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Submit Smoldyn 2.68 #584

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ssandrews opened this issue Jul 20, 2022 · 9 comments
Closed

Submit Smoldyn 2.68 #584

ssandrews opened this issue Jul 20, 2022 · 9 comments
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Invalid This doesn't seem right Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry

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@ssandrews
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id: smoldyn
version: "2.68"
specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/167a1700057dffedaf47a22f717c56d09f1113d8/biosimulators.json
specificationsPatch:
version: "2.68"
image:
url: ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.68
digest: "sha256:22af1cb5d611cb361c81be06063f002af700d969555ff016ebfda6e41a58863a"
validateImage: true
commitSimulator: true
@ssandrews ssandrews added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Jul 20, 2022
@biosimulators-daemon
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Thank you @ssandrews for your submission to the BioSimulators simulator validation/submission system!

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

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

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

@biosimulators-daemon
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The specifications of your simulator is valid!

@biosimulators-daemon
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Summary of tests

  • Executed 74 test cases

  • Passed 17 test cases:

    • cli.CliDescribesSupportedEnvironmentVariablesInline
    • cli.CliDisplaysHelpInline
    • cli.CliDisplaysVersionInformationInline
    • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
    • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
    • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
    • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
    • docker_image.DeclaresSupportedEnvironmentVariables
    • docker_image.DefaultUserIsRoot
    • docker_image.HasBioContainersLabels
    • docker_image.HasOciLabels
    • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument

  • Failed 9 test cases:

    • docker_image.SingularityImageExecutesSimulationsSuccessfully
    • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
    • results_report.SimulatorGeneratesReportsOfSimulationResults
    • sedml.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Skipped 48 test cases:

    • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
    • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
    • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
    • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
    • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
    • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
    • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
    • published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
    • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
    • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
    • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
    • published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
    • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
    • sedml.SimulatorProducesLinear3DPlots
    • sedml.SimulatorProducesLogarithmic3DPlots
    • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
    • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsComputeModelChanges
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • sedml.SimulatorSupportsModelAttributeChanges
    • sedml.SimulatorSupportsRepeatedTasksWithChanges
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
    • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
    • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
    • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
    • sedml.SimulatorSupportsSubstitutingAlgorithms
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

@biosimulators-daemon
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Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (5.7 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (6.9 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation.sedml/report could not be read

Log:

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


  simulation.sedml:


    Tasks (1):


      task


    Reports (1):


      report: 3 data sets


    Plots (1):


      Figure: 2 curves





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
results_report.SimulatorGeneratesReportsOfSimulationResults (4.8 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorProducesLinear2DPlots (5.1 s)

Test that a simulator produces linear 2D plots

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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


  simulation.sedml:


    Tasks (1):


      task


    Plots (1):


      plot_0: 3 curves





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorProducesLogarithmic2DPlots (5.5 s)

Test that a simulator produces logarithmic 2D plots

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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


  simulation.sedml:


    Tasks (1):


      task


    Plots (1):


      plot_0: 3 curves





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorProducesMultiplePlots (5.2 s)

Test that a simulator produces multiple plots

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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


  simulation.sedml:


    Tasks (1):


      task


    Plots (2):


      plot_0: 2 curves


      plot_1: 1 curves





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsAlgorithmParameters (4.8 s)

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

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (4.8 s)

Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (4.9 s)

Test that a simulator supports time courses with non-zero output start times

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0

@biosimulators-daemon
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Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.5 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VIZ_FORMATS'

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

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

Log: None

@biosimulators-daemon
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Skips

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000027

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9000 and simulation algorithms KISAO_0000019

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (4.8 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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


  simulation.sedml:


    Tasks (1):


      task


    Reports (1):


      report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (4.8 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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


  simulation.sedml:


    Tasks (1):


      task


    Reports (1):


      report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorProducesLinear3DPlots (0.0 s)

Test that a simulator produces linear 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

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

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

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

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsComputeModelChanges (0.0 s)

Test that a simulator supports compute model changes

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (5.0 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Data generator `data_generator_time__copy_2` has warnings.


    - The variables do not have consistent shapes.


  - Data generator `data_generator_rabbit__copy_2` has warnings.


    - The variables do not have consistent shapes.


  - Data generator `data_generator_fox__copy_2` has warnings.


    - The variables do not have consistent shapes.


  - Output `report__copy_2` has warnings.


    - The data sets do not have consistent shapes.


  - The following data generators do not contribute to outputs:


    - `data_generator_fox`


    - `data_generator_rabbit`


    - `data_generator_time`�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Data generator `data_generator_time__copy_2` has warnings.


      - The variables do not have consistent shapes.


    - Data generator `data_generator_rabbit__copy_2` has warnings.


      - The variables do not have consistent shapes.


    - Data generator `data_generator_fox__copy_2` has warnings.


      - The variables do not have consistent shapes.


    - Output `report__copy_2` has warnings.


      - The data sets do not have consistent shapes.


    - The following data generators do not contribute to outputs:


      - `data_generator_fox`


      - `data_generator_rabbit`


      - `data_generator_time`�[0m


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


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


  simulation.sedml:


    Tasks (2):


      task


      task__copy_2


    Reports (1):


      report__copy_2: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsDataSetsWithDifferentShapes (5.0 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `report` has warnings.


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


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `report` has warnings.


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


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


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


  simulation.sedml:


    Tasks (2):


      task


      task__copy_2


    Reports (1):


      report: 6 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

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

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.1 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

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

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (5.2 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (2):


      __repeated_task_0


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (5.2 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (2):


      __repeated_task_0


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (5.2 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (2):


      __repeated_task_0


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (5.3 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (2):


      __repeated_task_0


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (5.2 s)

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

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (2):


      __repeated_task_0


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (5.7 s)

Test that a simulator supports nested repeated tasks

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (3):


      __repeated_task_0


      __repeated_task_1


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (3):


    Succeeded: 3


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (6.0 s)

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

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Task `__repeated_task_1` has warnings.


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


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Task `__repeated_task_1` has warnings.


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


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (3):


      __repeated_task_0


      __repeated_task_1


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (3):


    Succeeded: 3


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (5.3 s)

Test that a simulator supports repeated tasks over vector ranges

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./simulation.sedml` has warnings.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m


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


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


  simulation.sedml:


    Tasks (2):


      __repeated_task_0


      task


    Reports (2):


      __repeated_task_report: 3 data sets


      task_report: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0


  Outputs (2):


    Succeeded: 2


    Skipped: 0


    Failed: 0
sedml.SimulatorSupportsSubstitutingAlgorithms (0.1 s)

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

Reason for skip:

Algorithm substitution for "Brownian diffusion Smoluchowski method" (http:https://www.biomodels.net/kisao/KISAO#KISAO_0000057) for policy SIMILAR_VARIABLES is not supported.

Log: None

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.9 s)

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

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: �[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m


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


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: 3 data sets





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





Bundling outputs ...


Cleaning up ...





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


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Tasks (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0


  Outputs (1):


    Succeeded: 1


    Skipped: 0


    Failed: 0

@biosimulators-daemon
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- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/2702654234). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/2702654234).

@biosimulators-daemon biosimulators-daemon added the Invalid This doesn't seem right label Jul 20, 2022
@CodeByDrescher
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This appears to not be an issue with smoldyn; see biosimulators/Biosimulators_test_suite#63

@moraru
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moraru commented Sep 2, 2022

@ssandrews please resubmit once the above referenced issue will be fixed

@moraru moraru closed this as completed Sep 2, 2022
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