Submit Neuron 8.0.0

id: neuron
version: 8.0.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/dc6b86d7247f2767fbea4b0db41348ae12d3bf68/biosimulators-neuron.json
specificationsPatch:
version: 8.0.0
image:
url: ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0
digest: "sha256:0e4938c4b152300338e8d4ddec7b6c980ed8ef660075dd609a5c9c3a1129d02a"
validateImage: true
commitSimulator: true

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.

The specifications of your simulator is valid!

Warnings
docker_image.DeclaresSupportedEnvironmentVariables (0.4 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'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - '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: None

docker_image.HasBioContainersLabels (0.3 s)

Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Summary of tests

Executed 73 test cases

Passed 29 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 44 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
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-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000027

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (1.5 s)

Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (1.4 s)

Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (1.5 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.9 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsAlgorithmParameters (0.9 s)

Test that a simulator supports setting the values of parameters of algorithms
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (0.9 s)

Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsModelAttributeChanges (1.5 s)

Test that a simulator supports changes to the attributes of model elements
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (1.4 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.9 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (9.8 s)

Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NEURON` was not able to execute `/tmp/tmpkjboj31z.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpuylz9goo.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:31:24,983 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpuylz9goo.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpuylz9goo.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:31:24,984 - pyneuroml.pynml - INFO - Executing: (java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpuylz9goo.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpuylz9goo.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:31:25,256 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpuylz9goo.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpuylz9goo.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

      pyNeuroML >>> 2021-11-25 04:31:25,257 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpuylz9goo.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (10.6 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NEURON` was not able to execute `/tmp/tmptrkmwk6o.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpxccgdn85.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:31:35,565 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmpxccgdn85.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5668M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpxccgdn85.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:31:35,566 - pyneuroml.pynml - INFO - Executing: (java -Xmx5668M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpxccgdn85.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5668M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpxccgdn85.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:31:35,837 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5668M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmpxccgdn85.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpxccgdn85.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

      pyNeuroML >>> 2021-11-25 04:31:35,837 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmpxccgdn85.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (10.8 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NEURON` was not able to execute `/tmp/tmp5kalkyns.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp11ecls0n.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:31:46,365 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp11ecls0n.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp11ecls0n.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:31:46,366 - pyneuroml.pynml - INFO - Executing: (java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp11ecls0n.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp11ecls0n.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:31:46,633 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp11ecls0n.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp11ecls0n.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

      pyNeuroML >>> 2021-11-25 04:31:46,633 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp11ecls0n.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (10.6 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NEURON` was not able to execute `/tmp/tmpn4x332ku.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmptct8jtel.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:31:57,060 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmptct8jtel.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmptct8jtel.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:31:57,061 - pyneuroml.pynml - INFO - Executing: (java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmptct8jtel.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmptct8jtel.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:31:57,333 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5671M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmptct8jtel.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmptct8jtel.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

      pyNeuroML >>> 2021-11-25 04:31:57,333 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmptct8jtel.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (10.8 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NEURON` was not able to execute `/tmp/tmp7lxng3d7.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp04ac4s82.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:32:07,868 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp04ac4s82.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp04ac4s82.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:32:07,869 - pyneuroml.pynml - INFO - Executing: (java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp04ac4s82.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp04ac4s82.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:32:08,161 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5667M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp04ac4s82.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp04ac4s82.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

      pyNeuroML >>> 2021-11-25 04:32:08,161 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp04ac4s82.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (11.1 s)

Test that a simulator supports nested repeated tasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `NEURON` was not able to execute `/tmp/tmptfjojzy2.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp8kenjif8.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:32:18,457 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp8kenjif8.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp8kenjif8.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:32:18,458 - pyneuroml.pynml - INFO - Executing: (java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp8kenjif8.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp8kenjif8.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:32:18,720 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5672M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp8kenjif8.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp8kenjif8.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

      pyNeuroML >>> 2021-11-25 04:32:18,721 - pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp8kenjif8.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:247)

       jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:472)

       jNeuroML >>

    `NEURON` was not able to execute `/tmp/tmpnlzp5lgo.xml`

      pyNeuroML >>> pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp425bzajd.xml and running with jNeuroML_NEURON

      pyNeuroML >>> 2021-11-25 04:32:18,889 - pyneuroml.pynml - INFO - Loading LEMS file: tmp/tmp425bzajd.xml and running with jNeuroML_NEURON

      pyNeuroML >>> pyneuroml.pynml - INFO - Executing: (java -Xmx5673M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp425bzajd.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> 2021-11-25 04:32:18,890 - pyneuroml.pynml - INFO - Executing: (java -Xmx5673M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp425bzajd.xml"  -neuron -run -compile -nogui -I '') in directory: .

      pyNeuroML >>> pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5673M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp425bzajd.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> 2021-11-25 04:32:19,169 - pyneuroml.pynml - CRITICAL - *** Problem running command:

             Command 'java -Xmx5673M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.11.0-jar-with-dependencies.jar"  "tmp/tmp425bzajd.xml"  -neuron -run -compile -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>> pyneuroml.pynml - CRITICAL -  jNeuroML >>   jNeuroML v0.11.0

       jNeuroML >>  (INFO) Reading from: /tmp/tmp425bzajd.xml

       jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

       jNeuroML >>  Search directories are: [/, /tmp, /tmp, /]

       jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

       jNeuroML >>

       jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

       jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

       jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

       jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

       jNeuroML >>  	at org.neuroml.JNeuroML.loadLemsFile(JNeuroML.java:258)

       jNeuroML >>  	at org.neuroml.JNeuroML. ...

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of neuron to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.


[CP Staging] Fix report and personal detail options are persisted after switching account

Details

We have a context provider to cache the report and personal detail options which is put in App.tsx component. Signing out won't clear the cache, so this PR moves it to the AuthScreen.
Fixed Issues

$ https://github.com/Expensify/App/issues/39710
PROPOSAL: https://github.com/Expensify/App/issues/39710#issuecomment-2040229758
Tests

Same as QA Steps

[x] Verify that no errors appear in the JS console

Offline tests

Same as QA Steps
QA Steps

Sign in as user A
Open the new chat page
Note down the recent and contact list
Log out and sign in as user B
Open the new chat page
Verify the recent and contact list from user A are not shared with user B

[x] Verify that no errors appear in the JS console

PR Author Checklist

[x] I linked the correct issue in the ### Fixed Issues section above
[x] I wrote clear testing steps that cover the changes made in this PR

[x] I added steps for local testing in the Tests section
[x] I added steps for the expected offline behavior in the Offline steps section
[x] I added steps for Staging and/or Production testing in the QA steps section
[x] I added steps to cover failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[x] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)
[x] I tested this PR with a High Traffic account against the staging or production API to ensure there are no regressions (e.g. long loading states that impact usability).

[x] I included screenshots or videos for tests on all platforms
[x] I ran the tests on all platforms & verified they passed on:

[x] Android: Native
[x] Android: mWeb Chrome
[x] iOS: Native
[x] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

[x] I verified there are no console errors (if there's a console error not related to the PR, report it or open an issue for it to be fixed)
[x] I followed proper code patterns (see Reviewing the code)

[x] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick)
[x] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[x] I verified that comments were added to code that is not self explanatory
[x] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[x] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method

[x] If any non-english text was added/modified, I verified the translation was requested/reviewed in #expensify-open-source and it was approved by an internal Expensify engineer. Link to Slack message:

[x] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[x] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is either coming verbatim from figma or has been approved by marketing (in order to get marketing approval, ask the Bug Zero team member to add the Waiting for copy label to the issue)
[x] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[x] I verified the JSDocs style guidelines (in STYLE.md) were followed

[x] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[x] I followed the guidelines as stated in the Review Guidelines
[x] I tested other components that can be impacted by my changes (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar are working as expected)
[x] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[x] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[x] I verified that if a function's arguments changed that all usages have also been updated correctly
[x] If any new file was added I verified that:

[x] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[x] If a new CSS style is added I verified that:

[x] A similar style doesn't already exist
[x] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(theme.componentBG))

[x] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[x] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[x] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[x] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[x] If the PR modifies the UI (e.g. new buttons, new UI components, changing the padding/spacing/sizing, moving components, etc) or modifies the form input styles:

[x] I verified that all the inputs inside a form are aligned with each other.
[x] I added Design label and/or tagged @Expensify/design so the design team can review the changes.

[x] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[x] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.

Screenshots/Videos

Android: Native

https://github.com/Expensify/App/assets/50919443/6d22efa0-1598-47d6-8f74-d074a4addf1a

Android: mWeb Chrome

https://github.com/Expensify/App/assets/50919443/7a9e32a2-c029-4d21-a3d9-06d55b9c8381

iOS: Native

https://github.com/Expensify/App/assets/50919443/c10ac864-1cd5-4827-b678-ef3b54c03bf3

iOS: mWeb Safari

https://github.com/Expensify/App/assets/50919443/39960b1a-5194-4572-a467-5332bb94603d

MacOS: Chrome / Safari

https://github.com/Expensify/App/assets/50919443/e583d50f-63be-4db7-9cbd-e5684a3070e6

MacOS: Desktop

https://github.com/Expensify/App/assets/50919443/82450115-7027-4c93-b8ed-ec71b08d4f35

Pending mobile recording..

Rerunning perf tests

:hand: This PR was not deployed to staging yet because QA is ongoing. It will be automatically deployed to staging after the next production release.

🚀 Deployed to staging by https://github.com/jasperhuangg in version: 1.4.60-13 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅

🚀 Deployed to production by https://github.com/Julesssss in version: 1.4.60-13 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅


SSL Certificate

Problem
I followed along #60 in an attempt to enable TLS on the broker but when starting the broker I encountered the exception System.InvalidOperationException: The certificate for TLS encryption must contain the private key despite the certificate having the key.
Solution
To fix the issue, I first had to mark the certificate as Exportable:
var certificate = new X509Certificate2(filePathToCertificate, password, X509KeyStorageFlags.Exportable);

Then, when setting the options for the broker, the certifciate needs to be exported as a Pfx certificate (which contains the private key):
options.TlsEndpointOptions.Certificate = certificate.Export(X509ContentType.Pfx);
options.TlsEndpointOptions.IsEnabled = true;

Recommendation
Update the Wiki with this information.

Duplicate of #124.  Recommendation stands.

Thank you for the detailed explanation. I will update the Wiki soon. But you can do it as well if you like.

I just made the update.  Thanks!

Can you connect using TLS?

@inforaudio I am able to.  Our application uses two different clients:  the MQTT node.js package and the ESP32 MQTT Client.  Both are able to connect using TLS to a broker built using MQTTNet running on a Windows VM we are hosting via Microsoft Azure.

But this library is no possible use in Xamarin.
What platform do you use for made the APP? and use this library?

But this library is no possible use in Xamarin.

I have not tried using it in Xamarin.

What platform do you use for made the APP? and use this library?

I created a console application using Visual Studio that uses this library.

thanks for answer.
and do you know a simple library for use MQTT with SSL over Xamarin

Have you tried Xamarin's broker/client? https://github.com/xamarin/mqtt
On Thu, Mar 14, 2019 at 2:45 PM inforaudio<EMAIL_ADDRESS>wrote:

thanks for answer.
and do you know a simple library for use MQTT with SSL over Xamarin
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I think that this library dont run in SSL /TLS mode,
There are some question ask about it, wiht problem with this theme/topic
And there are nothing information about TLS /SSL in the library

Why do you think it is not able to run TLS in Xamarin?
I can connect with the test broker from hivemq without problems in Xamarin.
The only thing I need to do is to use WithTls in the client options builder.

Hello:
I have some days try with it, and i cant made it.
if only add:
.WithTls()
Show the exception.
MQTTnet.Exceptions.MqttCommunicationException: A call to SSPI failed, see inner exception. ---> System.Security.Authentication.AuthenticationException: A call to SSPI failed, see inner exception. ---> Mono.Btls.MonoBtlsException: Ssl error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED
I add
MqttClientOptionsBuilderTlsParameters tls = new MqttClientOptionsBuilderTlsParameters();
tls.AllowUntrustedCertificates = true;
tls.UseTls = true;
tls.IgnoreCertificateChainErrors = true;
and
.WithTls(tls)
And show the exception
MQTTnet.Exceptions.MqttCommunicationException: A call to SSPI failed, see inner exception. ---> System.Security.Authentication.AuthenticationException: A call to SSPI failed, see inner exception. ---> Mono.Btls.Mon
the code is like your example..
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using Xamarin.Forms;
using MQTTnet.Client;
using MQTTnet.Protocol;
using MQTTnet.Client.Options;
using System.Security.Cryptography.X509Certificates;
using System.IO;
namespace App24
{
public partial class MainPage : ContentPage
{
    public MainPage()
    {
        InitializeComponent();

        RunAsync();

        async Task RunAsync()
        {
            try
            {

                var factory = new MQTTnet.MqttFactory();
                var client = factory.CreateMqttClient();
                var clientOptions = new MqttClientOptionsBuilder()
                 .WithClientId("foo")
                 .WithTcpServer("<IP_ADDRESS>", 8883)
                 .WithCredentials("", "")
                 .WithTls()
                //.WithTls(true, false, false, serverCertificate.Export(X509ContentType.Cert))
                //.WithTls(true, false, false, serverCertificate.Export(X509ContentType.Cert))
                .WithCleanSession()
                 .WithProtocolVersion(MQTTnet.Formatter.MqttProtocolVersion.V311)
                 .WithKeepAlivePeriod(TimeSpan.FromSeconds(60))
                 .WithCommunicationTimeout(TimeSpan.FromSeconds(30))
                 .Build();

                client.Connected += async (s, e) =>
                {
                    Console.WriteLine("### CONNECTED WITH SERVER ###");

                    await client.SubscribeAsync(new MQTTnet.TopicFilterBuilder().WithTopic("#").Build());

                    Console.WriteLine("### SUBSCRIBED ###");
                };

                client.Disconnected += async (s, e) =>
                {
                    Console.WriteLine("### DISCONNECTED FROM SERVER ###");
                    await Task.Delay(TimeSpan.FromSeconds(5));

                    try
                    {
                        //await client.ConnectAsync(clientOptions);
                        await client.ConnectAsync(clientOptions);
                    }
                    catch
                    {
                        Console.WriteLine("### RECONNECTING FAILED ###");
                    }
                };

                try
                {
                    await client.ConnectAsync(clientOptions);
                    Console.WriteLine(" Conectando : ......................");
                }
                catch (Exception exception)
                {
                    Console.WriteLine("### CONNECTING FAILED ###" + Environment.NewLine + exception);
                }

                Console.WriteLine("### WAITING FOR APPLICATION MESSAGES ###");

                while (true)
                {
                    Console.ReadLine();

                    //client.SubscribeAsync(new TopicFilter("test", MqttQualityOfServiceLevel.AtMostOnce));

                    var applicationMessage = new MQTTnet.MqttApplicationMessageBuilder()
                        .WithTopic("A/B/C")
                        .WithPayload("Hello World2")
                        .WithAtLeastOnceQoS()
                        .Build();

                    await client.PublishAsync(applicationMessage);
                }
            }
            catch (Exception exception)
            {
                Console.WriteLine(exception);
            }
        }

    }
}

}

OK this seems to be a platform specific issue. Are you able to connect to hivemq test broker (broker.hivemq.com) with TLS? If yes the problem may be caused by your environment.
Additionally you can attach an event handler to the static validation callback at the TLS options object.  Maybe the properties you set are not covering your problem while validating.

Thanks so much by your answer.
I try to connect to: broker.hivemq.com
and the answer is  nothing.
MQTTnet.Exceptions.MqttCommunicationException: The client is not connected.
at MQTTnet.Client.MqttClient.ThrowIfNotConnected () [0x00021] in <6fb0ae0760d243c8a0c3422110b350c4>:0
at MQTTnet.Client.MqttClient.PublishAsync (MQTTnet.MqttApplicationMessage applicationMessage, System.Threading.CancellationToken cancellationToken) [0x0000e] in <6fb0ae0760d243c8a0c3422110b350c4>:0
at MQTTnet.Client.MqttClientExtensions.PublishAsync (MQTTnet.Client.IMqttClient client, MQTTnet.MqttApplicationMessage applicationMessage) [0x00023] in <6fb0ae0760d243c8a0c3422110b350c4>:0
at App24.MainPage+<<-ctor>g__RunAsync|0_0>d.MoveNext () [0x0023b] in C:\Users\Pablo\source\repos\App24\App24\App24\MainPage.xaml.cs:170
So, here https://github.com/mqtt/mqtt.github.io/wiki/public_brokers
you can see that dont work in SSL only
address | broker.hivemq.com
port | 1883, 8000 (WebSockets)

In broker broker.hivemq.com, we try to connect with desktop client like MQTTBOX and MQTTFX and cant connect by SSL.
And in my Broker, we can connect whit this clients.
always with CA signed server certificate

Hello:
We ty to connect to other public broker and we can connect to mqtt.fluux.io properly..
WONDERFULL.
But try to connect to other server MQTT and cant connect, show this message.
One have seft signed certificate and other have lets encrypt certificate
MQTTnet.Exceptions.MqttCommunicationException: A call to SSPI failed, see inner exception. ---> System.Security.Authentication.AuthenticationException: A call to SSPI failed, see inner exception. ---> Mono.Btls.MonoBtlsException: Ssl error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED03-15 13:27:56.230 I/mono-stdout(27658): MQTTnet.Exceptions
Really what can looking for in the broker?? What need the broker? How can solved it?
At this broker connect other clients by SSL without problem MQQTBOX MQTT.FX etc..


Fixes a bug with MigrationCreator

Related to laravel/framework#31978, this commit fixes #333 and #332

Would be great to have this implemented as well as having Baum work with Laravel 7 . If current author @etrepat no longer has the time for it perhap @ChrisThompsonTLDR can set up a repository and composer package based on it?

Do see now there is version 2 as well https://github.com/etrepat/baum/tree/v2 . Version that is more up-to-date


Use of undeclared identifier compiler error for AVX intrinsics

A customer tried to run scip-clang and was seeing these errors:
/usr/lib/llvm-14/lib/clang/14.0.3/include/avx512fintrin.h:9319:10: error: use of undeclared identifier '__builtin_ia32_reduce_add_q512'
  return __builtin_ia32_reduce_add_q512(__W);

The main effect of this error would be code nav for these intrinsics won't work. But apart from that, it should be OK.
However, we should still fix this, because the Clang we link in should have these intrinsics.

For ARM intrinsics, the problem may be due to this renaming. https://sourcegraph.com/github.com/llvm/llvm-project/-/commit/dba8fced969e2eca9e8650a874293927db17d131


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Receive ERROR: unable to download video data: HTTP Error 403: Forbidden only when ffmpeg installed

DO NOT REMOVE OR SKIP THE ISSUE TEMPLATE

[X] I understand that I will be blocked if I intentionally remove or skip any mandatory* field

Checklist

[X] I'm reporting a bug unrelated to a specific site
[X] I've verified that I have updated yt-dlp to nightly or master (update instructions)
[X] I've checked that all provided URLs are playable in a browser with the same IP and same login details
[X] I've checked that all URLs and arguments with special characters are properly quoted or escaped
[X] I've searched known issues and the bugtracker for similar issues including closed ones. DO NOT post duplicates
[X] I've read the guidelines for opening an issue

Provide a description that is worded well enough to be understood
OS: Ubuntu 24.04 LTS 64 (Running on a VM on Vultra cloud @ Los Angeles)
The Error: yt_dlp.networking.exceptions.HTTPError: HTTP Error 403: Forbidden (Please ref the Complete Verbose Output below)
Steps to replicate the error:

Initialize a VM on the cloud, and login in as user ubuntu
Install ubuntu-desktop via apt and reboot
Open firefox and login in to youtube.com via remote console
Open https://www.youtube.com/watch?v=sWbUDq4S6Y8 and watch by opening an new table on the firefox
Download the tools yt-dlp and the ffmpeg tool-set from the links below and add them to PATH (~/.bashrc):
-- https://github.com/yt-dlp/yt-dlp/releases/download/2024.07.02/yt-dlp
-- https://github.com/yt-dlp/FFmpeg-Builds/releases/download/latest/ffmpeg-n7.0-latest-linux64-gpl-7.0.tar.xz
Followed by update yt-dlp to the nightly version.
Connect to the VM via ssh and execute the command yt-dlp https://www.youtube.com/watch?v=sWbUDq4S6Y8 --cookies-from-browser firefox -v

Them, it will print the Complete Verbose Output.
However, if remove the ffmpeg, it will download the video with very low quality.
Provide verbose output that clearly demonstrates the problem

[X] Run your yt-dlp command with -vU flag added (yt-dlp -vU <your command line>)
[ ] If using API, add 'verbose': True to YoutubeDL params instead
[x] Copy the WHOLE output (starting with [debug] Command-line config) and insert it below

Complete Verbose Output
[debug] Command-line config: ['https://www.youtube.com/watch?v=ogOmQ86y0es', '--cookies-from-browser', 'firefox', '-v']
[debug] Encodings: locale UTF-8, fs utf-8, pref UTF-8, out utf-8, error utf-8, screen utf-8
[debug] yt-dlp version<EMAIL_ADDRESS>from yt-dlp/yt-dlp-nightly-builds [4862a2985] (zip)
[debug] Python 3.12.3 (CPython x86_64 64bit) - Linux-6.8.0-36-generic-x86_64-with-glibc2.39 (OpenSSL 3.0.13 30 Jan 2024, glibc 2.39)
[debug] exe versions: ffmpeg n7.0.1-20-g2df8aaa8c5-20240707 (setts), ffprobe n7.0.1-20-g2df8aaa8c5-20240707
[debug] Optional libraries: certifi-2023.11.17, requests-2.31.0, sqlite3-3.45.1, urllib3-2.0.7
[debug] Proxy map: {}
Extracting cookies from firefox
[debug] Extracting cookies from: "/home/ubuntu/snap/firefox/common/.mozilla/firefox/8vyoay9l.default/cookies.sqlite"
Extracted 46 cookies from firefox
[debug] Request Handlers: urllib
[debug] Loaded 1832 extractors
[youtube] Extracting URL: https://www.youtube.com/watch?v=ogOmQ86y0es
[youtube] ogOmQ86y0es: Downloading webpage
[debug] [youtube] Extracted SAPISID cookie
[youtube] ogOmQ86y0es: Downloading ios player API JSON
[debug] Loading youtube-nsig.5352eb4f from cache
[debug] [youtube] Decrypted nsig gHaFrFKY5BSdE5Oyrlm => lb6pj2McTpgdag
[debug] Loading youtube-nsig.5352eb4f from cache
[debug] [youtube] Decrypted nsig SkmSyYPGJfZi93Ly3C_ => 2lvo7ZuTfmlwhw
[youtube] ogOmQ86y0es: Downloading m3u8 information
[debug] Sort order given by extractor: quality, res, fps, hdr:12, source, vcodec:vp9.2, channels, acodec, lang, proto
[debug] Formats sorted by: hasvid, ie_pref, quality, res, fps, hdr:12(7), source, vcodec:vp9.2(10), channels, acodec, lang, proto, size, br, asr, vext, aext, hasaud, id
[debug] Default format spec: bestvideo*+bestaudio/best
[info] ogOmQ86y0es: Downloading 1 format(s): 303+251
[debug] Invoking http downloader on "https://rr1---sn-a5msenek.googlevideo.com/videoplayback?expire=1720386193&ei=Ma6KZpT9JbexsfIPxcqS2Ag&ip=2001%3A19f0%3A6001%3A496d%3A5400%3A5ff%3Afe01%3Adb68&id=o-AOh5GMpOoCa0c-d4JBLyyS3i3-<Deleted-by-poster>&itag=303&aitags=133%2C134%2C135%2C136%2C160%2C242%2C243%2C244%2C247%2C278%2C298%2C299%2C302%2C303%2C394%2C395%2C396%2C397%2C398%2C399&source=youtube&requiressl=yes&xpc=EgVo2aDSNQ%3D%3D&mh=Zc&mm=31%2C26&mn=sn-a5msenek%2Csn-n4v7snls&ms=au%2Conr&mv=m&mvi=1&pl=38&initcwndbps=302500&siu=1&bui=<Deleted-by-poster>-7di3mxQ&spc=<Deleted-by-poster>&vprv=1&svpuc=1&mime=video%2Fwebm&ns=n-nbfOnBRjNz_7D-bk1tXq0Q&rqh=1&gir=yes&clen=2061243156&dur=19001.216&lmt=1703250286450204&mt=1720364256&fvip=2&keepalive=yes&c=WEB&sefc=1&txp=5437434&n=2lvo7ZuTfmlwhw&sparams=expire%2Cei%2Cip%2Cid%2Caitags%2Csource%2Crequiressl%2Cxpc%2Csiu%2Cbui%2Cspc%2Cvprv%2Csvpuc%2Cmime%2Cns%2Crqh%2Cgir%2Cclen%2Cdur%2Clmt&sig=<Deleted-by-poster>-lvTsP-vhw8iRqDSdcGxUT_NemCM%3D&lsparams=mh%2Cmm%2Cmn%2Cms%2Cmv%2Cmvi%2Cpl%2Cinitcwndbps&lsig=<Deleted-by-poster>-<Deleted-by-poster>-<Deleted-by-poster>"
ERROR: unable to download video data: HTTP Error 403: Forbidden
Traceback (most recent call last):
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/networking/_urllib.py", line 396, in _send
    res = opener.open(urllib_req, timeout=self._calculate_timeout(request))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/urllib/request.py", line 521, in open
    response = meth(req, response)
               ^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/urllib/request.py", line 630, in http_response
    response = self.parent.error(
               ^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/urllib/request.py", line 559, in error
    return self._call_chain(*args)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/urllib/request.py", line 492, in _call_chain
    result = func(*args)
             ^^^^^^^^^^^
  File "/usr/lib/python3.12/urllib/request.py", line 639, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 403: Forbidden

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/YoutubeDL.py", line 3461, in process_info
    partial_success, real_download = self.dl(fname, new_info)
                                     ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/YoutubeDL.py", line 3199, in dl
    return fd.download(name, new_info, subtitle)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/downloader/common.py", line 466, in download
    ret = self.real_download(filename, info_dict)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/downloader/http.py", line 369, in real_download
    establish_connection()
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/downloader/http.py", line 120, in establish_connection
    ctx.data = self.ydl.urlopen(request)
               ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/YoutubeDL.py", line 4161, in urlopen
    return self._request_director.send(req)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/networking/common.py", line 117, in send
    response = handler.send(request)
               ^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/networking/_helper.py", line 208, in wrapper
    return func(self, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/networking/common.py", line 337, in send
    return self._send(request)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/bin/yt-dlp/yt_dlp/networking/_urllib.py", line 401, in _send
    raise HTTPError(UrllibResponseAdapter(e.fp), redirect_loop='redirect error' in str(e)) from e
yt_dlp.networking.exceptions.HTTPError: HTTP Error 403: Forbidden

Without ffmpeg you are most likely downloading format 18. This is a legacy format that isn't guarded by some of the restrictions of the rest of the formats (such as 303 and 251). You are getting 403'd with the non-legacy formats most likely because your account has been flagged for automated tool usage. See #10046


Arithmetic command of Sublime 3154 not styled properly

Using dev channel release 3154 which adds a new "Arithmetic" command to the command palette, the following happens (theme is Boxy Monokai):

Expected Behavior
The displayed result should fit in with the theme.
Current Behavior
The result value is in black on dark grey and overall looks unstyled.
Steps to Reproduce (for bugs)

Use Sublime dev channel release 3154
Open command palette and select arithmetic
Type an arithmetic expression

Your Environment

Boxy Theme: 5.2.0
Sublime Text: 3154
Platform: linux
Package Control: True
Dependencies:

mdpopups: 3.1.3
markdown: 2.6.9
pygments: 2.1a0
jinja2: 2.8

In general, the layout of the command palette is screwed after installing build 3154


Problem with 'https://github.com/vitusbenson/torch_advection.git'

I am attempting to install all the required packages, but I'm encountering an issue with the command pip3 install git+https://github.com/vitusbenson/torch_advection.git. It prompts me to enter a GitHub password.

Hey! Thanks for checking out our package! This is a mistake on my side, the torch_advection package is no longer necessary, you can just drop that requirement. I will update the readme when I am back in office.
Cheers
Vitus

#11  should fix this. Closing for now.


Add codecov reporting to travis

This is currently WIP. Depends on https://github.com/jhass/crystal-build-docker/pull/2. Doesn't currently work on OSX. Displays loads of errors to the build log.
This PR uses the kcov tool to provide coverage reports on crystal code. Example output here. I think there are bugs with the crystal debug line information, for example this empty line of documentation got 37 hits. I've seen similar impossible debug information when profiling using callgrind + kcachegrind so I suspect the issue is with crystal not kcov. I will shortly create an issue in the kcov repo reporting the ld errors in the build log.

This PR will likely help https://github.com/crystal-lang/crystal/issues/3801 once the coverage data is correct.

I like this, but would be better to decouple things a bit and use a Docker image to run kcov over a binary which is built on jhass docker image? I wouldn't expect changes in the Makefile to achieve this kind of reports.

@bcardiff running coverage reports is surely something someone does locally as well as on travis. kcov produces some great HTML reports so I see no reason not to include the functionality in the makefile. Besides, bin/ci would get ugly as it would have to build the all_spec binary using the makefile then run it seperately. On top of that the binary is dynamically linked so we'd need to install the correct library files into the new container. Overall I think this approach is the best.

Any progress on this? I've just rebased it on master since e811cf964dbb9887e12369c52247165c0e216aa4 broke it.

Do we want to proceed with this? This PR hasn't been touched in 2,5 years.
I tried building coverage report with kcov and it didn't show anything. Not sure if I did something wrong (but according to this PR there shouldn't be much to it) or if it just broke somewhere in between.
In any case, I figure we can close this because it would probably be easier to start anew.

I think with the debug location fixes in #8538 this PR will be viable again.
This is a good stress test, anyway.

We're actually doing pretty well!

@RX14 Wow, that's really nice!
I wonder if then we could get spec to include a way to generate a coverage. That would really be awesome.

I wonder if then we could get spec to include a way to generate a coverage. That would really be awesome.

That would be doable, though a generic --wrapper-program="kcov --include-path=src .build/coverage" would be my preference.
I'm not sure if we want to "bless" kcov, though i'm fine with it.

So, do we want to move forward with this PR? :+1:/:-1:?

For information, Travis CI is no longer used (#10078).
The coverage can still be added to GitHub Actions and Circle CI.

For information, Travis CI is no longer used (#10078).
The coverage can still be added to GitHub Actions and Circle CI.

Closing. PRs for adding code coverage to our current CI setup would be welcome.

Closing. PRs for adding code coverage to our current CI setup would be welcome.


Increase default AssetCacheSize and VersionCacheSize

Recommend setting AssetCacheSize and VersionCacheSize in /gevol/assets/.config/misc.xml to be set to reasonable values for modern systems so that we can get good better performance from GEE without hand tuning cache sizes.

Closed via PR #974


Add note for zsh users that recommends sourcing nvm before using it

Nvm can fail to install perfectly for zsh. Added a note for an easy workaround.

I think this might also be the case for bash? The install script should detect zsh and set up the zshrc entries for nvm, but that won't apply immediately to the shell you're running the install command from. So sourcing nvm.sh would be necessary at that time, but that should also be the same in bash.

It does finish the installation with telling the user to 'exec bash' or 'source ~/.nvm/nvm.sh'.
Hopefully that is all that's needed for bash users.


Package update: PreprocessMD.jl 2.0.0

Breaking changes were introduced in #103 and #116, so version has been updated from 1.0.0 to 2.0.0. Additionally, MLDemo() has been removed from the export list.

@JuliaRegistrator register


Invalid query build for null or empty value

NEST/Elasticsearch.Net version:
5.5.0, 6.0-alpha1
Elasticsearch version:
5.1.2
I need to filter query by field with empty string.
My code is:
searchRequest.Query = new BoolQuery { 	Should = new List<QueryContainer> 	{ 		new TermQuery() 		{ 			Field = "parentId", 			Value = "2" 		} 	}, 	Filter = new List<QueryContainer> 	{ 		new BoolQuery 		{ 			MustNot = new List<QueryContainer> 			{ 				new TermQuery 				{ 					Field = "accessoryProductImage", 					Value = "" 				} 			} 		} 	} };
So it is converted to {"query":{"bool":{"should":[{"term":{"parentId":{"value":"2"}}}]}}}
But if set value to MustNot for example
new TermQuery { 	Field = "accessoryProductImage", 	Value = "s" }
All are ok: {"query":{"bool":{"should":[{"term":{"parentId":{"value":"2"}}}],"filter":[{"bool":{"must_not":[{"term":{"accessoryProductImage":{"value":"d"}}}]}}]}}}
Bug is for all query (TermQuery, MutchQuery), where value or query (keyword) is null or empty. It's not only for filter.

This is a feature known as conditionless queries. You can use IsVerbatim = true to circumvent conditionless logic
searchRequest.Query = new BoolQuery
{
    Should = new List<QueryContainer>
    {
        new TermQuery()
        {
            Field = "parentId",
            Value = "2"
        }
    },
    Filter = new List<QueryContainer>
    {
        new BoolQuery
        {
            MustNot = new List<QueryContainer>
            {
                new TermQuery
                {
                    Field = "accessoryProductImage",
                    Value = "",
                    IsVerbatim = true // ensure this query is serialized, even though it's considered "conditionless"
                }
            }
        }
    }
};

Thank you.

No problem, thanks for raising @dimmasik 👍


fix: Use presets for cross compilation as they sometimes override C flags

Resolves #2004
Checklist:
Remove the checklist to signal you've completed it. Enable auto-merge if the PR is ready to merge.

[ ] If the pull request requires a cryptography review (e.g. cryptographic algorithm implementations) I have added the 'crypto' tag.
[ ] I have reviewed my diff in github, line by line and removed unexpected formatting changes, testing logs, or commented-out code.
[ ] Every change is related to the PR description.
[ ] I have linked this pull request to relevant issues (if any exist).

Blocking on folks who have an x86-64 mac testing it out

Closing as stale, reopen as needed.


tfa.optimizers.MovingAverage & tfa.optimizers.SWA future

Hi,
The average optimizer wrappers support only tf.keras.optimizers.legacy optimizers. Since TFA was deprecated, I doubt there will be not development work here to support the new APIs. Are there any plans to support average optimizers in https://github.com/keras-team/keras-core ? Is there any replacement compatible with newer Keras optimizers?

I suggest to open this ticket in Keras or Keras-core repo as feature request.


Error: Query has no results to return

Azure Data Studio Version:

Steps to Reproduce:

Download Azure Data Studio System Installer .zip (NOT THE USER INSTALLER)
On the computer I'm using I'm not Administrator but I have the Administrator credentials so: SHIFT + right click on the installer >Run as a different user > enter the Administrator user and password
Install a few plugin for metrics and performances

None of the dashboard is working and they are all saying Error: Query has no results to return. This happens with multiple plugins:

IDERA SQL DM Performance Insights:

but also Managed Instance Dashboard:

I believe the problem might rely in the non administrator user having installed the installer through the Administrator user/password.
I will make a few tests and keep you updated.

could you please try server report extension? the Idera extension is not working and we might need to remove it from the marketplace, the Managed Instance is for Azure Managed Instance, seems you are connecting to an on-prem SQL Server instance, server report extension will make more sense.

So strange, Server Report extension is working fine.
So:

IDERA SQL DM Performance Insights
Query Performance Insights
Managed Instance Dashboard

are all not working, and you should remove all of them?
That's a lot

IDERA extension will be removed because it is not properly maintained and stopped working.
Query Performance Insights: please read the extension's readme page, you need to some prep work before you can use it.

managed instance dashboard: this is for a special edition of SQL Server that Microsoft Azure offers. it should check the edition of the server and only show it for Managed Instance. Let me work with the extension author and have it fixed.
I am going to close this issue since nothing is wrong with the dashboard itself.

Alright, I also discovered that our Sysadmin removed the installation privilege for my user.
All good, thank you for your help