, target=None, target_namespaces=None)[source]#
    +class biosimulators_utils.sedml.data_model.RemoveElementModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None)[source]#

    Bases: ModelChange

    A removal of an element from a model

    @@ -2624,7 +2624,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.RepeatedTask(id=None, name=None, range=None, reset_model_for_each_iteration=None, changes=None, sub_tasks=None, ranges=None)[source]#
    +class biosimulators_utils.sedml.data_model.RepeatedTask(id: str | None = None, name: str | None = None, range: Range | None = None, reset_model_for_each_iteration: bool | None = None, changes: list[SetValueComputeModelChange] | None = None, sub_tasks: list[SubTask] | None = None, ranges: list[Range] | None = None)[source]#

    Bases: AbstractTask

    A repeated task

    @@ -2739,7 +2739,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.ReplaceElementModelChange(id=None, name=None, target=None, target_namespaces=None, new_elements=None)[source]#
    +class biosimulators_utils.sedml.data_model.ReplaceElementModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None, new_elements: str | None = None)[source]#

    Bases: ModelChange

    A replacement of an element of a model

    @@ -2832,7 +2832,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Report(id=None, name=None, data_sets=None)[source]#
    +class biosimulators_utils.sedml.data_model.Report(id: str | None = None, name: str | None = None, data_sets: list[DataSet] | None = None)[source]#

    Bases: Output

    A report

    @@ -2941,7 +2941,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.SedDocument(level=1, version=3, models=None, simulations=None, tasks=None, data_generators=None, outputs=None, styles=None, metadata=None)[source]#
    +class biosimulators_utils.sedml.data_model.SedDocument(level: int = 1, version: int = 3, models: list[Model] | None = None, simulations: list[Simulation] | None = None, tasks: list[AbstractTask] | None = None, data_generators: list[DataGenerator] | None = None, outputs: list[Output] | None = None, styles: list[Style] | None = None, metadata: Metadata | None = None)[source]#

    Bases: SedBase

    A SED-ML document

    @@ -3067,7 +3067,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.SedIdGroupMixin(id=None, name=None)[source]#
    +class biosimulators_utils.sedml.data_model.SedIdGroupMixin(id: str | None = None, name: str | None = None)[source]#

    Bases: ABC

    Object with an id and optional name

    @@ -3113,7 +3113,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.SetValueComputeModelChange(id=None, name=None, target=None, target_namespaces=None, variables=None, parameters=None, math=None, model=None, range=None, symbol=None)[source]#
    +class biosimulators_utils.sedml.data_model.SetValueComputeModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None, variables: list[Variable] | None = None, parameters: list[Parameter] | None = None, math: str | None = None, model: Model | None = None, range: Range | None = None, symbol: str | None = None)[source]#

    Bases: ComputeModelChange, Calculation

    A change that sets the value of an attribute of a model within an iteration of a repeated task

    @@ -3261,7 +3261,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Simulation(id=None, name=None, algorithm=None)[source]#
    +class biosimulators_utils.sedml.data_model.Simulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A simulation

    @@ -3318,7 +3318,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.SteadyStateSimulation(id=None, name=None, algorithm=None)[source]#
    +class biosimulators_utils.sedml.data_model.SteadyStateSimulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None)[source]#

    Bases: Simulation

    A steady-state simulation

    @@ -3476,7 +3476,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.SubTask(task=None, order=None)[source]#
    +class biosimulators_utils.sedml.data_model.SubTask(task: AbstractTask | None = None, order: int | None = None)[source]#

    Bases: SedBase

    A subtask of a repeated task

    @@ -3536,7 +3536,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Surface(id=None, name=None, x_scale=None, y_scale=None, z_scale=None, x_data_generator=None, y_data_generator=None, z_data_generator=None, style: Style | None = None)[source]#
    +class biosimulators_utils.sedml.data_model.Surface(id: str | None = None, name: str | None = None, x_scale: AxisScale | None = None, y_scale: AxisScale | None = None, z_scale: AxisScale | None = None, x_data_generator: DataGenerator | None = None, y_data_generator: DataGenerator | None = None, z_data_generator: DataGenerator | None = None, style: Style | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A surface in a 3D plot

    @@ -3737,7 +3737,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Task(id=None, name=None, model=None, simulation=None)[source]#
    +class biosimulators_utils.sedml.data_model.Task(id: str | None = None, name: str | None = None, model: Model | None = None, simulation: Simulation | None = None)[source]#

    Bases: AbstractTask

    A task

    @@ -3819,7 +3819,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.UniformRange(id=None, name=None, start=None, end=None, number_of_steps=None, number_of_points=None, type=None)[source]#
    +class biosimulators_utils.sedml.data_model.UniformRange(id: str | None = None, name: str | None = None, start: float | None = None, end: float | None = None, number_of_steps: int | None = None, number_of_points: int | None = None, type: UniformRangeType | None = None)[source]#

    Bases: Range

    A uniform range

    @@ -3928,7 +3928,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation(id=None, name=None, algorithm=None, initial_time=None, output_start_time=None, output_end_time=None, number_of_steps=None, number_of_points=None)[source]#
    +class biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None, initial_time: float | None = None, output_start_time: float | None = None, output_end_time: float | None = None, number_of_steps: int | None = None, number_of_points: int | None = None)[source]#

    Bases: Simulation

    A uniform time course simulation

    @@ -4048,7 +4048,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.Variable(id=None, name=None, target=None, target_namespaces=None, symbol=None, task=None, model=None)[source]#
    +class biosimulators_utils.sedml.data_model.Variable(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None, symbol: str | None = None, task: AbstractTask | None = None, model: Model | None = None)[source]#

    Bases: SedBase, SedIdGroupMixin

    A model variable

    @@ -4163,7 +4163,7 @@

    Submodules
    -class biosimulators_utils.sedml.data_model.VectorRange(id=None, name=None, values=None)[source]#
    +class biosimulators_utils.sedml.data_model.VectorRange(id: str | None = None, name: str | None = None, values: list[float] | None = None)[source]#

    Bases: Range

    A vector range

    @@ -5328,6 +5328,23 @@

    Submodules +
    +biosimulators_utils.sedml.utils.is_executable_task(doc: SedDocument, task: Task)[source]#
    +

    Check if a task actually has outputs that a simulator needs to find

    +
    +
    Parameters:
    +
      +

    • doc (SedDocument) – sedml document

      • +

    • task (Task) – task

      • +
    +
    +
    Returns:
    +

    bool value of whether the task is an “executable” one

    +
    +
    +

    +
    biosimulators_utils.sedml.utils.is_model_language_encoded_in_xml(language)[source]#
    @@ -6610,6 +6627,7 @@

    Submodulesget_variables_for_data_generators()
  • get_variables_for_task()
  • get_xml_node_namespace_tag_target()
    • +
  • is_executable_task()
  • is_model_language_encoded_in_xml()
  • remove_algorithm_parameter_changes()
  • remove_model_changes()
    • diff --git a/docs/source/biosimulators_utils.simulator.html b/docs/source/biosimulators_utils.simulator.html index 41853888..57a675da 100644 --- a/docs/source/biosimulators_utils.simulator.html +++ b/docs/source/biosimulators_utils.simulator.html @@ -8,7 +8,7 @@ - biosimulators_utils.simulator package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.simulator package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.simulator_registry.html b/docs/source/biosimulators_utils.simulator_registry.html index 37a5e1a5..e430245e 100644 --- a/docs/source/biosimulators_utils.simulator_registry.html +++ b/docs/source/biosimulators_utils.simulator_registry.html @@ -8,7 +8,7 @@ - biosimulators_utils.simulator_registry package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.simulator_registry package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.utils.html b/docs/source/biosimulators_utils.utils.html index b3ed13ee..113ce28f 100644 --- a/docs/source/biosimulators_utils.utils.html +++ b/docs/source/biosimulators_utils.utils.html @@ -8,7 +8,7 @@ - biosimulators_utils.utils package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.utils package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.viz.html b/docs/source/biosimulators_utils.viz.html index 3c8a8d9a..ef2980db 100644 --- a/docs/source/biosimulators_utils.viz.html +++ b/docs/source/biosimulators_utils.viz.html @@ -8,7 +8,7 @@ - biosimulators_utils.viz package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.viz package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.viz.vega.escher.html b/docs/source/biosimulators_utils.viz.vega.escher.html index 6e36c665..c0970002 100644 --- a/docs/source/biosimulators_utils.viz.vega.escher.html +++ b/docs/source/biosimulators_utils.viz.vega.escher.html @@ -8,7 +8,7 @@ - biosimulators_utils.viz.vega.escher package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.viz.vega.escher package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.viz.vega.ginml.html b/docs/source/biosimulators_utils.viz.vega.ginml.html index 3d9ce708..779af443 100644 --- a/docs/source/biosimulators_utils.viz.vega.ginml.html +++ b/docs/source/biosimulators_utils.viz.vega.ginml.html @@ -8,7 +8,7 @@ - biosimulators_utils.viz.vega.ginml package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.viz.vega.ginml package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.viz.vega.html b/docs/source/biosimulators_utils.viz.vega.html index ae00989c..df6dc1d6 100644 --- a/docs/source/biosimulators_utils.viz.vega.html +++ b/docs/source/biosimulators_utils.viz.vega.html @@ -8,7 +8,7 @@ - biosimulators_utils.viz.vega package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.viz.vega package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.viz.vega.sbgn.html b/docs/source/biosimulators_utils.viz.vega.sbgn.html index 2eaabff7..fefb9a28 100644 --- a/docs/source/biosimulators_utils.viz.vega.sbgn.html +++ b/docs/source/biosimulators_utils.viz.vega.sbgn.html @@ -8,7 +8,7 @@ - biosimulators_utils.viz.vega.sbgn package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.viz.vega.sbgn package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home + diff --git a/docs/source/biosimulators_utils.xml.html b/docs/source/biosimulators_utils.xml.html index 7c992408..e860c99f 100644 --- a/docs/source/biosimulators_utils.xml.html +++ b/docs/source/biosimulators_utils.xml.html @@ -8,7 +8,7 @@ - biosimulators_utils.xml package — BioSimulators utils 0.2.0 documentation + biosimulators_utils.xml package — BioSimulators utils 0.2.1 documentation @@ -36,7 +36,7 @@ - + @@ -124,8 +124,8 @@ - BioSimulators utils 0.2.0 documentation - Home - + BioSimulators utils 0.2.1 documentation - Home +