Explore providing an API for providing progress information

Some extensions have a need to make the user aware of long running operations that usually happen in the background. Here are a few examples.

the Java extension indicates the background installation of the Java language server
the Azure Functions extensions indicates the generation of code
the spell checking extension indicates checking in progress
the Python extension indicates running unit tests

Since VS Code does not provide an API extensions invent their own way of progress reporting usually using status bar contributions. Some use words, some use ascii art, some use glyphs. Some show the progress on the right side, some in the left side. This does not
We'll explore what kind of progress reporting capabilities are most helpful to extensions and how we could expose those in our API.

While there are many ways and locations to show progress we will focus an 'ambient progress' information presented in the status bar. Still, the solution developed here should be generic enough to allow for progress in other places, like progress inside an editor.
Option 1 - ProgressIndicator API
This is UX'ish API which allows extensions to create ProgressIndicators in the status bar. This is similar to the StatusBarItem-api. It give lots of freedom to extensions which can (but must not) cause headaches for the editor, for instance do we rely on extensions hide/disposing those indicators etc.
export interface ProgressIndicator {
	title: string;
	percentage: number;
	onDidCancel: Event<this>;
	show(): void;
	hide(): void;
	dispose(): void;
}

export namespace window {

	export function createStatusBarProgressIndicator(): ProgressIndicator;
}

Pros:

flexible

Cons:

flexible, extension might forget to hide/reset indicator etc
similar to the StatusBarItem API

Option 2 - declarative
The second options abstracts the UX element of a ProgressIndicator and simply allows extensions to provide a task/callback for which we will show progress. The interface is more simple and allows for less.
export interface Progress {
	message: string;
	precentage: number;
}

export namespace window {
	export function withStatusBarProgress<R>(task: (progress: Progress, token: CancellationToken) => Thenable<R>): Thenable<R>;
}

Pros:

limited
allows to restrict the lifecycle of Progress to the execution time of task

Cons:

limited, it's harder to fit an operation into this which isn't yet wrapped into a promise.

If I understand Option 2 correctly, this would mean one progress indicator managed by VS Code. This would be an issue if two extensions were executing simultaneous tasks and both wanted to indicate progress.
Also, I think many (perhaps the majority) of uses cases would involve showing an indeterminate progress indicator, e.g., a spinner, to simply indicate that a long running task is occurring. Whatever API you come up with should allow for this.

Option 2, and that's we one we are implementing, means that the API allows you to suggest to the editor to show progress in different places. One is the status bar, we now call that window progress, others are progress inside the viewlets, editors, or application wide progress (showing on the app icon). That doesn't mean only one progress can be shown at a time but we have UX limitation that don't allow us to show arbitrary progress indicators everywhere. For instance the little clock icons we render on top of the activity switcher can only show one activity at a time. Similar with progress inside editors. Still, all progress elements will stack. So, a latter task overlays the former but also reveals it again when finishing earlier.

My extension Color Picker shows own progress indicator in the status bar while NPM modules installation running.
Since the user might not see the status bar, I made it blink.

For important message, is an option of new API that make it stand out considered?
Also, can an extension do something when the task is forcibly aborted? For example, is the onDidCancel event fired when the user closes VS Code also?

When installation for something is aborted, files might be broken, and re-installation may fail.
An extension has to clean up the install directories.
(Sorry, my poor English)

Ok, I understood that. Thank you.
I think that a new event that is fired when VS Code is closed is needed for important task such as installation.

Api is now a single function with an options parameter
	/**
	 * A location in the editor at which progress information can be shown. It depends on the
	 * location how progress is visually represented.
	 */
export enum ProgressLocation {

	/**
	 * Show progress for the source control viewlet, as overlay for the icon and as progress bar
	 * inside the viewlet (when visible).
	 */
	SourceControl = 1,
	/**
	 * Show progress in the status bar of the editor.
	 */
	Window = 10
}

/**
 * Value-object describing where and how progress should show.
 */
export interface ProgressOptions {
	/**
	 * The location at which progress should show.
	 */
	location: ProgressLocation;

	/**
	 * A human-readable string which will be used to describe the
	 * operation.
	 */
	title?: string;
}

export function withProgress<R>(options: ProgressOptions, task: (progress: Progress<{ message?: string; percentage?: number }>) => Thenable<R>): Thenable<R>;

Verified by implementing an extension that uses the new API.

@aeschli Can you post your extension to github? I'm not quite following the API as posted above.

Use yo code to generate a sample extension and replace extension.ts with:
'use strict';

export function activate(context: vscode.ExtensionContext) {

    let disposable = vscode.commands.registerCommand('extension.sayHello', () => {

        vscode.window.withProgress({ location: vscode.ProgressLocation.Window, title: 'hello'}, p => {
            return new Promise((resolve, reject) => {
                p.report({message: 'Start working...' });
                let count= 0;
                let handle = setInterval(() => {
                    count++;
                    p.report({message: 'Worked ' + count + ' steps' });
                    if (count >= 10) {
                        clearInterval(handle);
                        resolve();
                    }
                }, 1000);
            });
        });
    });

    context.subscriptions.push(disposable);
}

@vazexqi I think you should go ahead and open an issue for adding a cancel event to withProgress.

@aeschli any plans on exposing also custom tooltip (like here) using public withProgress API?

No plans, but please file a new issue.


Fix/close context when done

Huge memory save on test-runner.

Now we open playwright and the browser only once. Then we create a context for each test
Got rid of slowmo. Swapped it with waiting when needed (circa 40s time gain)
Test now run perfectly on the small runner. Non need for gh-large

Before:

After (peeks at like 300Mb):

Thank you, this is very satisfying. Looks good to be merged to me.

Looks great!
I'll close gh-large once merged 🎉


kitchen: detect, error when waypoints.json is missing, dont install heart.kit.js by default

Thanks!


Compliance for team request for SES

Describe the issue
The ENV Falcon team is wanting to use the Amazon Simple Email Service and wishes us to prioritize a compliance review of this service for tenant team usage and inclusion in the developer's toolkit / allowed list of services.
Which Sprint Goal is this issue related to?

Note: 'Milestone' is a ZenHub term that we use synonymously with 'Sprint'.

The 'Milestone' description (created in ZenHub) should clearly list Sprint Goals. This section should indicate which 'goal' this issue is related to.
Additional context

Contact Max Wardle on team Falcon (he's a gov employee so Teams is fine)
There currently are several teams using the compliant BC Gov Common Hosted Email Service (https://developer.gov.bc.ca/About-the-Messaging-Common-Service), but we are unsure of the operational capacity of this product (industrialized, supported 24/7, on a platform with 7 9's uptime etc)
There is a review in flight over the GoC Notify Service (Greg F)

Definition of done

Compliance review of SES service done
Decision of inclusion into developer toolkit (or not)
Connect back to Falcon with update on timeline before June 15

proposed meeting with NRM on 14th.

meeting planned with nrm on 14th.

deprioritized due to other tools being used by NRM

Team Falcon ended up using GC Notify service but another team has come to us with a request for SES.

Not relevant anymore


fix: typo in default role prompt

Just a small typo in the default configuration.

good catch, thanks :pray:


Different results on different machine

While this may be slightly unrelated, I couldn't find out why the deepface models are returning different result for same code:
from deepface import DeepFace
from sklearn.datasets import fetch_lfw_pairs
from sklearn.metrics import accuracy_score

X = fetch_lfw_pairs(
    subset="test",
    funneled=False,
    # slice_=(slice(0, 250), slice(0, 250)),
    resize=1,
    color=True
  )

imgs, y = X.pairs, X.target

preds = []

for i in range(len(imgs)):
  img = imgs[i]

  img1 = img[0]
  img2 = img[1]
  img1 = img1[:,:,::-1]
  img2 = img2[:,:,::-1]

  result = DeepFace.verify(
      img1,
      img2,
      model_name="ArcFace",  # "DeepFace" # "ArcFace" # "Dlib" # "DeepID" # "OpenFace" # VGG-Face" # "Facenet"
      detector_backend="dlib",  # "mtcnn",  #"ssd" # "opencv",  # "retinaface",
      enforce_detection=False,
      )

  # print(f"Actual :", y[i], "Predicted :", result["verified"])
  preds.append(result["verified"])  # result

print("Accuracy :", 100*accuracy_score(y, preds))

Machine 1 (i.e. Google Colab) is returning 94% accuracy.
Machine 2 is returning 50% accuracy.
The library versions on two different platform is as follows:
             Machine 1                     Machine 2
deepface     0.0.75                        0.0.75
scikit-learn 1.0.2                         1.1.1
opencv       <IP_ADDRESS>                      <IP_ADDRESS>
tensorflow   2.8.2+zzzcolab20220527125636  2.7.0

Could scikit-learn version be the cause?

most probably it is because of the weight file in HOME/.deepface/weights. Delete them and let the library to re-install.

I retested after dekleting the weights, but the results are same.
md5sum of weight files are same on both:
dfe5b4da0a49aef19ec4c62673295d29  arcface_weights.h5


Set up PHPStan on GitHub Actions

This PR sets up PHPStan to run on GitHub Actions, as discussed in discussions#469.
Overview

[x] Sets up PHPStan to run on GitHub Actions on PHP 8.1 only
[x] Configures PHPStan to run the analysis on the examples, src and tests folders
[x] Generates the baseline so that static analysis passes immediately

Baseline
Because this PR aims to set up PHPStan and not address the errors it reports, I've generated a baseline to make the pipeline succeed. We'll then be able to incrementally fix the problems in future PRs.

The generated baseline produces different results on different operating systems.
The pipeline succeeds when running on macOS but fails when running on Ubuntu (in the GitHub Actions runner at least).
 ------ -----------------------------------------------------------
  Line   examples/92-client-benchmark-upload.php
 ------ -----------------------------------------------------------
  109    Call to an undefined method ChunkRepeater::getPosition().
  116    Call to an undefined method ChunkRepeater::getPosition().
  116    Call to an undefined method ChunkRepeater::getPosition().
 ------ -----------------------------------------------------------

 ------ -----------------------------------------------------------------------
  Line   examples/99-server-benchmark-download.php
 ------ -----------------------------------------------------------------------
         Ignored error pattern #^Call to an undefined method
         ChunkRepeater\:\:getSize\(\)\.$# in path
         /home/runner/work/http/http/examples/99-server-benchmark-download.php
         was not matched in reported errors.
 ------ -----------------------------------------------------------------------

It seems to complain about a method not being defined although the method is defined. I cannot find a reason for this currently.

For the reference: It looks like this wasn't closed intentionally (as discussed in https://github.com/reactphp/async/pull/64). We've recently started applying PHPStan on max level into our projects with https://github.com/reactphp/async/pull/76 and we'll go ahead with this and apply PHPStan on max level to all our projects in the future.
Thank you very much for your contribution and sparking this discussion! :+1:


Scrutinizer Auto-Fixes

@DaneEveritt requested this pull request.
It consists of patches automatically generated for this project on Scrutinizer:
https://scrutinizer-ci.com/g/PufferPanel/PufferPanel/

Closing since broken

Bug was reported and should be fixed by next week.


Remove lifetime from FileDescriptor trait

Also:

Type annotate handles declaration, instead of annotating every insert.
Add note about flush being unnecessary when writing to stderr

Addresses comments in #1495 and #1497

Looking good, aside from one nit. :)

@bors r+

:pushpin: Commit 0c2506411700591f218c03dca19b47388bd80f60 has been approved by RalfJung

:hourglass: Testing commit 0c2506411700591f218c03dca19b47388bd80f60 with merge 99a57a3f9e421c4fe0b1932c25103f2adbf54660...

:sunny: Test successful - checks-travis, status-appveyor
Approved by: RalfJung
Pushing 99a57a3f9e421c4fe0b1932c25103f2adbf54660 to master...


Hardcode videoIsTranscoded = true on livestreams

PR Checklist

Please check all that apply to this PR using "x":

[x] I have checked that this PR is not a duplicate of an existing PR (open, closed or merged)
[x] I have checked that this PR does not introduce a breaking change

PR Type
What kind of change does this PR introduce?

[x] Bugfix

Fixes
Fix quality selector not being shown on livestreams.
Issue Number: #232 (missing quality options under Auto (confirmed stream had em))
What is the current behavior?
No quality options on livestreams as it is not considered a transcoded stream
What is the new behavior?
Hardcode that livestreams are transcoded so those that are have quality selection, and those that don't just have a single quality.

Closing this. Not all livestreams are transcoded.

@akinwale @kekkyojin Please see the discussion in Slack. Also, currently livestreams are hardcoded to use HlsMediaSource, so any change in the backend when livestreams aren't HLS will require code changes as well.


feat(rust): add checkout_latest to Dataset

This is faster than doing dataset.checkout_version(dataset.latest_version_id().await?).await?, since we don't need to do an extra IOP to get the size and manifest path style of the version. (We do this in LanceDB right now.)

Codecov Report
Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 78.84%. Comparing base (fdbe4a8) to head (4081afe).

Files with missing lines
Patch %
Lines

rust/lance/src/dataset.rs
75.00%
0 Missing and 1 partial :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2991      +/-   ##
==========================================
- Coverage   78.84%   78.84%   -0.01%
==========================================
  Files         236      236
  Lines       73552    73556       +4
  Branches    73552    73556       +4
==========================================
+ Hits        57995    57997       +2
+ Misses      12553    12549       -4
- Partials     3004     3010       +6

Flag
Coverage Δ

unittests
78.84% <75.00%> (-0.01%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


First uplink to TTN always fails

The first uplink message to TTN always fails. This is true for Join, as well as for the first uplink sent in ABP mode. I am not sure if this is actually a problem in the firmware. I experienced the same problem with the original Murata firmware. I am just recording it here to make sure it is not forgotten.

It turns out that this is a problem in the US915 and AU915 regions and specifically only with gateways that do not listen on all 64 uplink channels defined in those regions. That includes pretty much all TTN gateways since those listen on the channels in the second subband (FSB2) only, i.e., channels 8 to 15.
Since the US915 and AU915 regions use all available uplink channels for Join, the device after a factory reset first transmits the Join on a channel in FSB1 (0-7), then on a channel in FSB2 (8-15), and so on. The first Join request will thus not be received by a majority of the gateways that are only configured to listen in FSB2. The FSB2 channels are defined as follows in the US915 region:
903.9 - SF7BW125 to SF10BW125
904.1 - SF7BW125 to SF10BW125
904.3 - SF7BW125 to SF10BW125
904.5 - SF7BW125 to SF10BW125
904.7 - SF7BW125 to SF10BW125
904.9 - SF7BW125 to SF10BW125
905.1 - SF7BW125 to SF10BW125
905.3 - SF7BW125 to SF10BW125

The solution is to update the channel mask in the device after a factory reset and prior to Join:
AT+FACNEW
AT+BAND=8
AT+MODE=1
AT+CHMASK=00FF00000000000000000000
AT+JOIN

It may be also necessary to manually configure the channel mask in ABP devices in the US915 and AU915 regions since there the network server cannot use the Join answer to update the channel mask in the device. The channel must can be updated by ADR, if the ABP device has ADR enabled.


Add coercion for joing using and equi-join

based on #2542

@erichwang do you have time to review this? If not, assign to @dain

This fixes the problem for JOIN ... USING, but it still fails with a regular equality joins:
SELECT * FROM (VALUES (1.0, 2.0)) x (a, b) JOIN (VALUES (1, 3)) y (a, b) ON x.a = y.b

@martint I add a commit to fix this one.

Merged, thanks!


Typings for imported icons

Hi!  Any way to have typings for imported icons?
import IconHome from '/@vite-icons/oi/home'

has the usual no typings found error.
Have to import them rather than auto-import because they're being used in a list like this:
  { title: 'Home', icon: IconHome, link: '/' },

Trying to build a list of menu items like so
const items = reactive([
  // @ts-ignore
  { title: 'Home', icon: IconHome, link: '/' },
  { title: 'Counter', icon: IconCounter, link: '/Counter' },
  { title: 'Fetch data', icon: 'oi-list-rich', link: '/Fetch-Data' }
])

The string icons don't get imported as a component, and I can't figure out how to inline import them so I"m trying to just do the standard import but I get typing errors.  Open to ideas.

You can import them with .vue
import MdiAlarmOff from<EMAIL_ADDRESS>
// vue-shim.d.ts
declare module '*.vue' {
  import { defineComponent } from 'vue'
  const Component: ReturnType<typeof defineComponent>
  export default Component
}

I actually tried that but couldn't get it to work in a Vitesse setup.


set up getDriverById endpoint

set up driver/:id/get endpoint to retrieve a certain driver's data

/cib get-driver-by-id-endpoint

Branch 13-get-driver-by-id-endpoint created!


NetKVM: add DmaRemappingCompatible to INF

Indicate that the driver is fully compatible with DMA remapping.
INF tested with

Windows HLK 2022 (InfVerifHLK.dll, 10.0.20348.1)
Windows HLK 1607 (InfVerifHLK.dll, 10.0.14393.4)
Windows HCK 2.1 (InfTest.exe, 6.3.9600.17298)

rerun tests


fix: creates the thinpool with the -Z option

This commit updates the lvcreate command used to create
the thinpool with the -Z option to enable zeroing. This removes
the requirement that the thin_pool_zero option be enabled in the
lvm.conf.
Signed-off-by: N Balachandran<EMAIL_ADDRESS>

/cherry-pick release-4.11


[Codegen] Ruby 3.0 compatibility

MAC build with ./bootstrap.sh
/Users/admin/.rvm/rubies/ruby-3.0.0/lib/ruby/3.0.0/set/sorted_set.rb:4:in rescue in <top (required)>': The SortedSetclass has been extracted from thesetlibrary.You must use thesorted_set` gem or other alternatives. (RuntimeError)
SortedSet was removed from stdlib in Ruby 3.0

Thanks for the report, we will fix it


Analog sensitivity setting

This is a suggestion regarding the addition of an analog stick sensitivity setting
I have re-written the code again based on your previous suggestions
I don't think it's appropriate to change the ADC value after the dead zone process, so I've done it in the current location.
However, the ADC values have changed significantly and the magnitude values need to be recalculated.
I am struggling with this point. If you have an evaluation, please let me know.
(This is a machine translation)

We'll take a look at this after the upcoming release. Thanks for submitting!

Then I'll close this request once.


Fix CMakeLists error

I realised that I forgot few lines to make deployment on Windows works... :sweat_smile:

I will try later, thanks ;)


[Content Submission] CRB classes

Here's the db files for classes and class features. The classes db just replaces the current classes db. the class features needs a new pack in the system json (set to class-features), then that can also be dropped in the packs folder. They should all be linking correctly between sheets.
CRB Classes.zip

Added to development a while back, just never marked it here.


Bump MSRV to 1.57

This will let us use dependencies that need Rust 2021 in examples.
As discussed at https://github.com/nrf-rs/microbit/pull/80#issuecomment-977001166 and https://github.com/nrf-rs/microbit/pull/83#issuecomment-1035592387 .

Should there be a changelog entry for this? It doesn't look like there's been one for previous bumps.

Since there's no other indication, documenting the bump in the ChangeLog (since it technically is a breaking change) would certainly make sense to me.


Added v!support and support to help command

upload your public key

wait no dont merge this yet, I forgot about slash commands so stuff may break

Just saw this. Keep it closed 👍

Just saw this. Keep it closed 👍


Move to script-driven extension instead of kernel extension

The package I want to suggest the idea to: AngouriMath.Interactive
Currently there's a class in AngouriMath.Interactive which inherits from KernelExtension. Instead, it is suggeted to move to running a dib-file with all necessary code, as shown in the link
https://github.com/dotnet/interactive/blob/main/docs/extending-dotnet-interactive.md#script-based-extensions

Not unless https://github.com/dotnet/interactive/issues/1808 is fixed

Current state:

On old dotnet-interactive version (see AngouriMathLab for the version) Jupyter works on old (21330.2) and new (21606.1) versionf of Formatting
On new dotnet-interactive version Jupyter doesn't work
VSC Notebooks work in both cases


Exclude docs/ directory from .sublime-package

The current FileManager.sublime-package is ~960KB. The docs/ directory may be not useful at local imho. By removing it from the package, FileManager.sublime-package reduces to ~34KB.

:+1: Clean and neat trick there. Thank you!

🎉

hey @jfcherng, I want to reuse this trick on MarkdownLivePreview, but I'm not sure I completely understand how it works.
I understand that the export-ignore tag tells git to ignore that target when archiving, but I haven't found any documentation from packagecontrol stating that they do use archives (although I get that it makes sense to do so). I've also unsuccessfully quickly browsed the code for some git archive command...
I figured I would just ask you because I'm guessing I'm missing something obvious: how did you know this would work?

I guess it's because Package Control directly downloaded the .zip file provided by Github.
https://github.com/wbond/package_control/blob/b2ac007/package_control/clients/github_client.py#L88
The above URL pattern is exactly the same with the one in the release page of a repository. (after a 302 redirection)

Oh I couldn't find that line by myself I guess :slightly_frowning_face: ... That's exactly what I wanted though, thank you very much Jack :slightly_smiling_face:


python312Packages.publicsuffixlist: <IP_ADDRESS>41127 -> <IP_ADDRESS>41129

Changelog: https://github.com/ko-zu/psl/blob/v<IP_ADDRESS>41129-gha/CHANGES.md

Things done

Built on platform(s)

[ ] 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/)
25.05 Release Notes (or backporting 24.11 and 25.05 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

[ ] Fits CONTRIBUTING.md.

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

nixpkgs-review result
Generated using nixpkgs-review.
Command: nixpkgs-review pr 360064

x86_64-linux

:fast_forward: 4 packages marked as broken and skipped:

python311Packages.parsedmarc
python311Packages.parsedmarc.dist
python312Packages.parsedmarc
python312Packages.parsedmarc.dist

:x: 3 packages failed to build:

pretalx
pretalx.dist
pretalx.static

:white_check_mark: 12 packages built:

parsedmarc
parsedmarc.dist
python311Packages.checkdmarc
python311Packages.checkdmarc.dist
python311Packages.publicsuffixlist
python311Packages.publicsuffixlist.dist
python312Packages.checkdmarc
python312Packages.checkdmarc.dist
python312Packages.publicsuffixlist
python312Packages.publicsuffixlist.dist
trustymail
trustymail.dist


The queuelist could not be loaded

after adding one or two blogs and adding them to the queue , then close the app and re run it , I see this error

I've some doubt this really happens the way you described it. I'm sure you've read my comment to the queue in the release notes, right?
I've just added each kind of blog for testing purpose, added them to the queue, restarted (the same version), and the queue was back.
Send me/attach the corresponding files from the Index folder for the blogs where this happens.

I encountered this problem in the VS environment for earlier version , and tested again with latest release ( not in VS ) and faced the same issue, not related to previously added blogs , just when I wanted to test
with one blog added or two, attaching the index file
when I tried to go through the code in the beginning, after running the app, and add blogs, theh close the app, I got exception on close , so I added below lines to avoid exception, but it seems like save on exit, correct me if am wrong, then I said to avoid testing on VS and try your latest release and the same result happened..not saving the blogs on exit,,, I think this is the issue, as I close the app while crwling
public void ReplaceAll(IEnumerable newBlogNames, IEnumerable newBlogTypes)
{
names.Clear();
names.AddRange(newBlogNames);
if (types != null)
{
types.Clear();   // types.Clear(); //
types.AddRange(newBlogTypes);
} // types.AddRange(newBlogTypes);
}

Works for me. Newest code, newest release, no issues. Even when I close the application during an active crawl or in VS.
As I've already said, I think you're mixing old code or saved queues with new one code/saved queues, thus the blogtypes is null since they weren't saved earlier in the queue save file as I've mentioned above (and in the release notes).
I've made the corresponding changes on the 25th August.

Did you try deleting your settings files? I'm not sure why this would help, but apparently it helped here.


Replace checkstyle plugin

We require a viable solution to fix the checkstyle errors right in IDE. Currently you have to compile and visit each class present in logs.
This should work something like eslint/prettier with visual indication of invalidly formatted lines.

current checkstyle plugin doesn't care about formatting like this:
  public Mono<Void> deleteConsumerGroupOffset(KafkaCluster cluster,
                                            String groupId,
                                              String topicName) {
    return adminClientService.get(cluster)
        .flatMap(adminClient -> adminClient.deleteConsumerGroupOffsets(groupId, topicName));
  }


 fuzzbug:

Thanks for filing an issue! Please fill out the TODOs below, and change <target> in the title to the corresponding fuzzing target.

Test case input

TODO_paste_the_base64_encoded_input_here

`cargo +nightly fuzz fmt` output

TODO_paste_cargo_fuzz_fmt_output_here

Stack trace or other relevant details

TODO_paste_the_report_here

Hi @Dees37. This issue appears to be incompletely filed. As such, I am closing it for now.
If you would like to fill out the requisite information to completely detail your issue, please reopen it at that time.
Thank you.


flatpickr is incorrectly positioned in version 2.6

Seems like there has been some kind of regression. When I upgraded from 2.58 to 2.6 I started to get the flatpickr displaying at the top left of the screen instead of next to the input element.
Your Environment

flatpickr version used: 2.6
Browser name and version: chrome
OS and version: windows 10

Hello,
Without knowing your config options, its impossible to help.
This issue isn't present neither in docs nor the fiddle
Kindly provide a fiddle that reproduces this regression and re-open the issue.
Thank you


flag package misleading msg on parsing issue

go version go1.12 windows/amd64
ISSUE 1
var minWordLen = flag.Int("min", 5, "Minimum word length.\n")
var maxWordLen = flag.Int("max", 5, "Maxmum word length, >= min.\n")
var filePtr = flag.String("file", "afile.txt", "input data file\n")
executing in bash: ./program.exe -min 1 -max 4 -file book.txt
Above works fine.
Fat finger and forget the "-" for the max option, and get a misleading error about: -file book.txt not found. Of course the file is present since reedit of command line works.
Was expecting some better message about garbage option data, of even that the int for min was invalid - that would have pointed the the error area better.
ISSUE 2 (maybe a bash issue and not Go?)
Run the command  and get output to stdout, then try to redirect like:
./program.exe -min 1 -max 4 -file book.txt -suffix 2
Above works fine.
./program.exe -min 1 -max 4 -file book.txt -suffix 2>OUT.file
No space before redirect, display help (option data), unexpected
Edit and add the space works fine.

Your ISSUE 2 is just how the Unix shell works.  2>OUT.file redirects file descriptor 2 to OUT.file, and the 2 is not passed to the program.  There is no Go problem there.  (In general, please file unrelated problems as separate issues on the issue tracker.  Thanks.)
For ISSUE 1, the error you mention is presumably coming from your program.  I don't see why it would be coming from the flag package.  Flag parsing stops before the first non-flag argument, which in this case would be max.  The remaining arguments 4 -file book.txt will all be passed to your program as normal non-flag arguments accessible via os.Args.  Can you suggest what the flag package could do differently here?

Issue 1: I agree ;-) this is what retirement does to you, I forgot cmdline
order of evaluation
2 Bugs in one report - forgive me, 35 years at Bell Labs we DID put
multiple issues in a report IF they were tightly related  to the same
code.I'll play by your rules.
Issue 2: Hummm.  I expected the cmdline to be parsed with some regex
findall/split based on something like -A-Za-z thus allowing for
all proper options to be evaluated and the left over "max 4" being passed
to the program which would be easy to decipher and err on.
But I'll cope.
Lastly a request? Why not allow an "or" in the option name like "n|number"
as we often did in shell case statements to accommodate power users as well
as novices?
Nice pkg by all means, especially the help text in the declaration and the
free formatting of help output. I've filed 100's of bugs in my career in
those area alone which would be much less likely,and certainly easier ti fix
this way.
Please close the report, blame my older gray matter.
On Fri, Jun 28, 2019 at 10:30 AM Ian Lance Taylor<EMAIL_ADDRESS>wrote:

Your ISSUE 2 is just how the Unix shell works. 2>OUT.file redirects file
descriptor 2 to OUT.file, and the 2 is not passed to the program. There
is no Go problem there. (In general, please file unrelated problems as
separate issues on the issue tracker. Thanks.)
For ISSUE 1, the error you mention is presumably coming from your program.
I don't see why it would be coming from the flag package. Flag parsing
stops before the first non-flag argument, which in this case would be max.
The remaining arguments 4 -file book.txt will all be passed to your
program as normal non-flag arguments accessible via os.Args. Can you
suggest what the flag package could do differently here?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/golang/go/issues/32830?email_source=notifications&email_token=AMNS5UYHXAYJJ5Y2IU6JLADP4YOAFA5CNFSM4H4FTTX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODY2HI7I#issuecomment-506754173,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AMNS5U3LA2BSUXBYDUIHGITP4YOAFANCNFSM4H4FTTXQ
.

You can define multiple flags with the same name using flag.StringVar and the like.  I can't recall ever seeing the idea of n|number before.  I'm not sure we could make such a change today.


Add simple pyTMD example scripts

First, many thanks for bringing a really amazing package to the community!
I am not an expert on tides, and I had not used TMD packages before. When starting with pyTMD, I had a bit of difficulty to do / find documentation / find examples about how to do really simple things (like, given a lon, lat, and time, get tide elevation and currents).
I have written a couple of small notebook "scripts" for getting an "as simple as possible" example of how to use the package (i.e. having just some pyTMD, without the widget etc present in the more advanced notebooks available so far). To make sure I use pyTMD correctly, I also compare with observations for both tide and current.
This results in the two notebooks committed here. I think this may be useful for other users who want a "least complexity example" of how to use pyTMD in a python script, so submitting these to the upstream.
Let me know if you are interested in including this. If yes, could you have a quick look, to triple check I am doing things correctly? :)

Sorry, I messed up with the signature of the commits - will open a new pull request in 2 minutes, coming soon :) .


Update A-Frame docs.

Change artoolkit to new arjs system, update debug to debugUIEnabled (could probably be shortened to debugUI?), and change example <a-cube> to <a-box>, as that's the valid markup in A-Frame.

Thanks! sorry for the delay... i was AFK


Feature/pfeeny listing updated on panel to sidebar

Pull Request Template
Issue
Addresses #80

[ ] This change addresses the issue in full
[x] This change addresses only certain aspects of the issue
[ ] This change is a dependency for another issue
[ ] This change has a dependency from another issue

Description
Created a new panel for the listing sidebar that includes the listing updated date.  This change creates the UI-component and implements it on the listing page.
Type of change

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] Prototype/POC (not to merge)
[ ] This change is a refactor/address technical debt
[ ] This change requires a documentation update
[ ] This change requires a SQL Script

How Can This Be Tested/Reviewed?
Open any listing and look in the upper right corner of the sidebar.  You should see the Listing Updated panel above the Application Due panel.

[x] Desktop View
[ ] Mobile View
[ ] Test A
[ ] Test B

Checklist:

[ ] My code follows the style guidelines of this project
[ ] I have performed a self-review of my own code
[ ] I have reviewed the changes in a desktop view
[ ] I have reviewed the changes in a mobile view
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes
[ ] Any dependent changes have been merged and published in downstream modules
[ ] I have assigned reviewers
[ ] I have updated the changelog to include a description of my changes

I don't see the change appear in mobile view. Should it be appearing there?

I think this could also be a candidate for an upstream change.


change got overwritten

my change was overwritten by: https://github.com/microsoft/azuredatastudio/commit/fb4e3c6a05aeae60b1bda673c2b8270db21cbebb#diff-09d5191ec912a707fecea55e7f97bb58
adding it back now.

FYI, I am going to merge directly and then kick off a build


Locations directory not found on JBoss

Hello,
We hit a strange bug when deploying flyway in our target environment, where some migration scripts are stored in JBoss "lib" directory (instead of the war).
I narrowed it down to this:

looking for db/migrations/module

works if directory exists in WAR classpath
does not work (not found) if directory exists in lib jars

looking for db/migrations/module/ (with a trailing slash)

works in all locations

However, when the locations are set, flyway normalize them and remove the trailing slash if there is one (in the com.googlecode.flyway.core.util.Location constructor). We workaround by putting two slashes at the end of our location, but it is rather ugly.
Obviously this is more of a bug in the classloaders behaviour, but since flyway does not give any control on how the URLs are retrieved, this is problematic. You may want to add a mean to pass location URLs directly.
Cheers,
Alexis.

Closing old issue for ancient JBoss version


Update license year

TO DO:

[ ] Wait to the next year (99% done)
[ ] Merge!

:octocat:

          2 Errors

:no_entry_sign:
Failing due to documentation issues, see below.

:no_entry_sign:
The core plugins are not at 100% doc’d - see below:

          1 Message

:book:
@m1guelpf is not a contributor yet, would you like to join the Danger org?

Core Docs Errors

  Generated by :no_entry_sign: Danger

Ace, thanks


File conflict for /opt/ros/noetic/lib/python3/dist-packages/libgtest.so between moveit_core and tf

Since the MoveIt release was merged recently in #29063, we have a file conflict reported on the buildfarm:
08:11:30   2967 'dpkg: error processing archive /tmp/apt-dpkg-install-UN3zrI/632-ros-noetic-tf_1.13.2-1focal.20210414.184309_amd64.deb (--unpack):'
08:11:30   2968 ' trying to overwrite '/opt/ros/noetic/lib/python3/dist-packages/libgtest.so', which is also in package ros-noetic-moveit-core 1.1.2-1focal.20210414.202258'

IMO, neither of those packages should install libgtest.so! Any ideas how this enters the debian package?

@tylerjw for your info

This is really odd.  I don't understand how the install into /opt/ros/noetic/lib/python3/dist-packages/ works and how we impact that.  Could this be something coming from a rosdep install run?  I don't think anything we are doing should be manually installing anything into there.
I'm not sure how to debug this.

Of course, we don't install anything manually in /opt/ros. This is done by the debian package that is built from our ROS packages. However, I haven't seen any install directive for libgtest in our sources. @sloretz,  has anything changed to catkin or the debian release process that could explain this issue?

@tylerjw, @rhaschke I have same problem, with pr2-controller-manager and moveit-core
Preparing to unpack .../ros-noetic-pr2-controller-manager_1.8.18-1focal.20210414.185725_amd64.deb ...
Unpacking ros-noetic-pr2-controller-manager (1.8.18-1focal.20210414.185725) ...
dpkg: error processing archive /var/cache/apt/archives/ros-noetic-pr2-controller-manager_1.8.18-1focal.20210414.185725_amd64.deb (--unpack):
 trying to overwrite '/opt/ros/noetic/lib/python3/dist-packages/libgtest.so', which is also in package ros-noetic-moveit-core 1.1.2-1focal.20210414.202258
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
Errors were encountered while processing:

It looks like setup.py is installing libgtest.so:
+ mkdir -p /homes/rhaschke/src/ros/install/lib/python3/dist-packages
+ /usr/bin/env PYTHONPATH=/homes/rhaschke/src/ros/install/lib/python3/dist-packages:/homes/rhaschke/src/ros/build/tf/lib/python3/dist-packages:/opt/ros/noetic/lib/python3/dist-packages CATKIN_BINARY_DIR=/homes/rhaschke/src/ros/build/tf /usr/bin/python3 /homes/rhaschke/src/ros/src/ros/tf/tf/setup.py egg_info --egg-base /homes/rhaschke/src/ros/build/tf build --build-base /homes/rhaschke/src/ros/build/tf install --root=/ --install-layout=deb --prefix=/homes/rhaschke/src/ros/install --install-scripts=/homes/rhaschke/src/ros/install/bin
running egg_info
...
running build
running build_py
...
running build_scripts
...
running install
running install_lib
creating /homes/rhaschke/src/ros/install/lib/python3/dist-packages/tf
copying /homes/rhaschke/src/ros/build/tf/lib/tf/broadcaster.py -> /homes/rhaschke/src/ros/install/lib/python3/dist-packages/tf
copying /homes/rhaschke/src/ros/build/tf/lib/tf/__init__.py -> /homes/rhaschke/src/ros/install/lib/python3/dist-packages/tf
copying /homes/rhaschke/src/ros/build/tf/lib/tf/listener.py -> /homes/rhaschke/src/ros/install/lib/python3/dist-packages/tf
copying /homes/rhaschke/src/ros/build/tf/lib/tf/transformations.py -> /homes/rhaschke/src/ros/install/lib/python3/dist-packages/tf
copying /homes/rhaschke/src/ros/build/tf/lib/tf/tfwtf.py -> /homes/rhaschke/src/ros/install/lib/python3/dist-packages/tf
copying /homes/rhaschke/src/ros/build/tf/lib/libgtest.so -> /homes/rhaschke/src/ros/install/lib/python3/dist-packages

@sloretz, is it possible that setup.py just installs all libs from <build space>/<package>/lib (libgtest.so is the only lib there) and this has changed?

We already debugged this some time ago and it's a problem in gtest's cmake files that can be worked around in catkin: https://github.com/ros/catkin/pull/1135

@mjcarroll, could you please have a look at https://github.com/ros/catkin/pull/1135 to unblock the upcoming Noetic release?

The catkin issue has been merged, so this one can probably be closed.

@mjcarroll, I guess catkin requires a new release before we can proceed with other packages?

What's the status of this ticket? It looks there's been a release of catkin since https://github.com/ros/catkin/pull/1135.

@jacobperron my problem on pr2 packages has been solved, thank you!
https://github.com/PR2/pr2_controllers/pull/401, https://github.com/PR2/pr2_kinematics/pull/15

Yes, problem is solved.


[Question] mujoco v4 environments need mujoco-py

Question
I tried to use mujoco v4 environments of gymnasium and I got error that need me to install mujoco-py. But I think v4 environments only need deepmind's mujoco, not mujoco-py which v3 environments need. Is that a bug or Did I misunderstand something? In fact, I can use mujoco v4 environments of gym 0.24.1 without mujoco-py.

Which OS are you using? Coz, Mujoco environments have some problems with Windows.

@maruya24 what environment is giving you the error? And how are you installing gymnasium? pip install gymnasium[mujoco] should work.
I'm not able to replicate the issue

I'm using macOS Ventura with Intel CPU. And I already done pip install gymnasium[mujoco] and stiil got following exception when I tried to use all mujoco v4 environments
You appear to be missing MuJoCo.  We expected to find the file here: /Users/Name/.mujoco/mujoco210

I think this message indicates that I need OpenAI's mujoco-py that is a legacy for mujoco v4 environments of gymnasium.

Could you uninstall mujoco_py?

Uninstalling mujoco-py greatly works. Now I can use mujoco v4 environments. Thank you for your suggestion.

Just for future readers, the issue is not that mujoco v4 environments needs the mujoco executable but rather that if mujoco py is installed then the mujoco executable needs to be installed.


UF-491 - Allow changing git folder name via system property

Continue to defaults to .niogit
Refactored test to check variation in the folder name

@ederign sure, reformatted code ;)


Custom Resolvers

This is a very useful plugin, but I would like to be able to have my own resolver, when wanting to make custom routes, for eg. an api.
This would probably also help with #83.

I also have the same issue... specifically the vite dev server can proxy/route /api/* to localhost:1234 but if you use a catch all you don't get hits to that api server when in production build.  In my case I'd like to have a way to turn off the catch all specifically for /api* routes.

@delaneyj I just want to generate routes for my server (I'm trying to do SSR)

I'll take a look at this. I'm working with Vite and Angular so it be great to support custom resolver

We will support custom resolver from v0.23.0, currently in beta.
Resolver's interface:
https://github.com/hannoeru/vite-plugin-pages/blob/e1496e02e003ca0a70b31a7a87e2c1ed4e2e2c99/src/types.ts#L18-L32


As an admin I want to produce a report on the All the countries in the world organised by largest population to smallest so that I can have easy access to population information

Connect to the existing database.
Add function to extract all the countries in the world filtered from largest population to smallest.
Display the country record.


Bug: SFML not found at build time on linux

The SFML library was not found at build time on linux Ubuntu

SFML version on client Cmake file needed to be delete because it's was not the good one


Skipping one of the scale test

This patch will skip one of the scale test as we are not supporting 'add-capacity' feature.


3D Doesn't Appear

Hello. I was looking to work on Gaussian Splat with Three.js and found this GitHub repository.
However, I immediately ran into a major obstacle.
Even after installing and uploading to the server, and testing with the codes provided in the sample, I can't see the ksplat on my server. The splat files we worked on also don't upload.
In the sample page console, there are a few more Views.js files that appear, but
Views.js doesn't show up in our console.
What could be the problem?

` import * as THREE from 'three';
import * as GaussianSplats3D from 'gaussian-splats-3d';
const viewer = new GaussianSplats3D.Viewer({
    'cameraUp': [0, -1, -0.54],
    'initialCameraPosition': [-3.15634, -0.16946, -0.51552],
    'initialCameraLookAt': [1.52976, 2.27776, 1.65898]
});
viewer.init();
let path = './shoose.splat';
viewer.loadFile(path, {
    'halfPrecisionCovariancesOnGPU': true
})
.then(() => {
    viewer.start();
});`

Thank you for your prompt response.
However, it seems like there are no errors catching on my debug console.
I am leaving the test URL here
https://bexcos.mycafe24.com/coor/ply/webgl3.html

I am leaving the test URL here
https://bexcos.mycafe24.com/coor/ply/webgl3.html

When I visit that URL, I see the follow error in the debug console:

That error means you don't have the necessary CORS headers set on your server that allow a SharedArrayBuffer to be used with web workers. The README talks about how to solve that problem: https://github.com/mkkellogg/GaussianSplats3D?tab=readme-ov-file#cors-issues-and-sharedarraybuffer
Or you can disable shared memory like I showed in the example above.

Thank you! Finally, 3D has come out.
I didn't know because I didn't get a console error.
Thank you very much for your kind and quick response.

Great!


Remove contract event topic limits

We have a few limits in the contract event topics:

No. topics <= 4
Topic byte size  < 64

These were some arbitrary limits put there initially, but are no longer needed. They are also not enforced consistently (diagnostic event contains a ContractEvent but we don't check that limit). Contract events are hashed into the transaction result, ~both contract and diagnostic~ contract events are included in the meta and is subject to limits and fees.

On second thought, these limits should not apply to diagnostic events (the current behavior is correct), since diagnostic events should be infallible (see https://github.com/stellar/rs-soroban-env/issues/962 to validate that).

I think it is necessary to more clearly spell out the event limits.

number of topics
single topic size limit
data size limit
Without these limits, contracts may DOS the downstream system by submitting many large events (each up to the metadata size limit).

The CAP also needs to be updated with the limits (https://github.com/stellar/stellar-protocol/pull/1371).

The 4 limit was chosen arbitrarily since that's the limit of topics in the evm. We don't need to follow that though because the topics are not indexed in the protocol like in Ethereum.

Based on recent discussions, downstream are more concerned with the meta data size to maintain than the number of topics. Thus we've decided to move the topics limit.
The meta size limit has been repurposed to event size limit in https://github.com/stellar/stellar-xdr/pull/127/files, and will be set to a much lower value ~10k to limit the downstream impact.


Dual lockup option update to config v2

Lock file needs to be updated

Lock file needs to be updated

It never works for me when I do that locally

Lock file needs to be updated

It never works for me when I do that locally

fixed


Test Release PR Creation

To be merged after the release is complete.

Looks like it's working!

Testing complete.


[3DS] CIA Format

I was wondering if you could make a CIA of this for the 3DS. I have made a banner image and sound for this.
Archive.zip

Done, it's added to the latest release. I swapped out the banner since there was something else I liked better, and I made a similar (but different) sound since that one wasn't working with bannertool, and I wanted to make the music part louder.

Nice!


something wrong about lgb.cv when using logloss or rmse

lgb.cv - rmse
import lightgbm as lgb
import numpy as np
import pandas as pd
feature = np.random.randint(1,10,size=(200000,5))
label = pd.DataFrame(np.random.randint(2, size=200000))
data = lgb.Dataset(data=feature,label=label)
params = {
        'learning_rate':0.1,
        'bagging_fraction': 0.8,
        'feature_fraction': 0.8,
        'num_leaves': 89,
        'reg_alpha': 0,
        'reg_lambda': 1,
        'bagging_freq': 7,
        'min_child_samples': 10,
       'objective':'binary',
       'metric':'rmse',
       'bagging_seed':2023}
res = lgb.cv(params, data, 1000,
                     nfold=5,
                     stratified=False,
                     shuffle=True,
                     metrics='rmse',
                     early_stopping_rounds=20,
                     verbose_eval=False,
                     show_stdv=False,
                     seed=2020)

###result

lgb.cv - logloss
import lightgbm as lgb
import numpy as np
import pandas as pd
feature = np.random.randint(1,10,size=(200000,5))
label = pd.DataFrame(np.random.randint(2, size=200000))
data = lgb.Dataset(data=feature,label=label)
params = {
        'learning_rate':0.1,
        'bagging_fraction': 0.8,
        'feature_fraction': 0.8,
        'num_leaves': 89,
        'reg_alpha': 0,
        'reg_lambda': 1,
        'bagging_freq': 7,
        'min_child_samples': 10,
       'objective':'binary',
       'metric':'logloss',
       'bagging_seed':2023}
res = lgb.cv(params, data, 1000,
                     nfold=5,
                     stratified=False,
                     shuffle=True,
                     metrics='logloss',
                     early_stopping_rounds=20,
                     verbose_eval=False,
                     show_stdv=False,
                     seed=2020)

###result

question
I know that for classification problems need the same logloss loss function，but why is there an error when using logloss, but not when using rmse?
### Tasks

of course
#lgb.cv-rmse
[LightGBM] [Info] Number of positive: 79805, number of negative: 80195
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.002291 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79711, number of negative: 80289
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001910 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79728, number of negative: 80272
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.002153 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79764, number of negative: 80236
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001885 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79828, number of negative: 80172
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001924 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498781 -> initscore=-0.004875
[LightGBM] [Info] Start training from score -0.004875
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498194 -> initscore=-0.007225
[LightGBM] [Info] Start training from score -0.007225
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498300 -> initscore=-0.006800
[LightGBM] [Info] Start training from score -0.006800
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498525 -> initscore=-0.005900
[LightGBM] [Info] Start training from score -0.005900
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498925 -> initscore=-0.004300
[LightGBM] [Info] Start training from score -0.004300

#lgb.cv-logloss
[LightGBM] [Info] Number of positive: 79805, number of negative: 80195
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.002173 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79711, number of negative: 80289
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001304 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79728, number of negative: 80272
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001855 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79764, number of negative: 80236
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001528 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] Number of positive: 79828, number of negative: 80172
[LightGBM] [Warning] Auto-choosing row-wise multi-threading, the overhead of testing was 0.001796 seconds.
You can set `force_row_wise=true` to remove the overhead.
And if memory is not enough, you can set `force_col_wise=true`.
[LightGBM] [Info] Total Bins 50
[LightGBM] [Info] Number of data points in the train set: 160000, number of used features: 5
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498781 -> initscore=-0.004875
[LightGBM] [Info] Start training from score -0.004875
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498194 -> initscore=-0.007225
[LightGBM] [Info] Start training from score -0.007225
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498300 -> initscore=-0.006800
[LightGBM] [Info] Start training from score -0.006800
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498525 -> initscore=-0.005900
[LightGBM] [Info] Start training from score -0.005900
[LightGBM] [Info] [binary:BoostFromScore]: pavg=0.498925 -> initscore=-0.004300
[LightGBM] [Info] Start training from score -0.004300
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_17268\3394599919.py in <module>
----> 1 res = lgb.cv(params, data, 1000,
      2                 nfold=5,
      3                 stratified=False,
      4                 shuffle=True,
      5                 metrics='logloss',

~\anaconda3\lib\site-packages\lightgbm\engine.py in cv(params, train_set, num_boost_round, folds, nfold, stratified, shuffle, metrics, fobj, feval, init_model, feature_name, categorical_feature, early_stopping_rounds, fpreproc, verbose_eval, show_stdv, seed, callbacks, eval_train_metric, return_cvbooster)
    645         try:
    646             for cb in callbacks_after_iter:
--> 647                 cb(callback.CallbackEnv(model=cvfolds,
    648                                         params=params,
    649                                         iteration=i,

~\anaconda3\lib\site-packages\lightgbm\callback.py in _callback(env)
    254     def _callback(env: CallbackEnv) -> None:
    255         if not cmp_op:
--> 256             _init(env)
    257         if not enabled[0]:
    258             return

~\anaconda3\lib\site-packages\lightgbm\callback.py in _init(env)
    224             return
    225         if not env.evaluation_result_list:
--> 226             raise ValueError('For early stopping, '
    227                              'at least one dataset and eval metric is required for evaluation')
    228

ValueError: For early stopping, at least one dataset and eval metric is required for evaluation

Try "binary_logloss" instead of "logloss".

you are right,thank you very much.
------------------ 原始邮件 ------------------
发件人: "Michael @.>;
发送时间: 2023年7月14日(星期五) 晚上8:47
收件人: @.>;
抄送: @.>; @.>;
主题: Re: [microsoft/LightGBM] something wrong about lgb.cv when using logloss or rmse (Issue #5971)
Try "binary_logloss" instead of "logloss".
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: @.***>


Move newly created windows to last known zone Chrome and PWA

Description of the new feature / enhancement
Treat Chrome main window and installed PWA as separate apps.
Scenario when this would be used?
When using for example Chrome main window in one zone, and a PWA in other zone.
Supporting information
The option to "move newly created windows to last known zone" is great, because it disables the default Windows behavior of opening windows in cascade.
However, this option treats the main Chrome and the installed PWAs as the same program. I know that internally they are, but it would be great if FancyZones could differentiate between them. I usually use Chrome in one zone, for example, and the Gmail PWA in another, so I always have to move it manually.

/dup https://github.com/microsoft/PowerToys/issues/34572

reopening, thought this was a workspace issue.  Same style issue however


volcanosv_asm

你好，我使用这个软件的时候，报错是找不到[E::hts_open_format] Failed to open file "/public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_asm_output/chr1//phasing_result/AHTL-1_phased.bam" : No such file or directory
error: Error estimating alignment parameters.
caused by: Error reading indexed FASTA file.
caused by: Unknown sequence name.
请问该怎么解决呢？

Hi, thank you for trying out our tool!
It looks like the reference file and your BAM file might not match. Can you double-check what reference your BAM file was generated on?

Thank you very much for your response, but I've encountered a new issue now.
This is the error report information from the volcanosv.
Separate fragments
Map read_hp_og: 100%|██████████| 46475/46475 [00:00<00:00, 622965.54it/s]
Roughly assign unphased reads: 100%|██████████| 250657/250657 [01:44<00:00, 2396.87it/s]
2024-08-24 15:49:08 INFO     construct kmer database...
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//count_kmer_v1.py", line 83, in
with open(name_path,'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/volcanosv_asm_output/chr1//kmer_assign//reads.name'
2024-08-24 15:49:08 INFO     split hash by up block...
2024-08-24 15:49:08 INFO     load dict
2024-08-24 15:49:09 INFO     load name file
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//split_hash_by_hp.py", line 27, in
with open(name_file,'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/volcanosv_asm_output/chr1//kmer_assign//reads.name'
2024-08-24 15:49:09 INFO     assign unphased reads...
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//get_raw_kmer_overlap_count_unphased_est_pbs_v1.py", line 113, in
hash_files = [ up_dir + '/'+fname for fname in os.listdir(up_dir) if '.hash' in fname]
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/volcanosv_asm_output/chr1//kmer_assign//up_est_hash/'
2024-08-24 15:49:27 INFO     delete unphased hash files...
rm: cannot remove ‘/public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/volcanosv_asm_output/chr1//kmer_assign//up_est_hash/’: No such file or directory
2024-08-24 15:49:27 INFO     delete hash files...
rm: cannot remove ‘/public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/volcanosv_asm_output/chr1//kmer_assign//reads.seq’: No such file or directory
2024-08-24 15:49:27 INFO     delete kmer db...

Can you provide the command you use?

This's code that i run
source /public/home/maokaikai/miniconda3/bin/activate volcanosv && python /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm/volcanosv-asm.py -bam /public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/bam/ACB-3.bam -o /public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/volcanosv_asm_output -ref /public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/OS.fa -t 10 -chr 1 -dtype Hifi -px ACB-3

I've been updating this GitHub repo recently. I'm afraid that you have an unstable version. Can you try to clone this repo again and reinstall it?

ok，i try again

I install this software today. So i think it's not the reason.

I see. Were you able to recreate the result using the provided test data? https://zenodo.org/records/10520476.
I highly recommend trying the test data first.

I've tested the data, but the problem still occurs when running it. It's possible that there is an issue with this version of the software. Here are my execution command and the error message.
command ：
source /public/home/maokaikai/miniconda3/bin/activate volcanosv && python /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm/volcanosv-asm.py -bam /public/home/maokaikai/soft/VolcanoSV/data/Hifi_L2_hg19_minimap2_chr10.bam -o /public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output -ref /public/home/maokaikai/soft/VolcanoSV/data/genome.fa -t 10 -chr 10 -dtype Hifi -px Hifi_L2_hg19_minimap2_chr10
the error message：
2024-08-25 08:36:26 Calling potential SNVs using pileup...
2024-08-25 08:36:26 0 potential variants identified.
No candidate variants identified, printing empty VCF file...
[E::hts_open_format] Failed to open file "/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//phasing_result/Hifi_L2_hg19_minimap2_chr10_phased.bam" : No such file or directory
samtools index: failed to open "/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//phasing_result/Hifi_L2_hg19_minimap2_chr10_phased.bam": No such file or directory
2024-08-25 08:36:26 INFO     k-mer based reads partition...
2024-08-25 08:36:27 INFO     bam to seq...
[E::hts_open_format] Failed to open file "/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//phasing_result/Hifi_L2_hg19_minimap2_chr10_phased.bam" : No such file or directory
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//bamtoseq_with_kmer_filter.py", line 25, in
samfile = pysam.AlignmentFile(bam_path)
File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file /public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//phasing_result/Hifi_L2_hg19_minimap2_chr10_phased.bam: No such file or directory
2024-08-25 08:36:39 INFO     hash seq...
2024-08-25 08:36:39 INFO     start converting...
2024-08-25 08:36:39 INFO     parameters: {'in_file': '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//reads.seq', 'out_file': '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign///reads.hash', 'batch_size': 10000, 'f': <function convert..f at 0x2b6590ac5b80>, 'kmer_size': 12, 'n_thread': 100}
2024-08-25 08:36:39 INFO     creating hash ...
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//HashSeq.py", line 123, in
convert(in_file,
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//HashSeq.py", line 102, in convert
with open(in_file) as fp:
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//reads.seq'
2024-08-25 08:36:39 INFO     collect phasing info...
INFO:Prepare phasing information:Start extracting information
[E::hts_open_format] Failed to open file "/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//phasing_result/Hifi_L2_hg19_minimap2_chr10_phased.bam" : No such file or directory
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//prepare_info_v1.py", line 35, in
samfile = pysam.AlignmentFile(bam_path)
File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file /public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//phasing_result/Hifi_L2_hg19_minimap2_chr10_phased.bam: No such file or directory
2024-08-25 08:36:40 INFO     construct kmer database...
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//count_kmer_v1.py", line 80, in
read_hp_og_dc = pickle.load(open(read_hp_og_path,'rb' ))
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//phasing_info//read_hp_og.p'
2024-08-25 08:36:41 INFO     split hash by up block...
2024-08-25 08:36:41 INFO     load dict
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//split_hash_by_hp.py", line 25, in
dc = pickle.load(open(read_hp_dc_path,'rb'))
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//phasing_info//reads_pb.p'
2024-08-25 08:36:41 INFO     assign unphased reads...
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm//get_raw_kmer_overlap_count_unphased_est_pbs_v1.py", line 113, in
hash_files = [ up_dir + '/'+fname for fname in os.listdir(up_dir) if '.hash' in fname]
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//up_est_hash/'
2024-08-25 08:37:00 INFO     delete unphased hash files...
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//up_est_hash/’: No such file or directory
2024-08-25 08:37:00 INFO     delete hash files...
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//reads.seq’: No such file or directory
2024-08-25 08:37:00 INFO     delete kmer db...
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign//kmer_db_by_hap/’: No such file or directory
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign/.seq’: No such file or directory
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign/.hash’: No such file or directory
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign/*.name’: No such file or directory
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign/kmer_db_by_hap’: No such file or directory
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign/up_est_hash’: No such file or directory
2024-08-25 08:37:00 INFO     write fastq...
2024-08-25 08:37:00 INFO     Deleting old output files...
rm: cannot remove ‘/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//assembly//fastq_by_hap/*fastq’: No such file or directory
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm/volcanosv-asm.py", line 107, in
write_fastqs_general(f"{out_dir}/{prefix}.bam", f"{out_dir}/assembly/", f"{out_dir}/kmer_assign/", None, None)
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-asm/write_fastq_asm_general.py", line 80, in write_fastqs_general
dc_up = pickle.load(open(nearest_neighbor_dc,'rb'))
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/maokaikai/soft/VolcanoSV/data/volcanosv_asm_output/chr1//kmer_assign/unphased_reads_assignment_dippav_norm_asg.p'

I will try it out myself.

Hello, I apologize for the oversight; the test data works fine. I would like to know if your BAM file was aligned using minimap2. What version of minimap2 was used for alignment? Is the BAM file obtained by aligning sequencing data to the reference genome?

No apology. I'm glad the test data works for you.  We were using minimap 2.22-r1101. It is aligned to the reference.  I wonder what aligner are you using? Can you send me the command you used to generate the BAM file?

This is my version of minimap2 (2.21), and the command I allowed is as follows:
/public/home/pengyan/anaconda3/bin/minimap2 -ax map-hifi -t 8 /public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/OS.fa /public/home/pengyan/bioproject2/09.ACB_genome/06.pan-ACB-ECB/05.pan/01.SV/02.fastq/ACB-3.filt.fastq.gz --MD |/public/software/env01/bin/samtools view -@ 8 -bS |/public/software/env01/bin/samtools sort -@ 8 -o /public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/bam/ACB-3.bam && /public/software/env01/bin/samtools index /public/home/maokaikai/data/10.OS/08.VolcanoSV/02.OS/bam/ACB-3.bam

Your command looks fine to me. Is it possible that you extract a chr22 BAM file and send it to me? I can try running it.

my email is<EMAIL_ADDRESS>if the link is private

Hello, I just ran the program and found that the type was mistakenly set to ONT. However, I've encountered a new issue where the chromosome setting can only be up to 22; it doesn't work when it goes to 23.
volcanosv-asm.py: error: argument --chrnum/-chr: invalid choice: 24 (choose from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)

Can i just change this code?
parser.add_argument('--chrnum','-chr', type = int, choices=[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22] )

Hi, thank you for your advice! Due to the complexity of sex chromosomes (It is hard to perform phasing when there is a pair of chrX and chrY), the current version of VolcanoSV only works on autosomal chromosomes (chr1-22).
We might add this feature in the future, but for now, the usage of this tool is limited to chr1-22.

Hi Yan, let's discuss here so other people can reference your problem in the future.
Can you provide the command you use and the error message?
I'm trying your data at the meantime by the way.

Hi, I found the problem. Your BAM file contains some alignment records with None as sequence, which caused the error.  I changed some of my code and now it worked. I was able to generate 72M contigs file. You may try git pull and run it again.

Many thanks, I found another problem. The python script of volcanosv-vc-complex-sv.py and volcanosv-vc-small-indel.py have missed the parameter: "--prefix PREFIX"

Hi Yan, thank you so much for pointing it out! I'm working on the test of these 2 scipts today and I will let you know when I get it done.

Test done. Try git pull and run it again.

OK. thanks,i will trry.

OK. thanks,i will try.

Hi, when i used the "volcanosv-vc-small-indel.py" script, i obtained the bug as follows:
2024-08-30 03:11:06 INFO

pair SNP, indel

2024-08-30 03:11:06 INFO
/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//k8 /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//dipcall//dipcall-aux.js vcfpair  -p /data/maiziezhou_lab/CanLuo/Software/dipcall/hs37d5.PAR.bed         /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_small_indel/var_raw.pair.vcf.gz | /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//htsbox/htsbox bgzip > /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_small_indel/var_raw.dip.vcf.gz
/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//dipcall//dipcall-aux.js:60: Error: [File] Fail to open the file
var file = new File(fn_par);
^
Error: [File] Fail to open the file
at vcfpair (/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//dipcall//dipcall-aux.js:60:14)
at main (/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//dipcall//dipcall-aux.js:327:29)
at /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL//dipcall//dipcall-aux.js:333:1
2024-08-30 03:11:06 INFO

seperate multi-alt-allele

2024-08-30 03:11:06 INFO

filter 2-49 bp indel within None region

Writing to /tmp/bcftools.rUhaBk
[E::bcf_hdr_read] Input is not detected as bcf or vcf format
Could not read VCF/BCF headers from /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_small_indel/indel_2_49_raw.vcf
Cleaning
Traceback (most recent call last):
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL/volcanosv-vc-small-indel.py", line 233, in
call_var(
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL/volcanosv-vc-small-indel.py", line 149, in call_var
filter_vcf_by_size_bed(f'{output_dir}/var_raw_rf.dip.vcf',  output_dir,  bedfile)
File "/public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL/volcanosv-vc-small-indel.py", line 51, in filter_vcf_by_size_bed
subprocess.run(f"bcftools sort  {output_folder}/indel_2_49_raw.vcf -Ov -o {sorted_vcf_path}", shell=True, check=True)
File "/public/home/pengyan/anaconda3/envs/volcanosv/lib/python3.8/subprocess.py", line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'bcftools sort  /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_small_indel/indel_2_49_raw.vcf -Ov -o /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_small_indel/indel_2_49_sorted.vcf' returned non-zero exit status 255.

Can you send me the command you use?

Ok，I used multiple scripts and found that only the last one did not produce any results.
The script as follows:
source /public/home/pengyan/anaconda3/bin/activate volcanosv && python /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Large_INDEL/volcanosv-vc-large-indel.py -i /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_asm_output -o /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_large_indel_output -dtype ONT -bam /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/bam/MDJ-4.bam -ref /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/MDJZ.sort.fa -t 10 -px MDJ-4 && python /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Complex_SV/volcanosv-vc-complex-sv.py -i /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_asm_output -vcf /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_large_indel_output/volcanosv_large_indel.vcf -o /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_complex_sv -d ONT -bam /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/bam/MDJ-4.bam -ref /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/MDJZ.sort.fa -t 10 -px MDJ-4 && python /public/home/maokaikai/soft/VolcanoSV/bin/VolcanoSV-vc/Small_INDEL/volcanosv-vc-small-indel.py -i /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_asm_output -o /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/volcanosv_small_indel -bam /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/bam/MDJ-4.bam -ref /public/home/maokaikai/data/10.OS/08.VolcanoSV/01.MDJ/MDJZ.sort.fa -t 10 -px MDJ-4

I saw in the error there is an absolute path. I just changed it. Can you try git pull and see if the error still comes up?

OK, i will try.

Hi, i met a question when i  git pull.

Hi Yan, I apologize for my mistake. My "git push" wasn't successful earlier. I just pushed again and double-checked to ensure the code is updated. Can you try git pull again?
The absolute path should disappear now.

I've run into the process, thank you very much, but I don't know that the SNP information is in that file。

Hi Yan, you are very welcome!
We adopt Longshot's SNP call result as the final result, which is volcanosv_output/<chromosome_name>/phasing_result/<prefix>_phased.vcf.

Hi, ok, thanks!

Hi， If we divide chromosomes for variants detection, can we use bcftools to merge the VCFs obtained later? For example, SV also uses this software to merge?

It is possible. You may also use customized script to do it.

Hi, i found that the script of "volcanosv_large_indel" used the example data to run. I check the code and VCF. I found that the vcf file have error information as follows:

Hi Yan, I can't see the picture you sent. It shows "uploading 1.png". Can you try sending it again?

ok, i have upload this.

This didn't my reference genome. I guess that this is the test data. So, this software didn't change the path in software.

Sorry about the inconvenience. I will work on this issue in these couple of days. I will report back when I'm done.
Our paper is just out, so some part of the software is not so perfect. Thank you so much for your patience and feedback sincerely!

Hi Yan, I found the problem is that I used a default VCF header instead of generating a new one based on the reference. I just fixed that issue. Could you try git pull and rerun the large INDEL call?
Thank you so much for catching it!!

Very well done, thanks

And I set the -chr parameter, and the header of the output SV result is still the header of the instance data, and it has not been corrected (volcanosv-vc-large-indel.py)

Hi Yan, I've updated the code so you can do more than 22 chromosomes now.
For the VCF header, I double-checked and it was updated to extract every contig and its length from the given reference file. Therefore you might have seen more than one chromosome in your header.  To make it more intuitive, I just changed it to only write down the chromosome you specified.
You may try git pull and rerun your experiments. Thanks for the suggestions!

Hi，i meet a new question as follows. Some of  samples could get VCF, some of them don't.

It seems there is some signature of length 0 (which did not happen before). I just added handler to this exception. Please try git pull and run the failed chromosomes again.
Thank you for catching this!


Tablet/Desktop layout like Navigation Rail

Is your feature request related to a problem? Please describe.
Works flawlessly on mobile, but cannot adapt orientation for the bottom navbar for tablet/desktop (like Navigation Rail)
Describe the solution you'd like
(Like Navigation Rail) allow a boolean toggle to display the views either:

As the package currently does for mobile or,
In a row format for tablet/desktop where the bottom navbar persists in the left portion of the screen and the views take up the remaining space.

Describe alternatives you've considered
Have tried different methods for trying to make this work - row with body of widget being the screens and stack. Have also tried Navigation Rail and other packages.
Additional context
I have tried other packages that provide the view that I'm looking for but do not come close to the minimal code required for a persistent and state preserved features of this package.

If someone has implemented this feature in their fork, can you please link your fork? Much appreciated!


Packaging - Linux: Bundle harfbuzz / freetype symbols

This is an attempt to workaround the harfbuzz issue in #514 - where Oni2 is trying to load a newer version of the library, but the symbol is not available. This fixes it by including a harfbuzz locally with the version we need (it overrides the exclude list used by linuxdeploy).

Unfortunately, doesn't seem like this helps with #514 - we get a version mismatch in pango instead: /tmp/.mount_OnivimPkvcwA/usr/bin/Oni2: symbol lookup error: /usr/lib/x86_64-linux-gnu/libpangoft2-1.0.so.0: undefined symbol: hb_font_funcs_set_variation_glyph_func


feat(Analysis/MeanInequalities): Weighted QM-AM inequality

The inequality between the quadratic and arithmetic mean as a consequence of Jensen's inequality. Weighted version for positive real valued functions from a Finset. Fix notation for sums, switching to ∈ in place of in.

What about the generalization ∑ i ∈ s, w i * z i ≤ Real.rpow (∑ i ∈ s, w i * Real.rpow (z i) p)) (1 / p) for any 1 ≤ p? Furthermore, the right hand side increases as p increases.

the right hand side increases as p increases.

Yes, this is the one statement I really want

What about the generalization ∑ i ∈ s, w i * z i ≤ Real.rpow (∑ i ∈ s, w i * Real.rpow (z i) p) (1 / p) for any 1 ≤ p? Furthermore, the right hand side increases as p increases.

It would be a nice project to define the generalized weighted mean for any exponent p : EReal. For p = 0 the mean is the geometric mean, for p = ⊥ it's the minimum, and for p = ⊤ it's the maximum. That would subsume pretty much everything in this file.

Note that this generalised mean is basically the compact Lp norm.

I think these are generalizations in different directions, since the generalized mean also allows for negative exponents, and for weights given to each variable.

The negative exponents I agree with, but the general weights version is here.

Hello! Sorry for not replying, I was kinda busy. I formalised it like this because I wanted the IMO compendium version, but I think it's quite reasonable to have the version @acmepjz suggested, the proof needs almost no adjustments anyway, I think it might still be worthwhile to have a named lemma for the p = 2 case (even if it's just literally specifying p = 2 in the general case)

I'll get to it when I can spare the time


Examples using proj4 do not load correctly in CodeSandbox

Describe the bug
Most examples which use proj4 have "proj4": "^2.7.5" in the package.json.  The ^ is not understood by CodeSandbox and must be edited out before the example will load.
In some cases (e.g. Print to Scale) proj4 is completely missing.
To Reproduce
Open an example in CodeSandbox and see error.
Expected behavior
Examples should load without needing edits.

@mike-000 is it the same case for this example ? https://openlayers.org/en/latest/examples/d3.html
who dont work in CodeSandbox

No, that one does not show any errors, and d3 is loaded from unpkg.com, not via package.json.

but you confirm it doesn't work  in CodeSandbox ?

The example loads but renders an empty d3 svg.

@mike-000 Can you please report this to codesandbox.io? I think this is clearly their issue, because in devDependencies, they specify the parcel dependency with ^ as well.

I don't think CodeSandbox uses devDependencies as it still works when edited out.  And there is the still the issue of the missing proj4 in the Print to Scale package.json  The only obvious difference between that and other examples is it has resources specified in its html template, but I cannot see how that is related.


Editor (Android)

I don't know how globed did this, but it give me ignore damage only for spikes (collision with blocks working well) [Sorry for bad English]

fixed in v1.3.4


Move release notes out of publish container

- [ ] Determine whether release notes in the publish container are still needed, and if so, how and what alternatives should be considered
- [ ] Remove release notes in publish container if nothing uses them (consider older versions still within service interval)
- [ ] Use GitHub as the source for downloadable release notes instead of the publish container?

@MRayermannMSFT What do you think about the idea of including ReleaseNotes.md as part of a GitHub publish and using that to source in-app release notes instead of the publish container?

Since the combination of enabling static websites and using Azure Front Door (CDN) makes content in the publish storage account accessible, the release notes will remain where they are.


Bug: Unintended Popup Display on Non-Chromium Browsers

Description
The cookie consent popup is displaying unexpectedly on non-Chromium browsers, specifically Safari, Mozilla Firefox, and mobile browsers.
Step to reproduce

Open the site in Safari, Mozilla Firefox, or a mobile browser.
Navigate to any page that triggers the cookie consent popup.
Observe the unintended display of the popup.

Expected Behavior
The cookie consent popup should display consistently and as intended across all browsers, similar to its behavior on Chromium-based browsers.
Additional Information
This issue appears to be specific to non-Chromium browsers. No problems were observed during tests on Chrome and other Chromium-based browsers.

Fix in the 1.1.2 version of package !


Trigger onChange event when clearing date for the DateTimePicker

Q
A

Bug fix?
[x]

New feature?
[ ]

New sample?
[ ]

Related issues?
fixes #1277

What's in this Pull Request?
Clearing a date in the DateTimePicker control now triggers the onChange function.

Thanks @milanholemans for the fix!


Android - Composer text is cleared and reshown by itself

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Action Performed:

Open any chat
Type "a" into the composer
Wait for 5 seconds
Delete the text from the composer
After about 1 second, type "a" again

Expected Result:
The "a" should not be deleted and reshown back
Actual Result:
Notice carefully on the video that after executing all the reproduction steps above, I didn't press any key of the keyboard but after a few seconds, "a" is deleted and then reshown back.
Workaround:
Unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[x] Android / native
[ ] Android / Chrome
[ ] iOS / native
[ ] iOS / Safari
[ ] MacOS / Chrome / Safari
[ ] MacOS / Desktop

Version Number: 1.3.74-2
Reproducible in staging?: n/a
Reproducible in production?: n/a
If this was caught during regression testing, add the test name, ID and link from TestRail:
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Notes/Photos/Videos: Any additional supporting documentation
https://github.com/Expensify/App/assets/93399543/f9f1aaa1-2037-4181-b433-d9536c3bba05
Expensify/Expensify Issue URL:
Issue reported by: @bernhardoj
Slack conversation: https://expensify.slack.com/archives/C049HHMV9SM/p1695831843492359
View all open jobs on GitHub

No, If the bug is not reproducible by the QA team.


Roll Flutter Engine from a0925f158198 to 935dc94ecfaa (5 revisions)

https://github.com/flutter/engine/compare/a0925f158198...935dc94ecfaa
2023-05-11<EMAIL_ADDRESS>Roll Skia from 9cbc2c578e10 to a12a999cbd09 (2 revisions) (flutter/engine#41933)
2023-05-11<EMAIL_ADDRESS>Roll Skia from 1a29bd9a0147 to 9cbc2c578e10 (10 revisions) (flutter/engine#41932)
2023-05-11<EMAIL_ADDRESS>Roll Fuchsia Mac SDK from a3rrULFaXlwS8mfjW... to 2tQjI0g3aDmjHAtMw... (flutter/engine#41931)
2023-05-11<EMAIL_ADDRESS>Return fonts in a deterministic order. (flutter/engine#41907)
2023-05-11<EMAIL_ADDRESS>Turn @staticInterop tear-off into closure (flutter/engine#41885)
Also rolling transitive DEPS:
fuchsia/sdk/core/mac-amd64 from a3rrULFaXlwS to 2tQjI0g3aDmj
If this roll has caused a breakage, revert this CL and stop the roller
using the controls here:
https://autoroll.skia.org/r/flutter-engine-flutter-autoroll
Please CC aaclarke@google.com,rmistry<EMAIL_ADDRESS>on the revert to ensure that a human
is aware of the problem.
To file a bug in Flutter: https://github.com/flutter/flutter/issues/new/choose
To report a problem with the AutoRoller itself, please file a bug:
https://bugs.chromium.org/p/skia/issues/entry?template=Autoroller+Bug
Documentation for the AutoRoller is here:
https://skia.googlesource.com/buildbot/+doc/main/autoroll/README.md

Commit queue failed; closing this roll.


fix: Fix class not found error

I think it might be something related to this issue

Yeah maybe. That was OK. I closed PR. Thanks.


[python3:x64-linux] build failure

Host Environment

OS: openSUSE Tumbleweed
Compiler: gcc (SUSE Linux) 10.2.1 20200805 [revision dda1e9d08434def88ed86557d08b23251332c5aa]

To Reproduce
Steps to reproduce the behavior:
./vcpkg install python3
Failure logs
-- Installing x64-linux-rel share files...
-- Installing x64-linux-rel Python library files...
-- Installing x64-linux-rel done
-- Configuring x64-linux-dbg
-- Building x64-linux-dbg
-- Installing x64-linux-dbg Python library files...
-- Installing x64-linux-dbg done
-- Installing: /home/valery/Cache/vcpkg/packages/python3_x64-linux/share/python3/copyright
-- Performing post-build validation
There should be no empty directories in /home/valery/Cache/vcpkg/packages/python3_x64-linux
The following empty directories were found:

    /home/valery/Cache/vcpkg/packages/python3_x64-linux/lib
    /home/valery/Cache/vcpkg/packages/python3_x64-linux/debug/lib

If a directory should be populated but is not, this might indicate an error in the portfile.
If the directories are not needed and their creation cannot be disabled, use something like this in the portfile to remove them:

    file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/a/dir" "${CURRENT_PACKAGES_DIR}/some/other/dir")

Found 1 error(s). Please correct the portfile:
    /home/valery/Cache/vcpkg/ports/python3/portfile.cmake
-- Performing post-build validation done
Error: Building package python3:x64-linux failed with: POST_BUILD_CHECKS_FAILED
Please ensure you're using the latest portfiles with `./vcpkg update`, then
submit an issue at https://github.com/Microsoft/vcpkg/issues including:
  Package: python3:x64-linux
  Vcpkg version: 2020.06.15-unknownhash

Additionally, attach any relevant sections from the log files above.

Also, boost[core]:x64-linux cannot be build because of this issue.

I met a few related issues on opensuse. But sadly, I can't repro it on my ubuntu machine.

@JackBoosY I am on OpenSUSE, how can I help you to find the issue?

Please list the files existing in /home/valery/Cache/vcpkg/packages/python3_x64-linux.

❯ ls /home/valery/Cache/vcpkg/packages/python3_x64-linux
.rw-r--r-- 43 valery  1 Sep 10:02 BUILD_INFO
drwxr-xr-x  - valery  1 Sep 10:02 debug
drwxr-xr-x  - valery  1 Sep 10:01 include
drwxr-xr-x  - valery  1 Sep 10:01 lib
drwxr-xr-x  - valery  1 Sep 10:01 share

Can you find libpython3.8.a in /home/valery/Cache/vcpkg/buildtrees/python3 ?

Sorry for the delay. Yep, it located in the /home/valery/Cache/vcpkg/buildtrees/python3/src/v3.8.3-43b03f2bf0.clean-x64-linux-release

And also in
python3/make-build-x64-linux-release/lib64 on  master
❯ ls
.rwxr-xr-x 23M valery  1 Sep 10:01 libpython3.8.a
drwxr-xr-x   - valery  1 Sep 10:01 pkgconfig
drwxr-xr-x   - valery 31 Aug 14:37 python3.8

python3/make-build-x64-linux-release/lib64 on  master
❯ pwd
/home/valery/Cache/vcpkg/buildtrees/python3/make-build-x64-linux-release/lib64

https://github.com/microsoft/vcpkg/blob/a0536798eeb0786a4a27078c1b797ab7b6c41dd1/ports/python3/portfile.cmake#L180-L181
https://github.com/microsoft/vcpkg/blob/a0536798eeb0786a4a27078c1b797ab7b6c41dd1/ports/python3/portfile.cmake#L234-L235
These two places should be adapted to the situation you encounter.

Please unzip and replace this file to VCPKG_ROOT/ports/python3 and try again.

Sorry, the same issue:
-- Performing post-build validation
There should be no empty directories in /home/valery/Cache/vcpkg/packages/python3_x64-linux
The following empty directories were found:

    /home/valery/Cache/vcpkg/packages/python3_x64-linux/lib

If a directory should be populated but is not, this might indicate an error in the portfile.
If the directories are not needed and their creation cannot be disabled, use something like this in the portfile to remove them:

    file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/a/dir" "${CURRENT_PACKAGES_DIR}/some/other/dir")

Found 1 error(s). Please correct the portfile:
    /home/valery/Cache/vcpkg/ports/python3/portfile.cmake
-- Performing post-build validation done
Error: Building package python3:x64-linux failed with: POST_BUILD_CHECKS_FAILED
Please ensure you're using the latest portfiles with `./vcpkg update`, then
submit an issue at https://github.com/Microsoft/vcpkg/issues including:
  Package: python3:x64-linux
  Vcpkg version: 2020.06.15-unknownhash

Additionally, attach any relevant sections from the log files above.

@bio-punk Does your Visual Studio installed in the default path? And please make sure you installed the English Language Package.

@48d90782 Sorry, use this one

@48d90782 Sorry, use this one

It works 👍🏻  Thank you very much.

But also it need to be replaced in the boost package

@48d90782 Does this issue also exist on boost-python?

@48d90782 Does this issue also exist on boost-python?

Yep, I can guess, that on openSUSE this issue will exist in the all python related packages.

Because python3 and boost-python are constructed inconsistently, I don’t think so.

Ok, sure. Here is the issue from boost-python:
CMake Error at scripts/cmake/vcpkg_execute_build_process.cmake:141 (message):
    Command failed: /home/valery/Cache/vcpkg/downloads/tools/cmake-3.17.2-linux/cmake-3.17.2-Linux-x86_64/bin/cmake --build . --config Debug --target install -- -v
    Working Directory: /home/valery/Cache/vcpkg/buildtrees/boost-python/x64-linux-dbg
    See logs for more information:
      /home/valery/Cache/vcpkg/buildtrees/boost-python/install-x64-linux-dbg-out.log

Call Stack (most recent call first):
  scripts/cmake/vcpkg_build_cmake.cmake:91 (vcpkg_execute_build_process)
  scripts/cmake/vcpkg_install_cmake.cmake:24 (vcpkg_build_cmake)
  installed/x64-linux/share/boost-build/boost-modular-build.cmake:114 (vcpkg_install_cmake)
  installed/x64-linux/share/boost-build/boost-modular-build.cmake:119 (unix_build)
  ports/boost-python/portfile.cmake:12 (boost_modular_build)
  scripts/ports.cmake:79 (include)

Error: Building package boost-python:x64-linux failed with: BUILD_FAILED
Please ensure you're using the latest portfiles with `./vcpkg update`, then
submit an issue at https://github.com/Microsoft/vcpkg/issues including:
  Package: boost-python:x64-linux
  Vcpkg version: 2020.06.15-unknownhash

I can make another issue for this

@JackBoosY #13277

Let's make another PR to fix that.


RUM-1520 Logger integration tests

What does this PR do?
Creates the first real Integration Test class for the Logger and Logger.Builder classes.
So far overal public API (all modules together) is up to 4%

Codecov Report

Merging #1735 (c46c81e) into develop (764129c) will increase coverage by 0.00%.
The diff coverage is n/a.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #1735   +/-   ##
========================================
  Coverage    83.35%   83.35%
========================================
  Files          465      465
  Lines        16182    16179    -3
  Branches      2412     2411    -1
========================================
- Hits         13487    13485    -2
- Misses        2031     2037    +6
+ Partials       664      657    -7

see 24 files with indirect coverage changes


Sequentional optional parts do not fully match

When trying to write a simple group-by-4 mask, it was possible to enter only spaces after the first group of digits.
$('...').inputmask('9999[ 9999][ 9999]');

After entering the first four digits, it is possible to enter two spaces. This should not be possible according to the above mask? The workaround is to wrap the optional parts in eachother:
$('...').inputmask('9999[ 9999[ 9999]]');

Using version 3.1.33

May I hope for a fix soon?

@BugFixerr ,
I will fix it for the current milestone

To better understand the problem try .inputmask('9999[+9999][-9999]');

@GMTA , @BugFixerr ,
Fixed in the latest version.  Can you have a try.
How do you use the optionals?  With the greedy true (default) or false ?

Tested the latest version; could not trigger the bug anymore. Seems to be fixed! Thank you very much.