Submit CBMPy 0.7.25 - Githubissues

biosimulators-daemon commented 3 years ago

id: cbmpy version: 0.7.25 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_CBMPy/a7be1736fedd9a1d0bfd78f11e6300a2f52c098d/biosimulators.json specificationsPatch: version: 0.7.25 image: url: ghcr.io/biosimulators/biosimulators_cbmpy/cbmpy:0.7.25 validateImage: true commitSimulator: true

Changelog

Rerunning with fixed test suite (added missing requirement)

biosimulators-daemon commented 3 years ago

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

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

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

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

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Executed 60 test cases
Passed 8 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
Failed 16 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 36 test cases:
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- 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.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon commented 3 years ago

Failures

`combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories` (0.0 s)

Test that SED documents in nested directories can be executed

Exception:

  No module named 'libsbml'

Log:

`combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories` (0.0 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

  No module named 'libsbml'

Log:

`combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile` (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

`combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments` (0.0 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

  No module named 'libsbml'

Log:

`results_report.SimulatorGeneratesReportsOfSimulationResults` (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorProducesLinear2DPlots` (0.0 s)

Test that a simulator produces linear 2D plots

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorProducesLinear3DPlots` (0.0 s)

Test that a simulator produces linear 3D plots

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorProducesLogarithmic2DPlots` (0.0 s)

Test that a simulator produces logarithmic 2D plots

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorProducesLogarithmic3DPlots` (0.0 s)

Test that a simulator produces logarithmic 3D plots

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorProducesMultiplePlots` (0.0 s)

Test that a simulator produces multiple plots

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions` (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorSupportsAlgorithmParameters` (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports` (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorSupportsMultipleReportsPerSedDocument` (0.1 s)

Test that a simulator supports multiple reports per SED document

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorSupportsMultipleTasksPerSedDocument` (0.0 s)

Test that a simulator supports multiple tasks per SED document

Exception:

  No module named 'libsbml'

Log:

`sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes` (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

biosimulators-daemon commented 3 years ago

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (4.9 s)

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

Warnings:

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

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

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

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

Log:

`docker_image.DeclaresSupportedEnvironmentVariables` (0.3 s)

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

Warnings:

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

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

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

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

Log:

`docker_image.HasBioContainersLabels` (0.2 s)

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

Warnings:

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

Log:

biosimulators-daemon commented 3 years ago

Skips

`log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives` (0.0 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Reason for skip:

  No module named 'libsbml'

Log:

`log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments` (0.0 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Reason for skip:

  No module named 'libsbml'

Log:

`log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs` (0.0 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Reason for skip:

  No module named 'libsbml'

Log:

`log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks` (0.0 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Reason for skip:

  No module named 'libsbml'

Log:

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

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000263

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
```
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3972 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000088

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000496

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000027
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000027

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000027
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000029

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)

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

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 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:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

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

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsComputeModelChanges (0.0 s)

Test that a simulator supports compute model changes

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)

Test that a simulator supports data generators with different shapes

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)

Test that a simulator supports data generators with different shapes

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

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

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

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

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)

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

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)

Test that a simulator supports nested repeated tasks

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 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:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)

Test that a simulator supports repeated tasks over vector ranges

Reason for skip:
```
No module named 'libsbml'
```
Log:
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)

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

Reason for skip:
```
No module named 'libsbml'
```
Log:

biosimulators-daemon commented 3 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 [here](https://github.com/biosimulators/Biosimulators/actions/runs/761243849). 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/761243849).

biosimulators-daemon commented 3 years ago

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

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

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

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

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Executed 60 test cases
Passed 33 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
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
Failed 0 test cases
Skipped 27 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

biosimulators-daemon commented 3 years ago

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (7.3 s)

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

Warnings:

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

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

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

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

Log:

`docker_image.DeclaresSupportedEnvironmentVariables` (2.2 s)

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

Warnings:

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

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

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

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

Log:

`docker_image.HasBioContainersLabels` (2.2 s)

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

Warnings:

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

Log:

biosimulators-daemon commented 3 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 Algorithm: KISAO_0000263

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
```
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3972 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000088

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000496

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000027
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000027

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000027
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000029

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log:

`sedml.SimulatorProducesLinear2DPlots` (0.1 s)

Test that a simulator produces linear 2D plots

Reason for skip:

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

Log:

`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:

`sedml.SimulatorProducesLogarithmic2DPlots` (0.1 s)

Test that a simulator produces logarithmic 2D plots

Reason for skip:

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

Log:

`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:

`sedml.SimulatorProducesMultiplePlots` (0.1 s)

Test that a simulator produces multiple plots

Reason for skip:

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

Log:

`sedml.SimulatorSupportsComputeModelChanges` (0.3 s)

Test that a simulator supports compute model changes

Reason for skip:

The SED document is invalid.
- Model `model` is invalid.
  - The changes of the model are invalid.
    - Change 363 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[72]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_363` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[72]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 364 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[71]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_364` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[71]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 365 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[70]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_365` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[70]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 366 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[69]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_366` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[69]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 367 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[68]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_367` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[68]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 368 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[67]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_368` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[67]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 369 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[66]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_369` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[66]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 370 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[65]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_370` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[65]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 371 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[64]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_371` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[64]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 372 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[63]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_372` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[63]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 373 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[62]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_373` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[62]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 374 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[61]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_374` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[61]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 375 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[60]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_375` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[60]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 376 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[59]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_376` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[59]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 377 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[58]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_377` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[58]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 378 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[57]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_378` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[57]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 379 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[56]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_379` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[56]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 380 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[55]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_380` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[55]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 381 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[54]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_381` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[54]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 382 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[53]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_382` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[53]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 383 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[52]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_383` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[52]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 384 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[51]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_384` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[51]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 385 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[50]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_385` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[50]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 386 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[49]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_386` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[49]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 387 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[48]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_387` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[48]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 388 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[47]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_388` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[47]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 389 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[46]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_389` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[46]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 390 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[45]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_390` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[45]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 391 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[44]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_391` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[44]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 392 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[43]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_392` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[43]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 393 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[42]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_393` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[42]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 394 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[41]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_394` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[41]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 395 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[40]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_395` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[40]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 396 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[39]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_396` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[39]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 397 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[38]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_397` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[38]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 398 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[37]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_398` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[37]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 399 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[36]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_399` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[36]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 400 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[35]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_400` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[35]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 401 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[34]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_401` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[34]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 402 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[33]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_402` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[33]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 403 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[32]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_403` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[32]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 404 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[31]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_404` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[31]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 405 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[30]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_405` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[30]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 406 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[29]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_406` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[29]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 407 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[28]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_407` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[28]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 408 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[27]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_408` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[27]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 409 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[26]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_409` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[26]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 410 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[25]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_410` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[25]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 411 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[24]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_411` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[24]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 412 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[23]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_412` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[23]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 413 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[22]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_413` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[22]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 414 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[21]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_414` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[21]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 415 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[20]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_415` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[20]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 416 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[19]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_416` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[19]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 417 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[18]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_417` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[18]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 418 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[17]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_418` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[17]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 419 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[16]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_419` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[16]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 420 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[15]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_420` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[15]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 421 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[14]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_421` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[14]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 422 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[13]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_422` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[13]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 423 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[12]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_423` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[12]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 424 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[11]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_424` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[11]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 425 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[10]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_425` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[10]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 426 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[9]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_426` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[9]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 427 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[8]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_427` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[8]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 428 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[7]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_428` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[7]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 429 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[6]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_429` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[6]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 430 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[5]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_430` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[5]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 431 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[4]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_431` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[4]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 432 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_432` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 433 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_433` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 434 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.
      - Variable `__var_434` is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`.

Log:

`sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes` (0.1 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

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

Log:

`sedml.SimulatorSupportsDataSetsWithDifferentShapes` (0.1 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

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

Log:

`sedml.SimulatorSupportsModelAttributeChanges` (0.7 s)

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

Reason for skip:


The SED document is invalid.
- Model `model` is invalid.
  - The changes of the model are invalid.
    - Change 4 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/@fbc:required` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 5 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/@fbc:strict` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 12 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[95]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 13 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[95]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 28 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[94]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 29 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[94]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 51 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[93]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 52 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[93]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 74 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[92]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 75 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[92]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 103 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[91]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 104 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[91]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 126 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[90]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 127 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[90]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 155 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[89]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 156 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[89]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 180 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[88]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 181 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[88]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 201 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[87]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 202 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[87]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 223 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[86]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 224 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[86]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 240 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[85]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 241 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[85]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 257 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[84]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 258 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[84]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 278 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[83]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 279 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[83]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 304 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[82]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 305 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[82]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 327 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[81]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 328 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[81]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 358 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[80]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 359 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[80]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 383 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[79]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 384 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[79]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 411 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[78]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 412 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[78]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 434 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[77]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 435 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[77]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 452 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[76]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 453 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[76]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 474 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[75]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 475 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[75]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 496 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[74]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 497 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[74]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 512 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[73]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 513 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[73]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 542 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[72]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 543 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[72]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 568 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[71]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 569 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[71]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 598 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[70]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 599 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[70]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 614 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[69]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 615 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[69]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 631 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[68]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 632 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[68]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 655 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[67]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 656 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[67]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 695 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[66]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 696 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[66]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 720 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[65]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`.
    - Change 721 is invalid.
      - One or more namespaces required for target `/sbml:sbml[1]/sb ...

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

Your submission was committed to the BioSimulators registry. Thank you!

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

biosimulators / Biosimulators

Submit CBMPy 0.7.25 #190

Summary of tests

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)

results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)

sedml.SimulatorProducesLinear2DPlots (0.0 s)

sedml.SimulatorProducesLinear3DPlots (0.0 s)

sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

sedml.SimulatorProducesMultiplePlots (0.0 s)

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)

sedml.SimulatorSupportsAlgorithmParameters (0.0 s)

sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)

sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.1 s)

sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.9 s)

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)

docker_image.HasBioContainersLabels (0.2 s)

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 s)

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

sedml.SimulatorSupportsComputeModelChanges (0.0 s)

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)

sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)

sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (7.3 s)

docker_image.DeclaresSupportedEnvironmentVariables (2.2 s)

docker_image.HasBioContainersLabels (2.2 s)

Skips

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

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

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

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

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

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

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

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

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

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

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

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

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

`combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories` (0.0 s)

`combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories` (0.0 s)

`combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile` (0.0 s)

`combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments` (0.0 s)

`results_report.SimulatorGeneratesReportsOfSimulationResults` (0.0 s)

`sedml.SimulatorProducesLinear2DPlots` (0.0 s)

`sedml.SimulatorProducesLinear3DPlots` (0.0 s)

`sedml.SimulatorProducesLogarithmic2DPlots` (0.0 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.0 s)

`sedml.SimulatorProducesMultiplePlots` (0.0 s)

`sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions` (0.0 s)

`sedml.SimulatorSupportsAlgorithmParameters` (0.0 s)

`sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports` (0.0 s)

`sedml.SimulatorSupportsMultipleReportsPerSedDocument` (0.1 s)

`sedml.SimulatorSupportsMultipleTasksPerSedDocument` (0.0 s)

`sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes` (0.0 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (4.9 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (0.3 s)

`docker_image.HasBioContainersLabels` (0.2 s)

`log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives` (0.0 s)

`log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments` (0.0 s)

`log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs` (0.0 s)

`log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks` (0.0 s)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

`sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments` (0.0 s)

`sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges` (0.0 s)

`sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.0 s)

`sedml.SimulatorSupportsComputeModelChanges` (0.0 s)

`sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes` (0.0 s)

`sedml.SimulatorSupportsDataSetsWithDifferentShapes` (0.0 s)

`sedml.SimulatorSupportsModelAttributeChanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithChanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithVectorRanges` (0.0 s)

`sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes` (0.0 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (7.3 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (2.2 s)

`docker_image.HasBioContainersLabels` (2.2 s)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

`sedml.SimulatorProducesLinear2DPlots` (0.1 s)

`sedml.SimulatorProducesLinear3DPlots` (0.1 s)

`sedml.SimulatorProducesLogarithmic2DPlots` (0.1 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.1 s)

`sedml.SimulatorProducesMultiplePlots` (0.1 s)

`sedml.SimulatorSupportsComputeModelChanges` (0.3 s)

`sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes` (0.1 s)

`sedml.SimulatorSupportsDataSetsWithDifferentShapes` (0.1 s)