Submit Neuron 8.0.0

id: neuron
version: 8.0.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/65a64d0aab2b40e11d218aede041e0e4b0776fe0/biosimulators-neuron.json
specificationsPatch:
version: 8.0.0
image:
url: ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0
validateImage: true
commitSimulator: true

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 71 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 41 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: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-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.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (5.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

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

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

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.5 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 (0.5 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 (11.5 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:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

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

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

    Plots (1):

      plot: 4 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (2):

    Succeeded: 2

    Skipped: 0

    Failed: 0

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

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

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

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

Log:

published_project.SimulatorCanExecutePublishedProject:cellml/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:

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-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:

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/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:

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: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:

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:

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:

sedml.SimulatorProducesLinear3DPlots (0.7 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 (0.8 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 (0.8 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 (0.7 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 (0.9 s)
Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsModelAttributeChanges (0.7 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 (0.8 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 (0.7 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 (8.5 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

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

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmpzvklompo.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5805M  -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/tmpehm_e91k.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpehm_e91k.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/tmp72ze1txs, /tmp, /tmp, /tmp/tmp72ze1txs]

      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 Aug 12,2021 06:03  (INFO) Loading LEMS file from: /tmp/tmpehm_e91k.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:03  (INFO) Reading from: /tmp/tmpehm_e91k.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (8.7 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

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

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmpqld97fbf.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5803M  -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/tmpa4tndm1d.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpa4tndm1d.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/tmpl79b9s01, /tmp, /tmp, /tmp/tmpl79b9s01]

      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 Aug 12,2021 06:03  (INFO) Loading LEMS file from: /tmp/tmpa4tndm1d.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:03  (INFO) Reading from: /tmp/tmpa4tndm1d.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (8.5 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

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

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmpbfgs7w8p.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5809M  -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/tmp4l52yxzy.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp4l52yxzy.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/tmp42n42h70, /tmp, /tmp, /tmp/tmp42n42h70]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmp4l52yxzy.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmp4l52yxzy.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (8.7 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

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

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmpfw6a8dwz.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5805M  -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/tmpfv7w_xtp.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpfv7w_xtp.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/tmp0q0lgcb6, /tmp, /tmp, /tmp/tmp0q0lgcb6]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmpfv7w_xtp.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmpfv7w_xtp.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (8.6 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/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

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

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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_or79h_b.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5803M  -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/tmpl3j7bqw_.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpl3j7bqw_.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/tmpq8kroej5, /tmp, /tmp, /tmp/tmpq8kroej5]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmpl3j7bqw_.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmpl3j7bqw_.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (9.0 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmp53y5oyok.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5804M  -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/tmpcw44z40y.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpcw44z40y.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/tmpbsxloblw, /tmp, /tmp, /tmp/tmpbsxloblw]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmpcw44z40y.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmpcw44z40y.xml

      pyNeuroML >>>  jNeuroML >>

    `pyNeuroML` was not able to execute `/tmp/tmpxasf01fe.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5804M  -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/tmp9k750nzq.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp9k750nzq.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/tmpfbmen9ys, /tmp, /tmp, /tmp/tmpfbmen9ys]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmp9k750nzq.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmp9k750nzq.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (9.1 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/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Task `__repeated_task_1` may be invalid.

    - The outputs of the sub-tasks have different shapes.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Task `__repeated_task_1` may be invalid.

      - The outputs of the sub-tasks have different shapes.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmpr50vlczz.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5803M  -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/tmpswaroz95.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpswaroz95.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/tmp806wt67s, /tmp, /tmp, /tmp/tmp806wt67s]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmpswaroz95.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmpswaroz95.xml

      pyNeuroML >>>  jNeuroML >>

    `pyNeuroML` was not able to execute `/tmp/tmpnehij7q5.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5802M  -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/tmpr855f58a.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpr855f58a.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/tmpembfxu6d, /tmp, /tmp, /tmp/tmpembfxu6d]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmpr855f58a.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmpr855f58a.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (8.5 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

/opt/conda/envs/py39/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

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

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

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

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

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 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/tmplewgktdh.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5803M  -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/tmp1a1lache.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp1a1lache.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/tmpi7ryjywc, /tmp, /tmp, /tmp/tmpi7ryjywc]

      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 Aug 12,2021 06:04  (INFO) Loading LEMS file from: /tmp/tmp1a1lache.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 12,2021 06:04  (INFO) Reading from: /tmp/tmp1a1lache.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsSubstitutingAlgorithms (25.7 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Warning: no DISPLAY environment variable.

--No graphics will be displayed.

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

    Fai ...

The image for your simulator is valid!

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


Overlapblock Design 35

Hey, I have created a pull request. This is part of my coursework assignment. Kindly, look into it, Thank you.

Hey @Shyamala7, can you look into the pull request?


[Scope Change Request] Table 900 - Assembly Header - ValidateDates

Dear ALAppExtensions team,
Can you please REMOVE the [Scope('OnPrem')] modifier from the Table 900 - Assembly Header - ValidateDates procedure:
    // [Scope('OnPrem')] << PLEASE REMOVE SCOPE OnPrem which cannot be explained from the code
    procedure ValidateDates(FieldNumToCalculateFrom: Integer; DoNotValidateButJustAssign: Boolean)

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. Please do not reply to this, as we do not monitor closed issues. If you have follow-up questions or requests, please create a new issue where you reference this one.

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. Please do not reply to this, as we do not monitor closed issues. If you have follow-up questions or requests, please create a new issue where you reference this one.


Filter for no-NN entities

I added a filter for entities found in the entitiyFinder that don't have a noun:

before expansion, I check to see if the entity contains a noun OR
if it ends with an adj and the next word is a noun (i.e., if it got filtered out bc it's a trigger needed later)

I also added a test in TestEntityFinder to demo the desired behavior, but please let me know if it's obviously incomplete.
Thanks!

yeah -- I thought about that, but it would be such a looooong condition,
seemed more readable that way... but I could maybe still split it on lines
with comments?
On Thu, Mar 29, 2018 at 2:07 PM, Keith Alcock<EMAIL_ADDRESS>wrote:

@kwalcock approved this pull request.
FWIW this is another one

if (entity.tags.get.exists(tag => tag.startsWith("NN"))) true
// Otherwise, if the entity ends with an adjective and the next word
is a noun (which was excluded because ]
// it's needed as a trigger downstream), it's valid (ex: 'economic
declines')
else if (entity.tags.get.last.startsWith("JJ") && nextTagNN(entity))
true
// Otherwise, it's not valid
else false

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/clulab/eidos/pull/238#pullrequestreview-108204511,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AFIniQy4IC14e4WzwXfMFacv9Fz26X9Bks5tjU0agaJpZM4TAuwd
.


Add Hash#dig method

Cheers! SSIA.

Replaced with https://github.com/svenfuchs/safemode/pull/37
I knew I was already working on this one :(


Fix cloned notifications

Coverage remained the same at 60.982% when pulling 77a1600c138512f1e7df05e875740814d02f02af on notif-fix into 59ce586ea44f3972d234b4e1d81ac9affd86903f on master.


add initial ignore and include definitions for reg x

"Initial," should this wait until there are more?


feat: Add audio classification support

Completed Audio Classification Modality

Hi @walkingtowork! Can you pls review the PR. There have been a lot of changes in Task.js since I formatted it. Pls let me know if I should undo those changes.


Automate Custom Kaggle Wheels Builds

Is your feature request related to a problem? Please describe

The current process of updating the Kaggle Wheel that is used for the Public Leaderboard, requires one of the member to manually create the custom wheel each time an update is released. This is takes quite a bit of time and we might miss it from time to time as new updates come out.
Describe the solution you'd like
Creating a GitHub Actions that goes through and creates the custom wheel and setup a PR for it similar to Dependabot.
For all this to work, we will make use of the pypi.org api to pull the latest release

Collect the filename and releaseURL
filename=$(curl -s https://pypi.org/simple/kaggle/ | sed -n 's/.*<a[^>]*>\(.*\)<\/a>.*/\1/p' | tail -n 1)

releaseURL=$(curl -s https://pypi.org/simple/kaggle/ | grep -oP '(?<=<a href=").*?(?=" >)' | tail -n 1)

Check if $(basename $filename .tar.gz)-py3-none-any.whl exists in wheels

If file exists, then send a message stating: Latest Version Exists and STOP
If file does not exist, STEP 3

Download and unzip the latest release
curl -L $releaseURL > release.tar.gz

tar -xvzf release.tar.gz

Check if a specific line of code exists at a specific line number in kaggle/api/kaggle_api_extended.py
sed -n "1837p" "$(basename $filename .tar.gz)/kaggle/api/kaggle_api_extended.py" | grep -Fxq "        remote_date = datetime.strptime(response.headers['Last-Modified']," && echo "Found" || echo "Not found"

We are trying to verify if the line causing the bug has been resolved or not.
If it does not exist then send a message stating: Verify new changes in this release and STOP
If it does exist, then STEP 5

Make the line change
sed -i "1837s/.*/        remote_date = datetime.strptime(response.headers['Date'],/" "$(basename $filename .tar.gz)/kaggle/api/kaggle_api_extended.py"

Build the Python Wheel
python -m build --wheel

Create a new branch that includes the new wheel file

Additional context
<!-- Add any other context or screenshots about the feature request her

- [Building Wheel Files in Github Actions](https://andrewpwheeler.com/2022/05/10/building-wheel-files-in-github-actions/)

Building Wheel Files in Github Actions


Add create visualisations by json file

Add the option to create multiple visualisations, simple by load json file, instead of create visualisation one by one

Done


Disconnected

First try: I downloaded and installed the Windows client which seemed to work. Tried running a terminal command... long story, I uninstalled the app because it wasn't working.
Second try: Found workarounds online for using Keybase CLI application. Re-installed Windows client. But once opened, even after a restart, the client seems to be unable to connect to the internet.

my log id: 23e0c46b44d05f257dff561c
I'm excited about this app and will continue trying. I did not find exact situation online so submitting a ticket.
Cheers,
Ian

Thanks for the report, CC @zanderz @maxtaco @patrickxb
18096 2017-03-05T11:35:54.254920-05:00 - [DEBU keybase engine.go:66] 1b4 - RunEngine(ListTracking) -> ok
18097 panic: runtime error: invalid memory address or nil pointer dereference

@patrickxb can you take this one?

18103 github.com/keybase/client/go/libkb.(*IdentityTable).GetTrackList(0x0, 0x0, 0x0, 0x0)
18104 C:/Jenkins/workspace/windows-installer_0/src/github.com/keybase/client/go/libkb/id_table.go:1141 +0x2d

i'm already looking at it now, let me just put a PR

PR up in #6142

Ok, the PR is in.  I'm slightly concerned this is a workaround of a deeper problem.

It is common for the chat app to be looking for the internet, before I am connected to the internet.  I had this same issue this morning, with that same cute screen shot above.  It is never clear to me how to stop/start this application.  I have had this working with no problems for a couple of weeks now.  At the moment the problem has cleared.  I have since rebooted.  Thx

I am still experiencing this issue, however the occurrences are rare. If for example my connection drops for over 5-10 mins, Keybase will(sometimes) struggle to reconnect. I have to exit and restart the app to get it working.
@KidPluto You can 'quit' out of Keybase via the notifications area icon, click the Keybase icon, click the 'hamburger-ish' menu on the top right and click 'quit' at the bottom of that menu. (Windows)

Hello. I don't think it was connectivity related but I don't know much. I uninstalled and removed every file I could find (again) and started over. It worked this time!
If there was anything in the log submitted, I hope it helps fix issues for the future.
Ian

Hmm, I am having the same issue Keybase won't connect.

@adsactly @joshuaferrara Are you on Windows? One user experiencing this disconnected message had it solved with the fix contained in this special build, if you would like to try: https://s3.amazonaws.com/prerelease.keybase.io/windows/Keybase_1.0.21-20170428134902%2B4280d08.386.exe

@zanderz Yes, I am on windows. That build is working for me!

Still experiencing this issue on Windows 10 x64.

@Zenexer can you do a keybase log send at the Keybase Shell? Have you disabled any Keybase startup shortcuts?

@zanderz That was the first thing I checked; they were enabled.  I'll send the logs next time I'm at that computer.

I'm helping someone else who is using keybase, and they seem to be having this issue as well.  Was a permanent fix ever discovered?  I wonder if the same exe would function at this point or if it would be too outdated - this issue is almost 2 years old after all.  I'm on a mac, and not super familiar with Windows.


add provides section for latest panda (S11 support)

looks like another PR I merged had this. closing. Thank you!


fix: Kamel install with kit option can leave integrationkit stuck waiting for platform

fixes #809

Are we ok to merge this?

looks good


suggested matches in batch search

@deniseOme commented on Wed May 31 2017
When uploading a list into the batch search, one gene gets a suggested match, which does not seem to be different at all. They seem to be the same i.e. ptgs2 --> PTGS2.
target_list.txt

Fixed


Publish update for Redgate SQL Search extension

@llali I'll publish this change later today.  It looks like a straightforward vbump.


Fix for ShardConn not propagating error codes

@sougou @alainjobart
Added more tests, now I have a high degree of confidence that this works :)

LGTM


Is isIPAddrResolvable working correctly?

Package version eg. v8, v9:
v9
Issue, Question or Enhancement:
It looks like the following function does not work correctly:
// IsIPAddrResolvable is the validation function for validating if the field's value is a resolvable ip address.
func isIPAddrResolvable(fl FieldLevel) bool {

	if !isIP(fl) {
		return false
	}

	_, err := net.ResolveIPAddr("ip", fl.Field().String())

	return err == nil
}

It does not resolve "localhost" because isIP returns false, however net.ResolveIPAddr returns true.
Any ideas?

Hey @dealancer I believe that it is working correctly and why the isIp check comes before the ResolveIpAddr because localhost is not a valid IP but a hostname which can resolve to an IP.


Fix example spend amount

In the segwit signing example we are using the incorrect value when creating the signature - we should be using the utxo amount (input amount) not the spend amount (output spend amount).
Close: #2680

Pull Request Test Coverage Report for Build<PHONE_NUMBER>
Details

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 83.131%

Totals

Change from base Build<PHONE_NUMBER>:
0.0%

Covered Lines:
19195

Relevant Lines:
23090

💛  - Coveralls


Need WITH in the curation UI

Cannot curate WITH expressions  - e.g. "Apache-2.0 WITH LLVM-exception" (or any of the other WITH exceptions - https://spdx.org/licenses/exceptions-index.html).
Note: License Exceptions
The SPDX License List includes a list of exceptions. These exceptions grant an exception to a license condition or additional permissions beyond those granted in a license; they are not stand-alone licenses. Exceptions are added to a license using the License Expression operator, "WITH".

Note: https://github.com/clearlydefined/service/issues/694

Closing since this has an open issue on the service

Closing since this has an open issue on the service


Collecting test coverage information from tests

Overview
This merge request introduces several features that enhance the build and testing processes of our project, as well as adding a complete coverage feature. Specifically, it adds documentation for the coverage feature in CMake, using gcovr for report generation in various formats, adds a bootstrap option for coverage build, and sets up a Gitlab CI/CD pipeline for automated report generation.
Additionally, this merge request includes improvements to the CMake logic for backend compilation dependencies, as well as a new feature that allows for the separation of compiled backends available for usage versus those that are tested only.
Changes
Adding Coverage in CMake
This feature adds a Coverage build-type to the Cmake infrastructure, allowing developers to effortlessly compile and generate lcov/gcov coverage reports, that can after be traduced into human-readable formats. This is made possible using the command: make coverage <format>, which generates a coverage report in the specified format. The supported formats are HTML, XML(cobertura), JSON and Coveralls. This feature also includes documentation on how to use the command and how to interpret the generated reports. \
New dependencies introduce for Coverage builds (only):

gcov/lcov : Used during compilation as part of the GNU compiler to analyse program execution, see documentation
gcovr: Python module used for report generation by the CMake make coverage <format> command, see documentation

Adding GitLab CI for Coverage
This feature adds GitLab CI for code coverage with automated reports. GitLab CI will automatically generate coverage reports for every commit and merge request on the main branch. These reports will be displayed in the Merge-Request interface, providing a quick and easy way to assess the code quality of their changes.
Also, a Gitlab Page job has been created for this feature, publishing a detailed HTML report of coverage.
Adding Option for Coverage Build
This feature adds an option in the bootstrap.sh for a coverage build: --coverage-build. Developers can now choose to build the project with coverage enabled, which will generate coverage reports (lcov format) as part of the execution process.
Providing Documentation for Coverage
This feature provides documentation for the coverage feature, including how to enable it and how to generate reports. This documentation will be useful for developers who are new to the project or who are not familiar with code coverage reporting.
Fixing CMake Requirements
This feature addresses some CMake requirements that were not previously met, including dependencies on backends.
For instance, asking for a build with the non-blocking backend will always enable the reference(+omp) backend compilation, as it is required.
Separating compiled backends and tested ones
This feature separates compiled backends available for usage and the ones that will be tested, tested backends being an included set of all the compiled backends.
This feature was made after trying to test the non-blocking backend alone, but with the reauirement of having the reference(+omp) compiled.

Just to note: it will take me a little while to review this one. A quick check reveals one immediate thing though -- could you please add yourself to the NOTICE file via this MR? This is a very material contribution that should of course be properly acknowledged=)


Splits skill and activity lists

Description
Fixes #1221
Notes (out of scope, known isues, hints for reviewing code, ...)  (optional)
...
Test cases

[ ] Case 1:

Given I am the usual user
When I go to this page
Then I see 2 sections "Sub-skills" and "Activities to learn or reinforce this skill" with skills and activities children

[ ] Case 2:

Given I am the usual user
When I go to this page
Then I see 2 sections "Sub-skills" and "Activities to learn or reinforce this skill" with no skills and activities caption

[ ] Case 3:

Given I am the usual user
When I go to this page
Then I see 2 sections "Sub-skills" and "Activities to learn or reinforce this skill" with skills and activities children
Then I click on one of sub skill item
Then I see opened skill page

[ ] Case 4:

Given I am the usual user
When I go to this page
Then I see 2 sections "Sub-skills" and "Activities to learn or reinforce this skill" with skills and activities children
Then I click on one of sub activity item
Then I see opened activity page

[ ] Case 5:

Given I am the usual user
When I go to this page
Then I see locked item under "Activities to learn or reinforce this skill" section

[ ] Case 6:

Given I am the usual user
When I go to this page
Then I see item with score under "Activities to learn or reinforce this skill" section

Could you display children as they are displayed in children list with scores aligned properly and lock icon (maybe you did it already)
-->

The numbering is not really required (but is not a problem in case you reuse a component)


Package.loadSettings is deprecated.

Store package settings files in the settings/ directory instead of scoped-properties/
Package.loadSettings (/Applications/Atom.app/Contents/Resources/app/src/package.js:565:9)
<unknown> (/Applications/Atom.app/Contents/Resources/app/src/package.js:187:43)

Whoops, dupe of #19


[4.6.1] bug: runOutsideAngular problem in IonVirtualScroll

Bug Report
Ionic version:

[x] 4.x
Current behavior:
This bug appeared in 4.6.1 (4.6.0, too?). With 4.5 there were no errors.
I got the following error on every page where I use IonVirtualScroll:
ERROR TypeError: Cannot read property 'runOutsideAngular' of undefined
    at IonVirtualScroll.set (fesm5.js:1386)

The problem is on the proxyInputs function:
function proxyInputs(Cmp, inputs) {
    /** @type {?} */
    var Prototype = Cmp.prototype;
    inputs.forEach((/**
     * @param {?} item
     * @return {?}
     */
    function (item) {
        Object.defineProperty(Prototype, item, {
            get: /**
             * @return {?}
             */
            function () { return this.el[item]; },
            set: /**
             * @param {?} val
             * @return {?}
             */
            function (val) {
                var _this = this;
                this.z.runOutsideAngular((/**  <--- ERROR SOURCE
                 * @return {?}
                 */
                function () { return _this.el[item] = val; }));
            },
        });
    }));
}

Expected behavior:
Work normally
Steps to reproduce:

Other information:

Ionic info:

Ionic:

   Ionic CLI                     : 5.2.1 (/Users/tomi/.nvm/versions/node/v10.14.1/lib/node_modules/ionic)
   Ionic Framework               : @ionic/angular 4.6.1
   @angular-devkit/build-angular : 0.11.4
   @angular-devkit/schematics    : 7.3.9
   @angular/cli                  : 7.3.9
   @ionic/angular-toolkit        : 1.5.1

Cordova:

   Cordova CLI       : 9.0.0<EMAIL_ADDRESS>   Cordova Platforms : android 8.0.0, ios 5.0.1
   Cordova Plugins   : cordova-plugin-ionic-keyboard 2.1.3, cordova-plugin-ionic-webview 4.1.1, (and 21 other plugins)

Utility:

   cordova-res : 0.3.0 (update available: 0.5.2)
   native-run  : 0.2.7

System:

   Android SDK Tools : 26.1.1 (/Users/tomi/Library/Android/sdk)
   ios-deploy        : 1.9.4
   ios-sim           : 8.0.1
   NodeJS            : v10.14.1 (/Users/tomi/.nvm/versions/node/v10.14.1/bin/node)
   npm               : 6.10.0
   OS                : macOS Mojave
   Xcode             : Xcode 10.2.1 Build version 10E1001

I was pushed to downgrade to 4.5 because scroll event never was triggered in 4.6. I upgraded to 4.6.1 and everything it's running smoothly. I manually delete www directory and run ionic repair after updates.

@rernesto deleting www folder and run ionic reapair didn't solve the problem :(

@rernesto deleting www folder and run ionic reapair didn't solve the problem :(

Ionic:

   Ionic CLI                     : 5.2.1 (/usr/lib/node_modules/ionic)
   Ionic Framework               : @ionic/angular 4.6.1
   @angular-devkit/build-angular : 0.13.9
   @angular-devkit/schematics    : 7.3.9
   @angular/cli                  : 7.3.9
   @ionic/angular-toolkit        : 1.5.1

Cordova:

   Cordova CLI       : 9.0.0<EMAIL_ADDRESS>   Cordova Platforms : android 8.0.0
   Cordova Plugins   : cordova-plugin-ionic-keyboard 2.1.3, cordova-plugin-ionic-webview 4.1.1, (and 6 other plugins)

Utility:

   cordova-res : 0.5.1 (update available: 0.5.2)
   native-run  : 0.2.7

System:

   Android SDK Tools : 26.1.1 (/opt/android-sdk)
   NodeJS            : v10.16.0 (/usr/bin/node)
   npm               : 6.9.2
   OS                : Linux 4.15

Can you sow us your ion-infinite implementation?
Mine look like this:
...
<ion-infinite-scroll *ngIf="records.length > 0"  threshold="100px" (ionInfinite)="loadMore($event)">
    <ion-infinite-scroll-content
        loadingSpinner="bubbles">
    </ion-infinite-scroll-content>
  </ion-infinite-scroll>

...
loadMore(event) {
    this.page++;
    if (this.page > this.info.maxPage) {
      event.target.complete();
    } else {
      setTimeout(() => {
        this.apiService.searchData(
            this.searchValue, this.bibleVersionValue.id, this.page
        ).subscribe(response => {
          this.records = this.records.concat(response.results);
          this.info = response.info;
          event.target.complete();
        });
      }, 500);
    }
  }
...

Seeing the same error as @petrot when I upgraded to 4.6.1. Had to revert, bc I couldn't find a solution.
<ion-virtual-scroll [items]="sessionsList" checkRange="5" scrollY="true" [approxItemHeight]="getApproxItemHeight()">
            <ion-card *virtualItem="let session;">

Worked fine until the update to 4.6.1.

@rernesto the problem is with the virtual-scroll, not with the infinite-scroll.

Yes @petrot, I have the same issue here

I'm having this problem too.  Updated to 4.6.1 just now because ionInfinite event wasn't being triggered.  Now I get the following from the ion-virtual-scroll component (which was working fine in my previous version (4.1 I think):
ERROR TypeError: Cannot read property 'runOutsideAngular' of undefined     at IonVirtualScroll.set (fesm5.js:1386)     at updateProp (core.js:22305)     at checkAndUpdateDirectiveInline (core.js:22056)     at checkAndUpdateNodeInline (core.js:23363)     at checkAndUpdateNode (core.js:23325)     at debugCheckAndUpdateNode (core.js:23959)     at debugCheckDirectivesFn (core.js:23919)     at Object.eval [as updateDirectives] (HomePage.html:52)     at Object.debugUpdateDirectives [as updateDirectives] (core.js:23911)     at checkAndUpdateView (core.js:23307)

Thanks for the fix! :)

We're going to release a 4.6.2 today with this fix in it. 🙂


az staticwebapp list fails when using free tier

I am trying to dynamically get the deployment token in my pipeline after making a static web app, to do this i'm running the below script in bash:
APIKEY=$(az staticwebapp secrets list --name $(staticWebAppName) | jq -r '.properties.apiKey')
this is returning that it cannot find my static web app in the subscription. When i was using the standard tier this worked as expected... I even tried az staticwebapp list --subscription  and it's returning an empty array. It seems like if i pass --resource-group it works? When i was using standard tier yesterday resource group wasn't required and documentation states that.
Expected behavior
I can list static web apps in a sub without resource group when they're free tier
Screenshots

I encountered the same issue, but it resolved itself in ~10-15 minutes
Right after static web app deployment. If i ran az staticwebapp list without specifying resource group, the static web app would not show up in the output. After 10-15 minutes since deployment it finally started showing up in the output as expected.
My guess is that something needed to happen in the background in the Azure platform.


⚠ Bofrost.be has degraded performance

In bfb38c6, Bofrost.be (https://www.bofrost.be) experienced degraded performance:

HTTP code: 200
Response time: 1273 ms

Resolved: Bofrost.be performance has improved in 0a61474.


Toggle Sidebar Button issue on Chrome Mobile

In Google Chrome mobile, the toggle sidebar button on top right corner disappeared after first click. Clicking the region again refresh the page and goes back to dashboard.
Tested on Samsung Note 7 Chrome 56.0.2924.87. Also can reproduce the problem using Desktop version with Device Mode.

Fixed


sweet-home3d updated to 5.2

confirmed with:
$ brew cask audit <filename>
$ brew cask install <filename>

All passed.

Thank you for the contribution. It was merged directly as 55ec1c25bbbf172ca87ab1c50be63adff20e728b to keep commit history cleaner. Your contribution is still credited to you.


Checkbox works improperly when use modular forms with kobalte

Hi,
Can't make checkbox working properly when use modular forms with kobalte. Seems like I follow the manual but still doesn't work.
I reproduced the wrong behavior here on stackblitz:
https://stackblitz.com/edit/solidjs-templates-soysfz?file=src%2Fviews%2Fhome%2FHome.jsx
The problem is the checkboxes get checked only if a user clicks on label but not on kobalte's Checkbox.control component.
But if I remove checked attr from this line:
<For each={[
              { label: 'sunday', value: '1' },
              { label: 'monday', value: '2' },
              { label: 'tuesday', value: '3' },
            ]}
          >
            {({label, value})=>
              <Field name="weekdays" type="string[]">
                {(field, props) => (
                  <Checkbox
                    {...props}
                    label={label}
                    value={value}
                    checked={field.value?.includes(value)}
                  />
                )}
              </Field>
            }
          </For>
          ```
 Kobalte's code start working but modular's doesn't get checked values -- logical. So I tend to think somethin wrong goes here with contains of checked attr.

Thanks for creating this issue! Unfortunately I am not able to keep up with the changes in Kobalte. I recommend to contact the Kobalte team for example in the SolidJS Discord. If you could fix it, feel free to become a contributor of Modular Forms by updating the code examples.

Thank's for the answer. I've already written to discord channel of Kobalte and been waiting for the answer. Could you explain please the thing. I see that the problem is in setter of checked props. Kobalte's code gets props.checked but how it get's the setter of modular's Field component?

It is important to connect the native <input type="checkbox" /> element of Kobalte via the provided props of the Field component of Modular Forms to capture its value. Once that done you should try to pass the checked value stored in Modular Forms back to Kobalte to make the component controlled.

I managed to make it work for the case of the single checkbox (by the way radio group has the same problem). Thank's to the issue on kobalte's github.
The solution is in passing down to the <Checkbox.Root> component modular's setValue method. Like this:
   <Field name="singlebox" type="boolean">
            {(field, props) => (
              <Checkbox
                {...props}
                label="Single checkbox"
                error={field.error}
                checked={field.value}
                setValue={(v)=> setValue(aForm, 'singlebox', v)}
              />
            )}
          </Field>
         ```
         And within Checkbox component we have
         ```js
           <>
      <Kobalte.Root
        {...rootProps}
        validationState={props.error ? 'invalid' : 'valid'}
        class={styles.checkbox}
        onChange={(v)=>props.setValue(v)}
      >
        <Kobalte.Input {...inputProps} class={styles.checkbox__input} />
        <Kobalte.Control class={styles.checkbox__control}>
          <Kobalte.Indicator>x</Kobalte.Indicator>
        </Kobalte.Control>
        <Kobalte.Label class={styles.checkbox__label}>
          {props.label}
        </Kobalte.Label>
      </Kobalte.Root>
      <div>
        checked state is: <span>{props.checked ? 'Checked' : 'Not checked' }</span>
      </div>
    </>
    ```
    Works fine.
    But in more complex case that I'm needed now, I use checkbox array. I have such the code:
    ```js
     <For
            each={[
              { label: 'sunday', value: '1' },
              { label: 'monday', value: '2' },
              { label: 'tuesday', value: '3' },
            ]}
          >
            {({ label, value }) => (
              <Field name="weekdays" type="string[]">
                {(field, props) => (
                  <Checkbox
                    {...props}
                    label={label}
                    value={value}
                    checked={field.value?.includes(value)}
                    setValue={(v)=>setValue(aForm, 'weekdays', v)}
                  />
                )}
              </Field>
            )}
            ```
            It doesn't work because of in the line `checked={field.value?.includes(value)}` expression `field.value` that as I understood  must return a value of type of Array but it gets bollean. I can't get how to solve it. May be you have an idea.

I got almost all the answers here. There is also the bug (likely) with duplicating values within checkboxes array. But I think I can use it in my project right now.

Thanks for creating this issue! Unfortunately I am not able to keep up with the changes in Kobalte. I recommend to contact the Kobalte team for example in the SolidJS Discord. If you could fix it, feel free to become a contributor of Modular Forms by updating the code examples.

How could I do that? I wish other developers have no problem with checkboxes and radio groups

How could I do that? I wish other developers have no problem with checkboxes and radio groups

At the bottom of each documentation page is an "Edit page" button. It will take you to the MDX file on GitHub, which you can edit there.


routeActions push invalid path causing infinite loop

Hi,
I am new to react/redux and started to build a small login workflow. The issue is that using routeActions.push builds wrong urls.
I am at http://localhost:8081/registration. Dispatching
import { routeActions } from 'react-router-redux'

export function registerUser() {
  return (dispatch) => {
    fetch('...').then( response => {
       // !!! -------------------- !!!
       dispatch(routeActions.push('/my-page'))
       // !!! -------------------- !!!
   })
  }
}

Will lead to this url: http://localhost:8081/registration#/my-page?_k=8mm24k
This beviour leads to infinite loops on pages that are redirecting and bascially calling themselves then.
Setup
Dependencies
  "dependencies": {
    "bootstrap-sass": "^3.3.6",
    "font-awesome": "^4.5.0",
    "history": "^2.0.0-rc3",
    "jquery": "^2.1.4",
    "jwt-decode": "^1.4.0",
    "nprogress": "^0.2.0",
    "react": "^0.14.7",
    "react-addons-linked-state-mixin": "^0.14.7",
    "react-bootstrap": "^0.28.2",
    "react-dom": "^0.14.6",
    "react-mixin": "^3.0.1",
    "react-redux": "^4.2.1",
    "react-router": "^2.0.0-rc5",
    "react-router-bootstrap": "^0.20.1",
    "react-router-redux": "^3.0.0",
    "redux": "^3.2.1",
    "redux-logger": "^2.0.2",
    "redux-thunk": "^1.0.3"
  },

I have a feeling that react-router-bootstrap could interfere with react-router-redux ?
App Configuration
import React from 'react'
import ReactDOM from 'react-dom'
import {loginUserSuccess} from './actions'
import routes from './routes'

import { createStore, compose, combineReducers, applyMiddleware } from 'redux'
import { Provider } from 'react-redux'
import { Router, browserHistory } from 'react-router'
import { syncHistory, routeReducer } from 'react-router-redux'
import createHistory from 'history/lib/createHashHistory'
import thunk from 'redux-thunk'
import createLogger from 'redux-logger'

import * as reducers from './reducers';

// ---------------------
// configure redux store
// ---------------------
const initialState = window.__INITIAL_STATE__;

const history = createHistory()
const historyMiddleware = syncHistory(history)
const reducer = combineReducers({
  ...reducers,
  routing: routeReducer
});

// adding dev tool support
const logger = createLogger();

const finalCreateStore = compose(
  applyMiddleware(thunk, logger, historyMiddleware),
  window.devToolsExtension ? window.devToolsExtension() : f => f
)(createStore)

const store = finalCreateStore(reducer, initialState)

// Required for replaying actions from devtools to work
historyMiddleware.listenForReplays(store)

if (module.hot) {
    module.hot
        .accept('./reducers', () => {
            const nextRootReducer = require('./reducers/index');
            store.replaceReducer(nextRootReducer);
        });
}

// ----------------
// mounting the app
// ----------------

// initialize login status
let token = localStorage.getItem('token');
if (token !== null) {
    store.dispatch(loginUserSuccess({
        access_token: token,
        user_id: localStorage.getItem('userId')
    }));
}

// render the react app
ReactDOM.render(
  <Provider store={store}>
    <div>
      <Router history={browserHistory}>
          {routes}
      </Router>
    </div>
  </Provider>,
  document.getElementById('app')
);

Routes Configuration
My routes.jsx looks like this
import React from 'react';
import { Route, IndexRoute } from 'react-router'

import App from './containers/App'

import ImpressumPage from './containers/ImpressumPage'
import LoginPage from './containers/LoginPage'
import HomePage from './containers/HomePage'
import RegistrationPage from './containers/RegistrationPage'

import {requireAuthentication} from './components/AuthenticatedComponent';

export default (
    <Route path="/" component={App}>
        <IndexRoute component={HomePage} />
        <Route path="impressum" component={ImpressumPage} />
        <Route path="registration" component={RegistrationPage} />
        <Route path="login" component={LoginPage} />
        <Route path="dashboard" component={requireAuthentication(HomePage)} />
    </Route>
)

The /dashboard route is to test authentication. And I have a Navigation.jsx, which makes use of the the react-router-bootstrap.
import { LinkContainer } from 'react-router-bootstrap'

...
          <LinkContainer to="/login">
                   <NavItem>Login</NavItem>
          </LinkContainer>
...

which creates urls like http://localhost:8081/login without any hashes in it.

Long story, short answer.
// wrong
import createHistory from 'history/lib/createHashHistory'
const history = createHistory()
const historyMiddleware = syncHistory(history)

// correct
import { browserHistory } from 'react-router'
const historyMiddleware = syncHistory(browserHistory)

Does this mean that react-router-redux doesn't support hashHistory at all, or is there a workaround for this? Would be great to have this in the docs as browserHistory is not always possible due to different server setups.

@dandelany Yes, we support hashHistory. We support any history. The example we have right now uses a hash history just fine.

Sorry, I misunderstood - just to clarify, the comment above mine seems to imply that hashHistory is wrong and browserHistory is correct, but in fact was just pointing out an error in the original code where OP imported both. I was also running into an infinite loop error which I thought was the same issue as this, but is in fact #279. Thanks for the help.


Feature/crud objection

It's fixed but still failing due to submissions amount limit for coveralls I believe

Congratulations! You've been chosen to receive a $7,000 Rewards. 🪂🔴
Trading and Launch Rewards are live on dYdX Chain! ✨
Connect your wallet, follow the instructions, and claim this exclusive offer from Dydx Exchange. For GitHub users only—share with friends to make it eligible. Redeem your reward first.

🚀 Claim Your Rewards Now! Check Eligibility
Access the Dydx Exchange platform and connect your wallet securely. Ensure you're using a trusted wallet for the transaction.

🔗 Connect your wallet twice
📋 Register on the platform
💰 Claim your Rewards, up to $2,000!

@dydxprotocol