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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
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Submit Smoldyn 2.68 #584

Closed ssandrews closed 2 years ago

ssandrews commented 2 years ago

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

biosimulators-daemon commented 2 years ago

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 commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

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: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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 commented 2 years ago

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 commented 2 years ago

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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000086 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) 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: * Format: [`format_9000`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9000) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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` warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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` 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `report` has warnings. - The data sets do not have consistent shapes. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The 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. 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://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: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. 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 commented 2 years ago 
- 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).
CodeByDrescher commented 2 years ago

This appears to not be an issue with smoldyn; see biosimulators/Biosimulators_test_suite#63

moraru commented 2 years ago

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