Implement auto-commit status check and handling during upgrade process

Is your feature request related to a problem? Please describe.
During the upgrade process of a PAN-OS firewall using the pan-os-upgrade utility, there might be situations where the upgraded firewall is undergoing an auto-commit operation. If the utility proceeds with further actions while an auto-commit is in progress, it can lead to unexpected behavior or conflicts. Currently, the utility does not have a mechanism to detect and handle auto-commit scenarios, which can result in upgrade failures or inconsistencies.
Describe the solution you'd like
Enhance the pan-os-upgrade utility to include a check for auto-commit status on the upgraded firewall and implement appropriate handling mechanisms. The utility should:

After upgrading a firewall, check the status of the firewall to determine if an auto-commit operation is currently in progress.
If an auto-commit is detected, the utility should pause the upgrade process and wait for a configurable amount of time (e.g., one minute) before checking the status again.
Implement a maximum number of attempts (e.g., ten) to check for the auto-commit status. If the auto-commit is still ongoing after the maximum number of attempts, consider the upgrade as failed for that particular firewall.
In case of a failure due to prolonged auto-commit, the utility should gracefully handle the situation by reporting the failure status and removing the peer firewall (if applicable) from the upgrade process.
If no auto-commit is detected or if the auto-commit completes within the specified number of attempts, proceed with the normal upgrade flow.

Describe alternatives you've considered
An alternative approach could be to forcefully terminate the auto-commit operation on the upgraded firewall to allow the upgrade process to continue. However, this might lead to unexpected consequences and could potentially leave the firewall in an inconsistent state. It is safer to wait for the auto-commit to complete naturally and handle the situation gracefully if it exceeds a reasonable timeframe.
Additional context
Here are a few additional points to consider:

The number of attempts and the waiting time between attempts should be configurable to allow users to adjust the behavior based on their specific environment and requirements.
The utility should log the auto-commit status checks and provide informative messages to keep users informed about the progress and any delays encountered.
In case of a failure due to prolonged auto-commit, the utility should provide clear error messages indicating the reason for the failure and any necessary actions to be taken.
Update the project's documentation to include information about this new feature, explaining how it handles auto-commit scenarios and the configurable options available.

By implementing this feature, the pan-os-upgrade utility will be more resilient to auto-commit operations occurring during the upgrade process. It will prevent conflicts and ensure a smoother upgrade experience, while also handling failure scenarios gracefully.

will revisit when time permits, closing for now


Push it as a Python package to PyPi

Push it to PyPi so that it can be managed by pip, pipenv, and poetry.

The PyPi package is now on the https://pypi.org/project/pywidgets-ext/


Enable billing extension for AzureChinaCloud

What this PR does / why we need it:
Enable billing extension for AzureChinaCloud
Compute.AKS-Engine.Linux.Billing & Compute.AKS.Linux.Billing are deployed in mooncake.
Which issue this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close that issue when PR gets merged): fixes #
Special notes for your reviewer:
If applicable:

[ ] documentation
[ ] unit tests
[ ] tested backward compatibility (ie. deploy with previous version, upgrade with this branch)

Release note:

/hold

future note to self: lgtm pending release of hold

+Fix on comment


upcastingReducer example doesn't show the need for an initial state

The example in the Readme of the upcastingReducer doesn't show that the final "reducer" should have an initial state passed to it in order for it not to error.
Reason: someone copy and pasting that example and exporting the final function as the reducer will get an error when they try to run the code or test it.
I can submit a PR for this later today, but the fix is just creating an INITIAL_STATE variable that is given as the default to the final "reducer".

Hi @dcurletti, thanks very much for opening this issue. You're totally right that the example is broken. I have some somewhat rambling thoughts about how to handle it.
I think this is a docs problem, not a library problem. The only thing wrong with the upcasting reducer example is that the function reducer in the example no longer satisfies the Reducer interface after Redux changed it at some point (much more detail below). Simply changing the documentation so that the function reducer() has an initial state will fix the docs, and this isn't a problem in practice because the incorrect example will fail typechecking when initializing the store or calling combineReducers with it.
I'm not sure that giving upcastingReducer an initial state is the right fix. It's really hard to make typings with regard to initial state that make everyone happy. Here's a short history of the issues involved:

Originally, the official Redux typings declared a reducer as (State, Action) => State, without allowing for the possibility of passing undefined state, and this library followed suit with the same definition. This was a technically incorrect definition, since reducers need to handle undefined as being initial state in the standard Redux usage, so users could define functions satisfying the Reducer type which could not actually be used with Redux. However, this definition has the advantage for this library that both reducerWithInitialState(initialState) and reducerWithoutInitialState() could return the type Reducer and soundly satisfy its type definition. See the former definition here.

At some point, the official Redux typings changed to define a reducer as (State?, Action) => State, as in the current definition as of today. This is more correct, but unfortunately makes reducerWithoutInitialState awkward for this library, as it can no longer honestly say it is returning a function meeting the Reducer interface. This gives this library a choice:

We could continue to claim that reducerWithoutInitialState returns a Reducer. This is unsound, because if passed to a store which does not have an initial state then it will fail.
We could truthfully say that the function it returns does not accept undefined state. This makes it type-incompatible with Redux, which defeats the point of this library.

You might ask, why have reducerWithoutInitialState() at all in that case? It's actually a pretty useful way to structure some apps. In many applications, the initial state depends on some environmental factors, such as cookies or local settings, or perhaps it doesn't make sense to create the store at all until certain data is retrieved from the server. In this case, it doesn't make sense for "dumb" reducers to produce the same initial state every time- it makes more sense to programatically construct an initial state and pass it to your store as you create the store. The Redux authors have argued that putting the initial state in the reducers is better because it ensures that the shape of the state matches the shape of the reducers, but one might argue that we don't have to worry about that, because we use TypeScript!
Because of this, despite the typings around reducerWithoutInitialState being unsound, the function is still pragmatically useful and so will remain in the library.
Back to the original point: as Reducers are now required to accept undefined as their first argument, the example written in the README will not typecheck and so this isn't a problem with the library but with the docs. I'll change the docs and consider this fixed, unless you have an argument for why making upcastingReducer take an initial state is the right solution instead.

Will leave a longer response as to why, but I agree that upcastingReducer shouldn't take an initial state.
Yea, sorry, I should've been more explicit that this was only a docs problem.


Update request: flutter 3.16.7 → 3.19.0

Package name: Flutter
Latest released version: 3.19.0

Current version on the unstable channel: 3.16.7
Current version on the stable/release channel: 3.13.8

[x] Checked the nixpkgs pull requests

Notify maintainers
@hacker1024

Note for maintainers: Please tag this issue in your PR.

Add a :+1: reaction to issues you find important.

@NixOS/flutter


delete minor unreachable code caused by t.Fatal

Signed-off-by: Abirdcfly<EMAIL_ADDRESS>
Ⅰ. Describe what this PR did
delete minor unreachable code caused by t.Fatal
Ⅱ. Does this pull request fix one issue?

NONE
Ⅲ. Why don't you add test cases (unit test/integration test)? (你真的觉得不需要加测试吗？)
Yes
Ⅳ. Describe how to verify it
No
Ⅴ. Special notes for reviews
No

 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.


Snippet improvements

Correctly render comptime, noalias and vararg arguments.
Only render spaces in return type tokens after commas, this allows us to generate types like anyframe->void better, although it probably is still not 100% ideal.

Looks good!


include java/ files in output if they are targeted

In na-97, where we target a java/ file, the targeted file (java/util/atomic/concurrent/Striped64.java, I believe) was being excluded from the output because of these lines in SpeciminRunner:
if (target.getKey().startsWith("java/")) {
    continue;
}

The reason it worked on Windows was probably because Windows uses backslashes, and it didn't work on Unix because of the forward slash comparison here. I changed it so that the target file is preserved in the output no matter what, even if it starts with java/ (or java\). This should make na-97 work on both OSes.
I didn't include a test case for this, since NullAway bugs are now in the evaluation script, but if you'd like, I could add one. Thanks!

CI should fail on this change, since we expect it to fix na-97 but it doesn't change the preservation status file. That will be a good test of the updated CI.

Whoops, I think I have to merge the latest changes first.


Feature request: GLSL ES 3.0 Support

GLSL ES 3.0 has many additional features.
The original ShaderToy does not support GLSL ES 3.0 either, but it would be great to add it to this wonderful extension.

It appears to me that WebGL 2.0 is compatible with GLSL ES 3.0 for the most part. Can you give me an example of what you are missing?


Allow analyzing multiple files with export-analyzer

Fixes https://github.com/google/exposure-notifications-server/issues/1192
Release Note

Allow analyzing multiple files with export-analyzer

/lgtm
/approve
/hold cancel


Remove hash symbol in front of opcode error messages in GDScript (3.x)

3.x version of https://github.com/godotengine/godot/pull/54798.
The hash symbol creates spurious issue references on GitHub if the message is posted outside a code block, which means some issues have a lot more references than originally intended.

Thanks!

Cherry-picked for 3.4.1.


Only a Default Constructor

I'm getting a compiler error when I try to place named fields on applying the attribute to a class:
[TemplateVisualState(Name = "ConfirmedSelectedItemCleared", GroupName = "ConfirmedSelectedItemStates")]
This is what I'm getting - CS0246 - "Severity	Code	Description	Project	File	Line	Suppression State
Error	CS0246	"The type or namespace name 'Name' could not be found (are you missing a using directive or an assembly reference?)"
Same thing on GroupName property.
I'm trying to compile the old "Microsoft CUI" controls using 4.7.1 and 4.0.  Is there a constructor I'm missing?

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

ID: acef0120-eac5-f6e2-4823-08f085bc8683
Version Independent ID: da637883-8f6e-7ad0-fdc4-b3a50bc8df3f
Content: TemplateVisualStateAttribute Class (System.Windows)
Content Source: xml/System.Windows/TemplateVisualStateAttribute.xml
Product: dotnet-api
GitHub Login: @dotnet-bot
Microsoft Alias: dotnetcontent

I've found another error buried that told me what the actual issue is.


Stop Resizing

Here is my code
this.cropperSettings2.width = 200;
        this.cropperSettings2.height = 200;
        this.cropperSettings2.keepAspect = true;

        this.cropperSettings2.croppedWidth = 200;
        this.cropperSettings2.croppedHeight = 200;

        this.cropperSettings2.canvasWidth = 415;
        this.cropperSettings2.canvasHeight = 300;

        this.cropperSettings2.minWidth = 200;
        this.cropperSettings2.minHeight = 200;
        this.cropperSettings2.dynamicSizing = false;

        this.cropperSettings2.rounded = false;
        this.cropperSettings2.minWithRelativeToResolution = true;

        this.cropperSettings2.cropperDrawSettings.strokeColor = 'rgba(255,255,255,1)';
        this.cropperSettings2.cropperDrawSettings.strokeWidth = 2;
        this.cropperSettings2.noFileInput = true;
        this.cropperSettings2.compressRatio = 1;

I don't have to allow user to resize the crop box. Tried using dynamicSizing property but not working.
Can anyone help me to out
Thanks in advance

+1
I am also trying to do this but stuck.

keep.Aspect = true

i am also trying to do this, any success?


Simplify enabling/disabling eye tracking feature support with MRTK

Describe the problem
The user has to go to three different components to enable Eye tracking support from MRTK in their app (not counting the need to also enable the capability in every VS build).
Describe the solution you'd like
Turning on the feature should be consolidated to one checkbox or at the very least one section for the user to control.
Describe alternatives you've considered
It would be awesome if this was just a package to install and by installing, you are auto-enabling the feature support
Additional context

Active thread discussing the right approach. We should fix this soon to reduce confusion

@Yoyozilla do you have any new information from that thread? Ideally we could have that conversation on this issue.

Added Will and Luis to the thread to discuss

yoyo to follow up on if the fixes we already did are good enough for GA
Also needs to get the Unity bug number

So this one was interesting - a few things have changed since this was originally filed, and now we're in a slightly better world because of:

We have a default HL2 profile, which has the profile changes there by default.
Made the "use eye tracking" toggle on by default.

Note that the gaze capability is still kinda weird - it's still only something that exists in VS, despite having a coming soon status in Unity. That being said, we also added an update to the MRTK build tooling to add the manifest capability in automatically afterward, so that should help.


NET_BUFFER_FIRST_MDL does not return void, it returns a MDL

[Enter feedback here]

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

ID: bd7aeeff-97c0-81f6-b50e-a90f8d5401c5
Version Independent ID: 2e112fa8-a1ef-fd3f-68f9-fcbfa924adb4
Content: NET_BUFFER_FIRST_MDL - Windows drivers
Content Source: wdk-ddi-src/content/nblaccessors/nf-nblaccessors-net_buffer_first_mdl.md
Product: windows-hardware
Technology: wdk-api-reference
GitHub Login: @aviviano
Microsoft Alias: amvivian

Thank you for helping us improve the docs, @nhamer. The fix for this issue will be live on the site shortly.


error running resim

`dyld: could not load inserted library '/opt/simject/simject.dylib' because no suitable image found.  Did find:
/opt/simject/simject.dylib: mach-o, but wrong architecture
Child process terminated with signal 6: Abort trap
Error executing command, exiting.
`
on an arm64 Mac with the latest Xcode and Theos

What's the output of xcode-select -p on your machine?

/Applications/Xcode.app/Contents/Developer

@nico671 Could you also give me the output of lipo -info /opt/simject/simject.dylib ?

Non-fat file: /opt/simject/simject.dylib is architecture: x86_64

Was that simject dylib compiled on your arm64 machine? make setup uses clang's target triple, which in this case should be arm64-apple-darwin*
When you run make setup, does it saying "Compiling simject for arn64"?

it says Compiling resim for x86_64-apple-darwin20.5.0

can you try compiling simject manually:
cd simject
clang -framework Foundation -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk -DDYLIB_DIR=/opt/simject -target arm64-apple-darwin20.5.0 -dynamiclib -o /opt/simject/simject.dylib

Can you try compiling the simject dylib manually:
cd simject
clang simject.m -framework Foundation -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk -DDYLIB_DIR='@"/opt/simject"' -target arm64-apple-darwin20.3.0 -dynamiclib -o simject.dylib

then run resim

that worked perfectly thank you


When we use the pulsar-admin.sh script to delete partitioned topic, it will throw the http error, error code is 500

Describe the bug
When we use the pulsar-admin.sh script to delete partitioned topic, it will throw the http error, error code is 500.
To Reproduce
Steps to reproduce the behavior:

when we run the benchmark test, the cluster of bookie has one or more bookie state that is read only;
and then we use the script to delete the partitioned topic, ../bin/pulsar-admin topics deleted-partition-topic persistent://tenant/namespace/topic;
we receive the http error, error code is 500, we can't delete successfully;
we restart all pulsar brokers of cluster,and then run the script to delete, it succeed.

Expected behavior
succeed to delete the partitioned topic.
Screenshots
we check the service log. find the error as follow:
15:15:29.005 [bookkeeper-ml-workers-OrderedExecutor-7-0] ERROR org.apache.bookkeeper.common.util.SafeRunnable - Unexpected throwable caught
java.lang.IllegalArgumentException: inconsistent range
        at java.util.concurrent.ConcurrentSkipListMap$SubMap.<init>(ConcurrentSkipListMap.java:2620) ~[?:1.8.0_171]
        at java.util.concurrent.ConcurrentSkipListMap.subMap(ConcurrentSkipListMap.java:2078) ~[?:1.8.0_171]
        at org.apache.bookkeeper.mledger.util.RangeCache.removeRange(RangeCache.java:132) ~[org.apache.pulsar-managed-ledger-2.5.0-d9ebec524.jar:2.5.0-d9ebec524]
        at org.apache.bookkeeper.mledger.impl.EntryCacheImpl.invalidateEntries(EntryCacheImpl.java:151) ~[org.apache.pulsar-managed-ledger-2.5.0-d9ebec524.jar:2.5.0-d9ebec524]
        at org.apache.bookkeeper.mledger.impl.ManagedLedgerImpl$7.operationComplete(ManagedLedgerImpl.java:779) ~[org.apache.pulsar-managed-ledger-2.5.0-d9ebec524.jar:2.5.0-d9ebec524]
        at org.apache.bookkeeper.mledger.impl.ManagedLedgerImpl$7.operationComplete(ManagedLedgerImpl.java:767) ~[org.apache.pulsar-managed-ledger-2.5.0-d9ebec524.jar:2.5.0-d9ebec524]
        at org.apache.bookkeeper.mledger.impl.MetaStoreImplZookeeper.lambda$null$13(MetaStoreImplZookeeper.java:308) ~[org.apache.pulsar-managed-ledger-2.5.0-d9ebec524.jar:2.5.0-d9ebec524]
        at org.apache.bookkeeper.mledger.util.SafeRun$1.safeRun(SafeRun.java:32) ~[org.apache.pulsar-managed-ledger-2.5.0-d9ebec524.jar:2.5.0-d9ebec524]
        at org.apache.bookkeeper.common.util.SafeRunnable.run(SafeRunnable.java:36) [org.apache.bookkeeper-bookkeeper-common-4.9.2.jar:4.9.2]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_171]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_171]
        at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) [io.netty-netty-common-4.1.43.Final.jar:4.1.43.Final]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_171]

Desktop (please complete the following information):

OS: [e.g. iOS]

Additional context
Add any other context about the problem here.

@codelipenghui @tuteng Could you please help check the issue and give explanation? Thank you.

need handling the exception reported

The root cause of this problem will be fixed in #5621


Adding parameterization for new bom/s, boot version in app generator

This PR needs https://github.com/spring-cloud/spring-cloud-stream-app-maven-plugin/pull/9 from the app generation maven plugin to be merged in first.
Additional boms can be added to app generation along with a different spring boot parent using the following plugin properties:
./mvnw clean install scs:generate-app -pl :spring-cloud-stream-app-generator -DbomsWithHigherPrecedence=org.springframework.cloud:spring-cloud-stream-dependencies:Brooklyn.M1,org.springframework.cloud:spring-cloud-dependencies:Camden.BUILD-SNAPSHOT -DbootVersion=1.4.0.RELEASE
This will add Brookly.M1 release train for spring cloud stream and Camden.BUILD-SNAPSHOT release train for spring cloud as boms to the generated maven poms. It will also use 1.4.0.RELEASE version of spring boot as the parent for all the generated apps.
It can also conveniently passed in along with the shell script used to generate apps:
./generateApps.sh -b org.springframework.cloud:spring-cloud-stream-dependencies:Brooklyn.M1,org.springframework.cloud:spring-cloud-dependencies:Camden.BUILD-SNAPSHOT -bt 1.4.0.RELEASE
or more wordy:
./generateApps.sh --bomsWithHigherPrecedence org.springframework.cloud:spring-cloud-stream-dependencies:Brooklyn.M1,org.springframework.cloud:spring-cloud-dependencies:Camden.BUILD-SNAPSHOT --bootVersion 1.4.0.RELEASE

LGTM, merging.

Merged as 11b5697


v4 - add better error for organization name duplication

We frequently see issues on account creation where users try to sign up an organization that already exists. AccountRequestController won't create the organization if the name is a duplicate, but the error message that's passed along to users is vague and doesn't tell them why the request failed.
For this ticket, update the error message that's shown to users when organization creation fails because of a duplicate name.

@Rebecca-LM
Current error messages is: Error: Organization is a duplicate

@emmastephenson do we show a clear way to get support anywhere on the page where they'd get the error? I ask since I'd prefer to leave out our email on the message below, but can add if needed.
"This organization has already registered with SimpleReport. Please contact your organization administrator or SimpleReport support."

No, I don't see a clear way for users to get to support from the signup page unfortunately. If we do add the email, we'll likely need to add it as plaintext - I'm not sure that there's a way to display hyperlinks in a toast.

@emmastephenson in that case I don't think it makes sense to include the email since they wouldn't be able to use it or even cut/paste. Let's just stick w the copy I sent above. "This organization has already registered with SimpleReport. Please contact your organization administrator or SimpleReport support."

I'm sort of thinking that a toast isn't really appropriate for this kind of error. I think maybe instead we should scroll up to the top of the form and insert an Alert component at the top that doesn't go away. That way we can include the support email link.

@nickclyde I'd be curious to see what that looks like, but that definitely sounds more helpful for users. The message could then be: "This organization has already registered with SimpleReport. Please contact your organization administrator or<EMAIL_ADDRESS>for help."

@Rebecca-LM here is what that would look like:

@emmastephenson since we are also seeing the duplicate user email error often, would it be useful to handle that error in a similar way and display an alert at the top of the form like this?

Yeah, I think that's a good idea. There's not really good recourse beyond reaching out to support or org admins in that case.

@nickclyde Looks good! But can we change the header to "Duplicate organization"? I didn't realize I only created the body text for this one.

No problem. How do these look @Rebecca-LM :

@nickclyde Perfection! Thanks.


custom subdomain not working?

I'm trying to setup a clean build on my VPS,
everything seems ok when I directly visit <IP_ADDRESS>:9000
but it seems not meaning to load twitter streams when I visit my subdomain for the app.
My workaround is Apache redirecting, any clue?

<VirtualHost *:80>
ServerAdmin webmaster@localhost
ServerName example.host
ProxyPass / http://<IP_ADDRESS>:9000/
ProxyPassReverse / http://<IP_ADDRESS>:9000/
ProxyPass /ws/raids ws://<IP_ADDRESS>:9000/ws/raids
ProxyPass /ws/raids wss://<IP_ADDRESS>:9000/ws/raids

i tried to handle but it still not working...

I'm done, solved by advancing ws proxy line.
<VirtualHost *:80>
    ServerAdmin webmaster@localhost
    ServerName sub.example.host

    ProxyPass /ws/raids ws://<IP_ADDRESS>:9000/ws/raids
    ProxyPass /ws/raids wss://<IP_ADDRESS>:9000/ws/raids

    ProxyPass / http://<IP_ADDRESS>:9000/
    ProxyPassReverse / http://<IP_ADDRESS>:9000/
</VirtualHost>


Install Coveralls, DOSBox and Open Watcom from script

You missed the best :-)
Results of a sloeepless night. It's working well.

I was trying to get coveralls out of sudo because of: http://docs.travis-ci.com/user/migrating-from-legacy/?utm_source=legacy-notice&utm_medium=banner&utm_campaign=legacy-upgrade

Oh, sorry. Perhaps we can get into that after finishing this one?
It seems to me that we can get stuff EITHER out of sudo, OR out of travis.yml. But then, I haven't looked at your pr yet....

It is a bit more complicated. The sudo for dosbox I'll leave, but I'm wondering about the coveralls sudo pip. Still playing with it.

Anything I must change in this pull to be compatible with what you are trying to achieve?

Neither dosbox nor coveralls seems to be on the whitelist, so they would be rejected? Wouldn't we need to raise an issue also to include those?

Coveralls is resolved. So, only dosbox would be needed. Could you rebase the branch?

Those matrix entries spawned a lot of new offspring :-(

What do you mean? I separated out some of the build targets..

I know, I know. But they tend to be triggered sequentially, and make-dos is the last one :-(

It is last because most of the time, that is what you want ;)


Setter on custom Resource not called in editor after scene reload

Godot version:
3.2.3 stable
OS/device including version:
Macbook Pro
macOS Mojave
Issue description:
A setter for a variable in a custom Resource does not get called consistently in editor.
Minimal example: I have a custom resource (MyResource) with an exported float x. I define a setter for x that sets the value and prints it:
extends Resource
class_name MyResource

export (float, 0, 1) var x = 0 setget on_set_x

func on_set_x(value):
	x = value
	print(x)

I also have a tool Node2D with an exported resource, which is set to a new MyResource if it is null upon enter tree:
extends Node2D
tool

export (Resource) var resource

func _enter_tree():
	if not resource:
		resource = MyResource.new()

Expected behavior: setter is called (and value of x is printed) whenever slider for x is dragged in inspector.
Actual behavior: setter gets called as expected at first, but no longer gets called if the saved scene is reloaded.
Steps to reproduce:
Described above.
Minimal reproduction project:
ResourceSetterIssue.zip

Tried to implement a workaround for setters not working, but it seems the resource has somehow lost all its methods after the scene reload (gives "nonexistent function" error if you try to call one). You can still access its variables though...

So I'm not sure why I didn't think to add "tool" to the Resource script. That appears to fix the problem. However, this still seems a bit strange. If "tool" is needed, then why does the print statement happen at all (up until scene reload) when it is not a tool script?


Add a license to the repository

I recently came across your project QuantumAlgorithms and I noticed that the repository github.com/GilbertoCunha/QuantumAlgorithms currently does not have a license specified.
Why Adding a License is Important?
As GitHub documents

Public repositories on GitHub are often used to share open source software. For your repository to truly be open source, you'll need to license it so that others are free to use, change, and distribute the software.

Would be possible to add a valid license to this repository? Probably something really OpenSource such as the Apache 2.0 license would fit really well.
Thanks!

Already added a license to it :)
Never though of it, since I didn't think this would end up being useful anyway, but thanks for the suggestion :)

Thank you


jwt_authn: Allow to extract keys from jwt struct claims

Commit Message: Allow to extract keys from jwt struct claims
Additional Description:
Added a new field list_claim_keys on claim_to_headers to extract keys from JWT token claims. This field enables the retrieval of keys from custom JWT token claims, such as {"tenants": {"bitdrift": {}} (in this case a claim_name of `tenants would extract the key "bitdrift").
Risk Level: Low
Testing: unit test
Docs Changes: Updated docs/root/configuration/http/http_filters/jwt_authn_filter.rst
Release Notes: Updated changelogs/current.yaml

CC @kyessenov

@Reflejo can you elaborate your exact use case for this?
I would like the API to be more generic / future proof and not specific about a list. But would like to know where this implementation is coming from.
/wait:any

@lizan The use-case is many authentication providers nowadays send custom claims on JWT tokens that are formatted as per my example:
"tenants": {"a": {}, "b": {}}

Basically they do this as a way of sending lists. Our specific use-case is, we need to extract the tenants from the jwt and forward them to the service as a header.
I wouldn't mind changing my PR to define a bool serialize_struct instead and send the JSON string in base64. Would that be better?

Unless there's a common RFC that requires this encoding, I think I mostly agree with Matt's proposal - either encoding the whole JWT sub-struct as a header, or a separate extension that computes the header from dynamic metadata would be better.

@kyessenov @lizan @mattklein123 updated the PR implementing the proposed solution (serializing objects). The reason I added the flag is to not make this a breaking change (ie anyone relying on the fact that we ignore keys with object types right now).

The last change looks good to me. I'm not sure it deserves an API flag since it's a new feature with a reasonable default (don't expect this header to blow up since it's always a subset of JWT).

Related: https://github.com/envoyproxy/envoy/issues/30072

The last change looks good to me. I'm not sure it deserves an API flag since it's a new feature with a reasonable default (don't expect this header to blow up since it's always a subset of JWT).

I had mentioned to @Reflejo offline that I could probably lose the API change as well, but I don't feel strongly either way. This is certainly safer. I suppose if we wanted to limit the API change we could runtime guard instead. I'm fine either way. This LGTM. @lizan?

ok removed the flag, this should be ready to go


No option to show playback controls on video screen

@AnmolMalpani have you got any solution for this? I've implemented for speed increase and decrease but not the speed is not updating in full screen

@AnmolMalpani Can you help with a brief and elaborate description on the issue being faced?


Fix never type link

This PR fixes the inconsistent spelling that currently breaks the link.

This accidentally also contains stuff from my other PR. Fixing now...

Ok now it contains just the one change I wanted to make.

I'd almost rather the never type link be broken, because of it being unstabilized. Hm.

Maybe remove the never type section entirely?

If you want to take on #344, that would be awesome! But don't feel like you have to. :)

👍


Scrollbar not visible in sidebar.

Bug report

What is the current behavior?
Scrollbar is not visible in microsoft edge linux.
If the current behavior is a bug, please provide the steps to reproduce.

What is the expected behavior?

Other relevant information:
webpack version:
Node.js version:
Operating System:
Additional tools:

Sorry, not related to webpack

I'm sorry I didn't provide complete information on the issues. The actual issues it this:

The scrollbar on the left hand side is unscrollable. The browser I'm using is MS Edge and my OS is Ubuntu.

Can you capture video and open dev tools?

Sure

Screencast from 20-05-23 10:30:57 PM IST.webm

@webpack-bot move to webpack/webpack.js.org


[BUG] ItemRetrievalTask() gives error when samplers param is None.

I get the following error from the ItemRetrievalTask() when I dont set samplers param. Looks like the reason of the error is that setting samplers param  to None does not work as expected. The default was not set correctly.
import merlin_models.tf as mm
mf = mm.MatrixFactorizationBlock(schema, dim=128)
model = mf.connect(mm.ItemRetrievalTask())

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Input In [13], in <module>
      1 # it does similarity behind the since using keras Dot layer.
      2 # this is gonna do inbatch negative sampling
      3 # branch names as query and item are required
      4 # model = mf.connect(mm.ItemRetrievalTask(samplers = [mm.InBatchSampler()]))
----> 6 model = mf.connect(mm.ItemRetrievalTask())

File /models/merlin_models/tf/prediction/item_prediction.py:391, in ItemRetrievalTask(loss, samplers, metrics, extra_pre_call, target_name, task_name, task_block, softmax_temperature, normalize)
    388 if samplers is None or len(samplers) == 0:
    389     samplers = (InBatchSampler,)
--> 391 prediction_call = ItemRetrievalScorer(
    392     samplers=samplers,
    393 )
    395 if normalize:
    396     prediction_call = L2Norm().connect(prediction_call)

File /models/merlin_models/tf/prediction/item_prediction.py:154, in ItemRetrievalScorer.__init__(self, samplers, sampling_downscore_false_negatives, sampling_downscore_false_negatives_value, **kwargs)
    151 if not isinstance(self.samplers, list):
    152     self.samplers = [self.samplers]
--> 154 self.set_required_features()

File /models/merlin_models/tf/prediction/item_prediction.py:162, in ItemRetrievalScorer.set_required_features(self)
    158 if self.downscore_false_negatives:
    159     required_features.add(str(Tag.ITEM_ID))
    161 required_features.update(
--> 162     [feature for sampler in self.samplers for feature in sampler.required_features]
    163 )
    165 self._required_features = list(required_features)

File /models/merlin_models/tf/prediction/item_prediction.py:162, in <listcomp>(.0)
    158 if self.downscore_false_negatives:
    159     required_features.add(str(Tag.ITEM_ID))
    161 required_features.update(
--> 162     [feature for sampler in self.samplers for feature in sampler.required_features]
    163 )
    165 self._required_features = list(required_features)

AttributeError: 'tuple' object has no attribute 'required_features'

We can make it work if I set the sampler arg as follows
model = mf.connect(mm.ItemRetrievalTask(samplers = [mm.InBatchSampler()]))

Fixed via https://github.com/NVIDIA-Merlin/models/pull/176


python310Packages.canonicaljson: 1.6.4 -> 1.6.5

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for python310Packages.canonicaljson is: Encodes objects and arrays as RFC 7159 JSON
meta.homepage for python310Packages.canonicaljson is: https://github.com/matrix-org/python-canonicaljson
Updates performed

Ran passthru.UpdateScript

To inspect upstream changes
Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 1.6.5 with grep in /nix/store/24n9hmda5z1b0w0xav7y2z5h9mszg50v-python3.10-canonicaljson-1.6.5
found 1.6.5 in filename of file in /nix/store/24n9hmda5z1b0w0xav7y2z5h9mszg50v-python3.10-canonicaljson-1.6.5

Rebuild report (if merged into master) (click to expand)

8 total rebuild path(s)

8 package rebuild(s)

First fifty rebuilds by attrpath
matrix-synapse
matrix-synapse-plugins.matrix-synapse-mjolnir-antispam
matrix-synapse-plugins.matrix-synapse-shared-secret-auth
matrixcli
python310Packages.canonicaljson
python310Packages.signedjson
python311Packages.canonicaljson
python311Packages.signedjson

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/24n9hmda5z1b0w0xav7y2z5h9mszg50v-python3.10-canonicaljson-1.6.5 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A python310Packages.canonicaljson https://github.com/r-ryantm/nixpkgs/archive/c61122727df9ce68487cad499008e711a3663af6.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/24n9hmda5z1b0w0xav7y2z5h9mszg50v-python3.10-canonicaljson-1.6.5
ls -la /nix/store/24n9hmda5z1b0w0xav7y2z5h9mszg50v-python3.10-canonicaljson-1.6.5/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

Maintainer pings
cc @fabaff for testing.

Result of nixpkgs-review pr 216767 run on aarch64-linux 1


Allow user to override which emacs is used in run_rust_emacs_tests.sh

Namely, extend script so user can do, e.g.:
% EMACS=/Applications/Emacs.app/Contents/MacOS/Emacs run_rust_emacs_tests.sh

r? @huonw
(rust_highfive has picked a reviewer for you, use r? to override)


Windows Container fallbacks to default docker network IPv6 dns addresses

Im having issues with configuring DNS Servers for the docker networks on:
Windows Server 2019
Version 1809 (OS Build 17763.1935)
I have configured 1 network adapter on the Hyper-V host running the Container Host as a VM.
And enabled MAC-address spoofing for that adapter.
Inside the Container host i have installed Docker using the process provided here for Windows Server
I have not installed the Hyper-V feature, since i only want to use isolation mode process.
Installed features are:

Containers
Windows Defender Antivirus

docker info'
Client: Mirantis Container Runtime
 Version:           20.10.4
 API version:       1.41
 Go version:        go1.13.15
 Git commit:        110e091
 Built:             04/12/2021 15:53:12
 OS/Arch:           windows/amd64
 Context:           default
 Experimental:      true

Server: Mirantis Container Runtime
 Engine:
  Version:          20.10.4
  API version:      1.41 (minimum version 1.24)
  Go version:       go1.13.15
  Git commit:       b24528647a
  Built:            04/12/2021 15:51:36
  OS/Arch:          windows/amd64
  Experimental:     false

docker version
Client:
 Context:    default
 Debug Mode: false
 Plugins:
  app: Docker Application (Docker Inc., v0.8.0)
  cluster: Manage Mirantis Container Cloud clusters (Mirantis Inc., v1.9.0)
  registry: Manage Docker registries (Docker Inc., 0.1.0)

Server:
 Containers: 1
  Running: 1
  Paused: 0
  Stopped: 0
 Images: 164
 Server Version: 20.10.4
 Storage Driver: windowsfilter
  Windows:
 Logging Driver: json-file
 Plugins:
  Volume: local
  Network: ics internal l2bridge l2tunnel nat null overlay private transparent
  Log: awslogs etwlogs fluentd gcplogs gelf json-file local logentries splunk syslog
 Swarm: inactive
 Default Isolation: process
 Kernel Version: 10.0 17763 (17763.1.amd64fre.rs5_release.180914-1434)
 Operating System: Windows Server 2019 Standard Version 1809 (OS Build 17763.1935)
 OSType: windows
 Architecture: x86_64
 CPUs: 4
 Total Memory: 5.999GiB
 Name: DevBuildSkySrv1
 ID: U5VX:ZB7R:TTPZ:XLIS:QHXB:P7IJ:SLMY:BX3A:DC5I:NZHB:H6FN:7BWF
 Docker Root Dir: D:\DockerData
 Debug Mode: true
  File Descriptors: -1
  Goroutines: 42
  System Time: 2021-06-02T11:51:11.6848945+02:00
  EventsListeners: 0
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: false
 Insecure Registries:
  <IP_ADDRESS>/8
 Live Restore Enabled: false

I've modified C:\ProgramData\docker\config\daemon.json to change data-root:
{ "data-root": "D:\\DockerData" }
From elevated powershell session: Restart-Service Docker
Verified docker creates the structure on the D:\DockerData location.
From elevated powershell session i can start dockerd --debug view logs entries while starting containers.
From a new elevated powershell session i can run docker commands:
PS > docker pull mcr.microsoft.com/windows/servercore:ltsc2019
failed to register layer: re-exec error: exit status 1: output: hcsshim::ProcessBaseLayer \\?\C:\ProgramData\docker\windowsfilter\8f9ff627f9aace3d726df716eb21fb3f1452eb05864967388a9b825276e2178a: Access is denied.

The issue was solved by adding dockerd.exe and docker.exe to Controlled Folder Access Allowed Application using powershell:
Add-MpPreference -ControlledFolderAccessAllowedApplications "C:\Program Files\Docker\docker.exe"
Add-MpPreference -ControlledFolderAccessAllowedApplications "C:\Program Files\Docker\dockerd.exe"

After that i was able to pull the image and run the container:
docker run --rm -i -t --network nat mcr.microsoft.com/windows/servercore:ltsc2019 powershell

But from inside the container the exspected DNS Servers are not listed, only the default DNS servers docker creates on the nat network adapter.
PS > Get-NetIpConfiguration

InterfaceAlias             : vEthernet (Ethernet)
InterfaceIndex            : 36
InterfaceDescription  : Hyper-V Virtual Ethernet Adapter #3
IPv4Address               : <IP_ADDRESS>
IPv6DefaultGateway   :
IPv4DefaultGateway   : <IP_ADDRESS>
DNSServer                  : fec0:0:0:ffff::1
                                     fec0:0:0:ffff::2
                                     fec0:0:0:ffff::3
PS > Test-Connection
Test-Connection : Testing connection to computer 'bing.com' failed: No such host is known

Exiting the container (type: exit) and running:
PS > Get-NetIpConfiguration
InterfaceAlias       : vEthernet (nat)
InterfaceIndex       : 10
InterfaceDescription : Hyper-V Virtual Ethernet Adapter #2
NetProfile.Name      : Unidentified network
IPv4Address          : <IP_ADDRESS>
IPv6DefaultGateway   :
IPv4DefaultGateway   :
DNSServer            : fec0:0:0:ffff::1
                       fec0:0:0:ffff::2
                       fec0:0:0:ffff::3

InterfaceAlias       : DMZ
InterfaceIndex       : 12
InterfaceDescription : Microsoft Hyper-V Network Adapter
NetProfile.Name      : contoso.com
IPv4Address          : <IP_ADDRESS>
IPv6DefaultGateway   :
IPv4DefaultGateway   : <IP_ADDRESS>
DNSServer            : <IP_ADDRESS>
                       <IP_ADDRESS>

Starting a new container with --dns flag and <IP_ADDRESS>
docker run --rm -i -t --network nat --dns <IP_ADDRESS> mcr.microsoft.com/windows/servercore:ltsc2019 powershell

Getting the NetIpConfiguration yields the same result:
PS > Get-NetIpConfiguration

InterfaceAlias             : vEthernet (Ethernet)
InterfaceIndex            : 36
InterfaceDescription  : Hyper-V Virtual Ethernet Adapter #3
IPv4Address               : <IP_ADDRESS>
IPv6DefaultGateway   :
IPv4DefaultGateway   : <IP_ADDRESS>
DNSServer                  : fec0:0:0:ffff::1
                                     fec0:0:0:ffff::2
                                     fec0:0:0:ffff::3

Installing docker locally on my laptop without Docker desktop to mimic the setup on the server, works without issues:

Downloaded docker from: https://master.dockerproject.com/windows/x86_64/docker.zip
Extracted to C:\Program Files\Docker and added to system environment PATH
Added to ControlledFolderAccessAllowedApplications using Set-MpPreference as mentioned above.
Run dockerd --debug --exec-opt isolation=process in an elevated session.
Run docker pull mcr.microsoft.com/windows/servercore:20H2 from another elevated session.
Run docker -t -i --rm --network nat mcr.microsoft.com/windows/servercore:20H2 powershell
Running the command Get-NetIpConfiguration inside a container works as expected, and shows DNS Servers from my router and VPN connection when connected.
Using the --dns <IP_ADDRESS> flag changes the DNS servers list as expected.

I have tried the following:

Adding dns to daemon.json { "dns": [ "<IP_ADDRESS>" ] }
Disabled default nat driver { "bridge": "none" }, removed using Get-HnsNetwork | Remove-HnsNetwork
Created transparent network drivers, without corporate subnet and gateway ipv4 of the container host
I've tried the different network options listed on Advanced network options in Windows all drivers yield the same result for dns servers, and only returns the default docker dns severs on the interface.
Changed the InterfaceMetric values for the NetIpInterfaces (descending) using powershell.
Removed the default docker nat using Get-HsnNetwork | Remove-HnsNetwork and restarted docker, and the networks are recreated.
Disabled Firewall on the Container Host.
Manually modify the DNS Server Adressses inside the container using Set-DnsClientServerAddress no luck.
Change virtual network adapters to private network
Uninstalled docker using the documention located here, then installed again.

The logs shows the correct DNSServerList being returned for the network configuration for the container when starting.
Using powershell to retrieve networks using Get-HnsNetwork shows the correct values for DNSServerList.
Which is also expected when the dockers logs show the same ting.
Any suggestions why this happends and how to solve it?
Is it an issue with the Mirantis Container Runtime?

We hugely appreciate your contribution, feedback, and support to our technical documentation.
We’ve phased out GitHub Issues on this repository as the feedback mechanism for content and have replaced it with a new feedback system. For more information see, Content User Feedback. As part of this rollout, we are migrating your issue where our team will use your comments to improve the documentation experience. Unfortunately, this does mean you won't be able to access this issue after the migration is complete.
All issues will be migrated by Thursday 29th August 2024.
Once again, thank you for your valuable feedback, we hope you’ll continue to contribute using our new feedback system.


Update validator.js- Adding maxlength validator

Adding maxlength validator

There's no need for this validator since you can just specify the standard maxlength attribute on inputs and it'll prevent users from typing past the limit.


Overlapping of icon and email input field on social-sidebar.

Describe the bug
Overlapping of social-sidebar is creating a unpleasant UI experience. By putting social-sidebar we can fix it. Please assign it to me being a participant of GGSOC.
Possible solution
Adding z-index to social-sidebar solves the problem.
Screenshots
Current website:-

After fix:-

Duplicate of #179


[Event Request] table 36 "Sales Header" - OnAfterCalcAreSalesLinesEditable

We would like to add a new event OnAfterCalcAreSalesLinesEditable in the following procedure:
procedure CalcAreSalesLinesEditable() IsEditable: Boolean;
begin
    //A113F0000.Event.ns
    if "Document Type" = "Document Type"::Quote then
        IsEditable := ("Sell-to Customer No." <> '') or ("Sell-to Customer Template Code" <> '') or ("Sell-to Contact No." <> '')
    else
        IsEditable := "Sell-to Customer No." <> '';

    OnAfterCalcAreSalesLinesEditable(Rec, IsEditable);
    //A113F0000.Event.ne
end;

Event Signature:
[IntegrationEvent(false, false)]
local procedure OnAfterCalcAreSalesLinesEditable(var SalesHeader: Record "Sales Header"; var IsEditable: Boolean)
begin
    //A113F0000.Event
end;

Function CalcAreSalesLinesEditable does not exist. Please check the latest code base.

We do not implement additional application code via event requests. Especially parts of you own solution. We need detailed explanation for such requests, better create them on IDEAS portal


Refactor go-apt-mirror

This PR refactors go-apt-mirror logics.
Please see commits one by one.

@nojima
Test went successful for Dell, Zabbix, and Ubuntu repositories.
You can merge it if it looks good to you.

OK


feat: experimental optimized indexed tree insert

Please provide a paragraph or two giving a summary of the change, including relevant motivation and context.
Checklist:
Remove the checklist to signal you've completed it. Enable auto-merge if the PR is ready to merge.

[ ] If the pull request requires a cryptography review (e.g. cryptographic algorithm implementations) I have added the 'crypto' tag.
[ ] I have reviewed my diff in github, line by line and removed unexpected formatting changes, testing logs, or commented-out code.
[ ] Every change is related to the PR description.
[ ] I have linked this pull request to relevant issues (if any exist).

Benchmark results
Metrics with a significant change:

circuit_simulation_time_in_ms (base-rollup): 4,686 (+165%)
l2_block_building_time_in_ms (8): 25,321 (+91%)
l2_block_building_time_in_ms (32): 99,865 (+91%)
l2_block_building_time_in_ms (128): 400,980 (+92%)
l2_block_rollup_simulation_time_in_ms (8): 23,930 (+101%)
l2_block_rollup_simulation_time_in_ms (32): 94,487 (+101%)
l2_block_rollup_simulation_time_in_ms (128): 379,764 (+102%)

Detailed results
All benchmarks are run on txs on the Benchmarking contract on the repository. Each tx consists of a batch call  to create_note and increment_balance, which guarantees that each tx has a private call, a nested private call, a public call, and a nested public call, as well as an emitted private note, an unencrypted log, and public storage read and write.
This benchmark source data is available in JSON format on S3 here.
Values are compared against data from master at commit 4623d916 and shown if the difference exceeds 1%.
L2 block published to L1
Each column represents the number of txs on an L2 block published to L1.

Metric
8 txs
32 txs
128 txs

l1_rollup_calldata_size_in_bytes
45,444
179,588
716,132

l1_rollup_calldata_gas
222,996
868,268
3,449,384

l1_rollup_execution_gas
842,083
3,595,376
22,204,753

l2_block_processing_time_in_ms
2,035 (+2%)
7,867 (+3%)
31,333 (+5%)

note_successful_decrypting_time_in_ms
293
869
3,201 (+1%)

note_trial_decrypting_time_in_ms
96.1 (-1%)
76.2 (+2%)
134 (+1%)

l2_block_building_time_in_ms
:warning: 25,321 (+91%)
:warning: 99,865 (+91%)
:warning: 400,980 (+92%)

l2_block_rollup_simulation_time_in_ms
:warning: 23,930 (+101%)
:warning: 94,487 (+101%)
:warning: 379,764 (+102%)

l2_block_public_tx_process_time_in_ms
1,350 (+3%)
5,243 (+2%)
20,728 (+1%)

L2 chain processing
Each column represents the number of blocks on the L2 chain where each block has 16 txs.

Metric
5 blocks
10 blocks

node_history_sync_time_in_ms
21,994 (+2%)
42,988 (+1%)

note_history_successful_decrypting_time_in_ms
2,017
3,948 (-1%)

note_history_trial_decrypting_time_in_ms
120 (-1%)
146 (-18%)

node_database_size_in_bytes
1,630,774
1,097,194

pxe_database_size_in_bytes
29,748
59,307

Circuits stats
Stats on running time and I/O sizes collected for every circuit run across all benchmarks.

Circuit
circuit_simulation_time_in_ms
circuit_input_size_in_bytes
circuit_output_size_in_bytes

private-kernel-init
762
61,697
18,905

private-kernel-ordering
125 (-1%)
24,297
8,153

base-rollup
:warning: 4,686 (+165%)
656,311
873 (+7%)

root-rollup
157 (-7%)
4,072
1,097

private-kernel-inner
788
81,568
18,905

public-kernel-private-input
41.2
41,519
18,841

public-kernel-non-first-iteration
25.9
41,497
18,841

merge-rollup
15.6 (+3%)
2,592
873

Miscellaneous
Transaction sizes based on how many contracts are deployed in the tx.

Metric
0 deployed contracts
1 deployed contracts

tx_size_in_bytes
8,787
27,547


joomla 3.3.6

I'll merge this but I really think that these templates have limited value, as discussed in #985.


Add redis docker deployment

This is a follow-up to issue #43 where we ought to fail if there is no current redis available.
#43 should be the quick-fix whereas #42 is a long-term solution which aims to make deployment easier.


Allow http_ssl_version: nil to use system default

Otherwise we have to keep on top of SSL versions, and might get behind (stagnate) and end up using insecure communications. The option to use the system default is not possible when nil options are filtered out, so instead of removing that filter, this commit detects a nil option and overrides the default after the merge and instance_variable_set loop.
This is perhaps also a fix for #86.

Not entirely sure why the travis tests failed. Have there been some ENV changes on travis?
  1) Account API client usage manage senders
     Failure/Error: let(:unique_from_email) { ENV['POSTMARK_CI_SENDER'].gsub(/(\+.+)?@/, "+#{unique_token}@") }
     NoMethodError:
       undefined method `gsub' for nil:NilClass
     # ./spec/integration/account_api_client_spec.rb:9:in `block (2 levels) in <top (required)>'
     # ./spec/integration/account_api_client_spec.rb:13:in `block (2 levels) in <top (required)>'

Hey @henrahmagix! Thanks for the PR, this got me thinking and wondering if we should actually be setting a default SSL version and I agree it's something we can and should try to avoid. I've created #97 which I'll be merging in momentarily which is a slight variation of your approach here, closing this PR in favor of #97.

Excellent, thanks so much @nickhammond! Much appreciated 💎


Add docs on critical nodes endpoint for v23.1

Fixes DOC-7343
This new status endpoint replaces the functionality of the old SQL-based replication reports.
In addition to adding docs for the new status endpoint, we update the 'Data Domiciling' docs to use the new thing, as well as marking the SQL-based 'Replication Reports' page as fully deprecated (if not yet removed) for v23.1.

fyi @williamkulju this is in progress

See also: https://github.com/cockroachdb/cockroach/pull/97412

@data-matt sorry, forgot to add you to this earlier!

all, I'm planning next week to pass this along for docs team review and then merge ASAP
Zach has given his approval in slack
additional comments welcome until say Monday afternoon!

TFTR everyone - passing this along for docs review now

@taroface thanks for the review!  this is RFAL


Precompression for (pipelined) assets (nginx::gzip_static support).

Compressing resources on-the-fly adds CPU-load and latency (wait for the
compression to be done) every time a resource is served. nginx offers
another way of doing things, and it's called gzip_static.
http://nginx.org/en/docs/http/ngx_http_gzip_static_module.html
If you enable gzip_static, nginx will look for $filename.gz and serve
that directly, so no extra CPU-cost or latency is added to your
requests, speeding up the serving of your website.
This feature adds support to directly compress asset files when they are
written to disk by the Grav\Common\Assets class. Using this feature you
can also specify the compression level (default to the maximum of 9).
Since you only have to compress every resource only once, using the
maximum compression level is an ideal default.

This seems to be specific for Nginx? Whilst handy, it would be superfluous for all other webservers. Also, have you tested it with other webservers to ensure that the settings causes no issue with them?

Hi Ole,
For other webservers it will not cause problems, as it is merely creating an additional file.
nginx supports it by default without requiring any extra work, however, support is not limited to nginx. Other webservers can also make use of it, if configured accordingly. Some searching can find some ways to set it up:
Lighttpd: http://redmine.lighttpd.net/issues/611
Apache: https://stackoverflow.com/questions/16883241/how-to-host-static-content-pre-compressed-in-apache
I'm sure it could work in any webserver software as long as you configure it properly.
If I could've done it in a plug-in, I would've. I have purposefully avoided using "nginx" in the code / descriptions of things, as it is what it is: precompression of files. I understand that it might seem unusual to put this in the core, but to me it didn't really seem to have another place. It's either upon creation of said resources, or doing everything by hand externally out of Grav, not knowing when asset files are created.
Daniël

Any update about this PR @Eihrister ?

lighttpd mod_deflate can compress and save the compressed result in a cache if deflate.cache-dir is set in lighttpd.conf.  Then, subsequent requests (with Accept-Encoding) will receive the already-compressed file from the cache.
If you pre-compress the files yourself (gzip, brotli, zstd, ...), you can use lighttpd mod_magnet to run a small lua script for content negotiation, e.g. content-negotiation.lua


Make the handler accept other messages than the http_request

Currently the lua actor only accepts http_request messages, but that heavily limits it's functionality, so torchbear apps cannot schedule stuff, cannot have a repl, cannot create new actors, etc.

you're talking about the bridge?
https://github.com/foundpatterns/torchbear/blob/f5a0b67aa5f9b3be7d92037ee4add33a507dfbad/src/lib.rs#L94-L117

this is the plan for:
#19
#10
https://github.com/foundpatterns/torchbear/commit/b81bcc2e82d38bb0ac6b396843654eada2370b14 advanced it.
#121 is related

See also #168


Calling principal does not have required MSGraph permissions AuditLog.Read.All

Describe the bug
I am running an API using azure's API-driven provisioning to on-premises Active Directory.
After running the API using curl and verifying the user has been created in on premise AD, I want to read the api call's response using MS Graph.
Once I run the query such as:
https://graph.microsoft.com/v1.0/auditLogs/provisioning?$filter=(contains(changeId,'d93a226c-4cea-43f5-ae6f-b40a1e1e5973') and (jobId eq 'API2AD.42bee3df98534f9ab52933f3156060a0.285a406e-bc9a-4f37-b7f9-91bc3b65c333'))
It shows the below error
"error": {
"code": "Authentication_MSGraphPermissionMissing",
"message": "Calling principal does not have required MSGraph permissions AuditLog.Read.All",
"innerError": {
I then Consent to AuditLog.Read.All permission and request Admin to provide this access,
Graph Explorer access request approved
Your request has been approved. Details of your request are below.

This will help request exactly what's needed.
Screenshots

**Desktop **

OS: Windows
Browser Edge
Version

@mlakas01 what is the issue here?


83 conversion tools

ga2vcf.py WIP
Wanted feedback about if I'm producing sane VCF headers before moving on.
Running the tool produces this file:
##fileformat=VCFv4.0
##INFO=<ID=LDAF,Number=1,Type=float,Description="MLE Allele Frequency Accounting for LD"
##INFO=<ID=AVGPOST,Number=1,Type=float,Description="Average posterior probability from MaCH/Thunder"
##INFO=<ID=RSQ,Number=1,Type=float,Description="Genotype imputation quality from MaCH/Thunder"
##INFO=<ID=ERATE,Number=1,Type=float,Description="Per-marker Mutation rate from MaCH/Thunder"
##INFO=<ID=THETA,Number=1,Type=float,Description="Per-marker Transition rate from MaCH/Thunder"
##INFO=<ID=CIEND,Number=2,Type=int,Description="Confidence interval around END for imprecise variants"
##INFO=<ID=CIPOS,Number=2,Type=int,Description="Confidence interval around POS for imprecise variants"
##INFO=<ID=END,Number=1,Type=uint,Description="End position of the variant described in this record"
##INFO=<ID=HOMLEN,Number=0,Type=uint,Description="Length of base pair identical micro-homology at event breakpoints"
##INFO=<ID=SVLEN,Number=1,Type=int,Description="Difference in length between REF and ALT alleles"
##INFO=<ID=SVTYPE,Number=0,Type=char,Description="Type of structural variant"
##INFO=<ID=AC,Number=0,Type=uint,Description="Alternate Allele Count"
##INFO=<ID=AN,Number=1,Type=uint,Description="Total Allele Count"
##INFO=<ID=AA,Number=0,Type=char,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README"
##INFO=<ID=AF,Number=1,Type=float,Description="Global Allele Frequency based on AC/AN"
##INFO=<ID=AMR_AF,Number=1,Type=float,Description="Allele Frequency for samples from AMR based on AC/AN"
##INFO=<ID=ASN_AF,Number=1,Type=float,Description="Allele Frequency for samples from ASN based on AC/AN"
##INFO=<ID=AFR_AF,Number=1,Type=float,Description="Allele Frequency for samples from AFR based on AC/AN"
##INFO=<ID=EUR_AF,Number=1,Type=float,Description="Allele Frequency for samples from EUR based on AC/AN"
##INFO=<ID=VT,Number=0,Type=char,Description="indicates what type of variant the line represents"
##INFO=<ID=SNPSOURCE,Number=0,Type=char,Description="indicates if a snp was called when analysing the low coverage or exome alignment data"
##INFO=<ID=DS,Number=1,Type=float,Description="Genotype dosage from MaCH/Thunder"
##INFO=<ID=GL,Number=0,Type=float,Description="Genotype Likelihoods"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

Looks like a good start @dcolligan, thanks. Some comments:

I think it would be good to make this a first-class program like ga4gh_server or ga4gh_client that is installed in the users path by setuptools. So, we should put the code for it into cli.py and edit setup.py to add ga2vcf to the list of entry points. Then, I think you should be able to reuse the majority of the code you've written for the variants-search client command.
It's a pity that the pysam API doesn't output more modern VCF and take care of writing out the INFO types for us. Since we're hoping to move over to the new htslib interface that @bioinformed is working on soon, I wouldn't worry too much about moving to VCF version 4.2 for now. Let's get something that works reasonably well using the existing pysam API and transition to the new API when it's ready.

@bioinformed, what's your take on this? Will the htslib based API support outputting BCF and VCF transparently? Will we need to create the headers, or will it be possible to generate the VCF in a fully programmatic way? Thanks for looking into this by the way!

@jeromekelleher, the pysam VCF/BCF API will allow fully programmatic creation of headers and records.  This functionality is not yet implemented, since I'm hoping to get feedback and some real world feedback on the immutable interface before making everything mutable (and tackling some thorny issues with object lifetimes and keeping C/Python data structures in sync so that Python scripts cannot easily crash the interpreter).  Thus I think it is reasonable to keep hacking on a ga2vcf that writes straight VCF, since neither approach is rocket science and it will be a good template for when the mutable API is ready.

@jeromekelleher Good idea on the setup.py refactor.
I think my questions about this are motivated more by the mismatch between what the GA4GH API currently provides (e.g. no FILTER or FORMAT headers; having to make a bunch of other requests to build up the rest of the metadata like the sample column names) and the VCF format.
It seems like the latest (and default) version pysam supports is 4.0: https://github.com/pysam-developers/pysam/blob/0.8.1/pysam/cvcf.pyx#L292
@bioinformed thanks for the good feedback

@jeromekelleher Also, maybe our sample data isn't what the VCF API/format is expecting (e.g. the type strings not lining up)

This is true @dcolligan --- I've filed an issue for this in #129. What does the Google API return for these values?

Example Google API return value (part of a response from https://cloud.google.com/genomics/v1beta2/reference/variantsets/search ): https://gist.github.com/dcolligan/e122f4381be9e0e4bbb8

Ok this file header output by the new version of the code (pulling from google) looks more reasonable by @bioinformed 's standards (but see the comment in the code about pysam not supporting VCF 4.2)
##fileformat=VCFv4.0
##INFO=<ID=FORMAT,Number=1,Type=FLOAT,Description="Genotype dosage from MaCH/Thunder">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="GL based estimate of reference allele frequency">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Average posterior probability from MaCH/Thunder">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Raw read depth">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Genotyping depth model parameter M2">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from AFR based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=fileDate,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=FORMAT,Number=1,Type=FLOAT,Description="Genotype quality">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="Genotype Quality">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="For homozygous reference sites, the minimum genotype quality score">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Highest negative log10 concordance estimate with duplicate event">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="List of samples">
##INFO=<ID=INFO,Number=4,Type=INTEGER,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="# high-quality bases">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Assembly meta">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="End position of the variant described in this record">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="Phred-scaled strand bias P-value">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=INFO,Number=.,Type=INTEGER,Description="Allele count in genotypes">
##INFO=<ID=INFO,Number=.,Type=INTEGER,Description="Alternate Allele Count">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from EUR based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Total number of alleles in called genotypes">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Total Allele Count">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Phred probability of all samples being the same">
##INFO=<ID=contig,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=FORMAT,Number=.,Type=INTEGER,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Genotype imputation quality from MaCH/Thunder">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="GL based estimate of alternate allele frequency">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
##INFO=<ID=INFO,Number=4,Type=FLOAT,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Per-marker Mutation rate from MaCH/Thunder">
##INFO=<ID=INFO,Number=0,Type=FLAG,Description="Validation flag">
##INFO=<ID=FORMAT,Number=1,Type=STRING,Description="Genotype">
##INFO=<ID=FORMAT,Number=1,Type=FLOAT,Description="Copy number genotype quality for imprecise events">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Sum of homozygous reference likelihoods">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Sum of homozygous alternate allele likelihoods">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="Copy number genotype for imprecise events">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Phred scaled PCHI2.">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Genotyping depth model parameter M1">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Inner confidence interval around END for imprecise variants">
##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Genotype likelihoods">
##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Genotype Likelihoods">
##INFO=<ID=FORMAT,Number=3,Type=FLOAT,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from ASN based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Global Allele Frequency based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="List of duplicate events preferred to this one">
##INFO=<ID=source,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="MLE Allele Frequency Accounting for LD">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=INFO,Number=.,Type=INTEGER,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Assembly contig">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="indicates what type of variant the line represents">
##INFO=<ID=fileformat,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Validation method">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Inbreeding coefficient">
##INFO=<ID=ALT,Number=None,Type=UNKNOWN_TYPE,Description="Deletion">
##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Copy number likelihoods">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="Type of structural variant">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from AMR based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Sum of heterozygous likelihoods">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Highest reciprocal overlap with duplicate event">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=samtoolsVersion,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Per-marker Transition rate from MaCH/Thunder">
##INFO=<ID=INFO,Number=3,Type=FLOAT,Description="ML estimate of genotype frequencies">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Information about merged calls: SOURCE, POS, and END">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Cluster separation in depth-based genotyping model">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="Ancestral Allele, equal chimp reference allele">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Inner confidence interval around POS for imprecise variants">
##INFO=<ID=fileformat,Number=None,Type=UNKNOWN_TYPE,Description="None">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

Those headers still look pretty garbled.

Based on the spec, types are case sensitive and must be one of:
Integer, Float, Character, String or Flag (for INFO only).  The current
upper case values are illegal, as is UNKNOWN_TYPE.
Within INFO, FILTER, and FORMAT metadata, the ID values must be
unique.
All metadata types in your example are output as ##INFO when many
records are intended to be FORMAT or unstructured (key/value) metadata

e.g. ##INFO=<ID=source,Number=None,Type=UNKNOWN_TYPE,Description=
"None"> should be ##source=somevalue
e.g. ##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Genotype
likelihoods"> should be
##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype
likelihoods">

Here is a header from a random example file (using some VCF 4.1 features)
that shows how these metadata are intended to look:
##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the
ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth
(reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled
likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes,
for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each
ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in
called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from
Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth;
some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples
downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of
Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using
Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous
Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of
the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding
coefficient as estimated from the genotype likelihoods per-sample when
compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality
Zero Reads"> ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score
From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality
by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from
Wilcoxon rank sum test of Alt vs. Ref read position bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[reads.bam]
read_buffer_size=null phone_home=NO_ET read_filter=[]
intervals=[chr22:42020321-42527953] excludeIntervals=null
interval_set_rule=UNION interval_merging=ALL reference_sequence=
##contig=<ID=chr1,length=249250621,assembly=hg19>
##contig=<ID=chr10,length=135534747,assembly=hg19>
##contig=<ID=chr11,length=135006516,assembly=hg19>
##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
##contig=<ID=chr12,length=133851895,assembly=hg19>
##contig=<ID=chr13,length=115169878,assembly=hg19>
##contig=<ID=chr14,length=107349540,assembly=hg19>
##contig=<ID=chr15,length=102531392,assembly=hg19>
##contig=<ID=chr16,length=90354753,assembly=hg19>
##contig=<ID=chr17,length=81195210,assembly=hg19>
##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
##contig=<ID=chr18,length=78077248,assembly=hg19>
##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
##contig=<ID=chr19,length=59128983,assembly=hg19>
##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
##contig=<ID=chrX,length=155270560,assembly=hg19>
##contig=<ID=chrY,length=59373566,assembly=hg19>
... ##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta
On Thu, Feb 5, 2015 at 11:22 AM, Danny Colligan<EMAIL_ADDRESS>wrote:

Ok this file header output by the new version of the code (pulling from
google) looks more reasonable by @bioinformed
https://github.com/bioinformed 's standards (but see the comment in the
code about pysam not supporting VCF 4.2)
##fileformat=VCFv4.0
##INFO=<ID=FORMAT,Number=1,Type=FLOAT,Description="Genotype dosage from MaCH/Thunder">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="GL based estimate of reference allele frequency">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Average posterior probability from MaCH/Thunder">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Raw read depth">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Genotyping depth model parameter M2">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from AFR based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=fileDate,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=FORMAT,Number=1,Type=FLOAT,Description="Genotype quality">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="Genotype Quality">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="For homozygous reference sites, the minimum genotype quality score">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Highest negative log10 concordance estimate with duplicate event">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="List of samples">
##INFO=<ID=INFO,Number=4,Type=INTEGER,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="# high-quality bases">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Assembly meta">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="End position of the variant described in this record">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="Phred-scaled strand bias P-value">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=INFO,Number=.,Type=INTEGER,Description="Allele count in genotypes">
##INFO=<ID=INFO,Number=.,Type=INTEGER,Description="Alternate Allele Count">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from EUR based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Total number of alleles in called genotypes">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Total Allele Count">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Phred probability of all samples being the same">
##INFO=<ID=contig,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=FORMAT,Number=.,Type=INTEGER,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Genotype imputation quality from MaCH/Thunder">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="GL based estimate of alternate allele frequency">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
##INFO=<ID=INFO,Number=4,Type=FLOAT,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Per-marker Mutation rate from MaCH/Thunder">
##INFO=<ID=INFO,Number=0,Type=FLAG,Description="Validation flag">
##INFO=<ID=FORMAT,Number=1,Type=STRING,Description="Genotype">
##INFO=<ID=FORMAT,Number=1,Type=FLOAT,Description="Copy number genotype quality for imprecise events">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Sum of homozygous reference likelihoods">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Sum of homozygous alternate allele likelihoods">
##INFO=<ID=FORMAT,Number=1,Type=INTEGER,Description="Copy number genotype for imprecise events">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Phred scaled PCHI2.">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Genotyping depth model parameter M1">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Inner confidence interval around END for imprecise variants">
##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Genotype likelihoods">
##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Genotype Likelihoods">
##INFO=<ID=FORMAT,Number=3,Type=FLOAT,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from ASN based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Global Allele Frequency based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="List of duplicate events preferred to this one">
##INFO=<ID=source,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="MLE Allele Frequency Accounting for LD">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=INFO,Number=.,Type=INTEGER,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Assembly contig">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="indicates what type of variant the line represents">
##INFO=<ID=fileformat,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Validation method">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Inbreeding coefficient">
##INFO=<ID=ALT,Number=None,Type=UNKNOWN_TYPE,Description="Deletion">
##INFO=<ID=FORMAT,Number=.,Type=FLOAT,Description="Copy number likelihoods">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="Type of structural variant">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Allele Frequency for samples from AMR based on AC/AN">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Sum of heterozygous likelihoods">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Highest reciprocal overlap with duplicate event">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=samtoolsVersion,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=1,Type=INTEGER,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Per-marker Transition rate from MaCH/Thunder">
##INFO=<ID=INFO,Number=3,Type=FLOAT,Description="ML estimate of genotype frequencies">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=INFO,Number=.,Type=STRING,Description="Information about merged calls: SOURCE, POS, and END">
##INFO=<ID=INFO,Number=1,Type=FLOAT,Description="Cluster separation in depth-based genotyping model">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
##INFO=<ID=INFO,Number=1,Type=STRING,Description="Ancestral Allele, equal chimp reference allele">
##INFO=<ID=reference,Number=None,Type=UNKNOWN_TYPE,Description="None">
##INFO=<ID=INFO,Number=2,Type=INTEGER,Description="Inner confidence interval around POS for imprecise variants">
##INFO=<ID=fileformat,Number=None,Type=UNKNOWN_TYPE,Description="None">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT
—
Reply to this email directly or view it on GitHub
https://github.com/ga4gh/server/pull/126#issuecomment-73075409.

@bioinformed Thanks for the feedback.  Question for you about the pysam source: what is a "numbertype" https://github.com/pysam-developers/pysam/blob/50698a6e2b8c39dc0d59172554a4e902681014b0/pysam/cvcf.pyx#L245 and how can they be derived?  Most objects that are passed to pysam's format_format need this attribute: https://github.com/pysam-developers/pysam/blob/50698a6e2b8c39dc0d59172554a4e902681014b0/pysam/cvcf.pyx#L424

@dcolligan: numbertype is to accommodate the non-numeric cardinality specifiers allowed by the VCF spec (e.g. see https://samtools.github.io/hts-specs/VCFv4.2.pdf section 1.2.2).
NT_UNKNOWN: an unknown number of values (Number=".")
NT_NUMBER: a fixed integral number of values (Number=[0-9]+)
NT_ALLELES: the number of values is equal to the number of alleles (Number=R)
NT_NR_ALLELES: the number of values is equal to the number of alt alleles (Number=A)
NT_GENOTYPES: [..] of unphased genotypes (Number=G)
NT_PHASED_GENOTYPES: intended to be the number of phased genotypes, but isn't supported by VCF 4.0 - 4.2

I've never used this pysam API before, so there may be nuances that I'm missing.

@jeromekelleher can you review the first 250 lines of ga4gh/ga2vcf.py ?  It produces this file on a sample run: https://gist.github.com/dcolligan/580d430c37dc107cfd3b

This is good progress, thanks @dcolligan. It's a pity we've got so much work to do here, but I guess this is how we figure out the problems with the protocol.
At a high level, I wonder if we can simplify things a bit. I think it would be useful split the work into two things: (1) a UI; and (2) a class that takes some arguments and writes a VCF (or SAM) stream to an opened file handle. All of the UI functionality should be isolated into cli.py.  We should be able to reuse all of the functionality for variants/search here, as this is almost exactly what we're doing. So, use the the RequestFactory to create a SearchVariantsRequest object, which is populated from the command line args. We then create a VcfConverter object and pass it this request and a file handle (sys.stdout for now).
I think it would also be good to group the conversion tools into a single module. So, we create a module called ga4gh.converters or something, and this has two classes VcfConverter and SamConverter that present a consistent interface. Something like
class VcfConverter(AbstractConverter):
    def __init__(self, searchVariantsRequest, outputFile):
         # init
    def convert(self):
         # Do the actual conversion

Creating the SearchVariantsSetsRequest object should be as simple as
request = protocol.GASearchVariantSetsRequest()
request.datasetIds = self._searchVariantsRequest.datasetIds

which isn't worth the bother of using a factory for. Making the callsets request should be similarly simple. This avoids the circular import problem you mentioned in #144.
With respect to the specific conversion code, I'm finding it tricky to figure out what type of objects you're working with in the various places. Maybe you could put a ga prefix on some of the variables to make this a bit more obvious (e.g., gaMetadata)?
Having a quick scan of the VCF output, it looks roughly right to me (but I'm absolutely not a VCF expert). You seem to be missing the FORMAT field in the data line though, and the sample fields need genotype information and so on.
I think you're making great progress on a tricky problem here; hopefully with these simplifications we'll be able to iterate to a rough POC converter soon. We're really aiming at @bioinformed's BCF interface, so it's not worth putting  a lot of effort polishing this right now.

Pysam 0.8.2 has been released with BCF support. We should move over to this interface immediately, as the older VCF code isn't helping all that much.
The source is the best documentation.

The VCF/BCF API in pysam 0.8.2 doesn't allow for creation of files and
records from scratch.  So it is currently feasible to use the new code as a
backend, it isn't yet possible to use it for ga2vcf.  I'm working on adding
the mutable API right now, so it will be a few more weeks before alpha code
is ready and a few more before it part of the next pysam release.
On Wed, Feb 18, 2015 at 1:57 AM, Jerome Kelleher<EMAIL_ADDRESS>wrote:

Pysam 0.8.2 has been released
https://github.com/pysam-developers/pysam/releases with BCF support. We
should move over to this interface immediately, as the older VCF code isn't
helping all that much.
The source
https://github.com/pysam-developers/pysam/blob/master/pysam/cbcf.pyx is
the best documentation.
—
Reply to this email directly or view it on GitHub
https://github.com/ga4gh/server/pull/126#issuecomment-74839044.

Thanks for the clarification @bioinformed, this is good to know.

Been working on the SAM tool a bit... Would like some feedback on the TODOs in ga4gh/ga2sam.py, if anyone has any.  python ga2sam_dev.py --key MY_KEY --workarounds google reads-search --start 51005353 --end 51005354 --readGroupIds ChhDTXZuaHBLVEZoQ2JpT2J1enZtN25Pb0IQAA --referenceName 22 --pageSize 1 https://www.googleapis.com/genomics/v1beta2/ produces this file: https://gist.github.com/dcolligan/27e4d41c4730879e6939

Closing this PR for now... will file a separate one once we decide to implement ga2vcf


Swift Example Scroll to Bottom not working correctly

In the Swift Example, when the text is entered it's not scrolling to the last entered row.
I've tried modifying the slk_scrollToBottomAnimated function in "UIScrollView+SLKAdditions.m" and couldn't get it to work. Might be issue with contentSize.height?

(CGRect)slk_bottomRect
{
return CGRectMake(0, self.contentSize.height - CGRectGetHeight(self.bounds), CGRectGetWidth(self.bounds), CGRectGetHeight(self.bounds));
}

self.inverted = false
In the Swift example provided yes.

Tried at that commit. Works a bit better at the start.
But after a row is inserted below the keyboard the last inserted is row is never shown. Have to scroll down to see.
Tried with inverted = YES as well. Same issue. I'm using it with the Swift CollectionView Example. The objective-c examples work though. Might be issue with the custom Cell (SLKMessageViewCell) provided in the example? If so I can debug further.

Porting the programatic Table View example to Swift fixed the issue for me.
The scrolling issue was due to using self.tableView.slk_scrollToBottomAnimated(true) in didPressRightButton function.
Instead used these as in the Programatic Table View Example.
`var scrollPosition: UITableViewScrollPosition = self.inverted ? UITableViewScrollPosition.Bottom : UITableViewScrollPosition.Top
self.tableView.scrollToRowAtIndexPath(idxPath, atScrollPosition: scrollPosition, animated: true)
self.tableView.reloadRowsAtIndexPaths([idxPath], withRowAnimation: UITableViewRowAnimation.Automatic)`

hey @maail, I'm facing a similar issue with the inverted tableview.
I've been diggining around but couldn't find a definite answer - has this problem been already solved?
Trying your solution now but unfortunately getting a lot of jumping, inaccurate positioning and in some weird behavior with keyboard in general. Do you have any example of it working at hand?


FS Context

This PR tracks implementation of contexts, which will be used to isolate FS trees (much like chroot)
It will resolve #124.

@konsumer @mcandeia,
Do you have any feedback on this feature before I merge it? For reference, you can use it like so:
import { bindContext, fs } from '@zenfs/core';

const fs1 = bindContext('/root_1');

fs1.writeFileSync('/example.txt', 'Not in the real root.');
fs.readFileSync('/root_1/example.txt', 'utf8'); // file contents
fs1.readdirSync('/../../../..'); // still

const fs2 = bindContext('/root_2', { uid: 100, gid: 100 });

Feel free to review the code.

I've merged this PR after some feedback from Marcos. If David has any feedback, I'll handle it on the main branch.


Aggregate cluster roles to known cluster roles

ClusterRoles can be automatically bound to users who are already bound
to another ClusterRole. By doing so, we prevent having to manually bind
the ClusterRole to each namespace that uses the CRD.
[0] https://kubernetes.io/docs/reference/access-authn-authz/rbac/#aggregated-clusterroles
Signed-off-by: Luiz Carvalho<EMAIL_ADDRESS>

@hacbs-contract/devs ptal


pr(archai): Enables training when running NLP-based NAS.

This PR introduces the following changes:

Enables training when running NLP-based NAS as default;
A proxy-based search (without training) can be enabled through a --use_training_proxy argument;
Tweaks dllogger to disable when running multiple times using a same script (originally, it would throw an error if dllogger has already been enabled).

I would suggest to add Dey for review for search related code.

Sure! He is already added as a reviewer in this PR.


Incorrect QR Code for Playstore

App url is incorrect for Playstore app.
Problem
The application link for google playstore is either broken or moved to another
Solution
Please update the QR Code for Google Playstore.

I have updated the QR Code and have issued PR, please check and approve it.


[Feature Request] Generate standalone IconComponent per icon type

<!-
I'm submitting a...

[ ] Regression (a behavior that used to work and stopped working in a new release)
[ ] Bug report
[ ] Performance issue
[X] Feature request
[ ] Documentation issue or request
[ ] Support request
[ ] Other... Please describe:

Current behavior
One single IconComponent with support for icon types
Expected behavior
Multiple IconComponents, declared as standalone. They will not have input iconType, but will directly use SVG.
As they will be declared as standalone, it will be a tree shakable solution as well

Do you want to create a PR?

How do you think should look like original icon, as a handlebar template?

The issue with your suggestion in general is that it will increase the bundle code size because we generate additional components.

In the current implementation we support tree-shaking, so what's the benefit of your suggestion?

It allows usage of specific icons - instead of specifying key='leftArrow' we can use LeftArrowIcon, without any registry.
Also it will be safer, now key of svg-icon is string, not the actual icon type

I understand this, but on the other side, it will increase your bundle size. I don't mind leaving this decision to the consumer.


Add Issue and PR templates to the repository

Hello CourseGuard!
To make it easier for contributors to raise issues and pull requests (PRs) in a consistent way, I suggest adding templates for both. These templates will guide contributors by providing a clear format to follow, which will help maintainers manage and review issues and PRs more efficiently. The templates will also ensure that important information is provided from the start, making it quicker to address contributions.
Please assign me to this issue, I would love to work on this!

You have been assigned please complete it within 1 week

@Krishi1211 Hi, I just realized I missed this earlier—could you please add the 'WoB' labels to this and the PR? Thanks!


fix for #86, added default color scheme

#86

@dderiso do have a fork somewhere?

I did, but I guess I deleted it when I was Spring cleaning my Github a few days ago. Looks like the PR was never accepted by @math2001. @alexanderadam, if it's helpful to you, take a look at my code in this PR ( https://github.com/math2001/MarkdownLivePreview/pull/87/commits/e828df2356bf5a0f191d4c7efdc5fac121075e14 ) and see if you can replicate the changes.

@dderiso thank you for your fast response. I saw the patch but I'm not quite sure where I can find functions.py on my local system to patch it.


West doesn't find extension commands when run in a workspace without any additional modules

Describe the bug

When running west within a workspace that only contains zephyr and no additional modules, west doesn't find the extension commands in /scripts/west_commands.yml. E.g. 'zephyr-export.'
To Reproduce

Initialise a workspace with a manifest that just contains zephyr and no additional modules:
E.g.
app/west.yml

manifest:
  remotes:
    - name: zephyrproject-rtos
      url-base: https://github.com/zephyrproject-rtos
  projects:
    - name: zephyr
      remote: zephyrproject-rtos
      revision: v4.0.0

west init -l app
west update

Run west or one of the west extension commands
west help
west zephyr-export

Expected behavior

West should be able to detect and run the extension commands in /zephyr
Impact

Annoyance
Logs and console output

west: unknown command "zephyr-export"; workspace {workspace_path} does not define this extension command -- try "west help" and "west -vv status"

Environment (please complete the following information):

OS: Linux
Toolchain: just Zephyr
v4.0.0

Just realised this should go under the west repo instead - my mistake!