Index

_

_archive_has_master (biosimulators_test_suite.test_case.combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories attribute) (biosimulators_test_suite.test_case.combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories attribute) (biosimulators_test_suite.test_case.combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile attribute) (biosimulators_test_suite.test_case.combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments attribute) (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute) (biosimulators_test_suite.test_case.published_project.SingleMasterSedDocumentCombineArchiveTestCase attribute) _expected_report_ids (biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase attribute) (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute)

_expected_reports (biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleTasksPerSedDocument attribute) _keep_one_task_one_report (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute) _model_change_filter (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute) _published_projects_test_case (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute) _remove_algorithm_parameter_changes (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute) _remove_plots (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute) _use_single_variable_data_generators (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase attribute)

A

a_tol (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) add_comment_to_issue() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction class method) add_time_data_set() (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase method) AlertType (class in biosimulators_test_suite.data_model) App (class in biosimulators_test_suite.exec_cli) App.Meta (class in biosimulators_test_suite.exec_cli)

archive (biosimulators_test_suite.test_case.published_project.ExpectedResultOfSyntheticArchive attribute) are_array_shapes_equivalent() (in module biosimulators_test_suite.test_case.utils) arguments (biosimulators_test_suite.exec_cli.BaseController.Meta attribute) assert_no_extra_datasets (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) assert_no_extra_plots (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) assert_no_extra_reports (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) assert_no_missing_plots (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute)

B

base_controller (biosimulators_test_suite.exec_cli.App.Meta attribute) BaseController (class in biosimulators_test_suite.exec_cli) BaseController.Meta (class in biosimulators_test_suite.exec_cli) biosimulators_api_client_id (biosimulators_test_suite.config.Config attribute) biosimulators_api_client_secret (biosimulators_test_suite.config.Config attribute) biosimulators_audience (biosimulators_test_suite.config.Config attribute) biosimulators_auth_endpoint (biosimulators_test_suite.config.Config attribute) biosimulators_curator_gh_ids (biosimulators_test_suite.config.Config attribute) biosimulators_default_image_version (biosimulators_test_suite.config.Config attribute) biosimulators_default_specifications_version (biosimulators_test_suite.config.Config attribute) biosimulators_dev_api_endpoint (biosimulators_test_suite.config.Config attribute) biosimulators_docker_image_url_pattern (biosimulators_test_suite.config.Config attribute) biosimulators_docker_registry_token (biosimulators_test_suite.config.Config attribute) biosimulators_docker_registry_url (biosimulators_test_suite.config.Config attribute) biosimulators_docker_registry_username (biosimulators_test_suite.config.Config attribute) biosimulators_prod_api_endpoint (biosimulators_test_suite.config.Config attribute) biosimulators_test_suite module biosimulators_test_suite.config module biosimulators_test_suite.data_model module biosimulators_test_suite.exceptions module biosimulators_test_suite.exec_cli module biosimulators_test_suite.exec_core module biosimulators_test_suite.exec_gh_action module biosimulators_test_suite.results module biosimulators_test_suite.results.data_model module

biosimulators_test_suite.results.io module biosimulators_test_suite.test_case module biosimulators_test_suite.test_case.cli module biosimulators_test_suite.test_case.combine_archive module biosimulators_test_suite.test_case.docker_image module biosimulators_test_suite.test_case.log module biosimulators_test_suite.test_case.published_project module biosimulators_test_suite.test_case.results_report module biosimulators_test_suite.test_case.sedml module biosimulators_test_suite.test_case.utils module biosimulators_test_suite.utils module biosimulators_test_suite.warnings module build_synthetic_archives() (biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase method) (biosimulators_test_suite.test_case.published_project.ConfigurableMasterCombineArchiveTestCase method) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsAlgorithmParameters method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsModelAttributeChanges method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleReportsPerSedDocument method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleTasksPerSedDocument method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsSubstitutingAlgorithms method)

C

case (biosimulators_test_suite.results.data_model.TestCaseResult attribute) cases (biosimulators_test_suite.exec_core.SimulatorValidator attribute) cli (biosimulators_test_suite.exec_core.SimulatorValidator attribute) CliDescribesSupportedEnvironmentVariablesInline (class in biosimulators_test_suite.test_case.cli) CliDisplaysHelpInline (class in biosimulators_test_suite.test_case.cli) CliDisplaysVersionInformationInline (class in biosimulators_test_suite.test_case.cli) CombineArchiveHasSedDocumentsInNestedDirectories (class in biosimulators_test_suite.test_case.combine_archive)

CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (class in biosimulators_test_suite.test_case.combine_archive) CombineArchiveTestCase (class in biosimulators_test_suite.test_case.combine_archive) commit_simulator() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) compatible_with_specifications() (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method) Config (class in biosimulators_test_suite.config) ConfigurableMasterCombineArchiveTestCase (class in biosimulators_test_suite.test_case.published_project) console (biosimulators_test_suite.data_model.OutputMedium attribute)

D

DeclaresSupportedEnvironmentVariables (class in biosimulators_test_suite.test_case.docker_image) DefaultUserIsRoot (class in biosimulators_test_suite.test_case.docker_image) description (biosimulators_test_suite.data_model.TestCase attribute) (biosimulators_test_suite.exec_cli.BaseController.Meta attribute) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute)

docker_hub_token (biosimulators_test_suite.config.Config attribute) docker_hub_username (biosimulators_test_suite.config.Config attribute) does_submission_have_approved_label() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) dry_run (biosimulators_test_suite.exec_core.SimulatorValidator attribute) duration (biosimulators_test_suite.results.data_model.TestCaseResult attribute)

E

environment (biosimulators_test_suite.test_case.published_project.ExpectedResultOfSyntheticArchive attribute) eval() (biosimulators_test_suite.data_model.TestCase method) (biosimulators_test_suite.test_case.cli.CliDescribesSupportedEnvironmentVariablesInline method) (biosimulators_test_suite.test_case.cli.CliDisplaysHelpInline method) (biosimulators_test_suite.test_case.cli.CliDisplaysVersionInformationInline method) (biosimulators_test_suite.test_case.docker_image.DeclaresSupportedEnvironmentVariables method) (biosimulators_test_suite.test_case.docker_image.DefaultUserIsRoot method) (biosimulators_test_suite.test_case.docker_image.HasBioContainersLabels method) (biosimulators_test_suite.test_case.docker_image.HasOciLabels method) (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) eval_case() (biosimulators_test_suite.exec_core.SimulatorValidator method) eval_outputs() (biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase method) (biosimulators_test_suite.test_case.log.LoggingTestCase method) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase method) (biosimulators_test_suite.test_case.results_report.SimulatorGeneratesReportsOfSimulationResults method) (biosimulators_test_suite.test_case.sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleReportsPerSedDocument method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleTasksPerSedDocument method)

exception (biosimulators_test_suite.data_model.AlertType attribute) (biosimulators_test_suite.results.data_model.TestCaseResult attribute) exception_traceback (biosimulators_test_suite.results.data_model.TestCaseResult attribute) exec_core() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) exec_sedml_docs_in_archive() (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method) EXEC_WITH_SINGULARITY (biosimulators_test_suite.test_case.docker_image.SingularityImageExecutesSimulationsSuccessfully attribute) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute) EXPECTED_LABELS (biosimulators_test_suite.test_case.docker_image.HasBioContainersLabels attribute) (biosimulators_test_suite.test_case.docker_image.HasOciLabels attribute) expected_plots (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) expected_reports (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) ExpectedResultOfSyntheticArchive (class in biosimulators_test_suite.test_case.published_project) ExpectedSedDataSet (class in biosimulators_test_suite.data_model) ExpectedSedPlot (class in biosimulators_test_suite.data_model) ExpectedSedReport (class in biosimulators_test_suite.data_model)

F

failed (biosimulators_test_suite.results.data_model.TestCaseResultType attribute) filename (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) find_cases() (biosimulators_test_suite.exec_core.SimulatorValidator method) (in module biosimulators_test_suite.test_case.published_project) find_cases_in_module() (biosimulators_test_suite.exec_core.SimulatorValidator method)

from_dict() (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method) from_json() (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method) FUNCTONAL_RANGE_USES_VARIABLES (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges attribute)

G

get_auth_headers_for_biosimulations_api() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) get_description() (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method) get_expected_reports() (biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase method) get_initial_message() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method)

get_simulator_docker_image() (biosimulators_test_suite.data_model.TestCase method) get_singularity_image_filename() (in module biosimulators_test_suite.utils) gh_action_run (biosimulators_test_suite.results.data_model.TestResultsReport attribute) gh_issue (biosimulators_test_suite.data_model.OutputMedium attribute) (biosimulators_test_suite.results.data_model.TestResultsReport attribute)

H

handlers (biosimulators_test_suite.exec_cli.App.Meta attribute) HAS_CHANGES (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables attribute)

HasBioContainersLabels (class in biosimulators_test_suite.test_case.docker_image) HasOciLabels (class in biosimulators_test_suite.test_case.docker_image) help (biosimulators_test_suite.exec_cli.BaseController.Meta attribute)

I

id (biosimulators_test_suite.data_model.TestCase attribute) (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute) IgnoredTestCaseWarning InvalidOutputsException InvalidOutputsWarning is_concrete() (biosimulators_test_suite.test_case.log.LoggingTestCase method) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives method) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments method) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs method) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithVectorRanges method)

is_curated_archive_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) is_curated_sed_algorithm_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) (biosimulators_test_suite.test_case.sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsAlgorithmParameters method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsSubstitutingAlgorithms method) is_curated_sed_doc_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) is_curated_sed_model_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) is_curated_sed_report_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) is_curated_sed_simulation_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) is_curated_sed_task_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method) (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase method) is_other_version_of_simulator_validated() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) is_simulator_approved() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) is_submission_latest_version_of_simulator() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) is_success_expected (biosimulators_test_suite.test_case.published_project.ExpectedResultOfSyntheticArchive attribute) issue_number (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction attribute)

L

label (biosimulators_test_suite.exec_cli.App.Meta attribute) (biosimulators_test_suite.exec_cli.BaseController.Meta attribute)

log (biosimulators_test_suite.results.data_model.TestCaseResult attribute) log_std_out_err (biosimulators_test_suite.exec_core.SimulatorValidator attribute) LoggingTestCase (class in biosimulators_test_suite.test_case.log)

M

main() (in module biosimulators_test_suite.exec_cli) minimum_number_of_synthetic_uniform_time_steps (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) MIXED_SUB_TASK_TYPES (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes attribute) model_format (biosimulators_test_suite.data_model.SedTaskRequirements attribute) model_format_features (biosimulators_test_suite.data_model.SedTaskRequirements attribute) modify_simulation() (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes method) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes method) module biosimulators_test_suite biosimulators_test_suite.config biosimulators_test_suite.data_model biosimulators_test_suite.exceptions biosimulators_test_suite.exec_cli biosimulators_test_suite.exec_core biosimulators_test_suite.exec_gh_action biosimulators_test_suite.results biosimulators_test_suite.results.data_model biosimulators_test_suite.results.io biosimulators_test_suite.test_case biosimulators_test_suite.test_case.cli biosimulators_test_suite.test_case.combine_archive biosimulators_test_suite.test_case.docker_image biosimulators_test_suite.test_case.log biosimulators_test_suite.test_case.published_project biosimulators_test_suite.test_case.results_report biosimulators_test_suite.test_case.sedml biosimulators_test_suite.test_case.utils biosimulators_test_suite.utils biosimulators_test_suite.warnings

N

name (biosimulators_test_suite.data_model.TestCase attribute) (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute) NUM_NESTED_RANGES (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges attribute) NUM_NESTED_REPEATED_TASKS (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithVectorRanges attribute)

NUM_SUB_TASKS (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithVectorRanges attribute)

O

output_medium (biosimulators_test_suite.data_model.TestCase attribute) (biosimulators_test_suite.exec_core.SimulatorValidator attribute) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute)

OutputMedium (class in biosimulators_test_suite.data_model)

P

passed (biosimulators_test_suite.results.data_model.TestCaseResultType attribute) post_entry_to_biosimulators_api() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method)

published_projects_test_cases (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute) pull_docker_image (biosimulators_test_suite.config.Config attribute) push_image() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method)

R

r_tol (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) RANGE_LENS (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes attribute) RANGE_TYPE (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithVectorRanges attribute) reduce_array_shape() (in module biosimulators_test_suite.test_case.utils)

REPORT_ERROR_AS_SKIP (biosimulators_test_suite.test_case.log.LoggingTestCase attribute) (biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsModelAttributeChanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsSubstitutingAlgorithms attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes attribute) results (biosimulators_test_suite.results.data_model.TestResultsReport attribute) run() (biosimulators_test_suite.exec_core.SimulatorValidator method) (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) runbiosimulations_api_client_id (biosimulators_test_suite.config.Config attribute) runbiosimulations_api_client_secret (biosimulators_test_suite.config.Config attribute) runbiosimulations_api_endpoint (biosimulators_test_suite.config.Config attribute) runbiosimulations_audience (biosimulators_test_suite.config.Config attribute) runbiosimulations_auth_endpoint (biosimulators_test_suite.config.Config attribute) runtime_failure_alert_type (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute)

S

SED_DOCUMENT_LOCATIONS_ARE_NESTED (biosimulators_test_suite.test_case.combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories attribute) (biosimulators_test_suite.test_case.combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories attribute) (biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase attribute) sed_documents (biosimulators_test_suite.test_case.published_project.ExpectedResultOfSyntheticArchive attribute) SED_DOCUMENTS_HAVE_SAME_NAMES (biosimulators_test_suite.test_case.combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories attribute) (biosimulators_test_suite.test_case.combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories attribute) (biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase attribute) SedTaskRequirements (class in biosimulators_test_suite.data_model) simulation_algorithm (biosimulators_test_suite.data_model.SedTaskRequirements attribute) simulation_results_isnan() (in module biosimulators_test_suite.utils) SimulatorCanExecutePublishedProject (class in biosimulators_test_suite.test_case.published_project) SimulatorGeneratesReportsOfSimulationResults (class in biosimulators_test_suite.test_case.results_report) SimulatorProducesLinear2DPlots (class in biosimulators_test_suite.test_case.sedml) SimulatorProducesLinear3DPlots (class in biosimulators_test_suite.test_case.sedml) SimulatorProducesLogarithmic2DPlots (class in biosimulators_test_suite.test_case.sedml) SimulatorProducesLogarithmic3DPlots (class in biosimulators_test_suite.test_case.sedml) SimulatorProducesMultiplePlots (class in biosimulators_test_suite.test_case.sedml) SimulatorProducesReportsWithCuratedNumberOfDimensions (class in biosimulators_test_suite.test_case.sedml) SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (class in biosimulators_test_suite.test_case.log) SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (class in biosimulators_test_suite.test_case.log) SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (class in biosimulators_test_suite.test_case.log) SimulatorReportsTheStatusOfTheExecutionOfSedTasks (class in biosimulators_test_suite.test_case.log) SimulatorRuntimeErrorWarning SimulatorSupportsAlgorithmParameters (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsModelAttributeChanges (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (class in biosimulators_test_suite.test_case.sedml)

SimulatorSupportsMultipleReportsPerSedDocument (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsMultipleTasksPerSedDocument (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithFunctionalRanges (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithLinearUniformRanges (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithMultipleSubTasks (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsRepeatedTasksWithVectorRanges (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsSubstitutingAlgorithms (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (class in biosimulators_test_suite.test_case.sedml) SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (class in biosimulators_test_suite.test_case.sedml) SimulatorValidator (class in biosimulators_test_suite.exec_core) SingleMasterSedDocumentCombineArchiveTestCase (class in biosimulators_test_suite.test_case.published_project) singularity_image_dirname (biosimulators_test_suite.config.Config attribute) SingularityImageExecutesSimulationsSuccessfully (class in biosimulators_test_suite.test_case.docker_image) skip_reason (biosimulators_test_suite.results.data_model.TestCaseResult attribute) skipped (biosimulators_test_suite.results.data_model.TestCaseResultType attribute) skipped_simulators (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) SkippedTestCaseException specifications (biosimulators_test_suite.exec_core.SimulatorValidator attribute) summarize_results() (biosimulators_test_suite.exec_core.SimulatorValidator static method) synthetic_archives_dir (biosimulators_test_suite.exec_core.SimulatorValidator attribute) SyntheticCombineArchiveTestCase (class in biosimulators_test_suite.test_case.published_project)

T

task_requirements (biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject attribute) test_case_timeout (biosimulators_test_suite.config.Config attribute) test_suite_version (biosimulators_test_suite.results.data_model.TestResultsReport attribute) TEST_TIME (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes attribute) TestCase (class in biosimulators_test_suite.data_model) TestCaseException

TestCaseResult (class in biosimulators_test_suite.results.data_model) TestCaseResultType (class in biosimulators_test_suite.results.data_model) TestCaseWarning TestResultsReport (class in biosimulators_test_suite.results.data_model) TimeoutException to_dict() (biosimulators_test_suite.results.data_model.TestCaseResult method) (biosimulators_test_suite.results.data_model.TestResultsReport method) trigger_conversion_of_docker_image_to_singularity() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) type (biosimulators_test_suite.results.data_model.TestCaseResult attribute)

U

UNIFORM_RANGE_TYPE (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges attribute) (biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges attribute)

UniformTimeCourseTestCase (class in biosimulators_test_suite.test_case.published_project) user_to_exec_in_simulator_containers (biosimulators_test_suite.config.Config attribute)

V

validate_image() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) VALIDATE_OUTPUT_LOGS (biosimulators_test_suite.test_case.log.LoggingTestCase attribute) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs attribute) validate_permissions() (biosimulators_test_suite.exec_gh_action.ValidateCommitSimulatorGitHubAction method) VALIDATE_SED_DOCUMENT_LOGS (biosimulators_test_suite.test_case.log.LoggingTestCase attribute) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments attribute) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs attribute) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks attribute)

VALIDATE_TASK_LOGS (biosimulators_test_suite.test_case.log.LoggingTestCase attribute) (biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks attribute) ValidateCommitSimulatorGitHubAction (class in biosimulators_test_suite.exec_gh_action) verbose (biosimulators_test_suite.exec_core.SimulatorValidator attribute)

W

warning (biosimulators_test_suite.data_model.AlertType attribute) warnings (biosimulators_test_suite.results.data_model.TestCaseResult attribute) WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (class in biosimulators_test_suite.test_case.combine_archive)

WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (class in biosimulators_test_suite.test_case.combine_archive) working_dirname (biosimulators_test_suite.exec_core.SimulatorValidator attribute) write_test_results() (in module biosimulators_test_suite.results.io)