search

biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
13 stars 0 forks source link

Submit PySceS 0.9.9 #188

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: pysces version: 0.9.9 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/f6d26aa178ca791b0c8c630d65a9ebf09e7ee422/biosimulators.json specificationsPatch: version: 0.9.9 image: url: ghcr.io/biosimulators/biosimulators_pysces/pysces:0.9.9 validateImage: true commitSimulator: true

Changelog

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

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 (0.0 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 (6.8 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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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/761216007). 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/761216007).
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

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (5.9 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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (4.2 s)

Required model formats and simulation algorithms for SED tasks:

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:

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