Error starting Adapter (v1.0.1)

Hi
I am trying to reinstall ioBroker, moving to a new HW platform.
It works with the GATEWAY in the current production
eNet used to work, but V1.0.1 and V1.0.0 cause issues
in v.1.0.0, the adapter seems to work, but the traffic light remains yellow.
in v1.0.1, the log keeps showing:
instance system.adapter.enet.0 terminated with code 10 (Cannot find start file of adapter)

Hello,
the eNet Server is currently not supported.
I'm still working on it.

Hi

THX THX THX!!!

am using the GATEWAY setting and it doesn’t work.

What is the last version BEFORE 1.0.0, so I could manually install that one?
Again: THX!
Nico
Sebastian Schultz<EMAIL_ADDRESS>schrieb am Sa. 9. Feb. 2019 um
19:58:

Hello,
the eNet Server is currently not supported.
I'm still working on it.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/SebastianSchultz/ioBroker.enet/issues/9#issuecomment-462070096,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AULYhnfXHtLaCtgjaol7FuNglWQs-ZMmks5vLxpNgaJpZM4ayrJt
.

1.0.1 is the current working Version.
I had installed it via Github URL and it works without any errors.
Can you please try to uninstall the Adapter completely and install it via Github URL?
If this doesn't work I Need a debug log.

Hi
Thank you for your efforts.
versions 1.0.0 and 1.0.1 still dont work for me, BUT: 0.0.4 does it, so I am fine with
sudo iobroker stop
sudo npm install<EMAIL_ADDRESS>--production
sudo iobroker upload enet
sudo iobroker start
THX

Hi,
are there any news on this topic? I had the same problem with and switched back to 0.0.4 to solve it, but would rather like to use the newest version.
Thanks,
Rainer

Do you get any error messages in log if you set the adapter in debug mode?
Do you run the adapter in gateway or server mode?

Thanks for your help!
Adapter is running in gateway mode. Error message is the same as daNick73 reported:
instance system.adapter.enet.0 terminated with code 10 (Cannot find start file of adapter)
During adapter installation I get this warning (don't know if it helps):
$ ./iobroker add enet  --host RaspberryPi01
NPM version: 6.4.1
npm install iobroker.enet --production --save --prefix "/opt/iobroker" (System call)
npm WARN enoent ENOENT: no such file or directory, open '/opt/iobroker/node_modules/follow-redirects/package.json'

I don't know what's wrong at your installation I had done the following:

Uninstalled ALL instances of the eNet adapter
Uninstalles the eNet adapter from iobroker
Installed the eNet adapter from the following Github URL: https://github.com/SebastianSchultz/ioBroker.enet
Added a new instance of the eNet adapter and configured it

The adapter ist starting and working without any error messages...
Can you please try this?

Thanks, but this did not solve the problem.
I then tried the following (see https://forum.iobroker.net/topic/7198/adapter-cannot-find-start-file):

Rename main.js in /opt/iobroker/node_modules/iobroker.enet to mainorg.js
Add a file main.js in this directory which contains just this line:
require('./mainorg');
Restarted iobroker and created a new instance of enet
=> No more errors, adapter seems to be running

Does this give you a hint to solve this issue? There is obviously a problem with resolving path names.

Do you use the adapter / ioBroker on a windows machine or a raspberry?
Or something other system?

On a Raspberry Pi3+.
Am 14.05.19, 00:41, Sebastian Schultz<EMAIL_ADDRESS>schrieb:
Do you use the adapter / ioBroker on a windows machine or a raspberry?
Or something other system?
—You are receiving this because you commented.Reply to this email directly, view it on GitHub, or mute the thread.
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Thanks for your input.
It seems a raspberry/linux specific problem...
I think (like you) it's a path resolving issue.
I will investigate this further and implement a solution in the next update,

Thanks a lot!

Just in case it helps:
My HW platform was also a Raspberry 3

I set the startfile in io-package.json.
Can you please uninstall the adapter and reinstall it here from GitHub url (https://github.com/SebastianSchultz/ioBroker.enet).
Can ou please report if the error still occurs?

Yes, thanks, I will do next weekend when I am back at home

Hello,
do you have any update on this issue?

Hi,
sorry for my late answer, I did not find time to continue my private projects.
Tonight, I installed the adapter with the modified io-package.json and it runs.
I still have a problem with my scripts. setState doesn't seem to work any longer. Test script:
console.log(getState("enet.0.channel22.STATE").val);
setState("enet.0.channel22.STATE", true);
console.log(getState("enet.0.channel22.STATE").val);
produces this:
javascript.0 script.js.Test: false
javascript.0 script.js.Test: false
and this warning message:
javascript.0  script.js.Test: setForeignState(id=enet.0.channel22.STATE, state=true)  - was not executed, while debug mode is active

Have you tried to set the value in the objects tab instead in a script?
Because of the periodically readout of the actual values of the channels from the gateway it is possible that this readout overwrites vour value?

Yes, I tried to set the value in the objects tab. This doesn't work either.
But: Both run with version 0.0.4 of the adapter, which I am still using use as backup until now.

Have you only replaced io-package.json?
Then that doesn't work.
You have to reinstall the adapter via Github URL. to get it working.
Can you please uninstall the adapter and reinstall it via Github URL?

Good point. Of course I installed the complete package, but I am not sure if everything was done in the right way.
So, what is the easiest and safest way to uninstall the old adapter and reinstall the new one from Github URL?

First uninstall all instances of the adapter and the adapter itself via console command "iobroker del enet"
Then on the "adapter" tab click on the Github logo (expert mode enabled) and enter the following url to install from Github: "https://github.com/SebastianSchultz/ioBroker.enet"
That's all :)

Ok, thanks. Installation done, created and activated an instance of the adapter. Adapter starts, no errors in the log, so the "Error starting Adapter" seems to be solved.
But when I try to change the STATE of an object in the objects tab (e.g. to true to switch on a light), it is immediately set back to false. So I cannot change any states, just read them out. I guess this is not the intended behavior. At least, with version 0.0.4 this worked.
By the way, during installation I get warnings, see attached file.
output.txt

You wrote before "Because of the periodically readout of the actual values of the channels from the gateway it is possible that this readout overwrites vour value?" Yes, it looks like that, but how can I use the adapter then to control the actors through the gateway?

One additional info: With the old version 0.0.4 the behavior is as follows: When I set the STATE of a channel to true, the connected actor (in my case a light) is switched on. The STATE variable immediately switches back to false (my interpretation: it reads out an old value from the gateway), while the actor is still on. After a second or two the STATE variable switches to true (because the STATE variable is now updated in the gateway?) and hence correctly shows the state of the actor. Changing from true to false (in my case switch off the light) shows the same behavior. The behavior is somewhat strange but finally ok, because the actors can be controlled, which is not the case with version 1.0.1. All tests have been done on the objects tab.
Is there a timing problem with version 1.0.1 so that the channel value is not really changed?

Hello Rainer,
I hevae to investigate and test this at my very simple eNet example installation (only one switching actor and 1 blind actor).
Currently I have not much time but I will check it.
I come back to you if I have new information OK?!

Sure, thanks a lot. I'll stay on version 0.0.4 until then.

Hello Rainer,
I think I found the bug. A little mistake with big effects :)
an you please reinstall the adapter from the GitHub url and check if it works at your ioBroker installation? Pleaese give me a feedback :)

Looks good. The STATE variable still behaves strangely as described above, but I can switch the actors now.  As the object model has changed from version 0.0.4 to version 1.0.1 I have to adapt my scripts, but this is not a big job.
So thanks for the bug fix and your work here!


GROOVY-9751, GROOVY-9463: STC: add type checking of method pointer expressions

Previously, the inferred type of a.&b was simply Closure.  This was a problem for return type inferencing of expressions like list.collect(service.&transform) (see GROOVY-9751).  Also, once the reference method(s) can be resolved, it was not much of a leap to add STC error for unknown condition (see GROOVY-9463).
https://issues.apache.org/jira/browse/GROOVY-9751
https://issues.apache.org/jira/browse/GROOVY-9463

Proposed PR merged, thanks!


Please ignore ffuure

Please ignore ffuure

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


fix(customize) only a template without plugins failed

fixes #582

@flrgh had to rebase and force-push after merging the other PR, now the approval is gone, and the PR needs a new approval... a 👍 would be most welcome (again)


Hamcrest <IP_ADDRESS> does not work with JDK 6

If I read https://github.com/hamcrest/JavaHamcrest/issues/65#issuecomment-68097018 correctly, Hamcrest <IP_ADDRESS> was supposed to work with JDK 6.
However, it was apparently compiled for JDK 7.
I've create a small sample project at https://github.com/marcphilipp/hamcrest-2-jdk6. It uses Maven to fetch java-hamcrest and hamcrest-java <IP_ADDRESS>. It's main class declares a simple assertion.
You can build a jar-with-dependencies using Maven:
$ mvn clean compile assembly:single

When executed using a JVM < 1.7 it fails with the following exception:
$ /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java -jar target/hamcrest-2-jdk6-0.0.1-SNAPSHOT-jar-with-dependencies.jar
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/hamcrest/CoreMatchers : Unsupported major.minor version 51.0
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at de.marcphilipp.hamcrest2.HamcrestTest.main(HamcrestTest.java:8)

When run using JDK 7 it gives the following (expected!) output:
$ /Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/bin/java -jar target/hamcrest-2-jdk6-0.0.1-SNAPSHOT-jar-with-dependencies.jar
Exception in thread "main" java.lang.AssertionError:
Expected: a string starting with "1.6.0"
     but: was "1.7.0_04-b20"
	at org.hamcrest.junit.MatcherAssert$1.mismatch(MatcherAssert.java:19)
	at org.hamcrest.junit.internal.Matching.checkMatch(Matching.java:20)
	at org.hamcrest.junit.MatcherAssert.assertThat(MatcherAssert.java:16)
	at org.hamcrest.junit.MatcherAssert.assertThat(MatcherAssert.java:12)
	at de.marcphilipp.hamcrest2.HamcrestTest.main(HamcrestTest.java:9)

JUnit 5 will depend on JDK 6, not JDK 7... so this issue is really critical for me. :-/

Rereading that comment thread, the eventual agreement was that the next release of Hamcrest would be <IP_ADDRESS> and would support Java 7 and above.
If JUnit 5 supports Java 6 and above, that will be fine if Hamcrest integration is taken out of JUnit and implemented in Hamcrest-JUnit instead.  Users of Hamcrest and Hamcrest-JUnit will be using Java 7+, and so can use JUnit 5, but JUnit 5 users who stick with Java 6 will have to do without Hamcrest.

I've released Hamcrest-JUnit <IP_ADDRESS>, which is compiled with JDK 1.6.


Test ghcr deploy script

Not sure how to test that properly. How about I create a release of this branch?

@anayden, sounds good, let's do it.

Oops, sorry for accidental merge, already reverted.

no problem, seems like GH does not have a possibility to reopen the PR_


Allow custom handlers to catch the cron job exceptions

I wanted to be able to use custom handlers for exceptions instead of waiting for the FailedRunsNotificationCronJob to run

Coverage increased (+0.04%) to 89.861% when pulling f20ab30b0a2ee85aa2032c5a384fe1dc2bc95a73 on pardo:master into 57bd91260bb658911880813dbac06f79483ac601 on Tivix:master.

@pardo closing in favor of #90. Would custom handlers for warnings work ok?

@sci-tab yes , my original idea was being able to track errors with sentry. Thanks!


priority not mixed with regular

Basically, LGTM, but I tried it and when writing an Infoton with ?priority,
/proc/bg.md shows for persist topic Green/Red.
I think this is only a typo in BGMonitorActor.scala in lines 107 and 109 - you misplaced the .p
They should be s"imp.${topicPartition.partition()}.p_offset" and s"indexer.${topicPartition.partition()}.p_offset"
So can you add one more commit to this PR?


WIP: BUG: Delaunay Cell Data

The DelaunayConformingQuadEdgeMeshFilter currently results in a
decoupling of the cell faces from their corresponding cell data.
This patch attempts to address this by re-assigning cell data
on either side of an edge to the new cell indices following the
edge flip.  In testing, this results in a dramatic improvement
in consistency.  Unfortunately, occasional inconsistencies are
still apparent.

PR Checklist

:no_entry_sign: Makes breaking changes
:no_entry_sign: Makes design changes
:no_entry_sign: Adds the License notice to new files.
:no_entry_sign: Adds Python wrapping.
[X] Adds tests and baseline comparison (quantitative).
:no_entry_sign: Adds test data.
:no_entry_sign: Adds Examples to ITKExamples
:no_entry_sign: Adds Documentation.

Refer to the ITK Software Guide for
further development details if necessary.

In the below meshes, the faces are colored according to their cell data.  I've displayed the input and output meshes on the left and right, respectively.
Here is a result before applying the patch:

Here is the result after applying the patch:

There does seem to be a big improvement in consistency, but unfortunately some errors still exist (see the pink face above Suzanne's right eye, and the green face in Suzanne's right ear).  I'd appreciate feedback on the patch, especially on whether these errors are inevitable or whether there is something I could be doing to further improve the consistency.

@dzenanz Thanks very much--just pushed the two requested changes.

Time to remove the WIP prefix?

@dzenanz Removed WIP, also re-factored into a convenience method.

Thank you @dzenanz for the review and merge!!  Happy holidays.  :-)


Prevent Targets having extra properties

Allow a valdiation to confirm that the target does not contain any properties other than those defined in the model.

We are going to support this by adding a parameter at validation time that will force a check of all properties on the target against the properties defined on the model.


Add new curated content file: HowToWriteGoodDocumentation.md

Create curated content file, following style of HowToEnablePerformancePortabilityForCseApps.md

Happy to pick up the baton here if needed.

Hi Damon -- Thanks for volunteering!  Let's start a new issue for details about documentation tools, as discussed during the minisymposium.  That is separate from this curation issue, which is just a pointer and brief description of another doc: https://ideas-productivity.org/wordpress/wp-content/uploads/2016/04/IDEAS-DocumentationHowToWriteGoodDocumentation-V0.1.pdf


[ENH,REF] Refactor visualisation and add temporal importance curves function

Refactors the visualisation package into series, results and estimator categories. Splits the different results functions into separate files based on the plot type. Moves a function for plotting collections from the clustering file to the series package.
Adds a function for plotting temporal importance curves, previously removed from classification.
This all needs better documentation and testing, but would prefer to leave that for another PR.

I was about to ask about testing, but then saw #1051

did you change the API?

The imports should still be the same, but i just noticed it would not matter because there is no vis page currently on the API 🙂. I can get to that, currently doing the rounds in the module


refactor pkg/application to use Appfile

Fixed e2e tests and added unit test. Also addressed #413 kubectl issue.


Add insert_by_period materialization

resolves #11

Description
Adding insert_by_period materialization.
The code is based on the insert_by_period materialization from the dbt-labs-experimental-features repo: https://github.com/dbt-labs/dbt-labs-experimental-features/tree/main/insert_by_period
Checklist

[x] I have run this code in development and it appears to resolve the stated issue
[ ] This PR includes tests, or tests are not required/relevant for this PR
[ ] I have updated the CHANGELOG.md with information about my change

Hi @septimit
Thank you for this contribution!
I have only one thing to add, can we change the Readme of this repo where we mention that we have no plans to implement this?

Can we change this to " custom macro provided"


max_per constraint validation incorrect for pods

max_per requires a value. pods doesn't enforce that:
https://github.com/mesosphere/marathon/blob/a1d7b569e795b5f8bf84cc7b22a66031b3a366ec/src/main/scala/mesosphere/marathon/api/v2/validation/PodsValidation.scala#L240
see correct impl for app constraints:
https://github.com/mesosphere/marathon/blob/6834f418470ca015522429d2629ebc7f125893fc/src/main/scala/mesosphere/marathon/state/AppDefinition.scala#L592

Patch is here: https://phabricator.mesosphere.com/D473

Picked


Enhancement: Add Password / Change Password

Coverage decreased (-1.9%) to 89.215% when pulling 891610626e09f7aa7e6cf039008dad85a51c3b4d on DericKJW:Password into 29f7f6e55a1e64360d12ea80fa9eab57b6cb0ae3 on CS2103AUG2017-F10-B2:master.

Coverage decreased (-1.6%) to 89.566% when pulling f081c74ecd1a6803fcec54669dfe7c834eb66ce2 on DericKJW:Password into 29f7f6e55a1e64360d12ea80fa9eab57b6cb0ae3 on CS2103AUG2017-F10-B2:master.

Coverage decreased (-1.6%) to 89.566% when pulling 3f58693e924342648a84a6f525274601aed96581 on DericKJW:Password into 29f7f6e55a1e64360d12ea80fa9eab57b6cb0ae3 on CS2103AUG2017-F10-B2:master.

try to add tests for password parsers and the coverage should be fine

Coverage decreased (-1.6%) to 89.566% when pulling 66699f4f38ba359cfe16c9e5798da84784de3a40 on DericKJW:Password into 29f7f6e55a1e64360d12ea80fa9eab57b6cb0ae3 on CS2103AUG2017-F10-B2:master.

Coverage decreased (-1.5%) to 89.613% when pulling d256c72c43ca3c98e9661aadb6723caf9bfda69d on DericKJW:Password into 29f7f6e55a1e64360d12ea80fa9eab57b6cb0ae3 on CS2103AUG2017-F10-B2:master.


Required field error is not disappear after fill

Hi,
With the autovalidate = false, the required error text will not disappear even after some text are entered. It will on be disappear after hitting the submit button. Can this be improved?
Thanks in advance.

Hi @jasonlaw.
I'll investigate and fix the issue as soon as I can.
Thank you for your contribution.

May be based on problems to do with state that I was planning to improve on in the next major version.

Pretty crucial, also good for checking the state of a form field such as if it's dirty.

And with autovalidate: true, when I enter the page with the form, all of the fields have errors which just doesn't look good but when I type into it, the error goes away which is good, but not how I want it so there are no good alternatives.

Good night,
Thank you very much for the prompt reply.
Sorry for the inconvenience, but would you have a forecast for such an improvement?
Thanks.
Cristian Regazzo

Fixed in v4.0.0


Add favicon

Great repo. I noticed there is no favicon. How does one add that?

I figured out. Go to https://www.favicon-generator.org/ to generate all the image files needed and upload them to images/ and it will also give you some html lines.
Change _includes/head/custom.html accordingly.


fix throw unbound exception when do type coercion

intro by PR #25609
Proposed changes
Issue Number: close #xxx

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

(From new machine)TeamCity pipeline, clickbench performance test result:
the sum of best hot time: 49.39 seconds
stream load tsv:          576 seconds loaded<PHONE_NUMBER>9 Bytes, about 123 MB/s
stream load json:         20 seconds loaded<PHONE_NUMBER> Bytes, about 112 MB/s
stream load orc:          65 seconds loaded<PHONE_NUMBER> Bytes, about 16 MB/s
stream load parquet:          31 seconds loaded 861443392 Bytes, about 26 MB/s
insert into select:          29.4 seconds inserted 10000000 Rows, about 340K ops/s
storage size:<PHONE_NUMBER>4 Bytes


I asked Wither if we could borrow your icon and he agreed to it. So I just credited both of you. :D


User Registration semantics (enabled >< accountLocked)

Hi,
I have a question about the proper use of user.enabled and user.accountLocked
By default the registration, create a  user with enabled=true and accountLocked = true.
When clicking the verification link https://github.com/grails-plugins/grails-spring-security-ui/blob/master/grails-app/controllers/grails/plugins/springsecurity/ui/RegisterController.groovy accountLocked is set to false.
This works but I wonder if by default, it should not be user.enabled = false and user.accountLocked = false. Locking is a manual decision to prohibit user access, enabled sounds the right place to handle opt-in registrations.
What do you think ?

Thank-you @wavyx for submitting this issue and bringing your perspective to our attention.
I do not have plans to modify the way user.enabled and user.accountLocked are utilized during registration.  It has worked well thus far ✨
If different functionality is desired, overriding the RegistrationController will allow you to use the fields in a way you feel makes more sense.
Thank-you again for your contribution.

@ddelponte glad to see you're still around to update this plugin ;)

Thanks @wavyx !  I'm slowly chipping away at the issues :)


(PYL-R1719) if expression used can be simplified

Description
The if expression used here can be simplified to increase the code readability. Example: python value = True if arg else False  This can be simplified into: python value = bool(arg)
Occurrences
There is 1 occurrence of this issue in the repository.
See all occurrences on DeepSource → deepsource.io/gh/themagicalmammal/Wikibot/issue/PYL-R1719/occurrences/

https://github.com/themagicalmammal/Wikibot/commit/9ec632911eb8fe4c5c8d3b13d37c12f52864e7e8


PL-500 - Setup the lab environment - Issue

PL-500 : Microsoft Power Automate RPA Developer
Setup the lab environment
Exercise 4 – Copy Lab Resources
Step 3.) Browse to C:\Labs\Resources\Funding manager app and double-click on the Woodgrove Bank Funding Manager.exe executable.
This is an issue identical to the issue raised in February: [https://github.com/MicrosoftLearning/PL-500T00-Microsoft-Power-Automate-RPA-Developer/issues/218]
Running the lab as instructed, it will prompt to install .Net when you launch the Woodgrove Bank Funding Manager.exe. [P1]. If you click yes, nothing will happening.
If you first run setup.exe it will prompt to install .Net and appears to complete that process but does eventually fail with this error [P2] stating it's due to a hash mismatch.
Then if you run the Woodgrove Bank Funding Manager.exe again, it'll launch without asking to install .Net and display the login page [P3].
[P1]

[P2]

[P3]

Thank you for raising this issue. We will update on this soon


Need a easy  filter sample. e.g. Create a thumbnail image every X seconds of the video

In FFmpeg wiki: https://trac.ffmpeg.org/wiki/Create a thumbnail image every X seconds of the video
we use cmd:
fmpeg -i input.flv -ss 00:00:14.435 -vframes 1 out.png
We get one picture in Specified time
ffmpeg -i input.flv -vf fps=1 out%d.png
then get lots of images. One picture per second.
How to use PyAV to achived the same goal ? Does anybody make a demo? Thanks.
BTW:  by use cmd:
ffmpeg -i input.flv-r 1 -y -f image2 -s 240*320 pc%3d.jpg
use '-r' arg  seems to be the same purpose， Which method is more efficient ?

I think you can do it more simple:

import av

count = 0
container = av.open('test_clips/test.mp4', 'r')

for packet in container.demux():
    if packet.stream.type == 'video':
        for frame in packet.decode():
            if count % 25 == 0:
                print(count)
            count += 1

Instead of print, you use a save image method.

@jb-alvarado unless I'm misreading the code, it seems to select every frame divisible by 25 yielding frames 0, 25, 50, .... But it doesn't give a frame rate of 1 fps. Do you know if we can achieve this using the fps filter especially when the input video can have any frame rate? Thanks!

When you want to have images as output you can use two methods:

before you use the modulo operator you read the fps from input file and use this as a modulo.
you use the fps filter, this one drops all other frames

When you want a video output the second method is better, but you have to look here in the issues and examples for a proper way to use filters in PyAV. My knowledge about PyAV is not so deep.
Here I have try one time to change the fps, but as I remember there was some issues, and of course the queue and pipe to ffplay is not necessary.

Thanks @jb-alvarado for a quick response. Unfortunately there are no examples for using filters. I've also asked a question in the Gitter channel for the project. Your solution here does give me some ideas but my problem is a little more complicated since I'm doing filtering on a video stream as opposed to a file on the disk. I'll see if I can come up with something. Thanks again!


Docker icon for Dockerfile and docker-compose.yml

Icon Path or AllIcons Field
DockerIcons.Icons.DockerFile_1 / DockerIcons.Icons.DockerComposeFile
What does it look like?

What Plugin?
https://plugins.jetbrains.com/plugin/7724-docker
How to get to it?
Create a file called Dockerfile

I submitted both in the same issue due to both being the same icon just with different letters (one is D and the other one is DC) so they can probably use the same exact icon.


Remove firewall rules for monitoring. Enable monitoring in other cluster providers

Heapster and Grafana are now accessible via the API server proxy. There is no need for firewall rules.
This change also helps enable monitoring outside of GCE.

LGTM


Collapse edges by double-click if node is already expanded

Hi,
It's useful to be able to expand edges of a node by a double click, it might be useful too to collapse them if we double click on an expanded node.

Hi, great feature request, but seems to be a duplicate of #50. Closing this one.
Please feel free to re-open if you think you need a different behavior from what's described there.


fix windows gpu build

copy cuda_runtime_api.h into build dir to fix gpu build on windows

Can one of the admins verify this patch?

jenkins, test this please.
@guschumue, do you need me to also run a windows gpu presubmit?

For this PR? Can not hurt of course but I had our Jenkins build it so I'm sure its good..


Bug: Backdrop scroll behavior.

If backdrop is enabled. (highlight element) It does not behave correctly on scroll. It does not move with the focused element.
Solution:

Disable scrolling while tour is enabled.
Or place the backdrop (highlight) correctly. Move with the element like in angular-ui-tour.

ngx-tour (bug)

angular-ui-tour (expected)

Bug discovered in current demo from 2019-03-07.
Compare with angular-ui-tour.

@Domvel

If you use "mat-sidenav-container", scrolling will be disabled by default when ui-tour is active
Feel free to create a PR addressing the issue in other cases

@hakimio Please let us know which scrolling do we need to disable, Is it Page scrolling, Container Scrolling or tour-step-template scrolling ?

@hakimio Any updates on this one please ?

@amitagrawal11 you should be able to see yourself which one of your divs/containers is scrolling when the tour is active by just inspecting the DOM. Solution is quite simple:

Before starting the tour add "no-scroll" class to that container

.no-scroll {
    overflow: hidden;
}

const body = document.body,
    mainSection = document.querySelector('.main-content');

mainSection.classList.add('no-scroll');

Add tour end event listener where you remove the class.

this.tourService.end$.subscribe(() => {
   this.enableScroll();
});

It's a bit tricky to come-up with general solution for everyone since scrolling is implemented differently from one app to the other and some have multiple scrollable containers.

@hakimio thanks for your response, It worked for me now.
But I can see another bug by disabling scrollbar onto container div i.e. suppose we have two tooltips on one page and first one is placed on the top of the page and second one is placed on bottom of the page. So problem is if I click on backtip/prevtip (while navigating from second tip to first tip) then page does not scroll and tip comes inconsistently.

Scrolling the page programmatically still works fine when overflow is hidden. That's not an issue.

Has this been resolved? I'm facing the same issue using mat-drawer

If you can reproduce the issue with the latest version of ngx-ui-tour library, open a new issue with reproduction in ngx-ui-tour repository.

You can also just use disablePageScrolling config in the new library.


custom path for hostkeys

Do the attributes work in libraries ? Are they called the way I did ?

Good morning,
we experience the following problem with this version:
undefined local variable or method sshd_custom_path'`
can you help out?

@chbiel Yeah, I see. This is a bug. Can you file a new ticket. The variable needs to be fetched properly. Until then I recommend to use the latest version before that release.

thanks, I will create it.
maybe a dumb question but is there an easy way provided by inspect to use a specific tag?
currently we run
inspec exec https://github.com/dev-sec/ssh-baseline.git --attrs /tmp/spec/global/attributes/ssh-baseline.yaml \
  --no-distinct-exit \
  --no-interactive \
  --no-color

is there something like inspec exec https://github.com/dev-sec/ssh-baseline.git#2.5.3 I am not aware of?
Thanks in advance

Yes you can. Back then when I built the feature in InSpec, I made it so that you can copy paste the github url:
inspec exec https://github.com/dev-sec/ssh-baseline/tree/2.5.1


Create Azure Workbooks resource

As a project developer, I want an Azure Workbook defined in IaC that includes the set of pre-built supporting queries, so that the visualization dashboard is deployed alongside existing project infrastructure

[ ] Azure Workbooks defined in IaC that implements the dashboard outlined in the design doc using the defined KQL queries and metrics

Mentioned in #336


[sil-cast-optimizer] Fix casting between Swift and CF types

If a Swift type T needs to be casted to a CF type, then we first cast T to its bridged NS type and then ref_cast the result to a corresponding CF type.
For example, if we need to cast String to CFString, we first cast String to NSString and then ref_cast the NSString to CFString.
Fixes rdar://problem/29745498

@swift-ci Please smoke test


Add api to set SLEEPONEXIT bit in SCR register

Thanks for the addition, I was almost 100% sure this was already in there :)
bors r+


New package: ReadCoverageDistributions v0.1.2

Registering package: ReadCoverageDistributions
Repository: https://github.com/Dinesh-Adhithya-H/ReadCoverageDistributions.jl
Created by: @Dinesh-Adhithya-H
Version: v0.1.2
Commit: 6eae56fd192b4e43154320442abec5fd44d1636f
Reviewed by: @Dinesh-Adhithya-H
Reference: https://github.com/Dinesh-Adhithya-H/ReadCoverageDistributions.jl/issues/2#issuecomment-873551854

@Dinesh-Adhithya-H please see the message above.  Once you fix the automerge issues you can register again the new revision without changing the version number and this pull request will be automatically updated.
[noblock]


Harp 7366 all fixes

Fixes from #852, #853 and additonally

optimize createLineGeometry
optimize allocation count in webMercatorTile2TargetWorld

Decoders tests please

Delivered in scope of #853, #882, #881


Limit max amount of signers when using "At least"

Currently it is possible to set the required signers to a number bigger than the actual amount of signers added to the treasury.

Fixed with this PR: https://github.com/ADAOcommunity/round-table/pull/55


Appstudio update hacbs-test-project-crwd

Pipelines as Code configuration proposal
To start the PipelineRun, add a new comment with content /ok-to-test
For more detailed information about running a PipelineRun, please refer to Pipelines as Code documentation Running the PipelineRun
To customize the proposed PipelineRuns after merge, please refer to Build Pipeline customization

Pipelines as Code CI has failed.There was an error creating the PipelineRun: hacbs-test-project-crwd-on-pull-request-
creating pipelinerun hacbs-test-project-crwd-on-pull-request- in namespace rhtap-demo-qzbl-tenant has failed.
Tekton Controller has reported this error: the namespace of the provided object does not match the namespace sent on the request

Pipelines as Code CI has failed.There was an error creating the PipelineRun: hacbs-test-project-crwd-on-pull-request-
creating pipelinerun hacbs-test-project-crwd-on-pull-request- in namespace rhtap-demo-vpfp-tenant has failed.
Tekton Controller has reported this error: the namespace of the provided object does not match the namespace sent on the request


Replace Camera.current with Camera.main to prevent it from grabbing scene camera

Camera.current can lead to infinite destroy -> spawn loop if you have scene view open.

I didn't know that Camera.current can be a scene view camera.
What do you mean by infinite destroy ? What will be destroyed ?

Anything using that script expecting game view camera is affected, but in this case it was the player ped being destroyed.
We probably shouldn't be adding that script to player controlled peds in the first place, but that's a story for another commit.

Aha, I get it. Thanks.


improve/document examples in wasmtime/cranelift/jit/

Hi, I just came from https://github.com/bytecodealliance/cranelift-jit-demo which is nice, document and pretty straightforward (although has some todo comments left there 3-4 years ago)
Improvement
Add more examples of different complexity (basic to medium and maybe some complex ones), document them with explanations of what's what (like it is done in cranelift-jit-demo)
Implementation
Think of some simple examples and use-cases that incorporate jit, it could be something like compiled regex or other type of state machine pattern, then add examples commenting every jit and cranelift-specific step to avoid confusion and provide guidance.
Show how to define functions, work with data, leave useful notes to external resources (at least to Wikipedia).
Benefit
Newcomers like me will be able to understand what is going on there and how they can use cranelift jit to build their own blazingly fast & feature packed language.
p.s. now I'm trying to explore cranelift-jit-demo and it is looking good so far, I like it.

I had considered hooking up my experimental regex compiler (https://github.com/jameysharp/pikevm) to cranelift-jit for fun, but I hadn't really thought about making it be useful documentation. Thanks for the suggestion!
I'm curious: what project do you want to use a JIT compiler in?
One way you can help is by keeping notes on things that you find confusing or surprising about Cranelift as you work on your project. We can help turn those notes into better documentation, or even better, fix Cranelift to be easier to use.
Also, I encourage you to join the #cranelift stream at https://bytecodealliance.zulipchat.com/.

Thanks for the response!

what project do you want to use a JIT compiler in?

Probably building a programming language of my own (at least trying my best) but for now just learning more stuff from it to become a bit more experienced. The reason I want JIT compiled language is that I like prototyping and iteration, but interpreted languages are not as fast to be useful in areas like gamedev or heavy simulations so I'm going to use JIT. In the past I've tried Julia programming language and found that is really nice but the problem is that it has GC so gamedev is basically no go (also it is a math-oriented functional language so some things are not so convenient as in e.g. Rust where you have "normal" mutability)
btw currently I'm working on a note-taking app called mem, it can be used to create notes, todos, readlists, dictionaries... but notably it will allow for creating "QA" cards so you can save questions you (or someone else) have to answer later.

Also, I encourage you to join the #cranelift stream at https://bytecodealliance.zulipchat.com/

thanks for that suggestion, not exactly sure if I'm gonna be there, but if I need some help I know where to go.


goenv local does not take effect?

Reproducible Steps:
goenv local 1.16.8

In the same shell:
goenv versions
  system
  1.14.4
  1.15.15
* 1.16.8 (set by /Users/codinghuang/codeDir/wiki/k8s-operator/docs/.go-version)
  1.17.1

In the same shell:
go version
go version go1.15.15 darwin/amd64

other info:
goenv
goenv 2.0.0beta11

the same problem. i resolved by comment the following lines, and source ~/.zsh

if above lines are not commented, every time you use 'go local 1.14.4', you should do source ~/.zsh, then go version
will change to what you want. I don't know whether this is a bug.

This is a configuration issue -- you shouldn't be blindly prepending $GOROOT/bin to the path but instead relying on goenv's shims in your path (which are put there by goenv init -). goenv local is doing nothing because the old $GOROOT from your shell startup is taking precedence over the shims.

It looks like the offending lines came from the README -- it looks like this feature is not that well thought-out and potentially breaks stuff badly. I personally don't use goenv init -/configure according to the README so I never ran into this.

I found my way here for this exact reason.  Use pyenv on a daily basis so expecting goenv to function similarly.  Following the instructions I added this in my zsh setup:
export GOENV_ROOT="$HOME/.goenv"
export PATH="$GOENV_ROOT/bin:$PATH"
if (( $+commands[goenv] )); then
  eval "$(goenv init -)"
  export PATH="$GOROOT/bin:$PATH"
  export PATH="$PATH:$GOPATH/bin"
fi

This results in the same issue OP describes.  Removing the exports from my if block like so
export GOENV_ROOT="$HOME/.goenv"
export PATH="$GOENV_ROOT/bin:$PATH"
if (( $+commands[goenv] )); then
  eval "$(goenv init -)"
fi

results the correct behavior I was looking for.
❯ which go
/home/me/.goenv/shims/go

❯ goenv versions
* system (set by /home/me/.goenv/version)
  1.17.0

❯ go version
go version go1.18.3 linux/amd64

❯ go local 1.17.0
go local: unknown command
Run 'go help' for usage.

❯ goenv local 1.17.0

❯ goenv versions
  system
* 1.17.0 (set by /home/me/.go-version)

❯ go version
go version go1.17 linux/amd64

Whats going on guys? We experienced the same issue and we had this in bash as instructed by INSTALL.md
export GOENV_ROOT="$HOME/.goenv"
export PATH="$GOENV_ROOT/bin:$PATH"
eval "$(goenv init -)"
export PATH="$GOROOT/bin:$PATH"
export PATH="$PATH:$GOPATH/bin"

Removing the bottom two line solves the issue, at least it looks like solved for now. What is the correct behavior?  If these lines are not needed, then why INSTALL.md tells (and says its recommended) you to add these? @neersighted @debo
https://github.com/syndbg/goenv/blob/0269402ebf9b82031c1bf35748ba5c9b895243d0/INSTALL.md?plain=1#L40-L44

I know i'm kinda necro-bumping, but I fiddled a bit more today and ended up with this in bashrc
export GOENV_ROOT="$HOME/.goenv"
export PATH="$PATH:$GOENV_ROOT/bin"
eval "$(goenv init -)"
unset GOROOT
unset GOPATH

I'm unsetting GOROOT and GOPATH because those values are only set at init. And as I navigate through different go version enabled directories, those env variables becomes wrong, so they become a source of confusion. unsetting them solves the confusion.
As I'm not putting not putting $GOPATH/bin,$GOROOT/bin in PATH, there is no conflict. all go commands are run by goenv shims, shims set the correct GOPATH/GOROOT env just before executing.


🐞 Bug Canceling save online alert box not working as expected

Is there an existing issue for this?

[X] I have searched the existing issues

Describe the bug
If the user clicks the project menu on the navbar and click save online browser alert shows up. If the user cancel the alert, the website still takes the user to edit project detail page which should not happen.
Steps To Reproduce

Go to  home page.
Click project menu and choose save online
Cancel the browser alert (the website will take you to the project edit page)
Click the browser back button
Sometimes you will see a flash red screen for a second and then show the home page

Expected Behavior
Should not take to the project edit page if the user cancel the browser alert
Screenshots
Watch till the end, the third try, after clicking the browser back button, show a flash red screen for a second and then take me to home page.
screen-capture.webm
Device Information [optional]
- OS:
- Browser:
- version:

Additional context
No response
Are you working on this issue?
Yes

Hello there, I'd like to be assigned this issue. Thanks!

@Harsh1s are you still working on it? if not by any chance i would like to work on it.

Actually i made a PR on the frontend repo to solve this issue. Waiting for a review.


I just lose the log when i use NLog

The code is in a console application.
code is simple :
        for (int i = 0; i < 26130; i++)
        {
            NLog.LogManager.GetLogger("mylog").Debug(i.ToString());
        }

the config setting :
1.
<target name="f" xsi:type="File" fileName="${basedir}/log/${logger}/${shortdate}.log"
                  layout="${longdate} ${callsite}  ${uppercase:${level}} ${message}"  />
  </targets>

<default-wrapper xsi:type="AsyncWrapper">
      <wrapper-target xsi:type="RetryingWrapper"/>
    </default-wrapper>
    <target name="f" xsi:type="File" fileName="${basedir}/log/${logger}/${shortdate}.log"
                  layout="${longdate} ${callsite}  ${uppercase:${level}} ${message}"  />
  </targets>

There is no problem in the first ,I get all 26130 log message,with a file size:1.58MB
But in the second ,I just get a log file with the size of :687KB....
I really confused about that . Can anybody tell me why?

That is expected behaviour.  The async wrapper will discard messages (configurable) when you write faster than it can handle. Writing only log messages I a for loop is of course not a real case you would use in practice.
Please check the internal log (set internal log level on trace) and see the docs of async wrapper.

I did not expect it so. Why it can not record all the information?

Please read https://github.com/NLog/NLog/wiki/AsyncWrapper-target

Is everything clear now @a14907 ?

Yes

Yes.@304NotModified

OK, I will close this one then :)


Kill ReadGroupSet

This really should live over here instead of in https://github.com/ga4gh/server/issues/737
See also: #380
Basically, a ReadGroupSet is a BAM file, but the fact that two read groups were in the same BAM file in and of itself doesn't really mean anything, semantically. I can glom together any arbitrary combination of ReadGroups from different samples, sequencers, and aligners into a single BAM file. The BAM spec supports it just fine.
You might complain that that would be a bad idea, and that putting two read groups from different samples/sequencers/pipelines into the same BAM is going to confuse people, because they might assume that they actually did belong to one sample/sequencer technology/alignment pipeline. But if it's these pieces of metadata that are important, then that metadata is what we should use to organize our ReadGroups. Having a ReadGroupSet that exists to represent a BAM file is only a good idea if we can enforce that being in the same BAM file actually means something consistent across data sets, and that the API endpoint you happen to be hitting against today hasn't grouped all of its reads into BAM files by first letter or some other useless convention.
If the point of ReadGroupSet is to represent particular application- or data-source-specific sets of ReadGroups (i.e. document the arrangement into BAM files upon import from some other repository, where being in a BAM file means something repository-specific), we would probably want a lighter-weight, less-fundamental-to-the-whole-API representation, where a ReadGroupSet is just an assertion that this other study grouped together these ReadGroups under this external identifier, with other-study-specific semantics.

For history, it looks like @dglazer originally introduced the object that is the modern ReadGroupSet as GARun in https://github.com/ga4gh/schemas/commit/dad54b11b2e0bc30474a76447ed54a3d172e87b7

A ReadGroupSet-like concept has a long history, all the way back to the beginning of ga4gh. The central question is: do we need a concept corresponding to a BAM file? I have been swaying between having or not having this concept, largely influenced by how we implement a read server.
Nonetheless, no matter what the history of ReadGroupSet is, for our file-based reference server, ReadGroupSet is important for two reasons. Technically, random access is achieved in a BAM, not in a read group. Having ReadGroupSet is more straightforward for implementation. Secondly, submission to a read server will rely on BAM/Cram files at least for some years.

Sorry. Clicked a wrong button. Overall, my opinion is we should keep this concept.

Agreed that ReadGroupSet should not be defined as `what was in a
BAM file'.  It should have documented semantics that are useful.
We need to look at the query required to obtain the same results
from the metadata to see if it should be dropped.  However,
there is a lot built around the implied meaning of a BAM.
adamnovak<EMAIL_ADDRESS>writes:

This really should live over here instead of in ga4gh/server#737
See also: #380
Basically, a ReadGroupSet is a BAM file, but the fact that two read groups were
in the same BAM file in and of itself doesn't really mean anything,
semantically. I can glom together any arbitrary combination of ReadGroups from
different samples, sequencers, and aligners into a single BAM file. The BAM
spec supports it just fine.
You might complain that that would be a bad idea, and that putting two read
groups from different samples/sequencers/pipelines into the same BAM is going
to confuse people, because they might assume that they actually did belong to
one sample/sequencer technology/alignment pipeline. But if it's these pieces of
metadata that are important, then that metadata is what we should use to
organize our ReadGroups. Having a ReadGroupSet that exists to represent a BAM
file is only a good idea if we can enforce that being in the same BAM file
actually means something consistent across data sets, and that the API endpoint
you happen to be hitting against today hasn't grouped all of its reads into BAM
files by first letter or some other useless convention.
If the point of ReadGroupSet is to represent particular application- or
data-source-specific sets of ReadGroups (i.e. document the arrangement into BAM
files upon import from some other repository, where being in a BAM file means
something repository-specific), we would probably want a lighter-weight,
less-fundamental-to-the-whole-API representation, where a ReadGroupSet is just
an assertion that this other study grouped together these ReadGroups under this
external identifier, with other-study-specific semantics.
—
Reply to this email directly or view it on GitHub.*

I strongly agree with keeping the concept of a ReadGroupSet -- that's the
fundamental unit of most genome browsing and analysis. See
https://github.com/ga4gh/schemas/pull/52 for the original discussion on why
we introduced ReadGroupSets in the first place.
(And note that the definition of a ReadGroupSet is not tied to BAM files,
although many servers may choose to use "being in a single BAM file" as a
good hint for "belong in the same ReadGroupSet".)

I support that we should keep ReadGroupSet.
The definition for Mark is "A set of ReadGroups that a user wants to keep connected together".  We should not try to define the possible purposes - there are many and people will think of new ones.
We should not define in terms of BAMs, but it seems reasonable to me to make a ReadGroupSet by default for an imported BAM.
Richard
Sent from my iPhone

On 12 Oct 2015, at 11:43 pm, David Glazer<EMAIL_ADDRESS>wrote:
I strongly agree with keeping the concept of a ReadGroupSet -- that's the
fundamental unit of most genome browsing and analysis. See
https://github.com/ga4gh/schemas/pull/52 for the original discussion on why
we introduced ReadGroupSets in the first place.
(And note that the definition of a ReadGroupSet is not tied to BAM files,
although many servers may choose to use "being in a single BAM file" as a
good hint for "belong in the same ReadGroupSet".)
—
Reply to this email directly or view it on GitHub.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

I am fine that ReadGroupSet is not tied to BAM (I was a strong supporter of generic ReadGroupSet in that old thread), but as we are moving closer to files, now it actually makes sense to let ReadGroupSet be a BAM. If repositories freely define ReadGroupSet, one submitted BAM may be represented in different ways. This will be confusing as users may get inconsistent results for the same data – not good. The most sensible way is to match a ReadGroupSet to a submitted BAM.
I guess ReadGroupSet will be similar to the "N" cigar operator in SAM. "N" was a generic operator, not only designed for splicing (though in the first spec, we did mention that "N" can be used for splicing). With tophat adopting "N" for splicing, "N" becomes the de facto operator for splicing. ReadGroupSet will probably go into the same route as there are no better use of this object.

The flexibility of generic definition of ReadGroupSet is forward
looking and I think important to maintain.
Given that people coming to this are bioinformaticans may come
in with assumptions on current practice, it's important to explicitly.
Here is my crack at a definition:
"A set of ReadGroups that a user wants to keep connected
together.  A ReadGroup may belong to multiple ReadGroupSets.
The semantics of this grouping are not restrict and are defined
by the data set creator.
While a common usage is all of the read groups in a set belong
to the same sample library sequenced with a single technology,
the API does not require these ReadGroupSet semantics and
it should not be assumed."
Richard Durbin<EMAIL_ADDRESS>writes:

I support that we should keep ReadGroupSet.
The definition for Mark is "A set of ReadGroups that a user wants to keep
connected together". We should not try to define the possible purposes - there
are many and people will think of new ones.
We should not define in terms of BAMs, but it seems reasonable to me to make a
ReadGroupSet by default for an imported BAM.
Richard
Sent from my iPhone

On 12 Oct 2015, at 11:43 pm, David Glazer<EMAIL_ADDRESS>wrote:
I strongly agree with keeping the concept of a ReadGroupSet -- that's the
fundamental unit of most genome browsing and analysis. See
https://github.com/ga4gh/schemas/pull/52 for the original discussion on why
we introduced ReadGroupSets in the first place.
(And note that the definition of a ReadGroupSet is not tied to BAM files,
although many servers may choose to use "being in a single BAM file" as a
good hint for "belong in the same ReadGroupSet".)
—
Reply to this email directly or view it on GitHub.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
—
Reply to this email directly or view it on GitHub.*

I am happy that when you import a BAM you make a ReadGroupSet.
Equally you should be able to define a new ReadGroupSet, and export it as a BAM.
For example, at Sanger we might start with a BAM with all the readgroups from a lane, which we might use for
some lane-based QC, then split into “lanelet” BAMs with individual readgroups, then merge lanelets that pass
QC into sample BAMs, then perhaps merge again into multi-sample BAMs.  Some of these might be transient
or even virtual.  Each of these, except for the individual readgroup lanelet one, could be a valid ReadGroupSet.
I would add to Mark’s documentation that if you import a BAM then you create a ReadSetGroup for it, and if you
want to export a BAM you make a ReadSetGroup for it.
Richard

On 13 Oct 2015, at 12:34, Heng Li<EMAIL_ADDRESS>wrote:
I am fine that ReadGroupSet is not tied to BAM (I was a strong supporter of generic ReadGroupSet in that old thread), but as we are moving closer to files, now it actually makes sense to let ReadGroupSet be a BAM. If repositories freely define ReadGroupSet, one submitted BAM may be represented in different ways. This will be confusing as users may get inconsistent results for the same data – not good. The most sensible way is to match a ReadGroupSet to a submitted BAM.
I guess ReadGroupSet will be similar to the "N" cigar operator in SAM. "N" was a generic operator, not only designed for splicing (though in the first spec, we did mention that "N" can be used for splicing). With tophat adopting "N" for splicing, "N" becomes the de facto operator for splicing. ReadGroupSet will probably go into the same route as there are no better use of this object.
—
Reply to this email directly or view it on GitHub https://github.com/ga4gh/schemas/issues/437#issuecomment-147690017.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

A data management issue that we are solving by removing the "BAM
is a ReadGroupSet" restriction has to with with BAM top-up.
The Broad's sequencing pipeline is based on making the best use
of their capacity with conflicting demands.  Lanes maybe
allocated to a given sample library over multiple runs.
Sometimes they are done months apart.
For TCGA, BAMs would be release for analysis when sufficient
read groups were ready.  Sometime latter, more read groups would
be sequenced.  The single-BAM assumptions of many of the tools
necessitated create a new BAM with both the old and read groups.
Sometimes the old BAM was suppressed, although if publications
were done using the old BAM, it was kept live.
This both consumed a significant amount of storage, it also cause
a great amount of confusion for users.
This is a use case were one would have a multiple ReadGroupSets
sharing ReadGroups and not having a one-to-one correspondence
with the original BAMs.
Richard Durbin<EMAIL_ADDRESS>writes:

I am happy that when you import a BAM you make a ReadGroupSet.
Equally you should be able to define a new ReadGroupSet, and export it as a
BAM.
For example, at Sanger we might start with a BAM with all the readgroups from a
lane, which we might use for
some lane-based QC, then split into “lanelet” BAMs with individual readgroups,
then merge lanelets that pass
QC into sample BAMs, then perhaps merge again into multi-sample BAMs. Some of
these might be transient
or even virtual. Each of these, except for the individual readgroup lanelet
one, could be a valid ReadGroupSet.
I would add to Mark’s documentation that if you import a BAM then you create a
ReadSetGroup for it, and if you
want to export a BAM you make a ReadSetGroup for it.
Richard

On 13 Oct 2015, at 12:34, Heng Li<EMAIL_ADDRESS>wrote:
I am fine that ReadGroupSet is not tied to BAM (I was a strong supporter of
generic ReadGroupSet in that old thread), but as we are moving closer to files,
now it actually makes sense to let ReadGroupSet be a BAM. If repositories
freely define ReadGroupSet, one submitted BAM may be represented in different
ways. This will be confusing as users may get inconsistent results for the same
data – not good. The most sensible way is to match a ReadGroupSet to a
submitted BAM.
I guess ReadGroupSet will be similar to the "N" cigar operator in SAM. "N"
was a generic operator, not only designed for splicing (though in the first
spec, we did mention that "N" can be used for splicing). With tophat adopting
"N" for splicing, "N" becomes the de facto operator for splicing. ReadGroupSet
will probably go into the same route as there are no better use of this object.
—
Reply to this email directly or view it on GitHub <https://github.com/ga4gh/
schemas/issues/437#issuecomment-147690017>.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
—
Reply to this email directly or view it on GitHub.*

So it sounds to me like there's consensus around:

Keeping ReadGroupSet around.
Divorcing ReadGroupSet from BAM files, and making it more obvious that it can and should be used for other kinds of read group grouping.

We already have a many-to-many ReadGroup/ReadGroupSet relationship, although I'm not sure we've implemented it in the reference server. We have a constraint that all the ReadGroups in a ReadGroupSet be aligned to the same ReferenceSet, but maybe we should drop that.
I would propose a PR adding in @diekhans 's description, and adding in a way to annotate ReadGroupSets with information about what they're being used for. We could add a type field, and fill it variously with something like "BAMFile", "SingleSample", "SingleSequencerRun", "ReadGroupsIAmInterestedIn", "Other", and so on. On the one hand we need to handle arbitrary kinds of ReadGroupSets, but on the other if a ReadGroupSet does correspond to a BAM file or a sample or something, that information should be machine-readable. Right?

A data management issue that we are solving by removing the "BAM
is a ReadGroupSet" restriction has to with with BAM top-up.

Divorcing ReadGroupSet from BAM files, and making it more obvious that it can and should be used for other kinds of read group grouping.

Are you all talking about the API or the reference server implementation? I don't think there is any language in the schemas repo which says ReadGroupSet == BAM file, but if there is I definitely agree that it should be removed.

We have a constraint that all the ReadGroups in a ReadGroupSet be aligned to the same ReferenceSet, but maybe we should drop that.

I disagree, but I'm also not seeing the motivation for that proposal.

Two questions:

What is the use case of many-to-many ReadGroupSet<=>ReadGroup relationship? Is anyone using that?

For one submitted BAM, if one repo keeps it in one ReadGroupSet, but another repo keeps it in two ReadGroupSets, users will get different results with the same set of queries. Dose it hurt interop?

The documentation is not clear on the relationship with read
groups and BAMs.  It kind of hints as a mapping, but isn't very
explicit:
"A ReadGroupSet is a collection of ReadGroups. If read
groups are equivalent to SAM files, then a read group set can be
a collection of SAM files that were generated from a single
sequencing run.  All read groups in the set are required to map
to the same referenceSet."
We are wanting contributors to step up and improve the specification
in the documentation branch and make it rigorous.
The naming of ReadGroup* is a bit misleading, as read groups
exist independent of a reference.  A far clearer name would be
AlignedReadGroup.
CH Albach<EMAIL_ADDRESS>writes:

A data management issue that we are solving by removing the "BAM
is a ReadGroupSet" restriction has to with with BAM top-up.

Divorcing ReadGroupSet from BAM files, and making it more obvious that it
can and should be used for other kinds of read group grouping.

Are you all talking about the API or the reference server implementation? I
don't think there is any language in the schemas repo which says ReadGroupSet =
= BAM file, but if there is I definitely agree that it should be removed.
We have a constraint that all the ReadGroups in a ReadGroupSet be aligned
to the same ReferenceSet, but maybe we should drop that.

I disagree, but I'm also not seeing the motivation for that proposal.
—
Reply to this email directly or view it on GitHub.*

See my mail on the Broad sequencing pipeline.  Many to many
ReadGroupSet<=>ReadGroup is an important use case.

ReadGroupSet for a given data set must be defined
consistently across servers or it will not be interoperable.
This needs to be independent of who BAMs are submitted..
Data interoperability is even a harder problem than API
interoperability.

Heng Li<EMAIL_ADDRESS>writes:

What is the use case of many-to-many ReadGroupSet<=>ReadGroup relationship?
Is anyone using that?

For one submitted BAM, if one repo keeps it in one ReadGroupSet, but
another repo keeps it in two ReadGroupSets, users will get different
results with the same set of queries. Dose it hurt interop?

—
Reply to this email directly or view it on GitHub.*

I think we should keep that all ReadGroups in a ReadGroupSet must be aligned to the same ReadGroupSet.
Richard
Sent from my iPhone

On 13 Oct 2015, at 12:38 pm, adamnovak<EMAIL_ADDRESS>wrote:
So it sounds to me like there's consensus around:
Keeping ReadGroupSet around.
Divorcing ReadGroupSet from BAM files, and making it more obvious that it can and should be used for other kinds of read group grouping.
We already have a many-to-many ReadGroup/ReadGroupSet relationship, although I'm not sure we've implemented it in the reference server. We have a constraint that all the ReadGroups in a ReadGroupSet be aligned to the same ReferenceSet, but maybe we should drop that.
I would propose a PR adding in @diekhans 's description, and adding in a way to annotate ReadGroupSets with information about what they're being used for. We could add a type field, and fill it variously with something like "BAMFile", "SingleSample", "SingleSequencerRun", "ReadGroupsIAmInterestedIn", "Other", and so on. On the one hand we need to handle arbitrary kinds of ReadGroupSets, but on the other if a ReadGroupSet does correspond to a BAM file or a sample or something, that information should be machine-readable. Right?
—
Reply to this email directly or view it on GitHub.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

@diekhans  We are talking about the final product, not intermediate data processing. At broad, we only have one set of BAMs. BAMs don't have a many-to-many relationship.

@lh3 I am talking about the final BAMs releases for public
analysis by Broad for TCGA.  They incremental released updated
BAMs with new read groups.  They initially wanted to suppress
the old versions of the BAMs.  That proved problematic when
papers were publish against the old version.
I can introduce you to the former head of the Broad group
handling TCGA, who is now at NY Genome Center.
Heng Li<EMAIL_ADDRESS>writes:

@diekhans We are talking about the final product, not intermediate data
processing. At broad, we only have one set of BAMs. BAMs don't have a
many-to-many relationship.
—
Reply to this email directly or view it on GitHub.*

1000g also have three versions: pilot, phase1 and phase3. They are separate datasets or different versions of one dataset. We wouldn't want to mix all three versions at the same time. In one version of a dataset, BAMs and read groups have a one-to-many relationship.

Absolutely, it is versioning, but it's data should be able to
represent.  TCGA is an important use case.
What is the issues with having ReadGroups in multiple
ReadGroupsSets?  Users should not just naively select all
ReadGroupsSets for analysis.
Heng Li<EMAIL_ADDRESS>writes:

That is versioning, which is different. For each version, we only have one set
of BAMs. Users would not want to interact with all versions at the same time.
—
Reply to this email directly or view it on GitHub.*

Hi @lh3, you are assuming semantics for dataset that are not
defined.
With this model, every BAM in TCGA would have to be it's own
dataset, as the BAMs we updated independently and in unpredictable
pattern.
I think it's a mistake define `what to analyze together', which
I think is what you are suggesting, statically as DataSet,
rather than dynamically through queries.
Heng Li<EMAIL_ADDRESS>writes:

1000g also have three versions: pilot, phase1 and phase3. They are separate
datasets or different versions of one dataset. We wouldn't want to mix all
three versions at the same time. In one version of a dataset, BAMs and read
groups have a one-to-many relationship.
—
Reply to this email directly or view it on GitHub.*

Ok. This winds back to Dataset. It will be a mess if we put SGDP and 1000g (both fully public) in one dataset, or put two freezes of 1000g in one dataset, or put 1000g whole-genome and exome data in one dataset. There are logical constraints on Datasets, not just permission. Anyway, as this issue depends on Dataset, I have no comments to add. Overall, I put -1 on this issue, but this -1 is for a different reason from others'.

BAMs may not have a many to many relationship at Broad, but I believe that is because of Broad not wanting to duplicate data.
If they can be virtual, as they are in the schema, then I think there are good reasons to deal with a ReadGroup being in multiple
ReadGroupSets, and we should allow it.  I don’t see any reason why not to.
Richard

On 13 Oct 2015, at 19:16, Heng Li<EMAIL_ADDRESS>wrote:
@diekhans https://github.com/diekhans We are talking about the final product, not intermediate data processing. At broad, we only have one set of BAMs. BAMs don't have a many-to-many relationship.
—
Reply to this email directly or view it on GitHub https://github.com/ga4gh/schemas/issues/437#issuecomment-147800488.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

thanks @lh3, you are point out the semantics and use cases are
weakly defined.
I would not have consider it wrong to mix whole-genome and exome
in a data set.  Without clear definition, we will go in circles
;-)
Heng Li<EMAIL_ADDRESS>writes:

Ok. This winds back to Dataset. It will be a mess if we put SGDP and 1000g
(both fully public) in one dataset, or put two freezes of 1000g in one dataset,
or put 1000g whole-genome and exome data in one dataset. There are logical
constraints on Datasets, not just permission. Anyway, as this issue depends on
Dataset, I have no comments to add. Overall, I put -1 on this issue, but this
-1 is for a different reason from others'.
—
Reply to this email directly or view it on GitHub.*

I think the (clear) consensus here is that we should keep ReadGroupSet; can we close this issue?

+1 on close it
Documenting exact semantics of ReadGroupSet is already covered
by documentation tickets.
Jerome Kelleher<EMAIL_ADDRESS>writes:

I think the (clear) consensus here is that we should keep ReadGroupSet; can we
close this issue?
—
Reply to this email directly or view it on GitHub.*

I'm going to close this, and hopefully come back with a PR including some of Mark's language (if we don't have one already).

Please fork the documentation branch for the PR and pull against
it.  There are fix me comments in ReadGroupSet.  Our
bioinformatican who did the first pass over the doc found it
very confusing.
adamnovak<EMAIL_ADDRESS>writes:

I'm going to close this, and hopefully come back with a PR including some of
Mark's language (if we don't have one already).
—
Reply to this email directly or view it on GitHub.*


Bug 2119615: The unit field doesn't change if the size number is big enough in Disk modal

Signed-off-by: Dana Orr<EMAIL_ADDRESS>
📝 Description
🎥 Demo
Before:

After:

/lgtm


feat: add quic client class

Pull Request Checklist
Please check if your pull request fulfills the following requirements:

[x] The commit message follows our guidelines: https://gitlab.playpod.ir/alpha/backend/server-services-next/-/blob/main/CONTRIBUTING.md#commit-message-format
[x] Tests for the changes have been added / updated (for feat / fix / refactor)
[x] Docs for the changes have been added / updated (for feat / fix / refactor)

Pull Request Type
What kind of change does this pull request introduce?

[ ] Build: Changes that affect the build system or external dependencies
[ ] CD: Changes to our CD configuration files and scripts
[ ] CI: Changes to our CI configuration files and scripts
[ ] Docs: Documentation only changes
[x] Feat: A new feature
[ ] Fix: A bug fix
[ ] Perf: A code change that improves performance
[ ] Refactor: A code change that neither fixes a bug nor adds a feature
[ ] Test: Adding missing tests or correcting existing tests

What is the current behavior?

Issue #484
What is the new behavior?

simplified making a client with a helper class named w_quic_client.

Does this Pull Request introduce a breaking change?

[ ] Yes
[x] No

Other information
Closes #484

@cthulhu-irl  thank you


Expression parser for parameters

Summary
close #2348
Details and comments
AST based parser is implemented under qiskit.tools. This parser accepts limited operators (+, -, *, /, **) and limited functions (defined under cmath). And the parser returns a tuple of expression (callable) and list of parameter names. This parser has no dependency on python evaluation function.
expr = '-P1*cos(P2)'
parsed_expr, params = parse_string_expr(expr)

value = parsed_expr(P1=1.0, P2=2.0)

@taalexander thank you for reviewing! Creating a grammar for arithmetic expresions may introduce additional dependency, so I prefer ast. In e5f90c7fc33d3ac3387ca0177c80aaa048ae6ba0, I replaced recursive call of _visit_node by ast.NodeTransformer. The main reasons of this are:

Could the params now be parsed as part of the AST? https://github.com/Qiskit/qiskit-terra/pull/2493#discussion_r287603348

Now params are parsed by AST as well. Arbitrary names for parameter are accepted. This is for parsing circuit parameters - such as theta, nu, etc...

They should support partial binding, provide a reasonably display of their operations and parameters when included in a printed circuit https://github.com/Qiskit/qiskit-terra/issues/2375#issue-442228477

QiskitExpression inheriting from NodeTransformer returns float or complex when all parameters are bound, otherwise it returns ast. NodeTransformer overwrite a node by ast.Num if parameters in its child nodes are bound.
parse_string_expr returns tuple of QiskitExpression and list of parameter names.
We can get Expression as follows
expr = '-P1*cos(P2)'
expression, params = parse_string_expr(expr)

value = expression(P1=1.0, P2=2.0)

Also we can specify partial biding
node = expression(P1=1.0, allow_partial_bind=True)

This returns partially evaluated abstract syntax tree.

After looking through the parameter expression I think it should still be possible to integrate with the ParameterExpression. We do not need to support the entire list of built-ins as is currently done (pulse doesn't actually use these right now, most expressions are of the form 2*np.pi*P1. If you were to define an expression ops module or something like this, we could then use this as the set of supported operations and as the AST is parsed, the expression could be dynamically built.

I moved parser under qiskit.pulse and changed its name from QiskitExpression to PulseExpression.
This parser receives an expression in str format (from backend), and I can see some differences in the format of expression from #2537 . @kdk is it difficult to define expressions in str format?
@taalexander for partial biding, functools.partial is returned instead of AST. but it is difficult to define params by args now. I propose to delete *args from arguments of parser and leave only **kwargs to remove ambiguity.
expr = 'P1+P2+P3'
expression, params = parse_string_expr(expr, partial_binding=True)

example:
expr = expression(P1=1.0, P2=2.0)
value = expr(P3=3.0)

it works (returns 6.0).
expr = expression(1.0, 2.0)
value = expr(P3=3.0)

it works (returns 6.0).
expr = expression(P1=1.0, P2=2.0)
value = expr(3.0)

it overwrites P1 and returns functools.partial (because P3 is not defined).


Add enmity

I'm not a developer of enmity, but their official AltStore source is outdated and invalid so I made a cloudflare worker that fetches the latest Enmity release from their github and turns it into an AltStore source.

We like that people are coming to help out on our community App Store in its infancy, but
since this provides the discord ipa with the source, we aren’t comfortable distributing it in our store as it provides the discord ipa.
We could reconsider a later date and maybe in the future we will implement a method for patching apps via the source. Sorry for the inconvenience for the moment.

@Spidy123222 We refuse to host that, yes, but just like "archived" apps section, we could put it in our trusted sources meaning "this works as we've tested it" but we won't host it, it'll be up to that user's country and discretion. I don't think by doing adding it to trusted sources, we'd be breaking anything unless the rest of the team disagrees?
@staticallyamazing What is the URL for your automatic CloudFlare Enmity source?

https://enmity-altstore.staticallyamazing.workers.dev/
the dev app is broken since the bundle ids don't match. might make a separate source for that. i don't have much time to maintain it but i could put the code on github.

Thanks @staticallyamazing - I saved this issue to come back later and think of the best way to handle this.


metric_score function should require pos_label value passed in

When I test Basics tutorial case, realize metric value reported by "score" function is not right. precision_score, recall_score and f1_score functions have "pos_label" argument set to 1 by default. In this case, labels passed in score function are composite of 1 and 2. pos_label should be set to 2 in this case. Otherwise, metric is calculated by mistake.
Regarding to MajorityLabelVoter, predict_prob could be sum(label_function_output) / total_label_function_count. This will generate probabilistic label. If k = 2, it could be continuous value in the range of [0, 1] instead of 0 or 1. This is to compare against Metal predict_prob values if draw AUC curves. Rank over labels are more useful than a single set of precision/recall/f1 score which assume a hard threshold of probability (it's 0.5 when k = 2).

Hi @ljx1110 ,
I'm not sure I totally understand the issue?  First of all, what do you mean by "composite of 1 and 2"?  Perhaps you could show me an example where you think the score is off?  You can always change pos_label if you want to have 1 mean positive and 2 mean negative, if that's the issue?  Otherwise I think the score function should be working fine
As for MajorityLabelVoter, we don't output probabilistic labels here- the full probability mass is put on the majority label (as per the docstring).  Overall however, we could definitely add in other metric reports like AUC curves and rank-based metrics for higher cardinality settings!

Hi Alex,
Sorry for the confusion. Let me clarify.
When we test Snorkel, our LF output is -1, 0 and 1. In our earlier discussion. To use Metal, I need to transit LF output from -1 -> 1 and 1 -> 2 . So, "1" means negative and "2" means positive.
In metric_score function, it doesn't pass in pos_label value. predict_score/recall_score/f1_score are always using default pos_label value as 1. In Basics case in tutorial, Ls[1] and Ys[1] are 1s and 2s. You assume 1 as pos_label, right?
label_model.score(Ls[1], Ys[1], metric=['precision', 'recall', 'f1']) ->
metric_score(Y, Y_p, metric, ignore_in_gold=[0]) ->
precision_score(gold, pred, pos_label=1, ignore_in_gold=[], ignore_in_pred=[])
I did manually set pos_label value to 2 for each metric function in our case.
What I mean is "score" function doesn't have pos_label variable exposed in the interface. It may be more convenient to add it and allow user to adjust it.
Please let me know if my understanding is wrong.

Just corroborating that I also had to write a method to translate labels to Metal language (1 for pos / 2 for neg) for my experiments and would be nice to avoid doing that

Active development is being moved to our main repo, https://github.com/snorkel-team/snorkel, where we use a different labeling convention (-1 for abstain, and 0...k-1 for actual labels).


webpack-dev-server/client is loaded twice

Version
4.1.1
Environment info
$ vue info

Environment Info:

  System:
    OS: Windows 10 10.0.18362
    CPU: (12) x64 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz
  Binaries:
    Node: 10.16.0 - C:\Program Files\nodejs\node.EXE
    Yarn: 1.21.0 - ~\AppData\Roaming\npm\yarn.CMD
    npm: 6.10.3 - C:\Program Files\nodejs\npm.CMD
  Browsers:
    Edge: 44.18362.449.0
  npmPackages:
    @vue/babel-helper-vue-jsx-merge-props:  1.0.0
    @vue/babel-plugin-transform-vue-jsx:  1.1.2
    @vue/babel-preset-app:  4.1.1
    @vue/babel-preset-jsx:  1.1.2
    @vue/babel-sugar-functional-vue:  1.1.2
    @vue/babel-sugar-inject-h:  1.1.2
    @vue/babel-sugar-v-model:  1.1.2
    @vue/babel-sugar-v-on:  1.1.2
    @vue/cli-overlay:  4.1.1
    @vue/cli-plugin-babel: ^4.1.0 => 4.1.1
    @vue/cli-plugin-eslint: ^4.1.0 => 4.1.1
    @vue/cli-plugin-router:  4.1.1
    @vue/cli-plugin-vuex:  4.1.1
    @vue/cli-service: ^4.1.0 => 4.1.1
    @vue/cli-shared-utils:  4.1.1
    @vue/component-compiler-utils:  3.1.0
    @vue/preload-webpack-plugin:  1.1.1
    @vue/web-component-wrapper:  1.2.0
    eslint-plugin-vue: ^5.0.0 => 5.2.3
    vue: ^2.6.10 => 2.6.10
    vue-eslint-parser:  5.0.0
    vue-hot-reload-api:  2.3.4
    vue-loader:  15.7.2
    vue-style-loader:  4.1.2
    vue-template-compiler: ^2.6.10 => 2.6.10
    vue-template-es2015-compiler:  1.9.1
  npmGlobalPackages:
    @vue/cli: (Not Found) 4.1.1

Steps to reproduce
Create a new Vue app using vue create, start it using yarn serve and open it in the browser.
What is expected?
webpack-dev-server/client is loaded once.
What is actually happening?
webpack-dev-server/client is loaded twice.
Details
As you can see in the screenshot below, sockjs-node/info is loaded twice, and there are two opened websocket connections, one from localhost and the other from the machine's IP <IP_ADDRESS>:

Looking at the generated bundle app.js, we can see that webpack-dev-server/client is loaded twice:
// http://localhost:8080/js/app.js
// ...
__webpack_require__(/*! D:\work\cs-vue-cli-4\node_modules\webpack-dev-server\client\index.js?http://localhost */"./node_modules/webpack-dev-server/client/index.js?http://localhost");
__webpack_require__(/*! D:\work\cs-vue-cli-4\node_modules\webpack\hot\dev-server.js */"./node_modules/webpack/hot/dev-server.js");
__webpack_require__(/*! D:\work\cs-vue-cli-4\node_modules\webpack-dev-server\client\index.js?http://<IP_ADDRESS>:8080/sockjs-node */"./node_modules/webpack-dev-server/client/index.js?http://<IP_ADDRESS>:8080/sockjs-node");
module.exports = __webpack_require__(/*! ./src/main.js */"./src/main.js");
// ...

Investigation
One of the clients - the second, webpack-dev-server/client/index.js?http://<IP_ADDRESS>:8080/sockjs-node - is added by vue-cli-service's serve command here: https://github.com/vuejs/vue-cli/blob/02f2436bdb44a435122e0de4b3924199b475983e/packages/%40vue/cli-service/lib/commands/serve.js#L145 so the question is, where is the first one webpack-dev-server/client/index.js?http://localhost coming from? My first guess was that it was automatically added by webpack-dev-server; indeed, going through the docs, I found the injectClient configuration option that specifies whether the dev server should inject the client or not. The weird thing is that the docs say the default value is false?!, but let's see what happens if we explicitly set it to false. So I added this to vue.config.js
// vue.config.js
module.exports = {
  devServer: {
    injectClient: false
  }
}

restarted yarn serve, and, lo and behold, the client is now only loaded once!

// http://localhost:8080/js/app.js
// ...
__webpack_require__(/*! D:\work\cs-vue-cli-4\node_modules\webpack\hot\dev-server.js */"./node_modules/webpack/hot/dev-server.js");
__webpack_require__(/*! D:\work\cs-vue-cli-4\node_modules\webpack-dev-server\client\index.js?http://<IP_ADDRESS>:8080/sockjs-node */"./node_modules/webpack-dev-server/client/index.js?http://<IP_ADDRESS>:8080/sockjs-node");
module.exports = __webpack_require__(/*! ./src/main.js */"./src/main.js");
// ...

My guess is that if hot is set to true https://github.com/vuejs/vue-cli/blob/02f2436bdb44a435122e0de4b3924199b475983e/packages/%40vue/cli-service/lib/commands/serve.js#L173 the dev server also sets injectClient to true by default.
Workaround
Set devServer.injectClient to false in vue.config.js:
// vue.config.js
module.exports = {
  devServer: {
    injectClient: false
  }
}

Fix
(assuming this is considered a bug)
Explicitly set injectClient to false in the WebpackDevServer options https://github.com/vuejs/vue-cli/blob/02f2436bdb44a435122e0de4b3924199b475983e/packages/%40vue/cli-service/lib/commands/serve.js#L164-L166

I'll make a PR this weekend.

If you confirmed this I can also make the PR. 🙂

Sure, go ahead


Add margin to shutting down dask workers to enable clean exit and reduce thrash

We are getting some dask thrashing because workers are being terminated by LSF before they have a chance to complete their data transfer to the scheduler, we are adding a 10m margin as the docking seems to be done nogil, and can take a while to spin down.

Codecov Report

Merging #573 (5e447aa) into main (d51307b) will increase coverage by 24.28%.
The diff coverage is n/a.

Additional details and impacted files


Require Python version >= 3.8

I would suggest to drop support for Python 3.7. It is end-of-life since yesterday and wasn't tested in CI anyway. If you feel like we should not require 3.8+, feel free to close the PR.
Again, the diff view from GH shows spurious changes. Seems to be an issue with mdx?

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint.


Add minimum step size property to adjustable objects (Like sliders)

Is your feature request related to a problem? Please describe.
if you have big fingers like me setting a exact number is difficult with steps this would be easier.
Describe the solution you'd like
a settable property for adjustable objects so you can set steps between min and max.
i am setting set-points for my lights inside HA to input_number sensors these have this minimum step size (5) but openhasp ignores them and sets numbers of 1

LVGL doesn't have a step parameter for sliders, but I think the same result can be achieved by multiplying / dividing the value by 5.
See the Thermostat example where this method is used to get 0.1 increments instead of 1. You could use the same logic to increase the increments to 5 in your application.


🐛 Bug Report: 401 Unauthorized Kubernetes Plugin

📜 Description
I am configuring the Kubernetes plugin (https://backstage.io/docs/features/kubernetes/). When I access the component in Backstage, the system shows the error below:
Errors: Request failed with 401 Unauthorized, {"error":{"name":"AuthenticationError","message":"Cannot read properties of undefined (reading 'getBaseUrl')","stack":"AuthenticationError: Cannot read properties of undefined (reading 'getBaseUrl')\n at DefaultIdentityClient.getIdentity (/Users/backstage/node_modules/@backstage/plugin-auth-node/src/identity/DefaultIdentityClient.ts:90:13)\n at AuthCompat.authenticate ( /Users/backstage/node_modules/@backstage/backend-common/src/auth/createLegacyAuthAdapters.ts:89:24)\n at HttpAuthCompat.credentials (/Users/backstage/node_modules/@backstage/backend-common/src/auth /createLegacyAuthAdapters.ts:218:25)\n at <anonymous> (/Users/backstage/node_modules/@backstage/plugin-kubernetes-backend/src/service/KubernetesBuilder.ts:403:27)"},"request" :{"method":"GET","url":"/api/kubernetes/clusters"},"response":{"statusCode":401}}

👍 Expected behavior
List cluster and pod details as per documentation
👎 Actual Behavior with Screenshots

👟 Reproduction steps

Install de plugin

kubectl create clusterrolebinding backstage-ingestion --clusterrole=cluster-admin --serviceaccount=kube-system:backstage-ingestion
kubectl apply -f - <<EOF
apiVersion: v1
kind: Secret
metadata:
  name: backstage-ingestion
  namespace: kube-system
  annotations:
    kubernetes.io/service-account.name: backstage-ingestion
type: kubernetes.io/service-account-token
EOF

---
apiVersion: v1
kind: ServiceAccount
metadata:
  name: backstage-service-account
  namespace: backstage
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRoleBinding
metadata:
  name: backstage-cluster-ro
subjects:
- namespace: backstage
  kind: ServiceAccount
  name: backstage-service-account
roleRef:
  apiGroup: rbac.authorization.k8s.io
  kind: ClusterRole
  name: system:aggregate-to-view
---
apiVersion: v1
kind: Secret
metadata:
  name: eks-secrets
  namespace: backstage
type: Opaque
data:
  SA_TOKEN: ${SA_TOKEN} #base64
  CA_DATA: ${CA_DATA} #base64

integrations:
  aws:
    mainAccount:
    accounts:
    - accountId: ${AWS_ACCOUNT_ID}
      accessKeyId: ${AWS_ACCESS_KEY_ID}
      secretAccessKey: ${AWS_SECRET_ACCESS_KEY}
      region: ${AWS_REGION}

 kubernetes:
  serviceLocatorMethod:
    type: 'multiTenant'
  clusterLocatorMethods:
    - type: 'config'
      clusters:
        - name: 'eks-production'
          url: https://${APISERVER_ENDPOINT}.gr7.${AWS_REGION}.eks.amazonaws.com
          authProvider: 'serviceAccount'
          serviceAccountToken: ${SA_TOKEN}
          caData: ${CA_DATA}
          skipMetricsLookup: true
          skipTLSVerify: false

I had try with AWS Access Key and Assume Role, but all the options returning the same error message.
📃 Provide the context for the Bug.
No response
🖥 Your Environment
No response
👀 Have you spent some time to check if this bug has been raised before?

[X] I checked and didn't find similar issue

🏢 Have you read the Code of Conduct?

[X] I have read the Code of Conduct

Are you willing to submit PR?
None

What's the contents of packages/backend/src/plugins/kubernetes.ts? I think that you'll need to pass in a discoveryApi to the createRouter method if you're using the old backend system still.

I added the newly required discovery api
import { CatalogClient } from '@backstage/catalog-client';
import { KubernetesBuilder } from '@backstage/plugin-kubernetes-backend';
import { Router } from 'express';
import { PluginEnvironment } from '../types';

export default async function createPlugin(
  env: PluginEnvironment,
): Promise<Router> {
  const catalogApi = new CatalogClient({ discoveryApi: env.discovery });
  const builder = await KubernetesBuilder.createBuilder({
    logger: env.logger,
    config: env.config,
    catalogApi,
    permissions: env.permissions,
    discovery: env.discovery,
  });
  const { router } = await builder.build();
  return router;
}

What's the contents of packages/backend/src/plugins/kubernetes.ts? I think that you'll need to pass in a discoveryApi to the createRouter method if you're using the old backend system still.

The is this:
import { KubernetesBuilder } from '@backstage/plugin-kubernetes-backend';
import { Router } from 'express';
import { PluginEnvironment } from '../types';
import { CatalogClient } from '@backstage/catalog-client';

export default async function createPlugin(
  env: PluginEnvironment,
): Promise<Router> {
  const catalogApi = new CatalogClient({ discoveryApi: env.discovery });
  const { router } = await KubernetesBuilder.createBuilder({
    logger: env.logger,
    config: env.config,
    catalogApi,
    permissions: env.permissions,
  }).build();
  return router;
}

https://backstage.io/docs/features/kubernetes/installation

Ah, you'll need to pass in discovery into the createBuilder. Do you want to raise a contribution to fix the docs? :pray:
import { KubernetesBuilder } from '@backstage/plugin-kubernetes-backend';
import { Router } from 'express';
import { PluginEnvironment } from '../types';
import { CatalogClient } from '@backstage/catalog-client';

export default async function createPlugin(
  env: PluginEnvironment,
): Promise<Router> {
  const catalogApi = new CatalogClient({ discoveryApi: env.discovery });
  const { router } = await KubernetesBuilder.createBuilder({
    logger: env.logger,
    config: env.config,
    catalogApi,
    discovery: env.discovery,
    permissions: env.permissions,
  }).build();
  return router;
}

Thanks @benjdlambert. I opened the PR to Backstage to fix the documentation
https://github.com/backstage/backstage/pull/23944

The mentioned PR is merged by now - is this issue fixed for you, @echalegre? :)

Yes. And I created a PR to fix the documentation too.

Nice! Feel free to link the PR with the documentation. I will close this issue now as it seems to be resolved.


Emphasize that odo is used for development not production

/kind docs

What mistake did you find / what is missing in the documentation?
Current we have:
OpenShift Do (odo) is a fast, iterative, and straightforward CLI tool for developers who write, build, and deploy applications on OpenShift.

Existing tools such as oc are more operations-focused and require a deep-understanding of Kubernetes and OpenShift concepts. odo abstracts away complex Kubernetes and OpenShift concepts for the developer, thus allowing developers to focus on what is most important to them: code.

We should elaborate on this and explain to the user that odo is meant for development and not production. We don't actually "deploy" applications to OpenShift, but rather write and build them.
Two action items:

An emphasis that it's meant for development use ONLY and we (potentially) have plans to deploy to production (whether that's knative, or something else, who knows).
Documentation on how to go from development (using odo) to using oc / deploying to production.

What is the relevance of it?
Elaborating on the basic functionality of odo and being more clear.

this should be higher up :)
odo -> a tool for devs to have standardised container test environment.
My naive question is -> what next? After the app is built, tested in containers, is it green to go to production off containers?

Needs docs

@pmacko1 Yeah, there is no "next step" solution after odo since we focus on just the "inner loop" process at the moment. We need to emphasize that odo is currently for development only and that current outer-loop solutions are in development.


RFP - openttd

Checklist

[x] The package I am requesting does not already exist on https://community.chocolatey.org/packages;
[x] There is no open issue for this package;
[x] The issue title starts with 'RFP - ';
[x] The download URL is public and not locked behind a paywall / login;

Package Details
Software project URL : https://www.openttd.org/
Direct download URL for the software / installer : https://cdn.openttd.org/openttd-releases/12.2/openttd-12.2-windows-win64.exe
Software summary / short description: OpenTTD is an open source simulation game based upon Transport Tycoon Deluxe

I searched the repo twice and that did not come up, closing my request, sorry for the thrash.


[Feature request] How to pass command line arguments to jupyter command

Hi everyone!
I use container for everything, so whenever I have to run a jupyter server with the following command line argument, exposing the ports accordingly :
--ip <IP_ADDRESS>

I try to use the Ijulia.notebook_cmd but it is not in the scope.
Any help?
Or feature request to have a string field to call:
notebook(cmd="--h")

Thanks

bump,
really need port and --no-browser


fix(inx): remove startup checks and revert influx update that breaks analytics

Description
This PR removes the unnecessary checks at startup that verify the protocol parameters. This behavior was also causing an issue where a protocol update would break Chronicle if the network name changed and Chronicle was restarted before it reached the milestone with the new params.
Notes to Reviewer

As a reviewer, please pay particular attention to the following areas when reviewing this PR and tick the above boxes after you have completed the steps.
INX Changes

[ ] Run chronicle using an INX connection.

I think we shouldn't remove the protocol parameter's check, because it's conceivable that a user accidentally connects Chronicle to a different node running in a different network, and then this would corrupt the database. Most users won't have the knowledge to fix the database after this, and switching to a new network name while keeping the previous data is not a standart/normal use-case.


Doesn't cast shadows on other objects

Nothing happens after enabling shadows from a light source.

Can you elaborate, maybe upload a project that reproduces the error? Also, which Godot version are you on?
Shadows seem to be working fine for me.

It's version 3.3.2.
Objects on the editor have default materials, and they're replaced with others that contain the shader when I run the game: https://youtu.be/IWvcZHnoDjo

Thanks!
I cannot repoduce the issue. I'm using this script
extends MeshInstance

const TOON_MATERIAL = preload("res://addons/flexible_toon_shader/FlexibleToonMaterial.tres")

func _ready():
	set_surface_material(0, TOON_MATERIAL.duplicate())

to dynamically assign the material to a MeshInstance. This is the result:

Can you make sure that use_albedo is true in the shader params of your material?

Oh it's very interesting that you say that since I have observed something similar for an unrelated project of mine. I thought it was just a mistake I made back then. I don't think the problem you're having is related to the toon material at all but is probably an issue with Godot itself.
If you can confirm that the issue persists with the built-in Godot materials as well, I'll close this issue and you should probably raise it in the main Godot repo.

I made a typo... I meant Camera in the Viewport, not a Mesh.

Yes, I get the same bug with Godot's default material.
Again I'm not using Godot's latest release so I'm unaware if it was fixed at some point.

Oh it's very interesting that you say that since I have observed something similar for an unrelated project of mine. I thought it was just a mistake I made back then. I don't think the problem you're having is related to the toon material at all but is probably an issue with Godot itself.
If you can confirm that the issue persists with the built-in Godot materials as well, I'll close this issue and you should probably raise it in the main Godot repo.

Not a bug from the engine, it's just the viewport needs to have a higher Size value for Shadow Atlas. I just tested this and it works.


.gitignore to remove build folder + eggs

Great job on this @PablocFonseca, pretty sure this will help a lot of users!
I forked your project and saw you were also versioning the build and Python egg-info. It makes it harder to check for code changes when working so I'd recommend copying Streamlit's gitignore and force removing the build + egg_info folders, what do you think ?
Cheers,
Fanilo

Done!

Done!