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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 AMICI 0.11.18 #376

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: amici version: 0.11.18 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_AMICI/159c1e1784a8e444421322c35adb23cad1efc0d9/biosimulators.json specificationsPatch: version: 0.11.18 image: url: ghcr.io/biosimulators/biosimulators_amici/amici:0.11.18 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 for 90 days 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 for 90 days 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 (4.6 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'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

  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 (0.5 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'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

  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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (26.2 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

The validation/submission of your simulator failed.

- A Singularity image could not be generated for the Docker image
- 
-   - Internal Server Error (500):

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

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 for 90 days 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 for 90 days 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 (4.1 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'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

  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 (0.6 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'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

  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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (26.4 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 amici to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.