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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 GillesPy2 1.5.5 #80

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

id: gillespy2 version: 1.5.5 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/e5db0434dc18125b8147f1335cb3c85a5e16e45b/biosimulators.json specificationsPatch: version: 1.5.5 image: url: ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.5 validateImage: true commitSimulator: true

biosimulators-daemon commented 3 years ago

Thank you @jonrkarr 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

Failures

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (2.4 s)

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

Exception:

  The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.5' could not execute the archive:

    Unknown error

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 20 data sets

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed.  Reason Given: name 'Clog' is not defined

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (2.4 s)

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

Exception:

  The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.5' could not execute the archive:

    Unknown error

Log:

  Found 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:
    __copy__simulation_1.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 20 data sets
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 20 data sets

  Executing SED-ML file 0: __copy__simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed.  Reason Given: name 'Clog' is not defined

exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (2.3 s)

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

Exception:

  The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.5' could not execute the archive:

    Unknown error

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 20 data sets

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed.  Reason Given: name 'Clog' is not defined

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint (2.5 s)

Required model formats and simulation algorithms for SED tasks:

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (11.1 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 (3.4 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`:

    GillesPy2: 1.5.5, CLI: 0.1.16, 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`:

    GillesPy2: 1.5.5, CLI: 0.1.16, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.6 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 (0.5 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.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (2.4 s)

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

Warnings:

  The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.5' could not execute the archive:

    Unknown error

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 20 data sets

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  Initial simulation time 50.0 is not supported. Initial time must be 0.
biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
jonrkarr commented 3 years ago

Rejecting GillesPy2 1.5.5 because it doesn't correctly handle species with ids that include "ln". This is fixed in GillesPy2 1.5.7.