Launching from Finder or Spotlight fails with: "Error installing battery limiter: undefined" in Ventura, but open command succeeds

Problem
Launching the "Battery" GUI app (/Applications/Battery.app) only works when invoked the following ways:

Running open /Applications/Battery.app from a terminal

And specifically does not work when invoked by:

Double-clicking /Applications/Battery.app from Finder
Running Battery from Spotlight
Adding /Applications/Battery.app to System Settings > Login Items > Open at Login and rebooting

Where this specific error is emitted:
Error message:

The error occurs regardless of the permissions of anything in ~/.battery. No log lines appear in ~/.battery/battery.log after the error occurs, no menulet appears in Notification Area, and no processes containing a "battery" string are spawned.
If I run open /Applications/Battery.app from a terminal, the Battery app starts and shows its menulet in the Notification Area:
Battery.app Notification Area menulet:

System state for error reproduction:

Mac OS: Ventura 13.3.1 (22E261)
Battery installed only ever from Homebrew cask (version 1.1.4), updated today
Nothing on the entire system has been installed outside of Homebrew, Nix, and the Mac App Store
Permissions opened for config directory: sudo chmod -Rc a+w ~/.battery
Battery app not already running (Mac OS likely does nothing when invoking an already-running app from Finder or Spotlight)

If I kill the Battery app by clicking "Quit" on its menulet dropdown menu, then all Finder or Spotlight invocations of Battery show the error dialogue shown above in this message, until battery is run with the command: open /Applications/Battery.app again.
So there is something wrong specifically with the Spotlight and Finder invocations of Battery.
Running processes
After running open /Applications/Battery.app:
$ ps aux | grep -i battery | egrep -v 'grep|tail'
nhooey           84631   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /bin/bash /usr/local/bin/battery discharge 80
nhooey           84619   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /bin/bash /usr/local/bin/battery maintain_synchronous 80 --force-discharge
nhooey           84450   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /Applications/Battery.app/Contents/Frameworks/battery Helper.app/Contents/MacOS/battery Helper --type=utility --utility-sub-type=network.mojom.NetworkService --lang=en-US --service-sandbox-type=network --user-data-dir=/Users/nhooey/Library/Application Support/battery --shared-files --field-trial-handle=1718379636,r,18185961855328760586,18097394644492592706,131072 --disable-features=SpareRendererForSitePerProcess --seatbelt-client=45
nhooey           84443   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /Applications/Battery.app/Contents/Frameworks/battery Helper (GPU).app/Contents/MacOS/battery Helper (GPU) --type=gpu-process --user-data-dir=/Users/nhooey/Library/Application Support/battery --gpu-preferences=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 --shared-files --field-trial-handle=1718379636,r,18185961855328760586,18097394644492592706,131072 --disable-features=SpareRendererForSitePerProcess --seatbelt-client=35
nhooey           84387   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /Applications/Battery.app/Contents/MacOS/battery

After clicking Quit in the Battery menulet in Notification Area:
nhooey           84631   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /bin/bash /usr/local/bin/battery discharge 80
nhooey           84619   0.0  0.0        0      0   ??  ?     5:05PM   0:00.00 /bin/bash /usr/local/bin/battery maintain_synchronous 80 --force-discharge

These last two shell processes are never spawned if battery is removed from System Settings > Login Items > Allow in Background section, but the /Applications/Battery.app GUI application continues to launch and work without issue.
This bug is similar to #15.

+1 same here with Version 1.1.4

Mine is not even working from the command line.
same error, undefined

I had the same problem but found that if I run "battery uninstall" from command line, the GUI installer then worked fine. I figure it manages to install the CLI tools, but fails for some reason to install the GUI. Repeated attempts to install fail because it is partially installed already.
Removing and reinstalling worked fine for me. Your mileage may vary :)

@SeargantSaxton: After upgrading with Homebrew today, my version of Battery is also now failing when launching with this method that worked before:

Running open /Applications/Battery.app from a terminal

@matphillips: Removing and reinstalling worked fine for me. Your mileage may vary :)

Uninstalling and reinstalling the battery cask with Homebrew doesn't fix the problem, running the Battery GUI with all 4 methods mentioned in the issue still fail with the same error message.

This is very strange and I have no idea what the source of this could me... If anyone has ideas, please let me know!

Workaround is to just use another equivalent app called “Aldente”. It’s not
all free, but it’s a lot more reliable, and the free version has enough
features.
I looked at the logging code in this app and it’s really lacking some basic
stuff. There’s not much chance that any of these bugs get fixed.
On Thu, Jul 20, 2023 at 18:47, Mentor Palokaj @.***>
wrote:

This is very strange and I have no idea what the source of this could
me... If anyone has ideas, please let me know!
—
Reply to this email directly, view it on GitHub
https://github.com/actuallymentor/battery/issues/133#issuecomment-1643779386,
or unsubscribe
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@.***>

It's also experience on MacOS 14.0 Sonoma. There is no workaround can be a remedy.

@SangTruongTan what is the manipulation and power cycle steps you took? Can it help me find the cause?

Hello @actuallymentor,
I've tried to use the GUI, but it was failed. So, I decided to interact with the CLI. During that time, I made some manipulation such as enable/disable charging, maintain battery level. Afterwards, I rebooted my Mac, when it was ready, I tried opening the GUI app and then it worked find (until now).

I had this issue and determined by running the executable in terminal that I had an error in my .bashrc. Removing those lines fixed the error.

@Tweoss
which lines you removed from the .bashrc file plz ?

@Tweoss
which lines you removed from the .bashrc file plz ?

@lucc70 Les lignes étaient pour une autre application qui n'était pas dans le PATH. Alors, malheureusement, l'erreur a prévenu l'ouverture du script de Battery. Peut-être vous pouvez commenter toutes les lignes dans votre .bashrc et ouvrir battery une fois plus?

@lucc70 @Tweoss @SangTruongTan @actuallymentor @nhooey @matphillips @rayshan @SeargantSaxton
You can fix that by following these steps.
I had the same probleme yesterday

Ensure that the Battery is installed, even if you have the following error message Error installing battery limiter: undefined just don't uninstall it.
Run this command in terminal

which battery

You should get this output
/usr/local/bin/battery

$\color{orange}{Step:2}$

Run the following command to update the Battery app from the command line.
this will call the shell script and download the latest script from the git repo and execute the installation via bash.

battery reinstall

Press any key to continue and hit enter, this will prompt you to enter the root password, since the shell script need root access to visudo and other privilege.
Here is a screen capture of the running command

Here is the latest version after the update via the CLI.

Thank you @rivolity!
Can someone else confirm this works for them too? It looks like that then the issue is an old version holding things up.
Please reopen is the above does not fix the issue for you.


HADOOP-18156. Address JavaDoc warnings in classes like MarkerTool, S3ObjectAttributes, etc (#4965)

Description of PR
just pushing #4965 through branch-3.3; if javadocs are happy will cherrypick.
not going to merge to 3.3.5
How was this patch tested?
For code changes:

[ ] Does the title or this PR starts with the corresponding JIRA issue id (e.g. 'HADOOP-17799. Your PR title ...')?
[ ] Object storage: have the integration tests been executed and the endpoint declared according to the connector-specific documentation?
[ ] If adding new dependencies to the code, are these dependencies licensed in a way that is compatible for inclusion under ASF 2.0?
[ ] If applicable, have you updated the LICENSE, LICENSE-binary, NOTICE-binary files?

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CloudFormation client - Tags parameter failing validation

Looking at the boto3 documentation, it appears that tagging of CloudFormation stacks should be possible through the create_stack or update_stack client functions.
When I attempt to create a stack via boto3, it's throwing the following botocore error.
botocore.exceptions.ParamValidationError: Parameter validation failed:
Unknown parameter in input: "Tags", must be one of: StackName, TemplateBody, TemplateURL, UsePreviousTemplate, StackPolicyDuringUpdateBody, StackPolicyDuringUpdateURL, Parameters, Capabilities, ResourceTypes, StackPolicyBody, StackPolicyURL, NotificationARNs
The syntax all looks correct and I'm using the majority of the other properties without issue.  Confirmed in the stable/final and confirmed that boto3 version is 1.2.3 (matches doc) and botocore is 1.3.22.  Currently running this from a Windows host, in case that matters.
Let me know if you need any additional information.

I was able to specify tags using the following (you'd need to provide a working TemplateBody):
cf.create_stack(StackName='foo', Tags=[{"Key": "a", "Value": "b"}, {"Key": "c", "Value": "d"}], TemplateBody='{}')

This is also show in the documentation: http://botocore.readthedocs.org/en/latest/reference/services/cloudformation.html#CloudFormation.Client.create_stack
Does using this type of format work for you?

I just tried it again and it looks like this issue is actually limited to the update_stack operation.  I took the exact "Tags" argument you provided and created a stack no problem.  I copied the same values to the update_stack operation in the same script and that's when I'm reproducing the error.

Ah I see. CloudFormation only supports Tags on create_stack. Updating the tags of a stack using update_stack is not currently part of their API. See: http://docs.aws.amazon.com/AWSCloudFormation/latest/APIReference/API_UpdateStack.html

@mtdowling I'm not sure if the API was updated recently, but updating the tags as part of UpdateStack is supported (you can see it on the link you posted).

Never mind, I see it was already updated: https://github.com/boto/botocore/blob/07422f03901f4bb30aaa8ec1e18f24628262c63b/botocore/data/cloudformation/2010-05-15/service-2.json#L377-L380


Guard closing quitCh with sync.Once to prevent double close

related #8144 #8166
See https://github.com/prometheus/prometheus/issues/8144#issuecomment-735814282
Signed-off-by: Mitsuo Heijo<EMAIL_ADDRESS>

You could instead revert 8166 and apply to the full function ?
pseudo code
var stopped bool
quitOnce.Do {
 stopped=true
  print(Quitting)
  close(quit)
}
if !stopped {
  print(Exit in progress)
}

Thanks good suggestion.
I think it's better only Handler.Quit(e.g. from main module) could read quitCh.

Thanks!


How to do SSR?

How to use type-route with server side rendering?
For example: https://github.com/bitttttten/oatmilk/blob/master/docs/server-rendering.md

Great question. Type Route almost has support for server side rendering. Basically when creating the router when doing server side rendering you'll want to use a "memory" router type instead of a "browser" router type. From there, however, it currently isn't possible to set the initial route from a given url using the "memory" router type. That'll take a small API change to be possible. Stay tuned. This is an important use case and I hope to get support out for it soon.

@zerkalica latest release has support for server-side rendering. I put together a brief guide explaining how to do it here: https://www.type-route.org/docs/guides/server-side-rendering. Feel free to reopen this issue if the guide isn't clear enough or open another issue if you encounter any bugs with the new feature.


add WebMention

i.e., please add WebMention to the features list.  thx.

upon further review of the WebMention spec, it appears that the spec does not define any API, or other specific functionality, to be implemented by a user agent and so adding it to caniuse's feature list would not be appropriate, IIUC.  if so, let's just close this issue with my apologies.


ui.gadgets: Allocating resources in graft* doesn't work as documented

I faced a problem drawing textures in a new window. when I create the gadget and add it to the listener using gadget. the image shows corretly, when I create the gadget and use open-window, the
image does not show up on the new window.
TUPLE: i-gadget < gadget
    image texture ;

: <i-gadget> ( path -- gadget )
    [ i-gadget new ] dip load-image >>image ;

M: i-gadget pref-dim*
    image>> dim>> [ 20 + ] map ;

M: i-gadget graft*
    dup find-gl-context
    dup image>> { 0 0 } <texture> >>texture drop ;

M: i-gadget ungraft*
    dup find-gl-context
    dup texture>> dispose
    f >>texture drop ;

M: i-gadget draw-gadget*
    [ { 10 10 } ] dip texture>> [ draw-texture ]
    curry with-translation ;

! In the listener

"vocab:images/sprites/game_drop.png" <i-gadget> gadget.

! the above works and shows the image in the listener

"vocab:images/sprites/game_drop.png" <i-gadget> "i-gadget" open-window

! the above opens a new window but the image does not show

I see that moving the texture creation code from graft* to draw-gadget* solves the issue. I'm wondering if this is a bug, since the documentation for graft* mentions that resources can be allocated on this method (and to use find-gl-context to ensure the correct GL context is setup before allocating the resources).
The modified the code shown below works correctly:
M: i-gadget graft*
     drop ;

M: i-gadget draw-gadget*
     [ { 10 10 } ] dip
     dup texture>> [ ]
     [ dup image>> { 0 0 } <texture> >>texture texture>> ] ?if
     [ draw-texture ] curry with-translation ;

<image-gadget> seems to have been implemented in the same way though (i.e.
setting up textures is done on the 1st call into draw-gadget*).

Yeah it looks like the docs are wrong. find-gl-context says that you can allocate gl resources in graft* but you can't because gl hasn't been initialized there. I believe your original code didn't work because <texture> calls glBindTexture and it happened before gl initialization. In fact, find-gl-context probably should throw an error or something if it is called before gl is ready to be used.

No my explanation was wrong. It turns out that if you just do some of the gl setup a little earlier, you can allocate textures in the graft* method no problem.


RxApp.MainThreadScheduler does not run on the UI Thread on WinRT

I've been playing around with the library the last couple of days and I think I've found a bug regarding the scheduling on Windows Phone 8.1 (not silverlight)
I notice here https://github.com/reactiveui/ReactiveUI/blob/2a6dd935af47c7040aef612935553aff584d5a7d/ReactiveUI/RxApp.cs#L79
that the property returned is based on the DefaultScheduler.
Shouldn't it be based on the CoreDispatcherScheduler? (http://rx.codeplex.com/SourceControl/latest#Rx.NET/Source/System.Reactive.Windows.Threading/Reactive/Concurrency/CoreDispatcherScheduler.cs)
I've run the following simple test on a viewmodel:
var backgroundScheduler = new EventLoopScheduler();
var currentScheduler = RxApp.MainThreadScheduler;

Observable
                .Interval(TimeSpan.FromMilliseconds(250), backgroundScheduler)
                .Take(20)
                .Select(o => string.Format("Title {0}", o))
                .ObserveOn(currentScheduler)
                .Subscribe(o => { this.MyList.Add(o); });

and it crashes with "bad thread" exception.
If I change to:
var currentScheduler = CoreDispatcherScheduler.Current;

the code runs fine.
My apologies if I'm missing something too obvious. I'm still trying to wire things up.

We haven't seen a repro project. Closing this.


Feature request: in console - scroll through the commands history

On up arrow key in console, scroll through the commands history, the default behaviour in any terminal app.

Commits 8f31ca16cac79c8d997985f83ea50acea02adc9d and 8f31ca16cac79c8d997985f83ea50acea02adc9d closes the issue.


keep getting GET / HTTP/1.1" 401 when logging first time to the app , Oops! You found a bug. Let us know how it happened! page

hello
i installed as was instructed in the README but i keep getting the : Oops! You found a bug. Let us know how it happened! page:
this is how i start it :
 bundle exec thin -e dev -R config.ru -p 7143 start
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/core_ext.rb:30: warning: constant ::Fixnum is deprecated
/usr/share/gems/gems/attic-0.5.3/lib/attic.rb:13: warning: constant ::Fixnum is deprecated
/usr/share/gems/gems/gibbler-0.8.9/lib/gibbler.rb:654: warning: constant ::Fixnum is deprecated
/usr/share/gems/gems/gibbler-0.8.9/lib/gibbler.rb:655: warning: constant ::Bignum is deprecated
2021-04-01 14:38:33 +0000 Thin web server (v1.8.0 codename Possessed Pickle)
2021-04-01 14:38:33 +0000 Maximum connections set to 1024
2021-04-01 14:38:33 +0000 Listening on <IP_ADDRESS>:7143, CTRL+C to stop
E(1617287918):  [:limit, :homepage, "88oij9uyld9inbygnn3j648n9hcl1yt", 5]
undefined method `join' for nil:NilClass
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/app/helpers.rb:162:in `err'
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/app/helpers.rb:75:in `rescue in carefully'
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/app/helpers.rb:41:in `carefully'
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/app/web/base.rb:10:in `publically'
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/app/web.rb:14:in `index'
/usr/share/gems/gems/otto-0.4.1/lib/otto.rb:281:in `call'
/usr/share/gems/gems/otto-0.4.1/lib/otto.rb:108:in `call'
/usr/share/gems/gems/rack-2.1.4/lib/rack/reloader.rb:51:in `call'
/usr/share/gems/gems/rack-2.1.4/lib/rack/common_logger.rb:35:in `call'
/usr/share/gems/gems/rack-2.1.4/lib/rack/urlmap.rb:77:in `block in call'
/usr/share/gems/gems/rack-2.1.4/lib/rack/urlmap.rb:61:in `each'
/usr/share/gems/gems/rack-2.1.4/lib/rack/urlmap.rb:61:in `call'
/usr/share/gems/gems/thin-1.8.0/lib/thin/connection.rb:86:in `block in pre_process'
/usr/share/gems/gems/thin-1.8.0/lib/thin/connection.rb:84:in `catch'
/usr/share/gems/gems/thin-1.8.0/lib/thin/connection.rb:84:in `pre_process'
/usr/share/gems/gems/thin-1.8.0/lib/thin/connection.rb:53:in `process'
/usr/share/gems/gems/thin-1.8.0/lib/thin/connection.rb:39:in `receive_data'
/usr/share/gems/gems/eventmachine-1.2.7/lib/eventmachine.rb:195:in `run_machine'
/usr/share/gems/gems/eventmachine-1.2.7/lib/eventmachine.rb:195:in `run'
/usr/share/gems/gems/thin-1.8.0/lib/thin/backends/base.rb:75:in `start'
/usr/share/gems/gems/thin-1.8.0/lib/thin/server.rb:162:in `start'
/usr/share/gems/gems/thin-1.8.0/lib/thin/controllers/controller.rb:87:in `start'
/usr/share/gems/gems/thin-1.8.0/lib/thin/runner.rb:203:in `run_command'
/usr/share/gems/gems/thin-1.8.0/lib/thin/runner.rb:159:in `run!'
/usr/share/gems/gems/thin-1.8.0/bin/thin:6:in `<top (required)>'
/usr/local/bin/thin:23:in `load'
/usr/local/bin/thin:23:in `<top (required)>'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/cli/exec.rb:63:in `load'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/cli/exec.rb:63:in `kernel_load'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/cli/exec.rb:28:in `run'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/cli.rb:494:in `exec'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/vendor/thor/lib/thor.rb:392:in `dispatch'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/cli.rb:30:in `dispatch'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/vendor/thor/lib/thor/base.rb:485:in `start'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/cli.rb:24:in `start'
/usr/local/share/gems/gems/bundler-2.2.15/exe/bundle:49:in `block in <top (required)>'
/usr/local/share/gems/gems/bundler-2.2.15/lib/bundler/friendly_errors.rb:130:in `with_friendly_errors'
/usr/local/share/gems/gems/bundler-2.2.15/exe/bundle:37:in `<top (required)>'
/usr/local/bin/bundle:23:in `load'
/usr/local/bin/bundle:23:in `<main>'
<IP_ADDRESS> - - [01/Apr/2021:14:38:38 +0000] "GET / HTTP/1.1" 401 - 0.0253
 new static route: /img (/img/favicon.png)
<IP_ADDRESS> - - [01/Apr/2021:14:38:38 +0000] "GET /img/favicon.png HTTP/1.1" 200 189 0.0004

and i keep getting this :

I have the same error - can anyone help?

Same here. :(

I get the same error. can anyone please help?

Downgrading the repo to the last commit from 2018 (before the latest pull request merges) has now allowed the site to work.

Thanks a lot! This worked for me @maraakate :)

i check out  this commit as recomended  :
* (HEAD detached at 346a2d3)

and then im getting this error :
<EMAIL_ADDRESS>onetimesecret]$ bundle exec thin -e dev -R config.ru -p 7143 start
/usr/share/gems/gems/thin-1.5.0/lib/thin/server.rb:104: warning: constant ::Fixnum is deprecated
/home/ec2-user/onetimesecret/onetimesecret/lib/onetime/core_ext.rb:30: warning: constant ::Fixnum is deprecated
/usr/share/gems/gems/attic-0.5.3/lib/attic.rb:13: warning: constant ::Fixnum is deprecated
/usr/share/gems/gems/gibbler-0.8.9/lib/gibbler.rb:654: warning: constant ::Fixnum is deprecated
/usr/share/gems/gems/gibbler-0.8.9/lib/gibbler.rb:655: warning: constant ::Bignum is deprecated
bundler: failed to load command: thin (/usr/local/bin/thin)
Traceback (most recent call last):
        33: from /usr/local/bin/bundle:23:in `<main>'
        32: from /usr/local/bin/bundle:23:in `load'
        31: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/exe/bundle:37:in `<top (required)>'
        30: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/friendly_errors.rb:130:in `with_friendly_errors'
        29: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/exe/bundle:49:in `block in <top (required)>'
        28: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/cli.rb:24:in `start'
        27: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/vendor/thor/lib/thor/base.rb:485:in `start'
        26: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/cli.rb:30:in `dispatch'
        25: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/vendor/thor/lib/thor.rb:392:in `dispatch'
        24: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
        23: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
        22: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/cli.rb:494:in `exec'
        21: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/cli/exec.rb:28:in `run'
        20: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/cli/exec.rb:63:in `kernel_load'
        19: from /home/ec2-user/.gem/ruby/gems/bundler-2.2.16/lib/bundler/cli/exec.rb:63:in `load'
        18: from /usr/local/bin/thin:23:in `<top (required)>'
        17: from /usr/local/bin/thin:23:in `load'
        16: from /usr/share/gems/gems/thin-1.5.0/bin/thin:6:in `<top (required)>'
        15: from /usr/share/gems/gems/thin-1.5.0/lib/thin/runner.rb:152:in `run!'
        14: from /usr/share/gems/gems/thin-1.5.0/lib/thin/runner.rb:187:in `run_command'
        13: from /usr/share/gems/gems/thin-1.5.0/lib/thin/controllers/controller.rb:71:in `start'
        12: from /usr/share/gems/gems/thin-1.5.0/lib/thin/controllers/controller.rb:181:in `load_rackup_config'
        11: from /usr/share/gems/gems/thin-1.5.0/lib/rack/adapter/loader.rb:33:in `load'
        10: from /usr/share/gems/gems/thin-1.5.0/lib/rack/adapter/loader.rb:33:in `eval'
         9: from config.ru:1:in `<main>'
         8: from config.ru:1:in `new'
         7: from /usr/share/gems/gems/rack-1.4.5/lib/rack/builder.rb:51:in `initialize'
         6: from /usr/share/gems/gems/rack-1.4.5/lib/rack/builder.rb:51:in `instance_eval'
         5: from config.ru:28:in `block in <main>'
         4: from /home/ec2-user/onetimesecret/onetimesecret/lib/onetime.rb:55:in `load!'
         3: from /usr/share/gems/gems/familia-0.7.1/lib/familia.rb:59:in `uri='
         2: from /usr/share/ruby/uri/common.rb:234:in `parse'
         1: from /usr/share/ruby/uri/rfc3986_parser.rb:73:in `parse'
/usr/share/ruby/uri/rfc3986_parser.rb:67:in `split': bad URI(is not URI?): "<%= (ENV['ONETIMESECRET_REDIS_URL'] || 'redis://user:CHANGEME@<IP_ADDRESS>:7179/0') + '?timeout=10&thread_safe=false&logging=false' %>" (URI::InvalidURIError)

Hi,
I am not in front of the server today; but I will give you more exact instructions on how I was able to make it work over the next day or so.  For what it's worth I am using Ubuntu 18 LTS, I only ran apt-get update/upgrade on it and have denied upgrading to version 20 (or whatever the latest LTS is).  Sorry for the somewhat vague instructions but I come from a mostly Windows environment.
Even after all of this it is not rendering the images properly on the site.  Everything else appears to work, but our email part is not working because it looks like the mailer gem does not support the proper authentication for our Office365 hosted noreply account in our organization.  We do have an SMTP relay for these kinds of situations, but I have not gotten a chance to set it up from our hosted OTS server to make sure that it works.
Otherwise, it DOES work and DOES have 'burn after reading' secrets.

I'm super late responding to this, sorry.
@maraakate Thanks for stepping in, I appreciated it. There's an upcoming release that includes these fixes, it's just taking us a while to get it over the line.
https://github.com/onetimesecret/onetimesecret/releases/tag/v0.11.0-RC1

Btw, if you're running from a clone of the git repo, you can make your own local branch:
$ git fetch
$ git co -b v0.11.0-RC1 origin/v0.11.0-RC1

This was all related to a change between ruby 1.9-2.6 and 2.7 btw.
@meiry you can open a new ticket for your error message if you please.


Spell GitHub correctly

😉

Thanks @koddsson 😊 Good spot, and appreciate you taking the time to fix in a PR 👍


Output RTSP stream

Would it be possible to either to render to screen AND output the same to an RTSP stream, or have the option to display either on screen OR output to RTSP?
I would like to ingest the RTSP stream into my frigate for recording.

Agreed! I'm grateful for what we have so far but I'd love the ability to output my thermal imaging to RTSP for viewing on other devices too.

+1


QUESTION: Can one federate the block storage across multiple block storage providers?

Hi! Great write up, and I will be taking it for a spin.  I was wondering if this, or others you may have stumbled across, allow me to store these blocks of information across mutiple providers with some redundancy like HDFS or something.  I am thinking that if any one provider does NOT have all the blocks I can a) feel even more comfortable about the content not being retrieved, b) if redundancy is done right, a provider going away and me losing files won't be a thing, and c) increased storage capacity by taking advantage of free tier options :)
Thanks!

This definitely wouldn't be hard to implement, but I decided not to include app-level redundancy because storage providers are already storing your data in a redundant fashion, such that you can reasonably expect them to never lose it. So it would be more technical complexity and month-to-month cost for very little benefit. I believe TahoeLAFS supports redundancy/federation though.
Thank you!


infer format option by providing a formatted example

It would be nice if there'd be an option to infer (most of the) format options by providing an example:
void fun () {
  int a = b + c;
  if (a) fun();
}

The parser would infer the parameters, eg:

space around operators
one-liners allowed

It would reject the example if the inferred options would not be idem-potent (ie if the formatting the input via the inferred options would change the input).

The odds of be implementing this are incredibly low.

it's by no mean urgent, could be picked up later by someone else if there's more interest.

clang-format started with the idea that this is the main use case. Infer style from input file via "majority voting" and then unify the style. Turned out that an external style definition is the main use case.


Improvement for k8s.io/docs/tasks/debug-application-cluster/crictl/

completely misses what docker has, and crictl hasn't.
docker commit
docker save
how to do that?

Within the context of Monitoring, Logging, and Debugging: how are the commands docker commit and docker save useful?
That explanation will help us decide if those omissions are a drawback or actually that it's OK given the scope of that page.

for debugging it's useful to do slight modifications to containers and save the results.
If another place is better to document how to do docker commit and docker save, by all means. A path to help existing docker users navigate how to do the same things with this new set of tools is sorely missing.

@hw-claudio if you'd like to either:

reshape this issue to be about new content, helping people who are used to Docker adapt to using Kubernetes
request a specific page about how to achieve the equivalent of docker save and docker commit for … a running Pod? (I'm not sure)

then please do.
Right now it's not clear to me what improvement addresses the need you've mentioned.
/language en
/triage needs-information

both things are useful, this is really a FAQ without an answer.
https://github.com/containerd/containerd/issues/4818
https://github.com/kubernetes/kubernetes/issues/80818
...
this is requested many times, but things just die off.
docker commit is considered an anti-pattern of course: you want to build containers from scratch from Dockerfile etc.
But then as the theory is put into practice, you get strange behavior and interactions between the K8S infrastructure and the workload running in the POD that needs to be debugged at runtime, and you want to save the state.
The group tending to the runtime operations might even not be the same group of people tending to the build process (of course, people should change to devops right? But then it's again about when the tire hits the road, this is not always possible). So doing things "properly" starting from scratch from the Dockerfile  is great in the normal case, but can become a disaster at debugging time when the clock is ticking, where quick feedback and validation of attempts is key, and when the people running the workload and attempting to understand what is wrong are different from the people producing the containers.
Just my opinion of course, but this is a fairly common missing feature I think.
Thanks

Maybe the question is “how do I get a shorter feedback loop but still run my code as if / actually in the target cluster”.
People use https://tilt.dev/, https://nocalhost.dev, https://squash.solo.io/, https://www.telepresence.io/, and other tools for that.

Hi there, PR wrangler here for this week.
Based on the documentation for triaging an issue, I'll close out this issue as it contains both lifecycle/stale and triage/needs-information labels.
Feel free to reopen with correct labels if it's still relevant.
/close

I think "how to docker commit in K8s?" is a FAQ and should be answered somewhere.

@guettli we have an issue you can use to discuss and report issues connected to the removal of dockershim: https://github.com/kubernetes/kuberetes/issues/106917
You can also log a new feature request, something like “document equivalent of docker commit for development on Kubernetes”. To do that, visit https://github.com/kubernetes/website/issues/new/choose

/reopen
/retitle Highlight development tools for that get feedback from running code within Kubernetes
/remove triage needs-information
/priority awaiting-more-evidence
/kind feature
We don't have a focus on documenting external tools (there's enough work on documenting Kubernetes itself that takes priority), but anyone who wants to work on this issue is welcome to; that's a benefit of open source.
If opening PRs, take account of What's Allowed in the content guide.
I'm also an editor for the blog. I would welcome a vendor-neutral survey of your options for this kind of development, especially one that mentions how using docker commit will require extra work after the dockershim removal.

/language en
/remove-triage needs-information

/remove-lifecycle stale


ActiveAdmin Layout was lost after overriding Controller action

Overriding a new controller without 'new!' does not display ActiveAdmin layout.  But then when I added 'new!' nested 'synchronization' form is not appearing although I did<EMAIL_ADDRESS> Not so sure what I'm doing wrong here.
case #1 (ActiveAdmin layout is gone)
ActiveAdmin.register Resource do
  controller do
      # This code is evaluated within the controller class
      def new
        @resource = Resource.new
        @resource.build_synchronization
      end
  end
end

case #2 (nested form synchronization does not appear)
ActiveAdmin.register Resource do
  controller do
      # This code is evaluated within the controller class
      def new
        @resource = Resource.new
        @resource.build_synchronization
        new!

      end
  end
end

views\admin\resources\new.html.erb
<%= semantic_form_for [:admin, @resource] do |form| %>
    <%= form.inputs "Resource", :id => "resource" do %>
        <%= form.input :name %>

    <% end %>

    <%= form.semantic_fields_for :synchronization do |sync| %>
        <% sync.inputs  :name => "Synchronization", :id => "synchronization"  do %>
            <%= sync.input :start_datetime, :as => :datetime %>
            <%= sync.input :repeat_interval, :as => :radio, :collection => @intervals %>
            <%= sync.input :repeat_type, :as => :select, :collection => ["Manual", "Automatic"] %>

        <% end %>

        <%= form.buttons %>
    <% end %>
<% end %>

models:
class Resource < ActiveRecord::Base
  has_one :synchronization
  accepts_nested_attributes_for :synchronization
end

class Synchronization < ActiveRecord::Base
  belongs_to :resource
  has_many :mappings
  accepts_nested_attributes_for :mappings
  #validates_presence_of :start_datetime
end

I'm also having a similar problem with rendering an erb new view. I've not managed find a workaround yet.

Try render :layout => 'active_admin'

It's been so long ago since I looked at this. I'll need to go back and check.


Integrate with State of Rust.

In a recent release team meeting we discussed having rfcbot take over the manual curation of State of Rust. Ths'd require commands to change the What's next?, move between columns, and add to State of Rust on RFC approval and merge.

So what we could do is have an rfcbot command @rfcbot status STATUS_DESCRIPTION_LINE which updates a new SQL column in the database for issues/PRs; Then, rfcbot will scan all issues labeled C-tracking-issue and add them to the project board if not there, and if they have changed label from B-RFC-Approved to B-unstable or something like that, it is also moved between the columns on the board.

Also cc #198 for an even more automated experience re. automatically making tracking issues.


Fatal error when executing Pangu

Hello!
I am getting a fatal error when executing Pangu. There seems to be a variable 'mult' within the cyp2d6_typer.py script that is being referenced before assignment. Can you recommend a solution to this problem?
This is the output to the terminal:
2024-01-30 11:30:20,342 | DEBUG | Alleles Identified: {'noSV': {'noSV_0': ('*2', '*34', '*39'), 'noSV_1': ('*39',)}, 'duplicate': {'duplicate_0': ('*41', '*2', '*34', '*39', '*119')}}
2024-01-30 11:30:20,343 | INFO | Calling Diplotype
2024-01-30 11:30:20,343 | WARNING | Multi-tandem DUP call -- check reads
2024-01-30 11:30:20,343 | ERROR | No DUP parent found for tandem *41
2024-01-30 11:30:20,525 | DEBUG | Alleles Identified: {'noSV': {'noSV_0': ('*3',), 'noSV_1': ('*4', '*10', '*39', '*74')}}
2024-01-30 11:30:20,526 | INFO | Calling Diplotype
2024-01-30 11:30:20,526 | INFO | Diplotype called: CYP2D6 *3/*4
2024-01-30 11:30:20,527 | DEBUG | Alleles Identified: {'noSV': {'noSV_0': ('*1',), 'noSV_1': ('*39',)}, 'duplicate': {'duplicate_0': ('*2', '*34', '*39')}}
2024-01-30 11:30:20,527 | INFO | Calling Diplotype
2024-01-30 11:30:20,527 | WARNING | Multi-tandem DUP call -- check reads
2024-01-30 11:30:20,527 | ERROR | No DUP parent found for tandem *2
Here is the python error:
Traceback (most recent call last):
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/bin/pangu", line 10, in
sys.exit(main_cli())
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/main.py", line 122, in main_cli
starTyper = main( parser )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/main.py", line 61, in main
typer.run( bamfile, vcffile )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 78, in run
self.diplotype._make_diplotype()
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 510, in _make_diplotype
self.haplotypes.append( ( f'{allele}x{dcount}', calls.pop(allele), mult ) )
UnboundLocalError: local variable 'mult' referenced before assignment

I actually have another error with a different sample. Here is that one:
Traceback (most recent call last):
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/bin/pangu", line 10, in
sys.exit(main_cli())
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/main.py", line 122, in main_cli
starTyper = main( parser )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/main.py", line 61, in main
typer.run( bamfile, vcffile )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 78, in run
self.diplotype._make_diplotype()
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 474, in _make_diplotype
nosv, dups, dels = [ Counter( [ calls[0] for calls in self.calls.get( atype, {} ).values() ] )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 474, in
nosv, dups, dels = [ Counter( [ calls[0] for calls in self.calls.get( atype, {} ).values() ] )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/016965f96f004ecaf59532db2b753d93/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 474, in
nosv, dups, dels = [ Counter( [ calls[0] for calls in self.calls.get( atype, {} ).values() ] )
IndexError: tuple index out of range

Hi! Sorry for getting back to your late. For the "out of range" error, I see this as the Pangu output:
2024-02-05 10:32:58,790 | INFO | Processing /srv/nfs/ngsdata/Projects/Tender_Pharmacogenetics/dragen_data_internal_samples/results/pacbio/50151577.M13_bc1004_F--M13_bc1055_R.pbaa_passed_cluster_sequences.bam
2024-02-05 10:33:00,337 | INFO | Identifying SV signatures
2024-02-05 10:33:00,502 | INFO | Phasing and Calling Alleles
2024-02-05 10:33:00,503 | DEBUG | Calling noSV
2024-02-05 10:33:00,504 | DEBUG | Attempting to phase noSV reads
2024-02-05 10:33:00,504 | DEBUG | Reseting HP for 7 noSV  reads
2024-02-05 10:33:00,711 | DEBUG | Positions used for read clustering: [42123210, 42123218, 42123225, 42123235, 42123236, 42123237, 42123238, 42123242, 42123243, 42123251, 42123253, 42123299, 42123307, 42123310, 42123311, 42123538, 42123630, 42123642, 42123651, 42124105, 42124797, 42125571, 42125619, 42125923, 42125979, 42126068, 42126131, 42126309, 42126389, 42126610, 42126913, 42127000, 42127206, 42127208, 42127355, 42127406, 42127607, 42127940, 42128498, 42128575, 42128667, 42128693, 42128944, 42129129, 42129131, 42129179, 42129753, 42129795, 42129808, 42129818, 42129949, 42130046, 42130481, 42130546, 42130558, 42130559, 42130564, 42130568, 42130570, 42130577, 42130691, 42130966, 42131468, 42131530, 42131790, 42132198, 42132208, 42132216, 42132374, 42132384, 42132560]
2024-02-05 10:33:07,406 | DEBUG | Alleles Identified: {'noSV': {'noSV_0': (), 'noSV_1': ('*2', '*34', '*39')}}
2024-02-05 10:33:07,406 | INFO | Calling Diplotype

Hi John! Was there any update on this? Was the Pangu output I provided helpful?

Hi!  Yes, thakn you for the extra info -- this was indeed enough to identify and fix the problem.  The latest version (0.2.4) should work -- let me know if you have any other issues!

fixed in 0.2.4

Hi! I pulled the new version, and it fixed some of my samples, but I am still having an issue on one. Can you take a look at these error messages?
2024-02-26 12:34:42,494 | INFO | Processing /srv/nfs/ngsdata/Projects/Tender_Pharmacogenetics/internal_samples_illumina_comparison/dragen_data_internal_samples/results/pacbio/50151589.M13_bc1009_F--M13_bc1050_R.pbaa_passed_cluster_sequences.bam
2024-02-26 12:34:44,373 | INFO | Identifying SV signatures
2024-02-26 12:34:44,568 | INFO | Phasing and Calling Alleles
2024-02-26 12:34:44,569 | DEBUG | Calling noSV
2024-02-26 12:34:44,570 | DEBUG | Attempting to phase noSV reads
2024-02-26 12:34:44,571 | DEBUG | Reseting HP for 4 noSV  reads
2024-02-26 12:34:44,791 | DEBUG | Positions used for read clustering: [42123210, 42123218, 42123225, 42123235, 42123236, 42123237, 42123238, 42123242, 42123243, 42123251, 42123253, 42123299, 42123307, 42123310, 42123311, 42123538, 42123630, 42124105, 42124797, 42125923, 42125979, 42126068, 42126131, 42126309, 42126389, 42126610, 42127000, 42127206, 42127208, 42127406, 42127940, 42128693, 42128944, 42129129, 42129795, 42129808, 42129818, 42129949, 42130046, 42130481, 42130546, 42130558, 42130559, 42130564, 42130568, 42130570, 42130577, 42130691, 42131468, 42131530, 42131790, 42132216, 42132374, 42132560]
2024-02-26 12:34:54,819 | DEBUG | Calling duplicate
2024-02-26 12:34:59,707 | DEBUG | Alleles Identified: {'noSV': {'noSV_0': ('*4', '*10', '*39', '*74'), 'noSV_1': ('*4', '*10', '*65', '*2', '*34', '*39', '*74')}, 'duplicate': {'duplicate_0': ('*2', '*34', '*39')}}
2024-02-26 12:34:59,707 | INFO | Calling Diplotype
2024-02-26 12:34:59,707 | WARNING | Multi-tandem DUP call -- check reads
2024-02-26 12:34:59,707 | ERROR | No DUP parent found for tandem *2
Traceback (most recent call last):
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/scripts/tmplftx9ucy.wrapper.py", line 16, in
shell(
File "/home/pbrennan/miniconda3/envs/snakemake/lib/python3.8/site-packages/snakemake/shell.py", line 287, in new
raise sp.CalledProcessError(retcode, cmd)
Here is the error:
Traceback (most recent call last):
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/3b24d641831797150e212867dfcbde2a/bin/pangu", line 10, in
sys.exit(main_cli())
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/3b24d641831797150e212867dfcbde2a/lib/python3.10/site-packages/pangu/main.py", line 126, in main_cli
starTyper = main( parser )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/3b24d641831797150e212867dfcbde2a/lib/python3.10/site-packages/pangu/main.py", line 65, in main
typer.run( bamfile, vcffile )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/3b24d641831797150e212867dfcbde2a/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 78, in run
self.diplotype._make_diplotype()
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/3b24d641831797150e212867dfcbde2a/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 516, in _make_diplotype
self.haplotypes.append( ( f'{allele}x{dcount}', calls.pop(allele), mult ) )
UnboundLocalError: local variable 'mult' referenced before assignment

Hi! Just checking in --  was there any update on this?

apologies!  I've been slammed recently -- I'll take a look and get back to you as soon as i can!

hi again, sorry for the long delay.  I just published an update that should fix that bug.  Please give it a try and let me know.

sorry for the hassle -- after I published the last result, something looked off and it turned out I created a bug with the fix to the last one.  These should all be fixed in v0.2.6 (just published).  thank yoo for your patience!!

Thanks John! Do you know when 2.6.0 will be available through conda?

i am guessing soon --  the bot has picked up the update https://github.com/bioconda/bioconda-recipes/pull/46752#event-12243649180, but it might still be updating mirrors??  not sure what the time delay is exactly.
if you really want to try it right away, you can also clone the repo and then pip install . from the cloned repo :)

Hi John! I was able to pull the version 2.6.0 from conda, but unfortunatly I am still getting an error.
2024-04-02 14:23:17,377 | INFO | Processing results/internal_pgx_samples_all_variants_forcegt_test_only/pacbio/50151589.M13_bc1009_F--M13_bc1050_R.pbaa_passed_cluster_sequences.bam
2024-04-02 14:23:18,514 | INFO | Identifying SV signatures
2024-04-02 14:23:18,635 | INFO | Phasing and Calling Alleles
2024-04-02 14:23:18,636 | DEBUG | Calling noSV
2024-04-02 14:23:18,637 | DEBUG | Attempting to phase noSV reads
2024-04-02 14:23:18,637 | DEBUG | Reseting HP for 4 noSV  reads
2024-04-02 14:23:18,775 | DEBUG | Positions used for read clustering: [42123210, 42123218, 42123225, 42123235, 42123236, 42123237, 42123238, 42123242, 42123243, 42123251, 42123253, 42123299, 42123307, 42123310, 42123311, 42123538, 42123630, 42124105, 42124797, 42125923, 42125979, 42126068, 42126131, 42126309, 42126389, 42126610, 42127000, 42127206, 42127208, 42127406, 42127940, 42128693, 42128944, 42129129, 42129795, 42129808, 42129818, 42129949, 42130046, 42130481, 42130546, 42130558, 42130559, 42130564, 42130568, 42130570, 42130577, 42130691, 42131468, 42131530, 42131790, 42132216, 42132374, 42132560]
2024-04-02 14:23:24,268 | DEBUG | Calling duplicate
2024-04-02 14:23:26,881 | DEBUG | Alleles Identified: {'noSV': {'noSV_0': ('*4', '*10', '*39', '*74'), 'noSV_1': ('*4', '*10', '*65', '*2', '*34', '*39', '*74')}, 'duplicate': {'duplicate_0': ('*2', '*34', '*39')}}
2024-04-02 14:23:26,881 | INFO | Calling Diplotype
2024-04-02 14:23:26,882 | WARNING | Multi-tandem DUP call -- check reads
2024-04-02 14:23:26,882 | ERROR | No DUP parent found for tandem *2
2024-04-02 14:23:26,882 | ERROR | Extra haplotypes called: [('*2x1', ['duplicate_0'], 1), ('*4', ['noSV_0']), ('*4', ['noSV_1'])]
Traceback (most recent call last):
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/bin/pangu", line 10, in
sys.exit(main_cli())
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/lib/python3.10/site-packages/pangu/main.py", line 127, in main_cli
starTyper = main( parser )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/lib/python3.10/site-packages/pangu/main.py", line 65, in main
typer.run( bamfile, vcffile )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 78, in run
self.diplotype._make_diplotype()
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 572, in _make_diplotype
self.diplotype = self.joinHaplotypes( self.haplotypes )
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 589, in joinHaplotypes
return '/'.join( h if type( h ) == str else h[0]
File "/mnt/stg_wgs/scripts/PGx_pipeline/.snakemake/conda/383bc07cbc5f0b8fea6f90a69550b588/lib/python3.10/site-packages/pangu/cyp2d6_typer.py", line 590, in
for h,lbls in haps )
ValueError: too many values to unpack (expected 2)
Could you take another look at this? Thanks!

yike, i'm so sorry you keep hitting these bugs!  it looks like this is a bit of an edge case where a parent tandem dup is not identified, and i had a typo in the conditional.  Its fixed in the bug_fix branch -- are you able to clone the bug_fix branch and pip install . to test it quick?  else i can just merge it in, but i'd rather avoid any more bugs before releasing a new version, if possible!   thanks!

Hi John! I just did a test, and the fix worked :)

thanks for checking!  i've merged the latest as v0.2.7.  It mightntake a couple days again for bioconda to auto-update the image.


Platforms

This is a rough first pass at adding support for full platforms.
Rather than adding items in config.json for every item on your HA network, this hopes to let homebridge find all of your items for you. The first example usage of this is Wink.
Wink support for specific accessories has been removed and replaced with a simple way to set it up as a platform.
Platforms have the same sort of pattern as accessories in that they take a json hash as an input. You can define it as anything you want for your Platform library to use what you need to fetch your items.
The most important function to implement is the accessories() function. Here is where you'll do your fetching of all of your accessories, turn them into the appropriate objects, and return them with the callback.
Once the accessories are returned, they are looped through and registered in the same exact manner that accessories are registered on an individual basis.
There's also no mention of this support in the README yet. I figured I'd wait till it was ready to land before writing that up.
This idea came out of the conversation on #10.
Comments welcome!

/cc @jnewland

The Wink platform example only supports lightbulbs. But there's nothing stopping another library from returning different TYPES of accessories from the accessories() function. Then, combined with the right definitions at the bottom of your library, you can support everything your platform does, hence bridging everything pretty much automatically.

This is fantastic!! I think this is perfectly done.
Would the accessories/Wink.js accessory still be needed? Or could you always get everything via the platform approach?

@nfarina I debated it, and possibility turning it into a more general library and putting it under /lib, but seeing that this is a HomeKit bridge, I can't come up with a single reason you'd want cherry picked devices.
This way is just way easier. Add creds and 💥 done. Why confuse with 2 different ways to add devices, right?
I figure, if it's a problem, we can just roll it back in.

Yes agreed with that conclusion. I only asked because accessories/Wink.js was still present in this PR :)
But yes, I think just a README update and this is good to go.

I only asked because accessories/Wink.js was still present in this PR :)

Nope, it was 🔥d in https://github.com/maddox/homebridge/commit/c4026e997af9ac13c6937fb3026f964b4b204453
It's just confusing cause the overall diff has it as a moved file with some changes.

But yes, I think just a README update and this is good to go.

Ok, i'll update the readme soon and submit it.

Ok, the README was updated.

Ah gotcha, OK awesome. Looks perfect! Merging!

This is great. I know what I'm doing tonight!


Check while being threatened wins a puzzle

Check while being threatened wins a puzzle - For example, in the first puzzle, bishop to g7 wins the puzzle (instead of displaying a player mistake message).

duplicated #17


feat: makefile for automating builds and deployments for dev environments

Description
This change introduces a makefile that automates common processes when building and developing NMS. Refer to CONTRIBUTING.md for more information details about the makefile.
Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code.
[x] I have made corresponding changes to the documentation.
[x] I have added tests that validate the behaviour of the software.
[x] I validated that new and existing unit tests pass locally with my changes.
[x] Any dependent changes have been merged and published in downstream modules.

I was testing and make rock has failed. I attached the full logs here: https://pastebin.ubuntu.com/p/TvWn6HKNrk/
make rock
make: building oci image with a local version of webconsole
mv rockcraft.yaml rockcraft_default.yaml
sed "s~source-type.*~~; s~source-tag.*~~; s~source: https.*~source: .\/build/webconsole-src~" rockcraft_default.yaml > rockcraft.yaml
rockcraft pack
'override-build' in part 'nms' failed with code 1.
Recommended resolution: Review the scriptlet and make sure it's correct.
Failed to execute rockcraft in instance.
Full execution log: '/home/gatici/.local/state/rockcraft/log/rockcraft-20241022-162747.266520.log'
make: [Makefile:95: artifacts/sdcore-nms.rock] Error 1 (ignored)
mv rockcraft_default.yaml rockcraft.yaml
Built rock with local webconsole
``


Clickable check lists

Context
In my student assignments, I include a checklist so that student can
check tasks as they are achieved to keep track of their progress through
the assignment. For now, they have to edit the underlying markdown
(double click, and replace - [ ] by - [x]) which is inconvenient and
error-prone.
Proposal
When a rendered markdown cell contains a check-list, enable to
check/uncheck a checkbox by a simple click in the check-box. Like
e.g. in github/gitlab issue trackers.
Note: this involves not only rendering of cells, but also editing
the underlying markdown. So this may well be out of scope of
jupyterlab-mystjs and/or may require coordination with the
progress with
prosemirror wysiwig cell editor.
Bonus: enable markdown cells that are read-only but for
checking/unchecking check boxes. This would require a
third value to the editable cell option:
non editable/checkable/editable, a change which goes even
further away of jupyterlab-mystjs.
Tasks and updates
No response

Prosemirror is something I always wanted to look at for next-level JupyterLab Markdown support. I know that Jason Grout also used to to add inline widgets, which was quite interesting.
@rowanc1 MDAST includes the token position information, right? If so, we should be able to do this.

We do have access to the token line numbers, so editing that x shouldn't be too difficult in this context. We probably want to keep some scope in check for how much the rendered view can edit the markdown, but this part seems very doable. I am tracking the underlying work here.
From the prosemirror/wysiwyg editor, I would vote to keep that out of scope of this repository. I absolutely want to work on that, and through open source work + curvenote have been working on these editors for >3 years. It will happen, just not sure if this extension is the best place for the wysiwyg push, which may appeal to slightly different users? Super open to feedback though if you think they should live in the same place!


Cant run EF 6.2.0 code first migrations on VSTS using migrate.exe

I get the following error when I run the migrate.exe on VSTS with following arguments. I have no clue what the error is suggesting. My.dll is in the same directory as migrate.exe.
D:\a\r1\a_Build My API\drop\Migrations\migrate.exe" My.dll /connectionString="Server=tcp:sqlserv-XXXX.database.windows.net,1433;Initial Catalog=sqldb-portal;Persist Security Info=False;User ID=sqluseracct;Password=mypass;MultipleActiveResultSets=False;Encrypt=True;TrustServerCertificate=False;Connection Timeout=30;" /connectionProviderName="System.Data.SqlClient" /startUpConfigurationFile:"My.dll.config" /verbose
Exception message:

2018-10-06T17:22:15.2556319Z System.Data.Entity.Migrations.Design.ToolingException: The type initializer for 'System.Data.Entity.Migrations.DbMigrationsConfiguration1' threw an exception.
2018-10-06T17:22:15.2556933Z    at System.Data.Entity.Migrations.Design.ToolingFacade.Run(BaseRunner runner)
2018-10-06T17:22:15.2557546Z    at System.Data.Entity.Migrations.Console.Program.Run()
2018-10-06T17:22:15.2557722Z    at System.Data.Entity.Migrations.Console.Program.Main(String[] args)
2018-10-06T17:22:15.2557855Z ERROR: The type initializer for 'System.Data.Entity.Migrations.DbMigrationsConfiguration1' threw an exception.
Stack trace:

Steps to reproduce
Include a complete code listing (or project/solution) that we can run to reproduce the issue.
Partial code listings, or multiple fragments of code, will slow down our response or cause us to push the issue back to you to provide code to reproduce the issue.
Further technical details
EF version: EntityFramework.6.2.0
Database Provider: (e.g. EntityFramework.SqlServer)

does "my.dll" depend on another assembly?  It could be that the runtime cannot load a dependency of my.dll

EF Team Triage: This issue is lacking enough information for us to be able to effectively triage it. In particular, it is missing the following information requested in the new issue template. Can you please provide this information?

Steps to reproduce

Ideally include a complete code listing that we can run to reproduce the issue.
Alternatively, you can provide a project/solution that we can run.
BTW we're not just doing this to be mean :smile:... we get a lot traffic on this project and it takes time to attempt to reproduce an issue based on fragments of information. In addition, our attempt is often unsuccessful as the exact conditions required to hit the issue are often not explicitly included in the code provided. To ensure we maximize the time we have to work on fixing bugs, implementing new features, etc. we ask that folks give us a self-contained way to reproduce an issue.
For a guide on submitting good bug reports, read Painless Bug Tracking.
BTW this is a canned response and may have info or details that do not directly apply to this particular issue. While we'd like to spend the time to uniquely address every incoming issue, we get a lot traffic on the EF projects and that is not practical. To ensure we maximize the time we have to work on fixing bugs, implementing new features, etc. we use canned responses for common triage decisions.

EF Team Triage: Closing this issue as the requested additional details have not been provided and we have been unable to reproduce it.
BTW this is a canned response and may have info or details that do not directly apply to this particular issue. While we'd like to spend the time to uniquely address every incoming issue, we get a lot traffic on the EF projects and that is not practical. To ensure we maximize the time we have to work on fixing bugs, implementing new features, etc. we use canned responses for common triage decisions.


Meeting minutes for August 5th

Signed-off-by: Thomas Steenbergen<EMAIL_ADDRESS>

@tsteenbe I've created this PR for the dangling branch on your behalf. Could you find the time to polish it so we can get this merged?

@tsteenbe @mnonnenmacher @fviernau @MarcelBochtler if there are no objection by the end of this day I'll simply finally merge this. It has been pending for long enough.


[jvm-package] remove the coalesce in barrier mode

Barrier mode doesn't allow coalesce operation, which should fail
all tests of xgboost4j-spark-gpu, but it doesn't. That's because
the test file is extremly small which result in only 1 PartitionedFile
and finally bypass the checking.
This PR makes at least multi-PartitionedFiles for a test file, and
then the existing tests can cover this PR

@trivialfis, please also port this PR back to 1.6.1
Thx


Bugfix/helm template csi driver cherrypick

Description
See #1002
How can this be tested?
See #1002
Checklist

[x] Unit tests have been updated/added
[x] PR is labeled accordingly
[x] I have read and understood the contribution guidelines

Not quite sure what happened. Out of curiosity I did the cherry-picking in Github Desktop. Maybe that messed up stuff. I'll start over.


Fall back to CPU for queries referencing hidden metadata columns

Signed-off-by: Andy Grove<EMAIL_ADDRESS>SPARK-37273 added support for reading hidden metadata columns and we do not support this on GPU.
This PR adds checks to see if the user is attempting to read any of the metadata columns (file_path, file_name, file_size, file_modification_time) and will fall back to CPU in this case.

build


Fix Swift 5.8 warning

This warning is new in Xcode 14.3 / Swift 5.8:
File: GetTriviaRequest.swift
Warning:
Heterogeneous collection literal could only be inferred to '[String : Any]'; add explicit type annotation if this is intentional

You can accept the suggested fix, which will silence the warning.

Due to CI/CD, fixing this issue is blocked by fixing #14


Uncaught Error: ENOENT: no such file or directory, open 'C:\tmp\atom.apib'

[Enter steps to reproduce below:]

...
...

Atom Version: 0.189.0
System: Microsoft Windows 7 Professional
Thrown From: api-blueprint-preview package, v0.3.0
Stack Trace
Uncaught Error: ENOENT: no such file or directory, open 'C:\tmp\atom.apib'
At C:\Users\Allen\AppData\Local\atom\app-0.189.0\resources\app\node_modules\q\q.js:128

Error: ENOENT: no such file or directory, open 'C:\tmp\atom.apib'
  at Error (native)
  at Object.fs.openSync (fs.js:544:18)
  at Object.module.(anonymous function) [as openSync] (ATOM_SHELL_ASAR.js:118:20)
  at Object.fs.writeFileSync (fs.js:1155:15)
  at ApiBlueprintPreviewView.module.exports.ApiBlueprintPreviewView.renderApiBlueprintText (C:\Users\Allen\.atom\packages\api-blueprint-preview\lib\api-blueprint-preview-view.coffee:83:8)
  at ApiBlueprintPreviewView.module.exports.ApiBlueprintPreviewView.renderApiBlueprint (C:\Users\Allen\.atom\packages\api-blueprint-preview\lib\api-blueprint-preview-view.coffee:80:8)
  at C:\Users\Allen\.atom\packages\api-blueprint-preview\lib\api-blueprint-preview.coffee:48:33
  at _fulfilled (C:\Users\Allen\AppData\Local\atom\app-0.189.0\resources\app\node_modules\q\q.js:794:54)
  at self.promiseDispatch.done (C:\Users\Allen\AppData\Local\atom\app-0.189.0\resources\app\node_modules\q\q.js:823:30)
  at Promise.promise.promiseDispatch (C:\Users\Allen\AppData\Local\atom\app-0.189.0\resources\app\node_modules\q\q.js:756:13)
  at C:\Users\Allen\AppData\Local\atom\app-0.189.0\resources\app\node_modules\q\q.js:516:49
  at flush (C:\Users\Allen\AppData\Local\atom\app-0.189.0\resources\app\node_modules\q\q.js:110:17)
  at process._tickCallback (node.js:357:13)

Commands
     -1:46.6 core:page-down (atom-text-editor.editor)
 27x -1:45.8 core:page-up (atom-text-editor.editor)
  2x -1:12.0 core:page-down (atom-text-editor.editor)
 10x -1:05.8 core:move-up (atom-text-editor.editor)
  3x -1:04.5 core:delete (atom-text-editor.editor)
  2x -1:02.0 core:move-right (atom-text-editor.editor)
     -1:01.5 editor:move-to-end-of-word (atom-text-editor.editor)
     -1:01.0 core:move-left (atom-text-editor.editor)
     -0:59.6 core:move-down (atom-text-editor.editor)
  2x -0:59.6 core:delete (atom-text-editor.editor)
     -0:57.5 core:move-down (atom-text-editor.editor)
  5x -0:54.1 core:move-up (atom-text-editor.editor)
     -0:52.6 core:save (atom-text-editor.editor)
  2x -0:49.9 editor:move-to-first-character-of-line (atom-text-editor.editor)
  7x -0:49.3 core:select-down (atom-text-editor.editor)
  2x -0:28.7 api-blueprint-preview:toggle (atom-text-editor.editor)

Config
{}

Installed Packages
# User
api-blueprint-preview, v0.3.0

# Dev
No dev packages

Are you still getting this error? As a workaround, what happens if you make a directory called C:\tmp?

Actually, this is a duplicate of #17. We need to check if the directory exists first, and if not then either create it or use C:\temp or something.


editor crashed 5 times in 5 minutes

i was just looking at code not even 50 lines long

and every time i go into the settings menu

What's your OS? RAM? Did you try atom --safe?

im running os x (10.10.4), 4GBs of ram. I don't know what atom safe is, i just found out about this editor last week

@AHL96 You can run atom in safe mode from the command line, which disables all non-bundled packages:
atom --safe
If you don't get the crashes then, there's probably a community package you have installed, messing with you.

Also, can you provide the crash reports which OSX recorded for those crashes, e.g. by pasting them in a gist and sharing a link here? You should be able to find those crash reports in Console.app.

I don’t know if it’s the same issue, but there’s this file that immediately crashes atom on linux (4gb ram), both safe and normal mode

@andya9 likley your issue is #979

@benogle Yes it is! thank’you very much for pointing it


Pnp support absolute paths to nix store 3.2.1

Merge changes from yarn 3.2.1 release branch

I guess it could have been cleaner to rebase our branch on top of upstream instead of merging upstream into ours
btw. any idea about the failing tests?

Unsure about all the tests, some are linting issues, some other are weird failures with access.


chore: run cargo fmt

#553
#552  👈
master

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Merge activity

Nov 5, 4:48 PM EST: A user started a stack merge that includes this pull request via Graphite.


GH-357 Conversation matching based on multiline replies

Failing test for GH-357 Conversation matching based on multiline replies
See @ss-parser Conversation matching fails on multi line replies #12
Types of changes

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

Checklist:

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

Coverage remained the same at 80.565% when pulling a37acc8edb076ae9492fd65277f8ed463ccec01e on rensdewolf:patch-1 into 4de7271526d2f5f67e1aa25ebdc4eb7d2d4f637f on superscriptjs:master.

Thanks! Published as 1.1.2.


New version: CUDAnative v3.0.0

Registering package: CUDAnative
Repository: https://github.com/JuliaGPU/CUDAnative.jl
Created by: @maleadt
Version: v3.0.0
Commit: 23509a048407bd41255f0ba23819008c5ecc19c4
Reviewed by: @maleadt
Reference: https://github.com/JuliaGPU/CUDAnative.jl/commit/23509a048407bd41255f0ba23819008c5ecc19c4#commitcomment-38042014

Let's hold this.


Internal Server Error due to wrong Request Content-Type [JIRA: RCS-151]

Hi, I was trying to use node-aws-sdk to set bucket policies but the SDK sends the request with the wrong Content-Type, "application/octet-stream". I'm not sure if there is something wrong on my side or if AWS S3 also supports this since it is its SDK.
To find the problem I was digging in the SDK code because the server response is just a 500 Internal Server Error. It could be nice to return at least something like "Unaccepted Content-Type in request".

There is a ML discussion where this issue starred, http://lists.basho.com/pipermail/riak-users_lists.basho.com/2015-March/016924.html.

@pmarques Thanks for reporting.
As you indicated, 500 error is a bug of riak cs.
Also, it will be better for riak cs to accept application/octet-stream and whatever other content-type header values because the content of bucket policy request body should be XML and there are no alternatives to negotiate.


Unknown MIME type for URL

Hello @ospfranco,
when I run the following code:
        LinkPreview.getPreview('https://www.macys.com/shop/product/jaywalker-mens-animal-print-jacket?ID=5219568&CategoryID=80617')             .then(data => console.debug(data));
I always get the following Promise Rejection. No matter which URL I use or even if its just a string:
Possible Unhandled Promise Rejection (id: 0): Object {   "error": "React-Native-Preview-Link: Unknown MIME type for URL.", }
Is there something obvious I'm missing?

@stevenpal could you check this out? I think it might have to do with the latest merged changes

Sorry about that. I’m pretty sure it’s an issue with how the headers and content-types of the response are being extracted. I think I may have coded that in a way that’s too specific to a platform (e.g. looking for “_headers”). Won’t be able to take a look until Monday, so if someone wants to take a look in the interim please do.

@kaiszybiak in the mean time you can revert to using an older version 1.3.1 maybe

@ospfranco @stevenpal Thanks for the quick response.

@kaiszybiak in the mean time you can revert to using an older version 1.3.1 maybe

Yes. I will check that.

New version is out, please check it out


Update numpy version to 1.22.1

Signed-off-by: Martin Gaievski<EMAIL_ADDRESS>Description
Upporting 304 to main
Issues Resolved
#280 #281
Check List

[X] Commits are signed as per the DCO using --signoff

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.
For more information on following Developer Certificate of Origin and signing off your commits, please check here.

Did you use pip compile to upgrade?

Codecov Report

Merging #305 (acf5e1f) into main (b22a2dc) will decrease coverage by 0.10%.
The diff coverage is n/a.

@@             Coverage Diff              @@
##               main     #305      +/-   ##
============================================
- Coverage     83.56%   83.46%   -0.11%
  Complexity      885      885
============================================
  Files           127      127
  Lines          3822     3822
  Branches        361      361
============================================
- Hits           3194     3190       -4
- Misses          466      470       +4
  Partials        162      162

Impacted Files
Coverage Δ

...org/opensearch/knn/training/TrainingJobRunner.java
49.29% <0.00%> (-5.64%)
:arrow_down:

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Just checking, did you use pip compile to upgrade?

Yes, the pip-compile gives the rc version 1.22.0rc1 which is the minimal that works, so I've picked the next minimum released one.


Host admins to see hosted accounts activity

Without this check, the feature does not work when selecting specific hosted collectives from the Host Activity log.

Ended up merging a similar fix in https://github.com/opencollective/opencollective-api/pull/8009


can not match with performance in readme

I test a 13b model on a A100-80G with benchmark_throughput.py.
The hf result is 0.2 requests/s, 85.25 tokens/s.
The vllm result is 4.94 requests/s, 2153.77 tokens/s.
The acceleration effect is obvious, but the gap with the readme(154.2 requests/s) is huge. Is this result correct? Or am I doing something wrong?
Besides, the vllm use _add_request to load all input and use _run_engine to do the inference. A bit strange why not use generate directly? If there is a lot of data, we can not use _add_request to load whole data at once.

@irasin
Awesome, sorry didn't notice the unit.
As for the second question, when inferring a large amount of data, it is impossible to load all through _add_request, right? So how do you do the inference? Combine batches by myself?

@irasin
Thank you for your reply. For generate, it is also necessary to load all the data at one time to form a list. When the amount of data is particularly large, loading is very time-consuming and requires a lot of memory. Is it considered to be able to automatically combine batch from generator? Such as
def generator():
    with open("data.txt") as f:
        for line in f.readlines():
            yield line

 outputs = llm.generate(generator())

I can't run the benchmark test because  the wrong dataset format.  Would you mind to show the dataset you used? thks!

I can't run the benchmark test because the wrong dataset format. Would you mind to show the dataset you used? thks!

Please check here for the dataset link!

Thanks @irasin for answering this!

I can't run the benchmark test because the wrong dataset format. Would you mind to show the dataset you used? thks!

Please check here for the dataset link!

Thanks @zhuohan123 for great help ! Got it!


Fix broken link

Signed-off-by: Vanessa Maegima<EMAIL_ADDRESS>

Docs for f0147e5b32da79af4ea9adf297aa61eb41bbc16f are browesable at: https://ci.foundries.io/projects/fio-docs/builds/1327/docs/artifacts/html/index.html


Corrected CFP close date for Flowcon

As listed here, flowcon's cfp closed 12th September.
https://www.papercall.io/flowcon

No worries!  We're all human after all, and it isn't like there is an automated test for this kind of stuff.  You're great, thank you for maintaining this list


Update repo summary URL

The URL at the top of https://github.com/adobe-type-tools/box-drawing/ is still http://adobe-type-tools.github.com/boxDrawing/ but the repo was since renamed, so it should be http://adobe-type-tools.github.com/box-drawing

Thanks for the hint, but the link seems to be broken throughout, even with the proper URL. (I think it would have re-directed to the proper URL anyway).
It seems I have to re-initialize the gh-pages branch.

Ah yeah when you rename its ok but if you migrate user -> org it breaks and you need to recreate the branch (pushing isn't enough)

Oh, Git.
Thanks. It’s fixed now.


Spyder freezes, stops running

Description
What steps will reproduce the problem?

nothing specific that will cause Spyder to freeze.  That's strange, is this something happening to you consistently? and is there any other condition for the freeze to happen (are you running something else that could be consuming machine resources)?
Let us know :)

Hi Daniel,
yes, it is strange and I haven't had any problems until now with Spyder.
And I only encountered freezes after I downloaded and ran
itertools.permutations, every time I ran it Spyder froze.
Since then I've uninstalled and reinstalled Spyder and it seems to be
running without any issues now.
I checked the CPU and memory consumption, both were fine until I ran
itertools.permutations, and memory suddenly hit close to or even 100%. I
have an XPS17 with an i7 CPU and 16 GB internal memory.
I hope it won't happen again, but I will notify you if it does.
Thanks,
Mikael
Den ons 9 juni 2021 kl 18:41 skrev Daniel Althviz Moré <
@.***>:

Hi @Helge99 https://github.com/Helge99 thanks for the feedback! That's
strange, is this something happening to you consistently? and is there any
other condition for the freeze to happen (are you running something else
that could be consuming machine resources)?
Let us know :)
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/spyder-ide/spyder/issues/15821#issuecomment-857901059,
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.

Thanks a lot for the description of the circumstances @Helge99 I will then close this issue but for sure let us know is you experience some issue again :)


Galaxy Dependencies (Fix #2)

Dependencies management relying on Galaxy.

@victorock - I would rather let the user install the dependencies however the user chooses. In almost all of my roles, I leave dependencies: [] empty, because a lot of people like a lot of my roles... but not all of my roles. If you wanted your own pip role to set up Python Pip inside a virtualenv, if I locked in my role (which currently doesn't work with virtualenvs all that well... but could be made to), then those users would not, therefore, be able to use this role.
It's a philosophical stance, and it does mean you have to either install the roles manually or use a requirements file (e.g. like the one in the tests dir), but it's something that makes my roles a lot more composable (e.g. don't have to lock in an all-geerlingguy-role system).

I agree.  I prefer to find the deps and install them as git submodules.

We could simply have a flag like "awx_solve_deps: yes/no". The point was to make it simply for new users to use it, without creating requirements.yml, etc, etc. With dependencies defined, ansible-galaxy pulls and solves all the deps, much more convenient (IMHO). When installing something, i'd expect to have deps covered during installation. Imagine having to know, discover and solve the deps of every single package in any repo...


[WIP] fs: gdrive: use pydrive2's simplified auth

Codecov Report

Merging #110 (81c1849) into main (876454b) will increase coverage by 0.26%.
The diff coverage is 16.66%.

@@            Coverage Diff             @@
##             main     #110      +/-   ##
==========================================
+ Coverage   65.94%   66.21%   +0.26%
==========================================
  Files          39       39
  Lines        2414     2365      -49
  Branches      284      227      -57
==========================================
- Hits         1592     1566      -26
+ Misses        793      772      -21
+ Partials       29       27       -2

Impacted Files
Coverage Δ

src/dvc_objects/fs/implementations/gdrive.py
45.31% <16.66%> (+14.11%)
:arrow_up:

src/dvc_objects/fs/system.py
63.23% <0.00%> (-20.59%)
:arrow_down:

tests/test_reflink.py
87.50% <0.00%> (-12.50%)
:arrow_down:

src/dvc_objects/fs/path.py
49.43% <0.00%> (-1.12%)
:arrow_down:

src/dvc_objects/fs/utils.py
41.48% <0.00%> (-0.44%)
:arrow_down:

src/dvc_objects/executors.py
31.11% <0.00%> (+0.67%)
:arrow_up:

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Style, not critical observation: My feeling that init is too large to be honest? Don't linters complain about this? I would probably try to split into some pieces to improve readability.

I agree, hurts me too, but that "config translation" logic is something that we have everywhere and is going to be handled by a special helper in the plugins. Keeping as is for now.

I agree, hurts me too, but that "config translation" logic is something that we have everywhere and is going to be handled by a special helper in the plugins. Keeping as is for now.

yeah, there are some "middle grounds" though .. just saying :) your call. (still a bit surprised that linters don't catch this)


streaming dataset with concatenating splits raises an error

Describe the bug
streaming dataset with concatenating splits raises an error
Steps to reproduce the bug
from datasets import load_dataset

# no error
repo = "nateraw/ade20k-tiny"
dataset = load_dataset(repo, split="train+validation")

from datasets import load_dataset

# error
repo = "nateraw/ade20k-tiny"
dataset = load_dataset(repo, split="train+validation", streaming=True)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
[<ipython-input-4-a6ae02d63899>](https://localhost:8080/#) in <module>()
      3 # error
      4 repo = "nateraw/ade20k-tiny"
----> 5 dataset = load_dataset(repo, split="train+validation", streaming=True)

1 frames
[/usr/local/lib/python3.7/dist-packages/datasets/builder.py](https://localhost:8080/#) in as_streaming_dataset(self, split, base_path)
   1030             splits_generator = splits_generators[split]
   1031         else:
-> 1032             raise ValueError(f"Bad split: {split}. Available splits: {list(splits_generators)}")
   1033
   1034         # Create a dataset for each of the given splits

ValueError: Bad split: train+validation. Available splits: ['validation', 'train']

Colab
Expected results
load successfully or throws an error saying it is not supported.
Actual results
above
Environment info

datasets version: 2.4.0
Platform: Windows-10-10.0.22000-SP0 (windows11 x64)
Python version: 3.9.13
PyArrow version: 8.0.0
Pandas version: 1.4.3

Hi! Only the name of a particular split ("train", "test", ...) is supported as a split pattern if streaming=True. We plan to address this limitation soon.

Hi, have you addressed this yet?

yes, same error occurs.
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
[<ipython-input-3-a6ae02d63899>](https://localhost:8080/#) in <cell line: 5>()
      3 # error
      4 repo = "nateraw/ade20k-tiny"
----> 5 dataset = load_dataset(repo, split="train+validation", streaming=True)

1 frames
[/usr/local/lib/python3.10/dist-packages/datasets/builder.py](https://localhost:8080/#) in as_streaming_dataset(self, split, base_path)
   1265             splits_generator = splits_generators[split]
   1266         else:
-> 1267             raise ValueError(f"Bad split: {split}. Available splits: {list(splits_generators)}")
   1268
   1269         # Create a dataset for each of the given splits

ValueError: Bad split: train+validation. Available splits: ['train', 'validation']

google colab, datasets==2.12.0
- huggingface_hub version: 0.14.1
- Platform: Linux-5.10.147+-x86_64-with-glibc2.31
- Python version: 3.10.11
- Running in iPython ?: No
- Running in notebook ?: No
- Running in Google Colab ?: No
- Token path ?: /root/.cache/huggingface/token
- Has saved token ?: False
- Configured git credential helpers:
- FastAI: 2.7.12
- Tensorflow: 2.12.0
- Torch: 2.0.0+cu118
- Jinja2: 3.1.2
- Graphviz: 0.20.1
- Pydot: 1.4.2
- Pillow: 8.4.0
- hf_transfer: N/A
- gradio: N/A
- ENDPOINT: https://huggingface.co/
- HUGGINGFACE_HUB_CACHE: /root/.cache/huggingface/hub
- HUGGINGFACE_ASSETS_CACHE: /root/.cache/huggingface/assets
- HF_TOKEN_PATH: /root/.cache/huggingface/token
- HF_HUB_OFFLINE: False
- HF_HUB_DISABLE_TELEMETRY: False
- HF_HUB_DISABLE_PROGRESS_BARS: None
- HF_HUB_DISABLE_SYMLINKS_WARNING: False
- HF_HUB_DISABLE_EXPERIMENTAL_WARNING: False
- HF_HUB_DISABLE_IMPLICIT_TOKEN: False
- HF_HUB_ENABLE_HF_TRANSFER: False

Hi!, still not fixed this, the truth is that it is an important update for what we want to train the entire dataset because we want to train fast, also should be enabled the function "[train:18%]" for streaming


docs: previous/next links at bottom of documents have unresolved characters

This is obviously wrong.
For comparison, here is docs.akuity.io:

You should be able to compare the two sites to determine how this might be fixed.

Indeed, it does appear correct locally, but it does not on the live docs site.

Re-opening.
Inexplicably, the preview build of #2871 at https://deploy-preview-2871.docs.kargo.io/ showed the problem resolved, but the problem is not resolved in production or edge docs (published from main), nor is resolved in more recent preview builds.
Logs confirm that the desired version of Node is being used.

sounds like cache issue - https://answers.netlify.com/t/cache-issue-on-netlify/8238

@Marvin9 I will check that. Thanks!
I had cleared it once before while we were troubleshooting this, but probably not since we actually solved it.


Run the test cases under ARM

@peterzhuamazon Peter is running such under ARM
Add @seraphjiang for visibility

I have set up a ARM docker env and run OS and OSD artifacts. Then run functional test successfully.
Cypress 5.6.0 is working in ARM.