Submit Brian 2 2.4.2 #474

biosimulators-daemon · 2021-11-24T23:50:58Z

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

Updated specifications now that there's a Docker image, CLI, and Python API
Updated model, simulation, archive formats in specs
Changed length of test simulation to work around bug in pyNeuroML ([BUG]: getPulseGenMethod for Brian 2 doesn't properly account for the simulation time line NeuroML/org.neuroml.export#77)

The text was updated successfully, but these errors were encountered:

biosimulators-daemon · 2021-11-24T23:53:26Z

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 · 2021-11-24T23:53:28Z

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 · 2021-11-25T00:18:50Z

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 · 2021-11-25T00:18:52Z

The specifications of your simulator is valid!

biosimulators-daemon · 2021-11-25T00:19:04Z

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 · 2021-11-25T00:19:06Z

The specifications of your simulator is valid!

biosimulators-daemon · 2021-11-25T00:21:28Z

Summary of tests

Executed 48 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 0 test cases
Skipped 41 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

biosimulators-daemon · 2021-11-25T00:21:29Z

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 · 2021-11-25T00:21:30Z

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
Algorithm: KISAO_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 · 2021-11-25T00:21:30Z

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 · 2021-11-25T00:21:43Z

Summary of tests

Executed 48 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 0 test cases
Skipped 41 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

biosimulators-daemon · 2021-11-25T00:21:44Z

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 · 2021-11-25T00:21:45Z

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
Algorithm: KISAO_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 · 2021-11-25T00:21:46Z

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 · 2021-11-25T01:30:10Z

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 · 2021-11-25T01:30:12Z

The specifications of your simulator is valid!

biosimulators-daemon · 2021-11-25T01:40:01Z

Summary of tests

Executed 48 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 17 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 24 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2021-11-25T01:40:02Z

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe 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�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe 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�[0m

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...
  �[31mThe COMBINE/OMEX did not execute successfully:
  
    The SED document did not execute successfully:
    
      negative dimensions are not allowed�[0m
  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

biosimulators-daemon · 2021-11-25T01:40:03Z

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 · 2021-11-25T01:40:03Z

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
Algorithm: KISAO_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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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: �[33mThe 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`�[0m


  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: �[33mThe 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`�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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`�[0m


  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: �[33mThe 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`�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    negative dimensions are not allowed�[0m

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: �[33mThe SED document is potentially incorrect.


  - Output `report` may be invalid.


    - The data sets do not have consistent shapes.�[0m


  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: �[33mThe SED document is potentially incorrect.


  - Output `report` may be invalid.


    - The data sets do not have consistent shapes.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    negative dimensions are not allowed�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    No module named 'tmppnvk7vqg_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    No module named 'tmp7o0yu71r_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    No module named 'tmpatah9gil_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    No module named 'tmp8o4weu6s_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    No module named 'tmpv93j0g3m_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe 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'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe 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'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed

  

    No module named 'tmpkmzr4oh1_brian2'�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    Algorithms cannot be substituted at policy 'NONE'.�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    negative dimensions are not allowed�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    Initial time must be 0, not 5e-05�[0m

biosimulators-daemon · 2021-11-25T01:40:04Z

- 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 · 2021-11-25T03:31:30Z

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 · 2021-11-25T03:31:33Z

The specifications of your simulator is valid!

biosimulators-daemon · 2021-11-25T03:54:08Z

Summary of tests

Executed 73 test cases
Passed 28 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 45 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2021-11-25T03:54:08Z

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 · 2021-11-25T03:54:09Z

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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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: �[33mThe SED document is potentially incorrect.


  - Output `report` may be invalid.


    - The data sets do not have consistent shapes.�[0m


  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: �[33mThe SED document is potentially incorrect.


  - Output `report` may be invalid.


    - The data sets do not have consistent shapes.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmpf2s2t2d5_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmpcxsqis2b_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmp743z9rxj_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmptpn_4z2j_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmpgc8_4q6w_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmp1nf27rjs_brian2'

  

    No module named 'tmptjlktaw6_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmptr5numl7_brian2'

  

    No module named 'tmpvbi_nq5j_brian2'�[0m

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: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  warnings.warn(termcolor.colored(message, Colors.warning.value), category)





WARNING    /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe 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.�[0m


  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: �[33mThe 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.�[0m


  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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No module named 'tmpdjx9tz14_brian2'�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    Algorithms cannot be substituted at policy 'NONE'.�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    Algorithm parameters are not supported.�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    Algorithm parameters are not supported.�[0m

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





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    Initial time must be 0, not 0.105�[0m

biosimulators-daemon · 2021-11-25T03:54:10Z

The image for your simulator is valid!

biosimulators-daemon · 2021-11-25T03:54:24Z

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.

biosimulators-daemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Nov 24, 2021

biosimulators-daemon added the Invalid This doesn't seem right label Nov 24, 2021

jonrkarr added the Approved label Nov 25, 2021

jonrkarr self-assigned this Nov 25, 2021

biosimulators-daemon removed the Invalid This doesn't seem right label Nov 25, 2021

biosimulators-daemon added the Invalid This doesn't seem right label Nov 25, 2021

biosimulators-daemon removed the Invalid This doesn't seem right label Nov 25, 2021

biosimulators-daemon added the Invalid This doesn't seem right label Nov 25, 2021

biosimulators-daemon removed the Invalid This doesn't seem right label Nov 25, 2021

biosimulators-daemon added the Validated label Nov 25, 2021

biosimulators-daemon closed this as completed Nov 25, 2021

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Submit Brian 2 2.4.2 #474

Submit Brian 2 2.4.2 #474

biosimulators-daemon commented Nov 24, 2021 •

edited by jonrkarr

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biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

Submit Brian 2 2.4.2 #474

Submit Brian 2 2.4.2 #474

Comments

biosimulators-daemon commented Nov 24, 2021 • edited by jonrkarr Loading

biosimulators-daemon commented Nov 24, 2021

biosimulators-daemon commented Nov 24, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

Summary of tests

biosimulators-daemon commented Nov 25, 2021

Warnings

biosimulators-daemon commented Nov 25, 2021

Skips

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

Summary of tests

biosimulators-daemon commented Nov 25, 2021

Warnings

biosimulators-daemon commented Nov 25, 2021

Skips

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

Summary of tests

biosimulators-daemon commented Nov 25, 2021

Failures

biosimulators-daemon commented Nov 25, 2021

Warnings

biosimulators-daemon commented Nov 25, 2021

Skips

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

Summary of tests

biosimulators-daemon commented Nov 25, 2021

Warnings

biosimulators-daemon commented Nov 25, 2021

Skips

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 25, 2021

biosimulators-daemon commented Nov 24, 2021 •

edited by jonrkarr

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