Submit PySceS 0.9.9

[biosimulators-daemon]

---

id: pysces version: 0.9.9 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/4c2d94d516f750fb42f819bfd1ada268d0e8b391/biosimulators.json specificationsPatch: version: 0.9.9 image: url: ghcr.io/biosimulators/biosimulators_pysces/pysces:0.9.9 validateImage: true commitSimulator: true

---

[biosimulators-daemon]

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 is available here.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 36 test cases

• Passed 27 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 9 test cases:

  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
  • 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-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling

Warnings

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.3 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Warnings:

  Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

  Extra plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1.pdf

  Log:

  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rw0jhdsi because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running
  
  PySCeS defaults to matplotlib's TKagg backend if not specified                      in the user configuration file, set "matplotlib_backend = <backend>" 
  Attempting alternate pitcon import ...
  Attempting alternate nleq2 import ...
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
  BIOMD0000000912_sim.sedml:
    Tasks (1):
      BIOMD0000000912_sim
    Reports (1):
      BIOMD0000000912_sim: 4 data sets
    Plots (1):
      plot_1: 3 curves
  
  Executing SED-ML file 0: BIOMD0000000912_sim.sedml ...
  
  Bundling outputs ...
  Cleaning up ...
  
  ============= SUMMARY =============
  Executed 1 COMBINE/OMEX archives:
  Archives (1):
    Succeeded: 1
    Skipped: 0
    Failed: 0
  Tasks (1):
    Succeeded: 1
    Skipped: 0
    Failed: 0
  Outputs (2):
    Succeeded: 2
    Skipped: 0
    Failed: 0

  sedml.SimulatorProducesLinear2DPlots (0.0 s)

  Test that a simulator produces linear 2D plots

  Warnings:

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

  Log:

  sedml.SimulatorProducesLinear3DPlots (0.0 s)

  Test that a simulator produces linear 3D plots

  Warnings:

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

  Log:

  sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)

  Test that a simulator produces logarithmic 2D plots

  Warnings:

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

  Log:

  sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

  Test that a simulator produces logarithmic 3D plots

  Warnings:

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

  Log:

  sedml.SimulatorProducesMultiplePlots (0.0 s)

  Test that a simulator produces multiple plots

  Warnings:

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

  Log:

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

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.