Submit NetPyNE <IP_ADDRESS>

id: netpyne
version: <IP_ADDRESS>
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/27c2c97bc9192984e719880a96c1c3d1b4611b72/biosimulators-netpyne.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>
digest: "sha256:de1be2b99fec6bef8322fa9a3a691c5db0874bc298d173a5e5ca2cb6db617e4f"
validateImage: true
commitSimulator: true

Changelog

restarted because API was down\
restarted because API was down

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The validation/submission of your simulator failed.
- HTTPSConnectionPool(host='api.biosimulators.org', port=443): Max retries exceeded with url: /simulators/validate (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f02166aceb0>: Failed to establish a new connection: [Errno 110] Connection timed out'))

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.
If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 73 test cases

Passed 25 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 4 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks

Skipped 44 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
sedml.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
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (13.7 s)

Test that simulator logs the execution of COMBINE/OMEX archives
Exception:
Expecting value: line 1 column 1 (char 0)

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (13.6 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Exception:
Expecting value: line 1 column 1 (char 0)

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (13.9 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Exception:
Expecting value: line 1 column 1 (char 0)

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (13.6 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Exception:
Expecting value: line 1 column 1 (char 0)

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

Warnings
docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)

Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-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: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (1.1 s)

Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.9 s)

Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (1.0 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.9 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsAlgorithmParameters (1.0 s)

Test that a simulator supports setting the values of parameters of algorithms
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (1.0 s)

Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsModelAttributeChanges (1.0 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: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.9 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (1.0 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (14.0 s)

Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmp_92np2fx.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpye4igu_6.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:04:16,660 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpye4igu_6.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpye4igu_6.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:04:16,661 - pyneuroml.pynml - INFO - Executing: (java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpye4igu_6.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpye4igu_6.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:04:16,973 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpye4igu_6.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpye4igu_6.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:04:16,973 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpye4igu_6.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (14.0 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmp38naetta.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpgwudc2e0.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:04:30,638 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpgwudc2e0.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgwudc2e0.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:04:30,639 - pyneuroml.pynml - INFO - Executing: (java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgwudc2e0.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgwudc2e0.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:04:30,969 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgwudc2e0.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpgwudc2e0.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:04:30,969 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpgwudc2e0.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (14.1 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpzeuu5vgg.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmphcmoxbvp.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:04:44,777 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmphcmoxbvp.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5670M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmphcmoxbvp.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:04:44,778 - pyneuroml.pynml - INFO - Executing: (java -Xmx5670M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmphcmoxbvp.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5670M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmphcmoxbvp.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:04:45,093 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5670M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmphcmoxbvp.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmphcmoxbvp.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:04:45,093 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmphcmoxbvp.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (14.0 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpg1anyxwy.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp0s2m6h7i.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:04:58,824 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp0s2m6h7i.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5666M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0s2m6h7i.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:04:58,825 - pyneuroml.pynml - INFO - Executing: (java -Xmx5666M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0s2m6h7i.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5666M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0s2m6h7i.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:04:59,142 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5666M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0s2m6h7i.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp0s2m6h7i.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:04:59,143 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp0s2m6h7i.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (13.9 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpe4mewy2s.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpr3e591zw.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:05:12,799 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpr3e591zw.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5662M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpr3e591zw.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:05:12,800 - pyneuroml.pynml - INFO - Executing: (java -Xmx5662M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpr3e591zw.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5662M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpr3e591zw.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:05:13,109 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5662M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpr3e591zw.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpr3e591zw.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:05:13,109 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpr3e591zw.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (14.6 s)

Test that a simulator supports nested repeated tasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmphaim5bv6.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp7a2c4gl0.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:05:26,855 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp7a2c4gl0.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp7a2c4gl0.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:05:26,856 - pyneuroml.pynml - INFO - Executing: (java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp7a2c4gl0.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp7a2c4gl0.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:05:27,169 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp7a2c4gl0.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp7a2c4gl0.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:05:27,169 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp7a2c4gl0.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

    `NetPyNe` was not able to execute `/tmp/tmp54zecnu8.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpg4ubuef4.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:05:27,365 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpg4ubuef4.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpg4ubuef4.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:05:27,366 - pyneuroml.pynml - INFO - Executing: (java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpg4ubuef4.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpg4ubuef4.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:05:27,689 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpg4ubuef4.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpg4ubuef4.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:05:27,689 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpg4ubuef4.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (14.8 s)

Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpaewixq7d.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp0r3bxc9y.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 02:05:41,653 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp0r3bxc9y.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0r3bxc9y.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 02:05:41,654 - pyneuroml.pynml - INFO - Executing: (java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0r3bxc9y.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0r3bxc9y.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 02:05:41,969 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp0r3bxc9y.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp0r3bxc9y.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 02:05:41,970 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp0r3bxc9y.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

    `Ne ...

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
-
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1585520786). 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/1585520786).

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 73 test cases

Passed 25 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 4 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks

Skipped 44 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
sedml.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
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (13.6 s)

Test that simulator logs the execution of COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

"Unauthorized"

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (13.7 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

"Unauthorized"

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (13.7 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

"Unauthorized"

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (13.8 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

"Unauthorized"

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

Warnings
docker_image.DeclaresSupportedEnvironmentVariables (0.4 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.3 s)

Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-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: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (1.1 s)

Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.9 s)

Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (1.0 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.9 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsAlgorithmParameters (1.0 s)

Test that a simulator supports setting the values of parameters of algorithms
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (1.0 s)

Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsModelAttributeChanges (1.1 s)

Test that a simulator supports changes to the attributes of model elements
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.9 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (1.1 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (14.1 s)

Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpputfa51f.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpqsnxcmjz.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:20:13,496 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpqsnxcmjz.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpqsnxcmjz.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:20:13,497 - pyneuroml.pynml - INFO - Executing: (java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpqsnxcmjz.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpqsnxcmjz.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:20:13,810 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5660M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpqsnxcmjz.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpqsnxcmjz.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:20:13,810 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpqsnxcmjz.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (14.0 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpbd6wlrmg.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpmvdf5msw.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:20:27,539 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpmvdf5msw.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpmvdf5msw.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:20:27,540 - pyneuroml.pynml - INFO - Executing: (java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpmvdf5msw.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpmvdf5msw.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:20:27,856 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5661M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpmvdf5msw.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpmvdf5msw.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:20:27,857 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpmvdf5msw.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (14.1 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpnf6wza4p.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpyv3ujdzs.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:20:41,641 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpyv3ujdzs.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5658M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpyv3ujdzs.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:20:41,642 - pyneuroml.pynml - INFO - Executing: (java -Xmx5658M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpyv3ujdzs.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5658M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpyv3ujdzs.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:20:41,966 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5658M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpyv3ujdzs.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpyv3ujdzs.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:20:41,966 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpyv3ujdzs.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (14.0 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpq77ezybp.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpgy7qf679.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:20:55,676 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpgy7qf679.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5656M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgy7qf679.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:20:55,676 - pyneuroml.pynml - INFO - Executing: (java -Xmx5656M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgy7qf679.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5656M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgy7qf679.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:20:55,981 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5656M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpgy7qf679.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpgy7qf679.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:20:55,982 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpgy7qf679.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (14.1 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmp5fo5457d.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp5ysdztgr.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:21:09,841 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp5ysdztgr.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp5ysdztgr.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:21:09,842 - pyneuroml.pynml - INFO - Executing: (java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp5ysdztgr.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp5ysdztgr.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:21:10,161 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp5ysdztgr.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp5ysdztgr.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:21:10,162 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp5ysdztgr.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (14.6 s)

Test that a simulator supports nested repeated tasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NetPyNe` was not able to execute `/tmp/tmpxz64p8_8.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpob1878gh.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:21:23,871 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpob1878gh.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5653M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpob1878gh.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:21:23,872 - pyneuroml.pynml - INFO - Executing: (java -Xmx5653M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpob1878gh.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5653M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpob1878gh.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:21:24,182 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5653M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpob1878gh.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpob1878gh.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:21:24,183 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpob1878gh.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

    `NetPyNe` was not able to execute `/tmp/tmpmc3yma1x.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpetifeugr.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> 2021-12-16 04:21:24,372 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpetifeugr.xml and running with jNeuroML_NetPyNE

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpetifeugr.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> 2021-12-16 04:21:24,373 - pyneuroml.pynml - INFO - Executing: (java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpetifeugr.xml"  -netpyne -run -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpetifeugr.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-12-16 04:21:24,690 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5654M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpetifeugr.xml"  -netpyne -run -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpetifeugr.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

      pyNeuroML >>> 2021-12-16 04:21:24,690 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpetifeugr.xml

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

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

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

       jNeuroML >>

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

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

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

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

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

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

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

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:535)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (14.7 s)

Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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