Submit NetPyNE <IP_ADDRESS>

id: netpyne
version: <IP_ADDRESS>
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/494eeea5e89fb5c2e221ceef64a272fe456ccd41/biosimulators-netpyne.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>
validateImage: true
commitSimulator: true

Changelog

Added CVODE example COMBINE archive

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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

We created the GitHub group @biosimulators/netpyne to manage permissions to change the specifications of NetPyNe and added you (@biosimulators-daemon) to this group. You can manage permissions to change the specifications of NetPyNe at https://github.com/orgs/biosimulators/teams/netpyne/members.

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (14.4 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (5.9 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'

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:

docker_image.HasBioContainersLabels (1.0 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

Summary of tests

Executed 64 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 57 test cases:

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell
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-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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:smoldyn/Lotka-Volterra
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

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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.

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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 65 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
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Skipped 41 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
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-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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:smoldyn/Lotka-Volterra
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
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

Failures
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.1 s)
Test that SED documents in nested directories can be executed
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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.
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (4.7 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Exception:
No reports were generated

Log:
The COMBINE/OMEX archive is invalid.

  - The SED-ML file at location `simulation.sedml` is invalid.

    - Simulation `simulation` is invalid.

      - Algorithm has an invalid KiSAO id `KISAO_00000019`.

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/Hodgkin-Huxley-cell-CVODE.omex', '-o', '/tmp/out']' command failed.  (See above for error)

results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times
Exception:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (7.7 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (2.4 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'

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:

docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (4.7 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Warnings:
Plots were not produced:
  simulation.sedml/plot

Log:
The COMBINE/OMEX archive is invalid.

  - The SED-ML file at location `simulation.sedml` is invalid.

    - Simulation `simulation` is invalid.

      - Algorithm has an invalid KiSAO id `KISAO_00000019`.

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/Hodgkin-Huxley-cell-CVODE.omex', '-o', '/tmp/out']' command failed.  (See above for error)

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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:

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:

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:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

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:

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:

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:

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:

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:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

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:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
The SED document is invalid.
  - Simulation `simulation` is invalid.
    - Algorithm has an invalid KiSAO id `KISAO_00000019`.

Log:

- 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 [here](https://github.com/biosimulators/Biosimulators/actions/runs/905282661). 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/905282661).

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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (7.9 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.9 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'

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:

docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (10.9 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

    Plots (1):

      plot: 4 curves

Executing SED-ML file 0: 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 (2):

    Succeeded: 2

    Skipped: 0

    Failed: 0

Summary of tests

Executed 65 test cases

Passed 29 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
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 36 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
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-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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:smoldyn/Lotka-Volterra
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
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

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:

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:

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:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 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:

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:

sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsModelAttributeChanges (0.0 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:

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 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:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (6.7 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmp13r5ekqj.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5912M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp6nipxhpq.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp6nipxhpq.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpspn4x27_, /tmp, /tmp, /tmp/tmpspn4x27_]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmp6nipxhpq.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmp6nipxhpq.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (6.6 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpx56xtzhq.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5916M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp3cxz7vlv.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp3cxz7vlv.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpxmsfqpqr, /tmp, /tmp, /tmp/tmpxmsfqpqr]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmp3cxz7vlv.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmp3cxz7vlv.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (6.6 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmp8okvtff7.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5914M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp3wkctnxv.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp3wkctnxv.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmprv8quado, /tmp, /tmp, /tmp/tmprv8quado]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmp3wkctnxv.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmp3wkctnxv.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (6.5 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpf04rz5rs.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5917M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpata7771g.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpata7771g.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpbgp9nctt, /tmp, /tmp, /tmp/tmpbgp9nctt]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmpata7771g.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmpata7771g.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (6.5 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpej51rz_n.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5913M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpuj9awsry.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpuj9awsry.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpppvb_lwk, /tmp, /tmp, /tmp/tmpppvb_lwk]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmpuj9awsry.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmpuj9awsry.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (7.2 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpvvi53_rv.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5912M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp2ht0q39i.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp2ht0q39i.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpsy7bwb_p, /tmp, /tmp, /tmp/tmpsy7bwb_p]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmp2ht0q39i.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmp2ht0q39i.xml

      pyNeuroML >>>  jNeuroML >>

    `pyNeuroML` was not able to execute `/tmp/tmp98wfkx5f.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5912M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpl6_yktch.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpl6_yktch.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp160ca9mg, /tmp, /tmp, /tmp/tmp160ca9mg]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmpl6_yktch.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmpl6_yktch.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (7.2 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:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpl0sna4q6.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5916M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpftieqnyw.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpftieqnyw.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp_bp3y_sx, /tmp, /tmp, /tmp/tmp_bp3y_sx]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmpftieqnyw.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmpftieqnyw.xml

      pyNeuroML >>>  jNeuroML >>

    `pyNeuroML` was not able to execute `/tmp/tmpf2r57qu5.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5916M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmphyasun0v.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmphyasun0v.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp109o_ak4, /tmp, /tmp, /tmp/tmp109o_ak4]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmphyasun0v.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmphyasun0v.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (6.7 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpczfxhcfw.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5919M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpp8ycydbc.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpp8ycydbc.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpisajplz6, /tmp, /tmp, /tmp/tmpisajplz6]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Loading LEMS file from: /tmp/tmpp8ycydbc.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:31  (INFO) Reading from: /tmp/tmpp8ycydbc.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsSubstitutingAlgorithms (4.9 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 execution of the COMBINE/OMEX archive did not fail as expected

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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    No algorithm can be substituted for 'LSODA' (KISAO_0000088) at substitution policy 'NONE'. Algorithms can only be substituted for the following algorithms:

      KISAO_0000019: CVODE

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.9 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Initial time must be 0, not 5e-05

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of netpyne to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

Summary of tests

Executed 65 test cases

Passed 29 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
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 36 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
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-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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:smoldyn/Lotka-Volterra
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (8.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (2.3 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'

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:

docker_image.HasBioContainersLabels (0.9 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (14.2 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

    Plots (1):

      plot: 4 curves

Executing SED-ML file 0: 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 (2):

    Succeeded: 2

    Skipped: 0

    Failed: 0

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:

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:

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:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

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
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

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:

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:

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:

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:

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:

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:

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:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 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:

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:

sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsModelAttributeChanges (0.0 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:

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 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:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (7.9 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpfozt_3e8.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5919M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpylvn7f01.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpylvn7f01.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp_8hzo0xk, /tmp, /tmp, /tmp/tmp_8hzo0xk]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:32  (INFO) Loading LEMS file from: /tmp/tmpylvn7f01.xml

      pyNeuroML >>>  jNeuroML >>  INFO Jun 04,2021 06:32  (INFO) Reading from: /tmp/tmpylvn7f01.xml

      pyNeuroML >>>  jNeuroML >>

ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['biosimulators-netpyne', '-i', '/tmp/in/archive.omex', '-o', '/tmp/out']' command failed.  (See above for error)

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (7.8 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
'NoneType' object has no attribute 'ndim'

Log:
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 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpi8nrtupk.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5924M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp_ov6_e1s.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp_ov6_e1s.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmph_pwqvdo, /tmp, /tmp, /tmp/tmph_pwqvdo]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)