Submit NetPyNE 1.0.0.2

[biosimulators-daemon]

---

id: netpyne version: 1.0.0.2 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/bd9ddb6e2e1db3471bc6ad1cab4d39ccf36f627c/biosimulators-netpyne.json specificationsPatch: version: 1.0.0.2 image: url: ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:1.0.0.2 validateImage: true commitSimulator: true

---

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 66 test cases

• Passed 30 test cases:

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

• Failed 0 test cases

• Skipped 36 test cases:

  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (5.4 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

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

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

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.3 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

  Docker images for simulation tools should declare the environment variables that they support.

  The Docker image does not declare the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

docker_image.HasBioContainersLabels (0.9 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (12.2 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9004 Algorithm: KISAO_0000019

  Warnings:

  Unexpected reports were produced:
  simulation.sedml/plot

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
    Plots (1):
  
      plot: 4 curves
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Tasks (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  

[biosimulators-daemon]

Skips

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

Required model formats and simulation algorithms for SED tasks:

• Format: format_3972 Algorithm: KISAO_0000263

  Reason for skip:

  Case requires model formats format_3972 and simulation algorithms KISAO_0000263

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_3972 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_3972 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_3240 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_3240 and simulation algorithms KISAO_0000019

  Log:

  published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_9004 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_9004 and simulation algorithms KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000088

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000088

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000496

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000496

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000560

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000560

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000560

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000560

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

• Format: format_2585 Algorithm: KISAO_0000027

• Format: format_2585 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

• Format: format_2585 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000027

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000027

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000029

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000029

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000437

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000437

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000449

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_9001 Algorithm: KISAO_0000057

  Reason for skip:

  Case requires model formats format_9001 and simulation algorithms KISAO_0000057

  Log:

  sedml.SimulatorProducesLinear3DPlots (0.0 s)

  Test that a simulator produces linear 3D plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

  Test that a simulator produces logarithmic 3D plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

  Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

  Reason for skip:

  'cython_function_or_method' object has no attribute 'rpartition'

  Log:

  sedml.SimulatorSupportsAlgorithmParameters (0.0 s)

  Test that a simulator supports setting the values of parameters of algorithms

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsComputeModelChanges (0.0 s)

  Test that a simulator supports compute model changes

  Reason for skip:

  'cython_function_or_method' object has no attribute 'rpartition'

  Log:

  sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

  Test that a simulator supports changes to the attributes of model elements

  Reason for skip:

  'cython_function_or_method' object has no attribute 'rpartition'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  'cython_function_or_method' object has no attribute 'rpartition'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

  Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

  Reason for skip:

  'cython_function_or_method' object has no attribute 'rpartition'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (7.0 s)

  Test that a simulator supports repeated tasks over functional ranges

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      __repeated_task_0
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (2):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmpt4_6z4o2.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5937M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpi66as8j8.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpi66as8j8.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp49zvbv8b, /tmp, /tmp, /tmp/tmp49zvbv8b]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmpi66as8j8.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmpi66as8j8.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (7.0 s)

  Test that a simulator supports repeated tasks over uniform ranges

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      __repeated_task_0
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (2):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmp6t4medm2.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5939M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpmqp7ckg7.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpmqp7ckg7.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp298jexnz, /tmp, /tmp, /tmp/tmp298jexnz]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmpmqp7ckg7.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmpmqp7ckg7.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (7.0 s)

  Test that a simulator supports repeated tasks over uniform ranges

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      __repeated_task_0
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (2):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmpqxc_gnk8.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5932M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp9wycnxbn.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp9wycnxbn.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpfivq00f0, /tmp, /tmp, /tmp/tmpfivq00f0]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmp9wycnxbn.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmp9wycnxbn.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (7.0 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      __repeated_task_0
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (2):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmp_fcbxdzl.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5936M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp1b2ho5w1.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp1b2ho5w1.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp1lr0zihh, /tmp, /tmp, /tmp/tmp1lr0zihh]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmp1b2ho5w1.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmp1b2ho5w1.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (7.1 s)

  Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      __repeated_task_0
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (2):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmpi01psymy.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5936M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpjirt_brw.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpjirt_brw.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpu0nd6oer, /tmp, /tmp, /tmp/tmpu0nd6oer]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmpjirt_brw.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmpjirt_brw.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (7.7 s)

  Test that a simulator supports nested repeated tasks

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (3):
  
      __repeated_task_0
  
      __repeated_task_1
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (3):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 2
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmpl4izf7_1.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5939M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp089d9o60.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp089d9o60.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp8tmo7lya, /tmp, /tmp, /tmp/tmp8tmo7lya]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmp089d9o60.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmp089d9o60.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
    `pyNeuroML` was not able to execute `/tmp/tmpxdb39yfy.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5954M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmphwotwqm3.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmphwotwqm3.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp2eq6agqq, /tmp, /tmp, /tmp/tmp2eq6agqq]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Loading LEMS file from: /tmp/tmphwotwqm3.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:45  (INFO) Reading from: /tmp/tmphwotwqm3.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (7.5 s)

  Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (3):
  
      __repeated_task_0
  
      __repeated_task_1
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (3):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 2
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmpe7zxs326.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5940M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpwokwo4e3.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpwokwo4e3.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpm2h6mccc, /tmp, /tmp, /tmp/tmpm2h6mccc]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:46  (INFO) Loading LEMS file from: /tmp/tmpwokwo4e3.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:46  (INFO) Reading from: /tmp/tmpwokwo4e3.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
    `pyNeuroML` was not able to execute `/tmp/tmpnvmb1pm0.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5940M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpevuxyrg0.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpevuxyrg0.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpdevkhkml, /tmp, /tmp, /tmp/tmpdevkhkml]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:46  (INFO) Loading LEMS file from: /tmp/tmpevuxyrg0.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:46  (INFO) Reading from: /tmp/tmpevuxyrg0.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (7.0 s)

  Test that a simulator supports repeated tasks over vector ranges

  Reason for skip:

  'NoneType' object has no attribute 'ndim'

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      __repeated_task_0
  
      task
  
    Reports (2):
  
      __repeated_task_report: 5 data sets
  
      task_report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (2):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (2):
  
    Succeeded: 1
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    `pyNeuroML` was not able to execute `/tmp/tmpqlrimoyr.xml`:
  
      pyNeuroML >>> *** Problem running command: 
  
      pyNeuroML >>>        Command 'java -Xmx5941M  -Djava.awt.headless=true -jar  "/opt/conda/envs/py39/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpwz6og1v8.xml"  -nogui -I ''' returned non-zero exit status 1.
  
      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
  
      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpwz6og1v8.xml with jLEMS, NO GUI mode...
  
      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml
  
      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp4fmdcaex, /tmp, /tmp, /tmp/tmp4fmdcaex]
  
      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]
  
      pyNeuroML >>>  jNeuroML >>  
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)
  
      pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)
  
      pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:46  (INFO) Loading LEMS file from: /tmp/tmpwz6og1v8.xml
  
      pyNeuroML >>>  jNeuroML >>  INFO Jun 06,2021 03:46  (INFO) Reading from: /tmp/tmpwz6og1v8.xml
  
      pyNeuroML >>>  jNeuroML >>  
  
      
  

  sedml.SimulatorSupportsSubstitutingAlgorithms (4.9 s)

  Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.

  Reason for skip:

  The execution of the COMBINE/OMEX archive did not fail as expected

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (1):
  
    Succeeded: 0
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    No algorithm can be substituted for 'LSODA' (KISAO_0000088) at substitution policy 'NONE'. Algorithms can only be substituted for the following algorithms:
  
      KISAO_0000019: CVODE
  

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.9 s)

  Test that a simulator supports multiple time courses with non-zero initial times

  Reason for skip:

  ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (1):
  
    Succeeded: 0
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    Initial time must be 0, not 5e-05
  

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