webpack watch mode not working....

General Information:
webpack version: 1.13.2
OS: Windows 10 Anniversary Update and webpack is running in Windows Subsystem for Linux(The new bash on Ubuntu)
I"m trying to run webpack in watch mode by using:
webpack --watch

and by also setting watch mode in config:
context: path.join(__dirname, '/src'),
devtool: debug ? 'inline-sourcemap' : null,
entry: './js-src/scripts.js',
watch: true,
module: {

All webpack does is run the transpiler and exit.
Example of output when running watch mode:
Hash: 045070ba2ed9ce40edf7
Version: webpack 1.13.2
Time: 2146ms
         Asset     Size  Chunks             Chunk Names
scripts.min.js  1.89 MB       0  [emitted]  main
    + 172 hidden modules

I'm not sure what i'm doing incorrect?

Could you please first post your question on stack overflow before you post here. Our issue template clearly encourages submitters to submit their questions/support there so that you have more accessible support. When you have submitted the question to stackoverflow, please provide the link there for easier access.

Could you please provide your full webpack configuration.

Since I think it's a possible issue I think this is the appropriate place:  Full webpack config:
var debug = process.env.NODE_ENV !== 'production';
var path = require('path');
var webpack = require('webpack');

module.exports = {
  context: path.join(__dirname, '/src'),
  devtool: debug ? 'inline-sourcemap' : null,
  entry: './js-src/scripts.js',
  watch: true,
  module: {
    loaders: [
      {
        test: /.js?$/,
        exclude: /(node_modules)|(bower_components)/,
        loader: 'babel-loader',
        query: {
          presets: ['react', 'es2015', 'stage-0']
        }
      }
    ]
  },
  output: {
    path: path.join(__dirname, '/src/wwwroot/static/js'),
    filename: 'scripts.min.js'
  },
  plugins: debug ? [] : [
    new webpack.optimize.DedupePlugin(),
    new webpack.optimize.OccurenceOrderPlugin(),
    new webpack.optimize.UglifyJsPlugin({ mangle: false, sourcemap: false }),
  ],
};

Thanks!

OS: Windows 10 Anniversary Update and webpack is running in Windows Subsystem for Linux(The new bash on Ubuntu)

Probably chokidar has an issue with this...

Their issue list has a few maybe related things. @mastrauckas is there any additional details that you think might be beneficial that we (you could also as well) could submit to @paulmillr?

@TheLarkInn I have no additional information.  Should I just put a ticket on their issue list and refer back to this ticket?

@mastercactapus I would be glad to help you (i've created chokidar). Are you able to set up a demo git repo that makes it easy to replicate the issue?

@paulmillr I can pull down any demo you want me too from git and run it.  I might not be able to do it until tomorrow though.

@paulmillr thank you very much!!

@mastrauckas I think you have a typo
devtool: debug ? 'inline-sourcemap' : null,
should be
devtool: debug ? 'inline-source-map' : null,

@rafde Thanks for noticing that.  I'll fix that tonight and see if it fixes the issue.

@rafde That didn't fix the issue.  @paulmillr what did you want me to demo?

Would be great to have a demo repository where i'll be able to reproduce the issue simply without hassle and messing with configs.

@paulmillr FWIW, I experience the exact same thing on a number of webpack projects in Windows Subsystem for Linux, which have wildly varying configs. Therefore I'm not sure prepping any particular repo will help.
All that said, I share Sokra's hunch that this is either in chokidar or simply a core bug in this fancy new Windows feature. So I cloned chokidar, ran tests, got 19 passes and 76 failures (gist: https://gist.github.com/eteeselink/0c7394eab588d0851d8633cc0ade7c3f). Running the same tests on plain windows gives 0 test failures. Node 6.5.0 on both "platforms". Removed node_modules and re-did npm install before running tests on either system.

@paulmillr Like @eteeselink said it might be a an issue in the Windows Subsystem.  Here is a demo project  https://github.com/mastrauckas/webpack-issue that is having an issue.  I you need me to do anything else please let me know.

What about webpack tests? Does everything pass on the subsystem?

Here is the result of running npm test for webpack.

@paulmillr here is the result of running npm test on chokidar

68 failing tests for webpack.
Basically this means Windows subsystem for Linux is broken and shitty. I'll see what we can do here but a more robust solution would be to cease using it until Windows developers would fix all issues.

@paulmillr that's a perfectly valid solution for me, FWIW. WSL is beta so some incompatibilities are to be expected, i guess.
I just discovered it's a known bug in WSL: https://github.com/Microsoft/BashOnWindows/issues/216. If I were @sokra I'd close this bug until MS fixes inotify.
For people who find this webpack issue, the issue linked above lets you vote on this on UserVoice: https://wpdev.uservoice.com/forums/266908-command-prompt-console-bash-on-ubuntu-on-windo/suggestions/13469097-support-for-filesystem-watchers-like-inotify

I'm going to reply to the bug @eteeselink  put a like to.

https://github.com/Microsoft/BashOnWindows/issues/216 has been closed

I've unistalled Bash on Windows 10 and webpack --watch still isn't working. Even with a very simple config like:
module.exports = {
    entry: './entry.js',
    output: {
        path: __dirname,
        filename: "bundle.js"
    }
};

Path to project is d:\_WWW\!_serwer_root\_test\webpack (if that is important). And entry.js just contains:
console.log('123');

Nevermind... The problem was the ! in the directory name :-/

Moved to https://github.com/webpack/webpack-cli/issues/17.

Try this workaround:
Add this to your webpack configuration file:
    watchOptions: {
        poll: true
    },

    poll: true
}```

Thank you. This solution works for me.

I am on webpack 3, and I have poll option enabled, still Webpack picks up first few writes and then doesn't do that. I have tried saving the files via emacs and atom.

I have similar problem on Linux Mint 18.2. After fix inotify issue works fun :)

@lahdo thank you!

This still doesn't work for me.
I run npm run watch and make a change to index.js and a build is not triggered:
webpack.config.js
const path = require('path');

console.log("__dirname: " + __dirname);

module.exports = {
	entry: "./public/js/index.js",
	output: {
		filename: "bundle.js",
		path: path.resolve(__dirname, 'public/js')
	},
	 watchOptions: {
        poll: true
    }
}

package.json
  "scripts": {
    "start": "nodemon ./app.js --exec babel-node -e js",
    "build": "webpack",
    "watch": "webpack --w"
  },

Environment:
node -v
v10.0.0
npm -v
5.6.0
Windows 10 Professional, 64 Bit

@lahdo I know, It's a ghost thread, but still - thank you, I've really struggled with this issue!

@lahdo thank you too, saved my day, literally!

For anyone stumbling upon this when using the node API, having
watchOptions: {
  poll: true
}

In the webpack config didn't work for me, I had to feed it into the compiler.watch function, not sure if this is intended.
const webpack = require('webpack');

const compiler = webpack({
  // these options do not seem to effect compiler.watch
  watchOptions: {
    poll: true,
  },
});

const watching = compiler.watch({
  poll: true // this works
}, (err, stats) => { // Stats Object
  console.log(stats);
});

For googlers,
On wsl 2 you have to set poll, poll: 1000 worked for me.

This just happened to me.
The compilation starts and finishes without any error, but it does not continue to watch for changes.
It acts as if watch is disabled.
My webpack.config.js is:
module.exports = () => ({
    entry: path.resolve(__dirname, 'src/index.ts'),
    mode: NODE_ENV,
    watch: true,
    target: 'node',
...
// rest of config (uninportant I think)
...
}

And I am running webpack via NODE_ENV=development webpack
I found the problem in my case is combination of
"webpack": "^4.44.2",
"webpack-cli": "^4.0.0",

If I change webpack-cli to version "^3.3.12" and update my deps, then everything works as expected.
Don't know why this is, but I hope it can help somebody solving the problem for themselves.
Also should mention that I am using:
yarn version - 1.22.4
node version - v14.13.0

@zatloeri Please create reproducible test repo and open an issue in webpack-cli

I had this problem, just updated webpack-cli from 4.0.0 to 4.1.0 and it fixed it!

@lahdo Thank you so much. It works.
Here is part of my Webpack setting.
module.exports = {
  watchOptions: {
    ignored: /node_modules/,
    poll: true
  }
};

"webpack": "4.31.0",
"webpack-cli": "3.3.2",
"webpack-dev-server": "3.10.3"
WSL 2
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.5 LTS
Release:        18.04
Codename:       bionic
FYI webpack watch option
https://webpack.js.org/configuration/watch/#watchoptionspoll
However, but I still don't understand that I don't have to set this option when I use Windows.
If someone can explain, I will appreciate it.
Thanks.


[WIP] Implement support for metrics in ark server

Add a metrics package to handle metric registration and publishing
Add a metricsAddress field to the server struct
Start a metrics endpoint as part of starting the controllers
Report backup status on backup completion

Starting a WorkInProgress PR to get some feedback on the approach here to add metrics. Related to #84  Adding some code to the discussion on the issue.

I will sign my next commit :)

Just did a very quick first pass

@ncdc Thanks for the quick review! I've made changes to address your comments. I will now start adding some metrics

I don't have any additional comments. Excited for this!


MacOS Ventura service is not working with default package

I've been trying to install macOS ventura in my NixOS computer but the rebuild process failed due to apparently something's wrong with the macOS module, you can reproduce this error with the snippet of the image below

Here's the underlying error

A workaround for me is to create the package directly from the flake itself.

Until then, everything else works as expected. I tried the macOS option and I want to say what you've been doing is great and it seems that it will save me a lot of money by saving me from buying a macOS just to do some app builds for iOS. :)

The nixosModule is tested in CI, there has to be something else going on in some code that you are not displaying in the screenshots, for example inside of ./system/configuration.nix.
I notice you have pkgs defined since you are inheriting it. Can you show me how you defined it?

Here you can find some definitions that I have on my computer

pkgs definition (flake)
MacOS ventura service

Also, I don't think it's relevant but you can find the mkSetup definition here
The macOS module is disabled because I already used it and I don't wanted it to consume space until the next time

You can find this other configuration that I have used and got the same result, it is from a computer at my work that has NixOS installed and is not complex like my personal flake. In fact, the first two screenshots are from that computer.

@luisnquin I see you're applying a lot of overlays, and I think you're doing expressing something wrong and clobbering the overlay from this flake somehow. It is not easy to debug, but I hope this gives you something to go on.

Currently busy travelling, but I'll get back to this if you don't figure it out, when I get home again.

Don't worry, I'm currently using the workaround I mentioned before. The issue might be when someone tries to start the service with the default package.

@luisnquin it definitely isn't that, because if you craft a barebones Nix flake without any of your code in it, this doesn't happen. The issue is in a nix expression you're including into your own config which includes other overlays. I'm fairly confident that it is your Nix code causing the problem at this time, having tested it myself. But debugging your config will be a bit time consuming for me right now, but I'm up for it when I get home.

Closing, as the issue cannot be reproduced and is likely an issue with the user's Nix expression, and not with the project.


Typo correction

Fix a typo.

@chenxu2394 Please sign the Contributor License Agreement!
Click here to manually synchronize the status of this Pull Request.
See the FAQ for frequently asked questions.

Thank you!


[BUG] SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x77820f]\n\ngoroutine 436 [running]:\ngo/types.(*Checker).handleBailout(0xc0007fa8c0,

Setting a Baseline
Please start by providing the necessary insights to ensure you can be helped swiftly
Which version of the Action are you using: <>
How does your configuration look like:
      - name: Go Vulnerability Check
        uses: Templum/govulncheck-action@v1
        with:
          go-version: 1.23.2

Logs:
Please share the output of the action, preferably turning the Action into Debug mode. This can be done by specifying an env called DEBUG and setting it to true.
Run Templum/govulncheck-action@v1
Run docker build --build-arg GOLANG_VERSION=1.23.2 --build-arg GH_PAT_TOKEN=$GH_PAT_TOKEN --build-arg GOPRIVATE=$GOPRIVATE --build-arg VULNCHECK_VERSION=v1.0.0 -q -f $GITHUB_ACTION_PATH/Dockerfile -t templum/govulncheck-action:local $GITHUB_ACTION_PATH

sha256:cd3800f950226dc2a17f71df466c92a8bf603a6023edaf8693f9a151f5f2a4dd
Run docker run --rm -v $(pwd):/github/workspace --workdir /github/workspace -e GITHUB_TOKEN=*** -e STRICT=false -e PACKAGE=./... -e SKIP_UPLOAD=false -e DEBUG=${DEBUG} -e GITHUB_REPOSITORY=joe-at-startupmedia/version-bump -e GITHUB_REF=refs/heads/master -e GITHUB_SHA=586064c60848a933d036562e68d07189482e438e templum/govulncheck-action:local
5:10AM INF GoEnvironment Details: GOPRIVATE= Go-Arch='amd64' Go-Os='linux' Go-Version='go1.23.2'
5:10AM INF Running govulncheck for package ./... in dir /github/workspace
5:10AM ERR govulncheck exited with none 0 code error="exit status 2" Stderr="panic: runtime error: invalid memory address or nil pointer dereference [recovered]\n\tpanic: runtime error: invalid memory address or nil pointer dereference\n[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x77820f]\n\ngoroutine 436 [running]:\ngo/types.(*Checker).handleBailout(0xc0007fa8c0, 0xc00081dbf0)\n\t/usr/local/go/src/go/types/check.go:404 +0x88\npanic({0x8891c0?, 0xc8e940?})\n\t/usr/local/go/src/runtime/panic.go:785 +0x132\ngo/types.(*StdSizes).Sizeof(0x0, {0x9d2fe0, 0xc95700})\n\t/usr/local/go/src/go/types/sizes.go:229 +0x30f\ngo/types.(*Config).sizeof(...)\n\t/usr/local/go/src/go/types/sizes.go:334\ngo/types.representableConst.func1({0x9d2fe0?, 0xc95700?})\n\t/usr/local/go/src/go/types/const.go:77 +0x86\ngo/types.representableConst({0x9d5d70, 0xc6ce60}, 0xc0007fa8c0, 0xc95700, 0xc00081b658)\n\t/usr/local/go/src/go/types/const.go:93 +0x173\ngo/types.(*Check
5:10AM INF govulncheck information Database=https://vuln.go.dev/ Protocol Version=v1.0.0 Scanner Version=v1.0.0
5:10AM INF Successfully scanned project
5:10AM INF Conversion yielded following stats Call Sites=0 Vulnerabilities=0
5:10AM INF Preparing Report for upload to Github Commit=586064c60848a933d036562e68d07189482e438e Ref=refs/heads/master
5:10AM INF Report was uploaded to GitHub sarif_id=406f82b8-8d0f-11ef-885c-0506fb72b015
5:10AM INF Successfully uploaded Sarif Report to Github, it will be available after processing

Bug Description
"panic: runtime error: invalid memory address or nil pointer dereference [recovered]\n\tpanic: runtime error: invalid memory address or nil pointer dereference\n[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x77820f]\n\ngoroutine 436 [running]:\ngo/types.(*Checker).handleBailout(0xc0007fa8c0,
Screenshots
https://github.com/joe-at-startupmedia/version-bump/actions/runs/11397804013/job/31713843122#step:6:156

This error is coming from the govulncheck binary and not from the action. Hence I would kindly ask you to see if you receive the same error when locally running the binary against your code base.
Alternatively you can also try to update the version of govulncheck, via the action parameter.

Thanks for the quick response.
This adjustment fixes it:
https://github.com/joe-at-startupmedia/version-bump/commit/968efddb023472fd5c00299cf36308c34e73da2f#diff-87db21a973eed4fef5f32b267aa60fcee5cbdf03c67fafdc2a9b553bb0b15f34R56
Workflow run:
https://github.com/joe-at-startupmedia/version-bump/actions/runs/11411930625/job/31757056950#step:6:1
Without looking into the issue too much, the default version is v1.0.0. When looking at the changelog for v1.0.1 the point of failure in the workflow above was specifically addressed (types.(*StdSizes).Sizeof). Maybe consider incrementing the default version by a patch or two?
https://go.googlesource.com/vuln/+/refs/tags/v1.0.1
In either case I will mark this as closed.

I will check what you have reported and adjust the version as needed.


Recently opened folder

I want "Recently opened folder"

Ctrl + R
or cmd + R if you are on a mac

thank you


expose reportedHostUuid to users in the host api

This is the field that is used by websocket-proxy and host-api to register hosts. It appears in rancher-server logs. So it would be good for debugging if we exposed this field in the API

Closed due to inactivity.


Add webhook handler for auto-mounting projected ServiceAccount tokens into Pods

How to categorize this PR?

/area security
/kind enhancement
What this PR does / why we need it:
This PR adds a webhook handler for auto-mounting projected ServiceAccount tokens into Pods in case their referenced ServiceAccount sets .automountServiceAccountToken=false.
Special notes for your reviewer:

~✅ Based on #4817 which should be merged first~
~Only the last four commits are relevant (the others belong to #4817)~

Release note:

`gardener-resource-manager` can now auto-mount projected `ServiceAccount` tokens into `Pod`s in case their referenced `ServiceAccount` sets `.automountServiceAccountToken=false`. Please consult [this document](https://github.com/gardener/gardener/blob/master/docs/concepts/resource-manager.md#auto-mounting-projected-serviceaccount-tokens) for more information.

@rfranzke seems like  /go/src/github.com/gardener/gardener/pkg/resourcemanager/webhook/projectedtokenmount/handler_test.go:247 is failing in verify. Can you check?

@BeckerMax done


[FEATURE REQ] mgmt, Java SDK PolicyDefinition - Mode and Metadata

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
Describe the solution you'd like
A clear and concise description of what you want to happen.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.
Information Checklist
Kindly make sure that you have added all the following information above and checkoff the required fields otherwise we will treat the issuer as an incomplete report

[ ] Description Added
[ ] Expected solution specified

expect fix in 2.39.0


Scenario text is not coming in console in windows!

hey, everyone, I am not getting a feature text in windows console.
Please find an attachment.

I hope you understand that just a single screenshot without much context or background into your suite setup makes it impossible to help you.
Please collect more context about your environment and open a new issue conforming to our very simple contribution guide. Then we will be able to help you.

Hey!!
I am using window 8. and having
behat - 3.2.1 version.
mink - 1.5.0
mink-extension - 2.0.1
drupal-extension - 3.0
mink-goutte driver - 1.0
PHPUnit - 3.7.37
SO here us my feature file -
Feature: Some terse yet descriptive text of what is desired
In order to realize a named business value
As an explicit system actor
I want to gain some beneficial outcome which furthers the goal
@blackbox @1
Scenario: User Visits at some site for the first time.
Given I am on "/"
And I should see "site's title"
Do i need to tell anytihng?

I added the information.
On Sun, Oct 30, 2016 at 4:39 PM, Konstantin Kudryashov <
<EMAIL_ADDRESS>wrote:

I hope you understand that just a single screenshot without much context
or background into your suite setup makes it impossible to help you.
Please collect more context about your environment and open a new issue
conforming to our very simple contribution guide
https://github.com/Behat/Behat/blob/master/CONTRIBUTING.md#submitting-an-issue.
Then we will be able to help you.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/Behat/Behat/issues/962#issuecomment-257144889, or mute
the thread
https://github.com/notifications/unsubscribe-auth/ARWCj6XsSiCvWikWgyLZj6EviXm4c48Fks5q5HragaJpZM4KjGel
.

--
Regards,
Karan Kural
Contact : +91 9999 812 027
Skype : karan.kural | Twitter : karan_kural


Ignore unknown JSON keys

Hello,
Thank you for keeping this library updated. I've been scratching my head for a while about this, I'm trying to get this serialiser factory to ignore any unknown keys, so as to not have to include loads of keys that I do not need. The Kotlin serialisation docs say that it can be accomplished with the ignoreUnknownKeys property, but it doesn't look like this library uses the Json builder at all. Is it possible to set this option in some way?

This library actually uses the Json Builder more or less.
You can create a Json object with the builder and call asConverterFactory on that json object.
val contentType = "application/json".toMediaType()
val retrofit = Retrofit.Builder()
  .baseUrl("https://example.com/")
  .addConverterFactory(Json {
    ignoreUnkownKeys = true
  }.asConverterFactory(contentType))
  .build()

Ah, that makes sense now. Thank you!


Cleanup AccessMarkerElimination.

In raw SIL, access markers are unconditionally retained. In canonical SIL,
markers are still removed prior to optimization.
A new flag, -sil-optimized-access-markers, allows testing access markers in
optimized builds, but it is not yet fully supported.

@swift-ci smoke test and merge.


chore(deps): upgrade dependencies

Upgrades project dependencies. See details in workflow run.

Automatically created by projen via the "upgrade-k8s-25-main" workflow

⚪ Backport skipped
The pull request was not backported as there were no branches to backport to. If this is a mistake, please apply the desired version labels or run the backport tool manually.
Manual backport
To create the backport manually run:
backport --pr 1429

Questions ?
Please refer to the Backport tool documentation


fix: :bug: concurrence printing issue on pos-app

Description

Issue: long delayInSeconds = 3; is not enough for printer to handle multiple print requests. the print job come later get failed immediatedly on line 98
Solution: Increase delayInSecond of printing to 10
Related Issues

Issue: #XXX
How Has This Been Tested

Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist

[ ] My code follows the code style of this project.
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

Screenshots (if appropriate)

This description is not true @tillpos-tony ...

long delayInSeconds = 3; is not enough for printer to handle ONE large print request or a delay in sending data to the printer.
The one print job TAKES longer than 10s get failed on line 98, all other print jobs will have to wait for this one print job until it fails. There is a chance that a serial of waiting job will fail the 10s delay like dominos, but hopefully the iPad job queue and the code locks will prevent that. To be determined


cudnn and combined char+word model

Hi,
Thanks for building this nice tool!

Do you have any plans to incorporate cudnn's LSTM implementation (e.g. from cudnn.torch) for speed-up?
Is there an option to use a combined char+word model in the same way as in the original language modelling work?

Hi!

we do not currently have plans to incorporate this
currently we do not support this, but I imagine this won't be too difficult to incorporate (basically, you will need to modify models.lua to be similar to the original LSTMTDNN.lua code, and also modify the inputs/gradients during training. Finally, you want to modify data.lua so you can get both characters and words as inputs).

Yoon


Beta - Add Different Margins to Each Side - Guide Page 404 Not Found

Challenge Name

https://beta.freecodecamp.org/en/challenges/basic-css/add-different-margins-to-each-side-of-an-element
Issue Description

When selecting the 'Get Hint' button, it re-directs you to the guides but there is no guide page for this challenge.
Returns Page not found.
Browser Information

Browser Name, Version: Chrome 64.0.3282.186 64-bit
Operating System: Windows 10 Pro 64-bit
Mobile, Desktop, or Tablet: Laptop
Your Code

Screenshot

URL: https://guide.freecodecamp.org/certificates/add-different-margins-to-each-side-of-an-element
SCREENSHOT:

@mstellaluna, The guide does not have these pages as the challenges are not in production yet. As soon as the new challenges make it to the master branch, the guide will be updated

Reason for close, see  https://github.com/freeCodeCamp/freeCodeCamp/issues/16817


Warnings give additional output

Something weird with the behavior of warnings from inside RMS.
warnings.warn(
                "Exporting to a subfolder is a deviation from the standard "
                "and could have consequences for later dependencies",
                UserWarning
            )

...gives this:
UserWarning: Exporting to a subfolder is a deviation from the standard and could have consequences for later dependencies
  collected/processed and subsequently both 'independent' and object dependent

Originally posted by @perolavsvendsen in https://github.com/equinor/fmu-dataio/issues/65#issuecomment-889681949

The extra sentence seems to be random:
UserWarning: Exporting to a subfolder is a deviation from the standard and could have consequences for later dependencies
  a final metadata file (or part of file if HDF) are collected and


Feature request: derive Clone for RawTag

Hi!
The way we set up communications with devices requires us to have RawTag cloneable. There is no risk of race conditions or anything like that that might result in concurrent access to the same tag. But what we do is create an abstraction over tags, which, when it's un-abstracted, requires a clone call. My guess is that by omitting both Copy and Clone you enforce local ownership and thus synchronized access at any time, but it severely limits architectural options. Would you agree on adding that Clone derive to RawTag? I don't know what other structs may be needed too, as I started using your nice library just yesterday. :)
And thanks for making this!

I do not think it's a good idea.
What about Arc<RawTag>?

I spoke with a colleague about this. We will wrap it in an Arc, but probably also in a mutex, because if your intent is to enforce local ownership, you should mark it as !Sync. So having both Mutex and Arc should be required to use that struct, if you want to synchronize tag access*. Feel free to close this issue now. Thank you! :)
*) I'm not sure if only tags require synchronization. The original documentation talks both about tags and the API itself, so I'm not sure whether one needs to synchronize over all calls to all (most) API functions.

you should use mutex to protect read/write. you cannot read and write at the same time，and get an error code if it's busy. with mutex，operations from different threads are in order.

I don't understand - what do you mean you "can't" read and write at the same time? Without Arc, you can't read and read at the same time either, because there's only one RawTag instance. If you wrap it in Arc, you can theoretically do do read twice or read and write at the same time. And if you get an error when busy, why not just derive Clone anyway?

with Arc，the tag only drop once.  if rawtag is clonable， it will drop multiple times if there are multiple instances for the same tag. that's the problem.

Oh, I didn't know you destroy the tag on drop. Alright, that makes sense. Thanks! :+1:


Update README.md

Simple text error.

I am closing this pull request as this was for the old version of the JFK Files demo that did not use Cognitive Search.


cleaning various kinds of details

This is just making several little changes, nothing serious.
A much more serious matter would be to avoid using the symbolic ring. SR is not meant for serious people.

Looks good; thank you.


update: net-libs/gnutls

Name: net-libs/gnutls
CVEs: CVE-2024-0567, CVE-2024-0553
CVSSs: 7.5, 7.5
Action Needed: upgrade to >= 3.8.3
Summary:

CVE-2024-0567: Fix assertion failure when verifying a certificate chain with a cycle of cross signatures
CVE-2024-0553: Fix more timing side-channel inside RSA-PSK key exchange

refmap.gentoo: https://bugs.gentoo.org/922262

Set to cvss/HIGH.


[LiveMetrics] report process counters for perf counters

WORK IN PROGRESS.
TODO: Need to deploy to App Service and compare to what App Service reports.
Changes

Implement Perf Counters by reading Process Counters.
update Demo project with stress test used for testing. REVERT THIS BEFORE MERGING
I'm sharing this so we can also review my testing methodology.

Testing
TODO: write description and share screenshots of testing

API change check
API changes are not detected in this pull request.

perf counter is called out in code comment, title and variables. We are not getting data from perf counter. Use an alternate name instead.

@cijothomas @rajkumar-rangaraj
I've addressed all feedback, please re-review.
I'll be out the rest of the week. If everything looks good feel free to merge. :)

The screenshot in the description has one with CPU showing above 100%.. That should never happen, if you are sending normalized values.

The screenshot in the description has one with CPU showing above 100%.. That should never happen, if you are sending normalized values.

I suggest that we evaluate what .NET Extension did and align on the algorithm. At minimum, if we want to introduce our own implementation, I want the algorithm to be carefully designed, reviewed (and backed by Math) and documented. https://github.com/dotnet/extensions/blob/main/src/Libraries/Microsoft.Extensions.Diagnostics.ResourceMonitoring/Linux/LinuxUtilizationProvider.cs

The screenshot in the description has one with CPU showing above 100%.. That should never happen, if you are sending normalized values.

I suggest that we evaluate what .NET Extension did and align on the algorithm. At minimum, if we want to introduce our own implementation, I want the algorithm to be carefully designed, reviewed (and backed by Math) and documented (e.g. this PR sets a good example). https://github.com/dotnet/extensions/blob/main/src/Libraries/Microsoft.Extensions.Diagnostics.ResourceMonitoring/Linux/LinuxUtilizationProvider.cs

Agree mostly. My thoughts are

AzMon distro or exporter should not be in the business of producing metrics. It should just bring in existing instrumentation libraries only. And so far, we seem to be sticking with this approach.
This particular PR is for the LiveMetrics feature. While it'd be nice to follow above here too, it may not be feasible/worth-the-effort. Considering LiveMetrics feature is not to store metrics anywhere permanent, the efforts to design and maintain an algorithm may not be worth it. (Its just for quick visual indication, not even queryable for later consumption, so carefully find the balance and avoid spending too much effort here)
We still need to do the basic accuracy part - i.e do not incorrectly tell what the CPU utilization is that of the machine, while actually showing just the single process cpu utilization. Do not state that the cpu utilization is normalized to take into account the number of cores, but send a non-normalized value. (these requires product changes too). (In fact, ApplicationInsights SDKs are lying in many cases - eg: In Linux or in AppService environmetns, app insights only sends process cpu and memory, but the UI shows it as Total Machine CPU and Memory, which is wrong, and that mistake should not be repeated here.) Again, this needs product change/support (And Mothra is already engaged with Product team to get the necessary changes)

Providing a summary of the issue before we exploring into the specifics:
In the Application Insights SDK, for the Windows environment, CPU metrics are collected for the entire operating system. In contrast, for Azure App Service and other non-Windows environments, process-level CPU metrics are utilized. When it comes to memory metrics, Windows uses the performance counter \Memory\Committed Bytes, while other environments rely on process-level private bytes.
Languages other than .NET typically read the OS-level counter to send these metrics, leading to inconsistencies in the data sent across different environments and languages.
Mothra has initiated a collaboration with the services team to establish clear guidelines on what exactly should be sent. Our objective is to ensure that the same metrics are sent from all environments and languages.
The services team has requested additional time to formalize this process. As an interim solution, both service and SDK teams have agreed to use process-level metrics for both CPU and memory. This temporary solution will be implemented in beta versions, and we will not release a Release Candidate (RC) or General Availability (GA) version until the standardization is finalized. This approach allows us to continue our work on filters in the meantime.

AzMon distro or exporter should not be in the business of producing metrics. It should just bring in existing instrumentation libraries only. And so far, we seem to be sticking with this approach.

This is correct, except for standard metrics. For live metrics, we don't want to take the dependency on the OpenTelemetry Metric SDK, as it will make the implementation very complex.

This particular PR is for the LiveMetrics feature. While it'd be nice to follow above here too, it may not be feasible/worth-the-effort.

Correct, it is not worth the effort.

Considering LiveMetrics feature is not to store metrics anywhere permanent, the efforts to design and maintain an algorithm may not be worth it. (Its just for quick visual indication, not even queryable for later consumption, so carefully find the balance and avoid spending too much effort here)

I have to agree with Cijo on this part. The algorithm used is very straightforward, and I don't see any issues with it. The LinuxUtilizationProvider  uses the same approach..

The screenshot in the description has one with CPU showing above 100%.. That should never happen, if you are sending normalized values.

This is not true. Mothra is trying to explain that using Process.UserProcessorTime plots an incorrect graph, and a small implementation is needed to solve it. He provided the accurate graph at the end of the description and has also validated the graph by onboarding the runtime metrics to the same app.
Finally, I need to acknowledge that we need to accurately capture the information in the changelogs.

The screenshot in the description has one with CPU showing above 100%.. That should never happen, if you are sending normalized values.
This is not true. Mothra is trying to explain that using Process.UserProcessorTime plots an incorrect graph, and a small implementation is needed to solve it. He provided the accurate graph at the end of the description and has also validated the graph by onboarding the runtime metrics to the same app.

Thanks! Yes I can see the description is pretty clear.


Code hints (IntelliSense) always show loading

Since the update of vscode to 1.27, the code hints have slowed down. The code hint does not appear until the beginning of the previous time, and it is always displayed 'loading' by pressing Ctrl + Space.
I uninstalled the vscode reinstall and still didn't solve it.
My operating system is win10(1803)，the vscode version is 1.28.2, I am in China.

What programming language is this? Have you installed an extension for that language?

I found this because of the installation of the vscode-flow-ide extension.


gcc12: 12.3.0 -> 12.4.0

Description of changes

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

@trofi
Heuristics: Are you capable of building this in your host?
On yes, please post the nixpkgs-review of it.
On no, please target staging.


Add /tweet command

We have a goofy little !tweet command for @core that's powered by MEE6. All it does is ping the @tweet-squad role. I don't like MEE6 so I want to migrate away from it.
Thought it would be fun to move this one over and add some funny messages.
TODO:

I'm struggling to test this locally
I'm unsure how to scope the command to certain permissions. This should be accessible only to @core, so maybe the ability to use @everyone is the most similar?

We should be able to limit the command to core-only in the discord settings instead of checking for @everyone permission. That would be my preferred approach. That way, people without permission can't even see the command.


new release?

I notice that compat has been updated for latest StringManipulation, but has not been released.
Is it worthwhile to release a new version?

Perfect! I will do this!

Hi @GregPlowman,
Sorry, I completely forgot! I will do this as soon as possible.

Done! Should be available soon. I am really sorry for the delay.

Thanks!


pipenv shell should respect your current shell.

I use Fish shell, but unfortunately running pipenv shell spawns a weird, foreign, and confusing bash shell.
It'd be nice if pipenv shell spawns my preferred shell. :)

Hey @jonparrott, this is because Fish doesn't update the SHELL variable in some cases (I don't know which). We use that to launch the subshell, so yours is likely defaulting back to /bin/bash.
The previously suggested workaround has been to update your profile/bashrc with the correct SHELL variable for Fish. I'm open to other ideas though for a better implementation if you have any 😁

Ah interesting. I thought that might be what's going on - thanks, I'm gonna close this for now.


Clear API definitions between UI and API

Feature Request
Description of Problem:
Currently the custom RPC call function defined on server is part of the RPC message UI need to send. We need a separation so what UI sends is not tied to internal function names. (also the interface name is used as "service" parameter of the rpc call)
Would be good to have a way to view catalog of possible messages that server and UI can send back and forward. This has been asked by other users of VUU as well
Potential Solutions:
TBC
Also need to provide documentations of all possible RCP messages  - been asked by several users

Might be best to wait for new RPC message type defined as outcome as https://github.com/finos/vuu/discussions/1447
Being tackled as part of this change https://github.com/finos/vuu/issues/1434

First cut implemented for a viewport RPC request and a response that can be success or failure.
New issue created for further follow up https://github.com/finos/vuu/issues/1502


GDScript 2.0: Unknown Function convert() in @GDScript scope

Godot version
4.0-beta1
System information
Zorin OS-16, Intel hd 5500HD
Issue description
Some Global Scope functions are "unknown" in GDscript. "convert", function is one such function. Not sure how/why this is possible.

Steps to reproduce
Use the convert function to any meaningful task should trigger the error.
Minimal reproduction project
No response

Seems related (same?) to #5523

@KoBeWi. It indeed looks to be the same. I guess a decision whether to remove or improve it was reached since this was from a year ago. I say just nuke the thing. One less "conversion" function to worry about among the many we already have. I guess not many used it either.

I have the same issue, I can't convert a variant from a Javascirpt.eval() rerturn to int in any way. This is VERY urgent for me so any kind of advice would be appreciated. I'm trying to get a browser parameter value.

@QushyQushy just type cast it. Use the as keyword or int(variant) or if you want some convoluted way use var_to_str() and then convert the str to int

@QushyQushy just type cast it. Use the as keyword or int(variant) or if you want some convoluted way use var_to_str() and then convert the str to int

It returns null sometimes so that was the issue. I just used an if statement.

Just wanted to point out that int("2") for example does not actually work to convert a string to number, I needed to also use str_to_var, so honestly either a working convert or a better casting system sound like a necessity to me.

PLEASE don't remove the convert function, i need it too!
It is very helpfull to have such utility.

@MikeSchulze what are you using it for?

@MikeSchulze what are you using it for?

I build the plugin GdUnit3 and current on migrate to Godot4.
I have a GdScript parser implemented to parse out  a function descriptor to hold all informations about all argument type and defaults.
class_name GdFunctionArgument
extends RefCounted

var _name: String
var _type: int
var _default_value :Variant

const UNDEFINED :Variant = "<-NO_ARG->"
const ARG_PARAMETERIZED_TEST = "test_parameters"

func _init(name :String, type :int = TYPE_MAX, default_value :Variant = UNDEFINED):
	_name = name
	_type = type
	_default_value = default_value

func name() -> String:
	return _name

func default() -> Variant:
	prints("get converted type %s of %s" % [_type, _default_value])
	return convert(_default_value, _type)

By nature, the parser reads everything from a file as string and I have to convert the default arguments final from string to the real type.

Did you try using str2var (3.x) / str_to_var (4.x)? This is the supported way to convert a string representation to a Variant.

Yes i use currently str_to_var but this is not save enough, i wrote my own convert now to handle the edge cases as well.
e.i. to convert a string "1" could be mean int could also mean a float.
I have the type already extracted from the scripts and want to convert in the right value.
So have a convert function with a type as argument would be great.

In #70080 I am proposing to replace the existing convert method with a new type_convert method. This method will always succeed and it also has a clearer name to make it obvious that we are converting types.


[routing-manager] new APIs to get state and new CLI commands

This commit adds new public OT APIs in border_routing.h to get the
current state of RoutingManager and to get the current favored
on-link prefix.
This commit also updates CLI br commands:

It moves the CLI br implementation into own cli_br module.
It adds br state to get the current state
It changes br omrprefix, br onlinkprefix, and br nat64prefix
to output both local and favored prefixes when no additional arg
is provided and allow the use of local or favored extra arg to
specify the type.
It updates the documentation of br related commands in the source
code and in cli/README.md.

In new push, updated the CLI code

Moved the br related code into its own module cli_br
Allow favored, local as extra arg for different prefix sub-commands (e.g., omrprefix local or omrprefix favored)

I'm checking the CLI import to openthread.io on this, since there are a lot of changes...
@kylorene FYI


Hamburger menu doesn't always appear on homepage when on mobile

I think it has something to do with the scroll to reveal I added. There's probably a way to disable it on mobile.
Edit - Definitely has to do with scroll to reveal. This will be fixed later.

Fixed this by not using data-aos="slide-left" anywhere. So basically the scroll to reveal won't work on slide ins from the left. Changed to "zoom-in" and "fade-up"


NIMBLE stack usage almost 10000 bytes (IDFGH-10004)

Answers checklist.

[X] I have read the documentation ESP-IDF Programming Guide and the issue is not addressed there.
[X] I have updated my IDF branch (master or release) to the latest version and checked that the issue is present there.
[X] I have searched the issue tracker for a similar issue and not found a similar issue.

IDF version.
v4.4.3
Operating System used.
Windows
How did you build your project?
Command line with idf.py
If you are using Windows, please specify command line type.
CMD
Development Kit.
WROVER-IE
Power Supply used.
USB
What is the expected behavior?
I use NIMBLE in central role. It is connected to a peripheral and MTU is 156. Peripheral sends a notification with payload size of 154 bytes. This will render in a fragmented frame since only 27 bytes can be sent in one frame.
When the central (WROVER) receives the data the stack usages is increased from til the high water mark 3500 bytes to 8000 bytes (I use function uxTaskGetStackHighWaterMark to monitor the stack usage of the BLE task).
I don't expect reception of 154 bytes of data to increase stack usage that much.
If I set stack size to 6000 the system will crash
What is the actual behavior?
BLE stack usage high water mark is almost 9000 bytes. Why is so much stack used to receive notification?
Steps to reproduce.

Step
Step
Step

Debug Logs.
***ERROR*** A stack overflow in task ble has been detected.

Backtrace: 0x4008207a:0x3ffe6d00 0x40092995:0x3ffe6d20 0x40095ebe:0x3ffe6d40 0x400944f1:0x3ffe6dc0 0x40092a90:0x3ffe6df0 0x40092a42:0xa5a5a5a5 |<-CORRUPTED
0x4008207a: panic_abort at C:/repo/esp_4_4_3/components/esp_system/panic.c:402

0x40092995: esp_system_abort at C:/repo/esp_4_4_3/components/esp_system/esp_system.c:128

0x40095ebe: vApplicationStackOverflowHook at C:/repo/esp_4_4_3/components/freertos/port/xtensa/port.c:394

0x400944f1: vTaskSwitchContext at C:/repo/esp_4_4_3/components/freertos/tasks.c:3505

0x40092a90: _frxt_dispatch at C:/repo/esp_4_4_3/components/freertos/port/xtensa/portasm.S:436

0x40092a42: _frxt_int_exit at C:/repo/esp_4_4_3/components/freertos/port/xtensa/portasm.S:231

More Information.
No response

sdkconfig.txt

Hi @JonasAxelsson ,
We tried to reproduce your issue as per mentioned configuration but not identified the stack overflow error for the configuration option  CONFIG_BT_NIMBLE_TASK_STACK_SIZE =10000.
Custom notification  with payload size 154 bytes is sent from bleprph to blecent and printed the value returned by uxTaskGetStackHighWaterMark() to trace the stack usage.
uxTaskGetStackHighWaterMark() returns the high water mark of the stack associated with xTask.  That is,the minimum free stack space there has been (in bytes) since the task started.The smaller the returned number the closer the task has come to overflowing its stack.
Also it is observed that there is not significant usage of stack for reviewing the notification from peripheral.I have attached the screenshot showing stack usage for the notification operation.

We can see that 8404 bytes memory is available after the task is created which is decreased up to 7604 bytes after notification is received.
To get more information about the issue can you please share the following things:

Code where you have traced the stack usage.
Examples which you have used  ( like blecent and bleprph etc.)
Console logs for stack usage.

Hi @JonasAxelsson ,
Any update on this ?

Closing the issue for now. Feel free to reopen the issue in case of any updates or further queries. Thanks.


Update list of cultures to be current with a recent Win10 installation

Need to rerun the culture generator on a recent Win10 machine to ensure we have all the latest cultures.

I'm running Windows 10 Enterprise, the .NET release key 393295 there are 809 cultures, I think we should consider the newly added culture that have been remove based on @Eilon comment in  https://github.com/aspnet/Localization/pull/96/files#r41166078

OK yep, I confirmed it. I just ran it here on Windows 10 Pro RTM and it updates to over 800 cultures.
@hishamco, feel free to send a PR that just includes the culture list update, assuming you are running Windows 10 RTM (build 10240).

@DamianEdwards I'm running the same version, I will send a PR soon
thanks

@Eilon It seems that something missed by using the tool. #104

Nope, this is auto generated by the CultureInfoGenerator command which is fetch all the cultures from the OS

Based on the discussion in this PR - https://github.com/aspnet/Localization/pull/104 it looks like other OSes have valid cultures which we need to add to our list or come up with a smarter way to identifying known cultures.

No longer needed due to https://github.com/aspnet/Localization/issues/111


Optimize caching in CI

In CI, we use the Swatinem/rust-cache GitHub Action to cache certain build artifacts across runs. However, it seems from the README that we might be using it in a suboptimal way. A few observations:

Zerocopy has only one dependency, and rust-cache only caches dependencies, not crate artifacts (note that zerocopy-derive has more dependencies - and dependencies that are expensive to compile - so presumably benefits much more than zerocopy)
We generate a custom cache key which includes:

A hash of the Cargo features, but this presumably shouldn't have any effect on dependencies (at least in our case, since none of our Cargo features depend on dependencies' Cargo features)
A hash of **/Cargo.lock, but this is documented to be the default behavior anyway

We should:

Figure out if there's a way to squeeze more benefit out for zerocopy (can we get rust-cache to cache any more artifacts?)
Don't include Cargo features in the cache
Don't include a hash of **/Cargo.lock in the cache
Go back over our use of rust-cache and its README with a fine toothed comb and see what else we're doing suboptimally

cc @Swatinem in case there's anything obvious that jumps out at you!

What do you mean by "crate artifacts"?

Don't include a hash of **/Cargo.lock in the cache

I've seen this used everywhere, presumably as a means to invalidate the cache when the dependencies change so not sure why we would want to change this.
If you feel like you need more fine-grained control we could definitely checkout https://github.com/actions/cache which is what the rust-cache wraps around.

Your caching does not work, and won’t work with the upstream actions/cache either because you are not running CI on the master branch. There is no cache reuse across PRs, only from branch bases.
As for the cache config:
        key: "${{ matrix.toolchain }}-${{ matrix.target }}-${{ env.FEATURES_HASH }}-${{ hashFiles('**/Cargo.lock') }}"

The toolchain and lockfile hashes are part of the autogenerated, so you don’t need to list those manually.
I also doubt the extreme fanout to all target and feature permutations is really necessary. As only dependencies are cached, the feature flags do not really matter, and you might just as well test multiple permutations in a single run.

There is no cache reuse across PRs, only from branch bases.

What solution do you suggest? One workaround is to create a workflow that updates the cache on each commit to main as described here.

simply run workflow on the main branch as well

Hey, would love your inputs on the above discussion @joshlf

@AntoniosBarotsis

What do you mean by "crate artifacts"?
Anything that would speed up future compilation of the crate itself (such as the incremental compilation cache).

Don't include a hash of **/Cargo.lock in the cache

I've seen this used everywhere, presumably as a means to invalidate the cache when the dependencies change so not sure why we would want to change this.
rust-cache already does this by default, so having it explicitly is redundant.

@Swatinem

Your caching does not work, and won’t work with the upstream actions/cache either because you are not running CI on the master branch. There is no cache reuse across PRs, only from branch bases.
To clarify, if we enable the same workflow on the main branch, we will get caching benefits when the workflow is triggered by a PR?

As for the cache config:
        key: "${{ matrix.toolchain }}-${{ matrix.target }}-${{ env.FEATURES_HASH }}-${{ hashFiles('**/Cargo.lock') }}"

The toolchain and lockfile hashes are part of the autogenerated, so you don’t need to list those manually.
Yeah, definitely agreed that we should get rid of those.

I also doubt the extreme fanout to all target and feature permutations is really necessary. As only dependencies are cached, the feature flags do not really matter, and you might just as well test multiple permutations in a single run.

Removing the feature flags makes sense to me. As for the targets, it seems like building with a different --target flag overwrites the build artifacts for other targets, so IIUC, it's still important to keep separate caches for different targets.
Specifically, I ran cargo check --target <target-a> && cargo check --target <target-b> && cargo check --target <target-a>, and the third invocation recompiled all of the dependency crates that had been compiled during the first invocation, leading me to believe that they were overwritten in the second invocation.
Thanks for your advice on this, btw! Good to know we've been doing all of this caching for absolutely no benefit whatsoever 😆

Hey @joshlf can I get started on this issue then?

Sure thing, @glokta1; thanks for volunteering!
Based on the preceding discussion, looks like the specific tasks are:

From the key, remove the matrix.toolchain, env.FEATURES_HASH, and hashFiles(...) components
Remove the job that generates the FEATURES_HASH environment variable
Make the ci.yml workflow run on push to main as well as on PRs

What do you mean by "crate artifacts"?

Don't include a hash of **/Cargo.lock in the cache

I've seen this used everywhere, presumably as a means to invalidate the cache when the dependencies change so not sure why we would want to change this.
If you feel like you need more fine-grained control we could definitely checkout https://github.com/actions/cache which is what the rust-cache wraps around.

Also there is an example configuration for Rust: https://github.com/actions/cache/blob/main/examples.md#rust---cargo

- uses: actions/cache@v3
  with:
    path: |
      ~/.cargo/bin/
      ~/.cargo/registry/index/
      ~/.cargo/registry/cache/
      ~/.cargo/git/db/
      target/
    key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}


Can't chat

Hi, great extension Siderite.
I found a small bug while playing a game, you can't chat.
When i disabled addon, i could.
Using firefox.
Thanks

Can't reproduce. Can you look at the developer tools console and tell me if there are any errors thee? What version of FF and what version of LiChess Tools are you using?

Thanks for the report!

Any update here? Since I can't reproduce it, I can't fix it.


workload identity tutorial (yaml file has some issue)

Describe the bug
After following the tutorial twice and doing all the steps as it is , we are unable to attain our goal.
ERROR
C:\Users\JamalAshraf>kubectl get pods
NAME          READY   STATUS   RESTARTS     AGE
quick-start   0/1     Error    1 (2s ago)   4s
C:\Users\JamalAshraf>kubectl logs quick-start
E1206 12:00:43.380355       1 main.go:60] "failed to get secret from keyvault" err="no Host in request URL" keyvault="azwi-ky-demo-013" secretName="my-secret"
Steps To Reproduce
Expected behavior
Logs
Environment

Kubernetes version (use kubectl version):
Cloud provider or hardware configuration:
OS (e.g: cat /etc/os-release):
Kernel (e.g. uname -a):
Install tools:
Network plugin and version (if this is a network-related bug):
Others:

Additional context

@Jamal8548 Please share the following

kubectl get pods -n <namespace where webhook is deployed>
kubectl get pod quick-start -o yaml
service account yaml
Logs from mutating webhook

Here is the troubleshooting guide: https://azure.github.io/azure-workload-identity/docs/troubleshooting.html

thanks but it is working now as in pod we need now :
KEYVALUT_URL


How to pass weights to a custom objective function when using random forest with Scikit-Learn-Like API

Hello, I am trying to develop a custom objective function as below.

I am using xgboost.XGBRFRegressor, so I created an objective function based on MSE and passed it to the objective parameter.
def gradient_se(y_true, y_pred):
    return -2 * (y_true - y_pred)

def hessian_se(y_true, y_pred):
    return 0 * (y_true + y_pred) + 2

def custom_se(y_true, y_pred):
    grad = gradient_se(y_true, y_pred)
    hess = hessian_se(y_true, y_pred)
    return grad, hess

xgb.XGBRFRegressor(max_depth=50, objective=custom_se, random_state=1).fit(x_train, y_train)

As I can only get the values of y_true and y_pred in the custom objective function, I have no idea how to assign weights to grad or hess. Currently, I defined a global WEIGHT, and assigned it dynamicly like this, which is calculated based on distance.
global WEIGHT
dis = np.sqrt(np.sum((coords[0] - coords_train) ** 2, axis=1))
WEIGHT = np.exp(-0.5 * (dis) ** 2)

Then, the gradient and hessian were modified using WEIGHT:
def gradient_se(y_true, y_pred):
    return -2 * WEIGHT * (y_true - y_pred)

def hessian_se(y_true, y_pred):
    return 0 * (y_true + y_pred) + 2 * WEIGHT

def custom_se(y_true, y_pred):
    grad = gradient_se(y_true, y_pred)
    hess = hessian_se(y_true, y_pred)
    return grad, hess

Am I correct by using this method? Or is there any alternative solution to this issue?
Thanks in advance!

It's correct.

Or is there any alternative solution to this issue?

Use the native interface instead, which passes a DMatrix object.
Use closure/callable instead of global variable.

# use callable
class MyObj:
    def __init__(self, weight: np.ndarray) -> None:
        self.weight = weight

    def __call__(self, y_true, y_predt) -> tuple[np.ndarray, np.ndarray]:
        return gradient(y_true, y_predt, self,weight), hessian(...)

# closure is simiar

Many thanks for your suggestion! I tried callable and it worked properly.
May I ask what did you mean of 'use the native interface'?  Did you mean I can create an objective function containing a DMatrix object to the objective parameter of  xgboost.XGBRFRegressor like this tutorial?
But I read this article and it shows the  objective parameter of xgboost.XGBRFRegressor should be like this:

Unfortunately, the RF regressor doesn't support custom objective.  Right now only gradient boosted ensemble supports it, xgb.XGBRegressor and xgb.XGBClassifier.
I saw that you have pasted a link to the "latest" doc instead of "stable".  The latest XGBoost has some improvements over the custom objective and evaluation function but hasn't been released yet.  The native interface is https://xgboost.readthedocs.io/en/latest/tutorials/custom_metric_obj.html#customized-objective-function .  From the snippet, you can see there's a xgb.train function.  xgb.XGBRegressor is a high level scikit-learn wrapper over this train function.

Thanks a lot!


typo in README.md

"compareLeftToRight" in README.md should be "composeLeftToRight".
As well as "compareTopToBottom".

Fixed in PR #22 .
Thank you!


[Feature] displayFormat prop with localization feature

It would be great use displayFormat prop with localization
Now, using displayFormat={"D MMMM YYYY"} just give 11 July 2023 despite set i18n={"fr"}

You can write like i18n={"fr-FR"}.
Please check #145.


Decouple BinaryInfo from the block encoder

Closes #2145.
Split
nodeEncodeBlockWithInfo  :: CodecConfig blk -> blk -> BinaryInfo Encoding

Up into
nodeGetBinaryBlockInfo :: blk -> BinaryBlockInfo
nodeEncodeBlock        :: CodecConfig blk -> blk -> Encoding

where BinaryBlockInfo is the former BinaryInfo without its blob
argument. This also means Binary(Block)Info is no longer a functor, closing
issue #2145.
The reason both were coupled is that we thought that the information would be
computed during encoding, making it more efficient to do both at the same
time. However, for all real ledgers, we use annotations, making it cheap to
compute the BinaryBlockInfo without any real encoding work to be done.
Splitting them up will make later refactorings of the encoders/decoders
easier.

bors merge


It would be better to disable the action 'Undelete by Date...' for one soft-deleted blob version

Storage Explorer Version: 1.20.0-dev
Build Number: 20210610.4
Branch: main
Platform/OS: Windows 10/ Linux Ubuntu 20.04/ MacOS Big Sur 11.3
Architecture: ia32/x64
How Found: From running test case
Regression From: Not a regression
Steps to Reproduce

Expand one storage account -> Blob Containers (make sure the blob versioning is enabled).
Create one blob container -> Upload one blob.
Delete the blob to create a blob version.
Disable the blob versioning.
Switch to 'All blobs and blobs without current version' -> Soft delete the blob version.
Right click the soft-deleted blob version -> Click 'Undelete'.
Check whether the action 'Undelete by Date...' is disabled.

Expected Experience
The action 'Undelete by Date...' is disabled.
Actual Experience
The action 'Undelete by Date...' is enabled.

I will take this issue and figure out what is the expected behavior of undelete on soft-deleted versions/snapshots.

@JasonYeMSFT FYI, there is a similar issue 508.


--node with require / module

Are there any plans to support more native-like require and module globals when using browserify --node ?
For example:
index.js
console.log(require.resolve('url'))

Prints url with node:
node index.js

However, throws an error with browserify:
browserify index.js --node | node

TypeError: Object function (e){var n=t[o][1][e];return s(n?n:e)} has no method 'resolve'
    at Object.<anonymous> ([stdin]:2:21)
    at s ([stdin]:1:254)
    at e ([stdin]:1:425)
    at [stdin]:1:443
    at Object.<anonymous> ([stdin]-wrapper:6:22)
    at Module._compile (module.js:456:26)
    at evalScript (node.js:536:25)
    at Socket.<anonymous> (node.js:154:11)
    at Socket.emit (events.js:117:20)
    at _stream_readable.js:943:16

Maybe require.resolve can fall back through to whatever require is already defined. This is how require() works across multiple bundles already.


updated doc links and changed cert to api.trustly.com

updated doc links and changed cert to api.trustly.com

@pontus-eliason since this repo seems to be alive again I added a few PRs to fix various issues, hope you have a chance to look at them.


Add sample describing how to use KEDA with GKE.

Description
This PR adds a sample describing how to use KEDA with GKE.
Tasks

[x] The contributing guide has been read and followed.
[x] The samples added / modified have been fully tested.
[x] Workflow files have been added / modified, if applicable.
[x] Region tags have been properly added, if new samples.
[x] All dependencies are set to up-to-date versions, as applicable.
[x] Merge this pull-request for me once it is approved.

@bourgeoisor Olivier could you please review this new sample?


html data attribute is not working in sass file

my below  [data-progress="#{$i}"] is not increment $i value ..i got as like it is.. it is considering as a string.
.loadingcontainer {
$i=1;
@while ($i <= 2) {
&[data-progress="#{$i}"] {
.loading-inset .loading-inset__percentage:before {
content: "#{$i}";
}
}
    $i : $i + 1;
}

}
The final CSS output i got like below
.loadingcontainer[data-progress="#{$i}"] {
.loading-inset .loading-inset__percentage:before {
content: "1";
}
}
.loadingcontainer[data-progress="#{$i}"] {
.loading-inset .loading-inset__percentage:before {
content: "2";
}
}

i am using "version": "0.9.0",

Please test with latest version of node-sass, that is; v2.0.0-beta.
Going by your example:
.loadingcontainer {
  $i:1;
  @while ($i <= 2) {
    &[data-progress="#{$i}"] {
     .loading-inset .loading-inset__percentage:before {
       content: "#{$i}";
      }
    }
    $i : $i + 1;
  }
}

node-sass 2.0.0-beta output:
.loadingcontainer[data-progress="1"] .loading-inset .loading-inset__percentage:before {
  content: "1"; }
.loadingcontainer[data-progress="2"] .loading-inset .loading-inset__percentage:before {
  content: "2"; }

Ruby sass v3.4.9 output:
.loadingcontainer[data-progress="1"] .loading-inset .loading-inset__percentage:before {
  content: "1";
}
.loadingcontainer[data-progress="2"] .loading-inset .loading-inset__percentage:before {
  content: "2";
}

Thanks for your reply. i did different way without change the version
In my case i can't update the sass version. i don't have control to update the sass version. so i got reference from https://github.com/sass/libsass/issues/309
my final code.
.loadingcontainer {
$i=1;
@while ($i <= 2) {
$x: ""#{$i}"";
&#{"[data-progress=" + $x + "]"} {
.loading-inset .loading-inset__percentage:before {
content: "#{$i}";
}
}
it is generating same as above your example..
.loadingcontainer[data-progress="1"] .loading-inset .loading-inset__percentage:before {
content: "1"; }
.loadingcontainer[data-progress="2"] .loading-inset .loading-inset__percentage:before {
content: "2"; }


docs(faq): add FI_PROVIDER answer for #19

This will help users to try a different Fabric provider.
Close #19.

What system do these instructions apply to?  I'd like to try it and better understand why that solves the problem.

It applies to Crusher. I guess it also applies to any system that has multiple FI_PROVIDER.

It applies to Crusher. I guess it also applies to any system that has multiple FI_PROVIDER.

Ah right, Ok.  I misread the diff. I thought there was something in there for libfabric 1.13, that was what I was asking about.  I'll validate this on Crusher shortly before merging this PR.


FIX Check canView() permission before rendering BaseElements

Fixes #253 by checking canView() permissions before rendering BaseElements.

Alrighty, reverted my prior changes and went with @kinglozzer's approach - thanks very much for your input!

Follow up at #265


Example NOx Binning Test Data

Example NOX Binning Data Created last year
Now with ascii text strings on sheet 5
Now in little Endian
NOX Bin Test Data.xlsx

Data provided as shown


New and improved Skor is now part of Hasura GraphQL Engine

New and improved version of Skor is now part of Hasura GraphQL Engine
A few months ago, we built the open source GraphQL Engine that gives you instant GraphQL APIs over any Postgres database. We have added all of Skor's existing features and even more to make it production ready:

Reliable: We capture every relevant action on the database as an event, even when Hasura is down! The events are delivered to your webhook as soon as possible with an atleast-once guarantee.

Scalable: What more, it even scales horizontally. If you are processing millions of events, just add more instances of GraphQL engine.

Use with Serverless: If you are using Skor, then avoid the pain of managing your webhook by moving to Serverless infrastructure. Check out these blog posts to get started

Use Hasura GraphQL Engine for production use cases

@shahidhk Would recommend these change.
In scalable, We can just say: Event delivery scales horizontally. If you want to process more events faster, just increase the number of instances of Hasura. (I'm in favour of gradually dropping graphql engine from our terminology)
In point 3:
3. Use with serverless: Webhook triggers on postgres events work especially great with serverless. We've put together a bunch of useful getting started's here.

I think we should add a point around there being a UI to configure event-triggers easily too. We have a nice GIF. You can get it from my blogpost.
I don't think you need to have the last line "Use HGE for production....."
We can also serve a deprecation notice saying that work on skor will now continue has a part of HGE.

@Sach97 Yes, absolutely. The one event will be picked by any one of the N Hasura instances and sent to the subscriber.

Oh that's nice thank's, that is exactly what I was searching for !


Exclude 'output' and 'git' schemes

Currently, this extension can make RO active file from workspace if opened output window or git diff. This PR fixes it.
Also, may be better toggle RO only for 'file' scheme...

I made a few  other changes so I didn't use this PR but did use your ideas, thank you.
I considered using only file schemes but there are more odd ones like scmInput and log so I am using just the four ignore scheme list for now.


[stable/filebeat] raised filebeat version to 6.4.0

What this PR does / why we need it:

raises filebeat version to 6.4.0

Which issue this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close that issue when PR gets merged): fixes #
Special notes for your reviewer:

/ok-to-test
/assign

/assign @seanknox

/assign @davidkarlsen

/lgtm


Obsolete 'detection of stimulus involved in cell cycle checkpoint' branch

Dear all,
The proposal has been made to obsolete the 'detection of stimulus involved in cell cycle checkpoint' branch. The reason for obsoletion is that these terms correspond to molecular functions. The terms impacted are:
GO:0090429 detection of endogenous biotic stimulus
GO:0072394 detection of stimulus involved in cell cycle checkpoint
GO:0072409 detection of stimulus involved in meiotic cell cycle checkpoint
GO:0072412 detection of stimulus involved in mitotic cell cycle checkpoint
GO:0072415 detection of stimulus involved in spindle checkpoint
GO:0072460 detection of stimulus involved in meiotic recombination checkpoint
GO:0072463 detection of stimulus involved in meiotic spindle assembly checkpoint
GO:0072475 detection of stimulus involved in mitotic spindle checkpoint
GO:0072484 detection of stimulus involved in spindle assembly checkpoint
GO:0072481 detection of stimulus involved in mitotic spindle orientation checkpoint
GO:0072469 detection of stimulus involved in cell size control checkpoint
GO:0072448 detection of stimulus involved in G1 cell size control checkpoint
GO:0072451 detection of stimulus involved in G2 cell size control checkpoint
GO:0072397 detection of stimulus involved in cytokinesis checkpoint
GO:1903819 detection of stimulus involved in mitotic cytokinesis checkpoint
GO:0072400 detection of stimulus involved in mitotic DNA integrity checkpoint
GO:1902401 detection of stimulus involved in mitotic DNA damage checkpoint
GO:0072442 detection of stimulus involved in mitotic DNA replication checkpoint
GO:0072427 detection of DNA damage stimulus involved in intra-S DNA damage checkpoint
GO:0072430 detection of DNA damage stimulus involved in mitotic G1 DNA damage checkpoint
GO:0072433 detection of DNA damage stimulus involved in mitotic G2 DNA damage checkpoint
GO:1903821 detection of stimulus involved in morphogenesis checkpoint
There is a single annotation to those terms, by MGI (MGI:1328317). There are no mappings, those terms are not present in any subsets.
You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/20976
Thanks, Pascale

What ticket had the discussion on this? The link just comes back to this ticket. Looking for suggested functions to replace?

It seems that it shouldn't be annotated to a "checkpoint" term.
in the abstract
"Notably, Trex1-deficient cells show defective G1/S transition and chronic ATM-dependent checkpoint activation, even in the absence of exogenous stress, correlating with persistent single-stranded DNA molecules produced in S phase, which accumulate in the ER."
So Trex1 isn't part of  checkpoint activation. However, in it's absence  abherrant DNA structures which are recognised by the  DNA integrity checkpoints accumulate.
When Trex1 is removed, a pathological situation arises and the checkpoint is activated. The gene product Trex1 itself isn't regulating the checkpoint is it?
"The data indicate chronic ATM-mediated checkpoint activation in Trex1−/− cells in the absence of exogenous DNA damage."
New MF terms will be created for "sensors" as required, but this doesn't appear to be a sensor. I would not make an annotation (other than of the are experiments to show the normal process of degrading DNA GO:0006308    DNA catabolic process ...in fact this seems to be removing toxic DNA-intermediates?)

Actually there are 2 annotations from 2 papers:

PMID:18045533 (the paper Val looked at)

In the results, the authors write "these data show that unstressed Trex1−/− MEFs are defective in G1/S transition.", and in the discussion the authors write "Trex1 acts on an ssDNA polynucleotide species arising from the processing of aberrant DNA replication intermediates, leading to chronic ATM-dependent checkpoint " - so really 'signaling' would be OK as a process

This supports an annotation to GO:0031571 mitotic G1 DNA damage checkpoint (we have changed the label to 'mitotic G1 DNA damage checkpoint signaling' in #20935)

PMID:23993650 -> I dont see 'checkpoint' being mentioned; DNA damage sensor would seem appropriate. Let me know if you want the term to be created.

Thanks, Pascale

"Trex1 acts on an ssDNA polynucleotide species arising from the processing of aberrant DNA replication intermediates, leading to chronic ATM-dependent checkpoint " - so really 'signaling' would be OK as a process

This isn't signalling though? A gene that is deleted thereby causing an increase in toxic by-products that are detected by a checkpoint isn't signalling. In a normal situation, this wouldn't occur, its a 'pathological' phenotype.  At least, from his data, my interpretation was that the cell is detecting, and trying to fix a problem, but because the problem is not correctable, the checkpoint is overwhelmed.
I see these phenotypes a lot in different mutants. For example, in fission yeast a 'cut' phenotype   occurs if the spindle checkpoint is 'overwhelmed' (162 genes so far). The checkpoint is usually activated because of some problem assembling the spindle or connecting the chromosomes. However, if a key component is absent, the problem is impossible to repair and the checkpoint eventually becomes overwhelmed/expires and cytokinesis proceeds even without correct chromosome segregation.
Similar problems occurs with DNA integrity checkpoints Most elongated inviable phenotypes (>460 genes)   result from a block at G2 checkpoints to fix interphase problems, these can be caused by defects in replication or even way upstream  (transcription, translation, splicing). The gene products which are absent, or mutated, have no role in signalling in a 'normal situation'.
If we do this, thousands of gene products could become annotated to signalling, because their mutation or absence results in checkpoint activation. Unfortunately, researchers sometimes refer to these obsevations as checkpoint activation or regulation, but the content is slightly different to 'real regulation'.
There are some instructions about this somewhere but I have no idea where they went (maybe on the wiki?). I'll try to track hem down as they should be added as comments to all of the checkpoint terms.
(disclaimer: I may have misinterpreted this paper due to lack of knowledge about this area in higher eukaryotes, but I don't see how a deficiency can be attributed to signalling in these cases)

done

GO:0009726 detection of endogenous stimulus (No annotations)


Not always signed out

In reference to #18
I'm not sure if this is related to settings I have with my google account but if I am in the health heroes app and I click the sign out -- I am redirected to the login page but I am then logged back in (with me doing nothing) and redirected to the app, logged in -- This happens pretty consistently, however some times it will log me out, take me to the login page and KEEP me logged out -- but the auto log back in happens pretty consistently too.

Can't repo anymore, closing

Happend again during demo so reopening.

This is happening to me consistently.  I have logged out, closed browser, returned to site to click Log in with Google and I do not have to enter password.  This will make it difficult to have different users try the application.


Add support for HomeWorks QSX systems

Add support for QSX processors by including their ProjectType string. Tested against QSX processor in HomeAssistant dev environment.
Add baseline support for Ketra lamps by adding SpectrumTune to the light section of _LEAP_DEVICE_TYPES, and for dimming them by adding GoToSpectrumTuningLevel support to set_value().
Fix a bug where when the color/color temperature of a Ketra lamp changes, the ColorTuningStatus message does not contain a Level attribute and pylutron-caseta incorrectly assumes that means the zone is off.
Add support for keypad button LEDs (creates switch devices for each button LED, subscribes to state from processor, and turns LEDs on and off from Home Assistant state changes).
Add tap_button function to send keypad button presses to the processor. This providers the necessary support to add button entities into the lutron_caseta Home Assistant component.

@cbw , looks great.  I'll be away until early next week.  I'll plan on merging after doing some tests then.
Thanks!

@danaues I'll keep hacking away on it in the meantime. As I got to know the code better, much of what you did for RA3 worked out of the box, but there are some additional HWQSX features I'd like to add as well. Enjoy your time away!

Added support for keypad button LEDs – presents them as switches to Home Assistant, subscribes to LED state from the processor, and turns LEDs on and off based on Home Assistant state changes.

Added the tap_button function to support sending keypad button presses to the Lutron Processor. I have a PR for the  lutron_caseta component I'll submit once this gets merged.

Hey @cbw
I haven't forgotten about this.  I'm working on getting my PR into the main pylutron_caseta source.  Having to make some changes to a few things based on the maintainers advice.  As soon as I have that all sorted out, we'll integrate your changes.

Now that your changes are merged, I'll go ahead and rebase against gurumitts and PR there

@cbw   Sounds great.  It will be great to have both systems supported.


rename asCSSPropertyValue to asCSSStringValue and use for generated CSS with font-family and content

more validation on values for file-icon / product-icon themes and icon registry
adopt the fileIconThemeData to the new css syntax

@mjbvz I adopted the fileIconThemeData to the new css string syntax. You want to have a look.
Note the different 'value' strings I added. Note that they are very limited (e.g. only hex colors) as the syntax for colors is much richer.


Kallisto support for RNAseq w/single-end reads?

Hello,
Is it possible to add this? I was trying to do fusion calls using Pizzly/Oncofuse, but got the error that the Pizzly-dependent Kallisto can't handle single-end reads (the terminal error actually suggested I open an "issue" :).
Thank you for any info on this!

Thanks David, sorry about not supporting it. We've been avoiding putting this in because users need to know up front what the fragment length distribution should look be since we can't calculate it from just the reads with single-end data, and in our experience most of the time the informatics people aren't getting that information upstream. Some folks have reported that kallisto is pretty sensitive to this parameter (https://www.biostars.org/p/253943/), so its important to get it right, and we are thinking that most folks won't have that information so we haven't supported it.
For fusions though, pizzly might be less sensitive to the parameter. If so then it would make sense to give this a go with single-end reads just for fusion calling. It would be worth checking if kallisto even calls fusions with single end reads: https://github.com/pachterlab/kallisto/issues/180 suggests that it might not be the case. Do you think you could run kallisto manually with a fragment size distribution guess and see if you can generate fusion calls from the single-end data? If not then I'll swap it to skip pizzly for single-end reads rather than give this error. If so then it would be useful to see how sensitive it is to fragment length guesses, and if it isn't too sensitive we could add a reasonable default.

Hi Rory,
Thank you for the quick reply! Yeah, I can give it a manual go. It looks
like for Illumina the average length should be ~190, so I should just be
able to do --single -l 190, and be (reasonably) safe. I might just try and
hack these flags into the bcbio_nextgen source (unless that sounds like a
horrible idea). In any event, I can understand why you wouldn't want to add
this in as default behavior to something as widely used as bcbio_nextgen.
Cheers!
On Fri, Aug 24, 2018 at 12:45 PM Rory Kirchner<EMAIL_ADDRESS>wrote:

Thanks David, sorry about not supporting it. We've been avoiding putting
this in because users need to know up front what the fragment length
distribution should look be since we can't calculate it from just the reads
with single-end data, and in our experience most of the time the
informatics people aren't getting that information upstream. Some folks
have reported that kallisto is pretty sensitive to this parameter (
https://www.biostars.org/p/253943/), so its important to get it right,
and we are thinking that most folks won't have that information so we
haven't supported it.
For fusions though, pizzly might be less sensitive to the parameter. If so
then it would make sense to give this a go with single-end reads just for
fusion calling. It would be worth checking if kallisto even calls fusions
with single end reads: pachterlab/kallisto#180
https://github.com/pachterlab/kallisto/issues/180 suggests that it
might not be the case. Do you think you could run kallisto manually with a
fragment size distribution guess and see if you can generate fusion calls
from the single-end data? If not then I'll swap it to skip pizzly for
single-end reads rather than give this error. If so then it would be useful
to see how sensitive it is to fragment length guesses, and if it isn't too
sensitive we could add a reasonable default.
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You are receiving this because you authored the thread.
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Thanks David, I’m super interested in hearing what the results are on your
dataset. In the meantime I can try doing pizzly calls on single end data
with the fusion dilution series with that default insert size and see how
much we lose.
On Fri, Aug 24, 2018 at 4:01 PM David Masica<EMAIL_ADDRESS>wrote:

Hi Rory,
Thank you for the quick reply! Yeah, I can give it a manual go. It looks
like for Illumina the average length should be ~190, so I should just be
able to do --single -l 190, and be (reasonably) safe. I might just try and
hack these flags into the bcbio_nextgen source (unless that sounds like a
horrible idea). In any event, I can understand why you wouldn't want to add
this in as default behavior to something as widely used as bcbio_nextgen.
Cheers!
On Fri, Aug 24, 2018 at 12:45 PM Rory Kirchner<EMAIL_ADDRESS>wrote:

Thanks David, sorry about not supporting it. We've been avoiding putting
this in because users need to know up front what the fragment length
distribution should look be since we can't calculate it from just the
reads
with single-end data, and in our experience most of the time the
informatics people aren't getting that information upstream. Some folks
have reported that kallisto is pretty sensitive to this parameter (
https://www.biostars.org/p/253943/), so its important to get it right,
and we are thinking that most folks won't have that information so we
haven't supported it.
For fusions though, pizzly might be less sensitive to the parameter. If
so
then it would make sense to give this a go with single-end reads just for
fusion calling. It would be worth checking if kallisto even calls fusions
with single end reads: pachterlab/kallisto#180
https://github.com/pachterlab/kallisto/issues/180 suggests that it
might not be the case. Do you think you could run kallisto manually with
a
fragment size distribution guess and see if you can generate fusion calls
from the single-end data? If not then I'll swap it to skip pizzly for
single-end reads rather than give this error. If so then it would be
useful
to see how sensitive it is to fragment length guesses, and if it isn't
too
sensitive we could add a reasonable default.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<
https://github.com/bcbio/bcbio-nextgen/issues/2491#issuecomment-415863423
,
or mute the thread
<
https://github.com/notifications/unsubscribe-auth/AMUKdrOynbLoqyVdD4dZyuFlnccihzx4ks5uUFfAgaJpZM4WLwYx
.

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Hi Rory,
As you had suggested, Kallisto/pizzly won't call fusions on sinlge-end
reads (at least, that was my experience). I simply commented out the
bcbio_nextgen assert failure for single-end reads in the kallisto script,
did my bcbio_nextgen runs with "fusion_caller: [pizzly, oncofuse]", and it
finished without error (aside from a warning that oncofuse isn't compatible
with hisat2). The fusion files in my pizzly directory were empty, just as
in the pachterlab/Kallisto issue you linked above. I did quite a bit of
poking around in other RNAseq-based fusion callers, and it appears that
this is a general limitation. So, for this dataset, I'll have to call
fusions from DNA or not at all. Thanks for your help!
On Fri, Aug 24, 2018 at 8:00 PM Rory Kirchner<EMAIL_ADDRESS>wrote:

Thanks David, I’m super interested in hearing what the results are on your
dataset. In the meantime I can try doing pizzly calls on single end data
with the fusion dilution series with that default insert size and see how
much we lose.
On Fri, Aug 24, 2018 at 4:01 PM David Masica<EMAIL_ADDRESS>wrote:

Hi Rory,
Thank you for the quick reply! Yeah, I can give it a manual go. It looks
like for Illumina the average length should be ~190, so I should just be
able to do --single -l 190, and be (reasonably) safe. I might just try
and
hack these flags into the bcbio_nextgen source (unless that sounds like a
horrible idea). In any event, I can understand why you wouldn't want to
add
this in as default behavior to something as widely used as bcbio_nextgen.
Cheers!
On Fri, Aug 24, 2018 at 12:45 PM Rory Kirchner<EMAIL_ADDRESS>wrote:

Thanks David, sorry about not supporting it. We've been avoiding
putting
this in because users need to know up front what the fragment length
distribution should look be since we can't calculate it from just the
reads
with single-end data, and in our experience most of the time the
informatics people aren't getting that information upstream. Some folks
have reported that kallisto is pretty sensitive to this parameter (
https://www.biostars.org/p/253943/), so its important to get it right,
and we are thinking that most folks won't have that information so we
haven't supported it.
For fusions though, pizzly might be less sensitive to the parameter. If
so
then it would make sense to give this a go with single-end reads just
for
fusion calling. It would be worth checking if kallisto even calls
fusions
with single end reads: pachterlab/kallisto#180
https://github.com/pachterlab/kallisto/issues/180 suggests that it
might not be the case. Do you think you could run kallisto manually
with
a
fragment size distribution guess and see if you can generate fusion
calls
from the single-end data? If not then I'll swap it to skip pizzly for
single-end reads rather than give this error. If so then it would be
useful
to see how sensitive it is to fragment length guesses, and if it isn't
too
sensitive we could add a reasonable default.
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Hi David,
Thanks for following up, that's super helpful information to have. I'll update the message to reflect this information.


Update hybrid ecdhe.sike known answer test to be more consistant

Issue # (if available):
N/A
Description of changes:
During this test's setup after setting the DRBG some methods can use random data from the DRBG which affects the ECHDE and SIKE keys. This moves the DRBG setup to right before the test starts to reduce the chance of that.
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Codecov Report

Merging #1050 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master    #1050   +/-   ##
=======================================
  Coverage   87.11%   87.11%
=======================================
  Files         167      167
  Lines       16000    16000
=======================================
  Hits        13938    13938
  Misses       2062     2062


send stats performances

Based on this capture ValueHistory contributes to the heaviness of str0m::session::Session::poll_packet

Tested locally these 2 alternatives
+        for _ in 0..1_000_000 {
+            h.push(now, 22);
+
+            // 1
+            h.sum_since(now - Duration::from_secs(1));
+            // 2
+            h.sum();
+
+            now += inc;
+        }

This goes from 2s to 0.05s

Did you run a test with proper profiling?
These kinds of microbenchmarks tend to be wildly wrong because the compiler optimizes away something that it won't be able to optimize away in the real usage.

in the same capture the sum_since / sum is gone completely


Introduce go modules

go test fails because we do not have dependency management systems introduced.
I added go modules (go.mod, go.sum) in order to introduce it and pass tests.

Go modules are supported in version branches, not in master.  If you would like to discuss why this is, I am happy to chat in gitter or even have a video call - but master must be kept modules-free.


Retry Mechanism like MQTT for message queuing

Like with MQTT is there a way to ensure that an intended message is delivered to the client whenever the client gets disconnected and re-establishes the socket connection.
With mobile devices depending on the network they continuous go online and offline and will messages when there was no network.
How can one ensure that the messages intended are queued up and delivered later when the client becomes available?

@astutesoftware SC is not a message queue; it's more lightweight.
There are many ways to make sure that clients receive a message after recovering from a lost connection.
You can store all messages in a log in the database (e.g. you could do it with MIDDLEWARE_PUBLISH_IN middleware) and when the client reconnects, they can fetch the latest log (snapshot) - That way they will get any missed messages.
If the sender goes offline, you can make the frontend wait for the connection to come back and then retry sending the message... You could store the unsent message in localStorage in case the user closes the browser before the message is sent while offline.
You can setup special channels unique to each user or category to check for read-acknowlegements. SC can support an infinite number of channels and they're cheap so you can create as many as you like.

@astutesoftware I store every message in a long term log database and then I store the last 7 days in another database that gets cleared every night (any message older than 7 days) to ensure quick queries on recent changes. Then if I really need to go back I can but it doesn't cause major slowdowns on recent queries because 10's of millions of rows is slow to query on lol. This works pretty well for us. Not sure if it helps but it might work for you.

Yes. @jondubois @happilymarrieddad - Thank you for your input.
Storing unsent message in localStorage is the way to go then.
I keep hearing this "Channels are cheap". On a group chat room - Is it advisable to subscribe to a channel and intercept via middleware OR create an individual channel for each participant and emit messages to all of them who are supposedly in a room (No subscription - Just intent that they are currently in a room) ?

@astutesoftware It depends on what your workload looks like. The advantage of using topic channels instead of private user channels is that you only have to check the user permissions once (e.g. inside MIDDLEWARE_SUBSCRIBE) and after that you can just keep publishing data to the target channel without having to do database lookups to see which users belongs to which groups/rooms.
Either way is fine though and allowing each user to have their own private channel is pretty useful for a lot of scenarios. The best solution for you probably comes down to efficiency and/or code complexity.


Add preliminary changelog for 2.5.0

Added a preliminary change log for 2.5.0.
There are 11 open PRs. We should review them and see if any of them can be merged before releasing 2.5.0-RC1.

Looks good so far.

hi @gkleiman - is there anything that can help push this along? It'd be great to see a new release soon


Example of dynamic argument in custom-directive.md is incorrect

In #2062, an example of dynamic argument for custom directive was added. However, the intension is not clear because

if it means dynamic arguments introduced in v2.6, the example should be mydirective:[argument]=dataproperty instead of mydirective:argument=[dataproperty]
if it means just passing the argument dynamically, the example should be mydirective:argument=dataproperty instead of mydirective:argument=[dataproperty]. But this is already described in the previous example v-demo:foo.a.b="message"

I think the following example may be close to the original intention.

https://jsfiddle.net/y0ftjLxs/

cc: @bk-dev @sdras

Pinging @sdras

If I'm totally honest, I was confused as well. Mainly because in my code base the syntax was different than what was outlined by @sdras. An example usage in my code base is <div v-my-directive:[dynamicArg]></div>. That said, I have never had a need to use =dataproperty to create statement.
My original goal was to pass a data property to a directive and when that data property changed the directive update hook would get invoked so the directive could react to the change. Doing something like 2) from @oohira's post would not have worked (at least not in my testing).

Yep, this was my fault for not reading through more thoroughly. I rewrote this section with clearer examples (thank you for the fiddle @oohira), but also rewrote the explanation to be more conversational in our docs style, and explain the problem space/use case. Let me know if that clears things up for you. Thanks for the issue!


Map test suites into distinct sessions within make

Each test suite implies its own infrastructure.   The systest/Makefile now reflects that.

wont fix