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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit Brian 2 2.4.2 #474

Closed biosimulators-daemon closed 2 years ago

biosimulators-daemon commented 2 years ago

id: brian2 version: 2.4.2 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/afb4fc5e7452ead7728c03608b4bfeea3db0cdc2/biosimulators-brian2.json specificationsPatch: version: 2.4.2 image: url: ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2 digest: "sha256:4932ba380f4917155c12dec1969cbf102b00f5e58f933cf5bf76a363b0cd8a48" validateImage: true commitSimulator: true

Changelog

biosimulators-daemon commented 2 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

- The simulator specifications from `https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/2f5ee2d7e53e5f47e98a260ac8dba1abb548c018/biosimulators-brian2.json` are invalid. The specifications of simulation tools must adhere to BioSimulators' schema. BioSimulators' schema is available in both JSON Schema and Open API Specifications formats. Documentation is available at https://api.biosimulators.org/.
- 
-   - Database ValidatorError (500): `/image/format` is invalid
-     
-       Path `format` is required.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

biosimulators-daemon commented 2 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)
Test that SED documents in nested directories can be executed Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
biosimulators-daemon commented 2 years ago

No test cases are applicable to your simulator. Please use this issue to share appropriate test COMBINE/OMEX files. The BioSimulators Team will add these files to this validation program and then re-review your simulator.

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.6 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)
Test that SED documents in nested directories can be executed Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
biosimulators-daemon commented 2 years ago

No test cases are applicable to your simulator. Please use this issue to share appropriate test COMBINE/OMEX files. The BioSimulators Team will add these files to this validation program and then re-review your simulator.

biosimulators-daemon commented 2 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (13.8 s)
Test that SED documents in nested directories can be executed Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: subdir/simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: subdir/simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (17.6 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots: subdir/simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets subdir__copy/simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: subdir/simulation.sedml ... Executing SED-ML file 2: subdir__copy/simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 2 SED documents: SED documents (2): Succeeded: 0 Skipped: 0 Failed: 2 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed The SED document did not execute successfully: negative dimensions are not allowed ```
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (13.4 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (16.6 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets simulation__copy.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Executing SED-ML file 2: simulation__copy.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 2 SED documents: SED documents (2): Succeeded: 0 Skipped: 0 Failed: 2 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed The SED document did not execute successfully: negative dimensions are not allowed ```
docker_image.SingularityImageExecutesSimulationsSuccessfully (17.3 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` The Docker image could not be successfully executed as a Singularity image: INFO: Convert SIF file to sandbox... The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed INFO: Cleaning up image... ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (12.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (11.7 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (11.7 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (11.8 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
results_report.SimulatorGeneratesReportsOfSimulationResults (12.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorProducesLinear2DPlots (12.1 s)
Test that a simulator produces linear 2D plots Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots: simulation.sedml: Tasks (1): task Plots (1): plot_0: 5 curves Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorProducesLogarithmic2DPlots (11.9 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots: simulation.sedml: Tasks (1): task Plots (1): plot_0: 5 curves Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorProducesMultiplePlots (11.5 s)
Test that a simulator produces multiple plots Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots: simulation.sedml: Tasks (1): task Plots (2): plot_0: 3 curves plot_1: 2 curves Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (11.6 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorSupportsMultipleReportsPerSedDocument (12.0 s)
Test that a simulator supports multiple reports per SED document Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (2): report_1: 3 data sets report_2: 3 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorSupportsMultipleTasksPerSedDocument (14.2 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): task task__test_suite_copy Reports (2): report: 5 data sets report__test_suite_copy: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed negative dimensions are not allowed ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (12.4 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
biosimulators-daemon commented 2 years ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (11.8 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (12.1 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorProducesLinear3DPlots (1.6 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (1.6 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (1.6 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (1.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.8 s)
Test that a simulator supports setting the values of parameters of algorithms Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (1.1 s)
Test that a simulator supports compute model changes Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (13.6 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Data generator `data_generator_time__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_v__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_m__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_h__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_n__copy_2` may be invalid. - The variables do not have consistent shapes. - Output `report__copy_2` may be invalid. - The data sets do not have consistent shapes. - The following data generators do not contribute to outputs: - `data_generator_h` - `data_generator_m` - `data_generator_n` - `data_generator_time` - `data_generator_v` warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:35:33,334 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Data generator `data_generator_time__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_v__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_m__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_h__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_n__copy_2` may be invalid. - The variables do not have consistent shapes. - Output `report__copy_2` may be invalid. - The data sets do not have consistent shapes. - The following data generators do not contribute to outputs: - `data_generator_h` - `data_generator_m` - `data_generator_n` - `data_generator_time` - `data_generator_v` warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Data generator `data_generator_time__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_v__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_m__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_h__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_n__copy_2` may be invalid. - The variables do not have consistent shapes. - Output `report__copy_2` may be invalid. - The data sets do not have consistent shapes. - The following data generators do not contribute to outputs: - `data_generator_h` - `data_generator_m` - `data_generator_n` - `data_generator_time` - `data_generator_v` warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:35:33,336 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Data generator `data_generator_time__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_v__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_m__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_h__copy_2` may be invalid. - The variables do not have consistent shapes. - Data generator `data_generator_n__copy_2` may be invalid. - The variables do not have consistent shapes. - Output `report__copy_2` may be invalid. - The data sets do not have consistent shapes. - The following data generators do not contribute to outputs: - `data_generator_h` - `data_generator_m` - `data_generator_n` - `data_generator_time` - `data_generator_v` warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (2): task task__copy_2 Reports (1): report__copy_2: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed negative dimensions are not allowed ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (13.7 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:35:47,124 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:35:47,125 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (2): task task__copy_2 Reports (1): report: 10 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed negative dimensions are not allowed ```
sedml.SimulatorSupportsModelAttributeChanges (1.6 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (1.5 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (1.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (12.8 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:36:43,288 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:36:43,289 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmppnvk7vqg_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (13.4 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:36:56,578 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:36:56,579 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmp7o0yu71r_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (13.1 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:09,621 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:09,623 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmpatah9gil_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (12.8 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:22,685 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:22,687 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmp8o4weu6s_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (13.1 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:35,763 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:35,764 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmpv93j0g3m_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (13.1 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:48,356 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:37:48,357 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 0 Skipped: 0 Failed: 3 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmp192bd3vz_brian2' No module named 'tmpt592mets_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (12.9 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:38:01,600 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:38:01,601 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 0 Skipped: 0 Failed: 3 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmpvtt93h_h_brian2' No module named 'tmpsbdepk4u_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (12.4 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:38:14,555 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 01:38:14,557 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 0 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 0 Skipped: 2 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed No module named 'tmpkmzr4oh1_brian2' ```
sedml.SimulatorSupportsSubstitutingAlgorithms (20.5 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Algorithms cannot be substituted at policy 'NONE'. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: negative dimensions are not allowed ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (9.5 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Initial time must be 0, not 5e-05 ```
biosimulators-daemon commented 2 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1501843010). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/1501843010).
biosimulators-daemon commented 2 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.7 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000086 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (1.8 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (1.7 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (1.7 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (1.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (1.1 s)
Test that a simulator supports setting the values of parameters of algorithms Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (1.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (57.8 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` Simulations with the same time courses should produce equivalent time data sets: Not equal to tolerance rtol=1e-07, atol=0 Mismatched elements: 21001 / 21001 (100%) Max absolute difference: 1.e-05 Max relative difference: 1. x: array([1.0000e-05, 2.0000e-05, 3.0000e-05, ..., 2.0999e-01, 2.1000e-01, 2.1001e-01]) y: array([0.0000e+00, 1.0000e-05, 2.0000e-05, ..., 2.0998e-01, 2.0999e-01, 2.1000e-01]) ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:43:02,681 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:43:02,682 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `report` may be invalid. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (2): task task__copy_2 Reports (1): report: 10 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 1 Skipped: 0 Failed: 0 Tasks (2): Succeeded: 2 Skipped: 0 Failed: 0 Outputs (1): Succeeded: 1 Skipped: 0 Failed: 0 ```
sedml.SimulatorSupportsModelAttributeChanges (1.8 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (1.7 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (1.3 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (28.6 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:45:46,817 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:45:46,819 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmpf2s2t2d5_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (29.5 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:46:15,629 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:46:15,631 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmpcxsqis2b_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (29.7 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:46:45,994 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:46:45,995 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmp743z9rxj_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (29.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:47:15,008 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:47:15,010 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmptpn_4z2j_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (27.8 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:47:43,863 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:47:43,864 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmpgc8_4q6w_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (29.8 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:48:12,009 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:48:12,011 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 1 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmp1nf27rjs_brian2' No module named 'tmptjlktaw6_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (29.2 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:48:41,903 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:48:41,904 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 1 Skipped: 0 Failed: 2 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmptr5numl7_brian2' No module named 'tmpvbi_nq5j_brian2' ```
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (28.9 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:49:10,839 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) [py.warnings] pyNeuroML >>> 2021-11-25 03:49:10,840 - py.warnings - WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (2): __repeated_task_0 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: No module named 'tmpdjx9tz14_brian2' ```
sedml.SimulatorSupportsSubstitutingAlgorithms (57.1 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Algorithms cannot be substituted at policy 'NONE'. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 1 Skipped: 0 Failed: 0 Tasks (1): Succeeded: 1 Skipped: 0 Failed: 0 Outputs (1): Succeeded: 1 Skipped: 0 Failed: 0 Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Algorithm parameters are not supported. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Algorithm parameters are not supported. ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (10.6 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.4.2' could not execute the archive: Unknown error ``` Log: ``` Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: simulation.sedml: Tasks (1): task Reports (1): report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (1): Succeeded: 0 Skipped: 0 Failed: 1 Outputs (1): Succeeded: 0 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Initial time must be 0, not 0.105 ```
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of brian2 to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.