Adding embedding methods?

Hi, I am Jisung from YY's group.
I'd like to contribute to this project regarding some network embedding methods that we have been implemented or invented.
Maybe we can put the basic Node2vec, SemAxis, or even method that we have been working for ScienceGenome project!
Let me know what you think! @ajgates42

Sure, that would be great.  The article titles are all easily accessible through the pub_df property of a database.  I haven't yet integrated abstracts from the MAG.  Is that enough for you to start?

Sure, that would be great. The article titles are all easily accessible through the pub_df property of a database. I haven't yet integrated abstracts from the MAG. Is that enough for you to start?

Yeah, Node2vec is just using the network information, so abstracts are not needed!

OK, I dont yet have a small test database setup, so the example to start with is likely APS---its small enough that development is possible.  The interface there is nearing stability, I'll review it tonight.  I think the Getting Started APS should work, but let me know if there's a problem.
Happy to video chat if that would be helpful for you to plan out your implementation.
Thanks for your help!

Hey @ajgates42 , do you have any plan for implementing a collaboration network or citation network?
If not, I can implement it also

Explicit functions for both networks are on the to-do list, but I haven't yet had a chance.
You're welcome to tackle either!
I had planned for network specific functions to be in 'networks.py' and NLP specific functions to be in 'nlp.py'

Hey @ajgates42 , do you have any plan for implementing a collaboration network or citation network?
I need the network for embedding, and if not, I can implement it also.

I actually needed the co-authorship network for a project, so I went ahead and added a basic implementation.  Feel free to expand on it if you want temporal co-authorships or other functionality.

Hey, I just checked your code, found some problems.

Maybe, numpy version problem?
Which version of NumPy are you using??

no, I just missed an enumerate when I transcribed over from a previous version.  Thanks for catching it!

In my case, it works well with this code
{aid:i for i, aid in enumerate(np.sort(mydblp.author2pub_df['AuthorId'].unique()))}
np.sort does not return the index.

Another error, I think coo_matrix is not subscriptable, so using csr-matrix?

OK, that's what I get for developing without checking on an example.  Thanks for your patience!
I've updated everything and included an example (Co-authorship network around Mark Newman in DBLP).  Definitely let me know if still gives some problems!

Perfect!!

Quick question! @ajgates42
I am writing down the codes for embedding, but if we make it faster, I need a numba library.
Is it okay to include numba library to dependency?

For now, leave the numba import in a try except (for example, as in the nlp for sklearn)
If we decide its needed package wide (actually a great idea to speed up some of the metric applys) then we can move it to a required dependency.

I am done with Node2vec and SemAxis, and try to make some examples.
I made a collaboration network with the focus_author with 'Albert-Laszlo Barabasi', 'Mark E. J. Newman'.
And made some 2D projection figures and SemAxis with two researchers.
Does it make sense to you? @ajgates42, you also included in this network:)
Archive.zip

'test.html' is 2-D projection of the embedding with UMAP, and 'semaxis.html' is the result of SemAxis:)

I am done with Node2vec and SemAxis, and try to make some examples.
I made a collaboration network with the focus_author with 'Albert-Laszlo Barabasi', 'Mark E. J. Newman'.
And made some 2D projection figures and SemAxis with two researchers.
Does it make sense to you? @ajgates42, you also included in this network:)
Archive.zip

Cool!! I'm take a deep look later this week.  Thanks!

Any comment?

Hi @jisungyoon,
I just took a look at the attached Archive, and all that I could find were the two figures.  Can you start a new branch with the code?  Without context for what I'm looking at, its a bit difficult to give any feedback.  The UMAP finds nice clusters of collaborators, but is there a reason SemAxis is only projected onto one dimension?
Thanks!
Alex

Hi @jisungyoon,
I just took a look at the attached Archive, and all that I could find were the two figures. Can you start a new branch with the code?

Yeah, I made some codes on my forked repository, I will make a pull request.

Without context for what I'm looking at, its a bit difficult to give any feedback. The UMAP finds nice clusters of collaborators, but is there a reason SemAxis is only projected onto one dimension?

The original purpose of the Semaxis is projecting the entities into some specific axis.

It usually used in word space, to characterize word semantics using many semantic axes.
In those examples, I define axis from two-person (Newman as a negative anchor and Barabasi as a positive anchor). Then, we can interpret persons with negative values as more Newman friendly people, and the person with positive values as more Barabasi friendly people.
Semaxis is quite useful when we find the relevant axis, it works for embedding with scientific mobility data in my ongoing proejct, also works on paper of YY.  https://arxiv.org/abs/2001.08199

#2

Forgot to close the issue


Submit COBRApy 0.20.0

id: cobrapy
version: 0.20.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/24216c4dec1b4e120fd102844e2de59b9775b8fc/biosimulators.json
specificationsPatch:
version: 0.20.0
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 is available here.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

The specifications of your simulator is valid!

The specifications of your simulator is valid!

Summary of tests

Executed 34 test cases

Passed 24 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 10 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (11.3 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

cli.CliDisplaysVersionInformationInline (4.7 s)
Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.4 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

sedml.SimulatorProducesLinear2DPlots (2.7 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (2.7 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (2.7 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.7 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (2.8 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/io.py:905: NoCurvesWarning: Plot None does not contain any curves
  NoCurvesWarning)
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (2):
      plot_0: 1 curves
      plot_1: 0 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

Summary of tests

Executed 34 test cases

Passed 24 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 10 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (11.3 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

cli.CliDisplaysVersionInformationInline (4.7 s)
Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.4 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

sedml.SimulatorProducesLinear2DPlots (2.7 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (2.7 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (2.7 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.7 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (2.8 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/io.py:905: NoCurvesWarning: Plot None does not contain any curves
  NoCurvesWarning)
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (2):
      plot_0: 1 curves
      plot_1: 0 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

The image for your simulator is valid!

The image for your simulator is valid!

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

The specifications of your simulator is valid!

The specifications of your simulator is valid!

Summary of tests

Executed 34 test cases

Passed 24 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 10 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (11.1 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

cli.CliDisplaysVersionInformationInline (5.0 s)
Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

sedml.SimulatorProducesLinear2DPlots (3.0 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (3.0 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (3.2 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.9 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (3.0 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/io.py:905: NoCurvesWarning: Plot None does not contain any curves
  NoCurvesWarning)
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (2):
      plot_0: 1 curves
      plot_1: 0 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

The image for your simulator is valid!

Summary of tests

Executed 34 test cases

Passed 24 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 10 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (11.1 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

cli.CliDisplaysVersionInformationInline (5.0 s)
Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  COBRApy: 0.20.0, CLI: 0.1.0, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

sedml.SimulatorProducesLinear2DPlots (3.0 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (3.0 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (3.2 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.9 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (1):
      plot_0: 1 surfaces

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (3.0 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/io.py:905: NoCurvesWarning: Plot None does not contain any curves
  NoCurvesWarning)
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  simulation.sedml:
    Tasks (1):
      task
    Plots (2):
      plot_0: 1 curves
      plot_1: 0 curves

Executing SED-ML file 0: simulation.sedml
  Found 1 tasks
    task
  Executing task 1: task
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times
Warnings:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

The image for your simulator is valid!

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

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


e2e,compute: Add sig-compute-serial e2e target

What this PR does
Before this PR:
After this PR:

Fixes #
Why we need it and why it was done in this way
The following tradeoffs were made:
The following alternatives were considered:
Links to places where the discussion took place:
Special notes for your reviewer
/cc none

Checklist
This checklist is not enforcing, but it's a reminder of items that could be relevant to every PR.
Approvers are expected to review this list.

[ ] Design: A design document was considered and is present (link) or not required
[ ] PR: The PR description is expressive enough and will help future contributors
[ ] Code: Write code that humans can understand and Keep it simple
[ ] Refactor: You have left the code cleaner than you found it (Boy Scout Rule)
[ ] Upgrade: Impact of this change on upgrade flows was considered and addressed if required
[ ] Testing: New code requires new unit tests. New features and bug fixes require at least on e2e test
[ ] Documentation: A user-guide update was considered and is present (link) or not required. You want a user-guide update if it's a user facing feature / API change.
[ ] Community: Announcement to kubevirt-dev was considered

Release note

NONE

/test pull-kubevirt-e2e-k8s-1.29-sig-compute

/test pull-kubevirt-e2e-k8s-1.29-sig-compute

/test pull-kubevirt-e2e-k8s-1.29-sig-compute

/cc @dhiller @xpivarc

/hold cancel

/override pull-kubevirt-fossa
fossa is failing on the main branch with the same issue[1] - not related to this PR.
[1] https://prow.ci.kubevirt.io/view/gs/kubevirt-prow/logs/push-kubevirt-fossa/1785802418752065536


TAT-127 create shell for spa

Set up scaffolding for vue app

Forked vue boilerplate template for initial setup
Built the four main pages for the app
Added a nav bar

@mehaase removed a few things from Mike's suggestions
Also the mobile menu is coming in the next PR


Random tests

This PR introduces a suite of unit tests for the random_number_generation.py located within the within the create_array directory. The primary functions in this file facilitate the creation of random AFArray objects allowing for the use of various random engines.
Shape: Ensures that a random AFArray with the correct shape is produced.
Random Engine: Ensures that the AFArray is created with the correct random engine and that the methods can properly handle invalid engines passed in.

I broke PR with auto-rebase on github. Sorry, my bad. Will fix by myself


Prioritize new files

There's gotta be a way to see date created metadata and sort by that when selecting random files.

Can't figure out an algorithm that would make a noticeable difference. Going with better sound file organization.


[Question] Filters object

Scope
I would like to rebuild the filter section of a ListView using a function rather than a static configuration.
I also would like to be I have a few questions than may help me in my analysis
Description

Item 1
Dynamically writing the filters seems easy enough. The filters() method in Listview.js is expecting an array of Fields which a custom method could provide.

Would you see added value to have an utility method inside ng-admin, able to deserialize a JSON into a Field ?

If I write a directive which can access the entity object (similar to the Create button). From there I can get the listview list of defined filters, but

Will that filter object contains the current state of the filters, i.e. the selected filters and their current values, or only the initial configuration of the filters?

Thanks for the help :)

@fzaninotto, @jpetitcolas any hints if you have a minute ?
Specifically regarding the second above point, I can access the listview filters using a directive, but not the current values of the filters. How could we go easily about grabbing this without reinventing the wheel ?

FYI problem was solved by using the llCtrl.search in our directive. Using this binding we can easily dynamically retrieve the filters

Hi @Phocea , I have the same problem, could you tell me what did you do for this? thank you very much


feat: support stricter type checking behavior as a Resolver configura…

This PR

Adds ResolverConfiguration that can be set when creating a new JSON evaluator. Configuration can be used to set stricter flag variants type checking (a couple of flavors).

Follow-up Tasks

Changes to go-sdk-contrib flagd provider will be needed to take advantage of this new functionality
Adding flagd command line flags to enable this will be needed

Apologies, I posted this too quickly. Let me close this for now and start at discussion on this new issue - https://github.com/open-feature/flagd/issues/1481.


MOP-405 Fixes invisible button on PDF signature on Samsung Android 9 and mem access crash on iOS

Syncs changes made directly in mobile-native repo:
https://github.com/servicetitan/mobile-native/pull/115

Not applicable to the recent PDF plugin


Remove -X flag from perl defaults.

"-X Disables all warnings regardless of use warnings or $^W".  See
"perldoc perlrun" or http://perldoc.perl.org/perlrun.html
With the current defaults, warnings are squashed.  For example:
$ perl -X -Mwarnings -c -e'BEGIN { 42 + undef }'
-e syntax OK
$ perl -Mwarnings -c -e'BEGIN { 42 + undef }'
Use of uninitialized value in addition (+) at -e line 1.
-e syntax OK
So, it's not clear from the current defaults whether Ale wants to remove
warnings or enable them.  As it stands, it's trying to do both and the
disabling appears to win.
This commit enables warnings by default.
I'm not familiar with Vader, but if this needs some tests, I'm happy to dig in and try to figure that out.

Cheers! :beers:

Thank you. I started using Ale last week and it has really been a huge improvement for me.  Also, fast merge!  🚀

The speed of merging can depend on whether or not I'm looking at my inbox at the time, etc.


can not run the  latest code

Description of the problem:
After I pull the  latest code ,I can not run because Android studio is always refreshing. for this,I wait for serveral hours.
Which library version are you using? E.g. 3.5.0.

ok. gradle version problem .


AsyncTargetWrapper loses MDLC context when puts event to parallel thread

Type:

Bug

NLog version:

4.5.0 rc2

Platform:
Checked only on .Net 4.5
Current NLog config (xml or C#, if relevant)
<nlog>
  <targets>
    <default-wrapper xsi:type="AsyncWrapper" overflowAction="Block" />
    <target name="aiTarget" type="ApplicationInsightsTarget"/>
  </targets>
  <rules>
    <logger name="System.*"    maxlevel="Info" final="true" />
    <logger name="Microsoft.*" maxlevel="Info" final="true" />
    <logger name="*" minlevel="Trace" writeTo="aiTarget" />
  </rules>
</nlog>

In case of a BUG:
Context:
There is disposable scope which adds data into MDLC when it's created and removes these data from MDLC when disposing.  Let's name it "scoped data".
LogEvent "X" is generated by Logger.Info(...) which is called inside of scope.

What is the current result?
Output of aiTarget does not contain "scoped data" for event "X".
What is the expected result?
Output of aiTarget should contain "scoped data" for event "X".
Did you checked the Internal log?
No
Please post full exception details (message, stacktrace, inner exceptions)
There were no any exceptions
Are there any work arrounds? yes/no
Yes, I had to create class derived from AsyncWrapperTarget which takes "scoped data" and adds it to logEvent.Properies collection before LogEvent is passed to parallel thread.
Is there a version in which it did worked?
Don't know.
Can you help us by writing an unit test?
Probably.

Remember you need to access the MDLC-properties using a layout-renderer ex: ${mdlc:item=PropertyName} -
https://github.com/NLog/NLog/wiki/MDLC-Layout-Renderer
Or by creating a custom layout renderer, and extract the value from the MappedDiagnosticsLogicalContext:
https://github.com/NLog/NLog/wiki/How-to-write-a-custom-layout-renderer

Also if you are using Microsoft ApplicationInsightsTarget:
https://github.com/Microsoft/ApplicationInsights-dotnet-logging/tree/develop/src/NLogTarget
Then you will notice they are not supporting MDLC-properties. You will have to implement your own.
Ofcourse the correct solution would be that it supported any number of properties. I guess NLog should implement an extension to TargetWithLayout called TargetWithProperties (Allow easy implementation of IncludeAllProperties, MDC, MLC, etc.)

Let me add some additional details.
I use code pretty close to the following:https://github.com/NLog/NLog.Extensions.Logging/blob/master/src/NLog.Extensions.Logging/Logging/NLogLogger.cs.
This scope implemetation has MDLContext under the hood.
So described bug occurs in the following case.
Assume that there code fragment:
using(logger.BeginScope(new Dictionary(){ {"key1", "value1"}, {"key2", "value2"} })) { logger.Info("Entering the scope"); // pretend that here goes some useful code logger.Info("Leaving the scope"); }
So it's expected that two log event will contain properties "key1" and "key2" when log target "print" them some how. And if target is synchronious it work as expected.
But please look what happens if target is wrapped with wrapper which uses queue and parallel thread:
using(logger.BeginScope(new Dictionary(){ {"key1", "value1"}, {"key2", "value2"} })) { // here MDLC contains "key1" and "key2" properties logger.Info("Entering the scope"); // here event has been added to queue of parallel thread // pretend that here goes some useful code logger.Info("Leaving the scope"); // here event has been added to queue of parallel thread } // here MDLC does not contain "key1" and "key2" properties
So if async wrapped target "prints" log event after leaving of the scope then events will be "printed" without "key1" and "key2" properties.
Does this description work for you?

Does this description work for you?

Not sure what you are trying to explain, but yes BeginScope can inject properties into MDLC, and when disposed then they are removed again.
Seems you didn't understand my first post. Please read it again, and explain what parts you don't understand about how you use the layout-renderer  in the output-target.

Seems you didn't understand bug description.
I do not have any questions about mdlc-layout-renderer in output target.
Moreover mdlc-layout-renderer is useless in the context of this bug.
Because it's impossible to configure output target with mdlc-layout-renderer since it's totally unpredictable which properties would be added inside of scope of BeginScope.
There are not question about ApplicationInsightsTarget.  It's exptected.
Please note that this bug description is about following points:

If ApplicationInsightsTarget (or Seq or other)  is used then context data of a scope is printed by target to output. So all work fine.
If working target is wrapper with AsyncWrapperTarget that underlying target does not print context data of a scope ever. Because when an event is printing a scope already is disposed and context data has been lost. Which is not exptected behavior of async wrapper.  Async wapper was supposed only to add asynchronicity but not losing of data.

There are not question about ApplicationInsightsTarget. It's pretty trivial and expected that target knows nothing about MDLC

That is the problem. NLog expects that the targets knows about MDLC, and knows how to capture the it also in async-mode. Special logic has to be implemented in all targets that wants to support MDLC-properties.
Believe that the NLogViewerTarget is the only target in the world that correctly support MDLC. For all other targets then the only option is to support usage of JsonLayout.
I'm not saying that this is super optimal. And I would prefer it was a lot easier to write NLog-targets that supported MDLC out of the box.
I'm still trying to wrap my brain around how the ApplicationInsightsTarget (or Seq) is able to capture MDLC-properties (coming from BeginScope), since they don't inspect MDLC-properties. So I cannot understand how you make BeginScope work when not using AsyncTargetWrapper.

how the ApplicationInsightsTarget (or Seq) is able to capture MDLC-properties
They didn't. The fastest workaround was found is to do something like that:

 private void AppendWithMdlcProperties(LogEventInfo logEvent)
        {
            foreach (var rawKey in MappedDiagnosticsLogicalContext.GetNames())
            {
                var key = GetPropertyBagKey(rawKey);
                var value = MappedDiagnosticsLogicalContext.Get(rawKey);
                if (!logEvent.Properties.ContainsKey(key))
                {
                    logEvent.Properties.Add(key, value);
                }
                else
                {
                    logEvent.Properties[key] = $"{logEvent.Properties[key]},{value}";
                }
            }
        }

And put it at the appropriate place to class derived from ApplicationInsightsTarget.
But in this case another issue occurs. How to do not append twice if there are two CustomApplicationInsightsTarget appears in the configuration.

They didn't. The fastest workaround was found is to do something like that:

Yes that explains it. You have met the pitfall of how NLog handles MDLC (or MDC, NDC, NDLC), that right now is rather cumbersome for custom targets. You need to signal to NLog that it should capture the async-data before doing the async-logging.
Normally this done by having a NLog-Layout on the Target that signals to NLog that it wants to render the async-data to a string-value before doing the async-logging.
I can see your case is a little different, since you just want to inject the async-data directly into the LogEventInfo-properties. I guess this will work fine if everyone can promise that the async-data-objects injected into BeginScope are immutable.
The problem is that modifying the NLog LogEventInfo any other place than in the logger itself will cause race-conditions. The same LogEventInfo object is forwarded to all relevant targets, and the unwritten contract is that no target should modify the LogEventInfo.
Your case could probably be handled by having the Logger-object itself to perform the capture of async-data, before broadcasting it to the destination targets.

The only workaround right now, when using NLog targets that doesn't support MDLC is to use the example Log<TState> Simple
https://github.com/NLog/NLog.Extensions.Logging/wiki/NLog-properties-with-Microsoft-Extension-Logging
Where you implement a helper method that injects the async-data into TState.

@datsis Have created an issue about improving the handling of MDLC-properties; #2466 (Maybe you have comments to the suggested solutions, or maybe have some yourself)

@datsis Made an attempt to make it easier to capture MDLC-properties when in async-mode. See #2467
The target just have to inherit from the new TargetWithContext, and then it will automatically have the ability to capture MDLC-properties, so they also work in async-mode.
Just have to call GetContextMdlc in the override of Write(LogEventInfo), instead of directly accessing the MDLC-container. You can see the very simple unit test how to use it.


need change tun device path when run  in termux

change/dev/net/tun to /dev/tun in tun_linux.go

Can you provide some more detail on why/how/what/where/when? We can't just change the path for tun_linux.go without affecting linux on everything that isn't termux.

sorry,I want to install nebula to my andriod plone, so i use termux ,
but i found the tun file path is not /dev/net/tun,this file path is /dev/tun,so i suggest  set a option in config.yml,if set use tun file path in config, use new tun file path, otherwise use default tun file path[/dev/net/tun]
this is my termux
# uname -a
Linux localhost 4.9.65-perf-g30ff678 #1 SMP PREEMPT Fri Oct 26 13:10:48 CST 2018 armv8l Android
# ls /dev/tun
/dev/tun
# ls /dev/net/tun
ls: cannot access '/dev/net/tun': No such file or directory

this is release v1.0
# ./nebula -version
Version: 1.0.0
# ./nebula -config config.yml
DEBU[0000] Trusted CA fingerprints                       fingerprints="[8fdddc001a0e6c8266707cb8df604ac93938eafbbd0d763983b47c0ba4cb493f]"
DEBU[0000] Client nebula certificate                     cert="NebulaCertificate {\n\tDetails {\n\t\tName: node_13\n\t\tIps: [\n\t\t\t<IP_ADDRESS>/24\n\t\t]\n\t\tSubnets: []\n\t\tGroups: []\n\t\tNot before: 2019-12-25 05:59:38 +0000 UTC\n\t\tNot After: 2020-12-19 10:11:44 +0000 UTC\n\t\tIs CA: false\n\t\tIssuer: 8fdddc001a0e6c8266707cb8df604ac93938eafbbd0d763983b47c0ba4cb493f\n\t\tPublic key: 47cba31fa2ff45dd9578b348ccc8580459159b3f832a386c22cb414041734b25\n\t}\n\tFingerprint: 69633d5badab2961dc6eb90ec6222a720b862a8b693bff5b3cdbc8063b4059d4\n\tSignature: 3a3ae8bfe48de52bcc8767b54701036e3a1231621e246945f7a744919f34c43fc2c8f5ded1f343f1ff3ff389c304a096c2676c80320dfaab5a35d63f76507e03\n}"
INFO[0000] Firewall rule added                           firewallRule="map[caName: caSha: direction:outgoing endPort:0 groups:[] host:any ip:<nil> proto:0 startPort:0]"
INFO[0000] Firewall rule added                           firewallRule="map[caName: caSha: direction:incoming endPort:0 groups:[] host:any ip:<nil> proto:1 startPort:0]"
INFO[0000] Firewall rule added                           firewallRule="map[caName: caSha: direction:incoming endPort:0 groups:[] host: ip:<IP_ADDRESS>/24 proto:0 startPort:0]"
INFO[0000] Firewall started                              firewallHash=eff5e716a65160ae2587067ad06a35ab4cdd9ac9b29fd6011ff375842d2f6635
FATA[0000] no such file or directory

after i change source code tun file path to /dev/tun ,it works
i suggest could custom the tun file in config

@labulaka521 fwiw, i ported nebula to android a couple of weeks ago and just doing some initial testing before releasing it to the entire app store.
Feel free to join the slack group nebulaoss.slack.com and I can add you to the alpha test if you'd like.
In the meantime, closing this issue. If you still have a need for nebua in termux once nebula for android is available, let me know and I'll reopen.

i can not join it ,because this group need invitate

Hello, I'm also interested in Android app.
Just did as @labulaka521 and this requires a rooted Android device, which is something not everyone is going to do.
@rawdigits: does your port require a rooted device, and in case would be possible to call Android VPN API to setup the TUN device without root?
Many thanks in advance.

This android build would be something you get from the Play store so no rooting required.

抱歉，我想将nebula安装到我的andriod plone上，所以我使用termux， 但是我发现tun文件路径不是/dev/net/tun，这个文件路径是 /dev/tun，所以我建议在config.yml中设置一个选项，如果设置使用tun文件路径配置，使用新的 tun 文件路径，否则使用默认的 tun 文件路径[/dev/net/tun] 这是我的 termux
# uname -a
Linux localhost 4.9.65-perf-g30ff678 #1 SMP PREEMPT Fri Oct 26 13:10:48 CST 2018 armv8l Android
# ls /dev/tun
/dev/tun
# ls /dev/net/tun
ls: cannot access '/dev/net/tun': No such file or directory

这是 v1.0 版本
# ./nebula -version
Version: 1.0.0
# ./nebula -config config.yml
DEBU[0000] Trusted CA fingerprints                       fingerprints="[8fdddc001a0e6c8266707cb8df604ac93938eafbbd0d763983b47c0ba4cb493f]"
DEBU[0000] Client nebula certificate                     cert="NebulaCertificate {\n\tDetails {\n\t\tName: node_13\n\t\tIps: [\n\t\t\t<IP_ADDRESS>/24\n\t\t]\n\t\tSubnets: []\n\t\tGroups: []\n\t\tNot before: 2019-12-25 05:59:38 +0000 UTC\n\t\tNot After: 2020-12-19 10:11:44 +0000 UTC\n\t\tIs CA: false\n\t\tIssuer: 8fdddc001a0e6c8266707cb8df604ac93938eafbbd0d763983b47c0ba4cb493f\n\t\tPublic key: 47cba31fa2ff45dd9578b348ccc8580459159b3f832a386c22cb414041734b25\n\t}\n\tFingerprint: 69633d5badab2961dc6eb90ec6222a720b862a8b693bff5b3cdbc8063b4059d4\n\tSignature: 3a3ae8bfe48de52bcc8767b54701036e3a1231621e246945f7a744919f34c43fc2c8f5ded1f343f1ff3ff389c304a096c2676c80320dfaab5a35d63f76507e03\n}"
INFO[0000] Firewall rule added                           firewallRule="map[caName: caSha: direction:outgoing endPort:0 groups:[] host:any ip:<nil> proto:0 startPort:0]"
INFO[0000] Firewall rule added                           firewallRule="map[caName: caSha: direction:incoming endPort:0 groups:[] host:any ip:<nil> proto:1 startPort:0]"
INFO[0000] Firewall rule added                           firewallRule="map[caName: caSha: direction:incoming endPort:0 groups:[] host: ip:<IP_ADDRESS>/24 proto:0 startPort:0]"
INFO[0000] Firewall started                              firewallHash=eff5e716a65160ae2587067ad06a35ab4cdd9ac9b29fd6011ff375842d2f6635
FATA[0000] no such file or directory

在我将源代码 tun 文件路径更改为之后/dev/tun，它可以工作， 我建议可以在配置中自定义 tun 文件

Why the proposal to specify or use the default tun path is not accepted, can I understand the specific reason?
@rawdigits


FlatButton has no debugFillProperties

Widget widget = new FlatButton(
          onPressed: (){},
          child: new Text('你好')
);
print(widget);

In console only print FlatButton，i want detailed widget information ,like this FlatButton(           onPressed: (){},            child: new Text('你好') )

This just needs a debugFillProperties method to be implemented on FlatButton.

@lishuhao To answer your question, for most objects in our framrwork just printing the object (e.g. a widget or BuildContext) should do what you want. You can often also do print('${object.toStringDeep()}'); to get the whole subtree. For FlatButton we happen to have forgotten to implement the code that gives you specific details.

@Hixie That solved my problem. Thank you very much!!

This looks to be fixed, can this issue be closed?

Yup!


Automatically get the rust version from the kani toolchain.toml

Right now, that's hardcoded in. Instead we should parse it from the toml

Doesn't Kani install the right rust toolchain version as part of its setup?


NDK_ROOT is undefined

I am using the DroneCodeSDK . But when I try to build for the android , I hit this command  sudo make android instal but I get this error
Makefile:152: *** NDK_ROOT is undefined, please point the environment variable to android-ndk root..  Stop.
Although I have set the NDK_ROOT in .bashrc. Also i have set NDK_ROOT from command prompt . I am using Ubuntu. I am not able to build the code for android. Please suggest how to get rid of this error.

@canopusTest is the env variable NDK_ROOT defined correctly?
Before doing make, try: echo $NDK_ROOT and check if the path is correct by doing ls $NDK_ROOT.
To manually set it to try out, do:
export $NDK_ROOT=/path/to/ndk/root

Yes , It is set to correct path and previous error are now fixed. But still I am getting some error while hitting the command "sudo make android install". This is the error " nstall configuration: "Debug"
-- Installing: /usr/local/lib/android/x86/libdronecode_sdk.so
CMake Error at core/cmake_install.cmake:36 (file):
file INSTALL cannot copy file
"/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/core/libdronecode_sdk.so"
to "/usr/local/lib/android/x86/libdronecode_sdk.so".
Call Stack (most recent call first):
cmake_install.cmake:38 (include)".
Please help me out to get the code compiled.

There are two things happening:-
Case 1). When I run command as "sudo make android install". Then I get the NDK_ROOT error.
I have set the paths as below
export NDK_ROOT=/home/akash/Android/Sdk/ndk-bundle
export ANDROID_TOOLCHAIN_CMAKE=/home/akash/Android/Sdk/ndk-bundle/build/cmake/android.toolchain.cmake
export ANDROID_CMAKE_BIN=/home/akash/Android/Sdk/cmake/3.6.4111459/bin/cmake
I have ensured that the paths are set correctly by running echo$NDK_ROOT I have echo all three paths and yet they are pointing to correct location. But still I am getting the error "Makefile:152: *** NDK_ROOT is undefined, please point the environment variable to android-ndk root.. Stop."
Case 2). When I run the command without sudo as "make android install" then I get the following error
" file INSTALL cannot copy file
"/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/core/libdronecode_sdk.so"
to "/usr/local/lib/android/x86/libdronecode_sdk.so".
Call Stack (most recent call first):
cmake_install.cmake:38 (include)
Makefile:93: recipe for target 'install' failed
make[1]: *** [install] Error 1
Makefile:86: recipe for target 'android_x86' failed
make: *** [android_x86] Error 2"
Please help me out to get this compiled.

@canopusTest aha!
So it looks like you need to specify env variables to pass them on to sudo:
https://stackoverflow.com/questions/8633461/how-to-keep-environment-variables-when-using-sudo
However, you don't need to install the Android artifacts into /usr/local of your system assuming you are not compiling this on an Android system. Best is to install them somewhere where you don't need sudo.
My scripts look like this but I have not verified if they still work in a while:
make INSTALL_PREFIX=$(pwd)/install BUILD_TYPE=$build_type android install
cp -r DroneCore/core/third_party/curl-android-ios/prebuilt-with-ssl/android/* install/lib/android/
cp -r DroneCore/core/third_party/curl-android-ios/curl/COPYING install/CURL_COPYING
mkdir -p install/include/curl
cp install/lib/android/include/curl/* install/include/curl/
rm -rf install/lib/android/include/

Thanks @julianoes  for the help so far. I would like to clearify that I am compiling the code on Ubuntu 16.04. I am following the instructions to build from here "https://sdk.dronecode.org/en/contributing/build.html" . I am compiling the code for an android app. When I use the command " make android install". I get the error Case 2). in above comment. I have checked the script and it looks like below:-
Install script for directory: /home/akash/Desktop/DroneCodeRetry/DronecodeSDK
Install shared libraries without execute permission?
if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
set(CMAKE_INSTALL_SO_NO_EXE "1")
endif()
if("${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/android/x86" TYPE SHARED_LIBRARY FILES "/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/core/libdronecode_sdk.so")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/android/x86/libdronecode_sdk.so" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/android/x86/libdronecode_sdk.so")
if(CMAKE_INSTALL_DO_STRIP)
execute_process(COMMAND "/home/akash/Android/Sdk/ndk-bundle/toolchains/x86-4.9/prebuilt/linux-x86_64/bin/i686-linux-android-strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/android/x86/libdronecode_sdk.so")
endif()
endif()
endif()
if("${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/dronecode_sdk" TYPE FILE FILES
"/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/core/connection_result.h"
"/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/core/system.h"
"/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/core/dronecode_sdk.h"
"/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/core/plugin_base.h"
)
endif()

This is where the code fails the compilation. This script is under the class "cmake_install.cmake" . I am not sure what is wrong in the script. Please let me know the compiling steps and building this code for android.
Thanks

Hm, two things:

Please put code and console output inside ``` here on github, that makes it easier to read.
You need to do make clean before you change the install directory, so:make clean # or maybe sudo make clean
make INSTALL_PREFIX=$(pwd)/install android install

I run the commands you mentioned, Below is the console output:-
  file INSTALL cannot find
  "/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/plugins/mission/third_party/json11/libjson11.so".```.

The cmake code from line 47 is as below:-

```if("${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
        file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/android/x86" TYPE FILE FILES "/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/plugins/mission/third_party/json11/libjson11.so")
        endif()

        if(NOT CMAKE_INSTALL_LOCAL_ONLY)
        # Include the install script for each subdirectory.
        include("/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/plugins/mission/third_party/json11/cmake_install.cmake")

        endif()```

Thanks.

Nice, I just ran into this as well. Pushing a fix in a second.

Please try #456.

Yes , I tried after a pull and now this is the newly introduced error from console output:-
CMake Error at plugins/mission/cmake_install.cmake:47 (file):
  file INSTALL cannot find
  "/home/akash/Desktop/DroneCodeRetry/DronecodeSDK/build/android_x86/plugins/mission/third_party/json11/libjson11.so".
Call Stack (most recent call first):
  plugins/cmake_install.cmake:39 (include)
  cmake_install.cmake:39 (include)

The fix is not merged yet. Please try the branch.

I do make the changes in the  plugins/mission/CMakeLists.txt file and then I run the below commands:-
make clean # or maybe sudo make clean
make INSTALL_PREFIX=$(pwd)/install android install
and it run all fine without any error on the terminal.
Please let me know to run the android sample app within the DroneCodeSDK , how can I import the code into Android Studio?

Thanks.

@julianoes Can you please check in, I will get back to you.

@julianoes Do you have any update for the same.

Not yet, sorry.

Okay , Can you please let me know if this issue is only for Android build or this issue exists fir iOS build too. ?

We are currently working on iOS, so that's closer to be usable.

Okay , How long will it take to get the iOS build ready ?

I'm hoping only about 2 weeks.

I this case I suggest you use the C++ API and wrap it yourself manually for now.

Is that the only left option ? This will take even more time.

You can try the Dronecode SDK in Swift using Cocoapods, see https://github.com/Dronecode/DronecodeSDK-Swift


Migrate kaybee importer #1011

Closing this PR for now, will re-open once models are open for storing commits


✨(react) add a mono DatePicker component

Mono Date Picker :

[X]  Clearable
[X]  Form data input
[X]  Min/Max range
[X]  Popover menu
[X]  Controlled
[X]  Non controlled
[X]  Month/Year dropdown menus
[X]  Native date / String value
[X]   States
[X]  Disabled
[x] Testing
[X] Tokens
[x]  Doc
[ ]  Changeset
[ ]  Time granularity
[ ]  Time dropdown menu

In a Nutshell
This is the first acceptable version of this component. I have asked few questions on the component's UX. They concern minor parts of its interactions. I am waiting for responses from the designer. Most of my questions are nit-picking.
Notes on React-Aria
Please note that react-aria provide several headless ui components that might be interesting to use. In example, they also have a select headless ui component. For now, I have used downshift to manage the logic of both dropdowns (Month and Year). Some parts could be refactored to be shared with the select component. We could also debate refactoring the select component to stick to components provides by react-aria.
React-aria props triggers warning as they pass non-native props to our button component (onPress and isDisabled). It's not directly related to this PR, but they provide a headless ui component that wraps a button. They explain in an articles' series why they propose such logic, to make sure they handle nicely all click/press events in an accessible way. Read more here
Using our wrapper button component, I could not use properly their popover headless ui component. Their popover detects clicks on the ref button element that has opened it, and block its onPress event. Thus, clicking on the ref button, which is outside the popover, closes the popover. In my case, clicking on the ref button that is not detected by their popover trigger twice the toggle function, and then close and reopen the popover. I have preferred to use a custom hook, that detect clicks outside the calendar menu.

👏 Special thanks to @NathanVss who has been a great mentor. He helped me opening this first PR on the DS. Hope to collaborate soon on more elements of the DS.

@jbpenrath @NathanVss by default, the component convert props date values to the local timezone of the user. Would you prefer the date picker converting it to a default common timezone, and make this timezone a props?

Few improvement ideas :

Remove reset button when input with value is disabled.

When user opens the "Year" dropdown, the scroll should positionned on the selected year.

I wonder if the calendar should be opened as soon as user clicks on the input.


Need to add watermarking for review copies

From James and Steve @ SIAM:
Regarding the “For review purposes only” issue with the review class of the macro, Steve here at SIAM mentioned that you can change the copyright notice and the footer at the very bottom of each page by adding:
\renewcommand{\footercopyright}{For review purposes only.}
<EMAIL_ADDRESS>Published by SIAM under the terms}
\copyrightlinetwo{of the Creative Commons 4.0 license}
to the preamble. This is set up in the definitions of \ps@plain and \ps@myheadings, which use the command \f@@terwithc@pyright (and a few related commands) that he defined a little above those. So if you are trying to set that up, that’s where to start looking.

Duplicate. Resolved. Didn't add watermarking but instead a note at the bottom of the page.


Add bypassFingerprinting option; useful when only prepending is needed

I believe this is possible from #52

@rickharrison It is not.
There is nothing I can do in customHash to make that - not appear in my file names.

You need to set it to null. We even have a test verifying this behavior.

You're right. Thanks for the clarification.

We probably need better documentation around this. Any help with adding docs via a PR would be greatly appreciated :)


fixes #203 enable configuration from dbt_project.yml

fixes #203 add support for selectors defined in dbt_project.yml

Hi @jlaneve, I've opened up a new PR rather than trying to work through a rebase #253
I'll close this one down now.


Add 2bp wiggle room to ivar primer trimming for tailedseq protocol

Issue: The tailedseq protocol results in some primer offset that was observed by scientists at CZB developing the protocol. This resulted in failure to trim all expected primers for samples processed using this "wet lab protocol".
Solution: This PR leverages the ivar trim primer offset parameter (-x) to allow for 2bp wiggle room associated with primer trimming for the tailedseq protocol (dependent on the input .bed file). Using 2bp wiggle room appeared to resolve the issues while limiting the impact on coverage.
Testing/verification: The trimming allowance was tested on real data for initial validation, run by the CZB scientists for verification, and an associated unit test was added.

@kislyuk I was able to rebase and the lint errors are resolved and the tests all pass now! (however, it looks like I changed way more files than I did for this PR).


mlvision text recognizer not working in some devices

when i run the code im getting the following error:
[ERROR:flutter/lib/ui/ui_dart_state.cc(157)] Unhandled Exception: PlatformException(textRecognizerError, Waiting for the text recognition model to be downloaded. Please wait., null)

Hi @PranayRaj2801,
Please provide flutter doctor -v, and a minimal complete reproducible code sample and the steps that shows the issue. Also mention the devices on which you tried.
Thanks.

Hi @PranayRaj2801,
Please provide flutter doctor -v, and a minimal complete reproducible code sample and the steps that shows the issue. Also mention the devices on which you tried.
Thanks.

[√] Flutter (Channel stable, v1.17.5, on Microsoft Windows [Version 10.0.18363.959], locale en-IN)
• Flutter version 1.17.5 at C:\src\flutter_windows_v1.12.13+hotfix.8-stable\flutter
• Framework revision 8af6b2f038 (3 weeks ago), 2020-06-30 12:53:55 -0700
• Engine revision ee76268252
• Dart version 2.8.4
[√] Android toolchain - develop for Android devices (Android SDK version 29.0.3)
• Android SDK at C:\Users\iail_\AppData\Local\Android\Sdk
• Platform android-29, build-tools 29.0.3
• ANDROID_HOME = C:\Users\iail_\AppData\Local\Android\Sdk
• ANDROID_SDK_ROOT = C:\Users\iail_\AppData\Local\Android\Sdk
• Java binary at: C:\Program Files\Android\Android Studio\jre\bin\java
• Java version OpenJDK Runtime Environment (build 1.8.0_212-release-1586-b04)
• All Android licenses accepted.
[√] Android Studio (version 3.6)
• Android Studio at C:\Program Files\Android\Android Studio
• Flutter plugin version 44.0.2
• Dart plugin version 192.7761
• Java version OpenJDK Runtime Environment (build 1.8.0_212-release-1586-b04)
[!] VS Code (version 1.44.1)
• VS Code at C:\Users\iail_\AppData\Local\Programs\Microsoft VS Code
X Flutter extension not installed; install from
https://marketplace.visualstudio.com/items?itemName=Dart-Code.flutter
[!] Connected device
! No devices available
! Doctor found issues in 2 categories.
edge_detection: 1.0.4
image_picker: 0.6.5+2
carousel_slider: 2.0.0
firebase_storage: 3.1.5
http: 0.12.0+4
firebase_ml_vision: 0.9.4
i tried on samsung M40(my device) and nexus 6 API28(emulator)

Hi @PranayRaj2801,
Will also need a minimal complete reproducible code sample that shows the issue you are facing.
Thanks.


Improve consistency in DB code amongst auth entities

User Story
As a Developer, I will use this work when I want to understand how we filter projects.
Audited where project filtering is handled on each auth entity:

Reviewing the above I came up with this set of choices as to how to make the above more consistent and thereby make our code easier to maintain.

Consensus seemed to be that (a) is most desirable, which entails the following work.
Definition of Done
Stage 1 – most consistency gains
Roles: Replace checkIfRoleIntersectsProjectsFilter with inline calls to projects_match. The code includes a check to call processError which will generate a 404 appropriately if project is filtered out.
Policies: For Delete and Update remove calls to p.queryPolicy and add inline calls to projects_match.
Stage 2 – fine-tuning: have everyone use RowsAffected instead of relying on processError:
This entails adding a check for RowsAffected after the DB for get/update/delete for each entity (role/policy/project/team/token), hence a total of 15 sites. Note that projects and tokens partially use RowsAffected already. The goal is to do this for all 15 occurrences.

I've got ideas for making this neater that are different from stage 1 and stage 2. Will outline before this comes up.

this work has been deprioritized, so closing.


remove absolute import paths entirely

These do not seem to work in Windows.

This is done and will be included in the next Release update. Closing.


A small flaw regarding the deployments table.

A default mechanism for train deployment is best_score, but why is the strategy field in the deployments table a fixed value most_recent? If it is to record the strategy during deployment, then it is best to be a variable. If it is to query during deployment, then it It seems like another redundant field. Maybe I don’t understand this table well enough. If possible, I’d like to ask you for advice!
`select pgml.train(
project_name => 'Diabetes Regression',
task => 'regression',
relation_name => 'pgml.diabetes',
y_column_name  => 'target',
algorithm=> 'linear'
);
select * from pgml.deployments
results :
id | project_id | model_id |  strategy   |         created_at
----+------------+----------+-------------+----------------------------
3 |          2 |        4 | most_recent | 2024-01-03 10:52:12.474621
5 |          2 |        7 | most_recent | 2024-01-03 10:55:03.908885
4 |          2 |        5 | most_recent | 2024-01-03 10:54:20.831898
2 |          2 |        2 | most_recent | 2024-01-03 10:47:02.574409
1 |          1 |        1 | most_recent | 2024-01-03 10:29:18.626135
`
Thank you for your continuous explanations these days. If I find new problems, I may need to trouble you. Thank you more.

This is a bug in https://github.com/postgresml/postgresml/blob/master/pgml-extension/src/orm/project.rs#L99
We should make this function take a parameter with the correct strategy to record in the database. }
To address question 4 in #1259 we should also expose this function to deploy by model.id in the api with a new "manual" strategy.

fixed with #1265

fixed with #1265

Wow, you are so quick at fixing bugs. It’s faster than I can find bugs. You are really awesome！


Show only titles on Non XML ERC875 asset cards

When an ERC875 token does not have an XML file, only show the title and blank out the other fields and icons which would normally have n/a
should be like below

Fixed in the PR - approve button pending @colourful-land @James-Sangalli


link for running cats not working

Challenge Make Images Mobile Responsive has an issue.
User Agent is: Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/49.0.2623.87 Safari/537.36.
Please describe how to reproduce this issue, and include links to screenshots if possible.
My code:
<link href="http://fonts.googleapis.com/css?family=Lobster" rel="stylesheet" type="text/css">

CatPhotoApp

Click here for cat photos.

Things cats love:

cat nip

laser pointers

lasagna

Top 3 things cats hate:

flea treatment

thunder

other cats

  <form action="/submit-cat-photo">
    <input type="radio" name="indoor-outdoor"> Indoor
    <input type="radio" name="indoor-outdoor"> Outdoor
    <input type="checkbox" name="personality"> Loving
    <input type="checkbox" name="personality"> Lazy
    <input type="checkbox" name="personality"> Crazy
    <input type="text" placeholder="cat photo URL" required>
    <button type="submit">Submit</button>
  </form>

Please check your spelling in your code. If you still need help, head over to the Help Room. Closing as not an issue with the site. Happy coding!

I copy the link straight from the site.

my case has not been resolved.  and the link provided is incorrect.

The issue is with the link that was provided to complete the assignment.  I've not able to move on because link is not being recognize, by going through the help portion of the site and it seems that others were having the same issues with the link provided.

@tspence33 There doesn't seem to be anything wrong with the link: http://bit.ly/fcc-running-cats
src is spelled incorrectly in your new img element.


Add support for CMake projects

Triggers extension when a compile_commands.json exists at root of workspace. Because there is no package.swift in the folder most of the extension will do nothing, but it will start the LSP server so code completion will be available.
Also look for CMake projects in the subfolders of workspaces.

See https://forums.swift.org/t/vs-code-swift-extension-and-cmake/62086


[Media Common] Bump up version to 21.2.3

Auto version bump up

@onabiull could you merge this PR then promote it?


Convert maternity-paternity-calculator to use ERB templates for questions

Looks good to me.

I've rebased on master and force pushed in preparation for merging.


[BUG] Bullet dissasembling

Version: [: mw3.0_sqr-0.7.21 BETA_mc1.12.2]
Describe the bug
When I craft bullets in the ammo press, for example: when I use one copper and one gunpowder to craft six bullets and I dissasemble it, I get six copper and six gunpowder, so it is basically a duplication bug.
To Reproduce
Steps to reproduce the behavior:
Craft bullets and dissasemble it and you get more materials than you used to make it.
Expected behavior
to not duplicate
Screenshots / Videos
N/A
Additional context
https://discord.com/channels/431403377977720862/1077574228326486046

In addition, the workbench recipe can use less materials to synthesize weapons and ammunition.
Convenient commands:
/recipe give @a *

Please use 0.1-Dev-5 and try again.
If the issue persist, please report the issue here


Usefulness of functions

There are some functions I wonder if they're useful or if they're in the right place.
This function isn't used anywhere:
https://github.com/freshworkstudio/transbank-web-services/blob/33d9da4c6014b7d12e92d45b7877b471f9b0156f/src/TransbankService.php#L9
And this one:
https://github.com/freshworkstudio/transbank-web-services/blob/33d9da4c6014b7d12e92d45b7877b471f9b0156f/src/WebpayWebService.php#L79
Is for PatPass only, Shouldn't this be in PatPass class?

Is far a I can remember, the first one is used to change the logger interface used on the implementation. We package provides one Logging implementation, but you can change it using that method.
The second one probably should need some refactor.


Duplicate projects in project list (admin) and ordering rules

There are duplicate projects in the list as shown offline.
Could we also order the projects alphabetically, from A to Z? (preferred), or have a toggle to order by oldest/newest?

At the moment delta doesn’t support sorting alphabetically by label. It can be achieved, but it has to be implemented on the backend side.


Ieee802154 switch to new net pkt API

Instead of using net_pkt_write in fragmentation, appending the frag to the packet is way more efficient (no allocation, de-allocation).

Codecov Report

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The diff coverage is n/a.

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=======================================
  Files         322      322
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  Branches    10768    10768
=======================================
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  Misses      17246    17246
  Partials     4905     4905

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indeed

@rlubos thing is now it does not copy anything (error message should be updated), so it can't be a memory allocation issue. But there is something fishy with comparing offset net_pkt_gen_len() now (see ieee802154_fragment.c:append_frag()

Got something. It was a tiny bit more complex than I thought due to the 6lo compressed header. It is not possible to compute the real packet size without decompressing it, but since decompressing for real would be killing the logic I tried to get, I added a 6lo function that makes a dry run of decompression, returning only the header size difference. It is a bit ugly to have this if (!dry_run) everywhere now, but that was the simplest way to achieve what I wanted. Code is also a bit more complex in fragmentation part, but it is in fact simple: it appends all fragments to pkt, the only specific one being the very first fragment (identified as such, that is) which takes the very first place in the list. Once all seems received (size fits the target size), reconstructing is done by reordering the fragments according to there offset. I added an  idea in the commit message how it could be optimized (i.e. running the dry run decompression the least possible).
@rlubos let me know if that works for you.


Extracting regional road network (Bay Area) using OSMnx

I tried using 'ox.graph_from_bbox' to get the drive network for the Bay Area but it took over 12 hours and still did not finish.
I'm running it on my mac, Python 3.6.4
appnope                   0.1.0
ca-certificates           2018.1.18                     0    conda-forge
certifi                   2018.1.18                py36_0    conda-forge
chardet                   3.0.4
click                     6.7
click-plugins             1.0.3
cligj                     0.4.0
cycler                    0.10.0
decorator                 4.2.1
descartes                 1.1.0
Fiona                     1.7.11.post1
geopandas                 0.3.0
idna                      2.6
ipykernel                 4.8.2
ipython                   6.2.1
ipython-genutils          0.2.0
jedi                      0.11.1
jupyter-client            5.2.2
jupyter-core              4.4.0
kiwisolver                1.0.1
matplotlib                2.2.0
munch                     2.2.0
ncurses                   5.9                          10    conda-forge
networkx                  2.1
numpy                     1.14.1
openssl                   1.0.2n                        0    conda-forge
osmnx                     0.7.2
pandas                    0.22.0
parso                     0.1.1
pexpect                   4.4.0
pickleshare               0.7.4
pip                       9.0.1                    py36_1    conda-forge
prompt-toolkit            1.0.15
ptyprocess                0.5.2
Pygments                  2.2.0
pyparsing                 2.2.0
pyproj                    <IP_ADDRESS>
python                    3.6.4                         0    conda-forge
python-dateutil           2.6.1
pytz                      2018.3
pyzmq                     17.0.0
readline                  7.0                           0    conda-forge
requests                  2.18.4
Rtree                     0.8.3
setuptools                38.5.1                   py36_0    conda-forge
Shapely                   1.6.4.post1
simplegeneric             0.8.1
six                       1.11.0
sqlite                    3.20.1                        2    conda-forge
tk                        8.6.7                         0    conda-forge
tornado                   5.0
traitlets                 4.3.2
urllib3                   1.22
wcwidth                   0.1.7
wheel                     0.30.0                   py36_2    conda-forge
xz                        5.2.3                         0    conda-forge
zlib                      1.2.11                        0    conda-forgeand OSMnx version are you using?
Code that reproduces the issue
north, south, east, west = 38.902, 36.855, -121.051, -123.711
G_roads_bb = ox.graph_from_bbox(north, south, east, west,network_type='drive')

@jesuslovesyiyi make sure you're using the latest versions of the packages. For OSMnx, that's v 0.7.3 (you're using 0.7.2).

OSMnx 0.7.3 added significant performance improvements for networkx 2.1.

@jesuslovesyiyi did that resolve this for you?

Thank you so much for asking. Yes, it did! You are awesome Geoff!


enter key

Important when there is no confirmation button to click on.
This does not seem to work for me:
http://jsfiddle.net/3xTM2/

ideas here did not seem to work:
https://codepen.io/hchiam/pen/XQGJoP
but I think this commit is good enough: 5f4d48f837b2ac85ae337f94c9d60720b840ea3f