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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 CBMPy 0.7.25 #85

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: cbmpy version: 0.7.25 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_CBMPy/bc67f88e3dd99e29a04825cf870b0f08ee3e3c92/biosimulators.json specificationsPatch: version: 0.7.25 image: url: ghcr.io/biosimulators/biosimulators_cbmpy/cbmpy:0.7.25 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 (10.7 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 (4.7 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`:

    SymPy not install (only required for optional, symbolic matrix support).

    ERROR: SymPy import error (required for symbolic matrix support only).

    INFO: No xlwt module available, Excel spreadsheet creation disabled

    No module named 'cplex'

    CPLEX not available

    *****
    Using GLPK
    *****

    Rational IO not available

    INFO: No xlrd module available, Excel spreadsheet reading disabled

    CBMPy environment
    ******************
    Revision: r689

    ***********************************************************************
    * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
    *                http://cbmpy.sourceforge.net                         *
    * Copyright(C) Brett G. Olivier 2014 - 2019                           *
    * Dept. of Systems Bioinformatics                                     *
    * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
    * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
    * Distributed under the GNU GPL v 3.0 licence, see                    *
    * LICENCE (supplied with this release) for details                    *
    ***********************************************************************

    CBMPy: 0.7.25.689, 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`:

    SymPy not install (only required for optional, symbolic matrix support).

    ERROR: SymPy import error (required for symbolic matrix support only).

    INFO: No xlwt module available, Excel spreadsheet creation disabled

    No module named 'cplex'

    CPLEX not available

    *****
    Using GLPK
    *****

    Rational IO not available

    INFO: No xlrd module available, Excel spreadsheet reading disabled

    CBMPy environment
    ******************
    Revision: r689

    ***********************************************************************
    * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
    *                http://cbmpy.sourceforge.net                         *
    * Copyright(C) Brett G. Olivier 2014 - 2019                           *
    * Dept. of Systems Bioinformatics                                     *
    * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
    * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
    * Distributed under the GNU GPL v 3.0 licence, see                    *
    * LICENCE (supplied with this release) for details                    *
    ***********************************************************************

    CBMPy: 0.7.25.689, 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 (2.7 s)

Test that a simulator produces linear 2D plots

Warnings:

  Simulator did not produce plots

Log:

  SymPy not install (only required for optional, symbolic matrix support).

  ERROR: SymPy import error (required for symbolic matrix support only).

  INFO: No xlwt module available, Excel spreadsheet creation disabled

  No module named 'cplex'

  CPLEX not available

  *****
  Using GLPK
  *****

  Rational IO not available

  INFO: No xlrd module available, Excel spreadsheet reading disabled
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-48vsz1ws 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.

  CBMPy environment
  ******************
  Revision: r689

  ***********************************************************************
  * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
  *                http://cbmpy.sourceforge.net                         *
  * Copyright(C) Brett G. Olivier 2014 - 2019                           *
  * Dept. of Systems Bioinformatics                                     *
  * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
  * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
  * Distributed under the GNU GPL v 3.0 licence, see                    *
  * LICENCE (supplied with this release) for details                    *
  ***********************************************************************

  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
  FBC version: 2
  M.getNumReactions: 95
  M.getNumSpecies: 72
  FBC.getNumObjectives: 1
  FBC.getNumParameters: 5
  FBC.getNumGeneProducts: 137
  Zero dimension compartment detected: c
  Zero dimension compartment detected: e
  FluxBounds process1: 0.003
  INFO: Active objective: obj
  Adding objective: obj
  FluxBounds process2: 0.001

  SBML3 load time: 0.107

  gplk_constructLPfromFBA time: 0.005035400390625

  glpk_analyzeModel FBA --> LP time: 2.384185791015625e-07

  analyzeModel objective value: 0.8739215069684909

  Objective obj: "maximize"
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: 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:

  SymPy not install (only required for optional, symbolic matrix support).

  ERROR: SymPy import error (required for symbolic matrix support only).

  INFO: No xlwt module available, Excel spreadsheet creation disabled

  No module named 'cplex'

  CPLEX not available

  *****
  Using GLPK
  *****

  Rational IO not available

  INFO: No xlrd module available, Excel spreadsheet reading disabled
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vdq0qs_r 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.

  CBMPy environment
  ******************
  Revision: r689

  ***********************************************************************
  * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
  *                http://cbmpy.sourceforge.net                         *
  * Copyright(C) Brett G. Olivier 2014 - 2019                           *
  * Dept. of Systems Bioinformatics                                     *
  * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
  * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
  * Distributed under the GNU GPL v 3.0 licence, see                    *
  * LICENCE (supplied with this release) for details                    *
  ***********************************************************************

  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
  FBC version: 2
  M.getNumReactions: 95
  M.getNumSpecies: 72
  FBC.getNumObjectives: 1
  FBC.getNumParameters: 5
  FBC.getNumGeneProducts: 137
  Zero dimension compartment detected: c
  Zero dimension compartment detected: e
  FluxBounds process1: 0.003
  INFO: Active objective: obj
  Adding objective: obj
  FluxBounds process2: 0.001

  SBML3 load time: 0.106

  gplk_constructLPfromFBA time: 0.005112409591674805

  glpk_analyzeModel FBA --> LP time: 2.384185791015625e-07

  analyzeModel objective value: 0.8739215069684909

  Objective obj: "maximize"
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (2.8 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

  Simulator did not produce plots

Log:

  SymPy not install (only required for optional, symbolic matrix support).

  ERROR: SymPy import error (required for symbolic matrix support only).

  INFO: No xlwt module available, Excel spreadsheet creation disabled

  No module named 'cplex'

  CPLEX not available

  *****
  Using GLPK
  *****

  Rational IO not available

  INFO: No xlrd module available, Excel spreadsheet reading disabled
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tbxzveg1 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.

  CBMPy environment
  ******************
  Revision: r689

  ***********************************************************************
  * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
  *                http://cbmpy.sourceforge.net                         *
  * Copyright(C) Brett G. Olivier 2014 - 2019                           *
  * Dept. of Systems Bioinformatics                                     *
  * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
  * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
  * Distributed under the GNU GPL v 3.0 licence, see                    *
  * LICENCE (supplied with this release) for details                    *
  ***********************************************************************

  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
  FBC version: 2
  M.getNumReactions: 95
  M.getNumSpecies: 72
  FBC.getNumObjectives: 1
  FBC.getNumParameters: 5
  FBC.getNumGeneProducts: 137
  Zero dimension compartment detected: c
  Zero dimension compartment detected: e
  FluxBounds process1: 0.003
  INFO: Active objective: obj
  Adding objective: obj
  FluxBounds process2: 0.002

  SBML3 load time: 0.108

  gplk_constructLPfromFBA time: 0.005189657211303711

  glpk_analyzeModel FBA --> LP time: 2.384185791015625e-07

  analyzeModel objective value: 0.8739215069684909

  Objective obj: "maximize"
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.6 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

  Simulator did not produce plots

Log:

  SymPy not install (only required for optional, symbolic matrix support).

  ERROR: SymPy import error (required for symbolic matrix support only).

  INFO: No xlwt module available, Excel spreadsheet creation disabled

  No module named 'cplex'

  CPLEX not available

  *****
  Using GLPK
  *****

  Rational IO not available

  INFO: No xlrd module available, Excel spreadsheet reading disabled
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3yuhqdet 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.

  CBMPy environment
  ******************
  Revision: r689

  ***********************************************************************
  * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
  *                http://cbmpy.sourceforge.net                         *
  * Copyright(C) Brett G. Olivier 2014 - 2019                           *
  * Dept. of Systems Bioinformatics                                     *
  * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
  * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
  * Distributed under the GNU GPL v 3.0 licence, see                    *
  * LICENCE (supplied with this release) for details                    *
  ***********************************************************************

  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
  FBC version: 2
  M.getNumReactions: 95
  M.getNumSpecies: 72
  FBC.getNumObjectives: 1
  FBC.getNumParameters: 5
  FBC.getNumGeneProducts: 137
  Zero dimension compartment detected: c
  Zero dimension compartment detected: e
  FluxBounds process1: 0.003
  INFO: Active objective: obj
  Adding objective: obj
  FluxBounds process2: 0.001

  SBML3 load time: 0.108

  gplk_constructLPfromFBA time: 0.005106449127197266

  glpk_analyzeModel FBA --> LP time: 2.384185791015625e-07

  analyzeModel objective value: 0.8739215069684909

  Objective obj: "maximize"
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: 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:

  SymPy not install (only required for optional, symbolic matrix support).

  ERROR: SymPy import error (required for symbolic matrix support only).

  INFO: No xlwt module available, Excel spreadsheet creation disabled

  No module named 'cplex'

  CPLEX not available

  *****
  Using GLPK
  *****

  Rational IO not available

  INFO: No xlrd module available, Excel spreadsheet reading disabled
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ku08m9zf 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.

  CBMPy environment
  ******************
  Revision: r689

  ***********************************************************************
  * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
  *                http://cbmpy.sourceforge.net                         *
  * Copyright(C) Brett G. Olivier 2014 - 2019                           *
  * Dept. of Systems Bioinformatics                                     *
  * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
  * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
  * Distributed under the GNU GPL v 3.0 licence, see                    *
  * LICENCE (supplied with this release) for details                    *
  ***********************************************************************

  /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
  FBC version: 2
  M.getNumReactions: 95
  M.getNumSpecies: 72
  FBC.getNumObjectives: 1
  FBC.getNumParameters: 5
  FBC.getNumGeneProducts: 137
  Zero dimension compartment detected: c
  Zero dimension compartment detected: e
  FluxBounds process1: 0.003
  INFO: Active objective: obj
  Adding objective: obj
  FluxBounds process2: 0.001

  SBML3 load time: 0.104

  gplk_constructLPfromFBA time: 0.005179643630981445

  glpk_analyzeModel FBA --> LP time: 2.384185791015625e-07

  analyzeModel objective value: 0.8739215069684909

  Objective obj: "maximize"
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: 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:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (2.9 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:

  SymPy not install (only required for optional, symbolic matrix support).

  ERROR: SymPy import error (required for symbolic matrix support only).

  INFO: No xlwt module available, Excel spreadsheet creation disabled

  No module named 'cplex'

  CPLEX not available

  *****
  Using GLPK
  *****

  Rational IO not available

  INFO: No xlrd module available, Excel spreadsheet reading disabled
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8npc1nkp 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.

  CBMPy environment
  ******************
  Revision: r689

  ***********************************************************************
  * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *
  *                http://cbmpy.sourceforge.net                         *
  * Copyright(C) Brett G. Olivier 2014 - 2019                           *
  * Dept. of Systems Bioinformatics                                     *
  * Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *
  * CBMPy is developed as part of the BeBasic MetaToolKit Project       *
  * Distributed under the GNU GPL v 3.0 licence, see                    *
  * LICENCE (supplied with this release) for details                    *
  ***********************************************************************

  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
  FBC version: 2
  M.getNumReactions: 95
  M.getNumSpecies: 72
  FBC.getNumObjectives: 1
  FBC.getNumParameters: 5
  FBC.getNumGeneProducts: 137
  Zero dimension compartment detected: c
  Zero dimension compartment detected: e
  FluxBounds process1: 0.009
  INFO: Active objective: obj
  Adding objective: obj
  FluxBounds process2: 0.001

  SBML3 load time: 0.119

  gplk_constructLPfromFBA time: 0.006440639495849609

  glpk_analyzeModel FBA --> LP time: 4.76837158203125e-07

  analyzeModel objective value: 0.8739215069684909

  Objective obj: "maximize"
  /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 cbmpy to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.