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Submit PySCeS 1.2.1 #691

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biosimulators-daemon opened this issue May 10, 2024 · 7 comments
Closed

Submit PySCeS 1.2.1 #691

biosimulators-daemon opened this issue May 10, 2024 · 7 comments
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Approved Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry Validated

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@biosimulators-daemon
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id: pysces
version: 1.2.1
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/2d97929994747fd30b5684393bb850839955b5eb/biosimulators.json
specificationsPatch:
version: 1.2.1
image:
url: ghcr.io/biosimulators/biosimulators_pysces/pysces:1.2.1
digest: "sha256:a9f364bd9e00c0bbfae9fa3c8adb6a63a593a5cc4d980df225399c5eb8bbe7e1"
validateImage: true
commitSimulator: true
@biosimulators-daemon biosimulators-daemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label May 10, 2024
@biosimulators-daemon
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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.

@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 48 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:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
    • results_report.SimulatorGeneratesReportsOfSimulationResults
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
    • sedml.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsComputeModelChanges
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • sedml.SimulatorSupportsModelAttributeChanges
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument
    • sedml.SimulatorSupportsRepeatedTasksWithChanges
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
    • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
    • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
    • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
    • sedml.SimulatorSupportsSubstitutingAlgorithms
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Failed 0 test cases

  • Skipped 26 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/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
    • 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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
    • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
    • sedml.SimulatorProducesLinear3DPlots
    • sedml.SimulatorProducesLogarithmic3DPlots
    • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions

@biosimulators-daemon
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Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.4 s)

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

Warnings:

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

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - '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/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/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:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

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.SimulatorProducesLinear3DPlots (0.1 s)

Test that a simulator produces linear 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.1 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 (0.1 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

@biosimulators-daemon
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The image for your simulator is valid!

@biosimulators-daemon
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Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of pysces to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

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