Submit PySceS 0.9.9 - Githubissues

Summary of tests

Executed 35 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
- exec_status_report.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.SimulatorGeneratesReportsOfSimultionResults
- 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 8 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

Warnings

`cli.CliDisplaysVersionInformationInline` (4.6 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`:

    Matplotlib backend set to: "TkAgg"
    Matplotlib interface not available
    Attempting alternate pitcon import ...
    Attempting alternate nleq2 import ...
    Continuation routines available (A)
    NLEQ2 routines available (A)
    SBML support available
    You are using NumPy (1.19.4) with SciPy (1.5.3)
    /opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
      38892959/120069679,11804845./141497517]])]
    Assimulo CVode available
    Parallel scanner is available

    PySCeS environment
    ******************
    pysces.model_dir = /root/Pysces/psc
    pysces.output_dir = /root/Pysces

    ***********************************************************************
    * Welcome to PySCeS (0.9.9) - Python Simulator for Cellular Systems   *
    *                http://pysces.sourceforge.net                        *
    * Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2020  *
    * Triple-J Group for Molecular Cell Physiology                        *
    * Stellenbosch University, ZA and VU University Amsterdam, NL         *
    * PySCeS is distributed under the PySCeS (BSD style) licence, see     *
    * LICENCE.txt (supplied with this release) for details                *
    * Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *
    ***********************************************************************
    PySCeS: 0.9.9, CLI: 0.1.4, Python: 3.7.9, OS: Linux debian 10.6 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`:

    Matplotlib backend set to: "TkAgg"
    Matplotlib interface not available
    Attempting alternate pitcon import ...
    Attempting alternate nleq2 import ...
    Continuation routines available (A)
    NLEQ2 routines available (A)
    SBML support available
    You are using NumPy (1.19.4) with SciPy (1.5.3)
    /opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
      38892959/120069679,11804845./141497517]])]
    Assimulo CVode available
    Parallel scanner is available

    PySCeS environment
    ******************
    pysces.model_dir = /root/Pysces/psc
    pysces.output_dir = /root/Pysces

    ***********************************************************************
    * Welcome to PySCeS (0.9.9) - Python Simulator for Cellular Systems   *
    *                http://pysces.sourceforge.net                        *
    * Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2020  *
    * Triple-J Group for Molecular Cell Physiology                        *
    * Stellenbosch University, ZA and VU University Amsterdam, NL         *
    * PySCeS is distributed under the PySCeS (BSD style) licence, see     *
    * LICENCE.txt (supplied with this release) for details                *
    * Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *
    ***********************************************************************
    PySCeS: 0.9.9, CLI: 0.1.4, Python: 3.7.9, OS: Linux debian 10.6 5.4.0-1032-azure, Machine: x86_64

Log:

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (3.7 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

Log:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a704wpvk 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.
Matplotlib interface not available
Attempting alternate pitcon import ...
Attempting alternate nleq2 import ...
/opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
38892959/120069679,11804845./141497517]])]
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
Found 1 tasks
  BIOMD0000000912_sim
Executing task 1: BIOMD0000000912_sim
Info: single compartment model: locating "Induction_of_tumor" in default compartment
Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
Writing file: /tmp/tmpe322qnc5.psc

SBML2PSC
in : /tmp/tmp3vobzxv2.xml
out: /tmp/tmpe322qnc5.psc
Using model directory: /tmp/Pysces/psc
/tmp/tmpe322qnc5.psc loading ..... 
Parsing file: /tmp/tmpe322qnc5.psc
Info: No reagents have been fixed

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

CVODE time for 5001 points: 0.42231297492980957
/opt/conda/envs/py/lib/python3.7/site-packages/tables/path.py:155: NaturalNameWarning: object name is not a valid Python identifier: 'BIOMD0000000912_sim.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)
/opt/conda/envs/py/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.SimulatorProducesLinear2DPlots` (4.1 s)

Test that a simulator produces linear 2D plots

Warnings:

Simulator did not produce plots

Log:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vudyrrnc 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.
Matplotlib interface not available
Attempting alternate pitcon import ...
Attempting alternate nleq2 import ...
/opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
38892959/120069679,11804845./141497517]])]
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
BIOMD0000000912_sim.sedml:
  Tasks (1):
    BIOMD0000000912_sim
  Plots (1):
    plot_0: 4 curves

Executing SED-ML file 0: BIOMD0000000912_sim.sedml
Found 1 tasks
  BIOMD0000000912_sim
Executing task 1: BIOMD0000000912_sim
Info: single compartment model: locating "Induction_of_tumor" in default compartment
Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
Writing file: /tmp/tmp57irturv.psc

SBML2PSC
in : /tmp/tmpxtr8x84i/./Caravagna2010.xml
out: /tmp/tmp57irturv.psc
Using model directory: /tmp/Pysces/psc
/tmp/tmp57irturv.psc loading ..... 
Parsing file: /tmp/tmp57irturv.psc
Info: No reagents have been fixed

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

CVODE time for 5001 points: 0.5399885177612305
/opt/conda/envs/py/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` (3.7 s)

Test that a simulator produces linear 3D plots

Warnings:

Simulator did not produce plots

Log:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lzsec37_ 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.
Matplotlib interface not available
Attempting alternate pitcon import ...
Attempting alternate nleq2 import ...
/opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
38892959/120069679,11804845./141497517]])]
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
BIOMD0000000912_sim.sedml:
  Tasks (1):
    BIOMD0000000912_sim
  Plots (1):
    plot_0: 4 surfaces

Executing SED-ML file 0: BIOMD0000000912_sim.sedml
Found 1 tasks
  BIOMD0000000912_sim
Executing task 1: BIOMD0000000912_sim
Info: single compartment model: locating "Induction_of_tumor" in default compartment
Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
Writing file: /tmp/tmp8f5mslx2.psc

SBML2PSC
in : /tmp/tmp4mqaw1vj/./Caravagna2010.xml
out: /tmp/tmp8f5mslx2.psc
Using model directory: /tmp/Pysces/psc
/tmp/tmp8f5mslx2.psc loading ..... 
Parsing file: /tmp/tmp8f5mslx2.psc
Info: No reagents have been fixed

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

CVODE time for 5001 points: 0.469008207321167
/opt/conda/envs/py/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` (3.7 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

Simulator did not produce plots

Log:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ci7fqiuq 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.
Matplotlib interface not available
Attempting alternate pitcon import ...
Attempting alternate nleq2 import ...
/opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
38892959/120069679,11804845./141497517]])]
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
BIOMD0000000912_sim.sedml:
  Tasks (1):
    BIOMD0000000912_sim
  Plots (1):
    plot_0: 4 curves

Executing SED-ML file 0: BIOMD0000000912_sim.sedml
Found 1 tasks
  BIOMD0000000912_sim
Executing task 1: BIOMD0000000912_sim
Info: single compartment model: locating "Induction_of_tumor" in default compartment
Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
Writing file: /tmp/tmp_c90vv6g.psc

SBML2PSC
in : /tmp/tmp7o3dim6g/./Caravagna2010.xml
out: /tmp/tmp_c90vv6g.psc
Using model directory: /tmp/Pysces/psc
/tmp/tmp_c90vv6g.psc loading ..... 
Parsing file: /tmp/tmp_c90vv6g.psc
Info: No reagents have been fixed

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

CVODE time for 5001 points: 0.4681262969970703
/opt/conda/envs/py/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` (3.8 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

Simulator did not produce plots

Log:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8qmmiidc 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.
Matplotlib interface not available
Attempting alternate pitcon import ...
Attempting alternate nleq2 import ...
/opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
38892959/120069679,11804845./141497517]])]
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
BIOMD0000000912_sim.sedml:
  Tasks (1):
    BIOMD0000000912_sim
  Plots (1):
    plot_0: 4 surfaces

Executing SED-ML file 0: BIOMD0000000912_sim.sedml
Found 1 tasks
  BIOMD0000000912_sim
Executing task 1: BIOMD0000000912_sim
Info: single compartment model: locating "Induction_of_tumor" in default compartment
Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
Writing file: /tmp/tmp72nbwm_5.psc

SBML2PSC
in : /tmp/tmpnhnh2yqo/./Caravagna2010.xml
out: /tmp/tmp72nbwm_5.psc
Using model directory: /tmp/Pysces/psc
/tmp/tmp72nbwm_5.psc loading ..... 
Parsing file: /tmp/tmp72nbwm_5.psc
Info: No reagents have been fixed

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

CVODE time for 5001 points: 0.4763193130493164
/opt/conda/envs/py/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` (3.8 s)

Test that a simulator produces multiple plots

Warnings:

Simulator did not produce plots

Log:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zu6xzw6s 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.
Matplotlib interface not available
Attempting alternate pitcon import ...
Attempting alternate nleq2 import ...
/opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
38892959/120069679,11804845./141497517]])]
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
BIOMD0000000912_sim.sedml:
  Tasks (1):
    BIOMD0000000912_sim
  Plots (2):
    plot_0: 2 curves
    plot_1: 2 curves

Executing SED-ML file 0: BIOMD0000000912_sim.sedml
Found 1 tasks
  BIOMD0000000912_sim
Executing task 1: BIOMD0000000912_sim
Info: single compartment model: locating "Induction_of_tumor" in default compartment
Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
Writing file: /tmp/tmpo6l249l2.psc

SBML2PSC
in : /tmp/tmpeqg6zn8_/./Caravagna2010.xml
out: /tmp/tmpo6l249l2.psc
Using model directory: /tmp/Pysces/psc
/tmp/tmpo6l249l2.psc loading ..... 
Parsing file: /tmp/tmpo6l249l2.psc
Info: No reagents have been fixed

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

CVODE time for 5001 points: 0.449873685836792
/opt/conda/envs/py/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)
/opt/conda/envs/py/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)

biosimulators / Biosimulators

Submit PySceS 0.9.9 #72

Summary of tests

Warnings

`cli.CliDisplaysVersionInformationInline` (4.6 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (3.7 s)

`sedml.SimulatorProducesLinear2DPlots` (4.1 s)

`sedml.SimulatorProducesLinear3DPlots` (3.7 s)

`sedml.SimulatorProducesLogarithmic2DPlots` (3.7 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (3.8 s)

`sedml.SimulatorProducesMultiplePlots` (3.8 s)

biosimulators / Biosimulators

Submit PySceS 0.9.9 #72

Summary of tests

Warnings

cli.CliDisplaysVersionInformationInline (4.6 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (3.7 s)

sedml.SimulatorProducesLinear2DPlots (4.1 s)

sedml.SimulatorProducesLinear3DPlots (3.7 s)

sedml.SimulatorProducesLogarithmic2DPlots (3.7 s)

sedml.SimulatorProducesLogarithmic3DPlots (3.8 s)

sedml.SimulatorProducesMultiplePlots (3.8 s)

`cli.CliDisplaysVersionInformationInline` (4.6 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (3.7 s)

`sedml.SimulatorProducesLinear2DPlots` (4.1 s)

`sedml.SimulatorProducesLinear3DPlots` (3.7 s)

`sedml.SimulatorProducesLogarithmic2DPlots` (3.7 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (3.8 s)

`sedml.SimulatorProducesMultiplePlots` (3.8 s)