Non-model plastome assembly, no reads mapped bowtie2

Hi! I want to use Fast-Plast to assemble cp genomes for a handful of non-model dicots. I have installed Fast-Plast but when I run it, the bowtie2 mapping step completes without mapping any reads. Can you help me figure out what is going on?
Here is the *Progess.log file contents:
Fri Jun  9 11:32:38 2017	Starting Fast-Plast v.1.2.6.
				Assemblying plastome with 0 single end libraries and 1 paired end libraries.
Fri Jun  9 11:32:38 2017	Determining best kmer sizes.
				K-mer sizes for SPAdes set at 55,87,121.
Fri Jun  9 11:32:39 2017	Starting read trimming with Trimmomatic.
				Using /home/derstudent/software/Trimmomatic-0.36/trimmomatic-0.36.jar.
Fri Jun  9 11:35:46 2017	Starting read mapping with bowtie2.
				Using bowtie2.
				Samples for All are not in current GenBank plastomes. Using one representative from each order to make bowtie2 indices.
Fri Jun  9 11:36:10 2017	Starting initial assembly with SPAdes.
				Using spades.py.
		******************ERROR: No mapped reads files were identified to run SPAdes.  Please check 2_Bowtie_Mapping.******************

Thank you!!

Can you check a couple of things?

Did Trimmomatic work? Are there reads in the 1_Trimmed_Reads directory? If not, rerun with the full path to your raw reads files and see if this takes care of the problem.

Are there bowtie2 indices in the 2_Bowtie_Mapping directory?  If not, let me know and I will check to make sure there isn't a bug in the code.

Thanks for getting back

Trimmomatic ran. There are *P1.fq, *P2.fq & *U.fq files in 1_Trimmed_reads/

No bowtie2 indices. There are 2 FASTA files in 2_Bowtie_Mapping/, one called All and one called All.fsa

Can you send the output of the error log?

$ cat Agma.4051_results_error.log
TrimmomaticPE: Started with arguments:
 -threads 40 /home/joshd/data/santalales/nickrent_wgs/wgs_reads/Acanthosyris_asipapote_Nickrent4051b.fastq.gz /home/joshd/data/santalales/nickrent_wgs/wgs_reads/Acanthosyris_asipapote_Nickrent4051.fastq.gz Acas.4051_0.trimmed_P1.fq Acas.4051_0.trimmed_U1.fq Acas.4051_0.trimmed_P2.fq Acas.4051_0.trimmed_U2.fq ILLUMINACLIP:/home/joshd/software/Fast-Plast_with_afin/bin/adapters/NEB-PE.fa:1:30:10 SLIDINGWINDOW:10:20 MINLEN:40
Using Long Clipping Sequence: 'ACACTCTTTCCCTACACGACGCTCTTCCGATC'
Using Long Clipping Sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Input Read Pairs: 4625323 Both Surviving: 4392854 (94.97%) Forward Only Surviving: 93347 (2.02%) Reverse Only Surviving: 87850 (1.90%) Dropped: 51272 (1.11%)
TrimmomaticPE: Completed successfully
No mapped reads files were identified to run SPAdes.  Please check 2_Bowtie_Mapping.

OK.  One more, can you send the output of *results_out.log?

  Reinstall Fast-Plast and give it a try.  I just tested it and it worked for me.
Also verify that bowtie2 is properly installed.
Best,
Michael

Thanks Michael, I reinstalled Fast-Plast but am getting the same result. The species I'm working with are all in Santalales.

I just checked and the code is working for on my install.  Here are some things for you to check.  If These are not the case, we will try something else.

Have you verified that bowtie2 is installed and working?
Did you provided the full path to your raw reads?
Are there trimmed read files properly filled?
Since you are using paired end data, did you provide both R1 and R2, and not R1 or R2 twice by accident?

Hmm ok I discovered that on lines 25-30 in my fast-plast.pl, where the paths to dependencies are defined, all dependencies except trimmomatic were define without full paths, like:
my $BOWTIE2="bowtie2"
I re-ran INSTALL.pl and provided the full paths (before, I had used PATH when asked for the paths), but fast-plast.pl was not changed. So I manually changed my fast-plast.pl so the full paths were in there.
I think I misunderstood what the installer did with when I used the PATH option to tell it where dependencies are–the dependencies were in the path at the time of installation but not when I actually ran fast-plast.pl. It's running now and has gotten past the bowtie2 step! Thanks!!

Great to hear it is working (at least past this step).  I will check the installation script to verify that "PATH" works, and if not, fix it.


Spark lineage producer always create a new entry instead of updating the existing

We have added the producer code below in our Python code and lineage is getting produced and seen in Spline UI. However every time the code is executed it is generating a new entry in the Spline UI. Is there a way to ensure that it overwrites the lineage metadata and shows only latest version of the lineage?
sc._jvm.za.co.absa.spline.harvester.SparkLineageInitializer.enableLineageTracking(spark._jsparkSession)

The goal of Spline is to capture all job executions, not just the last one. So it doesn't make sense to overwrite data.
To understand your question a bit better: How do you recognise that two lineages are the different versions of the same lineage and not just two completely different jobs?

I agree that the producer will be capturing and appending the lineage information in database, however in UI there should be a way to see the latest lineage based on target node.
As far as I understand in order to Identify the latest lineage we should refer to the target node and take the latest record. Hence I was looking for a way to only get the latest lineage for the Target dataset.

@rajendra-t the screenshot from your post is an event log page where you see all captured execution events. That view is just not designed for grouping per data source. Try the "Data Sources" view (from the main menu on the left hand side). It will show you all captured data sources with information about the latest write.

thanks @wajda, I can see the latest lineage in Data Sources tab.


WASM: config image pull interval

(This is used to request new product features, please visit https://discuss.istio.io for questions on using Istio)
Describe the feature request
I test it at local, the time that Istio proxy pull newer image is different, sometimes spend half an hour, sometimes spend 10 mins, looks like a random behavior.
I do not find any doc for its certain value, I think it would be better to make it configurable.
If I miss anything important, please tell me.
Describe alternatives you've considered
Affected product area (please put an X in all that apply)
[x] Docs
[ ] Installation
[ ] Networking
[ ] Performance and Scalability
[ ] Extensions and Telemetry
[ ] Security
[ ] Test and Release
[x] User Experience
[ ] Developer Infrastructure
Affected features (please put an X in all that apply)
[ ] Multi Cluster
[ ] Virtual Machine
[ ] Multi Control Plane
Additional context

there're two solution:

add a env(like WASM_INSECURE_REGISTRIES do) via MeshConfig.ProxyMetadata
make this configurable in WasmPlugin

@bianpengyuan WDYT?

Currently the image pulling happen on every listener update. We will implement pull policy to if not present, which should suffice what most people want (i.e. only pull once for the whole pod lifecycle).

@bianpengyuan can I check the timing of the listener update? I want a certain value for pull interval, it helps for end users. If only pull once, the remaining update of WASM image would lack. Now, the random interval is not acceptable for end users.

I think you should always tag your image differently if there is any change. You can specify sha256 (https://istio.io/latest/docs/reference/config/proxy_extensions/wasm-plugin/#WasmPlugin) + IfNotPresent pull policy (Note this is not yet implemented) if you really want to use the same image url for different images.

The case is that users always want to use the latest version.

IMO I don't think it is good approach to let proxy pull new images whenever it is available in an uncontrolled way. If you are absolutely sure this is what you want, I think we can add an env variable to pilot-agent which will could set expiry for cached Wasm modules.

IMO I don't think it is good approach to let proxy pull new image whenever it is available in an uncontrolled way. If you are absolutely sure this is what you want, I think we can add an env variable to pilot-agent which could set expiry for cached Wasm modules.

maybe we need a config like imagePullPolicy: Always

Now we have it.

IMO I don't think it is good approach to let proxy pull new image whenever it is available in an uncontrolled way. If you are absolutely sure this is what you want, I think we can add an env variable to pilot-agent which could set expiry for cached Wasm modules.

maybe we need a config like imagePullPolicy: Always

My key concern is pull/sync interval.

@daixiang0 as https://github.com/istio/istio/pull/39212 is merged, do you still need this?

Looks good, close it :)


Fails to build with Manjaro Linux 24.0.6

When installing this gem into a Manjaro Linux, I get an ERROR: Failed to build gem native extension.
Specs

Command: gem install or-tools
Ruby: ruby 3.3.4 (2024-07-09 revision be1089c8ec) [x86_64-linux]
OR Tools: v0.12.0
OS: Manjaro Linux 24.0.6

Specific Error
/home/dev/.rvm/gems/ruby-3.3.4@guard/gems/or-tools-0.12.0/ext/or-tools/vendor.rb:58:in `<top (required)>': Binary installation not available for this platform: manjaro  x86_64 (RuntimeError)

Full Error
> gem install or-tools
Building native extensions. This could take a while...
ERROR:  Error installing or-tools:
        ERROR: Failed to build gem native extension.

    current directory<EMAIL_ADDRESS>/home/dev/.rvm/rubies/ruby-3.3.4/bin/ruby extconf.rb
checking for rice/rice.hpp in<EMAIL_ADDRESS>yes
checking for -lstdc++fs... yes
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
        --with-opt-dir
        --without-opt-dir
        --with-opt-include=${opt-dir}/include
        --without-opt-include
        --with-opt-lib=${opt-dir}/lib
        --without-opt-lib
        --with-make-prog
        --without-make-prog
        --srcdir=.
        --curdir
        --ruby=/home/rodrigo/.rvm/rubies/ruby-3.3.4/bin/$(RUBY_BASE_NAME)
        --with-stdc++fs-dir
        --without-stdc++fs-dir
        --with-stdc++fs-include=${stdc++fs-dir}/include
        --without-stdc++fs-include
        --with-stdc++fs-lib=${stdc++fs-dir}/lib
        --without-stdc++fs-lib
        --with-stdc++fslib
        --without-stdc++fslib
        --with-or-tools-dir
        --without-or-tools-dir
        --with-or-tools-include=${or-tools-dir}/include
        --without-or-tools-include
        --with-or-tools-lib=${or-tools-dir}/lib
        --without-or-tools-lib
/home/dev/.rvm/gems/ruby-3.3.4@guard/gems/or-tools-0.12.0/ext/or-tools/vendor.rb:58:in `<top (required)>': Binary installation not available for this platform: manjaro  x86_64 (RuntimeError)

Build the OR-Tools C++ library from source, then run:
bundle config build.or-tools --with-or-tools-dir=/path/to/or-tools

        from extconf.rb:15:in `require_relative'
        from extconf.rb:15:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

<EMAIL_ADDRESS>
extconf failed, exit code 1

Gem files will remain installed in<EMAIL_ADDRESS>for inspection.
Results logged to<EMAIL_ADDRESS>

Hi @rofaccess, see the error message:
Build the OR-Tools C++ library from source, then run:
bundle config build.or-tools --with-or-tools-dir=/path/to/or-tools

Hello @ankane
I made a pull request to add support for Manjaro Linux.
I have tested the installation and use of the gem into my local project, and, it seems to work correctly. Tests also pass.
Sorry if I made a mistake in the contribution process, this is my first pull request to collaborate with a project.


Make the webview transparent when the map initialises instead of on app startup

I'm submitting a ...
[ ] question
[ ] any problem or bug report
[X] feature request
Hi!
This plugin makes the webview background transparent in order to show the maps underneath it, but the transparency is applied at app startup, which in my cases messes up some coool startup effects :)
Would it be possible to make the webview transparent when the map is initiated instead? If now technically messy, this would be a better approach, since the plugin wouldn't make any impact if not actually initialised.
With that said, this plugin is amazing. I've started converting my js-based map to this and I'm really surprised by the sheer amount of api support your have provided. Thanks so much for all your work on this!

This plugin changes the background when the map is created.
Did you read the code?
https://github.com/mapsplugin/cordova-plugin-googlemaps/blob/master/www/Map.js#L173

I'm not talking about the DOM, but the webview itself.

I see. But not acceptable.

The reason is ONLY one chance to change the background color of webview.


relu cooling off hotneurons

Connections between neurons are now inferred using the submodule NeuronNumbers, which contains coldneurons and hotneurons. Problem is that relu(hotneuron) should return hotneuron but is returning coldneuron.

Hmm, ok, problem is with isless(::NeuronState, ::Number) = true and the fact that relu is defined via relu(x) = ifelse(x<0, zero(x), x), so, since we have hotneuron < 0, relu returns zero(hotneuron), which is coldneuron.
Maybe we should have offneuron < coldneuron < any Number < hotneuron.


[zh] sync blog: 2023-03-01-introducing-kwok/

Add zh text to this blog. See preview.
content/zh-cn/blog/_posts/2023-03-01-introducing-kwok/

Fixes #39738

/approve


Miscellaneous docs fixes

I noticed some issues in the existing docs while thinking about where to add documentation for west, mostly in the getting started pages. Posting fixes for these separately.

Codecov Report

Merging #8260 into master will decrease coverage by <.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #8260      +/-   ##
==========================================
- Coverage   64.53%   64.53%   -0.01%
==========================================
  Files         420      420
  Lines       40109    40109
  Branches     6762     6762
==========================================
- Hits        25884    25883       -1
  Misses      11108    11108
- Partials     3117     3118       +1

Impacted Files
Coverage Δ

boards/posix/native_posix/timer_model.c
98.21% <0%> (-1.79%)
:arrow_down:

Continue to review full report at Codecov.

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Testing an image

I'm trying to test my own image. I've followed the instructions in the readme file. But when running test.py as the instructions say and checking the directory "checkpoints/output" I found that it's still empty without the image after colorization!

the checkpoints folder has four sub-folders: cifar10, places365, test -which contains the test image- and output -which's empty.

in the image what I've got when running

@RihamHazem
It looks like the program is either frozen or still running. Are you running on GPU?

I'm running on google Colab

Shitty repo.. test.py doesn't work

make sure the image is "jpg" not "jpeg" since it is hardcoded to find jpg and png extensions
make sure the image shape when read is grayscale and not grayscale with 3 channels for colors

Is it working now facing similar issue. Not generating colorize image nor giving error


Hello, I don't see logic about freezing routes and experts in TaskMoE.

Hello author, in the continuous learning and task transfer experiments, freezing experts and routing are mentioned, but I don’t see the relevant logic in TaskMoE.py. Does this logic exist elsewhere?

Thank you for your interest in our research. Codes for continual learning and task transfer will be open-sourced in the future.

Hello, thank you for your excellent work. Have you released the related code?

@YixiaoWang7 Thanks for your great work!
Could you release the related code for continual learning and task transfer?

Hello, thank you for your excellent work. I was wondering if the related code has been released?

We will release the code by the end of year.


[DO NOT MERGE][azure-template-cpp] publish version 1.0.0-beta.26

VALIDATION ONLY -- Update port for azure-template-cpp

This PR validates release automation... 2 checks have failed, all other checks have passed. Failure info:

OSX appears to be using a cached version of the .tar.gz (this is happening in part because I've been publishing the packages under the same release/tag)
The x86 windows build appears to be failing for unrelated reasons. I cannot re-queue a build.


Github repository setup: Allow to assign issues to users

It would be nice to be able to allow issues to be assigned to users so that they can work on them and have better visibility.

Like that?

Done. closing.


Backup user related data (DataSources etc)

survive harddrive crash

Current suggestion is to use mongodump tool on a regular basis e.g. weekly and store db dumps in the home partition as it is backed up by DESY

a cron job was created to dump mongodb on a daily basis


IOS11 v2.3.2  barcodes decoded with asterisk

I'm using Xamarin Forms on iOS11 using ZXing.Net.Mobile 2.3.2 and ZXing.Net.Mobile.Forms 2.3.2 and Xamarin.Forms <IP_ADDRESS>934.
These are the options I use
`
var options = new ZXing.Mobile.MobileBarcodeScanningOptions();
options.AutoRotate = true;
options.TryHarder = true;
options.TryInverted = true;
options.AssumeGS1 = false;
options.CharacterSet = "ISO-8859-1";
        options.PossibleFormats = new System.Collections.Generic.List<ZXing.BarcodeFormat>();
        options.PossibleFormats.Add(ZXing.BarcodeFormat.DATA_MATRIX);
        options.PossibleFormats.Add(ZXing.BarcodeFormat.All_1D);

        options.UseCode39ExtendedMode = false;

`
I'm using the options above and not the native AVCaptureEngine. Barcodes seem to be decoded in general, but the first, fifth, etc. character are always replaced by asterisks.
So instead of
0123456789
here http://barcode4j.sourceforge.net/images/example-code128.svg
I get
*1234*6789
This is a sample barcode that is well-known to work. It was created using barcode4j.
I've tried to alter options, but couldn't find any combination that returns a different result.
It doesn't matter whether I try to use Code128, Code39, datamatrix, etc. The behaviour is always the same regarding the asterisks.
Any ideas how to fix this?

Thanks for reporting this issue!  Unforunately it took me way too long to respond 😭.  Sorry, I apologize!  Recently the source code for this project was completely refactored to modernize it.  Many PR's were included in this effort, and many bugs were hopefully fixed.  Please try out the latest 3.x series of NuGet packages (currently in prerelease).  To try and make the project more maintainable in my spare time going forward, I've decided to close all existing issues to start with a clean slate.  If you're still experiencing this issue on the newest version, please open a new issue with as much detail as possible.  Thank you for your patience and understanding!  Happy scanning!


filter "parameters method" from swagger imports

In swagger files you can specify parameters for a path.
Insomnia added this parameters as methods. This simply filters this "parameters methods"

Can you please provide more detail on what this is actually doing? I'm not familiar enough with Swagger to know what this means.

In swagger you can write this to add parameters to all methods for a specific path.
At the moment if you import a swagger file the "parameters" will be interpretet as a method.
There might be a lot more wrong if the importer ignores this, but the most annoying are the extra useless requests that get "imported".
paths:
    /test/:
        parameters:
           ...
        get:


Update two-way demo to remove legacy componentWillUpdate method

Issue
The componentWillUpdate lifecycle method is set to be deprecated in React 17.0 and should be replaced with alternative approaches.
From this blog post: https://reactjs.org/blog/2018/03/27/update-on-async-rendering.html

One of the biggest lessons we’ve learned is that some of our legacy component lifecycles tend to encourage unsafe coding practices. They are:

componentWillMount
componentWillReceiveProps
componentWillUpdate

Note: React 17.0 is still a fair ways off, but this is an easy change to make at any time.
Current use
The componentWillUpdate lifecycle is used in the two-way gallery example:
http://kidjp85.github.io/react-id-swiper/#gallery
Using componentWillUpdate
componentWillUpdate(nextProps, nextState) {
  if (nextState.gallerySwiper && nextState.thumbnailSwiper) {
    const { gallerySwiper, thumbnailSwiper } = nextState

    gallerySwiper.controller.control = thumbnailSwiper;
    thumbnailSwiper.controller.control = gallerySwiper;
  }
}

Recommended change
I had a brief look and couldn't find an open repo to submit a pull request. Please point me in the right direction if I missed it.
Using componentDidUpdate
componentDidUpdate(prevProps, prevState) {
  const { gallerySwiper, thumbnailSwiper } = this.state
  if (gallerySwiper && thumbnailSwiper) {
    gallerySwiper.controller.control = thumbnailSwiper
    thumbnailSwiper.controller.control = gallerySwiper
  }
}

Hi @chicgeek , thanks for your suggestion. I am planning to rewrite whole library with new hooks apis. That will be a breaking chance for version 2.x.

That's great news, hope the rewrite goes well.
I suggest this change be made to the docs anyway. This old method will eventually cause issues for anyone who upgrades to React 17 and doesn't update react-id-swiper.
It's a small change to the docs to update current best practice. Better yet, it might prevent some headaches in the future for users, as well as prevent a new issues for you to respond to. 😄

Im trying to rewrite Thumbs Gallery With Two-way Control into hooks but i kinda struggle 🗡 is there a chance anyone has it?


Convert test_static.sh to test_static.py

Create platform independent style checking scripts.
Work in progress.

This checklist is used to make sure that common guidelines for a pull request are followed.

For new extensions:

[ ] My extension description/summary conforms to the Extension Summary Guidelines.

If this PR is for a new extension or change to an existing extension, use the following to try out the changes in this PR:
docker run -it microsoft/azure-cli:latest
export EXT=<NAME>
pip install --upgrade --target ~/.azure/cliextensions/$EXT "git+https://github.com/adewaleo/azure-cli-extensions.git@tosin/xplat-test-static#subdirectory=src/$EXT&egg=$EXT"


200 Add resumable uploads

Resolves #200

Can you briefly explain what exactly a resumable upload is, how it differs from the direct upload option and why a resumable upload is the preferred method for uploading? Resumable upload method is probably always preferred because it resumes your upload if you lose connection due to spotty internet. If you're uploading a large file and you lose connection after 98% progress you don't have to resume from the beginning.
We should probably preface the guide with this and add anchor links to jump to different parts of the guide (direct vs resumable upload method).

Updated!


[spark] make metadata columns passed across shuffles

Purpose
when there is a big subquery that need to involve shuffle to compute in delete condition, the metadata columns should be the output of DatasourceV2Relation, not just in the output of DataSourceV2ScanRelation, that can be computed correctly.

Tests

API and Format

Documentation

+1


No padding on iOS / iPadOS?

When I'm using the theme on my iPhone and iPad, there's no padding around the screen like is being shown in the preview imagine. Text begins touching the left-most edge of the screen, and continues all the way to the right-most. It needs a little buffer space.
iPhone 13, iPad Pro 11 (2018), both running current release OS, and Obsidian 1.0.5

Hey @dpmeltz, thanks for submitting an issue. Out of curiosity, have you enabled the beta WYSIWYG editor? That feature introduced some weird things in the css styling, so want to check if that's the source here too.

On desktop it's fine (not seeing issue with live preview), mobile is where I'm seeing the issue, so there's no beta wysiwyg to turn on.
I've turned all my community plugins off and still see like this.

On Nov 15, 2021, at 12:17 PM, Colin Eckert @.***> wrote:

Hey @dpmeltz, thanks for submitting an issue. Out of curiosity, have you enabled the beta WYSIWYG editor? That feature introduced some weird things in the css styling, so want to check if that's the source here too.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or unsubscribe.
Triage notifications on the go with GitHub Mobile for iOS or Android.

 I have "readable line length" in editor settings turned off. If I turn it on I get padding. Probably need something there.

Ahh ok cool. No worries, glad we could identify the issue. Thanks for using the theme! Let me know if you find any other issues :)


⚠ SceneTime has degraded performance

In a20f4d0, SceneTime ($ST) experienced degraded performance:

HTTP code: 200
Response time: 28005 ms

Resolved: SceneTime performance has improved in 61891f0 after 5 minutes.


statistics module

automatic trigger to collect statistics

@Morgan-Leon @zdp207 @jerrywalker0435 @EiddleChen : please check logic by UI design


docs(adr): ADR-002: Reports save/delete implementation

Description
This PR introduce the draft of the 2nd ADR related to reports save/delete operations.
Discussed before here: #575.

Author Checklist
All items are required. Please add a note to the item if the item is not applicable and
please add links to any relevant follow up issues.
I have...

[x] included the correct type prefix in the PR title
[ ] added ! to the type prefix if API or client breaking change
[x] targeted the correct branch (see PR Targeting)
[x] provided a link to the relevant issue or specification
[ ] followed the guidelines for building modules
[ ] included the necessary unit and integration tests
[ ] added a changelog entry to CHANGELOG.md
[ ] included comments for documenting Go code
[ ] updated the relevant documentation or specification
[ ] reviewed "Files changed" and left comments if necessary
[x] confirmed all CI checks have passed

Reviewers Checklist
All items are required. Please add a note if the item is not applicable and please add
your handle next to the items reviewed if you only reviewed selected items.
I have...

[ ] confirmed the correct type prefix in the PR title
[ ] confirmed ! in the type prefix if API or client breaking change
[ ] confirmed all author checklist items have been addressed
[ ] reviewed state machine logic
[ ] reviewed API design and naming
[ ] reviewed documentation is accurate
[ ] reviewed tests and test coverage
[ ] manually tested (if applicable)

Closing this because it has been splitted in two different ADRs


Adds ssh client to V2.0.0

SSH client for go-git.v2.

@alcortesm ping

Current coverage is 68.64%

Merging #3 into v2.0.0 will not affect coverage as of 0fb7605

@@            v2.0.0      #3   diff @@
======================================
  Files           13      13
  Stmts          877     877
  Branches       137     137
  Methods          0       0
======================================
  Hit            602     602
  Partial         71      71
  Missed         204     204

Review entire Coverage Diff as of 0fb7605

Powered by Codecov. Updated on successful CI builds.

LGTM

The current version does not implement the new AuthMethod functionality correctly and I have not understand what should the String() method does.
@mcuadros suggested I should take a look at ssh.AuthMethod, so all of them can be passed to the SSH client.
I have not fully understand all Máximo comments: I will need to think about it. Things will be much easier if the appropriate sections of go-git where documented.

Done.
But I still don't understand the purpose of having all this auth methods in go-git.client.ssh, there should be only one, that wraps a generic an externally generated []ssh.AuthMethod in a go-git.client.common.AuthMethod. Should we discuss about it?

I dont understand how the your AuthMethods works, how I should set for example the credentials here:
https://github.com/src-d/go-git/pull/3/files#diff-93a872f722160e3c55c4194ccfb29664R57ç
BTW can you squash

I have gotten myself into a squashing hell, let's continue this PR in a new one.


Update Duration Accumulation to support displaying durations longer than 24 hours

Problem
See #11 for description.
#Solution
I think there are two ways of doing this and also keeping it simple:

we use asHours instead of hours and just let the hours be the top most unit of time we aggregate with minute and second staying in their respective periods.
We use year as the top most unit of time we aggregate and update to include month and day. So year would aggregate endlessly with month, day, hour, minute, and second staying in their respective periods.

I decided on option 1 so that we minimize how soon really large numbers start to show up as the tracker is used.

Thanks so much! This looks great.

@Ellpeck I ran npm install and it changed some files so i committed that, should I revert that, or are those changes needed? Sorry, I'm a TS noob 😅

@Ellpeck no rush of course, just curious if when you have a chance, the version could be bumped, and a release for this could be cut? Or if you want me to open a PR that bumps the version so all you have to do is cut a release I can get that PR goin' for ya! Whatever flow and timeline works best for ya, just let me know 👍


export_to_shapefile

The following error occurs when performing a transformation SHP on a very simple model:
mymodel.export_to_shapefile('D:/admin')
error:
File "E:\APP\Anaconda3\envs\swmmio_env\lib\site-packages\swmmio\utils\spatial.py", line 219, in write_shapefile
w.line(parts=[row.coords])
TypeError: line() got an unexpected keyword argument 'parts'

@rhc123123 thanks for identifying this issue! I believe this is due to an API change in pyshp. Regardless, I think i have a patch to this over in #138 .


Fix TLV encoding for negative integer

Use signed magnitude representation instead of two's complement

OK with Wakaama client.

Integrated in master (commit : 0e0bd6e1fdd09ddbdabed1ca0841c483d56975d5)

Reverted in master with commit bbebd77bd5848449306a942cdb517fac77150bae.
Since the spec is ambiguous about the signed integer representation (Opened OMA issue: https://github.com/OpenMobileAlliance/OMA-LwM2M-Public-Review/issues/55#issuecomment-121798495), we will wait for a clarification before merging the fix.

Seems fixed in OMA-TS-LightweightM2M-V1_0-20150910-D


Zabbix plugin is not working wth Grafana 3.0.4.

Hi,
I have configured zabbix plugin in Grafana 3.0.4 but it is not working.

Thanks,
Saeedkm

@alexanderzobnin : Can you please help me to fix this

Hi! You must provide full zabbix api address with api_jsonrpc.php in url field.

Hi,
Where i can find this? it is in zabbix server or grafana ?
Thanks,
Saeedkm

Hi Alexander,
I can see only this after configuring zabbix.

Thanks,
Saeedkm

How this plugin works. only i can see zabbix server or all the servers from zabbix monitoring.

Check permissions for zabbix user.

I have given admin user only.

Do you really need http basic auth?

Even if

i remove that it is not coming.

It is not coming after removing that also.

Try to set checkbox Default.


Rercursion in Stateful Testing

Hi,
I am trying to do stateful testing with recursion limit 4.
Sometimes in testing I can see the recursion level goes only upto the level of 2 or 3.
As in below example, you can see the recurssion level has gone only till one level.

In the below image you will be able to see that the recursion level goes upto level 4

P.S: This is just a part of the execution
The scehma & the settings both the time were same.
Can you inform what would be the reason for variation in the recursion levels in different execution?
Thank You!!!

Hi!
Thanks for asking :) This config option limits the maximum depth, but the stateful testing doesn't guarantee that all generated sequences will reach that depth. Sometimes, the tested app doesn't respond with status codes needed to go to the next level. So the expected depth is less or equal to stateful-recursion-limit.
Let me know if that clarifies the observed behavior :)

Hi,
Thank you for the clarification.
It is clear that other than the response code there is no other reason for the expected depth to not be met.

Not sure if this is the right place to ask but I am unable to get stateful testing to work with PyTest . Does it work with PyTest or does just work in CLI for now ?

Does it work with PyTest

Yes, it works with pytest. Did any steps mentioned in the docs help? If not, then I'd appreciate a minimal schema example so I can debug it


out of 6 test images, 4 images, instance segmentation result not there only black image

in my trained model the total loss was near to 4.5 and the accuracy was 85%, why it is the case that the instance segmented images is appearing as black.
I used 220 images in training data for 2500 epochs(started training from snapshot with ur model), please help with the reason of above issue and also let me know the sample size of ur data. @MaybeShewill-CV please help

@him009verma The sample size used to train the model was [256, 512]. You may adjust the dbscan threshold to see if that helps. Visualizing the feature embedding layer will also help you with it. To visualize the feature embedding layer you may refer
https://github.com/MaybeShewill-CV/lanenet-lane-detection/blob/9154c1497291276f03fb70a33149b152aa74cda3/tools/test_lanenet.py#L122-L124

@MaybeShewill-CV thanks for the inputs will try these, sample size i mean the no. of images in the dataset.?, i want to know how much data is sufficient for this architecture to perform well as i have less manpower for the annotation task

@him009verma Can not tell the accurate sample counts for a well performed model which is task dependent. Make annotation data as much as you can:)

@MaybeShewill-CV hey I came across  a file name tusimple_ipm_remap.yml, can u please tell the how its created, i can see it has matrices of 640*640

@him009verma Check this https://github.com/MaybeShewill-CV/Easy-Ipm-Client . It's used to convert front-view image into bird view:)

@MaybeShewill-CV thanks ..!.. thats really helpfull, my data set is consisting the images where i already have the images in bird eye view ( i am using drone images) so still using this IPM will help or not, i have never used this so right now not in a situation to decide, your suggestion will help a lot...

@him009verma ipm will not offer you more help in this situation:)

@MaybeShewill-CV thanks for the inputs will try these, sample size i mean the no. of images in the dataset.?, i want to know how much data is sufficient for this architecture to perform well as i have less manpower for the annotation task

How did you generate the binary image and instance images from the own dataset?


Create Community Page

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Feature | Testing: unit + integration + functional e2e CI automation

What?

✅ Repo CLI:

create automated unit tests; initially to run at the time of creating a PR; then we could evaluate if pre/post release as well.
create automated tests, integration & functional; initially to run at the time of creating a PR; then we could evaluate if pre/post release as well.

Test leverage credentials
Test leverage project create

✅ Repo Ref Arch: create automated, functional tests; that run on-demand and at the moment of releasing a new version of the CLI; it is necessary to define well which accounts and layers will be included since it can become very complex depending the test-cases.

terratest is the reference tool here, we use it to test the modules eg: https://github.com/binbashar/terraform-aws-waf-owasp/tree/master/modules/waf-global/tests
The thing is that we are going to need to put together something that focuses on testing the ref-arch but using the leverage-cli.
To start with I can think of some workflows that take certain layers to do the init, plan, apply and destroy workflow. @diego-ojeda-binbash OJ has already been working on something related -> https://github.com/binbashar/le-devops-workflows

Eg Nat Gw Disable: https://github.com/binbashar/le-devops-workflows/actions/workflows/shared_network_natgw_disable.yaml
Eg Nat Gw Enable: https://github.com/binbashar/le-devops-workflows/actions/workflows/shared_network_natgw_enable.yaml

But it is not strictly oriented to testing, still the demo-app envs creation through ref-arch with automated and parameterized workflows could help a lot here and guide us on how to automate e2e functional tests scenarios. In other words It can serve as a base or inspiration for these e2e functional bb-leverage Ref Architecture for AWS tests.

Why?
Having the proper level of testings
➕ Makes the Process Agile
➕ Quality of Code
➕ Finds Software Bugs Early
➕ Facilitates Changes and Simplifies Integration
➕ Provides Documentation
➕ Debugging Process
➕ Design
➕ Reduce Costs

@diego-ojeda-binbash OJ we'll wait for your review and feedback here in order to segregate this Testing Epic in the proper specific issues. Thanks in advance!
CC: @binbashar/leverage-ref-architecture-aws-dev @binbashar/leverage-ref-architecture-aws-admin

Proposal for testing Ref Arch Repo:

Get all layers with changes:
Get all changed files (maybe via GitHub API?) -> dirname -> uniq -> loop over

If layer has tests folder:
Folder holds test file and .tfvars with expected values

Invoke bats

Layer directories can be concatenated and bats only invoked once
Bats test per layer:
Setup

Copy .tfvars to layer directory

Test

leverage tf init
leverage tf plan -detailed-exitcode
If exit code is 0:
3.1. leverage tf apply
3.2. leverage tf output -json
3.3. Use jq and bats_assert to compare against .tfvars
If exit code is not 0:
4.1. Post leverage tf plan output as comment to PR

Layers to test initially

apps-prd/base-identities

@angelofenoglio @diego-ojeda-binbash the testing approach looks very promising. Couldn't wait to see the 1st workflow in place 🙌🏼 💪🏼

Unit and Integration testing are considered done.
Functional testing will be implemented as a simple GH action in Ref Arch repo over a dummy layer where init, plan, apply, destroy commands will be executed checking for no errors.

@angelofenoglio thanks for everything, @juanmatias will be collaborating with this task from now on 💪🏼

@juanmatias let's create another issue in order to test the leverage CLI dependency package binaries that could be found here:

https://github.com/binbashar/le-docker-images/blob/master/terraform-awscli-slim/Dockerfile
https://github.com/binbashar/le-docker-leverage-toolbox/blob/master/Dockerfile

Eg test-cases (1st document and in a 2nd iteration automte)

levarage sso workflow
aws eks kubeconfig automated generation (aws eks update kubeconfig)

Regarding the Leverage CLI / RefArch integration
Prev Situation
tests were not working
Curr Situation
tests will work as soon as PR are merged in both  repos

https://github.com/binbashar/le-tf-infra-aws/pull/444
https://github.com/binbashar/leverage/pull/133

Notes
Things that have been done here:

set param with quotes due it being take as an int literal in other case

        client_payload: '{"leverage_branch": "${{ github.ref }}"}'

github app needed permissions for write in actions in order to trigger with dispatch
here: https://github.com/organizations/binbashar/settings/apps/bb-le-cli-ref-arch-trigger/permissions
permission: Actions (Workflows, workflow runs and artifacts)
also in the repo (https://github.com/binbashar/le-tf-infra-aws/) this action has to be confirmed

ref to branch in target repo added
by default the action will take main while we are using master, so this line was added to the source trigger action:

        ref: master

var scope fixed:
from this

        github_token: ${{ steps.authentication.output.token }}

to this

        github_token: ${{ steps.authentication.outputs.token }}

in refarch action switched from private clone to public one:
# from this
        git clone git@github.com:binbashar/leverage.git

# to this

        git clone https://github.com/binbashar/leverage.git

adding pipenv to the runner with this command in the target action

        if ! (which pipenv 2>/dev/null); then echo 'Installing pipenv...' && pip install pipenv && pipenv --python $(which python) ; else echo 'pipenv is already installed'; fi

added a step to set the toolbox version: Set Leverage Toolbox version
since tests are using a build.env already set in the refarch repo, there's a need of set the version based on the CLI version

credentials for aws

credentials are stored like this:

dependant profile (the one which needs to assume the role) in the .aws/config file
source profile credentials are stored in .aws/credentials file
the command aws configure set, when used to set the source profile, stores the access key id in the config file and then, for the source profile, stores the access key in config file and secret in credentials one.
but when using terraform there is a sort of a bug, and both the access key and the secret must be stored in the credentials file for the source profile

cc @exequielrafaela @angelofenoglio @diego-ojeda-binbash

@juanmatias as agreed we'll migrate all the test to the leverage cli repo instead of having them segregated in the ref arch one. Since this tests will give us a good testing baseline for the cli, we've also discussed about creating a new issue to start the discussions of the ref arch v1 specific minimum set of tests that could also help to have a better understanding of the different components versions (bringing more certainties for the current compatibility matrix that could be found in the doc).
CC: @diego-ojeda-binbash @angelofenoglio

A test was created in the Leverage CLI repo.
Now the test action has three jobs:

unit test
integration tests (make test-int)
integration_tests_cli_refarch

this last job does the following:

using leverage cli creates a project (step wich in turn will download refarch templates) and tries to init a layer
pulling the refarch repo and with the cli test layer:

init
apply
destroy

Please, @exequielrafaela @diego-ojeda-binbash @angelofenoglio , check this PR https://github.com/binbashar/leverage/pull/136


Electron 7.2.3

https://www.electronjs.org/releases/stable?version=7

Now when Electron 9.x is released, could we upgrade to the latest?
What the diff between with 7.x/8.x versions btw?


Pylance works with notebook on local server, but not with notebook on remote server

I'm using Visual Studio Code Remote - SSH (0.65.1)  extension  to connect to a remote server and work with ipython notebooks. Language server (Pylance) works fine for .ipynb files on the local server.  However, for .ipynb files on the remote server Pylance is not having any visual effect.
I have Python (2021.2.633441544), Pylance (2021.3.0)  and Jupyter (2021.3.619093157) extensions in both my local and remote server, same versions in both.
Environment data - local server

VS Code version: 1.54.1
Jupyter Extension version: 2021.3.619093157
Python Extension version: 2021.2.633441544
Language Server version: 2021.3.0
OS and version: Windows 10 Pro 10.0.18362
Python version: 3.8.5
Type of virtual environment used: virtualenv 20.0.31
Jupyter server running: Local

Environment data - remote server

Jupyter Extension version: 2021.3.619093157
Python Extension version: 2021.2.633441544
Language Server version: 2021.3.0
OS and version: Ubuntu 20.04 LTS
Python version: 3.8.5
Type of virtual environment used: virtualenv 20.0.31
Jupyter server running: Remote

Expected behaviour
Pylance-like intellisense (and theme with input code in boxes that separates it from output) for .ipynb files on remote server, just as it works on a local server.
Actual behaviour
No Pylance-like intellisense (and theme with input code in boxes) for .ipynb files on remote server.
Additional information
Pylance functionalities working on the local server notebook:

Pylance functionalities not working on the remote server notebook:

As shown here this issue affects readability:

Yes, thanks for the explanation, it's more clear now. I believe the issues that you are running into are mostly centered around how themes work with our remote support and the implementation of our old UI.
Can I ask you to check something out for me? Currently we are working on moving from an old webview based UI over to a new notebook UI that VS Code core is providing. This new notebook interface is available as the default in vscode insiders, which you can install safely next to stable vs code.
https://code.visualstudio.com/insiders/
Could you please try out your scenario in vscode - insiders? This new UI is what we are looking to move everyone to, so we're unlikely to fix a theming issue on the old UI at this point.

Yes, Pylance enhancements are working just perfect even in the remote server!

I think this new UI is a great improvement, very simple and effective. I'll be looking forward to it's release.

Awesome glad you like it. In the old UI vscode didn't support notebook style documents so we had to implement everything by hand in a webview (which was basically just a blank webpage that an extension could open in an editor window). In the new UI vscode core provides the basic notebook UI so everything feels and looks much more consistent with core vscode editors.
I'm going to actually close this issue now as we are not looking to make fixes in the old UI unless there are major braking issue. You can use the new UI in insiders for now (note that insiders does have minor issues from time to time as it's getting daily builds) and in stable when it fully rolls out.


HTTP Multipart POST support

Requested by Chris Cilino. labview HTTP Client supports it, but the rest API does not.

This should be working in release 1.3.0. Please download and test.


STAGES SHITTT

Describe your problem here.

Hey man, above image you can see i add agoti speakers using lua but it seems too big or enlarge whatever, tell me how to zoom out and i need to know speakers moving code man i work it out but it did't work [I KNOW MY ENGLISH IS SHIT ] help me out man
Are you modding a build from source or with Lua?
Lua
What is your build target?
Windows x64
Did you edit anything in this build? If so, mention or summarize your changes.
No response

Go to stages foleder find (stageurusing).json
And edit  "defaultZoom": 1, to 0.e

ar u gonna respond

sorry i had exam  in past days , did't see your response, thanks man  i have one more doubt

ar u gonna respond

sorry i had exam in past days , did't see your response, thanks for your time and i have one more doubt take a look
https://user-images.githubusercontent.com/87480185/193348091-ee3f4741-19c1-4ece-b9f5-667753b812ad.mp4
camera shitss

i coded but i miss something, solve this error: [Expected commajson(514)]
and thanks

hello kidboy?

ar u gonna respond

hello?

put a comma at the end of the "opponent" line

put a comma at the end of the "opponent" line

in opponent line? comma is already there

{
"directory": "",
"defaultZoom": 0.4,
"isPixelStage": false,
"boyfriend": [800, 200],
"girlfriend": [350, 230],
"opponent": [100, 100],

"camera_boyfriend": [0, 0],
"camera_opponent": [0, 0],
"camera_girlfriend": [0, 0],
"camera_speed": 1

}


CHEBI:86141 wrong CAS

The entry is about (9Z,12E), the CAS is about (9E,12Z).

Can you tell me where are you getting your CAS numbers from? We get our CAS number from ChemIDPlus. According to them, the CAS number for the (9Z,12E)-form is 2420-42-0 and the CAS number for the (9E,12Z)-form is 2420-55-5. They have made a mistake in naming the structures but the structures are drawn correctly.
These CAS numbers have been cross checked from this book (Link: https://books.google.co.uk/books?id=5irNBQAAQBAJ&pg=PA1426&lpg=PA1426&dq=2420-42-0&source=bl&ots=NjpkxXjUrL&sig=ACfU3U2z1buan2Hblrheoh924taXMOmaLw&hl=en&sa=X&ved=2ahUKEwi1gODEi-flAhUUi1wKHZQoC3QQ6AEwCnoECAcQAQ#v=onepage&q=2420-42-0&f=false).

Then the names have confused me, sorry.


Focus the quick pick back to the starting position

Accessibility issue we've seen on https://github.com/microsoft/azuredatastudio/issues/9232

Tracked with #92076.
Currently we use returnFocus() to pass the focus back to the current editor. We could instead first try to return it to the previous focus element the way you suggest.
https://github.com/microsoft/vscode/blob/master/src/vs/base/parts/quickinput/browser/quickInput.ts#L1527

Is there anything I need to do for this?

You can update the PR or I can take a look next milestone. 👍

@chrmarti what changes do you think @aaomidi should make to this PR? could you please add your comments directly?


IBM cloud foundry support?

Hi, thanks for your work. If possible, can this vnc app be deployed on IBM cloud foundry?
I tried to “git clone” this app and pushed to IBM CF, but it failed.

Hi, thanks for your work. If possible, can this vnc app be deployed on IBM cloud foundry? I tried to “git clone” this app and pushed to IBM CF, but it failed.

The app is normally built, like a docker image should be, there might be some custom config files of cloudfoundry like heroku.yml & app.json for Heroku, fork the project and modify accordingly. I don't exactly know what is cloud foundry but I've released docker images for latest and minimal version (purevnc minimal is in development so currently unavailable), so if cloud foundry has an option to directly deploy docker images with custom environment variables, you can do that else if you can get a VM instance, install docker and deploy the image manually or get a Ubuntu 20.04 LTS VM and install packages directly into it by following instructions from the Dockerfile. Close the issue if you are satisfied with the answer.

Try refering these docs.


New Tab: Pixels

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Add simple filter

Removed unused generic type from Filter

Codecov Report

Merging #98 (16f2aa9) into master (1e1feb6) will decrease coverage by 15.43%.
The diff coverage is 80.43%.

@@             Coverage Diff             @@
##           master      #98       +/-   ##
===========================================
- Coverage   83.90%   68.48%   -15.43%
===========================================
  Files          62       65        +3
  Lines        6506     6540       +34
  Branches      700      700
===========================================
- Hits         5459     4479      -980
- Misses        800     1849     +1049
+ Partials      247      212       -35

Impacted Files
Coverage Δ

...n/dev/evo/elasticmagic/transport/TransportError.kt
69.42% <44.44%> (-18.86%)
:arrow_down:

.../kotlin/dev/evo/elasticmagic/qf/AttrFacetFilter.kt
92.36% <60.00%> (-6.11%)
:arrow_down:

...ain/kotlin/dev/evo/elasticmagic/qf/SimpleFilter.kt
80.00% <80.00%> (ø)

...otlin/dev/evo/elasticmagic/qf/SimpleQueryFilter.kt
82.60% <82.60%> (ø)

...Main/kotlin/dev/evo/elasticmagic/qf/FacetFilter.kt
98.79% <87.50%> (ø)

...lin/dev/evo/elasticmagic/qf/AttrBoolFacetFilter.kt
98.34% <100.00%> (ø)

...in/dev/evo/elasticmagic/qf/AttrRangeFacetFilter.kt
74.50% <100.00%> (-23.00%)
:arrow_down:

...kotlin/dev/evo/elasticmagic/qf/FacetRangeFilter.kt
96.36% <100.00%> (ø)

...nMain/kotlin/dev/evo/elasticmagic/qf/PageFilter.kt
93.44% <100.00%> (-0.11%)
:arrow_down:

...ain/kotlin/dev/evo/elasticmagic/qf/QueryFilters.kt
88.67% <100.00%> (-1.89%)
:arrow_down:

... and 3 more

... and 34 files with indirect coverage changes
:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more


Issue adding service after initialization

I have a program that can toggle a service on/off at runtime but the service doesn't appear and I get an error in the terminal:
E NimBLEService: "ble_gatts_add_svcs, rc= 15, "
I have tried disconnecting attached devices (with a 100ms delay after requesting a disconnect) and stopping advertising before adding the service but the error still appears. The only reliable solution is to turn BLE off and back on again so that the service is added as BLE is starting up rather than at a later point in time.
I have a sample project here to demonstrate. See readme for more info..
https://github.com/olicooper/arduino-nimble-service-bug

When adding services after initialization, the server needs to reset the gatt/gap states. This will not occur until the clients have disconnected. This is a limitation in the NimBLE core at the moment.

Okay thanks for the info. I can see  NimBLEServer::resetGATT() but it is private, how do I do reset the state?
My code already disconnects clients by calling NimBLEServer::disconnect(bleConnHandle, BLE_ERR_REM_USER_CONN_TERM); then waits 100ms before stopping advertisements and creating the new service. The problem is still present despite doing that.
There is still a problem even when no clients have previously connected (the service is empty), so I think that is a separate problem?

 NimBLEServer::resetGATT() is called internally when the services are changed and after all connections are disconnected, no need to call it in your code.

My code already disconnects clients by calling NimBLEServer::disconnect(bleConnHandle, BLE_ERR_REM_USER_CONN_TERM); then waits 100ms before stopping advertisements and creating the new service.

Not sure why you're having issues there, i'll need to test it.

I seem to have forgotten about this one, I assume this is still an issue with the latest release, 1.3.7?

Yes is still here

I have tested the code provided. What you are seeing as the error is due to calling pService->start(). This call is not needed here because it will be started automatically when the gatts server is restarted. Removing that from the code removes the error. After this I can see the service gets added after the client devices have all disconnected and it shows in nRFconnect as expected.

Closing this, assuming resolved from my above recommendations. Please reopen if this issue is still persisting.


Duplicate Error registration

Bug description
After adding a custom module manager pylons.ModuleBasics, i get a runtime error regarding duplicate error registeration.
"error with code 2 is already registered: \"invalid proof\""
Stack:

I was hopeful you could tell me where Bdjuno calls the cosmos/types/errors registration function, so that i could ensure pylons app module is not also calling the error registration.

Hi @justyntemme could you pls show me the complete error message and the repository of pylons & of your bdjuno fork? It's probably an issue regarding the inconsistent dependency version.

Hi there, i think we have solved the inconsistent vendoring, but i will be sure to double check. As of right now i am using only forboles repository, making one small change to add the pylons.AppModule{}.
When i follow the steps outlined in the docs, it upgrades the deps to .55.5 instead of .44.4, but i don't think that is an issue. Here is the output
╰─⠠⠵ go get -u github.com/Pylons-tech/pylons
go get: added github.com/Pylons-tech/pylons v0.4.1
go get: upgraded github.com/cosmos/cosmos-sdk v0.44.4 => v0.44.5
go get: upgraded github.com/cosmos/iavl v0.17.2 => v0.17.3

I think i found it, it seems juno/v2 imports github.com/cosmos/cosmos-sdk v0.42.9 It seems that Bdjuno imports juno/v2 and not the updated juno/v3

Hey @justyntemme thanks for reporting that. We will update ibc-go package to higher version, in the meantime you can try updating juno version inside go.mod file to v2.0.1-0.20220303154752-50c37a0f96e7

It looks like when that is done, we are now both importing ibc-go/v2 and ibc-go/v3, leading us to the same error.
Is there currently a branch that has ibc-go v2, but uses cosmos .44.x on everything else, including the juno references? That may work best for us.
Here is the go.mod after running go mod tidy after changing the /juno/v2 reference to v2.0.1-0.20220303154752-50c37a0f96e7
	github.com/cosmos/ibc-go/v2 v2.0.0 // indirect
	github.com/cosmos/ibc-go/v3 v3.0.0-rc0 // indirect

Are you registering gaiaapp insidemain.go? Try to replace it with simapp instead

@justyntemme you may try the juno version v2.0.0-20220308070656-570bc10bf70a in which ibc-go is updated to v2. The ibc-go package should also be v2 in the gaia app dependency so I would suggest you use v6.0.4:
require (
    github.com/cosmos/gaia/v6 v6.0.4
    github.com/forbole/juno/v2 v2.0.0-20220308070656-570bc10bf70a
)

Let me know whether this helps.

Did not see this message from you, will try today and repeat back TY :D

I'm happy to report that fixed our issue, tysm this has been a huge pain for us. Will be VERY excited to issue a PR for a pylons branch of bdjuno 🥳


refactor: merge writer funcs into a single one

quick refactor to consolidate the two functions into a single one;
this makes testing a bit more straightforward

superseeded by https://github.com/syntasso/kratix/pull/151


How to override id type?

For ORM model, how do you override the id type to be UUID (String)? There is some stuff that forces id as int for query, and this is problematic.

I think this could be a bug by looking at the generated code when id is String. The primary key is assumed to be auto generated numeric field in the where clause and table creation. Will issue a fix for this.

Great, thanks @dukefirehawk !

@kevinelliott Have you tried the following annotation?
@PrimaryKey(columnType: ColumnType.varChar)
String? get id;

Take a look at email_indexed.dart in the angel_orm_test package. Let us know if this works.

@dukefirehawk Yes, when I try that, I get:
lib/marine/orm/managers/voyage_manager.dart:60:33: Error: Can't use 'id' because it is declared more than once.
      ..where!.id.equals(voyage.id!)
                                ^^
lib/marine/orm/managers/voyage_manager.dart:60:33: Error: The getter 'id' isn't defined for the class 'Voyage'.
 - 'Voyage' is from 'package:aggregation_server/marine/orm/models/voyage.dart' ('lib/marine/orm/models/voyage.dart').
Try correcting the name to the name of an existing getter, or defining a getter or field named 'id'.
      ..where!.id.equals(voyage.id!)
                                ^^
lib/marine/orm/managers/voyage_position_manager.dart:39:27: Error: Can't use 'id' because it is declared more than once.
      ..voyageId = voyage.id
                          ^^
lib/marine/orm/managers/voyage_position_manager.dart:39:27: Error: The getter 'id' isn't defined for the class 'Voyage'.
 - 'Voyage' is from 'package:aggregation_server/marine/orm/models/voyage.dart' ('lib/marine/orm/models/voyage.dart').
Try correcting the name to the name of an existing getter, or defining a getter or field named 'id'.
      ..voyageId = voyage.id
                          ^^
lib/marine/orm/models/voyage.g.dart:322:12: Error: Duplicated parameter name 'id'.
      this.id,
           ^^
lib/marine/orm/models/voyage.g.dart:319:13: Context: Other parameter named 'id'.
      {this.id,
            ^^
lib/marine/orm/models/voyage.g.dart:349:11: Error: 'id' is already declared in this scope.
  String? id;
          ^^
lib/marine/orm/models/voyage.g.dart:338:11: Context: Previous declaration of 'id'.
  String? id;
          ^^
lib/marine/orm/models/voyage.g.dart:391:15: Error: Duplicated parameter name 'id'.
      String? id,
              ^^
lib/marine/orm/models/voyage.g.dart:388:16: Context: Other parameter named 'id'.
      {String? id,
               ^^
lib/marine/orm/models/voyage.g.dart:608:23: Error: 'id' is already declared in this scope.
  static const String id = 'id';
                      ^^
lib/marine/orm/models/voyage.g.dart:602:23: Context: Previous declaration of 'id'.
  static const String id = 'id';
                      ^^
lib/marine/orm/models/voyage.g.dart:587:5: Error: Can't use 'id' because it is declared more than once.
    id,
    ^
lib/marine/orm/models/voyage.g.dart:584:5: Error: Can't use 'id' because it is declared more than once.
    id,
    ^
lib/marine/orm/models/voyage.g.dart:319:13: Error: Can't use 'id' because it is declared more than once.
      {this.id,
            ^^
lib/marine/orm/models/voyage.g.dart:322:12: Error: Can't use 'id' because it is declared more than once.
      this.id,
           ^^
lib/marine/orm/models/voyage.g.dart:405:24: Error: Can't use 'id' because it is declared more than once.
        id: id ?? this.id,
                       ^^
lib/marine/orm/models/voyage.g.dart:405:24: Error: The getter 'id' isn't defined for the class 'Voyage'.
 - 'Voyage' is from 'package:aggregation_server/marine/orm/models/voyage.dart' ('lib/marine/orm/models/voyage.dart').
Try correcting the name to the name of an existing getter, or defining a getter or field named 'id'.
        id: id ?? this.id,
                       ^^
lib/marine/orm/models/voyage.g.dart:408:24: Error: Can't use 'id' because it is declared more than once.
        id: id ?? this.id,
                       ^^
lib/marine/orm/models/voyage.g.dart:408:24: Error: The getter 'id' isn't defined for the class 'Voyage'.
 - 'Voyage' is from 'package:aggregation_server/marine/orm/models/voyage.dart' ('lib/marine/orm/models/voyage.dart').
Try correcting the name to the name of an existing getter, or defining a getter or field named 'id'.
        id: id ?? this.id,
                       ^^
lib/marine/orm/models/voyage.g.dart:408:9: Error: Duplicated named argument 'id'.
        id: id ?? this.id,
        ^^
lib/marine/orm/models/voyage.g.dart:430:21: Error: Can't use 'id' because it is declared more than once.
        other.id == id &&
                    ^
lib/marine/orm/models/voyage.g.dart:433:21: Error: Can't use 'id' because it is declared more than once.
        other.id == id &&
                    ^
lib/marine/orm/models/voyage.g.dart:454:7: Error: Can't use 'id' because it is declared more than once.
      id,
      ^
lib/marine/orm/models/voyage.g.dart:451:7: Error: Can't use 'id' because it is declared more than once.
      id,
      ^
lib/marine/orm/models/voyage.g.dart:472:24: Error: Can't use 'id' because it is declared more than once.
    return 'Voyage(id=$id, createdAt=$createdAt, updatedAt=$updatedAt, id=$id, vesselId=$vesselId, departurePortScheduledId=$departurePortScheduledId, departurePortActualId=$departurePortActualId, departureTimeScheduled=$departureTimeScheduled, departureTimeActual=$departureTimeActual, arrivalPortScheduledId=$arrivalPortScheduledId, arrivalPortActualId=$arrivalPortActualId, arrivalTimeScheduled=$arrivalTimeScheduled, arrivalTimeActual=$arrivalTimeActual, latestLatitude=$latestLatitude, latestLongitude=$latestLongitude, status=$status)';
                       ^
lib/marine/orm/models/voyage.g.dart:472:76: Error: Can't use 'id' because it is declared more than once.
    return 'Voyage(id=$id, createdAt=$createdAt, updatedAt=$updatedAt, id=$id, vesselId=$vesselId, departurePortScheduledId=$departurePortScheduledId, departurePortActualId=$departurePortActualId, departureTimeScheduled=$departureTimeScheduled, departureTimeActual=$departureTimeActual, arrivalPortScheduledId=$arrivalPortScheduledId, arrivalPortActualId=$arrivalPortActualId, arrivalTimeScheduled=$arrivalTimeScheduled, arrivalTimeActual=$arrivalTimeActual, latestLatitude=$latestLatitude, latestLongitude=$latestLongitude, status=$status)';
                                                                           ^
lib/marine/orm/models/voyage.g.dart:525:9: Error: Duplicated named argument 'id'.
        id: map['id'] as String?,
        ^^
Error: AOT compilation failed
Generating AOT kernel dill failed!

@dukefirehawk Any thoughts?

OK, so turns out it was just because I was extending Model. If I remove that, it all seemingly works (thus no collision there). Hopefully I'm not missing out on anything else by not extending!

We are currently looking into updating ORM to support models defined in multiple files. Will look into this issue together.

We are currently looking into updating ORM to support models defined in multiple files. Will look into this issue together.

Any update to this feature? Found out this was the missing info to why my attempts to create relationships was failing. Models NEEDED to be in a single file. This info should be prominent in the documentation. I was wondering how the examples were working importing private classes like:
@hasMany
List<_Book> get books;

@belongsTo
_Author get author;

Took me way too long to figure this out.


Invalid entities in the Vaccum Map Card

Firstly, thanks so much for putting together this repo and guide. I've had a Viomi S9 for the longest time and almost gave up on integrating it with HA.
I've followed your steps in the guide and it looks like some entities you're referencing don't seem to exist:
Invalid entities:

    select.viomi_v18_155a_clean_mode

    select.viomi_v18_155a_mopping_mode

    sensor.viomi_v18_155a_clean_time

Are these entities that you manually created?

No. They were created by the MIOT integration. Which integration are you using?

I'm using the miot integration as well - same as the one linked from your guide.
I've deleted the integration and forced it to recreate the entities, but those three entries still don't show up. Odd

what is the viomi device spec detected in the integration? i.e. is it viomi_v18? Can you list the entities in your setup?

Here is what I have.
Device: viomi.vacuum.v18
Firmware: 1.6.5_2254
Here are the entities (25 of them)
sensor.viomi_v18_155a_battery_level
vacuum.viomi_v18_155a_robot_cleaner
sensor.viomi_v18_155a_device_fault
sensor.viomi_v18_155a_door_state
number.viomi_v18_155a_mute
sensor.viomi_v18_155a_status
select.viomi_v18_155a_sweep_type
select.viomi_v18_155a_wide_dynamic_range_mode
switch.viomi_v18_155a_dust_collection
sensor.viomi_v18_155a_hypa_hours
sensor.viomi_v18_155a_hypa_life
select.viomi_v18_155a_mop_route
switch.viomi_v18_155a_remember_state
switch.viomi_v18_155a_repeat_state
sensor.viomi_v18_155a_main_brush_hours
sensor.viomi_v18_155a_main_brush_life
select.viomi_v18_155a_water_grade
sensor.viomi_v18_155a_mop_hours
sensor.viomi_v18_155a_mop_life
sensor.viomi_v18_155a_clean_use_time
sensor.viomi_v18_155a_clean_area
sensor.viomi_v18_155a_side_brush_hours
sensor.viomi_v18_155a_side_brush_life
sensor.mi_1676003610_message
sensor.mi_1676003610_244001062730_scene_history

Update: I figured it out. For some reason, those three entities are named differently on my device. Here is what they map to:

Yours
Mine

select.viomi_v18_155a_clean_mode
select.viomi_v18_155a_wide_dynamic_range_mode

select.viomi_v18_155a_mopping_mode
select.viomi_v18_155a_mop_route

sensor.viomi_v18_155a_clean_time
sensor.viomi_v18_155a_clean_use_time

One I replaced the entities in your card with the mapping above, it works!

Looks like the MIOT integration has renamed those entities in an update since the time I set my device up. I will update my code to reflect this.


Beter code

This code has a pattern of checking for null and providing a default value in WHERE like this:
    AND   (pc.ProductCategoryID = @ProductCategoryID or @ProductCategoryID IS NULL)

Better code would look like this:
    AND pc.ProductCategoryID = COALESCE(@ProductCategoryID,pc.ProductCategoryID)

Document Details
⚠ Do not edit this section. It is required for learn.microsoft.com ➟ GitHub issue linking.

ID: d1f2710f-b5a5-bb12-f204-3d332ef0356e
Version Independent ID: e838c337-fabe-5a2c-f605-ee389b321227
Content: Specify parameters - SQL Server
Content Source: docs/relational-databases/stored-procedures/specify-parameters.md
Service: sql
Sub-service: stored-procedures
GitHub Login: @WilliamDAssafMSFT
Microsoft Alias: wiassaf

Thanks @hoganlong for taking the time to great this issue. This code change would complicate the content by introducing the COALESCE syntax. We feel it brings more clarity to learners of all levels of experience to use the OR.


Spaces around operators

It'd be useful to have an option to be strict about having spaces around operators. This would encourage better written code and more normalized.
I'd say also add a space between if/for/while and parenthesis. i.e. 'if (' instead of 'if(' too.. but perhaps that's asking too much and depends a lot on the taste of the programmer.

Option white enforces whitespace around operators. Also whitespace between keyword and parenthesis like if ( is enforced...
I wrote a module to refine this options (see #28), but it never get productive...
We are working on a new parser right now. It's on my list after the change ;)


Create add proponent field

#1631
-Add proponent field
-Fetch proponents by ids

@djnunez-aot  We already have proponent info coming from project api response. Make use of that like rest of the column filter and place it between SubType and ENV Region fields. You don't need any back end calls in this ticket. Thanks


python venv install issue

Lynn reported:

For some reason I’m now getting an error at the setup python env step. I had been troubleshooting our HPC issue with Hunter and it had been passing this step previously, now it appears to be broken. I wonder if our HPC packages got an update? It seems like there could be an issue with python and/or pip versions? We’re missing pkg-config?

My response was:

I’ve seen this happen before and am not 100% sure what’s causing it or how to reproduce it but my understanding of the issue is that it has to do with running from github: when you do this, it installs the python venv in the cached repository directory (as opposed to the current work directory).  Doing it this way avoid having to re-create the venv for each run but it might be better to have the venv installed in the current work directory.

A workaround is to run nextflow drop stenglein-lab/tick_surveillance (or CDCgov/…) and then run again, forcing the code to be redownloaded (I believe this works).

I think, though am not positive, that the issue is related to something described in this release note:
https://docs.reportlab.com/releases/notes/whats-new-40/
reportlab is a python module required by toyplot, and reportlab switched to using the pyCairo package instead of other pacakges.  They say:
“The renderPM extension which lets you create bitmap versions of complex graphics now uses other python libraries which wrap up freetype, the font rendering engine, so that we don't need to worry about linking to it. Under the hood it uses PyCairo as a renderer by default (rather than the no-longer-supported libart), and freetype-py to render text glyphs”
pyCairo, in turn, requires pkg-config, which isn’t available in the python3 singularity images we are using.
This confirms that even though we are using a fixed python3 singularity image, installing modules using pip will download whatever is the latest versions of various python modules, and in this case, when a module changes one of its dependencies, it can break the pipeline.
So, the way the pipeline was handling python module dependencies is not ideal: it’s not fully reproducible.
I’m going to see if I can package fixed versions of required modules with the pipeline to really make it static.

Will close when confirmed fixed in other environments.

Lynn reported:

For some reason I’m now getting an error at the setup python env step. I had been troubleshooting our HPC issue with Hunter and it had been passing this step previously, now it appears to be broken. I wonder if our HPC packages got an update? It seems like there could be an issue with python and/or pip versions? We’re missing pkg-config?

My response was:

I’ve seen this happen before and am not 100% sure what’s causing it or how to reproduce it but my understanding of the issue is that it has to do with running from github: when you do this, it installs the python venv in the cached repository directory (as opposed to the current work directory).  Doing it this way avoid having to re-create the venv for each run but it might be better to have the venv installed in the current work directory.

A workaround is to run nextflow drop stenglein-lab/tick_surveillance (or CDCgov/…) and then run again, forcing the code to be redownloaded (I believe this works).

Note that this wasn't the issue - it was related to newer version of the reportlab module, as described above


{monitor} live test fixing

https://github.com/Azure/azure-cli/issues/18187
Description

Testing Guide

History Notes

[Component Name 1] BREAKING CHANGE: az command a: Make some customer-facing breaking change.
[Component Name 2] az command b: Add some customer-facing feature.

This checklist is used to make sure that common guidelines for a pull request are followed.

[ ] The PR title and description has followed the guideline in Submitting Pull Requests.

[ ] I adhere to the Command Guidelines.

[ ] I adhere to the Error Handling Guidelines.

monitor


(bug) Validate groups are an Array

After accidentally declaring a single element group as a Hash instead of a single element Array, The stack trace that resulted was difficult to troubleshoot. This commit adds validation that groups are always arrays.
!bug

Validate inventory groups are Arrays
Raise a validation error when a group resolves to a data structure other than an Array instead.

With an inventory like:
groups:
  name: ssh
  targets:
    - name: nix_target
      uri: example.com
  config:
    transport: ssh
    ssh:
      user: root
      password: password

This was hard to diagnose:
NoMethodError: undefined method `key?' for ["name", "ssh"]:Array
  /home/cas/working_dir/bolt/lib/bolt/inventory/group.rb:27:in `initialize'
  /home/cas/working_dir/bolt/lib/bolt/inventory/group.rb:72:in `new'
  /home/cas/working_dir/bolt/lib/bolt/inventory/group.rb:72:in `block in initialize'
  /home/cas/working_dir/bolt/lib/bolt/inventory/group.rb:72:in `map'
  /home/cas/working_dir/bolt/lib/bolt/inventory/group.rb:72:in `initialize'
  /home/cas/working_dir/bolt/lib/bolt/inventory/inventory.rb:25:in `new'
  /home/cas/working_dir/bolt/lib/bolt/inventory/inventory.rb:25:in `initialize'
  /home/cas/working_dir/bolt/lib/bolt/inventory.rb:87:in `new'
  /home/cas/working_dir/bolt/lib/bolt/inventory.rb:87:in `create_version'
  /home/cas/working_dir/bolt/lib/bolt/inventory.rb:77:in `from_config'
  /home/cas/working_dir/bolt/lib/bolt/cli.rb:62:in `inventory'
  /home/cas/working_dir/bolt/lib/bolt/cli.rb:410:in `execute'
  /home/cas/working_dir/bolt/exe/bolt:11:in `<top (required)>'
  /home/cas/working_dir/bolt/vendor/bundle/ruby/2.5.0/bin/bolt:23:in `load'
  /home/cas/working_dir/bolt/vendor/bundle/ruby/2.5.0/bin/bolt:23:in `<top (required)>'

@donoghuc I think this needs a rebase to pick up some changes to CI.

This is an incomplete solution. Filed a proper bug ticket. https://github.com/puppetlabs/bolt/issues/2430


fix vale ci

Pull request checklist
Use the following template to make sure your PR fits the Web3Signer documentation standard.
Before creating the PR
Make sure that:

[x] You've read the contribution guidelines.
[x] You've previewed your changes locally.

Describe the change

fix vale ci
and update common

Issue fixed

Failed CI
Impacted parts

For content changes:

[ ] Documentation content
[ ] Documentation page organization

For tool changes:

[ ] CircleCI workflow
[x] Build and QA tools (for example, lint or vale)
[ ] MkDocs templates
[ ] MkDocs configuration
[ ] Python dependencies
[ ] Node dependencies and JavaScript
[ ] Read the Docs configuration
[ ] GitHub integration

After creating your PR and tests have finished
Make sure that:

[ ] You've fixed any issues raised by the tests.
[ ] You've previewed your changes on Read the Docs
and added a preview link.

Preview

See sucesfull checks

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


DynamicMaskHead of MMDistributedDataParallel does not matches the length of CLASSES  in CocoDataset

While training a custom dataset having 2 coco classes with the config configs/queryinst/queryinst_swin_large_patch4_window7_fpn_300_proposals_crop_mstrain_400-1200_50e_coco.py
the model shows an error like this -
  Traceback (most recent call last):   File "tools/train.py", line 188, in <module>     main()   File "tools/train.py", line 184, in main     meta=meta)   File "/content/QueryInst/mmdet/apis/train.py", line 193, in train_detector     runner.run(data_loaders, cfg.workflow)   File "/usr/local/lib/python3.7/dist-packages/mmcv/runner/epoch_based_runner.py", line 127, in run     epoch_runner(data_loaders[i], **kwargs)   File "/usr/local/lib/python3.7/dist-packages/mmcv/runner/epoch_based_runner.py", line 45, in train     self.call_hook('before_train_epoch')   File "/usr/local/lib/python3.7/dist-packages/mmcv/runner/base_runner.py", line 307, in call_hook     getattr(hook, fn_name)(self)   File "/content/QueryInst/mmdet/datasets/utils.py", line 155, in before_train_epoch     self._check_head(runner)   File "/content/QueryInst/mmdet/datasets/utils.py", line 142, in _check_head     (f'Thenum_classes({module.num_classes}) in ' AssertionError: Thenum_classes(80) in DynamicMaskHead of MMDistributedDataParallel does not matches the length ofCLASSES2) in CocoDataset
The environment is google colab with Tesla-K80 GPU enabled at GPU:0
I've updated the classes in /content/QueryInst/mmdet/datasets/coco.py , /content/QueryInst/mmdet/core/evaluation/class_names.py and also in the base files of the corresponding config file.
Please help !!

Hi, @sagnik1511! Thanks for your interest on our work.
Actually, the error logs already told us what's wrong and what to do. It seems that your custom dataset has 2 classes only, while the configuration you used still built a mask head with 80 classes. Please make sure the number of class in your model config is consistent with your custom dataset.

Thanks for replying. Actually, I've updated all the num_classes in the model configs but figured out that there was no specific variable associated with the DynamicMaskHead, so added the num_classes there and the program is running now.

It's glad to see you have solved this problem and as such I'm closing this issue. Let us know if you have any questions in the future!

Hi, @sagnik1511! Thanks for your interest on our work.
Actually, the error logs already told us what's wrong and what to do. It seems that your custom dataset has 2 classes only, while the configuration you used still built a mask head with 80 classes. Please make sure the number of class in your model config is consistent with your custom dataset.

Thanks for replying. Actually, I've updated all the num_classes in the model configs but figured out that there was no specific variable associated with the DynamicMaskHead, so added the num_classes there and the program is running now.

I also encountered this problem. I would like to ask you where you have modified and solved this problem. I look forward to your answer. Thank you！

Search for the variable DynamicMaskHead in the repo. Maybe you'll find it in the configs. Then below that config dict add a line num_classes={number of classes you want }, and it's done.


Ubuntu 15.10 CUDA-capability

Is it possible to use this with Ubuntu 15.10 just by changing around some of the files from the installation instructions?

Yes. The only issue you'll run into is that for one of the installs it'll need to use gcc 4.9 to compile, it'll tell you in the error. Ubuntu 15 is on gcc 5. so when you run into that error change your .bashrc profile to include "export cc=/usr/bin/gcc-4.9" and "export "CXX=/usr/bin/g++-4.9".  Refresh bashrc. then run your install.   After it's all done switch it back to gcc 5 before you start anymore installs.
Didn't have any other issues.


[Wait for #2381][Tensor] Resolve SrcSharedTensorV2 cyclic dependency

This PR fixes the issue of SrcSharedTensorV2 containing TensorV2 which creates cyclic dependency.
(SrcSharedTensorV2 -> TensorV2 -> TensorBase -> SrcSharedTensorV2)
Changes proposed in this PR:

SrcSharedTensorV2 owns TensorBase instead of TensorV2.
Rename SrcSharedTensorV2 as SrcSharedTensorBase accordingly.
Add functions to create and get shared data tensor.

Self-evaluation:

Build test: [X]Passed [ ]Failed [ ]Skipped
Run test:   [X]Passed [ ]Failed [ ]Skipped

:memo: TAOS-CI Version: 1.5.20200925. Thank you for submitting PR #2382. Please a submit 1commit/1PR (one commit per one PR) policy to get comments quickly from reviewers. Your PR must pass all verificiation processes of cibot before starting a review process from reviewers. If you are new member to join this project, please read manuals in documentation folder and wiki page. In order to monitor a progress status of your PR in more detail, visit http://ci.nnstreamer.ai/.


Add renameat2 and change their flags' type to c_uint

Taking over #1508. This changes the type of some flags but it should've been c_uint.
Closes #1508

r? @Amanieu
(rust-highfive has picked a reviewer for you, use r? to override)

@bors r+

:pushpin: Commit b90fda7decf7cf4ae7401966ed59da12d4b4ac4d has been approved by Amanieu

:hourglass: Testing commit b90fda7decf7cf4ae7401966ed59da12d4b4ac4d with merge e3dd6080315b16b62669346c0fe9b91fef86d3a1...

:sunny: Test successful - checks-actions, checks-cirrus-freebsd-11, checks-cirrus-freebsd-12, checks-cirrus-freebsd-13
Approved by: Amanieu
Pushing e3dd6080315b16b62669346c0fe9b91fef86d3a1 to master...

The type change causes a build failure for openat (https://github.com/tailhook/openat/issues/35).  Should this have gone through a deprecation period per the breaking change policy?

Thanks for merging this!

The type change causes a build failure for openat (tailhook/openat#35). Should this have gone through a deprecation period per the breaking change policy?

@bgilbert I'd consider it as bugfix since renameat2 needs c_uint as their flag and the initial definition (i.e. c_int) should be wrong in that context. But hmm is there any use of the flags as c_int?

Well, it can be a bugfix and still be a breaking change. :slightly_smiling_face:  But meanwhile, openat has been updated with a workaround in https://github.com/tailhook/openat/pull/36.


feat: add rangeExtractor

closes #163

Love this. 🎉

Would you be up to adding an example to both the sandboxes and the docs?

:tada: This PR is included in version 2.8.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:

Would you be up to adding an example to both the sandboxes and the docs?

Yes, also would be good to update other example, something is wrong with Infinite Scrolling

@piecyk Sort of tangentially related, but I saw on the original issue #163 that an isVisible key value was in the works. I am wondering if this value could be used to memoize rows to also prevent rerenders on scroll. While this addition is helpful for performance, I think preventing row rerenders on scroll unnecessarily is probably something i'd appreciate for my infinite scrolling implementation

@jonahallibone you can do it now, by using memo on row. One problem is in dynamic context as the measureRef is re-crated for every range change, but you can always have an extra div wrapping the memo item.
Also we can move measureRef to measurements then problem that it's breaking memo will be resolved.


Adding local genomes: KeyError: assembly_acc

Hi!
I am trying to add some local genomes to my mtdb, following the tutorial/usage instructions. I keep getting the following error with the example:
# follow commands in tutorial
jgiDwnld -i Ustbr1 -a -g # this works

mtdb p Ustbr1.predb.tsv
##### output #####
Preparing run

Generating omes
Traceback (most recent call last):
  File "/home/toby/miniforge3/envs/mycotools/bin/predb2mtdb", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/toby/miniforge3/envs/mycotools/lib/python3.12/site-packages/mycotools/predb2mtdb.py", line 666, in cli
    omedb, failed = main(predb, refDB, wrk_dir, exit = exit, verbose = True,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/toby/miniforge3/envs/mycotools/lib/python3.12/site-packages/mycotools/predb2mtdb.py", line 598, in main
    omedb, failed = gen_omes(infdb, refdb, ome_col = 'ome', forbidden = forbidden,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/toby/miniforge3/envs/mycotools/lib/python3.12/site-packages/mycotools/predb2mtdb.py", line 306, in gen_omes
    refdb_accs = set([x for x in list(refdb['assembly_acc']) if x])
                                      ~~~~~^^^^^^^^^^^^^^^^
KeyError: 'assembly_acc'

I then tried with a small test sheet that is automatically generated by predb2mtdb and get the same error:
Here is the small test I am using:
#assembly_acc	previous_ome	genus	species	strain	version	assemblyPath	gffPath	genomeSource (ncbi/jgi/new)	useRestriction (yes/no)
GCA_927399515_3	laesul3	Laetiporus	sulphureus	NA	3	/data/toby/fungi_htt/1_sourcing_genomes/dtolGenomes/include/GCA_927399515.3_gfLaeSulp1.3_genomic.fna	/data/toby/fungi_htt/1_sourcing_genomes/dtolGenomes/include/GCA_927399515.3_gfLaeSulp1.3_genomic.gff3	new	no

Then output of mtdb p test_2.tsv :
Preparing run

Generating omes
Traceback (most recent call last):
  File "/home/toby/miniforge3/envs/mycotools/bin/predb2mtdb", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/toby/miniforge3/envs/mycotools/lib/python3.12/site-packages/mycotools/predb2mtdb.py", line 666, in cli
    omedb, failed = main(predb, refDB, wrk_dir, exit = exit, verbose = True,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/toby/miniforge3/envs/mycotools/lib/python3.12/site-packages/mycotools/predb2mtdb.py", line 598, in main
    omedb, failed = gen_omes(infdb, refdb, ome_col = 'ome', forbidden = forbidden,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/toby/miniforge3/envs/mycotools/lib/python3.12/site-packages/mycotools/predb2mtdb.py", line 306, in gen_omes
    refdb_accs = set([x for x in list(refdb['assembly_acc']) if x])
                                      ~~~~~^^^^^^^^^^^^^^^^
KeyError: 'assembly_acc'

Is there something locally that could be causing this issue?
Thanks in advance for your help!
Toby

This might be unrelated, but essentially I'm trying to add some genomes from the Darwin Tree of Life project to my database. Currently the assemblies are on NCBI but lacking annotations. I've done a quick + dirty annotation for the moment with augustus (as I don't need them for the moment, but I know they are required for MTDB), but the GFF3 curation is failing for all these genomes when I run:
mtdb update -i [primary_db] --predb predb.tsv

But here I don't get the key error, I just get GFF3 curation failed for [genome_name]. The augustus outputs are quite different from those in the existing db. I've tried to look in the documentation to see what fields are actually required but seem to have lost this now, do you have any advice on how to get these GFFs to play nicely? They currently look like this after I've messed with them a bit:
##gff-version 3
# This output was generated with AUGUSTUS (version 3.5.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initializing the parameters using config directory /home/toby/miniforge3/envs/mycotools/config/ ...
# neurospora_crassa version. Using default transition matrix.
# Looks like /data/toby/fungi_htt/1_sourcing_genomes/dtolGenomes/include/GCA_927399515.3_gfLaeSulp1.3_genomic.fna is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 4563458, name = OV656674.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
OV656674.1      AUGUSTUS        gene    1070    4795    0.68    +       .       ID=gene_g1
OV656674.1      AUGUSTUS        start_codon     1070    1072    .       +       0       Parent=gene_g1
OV656674.1      AUGUSTUS        CDS     1070    4792    0.68    +       0       ID=cds_g1.t1.cds;Parent=gene_g1
OV656674.1      AUGUSTUS        stop_codon      4793    4795    .       +       0       Parent=gene_g1
# protein sequence = [MRDSLLASLSRAGSPVPGRVAAATTLPIEASAVPPLANAPGPSGSAVAAATAIGADVSRYVTQRSREAVQAASSWVEL
# VALWPGSYREGVKPLMKEIWELAGSYAGATEAFERLSVHQKSPTTARTYPQHYAAVRIPAMQTSSEFGRTNDALSFKRELEDTVRNAKEAMLDVEYRA
# RSNEVHYLQTRLDPQKWVRDLHAVIERIYARDVQPFALEPPSLGGALGDGDVVMGDGGAQPPPPARDSWTVTKGARDERTFARNLAMHLIPRMMVVRR
# GAVANHREKQHAKESLKRAADTSAGASVPANLKQVVKAQVQAALASTSKGSVSIASVSLDIFLNPFTQTSSAKPKAPVAKPSGGGPTRSSGSKRPSGA
# AKRAKKNSKPYSTAGSGATADMRVVRRVFNLVGAQEDRSEDRAGRKREGEGQSESLADLLVKVLVSPWEYDRPSTYPDEILDLPSSVAQAVVWSRAPL
# ELIESARFRAGVHMGPNVSVPLELLVHASVGLNYLFASPPRASMVVRAWREFERRVRWSAVFVKESKTPYDPDYDSGRRSQKEPPLAPRAIEDGLLAG
# RQLLRSRVRHAHTARIVSRNVLLSSLVDVTPLLEVLKDNAYLIVPTDKNLGVAVVAAEWYVAECRKLLTNDVKIRSIDAYVAEILRSDLADKLEAVLL
# RHQSWLEDGNPQLWDYLRSTLIVRSGDGSAYLPEFKGLPKIHKTPWRMRPIVPGHSLIMSPSAKFVSKSLKPIIAQRPYVLESSRKLARDLSELRLLG

Thanks again!

I might be getting closer to solving this - sorry for all the separate messages! So I have managed to run:
mtdb update --init /data/toby/fungi_htt/1_sourcing_genomes/dtolGenomes/ --predb ../predb.tsv

And I have a successful mtdb file, along with the directories with faa, fna, and gff3, each with 31 non-empty files in them, as expected.
Now when I try to add this to my main db:
### reattach to the main database
mtdb -i /data/toby/fungi_htt/1_sourcing_genomes/mycotools_db/mycotoolsdb/
##### output
# Establishing fungi connection
# /data/toby/fungi_htt/1_sourcing_genomes/mycotools_db/mycotoolsdb/mtdb/20240717.mtdb

### add the new genomes
mtdb update -a /data/toby/fungi_htt/1_sourcing_genomes/dtolGenomes/mycotoolsdb/mtdb/20241010.mtdb

ERROR: some paths in addition MTDB do not exist:
        FNA: True; GFF3: True; FAA: True

I get the same error if I attach the new database and try to add the original one, which makes me think there is a potential issue with the resolution of filepaths when adding genomes from a new db in a different directory. I've checked the data dir of the new db with the genomes to add, and all files look as expected.

Hey Toby,
In response to your first message, I could not reproduce your error and I think I understand why through your next messages.

mtdb predb2mtdb is for adding genomes to an existing and initialized MTDB. you should have already initialized an MTDB. You can check if you are linked to an initialized MTDB by running mtdb on its own. You can initialize a new database from a predb using the command you attempted in 2.

mtdb update -i [primary_db] --predb predb.tsv - this command indicates to me you are not initialized. The -i flag means initialize, and what you are putting for [primary_db] should be the new initialization directory if you are initializing from a predb.tsv.

I have not accounted for Augustus GFF3s in curation. The one you're presenting me looks different from standard GFF3s. I would atttempt to use an Augustus GTF if you have it, some GTFs can be accounted for.

I think to summarize what you were doing incorrectly is that you were unlinked trying to add a predb to an existing database. You then attempted to initialize a new database with the predb, linked to the database you actually wanted, and tried to add the source MTDB you initialized to the one you actually wanted, but the database you were adding lacked paths because you were trying to add the source MTDB. You fixed your issue by linking to the correct database and just running predb2mtdb from there. Some of this is obfuscated and needs to be made easier.

Awesome thanks for the explanation! I think I confused myself and ended up linking + unlinking and all sorts! It all worked super well in the end - thanks for making such a great tool!


Unable to login, release 1.24.2

Unable to login with the new release, using sessionID to login since I play POE via Steam
As seen via the Procurement Gui
Procurement 1.24.2 Initialized.
Authenticating ....
[Error] Cloud flare clearance failed, please wait one minute and try again
Authenticating ....                                                                    [OK]
Fetching account name...
[Error] Error downloading account name, details logged to DebugInfo.log. Please open a ticket at https://github.com/Stickymaddness/Procurement/issues and include your DebugInfo.log
[23-12-2018 17:22] Failed to build HTTP request and get response for: method=GET, url='https://www.pathofexile.com/login', allowAutoRedirects=, requestData='': The remote server returned an error: (503) Server Unavailable. [23-12-2018 17:22] System.Exception: Cloud flare clearance failed, please wait one minute and try again ---> System.AggregateException: One or more errors occurred. ---> CloudFlareUtilities.CloudFlareClearanceException: Clearance failed after 3 attempt(s).    at CloudFlareUtilities.ClearanceHandler.<SendAsync>d__20.MoveNext()    --- End of inner exception stack trace ---    at System.Threading.Tasks.Task1.GetResultCore(Boolean waitCompletionNotification)
at POEApi.Transport.HttpTransport.CloudFlareSessionIdLogin()
--- End of inner exception stack trace ---
at POEApi.Transport.HttpTransport.CloudFlareSessionIdLogin()
at POEApi.Transport.HttpTransport.Authenticate(String email, SecureString password, Boolean useSessionID)
at POEApi.Model.POEModel.Authenticate(String email, SecureString password, Boolean offline, Boolean useSessionID)
at Procurement.ViewModel.LoginWindowViewModel.<>c__DisplayClass25_0.b__0()
at System.Threading.Tasks.Task.Execute()
[23-12-2018 17:23] Failed to build HTTP request and get response for: method=GET, url='https://www.pathofexile.com/login', allowAutoRedirects=, requestData='': The remote server returned an error: (503) Server Unavailable.
[23-12-2018 17:23] Failed to build HTTP request and get response for: method=GET, url='https://www.pathofexile.com/character-window/get-account-name', allowAutoRedirects=, requestData='': The remote server returned an error: (401) Unauthorized.
[23-12-2018 17:23] Error downloading account name, exception details: System.Net.WebException: The remote server returned an error: (401) Unauthorized.
at System.Net.HttpWebRequest.GetResponse()
at POEApi.Transport.HttpTransport.BuildHttpRequestAndGetResponse(HttpMethod method, String url, Nullable1 allowAutoRedirects, String requestData)    at POEApi.Transport.HttpTransport.PerformHttpRequest(HttpMethod method, String url, Nullable1 allowAutoRedirects, String requestData)
at POEApi.Transport.HttpTransport.GetAccountName()
at POEApi.Model.POEModel.GetAccountName()
[23-12-2018 17:23] System.Exception: Error downloading account name, details logged to DebugInfo.log. Please open a ticket at https://github.com/Stickymaddness/Procurement/issues and include your DebugInfo.log
at POEApi.Model.POEModel.GetAccountName()
at Procurement.ViewModel.LoginWindowViewModel.<>c__DisplayClass25_0.b__0()
at System.Threading.Tasks.Task.Execute()`

This definitely looks like your culprit, as I can use the same URL and get the page to open myself
[23-12-2018 17:34] Failed to build HTTP request and get response for: method=GET, url='https://www.pathofexile.com/character-window/get-account-name', allowAutoRedirects=, requestData='': The remote server returned an error: (401) Unauthorized.
[23-12-2018 17:34] Error downloading account name, exception details: System.Net.WebException: The remote server returned an error: **(401) Unauthorized.**

I have the same error and I'm not using Steam

This has been fixed in the newer releases of Procurement, if you still encounter issues please open a new ticket.


./stream.go:53: unknown websocket.Dialer field 'Jar'

Go/src/github.com/docker/go-dockercloud/dockercloud (master=)$ go test
# github.com/docker/go-dockercloud/dockercloud
./stream.go:53: unknown websocket.Dialer field 'Jar' in struct literal
FAIL	github.com/docker/go-dockercloud/dockercloud [build failed]

Do you have the latest version of gorilla websocket?

No, I did not! My bad.
Thanks a lot.
I'm still getting used to managing transitive dependencies in Go.


change loadtesting catalog

@qiaozha Please ask service team to change the service name in all sdk, and in the spec repo. For example, change specification/loadtestservice to specification/loadtesting.

/azp run


Fix brew tap command in readme

Thanks for the fix, this is currently WIP but I expect a first version to be ready very soon :).