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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit COBRApy 0.20.0 #70

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: cobrapy version: 0.20.0 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/01cfe3a4bc30552a6b96bec99c6ebdeab887c26c/biosimulators.json specificationsPatch: version: 0.20.0 validateImage: true commitSimulator: true

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 is available here.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (10.8 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:

cli.CliDisplaysVersionInformationInline (4.5 s)

Test that a command-line interface provides version information inline.

Warnings:

  Command-line interface should support the `-v` option for displaying version information inline.

  The command-line interface displayed the following when executed with `-v`:

    COBRApy: 0.20.0, CLI: 0.1.1, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

  Command-line interface should support the `--version` option for displaying version information inline.

  The command-line interface displayed the following when executed with `--version`:

    COBRApy: 0.20.0, CLI: 0.1.1, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)

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

Warnings:

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

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

  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 (0.4 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:

sedml.SimulatorProducesLinear2DPlots (2.5 s)

Test that a simulator produces linear 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation.sedml:
      Tasks (1):
        task
      Plots (1):
        plot_0: 1 curves

  Executing SED-ML file 0: simulation.sedml
    Found 1 tasks
      task
    Executing task 1: task
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (2.7 s)

Test that a simulator produces linear 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation.sedml:
      Tasks (1):
        task
      Plots (1):
        plot_0: 1 surfaces

  Executing SED-ML file 0: simulation.sedml
    Found 1 tasks
      task
    Executing task 1: task
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (2.7 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation.sedml:
      Tasks (1):
        task
      Plots (1):
        plot_0: 1 curves

  Executing SED-ML file 0: simulation.sedml
    Found 1 tasks
      task
    Executing task 1: task
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.8 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation.sedml:
      Tasks (1):
        task
      Plots (1):
        plot_0: 1 surfaces

  Executing SED-ML file 0: simulation.sedml
    Found 1 tasks
      task
    Executing task 1: task
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (2.7 s)

Test that a simulator produces multiple plots

Warnings:

  Simulator did not produce plots

Log:

  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/io.py:905: NoCurvesWarning: Plot None does not contain any curves
    NoCurvesWarning)
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
    simulation.sedml:
      Tasks (1):
        task
      Plots (2):
        plot_0: 1 curves
        plot_1: 0 curves

  Executing SED-ML file 0: simulation.sedml
    Found 1 tasks
      task
    Executing task 1: task
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (2.8 s)

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

Warnings:

  The specifications for the number of dimensions of each data set of algorithm `KISAO_0000437` differs from the actual number of dimensions, 1 != 0.

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation.sedml:
      Tasks (1):
        task
      Reports (1):
        report: 1 data sets

  Executing SED-ML file 0: simulation.sedml
    Found 1 tasks
      task
    Executing task 1: task
  /usr/local/lib/python3.7/site-packages/tables/path.py:155: NaturalNameWarning: object name is not a valid Python identifier: 'simulation.sedml'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
    check_attribute_name(name)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)

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

Warnings:

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

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)

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

Warnings:

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

Log:

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