[Feedback] Regarding testing of new features

I'm really enjoying the project but there are still many options missing regarding the XML files. That is not a problem in its self as I have no problem with patching those in myself and opening pull request but I'm unsure how to implement testing for those new features. In my last pull request I created a new test but I don't think that that would be feasible to do for each new element. Alternative I could create one test and gradually update them or maybe don't write a test at all? That's what I would like your feedback on, so I don't trash the repository while still ensuring correct translation from nix to XML.

If you're just updating files in generate-xml/ by adding more elements and attributes in the same way as the existing code, then you don't need to add new tests.
If you're doing something new or modifying generate-xml/generate.nix or generate-xml/xml.nix, etc., then you should make sure that is covered one way or another.

Thanks for the clarification


'viur build release' only updates to latest Version

Yes, here comes further information!
I want to stick to a specific version in project.json, and define this:
{
    "cli-version": "2.0.3",
    "default": {
        "builds": {
            "admin": {
                "command": "viur package install admin default 4.5.12",
                "kind": "exec",
                "version": "4.5.12"
            }
        }
    }
}

Then I run viur build release and the project.json looks like this:
{
    "cli-version": "2.0.3",
    "default": {
        "builds": {
            "admin": {
                "command": "viur package install admin",
                "kind": "exec",
                "version": "4.5.12"
            }
        }
    }
}

It is IMPORTANT that viur-cli uses the version specified as "version", and only updates when something like viur package update is being executed!!!

What about chaning the old format structure
{
    "cli-version": "2.0.3",
    "default": {
        "application_name": "my-project",
        "builds": {
            "admin": {
                "command": "viur package install admin default 4.5.12",
                "kind": "exec",
                "version": "4.5.12"
            },
            "dashboard": {
                "clean": "rm -rf deploy/static/dashboard && rm -rf sources/app/node_modules",
                "command": "build",
                "kind": "npm",
                "source": "app"
            },
            "scriptor": {
                "command": "viur package install scriptor default 2.1.2",
                "kind": "exec",
                "version": "2.1.2"
            }
        },
        "distribution_folder": "./deploy",
        "sources_folder": "./sources",
        "version": "$(year)-$(month)-$(day)-$(user)"
    },
    "format": "2.0.0"
}

generally to a new format structure
{
    "cli-version": "2.0.3",
    "default": {
        "application_name": "my-project",
        "builds": {
            "dashboard": {
                "clean": "rm -rf deploy/static/dashboard && rm -rf sources/app/node_modules",
                "command": "build",
                "kind": "npm",
                "source": "app"
            },
        },
        "packages": {
            "admin": "4.5.12",
            "scriptor": "2.1.2"
        },
        "distribution_folder": "./deploy",
        "sources_folder": "./sources",
        "version": "$(year)-$(month)-$(day)-$(user)"
    },
    "format": "2.0.0"
}

Before starting the Task of changing the format, i would like to fix the bug for the Version 2.1.0 deployment. Afterwards it is a generally good idea to rethink the way the ViUR Community wants to use the project json (As a document to customize their workflow by editing it or just as a collection of information about the project itself that should not be edited)


Add Typo3 Theme

Thanks for contributing to Wagtail! 🎉
Before submitting, please review the contributor guidelines https://docs.wagtail.io/en/latest/contributing/index.html and check the following:

Do the tests still pass? (https://docs.wagtail.io/en/latest/contributing/developing.html#testing)
Does the code comply with the style guide? (Run make lint from the Wagtail root)
For Python changes: Have you added tests to cover the new/fixed behaviour?
For front-end changes: Did you test on all of Wagtail’s supported browsers? Please list the exact versions you tested.
For new features: Has the documentation been updated accordingly?

Known issue: some automatically generated docs are wrapped in quote blocks. example

Thanks for this @allcaps!
Would it be possible to squash the commits, or split this into multiple PRs to make it easier to see what's going on?

@kaedroho I've extracted the content changes here: https://github.com/wagtail/wagtail/pull/6835

Since opening this pull request we have decided to create our own sphinx theme (sphinx_wagtail_theme) instead of trying to hack the typo3 theme to fit our needs - which is what this pull request is doing.
Content changes in this PR were merged seperately in https://github.com/wagtail/wagtail/pull/6835
Going to close this in favor of https://github.com/wagtail/wagtail/pull/6930


added integrations to article

Status
Ready/In Progress/In Hold (Reason for hold)
Related Issues
related: https://jira-hq.paloaltonetworks.local/browse/CIAC-2068
Description
Added the reply-mail commands to EWSO365 and gmail single user. therefore, added to the article that those integrations are now part of the email communication pack
Screenshots
Paste here any images that will help the reviewer

@yucohen I fixed several links that were broken and replaced links to graphics that were not correct.  Doc review completed.


System.String error.

Hi Russell.
First off, thanks for such an awesome script. I ran it in my test lab and all of the ADMX settings came across. However, I did have some GP push items in there that did not get copied over. I did note that there was a couple of system.string errors that occurred that may be related to this.
Method invocation failed because [System.String] does not contain a method named 'RemoveAll'
At C:\temp\CopyOfficeGPO2013to2016\Copy-OfficeGPOSettings.ps1:866 char:17
Method invocation failed because [System.String] does not contain a method named 'RemoveAll'.
At C:\temp\CopyOfficeGPO2013to2016\Copy-OfficeGPOSettings.ps1:867 char:17
Cheers.

Thank you for your feedback! We will take a look at the string errors. Can you provide some specifics on the Push items that didn't come over.  That would help us to figure out what we are missing.

Not a problem.
Interestingly, i reran the script with the push items removed and the same error occurred. so it might not be the push items that are a problem. I have attached the reports of the original Source and target policies so you can check out the push items anyway.
GPO_reports.zip
Also, I am a bit intrigued as to why, in this section,
$Paths = [string]"$sysvolDir$domain\Policies{$ID}\User\Registry.pol",
"$sysvolDir$domain\Policies{$ID}\Machine\Registry.pol";
$commentPaths = ("$sysvolDir$domain\Policies{$ID}\User\comment.cmtx",
"$sysvolDir$domain\Policies{$TargetID}\User\comment.cmtx"),
("$sysvolDir$domain\Policies{$ID}\Machine\comment.cmtx",
"$sysvolDir$domain\Policies{$TargetID}\Machine\comment.cmtx");
the $ID and $targetID are doubled up for $commentPaths and not for $Paths. The doubling up also does not seem to fit how it the Array elements for $commentPaths is used around line 858 onwards. But i could be competely wrong...

@jamiewhitehead is this still an issue? Please let us know if we need to dig further into the issue.

@jamiewhitehead Please let us know if this is still an issue and we can revisit.

Hi,
to be honest, I have not used the script for 4 months or so now. It was
certainly useful at the time, but most of my customers are on Office 2016
now.
Cheers.
On Sat, Oct 8, 2016 at 5:31 AM, AStigall<EMAIL_ADDRESS>wrote:

@jamiewhitehead https://github.com/jamiewhitehead Please let us know if
this is still an issue and we can revisit.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/OfficeDev/Office-IT-Pro-Deployment-Scripts/issues/89#issuecomment-252327342,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AQ4ezWsbTq29knCiY7D_kbQnR9hgSrJ9ks5qxpAYgaJpZM4HquZq
.


CDS-94177

Release Notes for CD 1.30.x
Includes issues from the following lists that are marked release candidate.
https://harness.atlassian.net/wiki/spaces/PD/pages/21705981968/NG+Release+SAAS+March+18th+2024+for+1.30.x-+Build
https://harness.atlassian.net/wiki/spaces/PIPE/pages/21705949229/Change+List+for+Pipeline+Service+Build+1.67

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step behind the Harness VPN and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app. Current Draft URL is: https://65facddd99b21a00aec8e809--harness-developer.netlify.app

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step behind the Harness VPN and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app. Current Draft URL is: https://65fbf705df8ffd9b59377509--harness-developer.netlify.app

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step behind the Harness VPN and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app. Current Draft URL is: https://65fd6170561236002a24b9e9--harness-developer.netlify.app

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step behind the Harness VPN and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app. Current Draft URL is: https://660292ce55b2e500a6d67c8e--harness-developer.netlify.app

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step behind the Harness VPN and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app. Current Draft URL is: https://6602bbf10cdeb1246a2668f5--harness-developer.netlify.app

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step behind the Harness VPN and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app. Current Draft URL is: https://6602be94d29313276a8ee71f--harness-developer.netlify.app


Color is muted when unlocking Atom on Macbook external monitor

Description
When unlocking mac OS on a macbook when atom is on a second monitor, the color of syntax highlighting is muted. The color fixes when the pane is updated by changing tabs. The screenshot below shows the muted color on the left, and the correct color (by changing the tab) on the right.
This does not appear to happen when waking the computer if atom is on the laptop screen. Its hard to tell, but the color appears to be fine for a split second, and then muted once the window is force-resized. This may happen on a desktop, but I don't have one to test with.

Steps to Reproduce

Open Atom on a second, external monitor on a macbook
Allow Mac to lock from inactivity OR lock from the lock in the toolbar. The System "Sleep" command will not work.
Wake the mac, and unlock the screen

Expected behavior: Color should appear normally
Actual behavior: Color is muted.
Versions
Atom    : 1.10.2
Electron: 0.37.8
Chrome  : 49.0.2623.75
Node    : 5.10.0

Does this occur in safe mode (atom --safe)?

Yes, it does

Based on the screenshot, it looks like the left side isn't sub-pixel rendered.

Left
Right

/cc @as-cii

@simurai Wow, good catch. I never would have thought to check that =)

@50Wliu I have successfully reproduced this issue on 2 of my coworkers machines, if that helps.


Support docker system-related API endpoints

Description
Add support for docker system as described in the docs
I looked but could not find any reference to it neither in the code or in any issue.
If this is duplicated let me know.
If this is the first time it is referenced, I would be interested in contributing this feature and would like to know if it would make sense and if there are any things I might need to check besides README etc.

Hi @rtfpessoa ,
Since this project went on mature status, please re-open this issue (if it still stands) to https://github.com/dmandalidis/docker-client. Thanks


UnboundLocalError

@emedvedev ,  @brishtiteveja
Hi,
I follow the steps above the file,when i run aocr train datasets/training.tfrecords  ,got the  error ：
File "/home/shengcheng/anaconda2/lib/python2.7/site-packages/aocr/model/model.py", line 351, in train
% (self.sess.run(self.global_step), step_time, loss, perplexity))
UnboundLocalError: local variable 'perplexity' referenced before assignment
I set perplexiy=100,then
2017-09-05 09:26:58.269298: I tensorflow/core/common_runtime/simple_placer.cc:697] Ignoring device specification /device:GPU:0 for node 'map_1/while/foldr/while/TensorArrayReadV3/Enter' because the input edge from 'map_1/while/foldr/TensorArray' is a reference connection and already has a device field set to /job:localhost/replica:0/task:0/device:CPU:0
I'm a beginner ,How should I change it?  If I want to train Chinese, do I also modify  other files ?
thank you very much indeed

local variable 'perplexity' referenced before assignment

This error was be fixed in the latest release. Just update the module.

If I want to train Chinese, do I also modify other files

If you want to train Chinese, you should modify the mapping in data_gen.py and the target_vocab_size parameter. When you train (and later, run) your model, it works with tokens (1, 2, 3) instead of characters (a, b, c). In your case, the tokens will be Chinese characters instead of latin alphabet, and target_vocab_size should be the number of possible characters + 10 for numbers + 3 for control characters.


feat: Implement GetSize for array

I hereby agree to the terms of the RisingWave Labs, Inc. Contributor License Agreement.
What's changed and what's your intention?
Implement the EstimateSize trait for array. The main part is estimated_heap_size. This is the first step to implement #6456

Checklist For Contributors

[x] I have written necessary rustdoc comments
[x] I have added necessary unit tests and integration tests
[x] I have added fuzzing tests or opened an issue to track them. (Optional, recommended for new SQL features #7934).
[x] I have demonstrated that backward compatibility is not broken by breaking changes and created issues to track deprecated features to be removed in the future. (Please refer to the issue)
[x] All checks passed in ./risedev check (or alias, ./risedev c)

Checklist For Reviewers

[x] I have requested macro/micro-benchmarks as this PR can affect performance substantially, and the results are shown.

Documentation

[x] My PR DOES NOT contain user-facing changes.

Click here for Documentation
Types of user-facing changes
Please keep the types that apply to your changes, and remove the others.

Installation and deployment
Connector (sources & sinks)
SQL commands, functions, and operators
RisingWave cluster configuration changes
Other (please specify in the release note below)

Release note

Maybe use https://github.com/singularity-data/risingwave/blob/7b0f2d21d278013faca232d399d0366352b240e0/src/common/src/collection/estimate_size.rs#L20 we maintained?

The implementation feels like it could be derive on a struct to recursively handle all its fields. Not sure how much we would like to invest on it.
Rest lgtm

We can have sth like crate get-size to derive it, but let's do it later.


Fix error of spark 2.4 k8s job

The job spark-integration-test-minikube-k8s is failed
due a reason "io.fabric8.kubernetes.client.KubernetesClientException:
404 page not found", and the spark community reply this
because too old a version of k8s we used, maybe some service
endpoints not existing.
This upgrades minikube to v0.34.1, upgrades kubernetes to v1.13.3.
And seems the tests passed, see the test patch:
https://github.com/theopenlab/spark/pull/14
Related-Bug: theopenlab/openlab#310

LGTM


heatmap and ui design

Also, since our app is probably going to start getting complicated, are we able to separate the UI and server elements as we didin the previous file structure?

Also, since our app is probably going to start getting complicated, are we able to separate the UI and server elements as we didin the previous file structure?

Yeah, I coincidentally deleted them last night but we need to separate them now.
Please don't approve the PR, we'll discuss it during the class.


Login panel not viewable in Safari and Firefox

Currently (Mai, 25th 2020) the login panel is not opening properly in Safari and Firefox. While #677 should fix issues with the fonts, something seems to be wrong with the polyfills as well. I attach a screenshot from Firefox that shows what happens if someone tries to open the Login dropdown. In Chrome everything is working as expected.

I can confirm this bug and would like to add, that this is reproducable on the official DSpace 7 demo page (https://dspace7-demo.atmire.com/) currently.
Console is showing several errors:


”Axente Sever” is listed in the drop-down menu

Description:
"Axente Sever" is listed in the drop-down menu alongside its corresponding county and commune, according to the law.
Precondition:
The website is up an running.

Step 1
Type "Axente Sever" in the search bar.

Expected results
The location is listed in the drop-down menu as "Comuna Axente Sever, SIBIU".


fluid.dataset and fluid.datasetquery objects missing

Hi, with download version 1.0.2 of FluCoMa-PD-Mac.dmg the fluid.dataset and fluid.datasetquery objects are missing. The respective helpfiles are there.

it is a library, they are all included in fluid_libmanipulation - see learn.flucoma.org/installation for a painless install.

Suggestion: link to learn.flucoma.org/installation in this readme


How to load the linear part in my code

Hello! I am new to machine learning and very appreciate your job. I have finished training and I donot know how to load the linear model in another file. Currently I load the Linear with the code below but the accuracy is Inconsistent with training process.
class linear(nn.Module):
    def __init__(self,n_features,n_classes):
        super(linear,self).__init__()
        self.model = nn.Linear(n_features,n_classes)

    def forward(self,x):
        return self.model(x)

linear_model = linear(model.inplanes,catagory_num).to(device)
linear_state = torch.load("linear.ckpt")["state_dict"]
linear_model.load_state_dict(linear_state,strict=False)

I changed my code but it still cannot work
    linear_model = linear(model.inplanes,catagory_num).to(device)
    linear_state = torch.load("linear.ckpt")["state_dict"]
    print(linear_state.keys())
    linear_state = {k:v for k,v in linear_state.items() if "classifier" in k}
    linear_model.load_state_dict(linear_state,strict=False)
    linear_model = linear_model.to(device)

Hi, can you explain a bit better what you are trying to do? Is there a specific reason why you didn't use main_linear.py

I have used main_linear.py to train the linear and then I want to load the linear and the encoder in another file. But I when I loaded them(ckpt files) with the above codes, the accuracy drop to only 1% in CIFAR100.
I use another files to load the linear because I need to use the contrastive models in another project.
Thanks a lot for your help.

I think the easiest way to do that is to pass a dummy backbone:
linear = METHODS["linear"](backbone=resnet18())
```
and then load a checkpoint using pytorch lightning:
```
linear.load_from_checkpoint("path_to_checkpoint")
```

Just to complement, what you are doing is just trying to load the linear classifier, and not the whole model (encoder + classifier). Also, there's a mismatch in names so the classifier is not being loaded as well. If you remove strict=False you will see an error poping up.

There is no error when I remove strict=False. But the accuracy is too low. I am sure I am using the correct test data set.

Ok, I have solved the problem, Thanks a lot.


Retain external transitions in envelopes

Retain external transitions in envelopes until they are added to the transition frontier. This is required because validations are done in different stages
Checklist:

[ ] Tests were added for the new behavior
[X] All tests pass (CI will check this if you didn't)
[ ] Serialized types are in stable-versioned modules
[ ] Does this close issues? List them:

Can we have
( ( external_transition_verified Envelope.Incoming.t
                            , state_hash )
                            With_hash.t
                          , state_hash )

rather than,
( ( external_transition_verified, state_hash )
                            With_hash.t) Envelope.Incoming.t

It seems more natural to me.  If you want the most outer layer to be With_hash, then it could convey that the hash include peer ip address.

The hash doesn't include the peer address.

@johnwu93 you mean the other way around? the way you request seems to be the way it already is. I agree that we should put the Envelope around the With_hash, not wrap the envelope with a With_hash.


refactor(ngSwitch):delete default directive restriction

delete the directive restriction to avoid code duplication since the default is already applied
Closes #10987

This is rebased #10987 to check on TravisCI


Post to FB - Other than feed/me

Can we have it to post on facebook other than just feed/me? something like post to particular page or group.

The core is limited to the feed. Please investigate adding a 3pillarlabs/socialauth plugin (check the wiki) and using it for other needs.


JS issue when using with @blueprintjs/core package

Discussed in https://github.com/idom-team/idom/discussions/452

Originally posted by rafaellichen July 28, 2021
Related issue ticket: https://github.com/palantir/blueprint/issues/4823
I tried to use @blueprintjs/core to render a button in the jupyter notebook with idom, but that results in js error in the browser console.
import idom
import idom_jupyter

blueprintjs = idom.web.module_from_template("react", "@blueprintjs/core", fallback="...")
bpbutton = idom.web.export(blueprintjs, "Button")

@idom.component
def ShowButton():
    return bpbutton()

ShowButton()

Tested using this environment: https://mybinder.org/v2/gh/idom-team/idom-jupyter/main?filepath=notebooks%2Fintroduction.ipynb
In the browser console, error: Uncaught (in promise) SyntaxError: Invalid or unexpected token
The error originates from the linked file core.js on: https://cdn.esm.sh/v43/<EMAIL_ADDRESS>Use text search to find the only code starting with 1.tolocal or t=1; this is where the error starts.

I still think it's syntax issue in the core.js file.Any other opinions?

it seems like a regular JS issue, but that piece of code looks syntactically correct as calling toLocaleString on a number is possible (https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Number/toLocaleString)

I'm going to close this in favor of the discussion for now. I'll recreate or reopen this issue once we determine what action needs to be taken in order to resolve the issue.

@rmorshea resolved by changing package build method


no such package '@gmock_archive//': Error downloading in Tensorflow (on ubuntu_X86 14.04)

I'm getting the following error when trying to run the configure command (on ubuntu_X86:14.04):
ERROR: /root/tf/tensorflow/tensorflow/workspace.bzl:221:3: no such package '@gmock_archive//': Error downloading
Please find the attached log for more details.
logfile.txt
Note- On ubuntu-ppc64le vm , configure command ran successfully.
Any suggestion/solution ?

Please provide details about what platform you are using  (operating system, architecture). Also include your TensorFlow version. Also, did you compile from source or install a binary?  Make sure you also include the exact command if possible to produce  the output included in your test case.   We ask for this in the issue submission template, because    it is really difficult to help without that information. Thanks!
Though, looking at the log file you provided and the errors like:
ERROR: /root/tf/tensorflow/tensorflow/workspace.bzl:221:3: no such package '@gmock_archive//': Error downloading [http://bazel-mirror.storage.googleapis.com/pkgs.fedoraproject.org/repo/pkgs/gmock/gmock-1.7.0.zip/073b984d8798ea1594f5e44d85b20d66/gmock-1.7.0.zip, http://pkgs.fedoraproject.org/repo/pkgs/gmock/gmock-1.7.0.zip/073b984d8798ea1594f5e44d85b20d66/gmock-1.7.0.zip] to /root/.cache/bazel/_bazel_root/8e11c3f2ede966708196f520db8b1e69/external/gmock_archive/gmock-1.7.0.zip: All mirrors are down: [Checksum was 49a998729226839bc06d6d4b8384af0c83e05e842b979193f43e1c3440e9cd16 but wanted 26fcbb5925b74ad5fc8c26b0495dfc96353f4d553492eb97e85a8a6d2f43095b, Checksum was dc73d26ce544ae4ba7f1ad6d305de0dee72bd953e4bfd9ba7170b2d5326946de but wanted 26fcbb5925b74ad5fc8c26b0495dfc96353f4d553492eb97e85a8a6d2f43095b] and referenced by '//external:gtest'

there seems to be some network error on the machine that might be truncating or corrupting the files.


Safari Users on Big Sur have Audio Distortion

Describe the bug
Audio on Safari 14.0.1 on Big Sur has massive amounts of distortion for the audio the Safari user is receiving. It is so bad that you can't understand what other people on the call are saying.
To Reproduce
Steps to reproduce the behavior:

Open a video call with one user in a stable browser (I.e. Chrome)
Have another user join in Safari on Big Sur.
User on Chrome starts talking, their audio will be heavily distorted for the user on Safari. Sometimes this seems to normalize after a variable amount of time.

Expected behavior
Audio should sound normal
Environment (please complete the following information):

OS: macOS 11.0.1
Browser: Safari 14.0.1
App Version: 0.2.1
SDK Version: 2.9.0
Node.js version: 14

Additional context
We've tested this on multiple different Macbooks (2013 MBP, multiple 2020 MBP's). We've tested it both on the demo app and our own version that we are running of Twilio Video.

Thanks for the bug report @jjp390!
We have experienced this same issue. It seems to happen intermittently, and it can resolve itself after a few seconds. While it happens, the audio is very distorted and almost sounds 'robotic'. We have seen this happen in rooms where all users are user Chrome.
We are still investigating the problem. I'll let you know as soon as we find anything.
In the meantime - there's a related ticket in the twilio-video repo:  https://github.com/twilio/twilio-video.js/issues/1304

@timmydoza any update on your investigation so far? We've also been experiencing similar issues quite frequently for the last three weeks or so. Any tips would be appreciated. Thanks!

We’re having a similar issue in Safari on iPadOS (latest version). The employee (using iPadOS) is always hearing the customer (on a ‘random’ device) with a robotic voice for the first minutes, similar the the video shared in https://github.com/twilio/twilio-video.js/issues/1304. Sometimes it also happens in the other direction.

We’re having a similar issue in Safari on iPadOS (latest version). The employee (using iPadOS) is always hearing the customer (on a ‘random’ device) with a robotic voice for the first minutes, similar the the video shared in https://github.com/twilio/twilio-video.js/issues/1304. Sometimes it also happens in the other direction.

Sorry @juan-ordonez - but the root cause of this issue hasn't been found. It's difficult to reproduce the issue.
How often does this issue occur for you? Please let us know if you have any ideas on how to reproduce the issue more reliably. Are there any specific steps that help? And what browser versions are you using?
@jhogervorst - it sounds like you may be encountering a separate issue. There's an audio issue that is specific to iOS 14.2. More info in the webkit bug and this github issue. Unfortunately, the only known fix is to upgrade to iOS 14.3.

Sorry @juan-ordonez - but the root cause of this issue hasn't been found. It's difficult to reproduce the issue.
How often does this issue occur for you? Please let us know if you have any ideas on how to reproduce the issue more reliably. Are there any specific steps that help? And what browser versions are you using?
@jhogervorst - it sounds like you may be encountering a separate issue. There's an audio issue that is specific to iOS 14.2. More info in the webkit bug and this github issue. Unfortunately, the only known fix is to upgrade to iOS 14.3.


Buffer source completion missing after last few commits

Hi, it may be on my end somehow, but I believe there may be an issue with some completion sources after the most recent commits.
Basically, I can't seem to get any completion besides LSP completion. For example, if I open a text file with some words in it, I get no completion for any of them even though they should provided with buffer completion enabled.
Below is my nvim-compe config:
require'compe'.setup {
  enabled = true;
  autocomplete = true;
  debug = false;
  min_length = 1;
  preselect = 'enable';
  throttle_time = 80;
  source_timeout = 200;
  incomplete_delay = 400;
  max_abbr_width = 100;
  max_kind_width = 100;
  max_menu_width = 100;
  documentation = true;

  source = {
    path = true;
    buffer = true;
    calc = true;
    vsnip = true;
    nvim_lsp = true;
    nvim_lua = true;
    spell = true;
    tags = true;
    snippets_nvim = true;
    treesitter = false;
  };
}

I am the latest neovim-nightly branch and latest version of this plugin.

I can't reproduce it.
Please provide minimal reproducible config that based on https://github.com/hrsh7th/nvim-compe/blob/master/misc/minimal.vim

@hrsh7th Thanks for the response. I actually see this when trying to trigger buffer completion with a minimal config:

Minimal config:
if has('vim_starting')
  set encoding=utf-8
endif
scriptencoding utf-8

if &compatible
  set nocompatible
endif

let s:plug_dir = expand('/tmp/plugged/vim-plug')
if !isdirectory(s:plug_dir)
  execute printf('!curl -fLo %s/autoload/plug.vim --create-dirs https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim', s:plug_dir)
end

execute 'set runtimepath+=' . s:plug_dir
call plug#begin(s:plug_dir)
Plug 'hrsh7th/nvim-compe'
call plug#end()
PlugInstall | quit

" Options or settings here.
set completeopt=menuone,noselect

let g:compe = {}
let g:compe.enabled = v:true
let g:compe.autocomplete = v:true
let g:compe.debug = v:false
let g:compe.min_length = 1
let g:compe.preselect = 'enable'
let g:compe.throttle_time = 80
let g:compe.source_timeout = 200
let g:compe.incomplete_delay = 400
let g:compe.max_abbr_width = 100
let g:compe.max_kind_width = 100
let g:compe.max_menu_width = 100
let g:compe.documentation = v:true

let g:compe.source = {}
let g:compe.source.path = v:true
let g:compe.source.buffer = v:true
let g:compe.source.calc = v:true
let g:compe.source.vsnip = v:true
let g:compe.source.nvim_lsp = v:true
let g:compe.source.nvim_lua = v:true
let g:compe.source.spell = v:true
let g:compe.source.tags = v:true
let g:compe.source.snippets_nvim = v:true
let g:compe.source.treesitter = v:true
let g:compe.source.omni = v:true

inoremap <silent><expr> <C-Space> compe#complete()
inoremap <silent><expr> <CR>      compe#confirm('<CR>')
inoremap <silent><expr> <C-e>     compe#close('<C-e>')
inoremap <silent><expr> <C-f>     compe#scroll({ 'delta': +4 })
inoremap <silent><expr> <C-d>     compe#scroll({ 'delta': -4 })

Thank you very very much!
I can reproduce it.
I will fix it soon.

I've fixed it. Thank you~.


Move prettyprinter and orderbook into a	"mdp" package

Breaking Change
The mdp pretty printer was not really setup as a proper module as there
was no good place to put it.  Also, the orderbook module is specific to
processing CME MDP messages.  By introducing a "mdp" package, we can have
a reasonable place to put both of these modules.

@tamboril Can you take a look at this and provide any feedback?
I ran into a problem with the pretty printer:
$ virtualenv x
$ source x/bin/activate
(x) $ python setup.py develop
(x) $ mdp_decoder.py --help
Traceback (most recent call last):
  File "/home/bud/src/sbedecoder/x/bin/mdp_decoder.py", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/home/bud/src/sbedecoder/scripts/mdp_decoder.py", line 15, in <module>
    import mdp_prettyprinter
ImportError: No module named mdp_prettyprinter

The issue is that the mdp_prettyprinter.py is in /scripts.  A workaround is to go ahead and add it to the scripts in setup.py but then it gets installed to /bin which doesn't seem right.  This change introduces a "mdp" package which gives us a place to put mdp3 specific code.


Page component

Here is a new component that should help us create pages that are consistent in terms of style and easier to make.
It retires PageHeader and SectionHeader.

Left minor unused stuff comments.
Biggest question is adoption by the team but only experience will tell. LGTM

Left minor unused stuff comments.
Biggest question is adoption by the team but only experience will tell. LGTM

So there are several things here:

It's simpler than tailwind (for someone who has not spent time on tailwind)
It avoids most of the inconsistencies (it always sets the right styles, it narrows down the spacing options…)
It's the only way if we want to manage darkmode efficiently some day

Yep yep :+1:


Contribute Converter codebase as it is at Apache Felix.

The Felix Community has agreed to migrating this codebase to Eclipse
(see https://www.mail-archive.com/dev%40felix.apache.org/msg52014.html)
This fixes #227

Thanks @bjhargrave I have amended the sources as requested.

I updated this PR to remove unnecessary changes (such as whitespace and removal of javadoc tags), format the code to our formatting rules, and remove a number of compiler warning introduced by the contributed changes.

The Felix Community has agreed to migrating this codebase to Eclipse
(see https://www.mail-archive.com/dev%40felix.apache.org/msg52014.html)

@bosschaert You should notify the Felix community that the code is now migrated and that they can now access the snapshots from https://oss.sonatype.org/content/repositories/snapshots/org/osgi/org.osgi.util.converter/1.0.8-SNAPSHOT/.
We, of course, welcome their contributions to improve the converter here!

A request has been made to perform a bugfix release of the Converter by the Apache Felix community. What would be the steps to perform this? https://www.mail-archive.com/dev%40felix.apache.org/msg52019.html

I think we need to do a first full release from the OSGi Specification Project before we can do bug fix releases of an artifact. Is there some specific fix in the code which Apache Felix has not already released? The email did not mention anything and just seemed to ask that we make a release.

For reference https://dev.eclipse.org/ipzilla/show_bug.cgi?id=23357 has approved this contribution.


Add pylint testing

Maintainers will complete the following section:

[x] Commit messages are descriptive enough
[x] "Signed-off-by:" line is present in each commit
[x] Code coverage from testing does not decrease and new code is covered

/packit copr-build

LGTM

/packit copr-build

no release notes, internal change only


Entities is initialized as a list, but code treats it as a set.

https://github.com/TStand90/tcod_tutorial_v2/blob/6e763f14a5a0345b6f3620c3ff3bd989145b5ac7/procgen.py#L92
Python 3.10 will break with other parts of the code such as.
for entity in self.game_map.entities - {self.player}:
TypeError: unsupported operand type(s) for -: 'list' and 'set'

It seems to be a simple fix - just declare it as {player}. I didn't make a pull request because I don't know in which part this "mistake" began, or if there's something else I'm missing.

GameMap's initializer always converts that input into a set, this part is missing from your code:
https://github.com/TStand90/tcod_tutorial_v2/blob/6e763f14a5a0345b6f3620c3ff3bd989145b5ac7/game_map.py#L14-L17
Your change would be a little more efficient though. Some classes would probably be better written with attrs.

Thank you, I missed that default when following your guide.
I believe it's not worth a change given that.


[CRASH] Game fails to start when installed with EnhancedVisuals

Logs
2023-05-31-2.log.gz
Mods

Version: MC 1.18.2
Modloader: Forge 40.2.4
EnhancedVisuals_FORGE_v1.6.4_mc1.18.2.jar
CreativeCore_FORGE_v2.6.16_mc1.18.2.jar
dawncraft-fixes-0.8.2.jar

These two errors are shown in console

[31/05/2023 00:44:37 a.m.] Exception in thread "main" org.spongepowered.asm.mixin.throwables.MixinApplyError: Mixin [enhancedvisuals.mixins.json:EntityAccessor] from phase [DEFAULT] in config [enhancedvisuals.mixins.json] FAILED during PREPARE
[31/05/2023 00:44:37 a.m.] Caused by: org.spongepowered.asm.mixin.transformer.throwables.MixinTargetAlreadyLoadedException: Critical problem: enhancedvisuals.mixins.json:EntityAccessor target net.minecraft.world.entity.Entity was loaded too early.

The log isn't match the issue. You should reproduce with only the three mods and provide the log

That log was before I tested with only those three mods sorry
2023-05-31-1.log.gz

To be honest I have no idea what causes this kind of error.

It seems other people also had this issue and it had somehow(?) been resolved: https://github.com/SpongePowered/Mixin/issues/388
Im hoping this too would somehow resolve but in the meantime, I will be downgrading some mods.

Can you reproduce with this? @DeshiDesu
dawncraft-fixes-0.8.2.zip

Can you reproduce with this? @DeshiDesu dawncraft-fixes-0.8.2.zip

It worked without any crashes! I will give you the log soon

As the https://github.com/SpongePowered/Mixin/issues/388 point out. I shouldn't call the logger from main class. Will publish a new version

Glad it helped 🙂


Add package bolt version 0.9.2

Merge Checklist

All boxes should be checked before merging the PR (just tick any boxes which don't apply to this PR)

[ ] The toolchain has been rebuilt successfully (or no changes were made to it)
[ ] The toolchain/worker package manifests are up-to-date
[ ] Any updated packages successfully build (or no packages were changed)
[ ] Packages depending on static components modified in this PR (Golang, *-static subpackages, etc.) have had their Release tag incremented.
[ ] Package tests (%check section) have been verified with RUN_CHECK=y for existing SPEC files, or added to new SPEC files
[ ] All package sources are available
[ ] cgmanifest files are up-to-date and sorted (./cgmanifest.json, ./toolkit/scripts/toolchain/cgmanifest.json, .github/workflows/cgmanifest.json)
[ ] LICENSE-MAP files are up-to-date (./SPECS/LICENSES-AND-NOTICES/data/licenses.json, ./SPECS/LICENSES-AND-NOTICES/LICENSES-MAP.md, ./SPECS/LICENSES-AND-NOTICES/LICENSE-EXCEPTIONS.PHOTON)
[ ] All source files have up-to-date hashes in the *.signatures.json files
[ ] sudo make go-tidy-all and sudo make go-test-coverage pass
[ ] Documentation has been updated to match any changes to the build system
[ ] Ready to merge

Summary

What does the PR accomplish, why was it needed?
Add package bolt version 0.9.2
Change Log

Change
Change
Change

Does this affect the toolchain?

YES/NO
Associated issues

NA

Links to CVEs

NA

Test Methodology

Pipeline build id: xxxx

Closing this as this needs to go to main.


[BUG] Duplicate Unique ID setting in OpenSearch transport

What is the bug?
OpenSearch's Security Plugin prevents connections that are not identified as a node.   As part of implementing security features, a transport header "extension_unique_id" was added to identify extension "nodes" to the plugin.
However, this header is being set twice and causing IllegalArgumentExceptions on initialization:
org.opensearch.bootstrap.StartupException: RemoteTransportException[[ad-extension][<IP_ADDRESS>:4532][internal:discovery/extensions]]; nested: IllegalArgumentException[value for key [extension_unique_id] already present];
	at org.opensearch.bootstrap.OpenSearch.init(OpenSearch.java:184) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.bootstrap.OpenSearch.execute(OpenSearch.java:171) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:104) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.cli.Command.mainWithoutErrorHandling(Command.java:138) ~[opensearch-cli-3.0.0.jar:3.0.0]
	at org.opensearch.cli.Command.main(Command.java:101) ~[opensearch-cli-3.0.0.jar:3.0.0]
	at org.opensearch.bootstrap.OpenSearch.main(OpenSearch.java:137) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.bootstrap.OpenSearch.main(OpenSearch.java:103) ~[opensearch-3.0.0.jar:3.0.0]
Caused by: org.opensearch.transport.RemoteTransportException: [ad-extension][<IP_ADDRESS>:4532][internal:discovery/extensions]
Caused by: java.lang.IllegalArgumentException: value for key [extension_unique_id] already present
	at org.opensearch.common.util.concurrent.ThreadContext$ThreadContextStruct.putSingleHeader(ThreadContext.java:590) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.common.util.concurrent.ThreadContext$ThreadContextStruct.putRequest(ThreadContext.java:584) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.common.util.concurrent.ThreadContext.putHeader(ThreadContext.java:401) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.transport.TransportService.lambda$connectionValidatorForExtensionConnectingToNode$15(TransportService.java:547) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.transport.ClusterConnectionManager.lambda$connectToNode$3(ClusterConnectionManager.java:158) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.action.ActionListener$1.onResponse(ActionListener.java:80) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.action.ActionListener$4.onResponse(ActionListener.java:180) ~[opensearch-3.0.0.jar:3.0.0]
	at org.opensearch.action.support.ThreadedActionListener$1.doRun(ThreadedActionListener.java:78) ~[opensearch-3.0.0.jar:3.0.0]

How can one reproduce the bug?
Start up an extension on a non-local node.
Start up OpenSearch and initialize the extension.
What is the expected behavior?
Extension is successfully initialized.
What is your host/environment?
Any remote host initialization: this has been seen in attempts to do performance testing on two servers, and in CI setup. It does not manifest when the extension node is local to the OpenSearch node, as the "localNode" code branches bypass the transport connection validation that throws the error.
Do you have any additional context?
The root cause is in the ExtensionsInitRequestHandler.  During the initial handling of a transport request by an extension, the header is added here:
https://github.com/opensearch-project/opensearch-sdk-java/blob/aa8886dee8301aeccdc1496ac67e9820860c4830/src/main/java/org/opensearch/sdk/handlers/ExtensionsInitRequestHandler.java#L77
That header is communicated back to OpenSearch with the response in this try block:
https://github.com/opensearch-project/opensearch-sdk-java/blob/aa8886dee8301aeccdc1496ac67e9820860c4830/src/main/java/org/opensearch/sdk/handlers/ExtensionsInitRequestHandler.java#L85-L89
However, because it is a transport connection, the response is asynchronous so the thread context on OpenSearch may not be immediately updated.
In the finally block immediately following this, the Extension creates a separate Transport Connection (if it has the right host and port, see #761, #769, and other related issues):
https://github.com/opensearch-project/opensearch-sdk-java/blob/aa8886dee8301aeccdc1496ac67e9820860c4830/src/main/java/org/opensearch/sdk/handlers/ExtensionsInitRequestHandler.java#L98-L101
Log files indicate this connection tends to update the header first, so when the earlier response is handled by an ActionListener, it causes the exception.
Possible fix 1:
See #767 to completely eliminate this second connection
Possible fix 2:
Have a different key for outbound vs. inbound Transport connections: the response on line 77 above could have "-outbound" appended to it, while the new connection on lines 98-101 could have "-inbound" appended.
Possible fix 3:
Check whether the header already exists on the connection.  Unfortunately given the multithreaded environment I'm not sure a simple conditional would work. It may be better to just catch the IllegalArgumentException and ignore this specific failure.
Possible fix 4:
In the ThreadContext header adding code, allow putting the same header twice.  Specifically, change
private static <T> void putSingleHeader(String key, T value, Map<String, T> newHeaders) {
    if (newHeaders.putIfAbsent(key, value) != null) {
        throw new IllegalArgumentException("value for key [" + key + "] already present");
    }
}

to
private static <T> void putSingleHeader(String key, T value, Map<String, T> newHeaders) {
    T oldValue = newHeaders.putIfAbsent(key, value);
    if (oldValue != null && !oldValue.equals(value)) {
        throw new IllegalArgumentException("different value for key [" + key + "] already present");
    }
}

Temporary workaround:
For near term testing "without security" change the connectToNodeAsExtension() back to connectToNode() in the SDK.

Links back to discussions on the original PR that connectToNodeAsExtension was introduced:

https://github.com/opensearch-project/opensearch-sdk-java/pull/619#discussion_r1174262875
https://github.com/opensearch-project/OpenSearch/pull/6866

It should not be setting the header twice and initially when implementing the TLS changes I only had putHeader called directly within ExtensionInitiRequestHandler here: https://github.com/opensearch-project/opensearch-sdk-java/blob/main/src/main/java/org/opensearch/sdk/handlers/ExtensionsInitRequestHandler.java#L77
I then faced a problem with connectToNode down below when it was performing a handshake with the cluster the header was not present. To fix that I explicitly set the header in connectToExtensionAsNode. A race condition may explain why it was not set during the call to connectToNode, but I'm still not positive.

We have a temporary fix that checks to see if the header is present before putting the header in the thread context.  Should I raise a PR with that change for now until we find the root cause?

@cwperks It's not consistent, but most of the time it occurs when running an extension, stopping it, and then running it again.

@ryanbogan @dbwiddis Can you post steps to reproduce the error? I am not able to reproduce this locally.

This is 100% reproducible in a cluster environment; set up a 1-CM 1-DataNode cluster using the CDK.  Shut down and start up the CM and observe the error.
I can work around the bug by changing the key used in the header in ExtensensionsInitResponseHandler, indicating that somehow this header is getting inserted in the map that later conflicts with the connectToNodeAsExtension call.
I'm really not sure what the purpose of adding the header to the OpenSearch transport connection from the SDK side is. Why don't we add that header on the OpenSearch side before we even establish the connection?

@dbwiddis Assuming that all transport actions are initiated from OpenSearch then it should be possible to populate the header similar to how the cluster name is populated here on all transport requests: https://github.com/opensearch-project/security/blob/d871af35da870118d5e5c5dbddff76452b9a4d9e/src/main/java/org/opensearch/security/transport/SecurityInterceptor.java#L151 as long as its possible to determine which extension a transport request is bound to.
I have been thinking about this header as another form of trusted cross cluster communication.


[Bug]: ViewAnnotationManager.swift throws error when running or building on iOS ^18

Mapbox Implementation
Mapbox
Mapbox Version
11.4.0
React Native Version
0.74.5
Platform
iOS
@rnmapbox/maps version
10.1.33
Standalone component to reproduce

iOS version 18.1 and Xcode 16.1
Install the related/latest versions
Run/build app then it throws error

Observed behavior and steps to reproduce
❌  (ios/Pods/MapboxMaps/Sources/MapboxMaps/Annotations/ViewAnnotationManager.swift:84:19)

  82 |     @available(*, deprecated, renamed: "allAnnotations", message: "Please use allAnnotations instead, or directly access ViewAnnotation itself")
  83 |     public var annotations: [UIView: ViewAnnotationOptions] {
> 84 |         idsByView.compactMapValues { [mapboxMap] id in
     |                   ^ cannot convert return expression of type '[UIView : ViewAnnotationOptions]' to return type 'Dictionary<String, Optional<JSONValue>>.RawValue'
  85 |             try? mapboxMap.options(forViewAnnotationWithId: id)
  86 |         }
  87 |     }

Expected behavior
Not to throw error due to ViewAnnotationManager.swift:84:19
Notes / preliminary analysis
No response
Additional links and references
This issue mentioned in https://github.com/rnmapbox/maps/issues/3640 but tagged as addressed and closed but still continues.

same problem


HELP !!!

Hi,
While running  mutational signatures, i have encountered the following error. I am not able to debug it. Please help me. I am a not tech guy, trying to understand my .maf file.
I am using Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa as my reference file.
It would be of a GREAT HELP if you can help me sorting out this issue.
Error as follows!!!
contigs in maf:
 [1] "chr10" "chr12" "chr22" "chr3"  "chr1"  "chr2"  "chr4"  "chr9"  "chr7"
[10] "chr16" "chr17" "chr19" "chr6"  "chr13" "chr11" "chr20" "chr18" "chr5"
[19] "chr14" "chr15" "chrX"  "chr8"  "chr21" "chrY"
missing reference contigs from fasta file.
 [1] "chr10" "chr12" "chr22" "chr3"  "chr1"  "chr2"  "chr4"  "chr9"  "chr7"
[10] "chr16" "chr17" "chr19" "chr6"  "chr13" "chr11" "chr20" "chr18" "chr5"
[19] "chr14" "chr15" "chrX"  "chr8"  "chr21" "chrY"
Contig names in MAF must match to contig names in reference fasta. Ignorinig 29573 single nucleotide variants from chr10, chr12, chr22, chr3, chr1, chr2, chr4, chr9, chr7, chr16, chr17, chr19, chr6, chr13, chr11, chr20, chr18, chr5, chr14, chr15, chrX, chr8, chr21, chrY
Error in trinucleotideMatrix(maf = laml, ref_genome = "/home/ateeqanees/mutation/centos/gr37.fasta",  :
  Zero mutations to analyze! Maybe add or remove prefix?

Thanks a Ton !!!
Zac

Hi,
Can you post your command ?
Also can you check if the chromosome names in input MAF file has 'chr' prefix ?

Hi,
Thanks a lot for quick reply,
I am using the following command:
lung.tnm = trinucleotideMatrix(maf = lung, ref_genome = '/GRCh38.dna_sm.primary_assembly.fa',
prefix = 'chr', add = TRUE, ignoreChr = 'chr23', useSyn = TRUE)
I have attached my .maf file, please have a look. It has the following column (first few)

Hugo_Symbol
Entrez_Gene_Id
Center
NCBI_Build
Chromosome

ANKRD23
200539
bcgsc.ca
GRCh37-lite
2

HOXD8
3234
bcgsc.ca
GRCh37-lite
2

CASP8
841
bcgsc.ca
GRCh37-lite
2

Please help me out, my knowledge in this is very limited.
Thanks a lot,
Zac
lung.zip

Hi,
No problem!
Anyways, its working fine for me.  You should note that,

your input MAF file uses GRCH37 (aka hg19) as reference genome but you're providing GRCh38 (ref_genome = '/GRCh38.dna_sm.primary_assembly.fa') as ref_genome.
Chromosome names in MAF file have no chr prefix, you should add one - which you already did. But make sure chromosome names in your reference genome also has chr prefix - in any case maftools will give an error/warnings if there is mismatch in the way chromsomes are named among input maf and reference genome file.

>lung = read.maf(maf = '~/Downloads/lung')

> lung
An object of class  MAF
                        ID     summary    Mean Median
 1:             NCBI_Build GRCh37-lite      NA     NA
 2:                 Center    bcgsc.ca      NA     NA
 3:                Samples          96      NA     NA
 4:                 nGenes        7607      NA     NA
 5:        Frame_Shift_Del         277   2.885    2.0
 6:        Frame_Shift_Ins         173   1.802    1.0
 7:           In_Frame_Del          79   0.823    0.0
 8:      Missense_Mutation       11568 120.500  106.0
 9:            Splice_Site         322   3.354    3.0
10: Translation_Start_Site          25   0.260    0.0
11:                  total       12444 129.625  114.5

> lung.tnm = trinucleotideMatrix(maf = lung, ref_genome = '~/NGS/ref_genomes/hg19.fa', prefix = 'chr', add = TRUE, useSyn = TRUE)
reading ~/NGS/ref_genomes/hg19.fa (this might take few minutes)..
contigs in fasta file:
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21" "chr22"
[23] "chrX"  "chrY"  "chrM"
contigs in maf:
 [1] "chr1"          "chr2"          "chr3"          "chr5"          "chr6"          "chr7"          "chr8"          "chr9"          "chr10"         "chr11"         "chr12"
[12] "chr13"         "chr14"         "chr16"         "chr17"         "chr18"         "chr19"         "chr20"         "chr22"         "chrX"          "chr4"          "chr15"
[23] "chrMT"         "chr21"         "chrGL000209.1" "chrGL000219.1" "chrY"          "chrGL000205.1" "chrGL000212.1" "chrGL000218.1" "chrGL000192.1" "chrGL000241.1" "chrGL000229.1"
missing reference contigs from fasta file.
[1] "chrMT"         "chrGL000209.1" "chrGL000219.1" "chrGL000205.1" "chrGL000212.1" "chrGL000218.1" "chrGL000192.1" "chrGL000241.1" "chrGL000229.1"
Contig names in MAF must match to contig names in reference fasta. Ignorinig 54 single nucleotide variants from chrMT, chrGL000209.1, chrGL000219.1, chrGL000205.1, chrGL000212.1, chrGL000218.1, chrGL000192.1, chrGL000241.1, chrGL000229.1
Extracting 5' and 3' adjacent bases..
Extracting +/- 20bp around mutated bases for background estimation..
Estimating APOBEC enrichment scores..
Performing one-way Fisher's test for APOBEC enrichment..
APOBEC related mutations are enriched in 25% of samples (APOBEC enrichment score > 2 ; 24 of 96 samples)
Creating mutation matrix..
matrix of dimension 96x96

Let me know if you still have issues.

Thanks a lot for this help, i will download the GRCH37 and work on it :) thanks a lot, its of great help for me !!! it means a lot...
Thanks again ,
Zac..

No problem at all.
Just a heads up,
If you're using maftools from Bioconductor, there is a major bug in trinucleotideMatrix function. This has been fixed in github repository, maybe you should install it from github and try..
library("devtools")
install_github(repo = "PoisonAlien/maftools")

HI,
Thanks a lot for your help, i have successfully executed the program and got some very good results.
Meanwhile, i am not able to save the matrix into .csv file. how can i save the 'laml.sign' into a .csv file for my future reference? I tried using the following code but its throws error.

write.csv(laml.sign, file = "ESCA_signature.csv",row.names=FALSE, na="")
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class "structure("NMFfit", package = "NMF")" to a data.frame

Thanks a lot for your kind help,
Have a great day ahead !!!
Zac

Hi,
Sorry for late reply. laml.sign is a list. So it contains,

scaled signatures
contribution of each signatures to each sample
cosine similariry matrix of identified signatures against all (30) validated signatures from Sanger.
NMF object

you can see by names(laml.sign)
You can access each element either by laml.sign[[1]] or laml.sign$
If you want to write to output file,
write.delim(laml.sign$signatures, file = "ESCA_signature.csv", row.names = TRUE, quote = FALSE)

Hi,
Thanks a lot for your kind help! it indeed helped me so much. Thanks again !
I have one last query to make, Is it possible to get all 30 genes signature? currently i am getting only 2 or 3 depending on the best p value(extractSignatures), can i get all detected signatures from my .maf against validated signatures?
I need to have all detected signatures against validated one, can we extract this from maftools? please let me know how this to be done.
Thanks a Ton, your help is indeed invaluable, highly appreciated.
Have a great day ahead,
Zac.

Hi,
sorry for late reply.
In short, No you can't detect all 30 signatures. maftools detects de-novo signatures and compares them to validated signatures for best match.
Also see here #62


I find some bugs

https://github.com/gnembon/fabric-carpet/issues/1118#issuecomment-927389553

@altrisi thanks you. but after my reading and testing that script, i find some issues.
https://github.com/Ghoulboy78/Scarpet-edit/blob/64543f220242657c0086c20a4ccfb138bc7dcce5/se.sc#L1943-L1945
seems that the area is not correct. maybe pos2=pos2+1 could fix that ?
https://github.com/Ghoulboy78/Scarpet-edit/blob/64543f220242657c0086c20a4ccfb138bc7dcce5/se.sc#L1957-L1961
seems that the one who writes the code incorrectly assumes that the map will remain its order.
https://github.com/Ghoulboy78/Scarpet-edit/blob/64543f220242657c0086c20a4ccfb138bc7dcce5/se.sc#L1963
I am concerned that the unnecessary use of parse_nbt here will disrupt some of the nbt types.

Ye... that part of the code is overdue for a rewrite anyways... We just havent had the time. I have fixed some of the issues on a private branch that I haven't touched for a while.


configure Go builder and test

Closed by https://github.com/Areso/Sailmaster/commit/59ba8d8d31d5ca3c3e66fda24bd4c8ff029a928d


Improve slack-access-token pattern.

Is your feature request related to a problem? Please describe.
The current Slack access token pattern is quite simple and thus prone to false-positives.
https://github.com/gitleaks/gitleaks/blob/839f114f2b2ca9429300e545aa5c93a2caf2e3d8/config/gitleaks.toml#L2602-L2608
It checks for strings with the prefix xoxp- followed by at least 10 alphanumeric characters, which tends to flag placeholders like xoxp-yourtokenhere. Actual Slack access tokens have multiple segments (e.g. xoxb-17653672481-19874698323-pdFZKVeTuE8sk7oOcBrzbqgy), so it should be straightforward to increase the accuracy of this pattern by looking for that.
cc @zricethezav

Slack has updated their tokens so this may be more complicated than initially thought.
Examples
Workspace Access Token
xoxe.xoxp-1-Mi0yLTMxNzcwMjQ0MTcxMy0zNjU5NDY0Njg4MTctNTE1ODE1MjY5MTcxNC01MTU4MDI0MTgyOTc5LWRmY2YwY2U4ODhhNzY5ZGU5MTAyNDU4MDJjMGQ0ZDliMTZhMjNkMmEyYzliNjkzMDRlN2VjZTI4MWNiMzRkNGQ

Workspace Refresh Token
xoxe-1-My0xLTMxNzcwMjQ0MTcxMy01MTU4MTUyNjkxNzE0LTUxODE4NDI0MDY3MzYtMjA5MGFkOTFlZThkZWE2OGFlZDYwYWJjODNhYzAxYjA5ZjVmODBhYjgzN2QyNDdjOTNlOGY5NTg2YWM1OGM4Mg

App Token
xapp-1-A362FGTH2KD-5157583564358-7f8b02421dcaaff6e54ad29273db9cf90d6a155e3c4a750566310008108ccf6d


MAVLink v2.0 integration

@bkueng I'd like to push this forward as a joint architecture effort.

Serialization functions: https://github.com/mavlink/c_library/blob/mavlink2/common/mavlink_msg_heartbeat.h
We need to change our API use to rely on those, rather on hand crafted stuff which doesn't scale.

Jenkins test this please

@bkueng I did all the plumbing, but the resulting packets are not yet correct MAVLink 1. Once they are fixed we should be pretty close.

@DonLakeFlyer This compiles and runs in SITL and successfully now delivers MAVLink 1 and MAVLink 2.

Jenkins test this please

Rebased and applied.


Correct parameter of setinputsizes: pyodbc.SQL_TIMESTAMP

The pyodbc returned a error when I tried to use the literal "SQL_TIMESTAMP" as parameter for setinputsizes(list_of_value_tuples). Eg: setinputsizes([pyodbc.SQL_TIMESTAMP]).
This is the syntax according to wiki Data Types:
https://github.com/mkleehammer/pyodbc/wiki/Data-Types
Luckly, I changed to "pyodbc.SQL_TYPE_TIMESTAMP" and it worked !
May review the wiki ?
Thanks.
Environment

Python: 3.7
pyodbc: 4.0.27
OS: Windows 10
DB: Microsoft SQL Server
driver: Microsoft SQL Server 13

Feel free to update the wiki with any corrections or improvements you may wish to offer.

Does anyone know why ODBC named most of these constants SQL_<DBTYPE> but the date and time constants SQL_TYPE_<DBTYPE?  For example, SQL_NUMERIC and SQL_TYPE_DATE?

Also, thanks for the Wiki update, whoever did it.

@mkleehammer SQL_xxx were there since ODBC 1.x, while the SQL_TYPE_xxx were introduced in ODBC 3.0. See https://docs.microsoft.com/en-us/sql/odbc/reference/appendixes/datetime-data-types for more information.


Getting error while deploying.

This is what I'm getting.

Could you run the deploy with the --debug flag? It may tell us more about the issue :)
firebase deploy --debug

'friendlypix-web-39f5a' is not a Firestore enabled project, but I can see it in the deployment history.


Detect Changes in Imported Files

Asset Mutator is working great for me, the only real issue left that I face is importing files. If you modify an imported file, it changes neither the modified date, nor the checksum of the original file that Asset Mutator examines.  Any ideas on how we could get it to detect changes in imported files?

v1.0b1 introduces a new always_remutate setting that can be utilized in development environments to make sure imports are always reprocessed.


Option for expanding folders

Just like search:
// Controls whether the search results will be collapsed or expanded.
//  - auto: Files with less than 10 results are expanded. Others are collapsed.
//  - alwaysCollapse
//  - alwaysExpand
"search.collapseResults": "auto",

Maybe it can also have a configurable number instead of hard-coded 10.
"referencesView.collapseResults": "alwaysCollapse" | "alwaysExpand" | %INT%

related to #21. challenge is that it is extensions with large results sets as each file needs to be opened from disk first...


Fix docs typos

Summary
Fix some typos in the docs.

Please note that Algolia's search index needs to be refreshed as well.

Test plan

Thank you!

Thank you!


Retries using with-items runs a retry even on objects that succeeded as well

We use the with-items to loop over and run an action.
If it fails for even one of them, it retries over all the items in the array again, instead of just retrying the failed ones.
For instance, if param1 was set to 1,2,3,4 in the below sample workflow:
version:                1.0
description:            Test retry workflow
input:
  - param1
  - slack_channel
tasks:
  split_list:
    action: core.noop
    next:
    - when: <% succeeded() %>
      do: print_val
      publish:
        - list_vals: <% ctx(param1).split(',') %>
  print_val:
    with: <% ctx(list_vals) %>
    action: core.local
    input :
      cmd : >
        val=<% item() %>;
        if [ $val -eq 2 ];then exit -1;fi
    retry:
      when: <% failed() %>
      count: 5
      delay: 2
    next:
      - when: <% succeeded() %>
        publish:
          - status: "SUCCESS"
      - when: <% failed() %>
        do:
          - send_failed_alert
        publish:
          - status: "FAILED"
  send_failed_alert:
    action: slack.chat.postMessage
    input:
      channel: "#<% ctx(slack_channel) %>"
      text: "ERROR: failed on param <% ctx(param1) %> failed"`

And here is the output of the run.

In current implementation, the retry is scoped to the task so it retry the task and not the items in the case of with items.  We can add an option in the retry spec to retry only failed items.

The following is one possible solution for the retry spec to support per-item retry.
    retry:
      items:
        when: <% some condition on the action execution for the item %>
        count: 3
        delay: 1

The following is one possible solution for the retry spec to support per-item retry.
    retry:
      items:
        when: <% some condition on the action execution for the item %>
        count: 3
        delay: 1

Your proposed solution per-item retry does not work.

@kyildiz It was a proposal and not supported yet.

you can wrap your action in a workflow and put the retry logic in the subworkflow for now as a workaround.


New Rules: CS EventStream Audit Events

Background
The Crowdstrike Eventstreams log source includes several audit events which provide security value. These detections provide some baseline coverage against these logs.
Changes

multiple new detections, covering user management and IP allowlist activity

Testing

Added multiple unit tests for each detection

Would love some eyes on the IP allowlisting rules. I'm concerned they may be too noisy!


Contestant is placed under wrong province

Link: https://ksn.toki.id/statistik/provinsi/SNZ
If you scroll to the bottom of the page, you will see a contestant from Palembang.

Thanks for reporting. It was indeed a mistake. Fixed!


[Feature Request]: Tag to disable the mod

Thank you for this mod and it's working great. I most of the time just AFK farm in this game and would like to turn this mod off when I'm not actually playing in the interest of saving my pc's resources for other things. It would be great if a user can just enable/disable this with a setting than manually tuning off all the options in the ini.

You could always just move the files out of the game folder. Would take less time than opening editing and saving too.


Can't run a cell after opening a second notebook and switching back to the first

Tracking VS Code bug: https://github.com/microsoft/vscode/issues/116516

Moving to validate

Validated. Scenario looks good to me now.


Add excluded to scope types

This is an enhancement proposal to the CycloneDX specification to add support for excluded components.
Currently, scope defines both required and optional components. This enhancement would be to support excluded components. Components may be excluded from runtime (and thus have reduce risk) due to a number of reasons, among them are test components, which are neither required for runtime or optional at runtime.

Included in CycloneDX 1.1


tf_smoke.py distributed computing doesn't work on minikube

I just started to learn K8S this month and found this CRD initiative to support Tensorflow on K8S really helpful. However, while I am able to run a local MNIST test on a single Pod in my minikube successfully, I am now stuck with distributed task tf_smoke.py. Here are the details:
minikube version: v0.24.1
tensorflow:1.4.0
tf_operator:gcr.io/tf-on-k8s-dogfood/tf_operator:v20171215-eb0fd5f
Below is the tf_smoke.yaml I used to create this tfjob. Since I already had a local copy of tensorflow 1.4, I just specified imagePullPolicy as  Never.
apiVersion: "tensorflow.org/v1alpha1"
kind: "TfJob"
metadata:
name: "tf-smoke"
spec:
replicaSpecs:
- replicas: 1
tfReplicaType: MASTER
template:
spec:
containers:
- image: registry.cn-hangzhou.aliyuncs.com/denverdino/tensorflow:1.4.0
imagePullPolicy: Never
name: tensorflow
command: ["python"]
args: [/workdir/script/tf_smoke.py]
volumeMounts:
- name: workdir
mountPath: /workdir
volumes:
- name: workdir
hostPath:
path: /home/docker/tensorflow_training
restartPolicy: OnFailure
- replicas: 2
tfReplicaType: WORKER
template:
spec:
containers:
- image: registry.cn-hangzhou.aliyuncs.com/denverdino/tensorflow:1.4.0
imagePullPolicy: Never
name: tensorflow
command: ["python"]
args: [/workdir/script/tf_smoke.py]
volumeMounts:
- name: workdir
mountPath: /workdir
volumes:
- name: workdir
hostPath:
path: /home/docker/tensorflow_training
restartPolicy: OnFailure
- replicas: 1
tfReplicaType: PS
Once I submit it by kubectl create -f tf_smoke.yaml, the master is constantly displaying
2017-12-21 10:03:28.949380: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:ps/replica:0/task:0
2017-12-21 10:03:28.949441: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:worker/replica:0/task:0
2017-12-21 10:03:28.949450: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:worker/replica:0/task:1
And the other 2 workers are just hanging there at 'INFO:root:Running Worker code'.
There are 2 things I don't understand.

The logs show all 3 pods have the same 'Started server with target: grpc://localhost:2222' even though minikube generated the cluster spec with unique hostname for each pod. Is this why the master fails to contact the other 2 workers since 2222 is occupied already by master?

{"cluster":{"master":["tf-smoke-master-jyab-0:2222"],"ps":["tf-smoke-ps-jyab-0:2222"],"worker":["tf-smoke-worker-jyab-0:2222","tf-smoke-worker-jyab-1:2222"]}

Why do we need to put the graph and ops in the master rather than worker?
if job_type == "ps":
logging.info("Running PS code.")
server.join()
elif job_type == "worker":
logging.info("Running Worker code.")
The worker just blocks because we let the master assign all ops.
server.join()
elif job_type == "master" or not job_type:
logging.info("Running master.")
with tf.device(device_func):
run(server=server, cluster_spec=cluster_spec)

Initially, I thought it was because I didn't create the ConfigMap which specifies grpcServerFilePath: /opt/mlkube/grpc_tensorflow_server/grpc_tensorflow_server.py. However, it still doesn't work even after I re-install tf-job with this tf-job-operator-config ConfigMap.
If anyone knows what is going wrong, please leave a comment. Thanks!

My guess would be some sort of networking issue with minikube. Can you try pinging the master from the workers e.g.
kubectl exec -ti tf-smoke-worker-jyab-0:2222 /bin/bash
ping tf-smoke-master-jyab-0

When you call tf.Server you are starting a TensorFlow server on port 2222 in another process. The python code that is executing locally on that work then connects to that gRPC server and uses that server to talk to the other gRPC servers in the cluster. It uses "localhost" because the server is running on the same machine (or virtual machine in the case of K8s POD).
When you start a distributed training job, the master waits for all the other replicas in the cluster (parameter servers, and workers) to check in before the job starts. That's what the log messages from the master indicates.
The log messages indicate the workers should be starting the server and waiting to be told what to do by the master.
So it looks like there is a problem with communication between the workers and master.
Can you provide a complete set of logs from the master and worker?
Are any of the containers getting restarted?

@jlewi Thanks for the reply. First of all, all the Pods are running without any container restart.

I also tried to verify the network connectivity. Surprisingly, It turns out that ping is not installed in the original tensorflow docker image. So I did this to get ping installed first.

echo "nameserver <IP_ADDRESS>" > /etc/resolv.conf
apt-get update
apt-get install inetutils-ping
Below are the hosts info on each Pod.
From master to workers

From work0 to master

So it looks like the 'virtual' IP addresses all pingable from one another. But since this is a minikube environment, localhost is used so I don't know if we can tell anything from this.
As for the log, workers logs are similar. Below is worker0 log
INFO:root:Tensorflow version: 1.4.0
INFO:root:Tensorflow git version: v1.4.0-rc1-11-g130a514
INFO:root:tf_config: {u'environment': u'cloud', u'cluster': {u'worker': [u'tf-smoke-worker-0uf4-0:2222', u'tf-smoke-worker-0uf4-1:2222'], u'ps': [u'tf-smoke-ps-0uf4-0:2222'], u'master': [u'tf-smoke-master-0uf4-0:2222']}, u'task': {u'index': 0, u'type': u'worker'}}
INFO:root:task: {u'index': 0, u'type': u'worker'}
INFO:root:cluster_spec: {u'worker': [u'tf-smoke-worker-0uf4-0:2222', u'tf-smoke-worker-0uf4-1:2222'], u'ps': [u'tf-smoke-ps-0uf4-0:2222'], u'master': [u'tf-smoke-master-0uf4-0:2222']}
INFO:root:server_def: cluster {
job {
name: "master"
tasks {
value: "tf-smoke-master-0uf4-0:2222"
}
}
job {
name: "ps"
tasks {
value: "tf-smoke-ps-0uf4-0:2222"
}
}
job {
name: "worker"
tasks {
value: "tf-smoke-worker-0uf4-0:2222"
}
tasks {
key: 1
value: "tf-smoke-worker-0uf4-1:2222"
and for master,
protocol: "grpc"
INFO:root:Building server.
2017-12-21 14:50:16.303408: I tensorflow/core/platform/cpu_feature_guard.cc:137] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX
E1221 14:50:16.303784801       1 ev_epoll1_linux.c:1051]     grpc epoll fd: 3
2017-12-21 14:50:16.321366: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job master -> {0 -> localhost:2222}
2017-12-21 14:50:16.321455: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job ps -> {0 -> tf-smoke-ps-0uf4-0:2222}
2017-12-21 14:50:16.321477: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job worker -> {0 -> tf-smoke-worker-0uf4-0:2222, 1 -> tf-smoke-worker-0uf4-1:2222}
2017-12-21 14:50:16.321770: I tensorflow/core/distributed_runtime/rpc/grpc_server_lib.cc:324] Started server with target: grpc://localhost:2222
INFO:root:Finished building server.
INFO:root:Running master.
INFO:root:Server target: grpc://localhost:2222
2017-12-21 14:50:26.352030: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:ps/replica:0/task:0
2017-12-21 14:50:26.352153: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:worker/replica:0/task:0
2017-12-21 14:50:26.352163: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:worker/replica:0/task:1
<repeating every 10 seconds>
2017-12-21 16:08:16.663648: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:ps/replica:0/task:0
2017-12-21 16:08:16.663843: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:worker/replica:0/task:0
2017-12-21 16:08:16.664279: I tensorflow/core/distributed_runtime/master.cc:221] CreateSession still waiting for response from worker: /job:worker/replica:0/task:1

Let me know your thought about this. In the meanwhile, I am also setting up a real cluster env to try this out. Thanks!

It looks in your shells you were pinging by ip address and not hostname. And I didn't see any entry in the hosts files for remote replicas. So maybe there is an issue with DNS lookup?
We also want to use the hostname for the services not the pods themselves. So in the example you gave the service names would be
tf-smoke-ps-0uf4-0
tf-smoke-master-0uf4-0
...

Can you run:
nslookup ${HOSTNAME}
for the names of some the services on one of the pods? And also try pinging that host.

@jlewi So I tried the same YAML and tf_smoke.py on a single K8S node and the issue was gone. I guess it's just an issue with Minikube then.


How to set the initial values of a form?

I want to populate a form with values I get dynamically (from a http request, etc).
Is the only option using <Field> or can I pass values through a <Provider>-like component
EDIT: Ended up doing something like
const fooAtom = fieldAtom({ value: 0 });

const fields = {
  foo: fooAtom,
}
type FormFields = typeof fields;

const myFormAtom = formAtom(fields);

interface FormProps {
  initialValues: {
    [Field in keyof FormFields]: any,
  }
}

const Form = ({ initialValues }) => {
  useFieldAtomInitialValue(fooAtom, initialValues.foo);
  return <form>...</form>
}

Yeah unfortunately due to the constraints of Jotai your solution and creating your form/field atom dynamically in your components are the only two options.


RevEng: Add DefaultValue fluent API into generated code

Part of #830.
Also investigate what to do about DefaultExpressions.

Done with the above 2 check-ins.


testing pullrequest auto-tester for a failing entry

This PR test should fail.

Status Flag 'Pre-Test Inspection' - Auto Inspected - Inspection Is Not Necessary for this Pull Request.

Status Flag 'Pull Request AutoTest' - Testing Jenkins Projects:

Pull Request Auto Testing STARTING (click to expand)

Build Information
Test Name: BSSW_PR_AutoTest

Build Num: 23
Status: STARTED

Jenkins Parameters

Parameter Name
Value

BSSW_SOURCE_BRANCH
pr-test-autotester-fail-01

BSSW_SOURCE_REPO
https://github.com/william76/betterscientificsoftware.github.io

BSSW_SOURCE_SHA
dbf4858b3d39d05d6d60eadc3293ca1623c2b4cc

BSSW_TARGET_BRANCH
develop

BSSW_TARGET_REPO
https://github.com/william76/betterscientificsoftware.github.io

BSSW_TARGET_SHA
20bb7a55bf9045a8685ba467e2471a14c0985c89

JENKINS_JOB_TYPE
Experimental

TEST_REPO_ALIAS
BSSW

Using Repos:

Repo: BSSW (william76/betterscientificsoftware.github.io)

Branch: pr-test-autotester-fail-01
SHA: dbf4858b3d39d05d6d60eadc3293ca1623c2b4cc
Mode: TEST_REPO

Pull Request Author: william76

Status Flag 'Pull Request AutoTest' - Jenkins Testing: 1 or more Jobs FAILED
Note: Testing will normally be attempted again in approx. 0:30:00. If a change to the Pull Request source branch occurs, the testing will be attempted again.

Pull Request Auto Testing has FAILED (click to expand)

Failure Message(s)
File: test/test_001_fail.md
Invalid value for property 'Topics', given value 'documentation'.
>>> Failed depenency check against property/value pair 'Categories'/'['Planning', 'Reliability', 'Collaboration', 'Crosscutting', 'Performance']'
>>> Allowable values are:
>>> - 'Continuous integration testing'
>>> - 'Debugging'
>>> - 'Design'
>>> - 'Discussion forums'
>>> - 'Funding sources and programs'
>>> - 'High-performance computing (HPC)'
>>> - 'Improving productivity and sustainability'
>>> - 'Licensing'
>>> - 'Performance at leadership computing facilities (LCFs)'
>>> - 'Performance portability'
>>> - 'Projects and organizations'
>>> - 'Reproducibility'
>>> - 'Requirements'
>>> - 'Software interoperability'
>>> - 'Software publishing and citation'
>>> - 'Strategies for more effective teams'
>>> - 'Testing'

Build Information
Test Name: BSSW_PR_AutoTest

Build Num: 23
Status: FAILED

Jenkins Parameters

Parameter Name
Value

BSSW_SOURCE_BRANCH
pr-test-autotester-fail-01

BSSW_SOURCE_REPO
https://github.com/william76/betterscientificsoftware.github.io

BSSW_SOURCE_SHA
dbf4858b3d39d05d6d60eadc3293ca1623c2b4cc

BSSW_TARGET_BRANCH
develop

BSSW_TARGET_REPO
https://github.com/william76/betterscientificsoftware.github.io

BSSW_TARGET_SHA
20bb7a55bf9045a8685ba467e2471a14c0985c89

JENKINS_JOB_TYPE
Experimental

TEST_REPO_ALIAS
BSSW


Adding configuration for the flyway-maven-plugin

Describe your changes
Adding configuration for the flyway-maven-plugin
Manual Test Scenarios and Output

Maven Goal: flyway:migrate
Output:

[INFO] Successfully validated 1 migration (execution time 00:00.036s)
[INFO] Creating Schema History table "public"."flyway_schema_history" ...
[INFO] Current version of schema "public": << Empty Schema >>
[INFO] Migrating schema "public" to version "1.0.0 - init schema"
[INFO] Successfully applied 1 migration to schema "public", now at version v1.0.0 (execution time 00:00.133s)

Maven Goal: flyway:info
Output:

[INFO] Schema version: 1.0.0
[INFO]
[INFO] +-----------+---------+-------------+------+---------------------+---------+----------+
| Category  | Version | Description | Type | Installed On        | State   | Undoable |
+-----------+---------+-------------+------+---------------------+---------+----------+
| Versioned | 1.0.0   | init schema | SQL  | 2024-03-03 22:33:29 | Success | No       |
+-----------+---------+-------------+------+---------------------+---------+----------+

Maven Goal: mvn flyway:clean -Dflyway.cleanDisabled=false
cleanDisabled by default is true inorder to avoid issues in the production database, so we have to disable it while executing the mvn goal
Output:

[INFO] Successfully dropped pre-schema database level objects (execution time 00:00.000s)
[INFO] Successfully cleaned schema "public" (execution time 00:00.071s)
[INFO] Successfully cleaned schema "public" (execution time 00:00.024s)
[INFO] Successfully dropped post-schema database level objects (execution time 00:00.000s)

Issue ticket number and link
#18 Add configuration for the flyway-maven-plugin
Checklist before requesting a review

[ Yes ] I have performed a self-review of my code
[ Not a Core Feature (Just a Plugin Configuration) ] If it is a core feature, I have added thorough tests.
[ No Documentation Needed ] I have made corresponding changes to the documentation
[ Yes ] I used the given Project Style Guide

Thanks for your contribution 😄


Upgrade curator version

https://github.com/apache/incubator-dolphinscheduler/issues/2020
the curator issue: https://github.com/apache/curator/pull/297  may cause InterProcessMutex.acquire() hang, we'd better upgrade its version

Codecov Report

Merging #2083 into dev will decrease coverage by 3.17%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##                dev   #2083      +/-   ##
===========================================
- Coverage     33.17%     30%   -3.18%
- Complexity     1554    1559       +5
===========================================
  Files           313     332      +19
  Lines         15529   17190    +1661
  Branches       1886    2132     +246
===========================================
+ Hits           5152    5157       +5
- Misses         9848   11504    +1656
  Partials        529     529

Impacted Files
Coverage Δ
Complexity Δ

...nscheduler/service/zk/DefaultEnsembleProvider.java
100% <100%> (ø)
6 <2> (?)

...scheduler/alert/template/AlertTemplateFactory.java
42.85% <0%> (-14.29%)
2% <0%> (ø)

...he/dolphinscheduler/api/service/LoggerService.java
91.3% <0%> (-8.7%)
7% <0%> (-1%)

...olphinscheduler/service/queue/TaskQueueZkImpl.java
0% <0%> (ø)
0% <0%> (?)

...hinscheduler/service/quartz/cron/CycleFactory.java
0% <0%> (ø)
0% <0%> (?)

...inscheduler/service/quartz/ProcessScheduleJob.java
0% <0%> (ø)
0% <0%> (?)

...lphinscheduler/service/process/ProcessService.java
0% <0%> (ø)
0% <0%> (?)

...pache/dolphinscheduler/service/log/LogPromise.java
0% <0%> (ø)
0% <0%> (?)

.../dolphinscheduler/service/zk/AbstractZKClient.java
0% <0%> (ø)
0% <0%> (?)

...dolphinscheduler/service/zk/ZookeeperOperator.java
0% <0%> (ø)
0% <0%> (?)

... and 12 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 3186545...a1d791e. Read the comment docs.

version is compatible with zookeeper.
+1


gcc 4.9.2/5.1.0 detects uninitialized variable in codec/decoder/core/src/mv_pred.cpp when compiling tests

codec/decoder/core/src/mv_pred.cpp: In function ‘void WelsDec::PredPSkipMvFromNeighbor(WelsDec::PDqLayer, int16_t*)’:
codec/decoder/core/src/mv_pred.cpp:158:51: error: ‘iLeftTopXy’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
     ST32 (iMvD, LD32 (pCurLayer->pMv[0][iLeftTopXy][15]));
                                                   ^
codec/decoder/core/src/mv_pred.cpp:99:71: error: ‘iLeftXy’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   iLeftType = ((iCurX != 0 && bLeftAvail) ? pCurLayer->pMbType[iLeftXy] : 0);
                                                                       ^
cc1plus: all warnings being treated as errors

Full output: https://gist.github.com/b9717bb9f32c43d15209
It works with gcc-4.8.4 and clang 3.6.0/3.6.1.

Actually, gcc 5.1.0 doesn't detect second one, only the first (iLeftTopXy). Might be gcc bug?

@HaiboZhu

This bug has been fixed in #2535 and no warnings output on newest GCC 5.4, close this issue.


add zh doc for multi-cluster-apps and quick-start

add zh doc for multi-cluster-apps and quick-start，and fix some link to /zh-doc/

@dixudx  please have a look at this pr☺


JSON Format Question

Is there an importance to the number on the read_sampling objects in the output JSON? Example: "SARS-CoV-2_1" or "SARS-CoV-2_2"
If there isn't a specific importance to the trailing number on those object keys, it would be great to place that in a JSON Array instead of objects with unique keys.
Something like:
"read_sampling": {
"SARS-CoV-2": [
{
"start": 26,
...
"pass": false
},
{
"start": 325,
...
"pass": false
}
]
}

The keys are the names of the amplicons. The format of those names could be anything, and indeed do vary between ARTIC v3, ARTIV v4, and midnight. It's extremely useful to be able to look up an amplicon by name, hence why it's a hash of name -> info.


Improvement suggestion [Expense Report sample]

On the form NewExpenseFormsucces on the NewExpense screen: use this Set(SelectedReport,NewExpenseForm.LastSubmit);
Navigate(ViewReport,None)
This will increase performance and also you will not be able to retrieve the wrong expanse. Before a refresh and the last function was used.
Kind regards,
Raymond Peters

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

ID: 379862e0-89e8-8e6b-b686-77d6836f0434
Version Independent ID: 29fc7f25-b6b5-26d2-69f3-eada7fff64b3
Content: Install and configure the Expense Report sample for canvas apps - PowerApps
Content Source: powerapps-docs/maker/canvas-apps/expense-report-install.md
Service: powerapps
GitHub Login: @caburk
Microsoft Alias: caburk

@Rpeters1977 Thanks for your feedback. For product-related feedback, visit the forum.
Closing this issue.

@mr-dang-msft


Markdown: don't allow inlines to break out of their containing block

I was running into this issue where an underscore in a url would cause the rest of the markdown document to appear in italics. And double line breaks, headers, etc. would not automatically close it. The main goal of this PR is to fix that and a couple other minor things.
Changes

Split the CODE mode into separate modes for inline (CODE_SPAN) and blocks (FENCED_CODE, INDENTED_CODE).
Enable endsWithParent: true on all inline elements (INLINE_HTML, LINK, CODE_SPAN, BOLD, ITALIC) and remove them from the top level mode.

However endsWithParent does not seem to work when the mode is used inside multiple other modes, so do a deepCopy of all the inline modes before using them. I'm totally open to other ways to workaround this. I'm not familiar with JS enough to know what the right approach here is.
Convert the inline modes from using regex literals to strings in order to do the copy.

Add a new default Paragraph mode which contains the inline elements. The Paragraph mode as well as the List mode ends whenever it recognizes the beginning of any of the other top level modes.
Update italics/bold so that underscore is not allowed within words https://spec.commonmark.org/0.29/#example-359.
Added a ITALICS_CHILD and BOLD_CHILD mode that only appears inside of ITALICS and BOLD. This is to handle edge cases around nesting italics/bold.
Updated the top level modes (BLANK_LINE, BLOCKQUOTE, HEADER, HORIZONTAL_RULE, FENCED_CODE, LINK_REFERENCE, LIST, INDENTED_CODE, PARAGRAPH) to begin/end at the beginning/ending of lines. Also updated them to accept unlimited white space in the front because they can all be nested inside of a list.
Updated the horizontal rule to better match https://spec.commonmark.org/0.29/#thematic-break

There is a failing test in /test/markup/dart/comment-markdown.txt. The asterisks get read as italics instead of a bulleted list. Removing the ///  it parses correctly as markdown, but as part of a dart it doesn't work for some reason. I couldn't figure out how to fix it. I'm thinking it has to due with newlines? Would appreciate help as to how to fix that test.
/// text.
/// * bullet
///   * sub-bullet

Had to tweak a couple of the markdown tests. **_ doesn't work anymore for bold + italics, because of the way it checks if the underscore is inside a word. Also the nested code blocks doesn't work... that seems like a small edge case though.  I think overall it is an improvement.
Checklist

[x] Added markup tests, or they don't apply here because...
[ ] Updated the changelog at CHANGES.md

Thanks for this! ...but this is very hard to review as-is.  It may need to be broken down into smaller chunks so that each item can be fully understood and discussed individually.  It also adds a lot of complexity and right now it's hard to see if that complexity is truly necessary or if these problems could perhaps be solved more simply.
If each of these items had been in a  separate commit that would be a lot easier to look thru.  Lets start with just one simple thing... HORIZONTAL_RULE.

Why is it now relevance 0?
Why does it now have has a className that it did not have before?

These types of changes should not be made in a large commit without any explanation or justification. That makes me very scary to try and process this as a whole unit for fear of all sorts of "hidden" changes like this.

so do a deepCopy of all the inline modes ... Convert the inline modes from using regex literals to strings

This is not necessary. endsWithParent does indeed alter the child modes (pulling in the end matcher based on the parent), so it will not work when blindly placed inside multiple parents.  I'd first take a look at whether this endsWithParent change was truly necessary.  You don't really say what problem you were trying to solve here... but if so you'd want to use hljs.inherit to make copies at the object level.  That's why it exists.
And we definitely want no more strings... the whole library is moving the direction of converting all strings to proper regex... so the reverse is definitely not what we want (though I think you only did that to copy them).

Also our recent trend is trying to find ways to make grammars simpler when possible (and often it's possible).  Not more complex... so for something like this it'd be better to take one item at a time and first understand the issue with the existing grammar.  It's quite possible there are grammar features (or patterns) you may not even be aware of or better ways to approach many of these things (with far less complexity).  Possibly not, but right now with them all mixed together it's very hard to say.
Are you ok with rewinding this and working thru and helping us understand each of these items on their own merits?

If we're going to take things one at a time I think the simple things to tackle first would be:

horizontal rule
Split the CODE mode into separate modes for inline (CODE_SPAN) and blocks (FENCED_CODE, INDENTED_CODE). (and what problem this is solving, etc)
Updated the top level modes (BLANK_LINE, BLOCKQUOTE, HEADER, HORIZONTAL_RULE, FENCED_CODE, LINK_REFERENCE, LIST, INDENTED_CODE, PARAGRAPH) to begin/end at the beginning/ending of lines. Also updated them to accept unlimited white space in the front because they can all be nested inside of a list.

Those three things alone would probably be a more manageable PR to review.

I was running into this issue where an underscore in a url would cause the rest of the markdown document to appear in italics. And double line breaks, headers, etc. would not automatically close it.

Off the top of my head fixing that might (possibly) only need to touch the URL rule.  Just because in Markdown double line break magically close things doesn't necessarily mean we have to build that logic into every mode in the grammar.  It's certainly possible this is a real improvement, but it also simply may be unneeded complexity.  Again, difficult to say without looking at individual tests/cases.  It's quite common that the first someone someone proposes (including myself) is often overly complex and that further thought and discussion leads to much simpler and more elegant solutions.

How about starting with disallowing underscores bolding/italicizing when inside words? The horizontal rule was just something I ran into while looking at the markdown spec and doesnt really matter. And its hard to explain the splitting and rearranging of the modes individually. It only works in conjunction with the addition of the paragraph mode etc.

How about starting with disallowing underscores bolding/italicizing when inside words?

Sure.

The horizontal rule was just something I ran into while looking at the markdown spec and doesnt really matter.

Your call - it'd probably be easy to sign off on - but we'd want to have a few markup tests to prove that the regex actually works on all the intended rule variants, etc... (which also serves to document the variants as well).

And its hard to explain the splitting and rearranging of the modes individually. It only works in conjunction with the addition of the paragraph mode etc.

So the individual code modes have no value on their own - apart from the paragraph stuff?  If so, then we could start by what problem we're trying to solve by adding a paragraph mode.  Over time I've slowly been removing contextual modes from grammars, so before we add a new one I want to make sure there isn't some simpler solution to the problem.

I was running into this issue where an underscore in a url would cause the rest of the markdown document to appear in italics.

An exact code example of this original issue would also be super useful to have attached.

Sure, here are some examples. Basically anything with an unescaped asterisk or underscore. Which is valid Markdown. Usually I run into it with urls www.example.com?test=foo_bar but it can happen in a lot of situations.

Example 1
# Rule of Identity, A*I=A

In this chapter we will learn about...

CommonMark.org:

GitHub:

Highlight.js:

Example 2
Next Steps:
1. Email<EMAIL_ADDRESS>2. ????
3. Profit!

CommonMark.org:

GitHub:

Highlight.js:

Example 3 https://gist.github.com/polygitapp/2f6d2e10e3de1b09c3f6530dde6a70e6
GitHub:

Highlight.js

Awesome... so I'd first take those 3 great test cases and add them all to markup/markdown/bold_italics.txt...
So the general idea is that _ should only work if proceeded by a space or something, right?  This is what look-behind is for, but of course we can't use that yet (browser support)... so at first glance I'd consider:

beforeMatch
matching all "word like things" with a separate rule to make sure no other rules trigger inside them (is there any Markdown actually allowed inside a word?)

We could also just include the space in the match, but that's dirty and I would consider it as a last resort.  All of these solutions should be <5 line patches.
That might still leave an edge case with nested bold/italic... but one thing/commit at a time.  Actually matching all word like things vs a beforeMatch might even leave you without an edge case... I'd first get the tests passing, make a small commit for that... then you could add an additional test for the nested bold/italics that might be an issue... and it will either pass or we'll have a second commit to tackle it.

What is the edge case with bold by the way, just something like:
**_bob went to the store_**

?

Any luck?

Closing for inactivity.  We'd still be happy to review these changes in smaller chunks (as mentioned), but we tend not to leave stale issues open if it seems like someone has moved on to other things.  This can be reopened at any time when a new revision is ready for review - or if easier an entirely new PR can also be opened.


(chaos-exporter): Add Unit Test Cases for function contains()

UNIT TEST
What happened:

Write the unit-test

What you expected to happen:

The test case should be written for function contains() - https://github.com/litmuschaos/chaos-exporter/blob/master/cmd/exporter/main.go

Anything else we need to know?:

Issue related to Repository: https://github.com/litmuschaos/chaos-exporter
Reference:- https://github.com/litmuschaos/chaos-operator/blob/master/pkg/controller/chaosengine/chaosengine_controller_test.go

Hi, if this issue is not taken I would like to start working on that :-)

Sure, go ahead! Don't forget to list this issue number in your PR, and please provide a link to PR here aswell.

@sebast26 Do you still working on this? If it's free I can take it.


more V2 work

FarcasterAccount token revocation not implemented yet.

hey! love this PR just a couple things
working on token revocation right now (specific, and all tokens)
but should we rename auth_token() to something like gen_auth_token() or get? the naming just feels a little off

just pushed some ground structure for token revocation, despite the API not being there yet, just make our future lives easier
question about auth_token still stands, though

https://github.com/TheLDB/farcaster-rs/issues/13

but should we rename auth_token() to something like gen_auth_token() or get? the naming just feels a little off

I think you're on to something. My thinking was Farcaster::functions() will call internally self.account.auth_token() to obtain Authentication Token when needed by reqwest. But get_auth_token() sounds equally good - do whatever feels more intuitive to you.
I would avoid get() as FarcasterAccount can possibly encapsulate more than just Authentication Token. That's why i tried to stick with auth_token for everything relating to Merkle V2 API token. Some of the non-public functions don't follow this convention as they basically act as a bridge to your auth code - and i thought of it as temporary btw.
As always i'm open for suggestions!
If we stick with above convention revoke_session_token should become revoke_auth_token propably?

cool, just made those changes.
thinking abt just leaving this branch & pr open so we can continue to work in here, then merge when we seem fit?
any thoughts

thinking abt just leaving this branch & pr open so we can continue to work in here, then merge when we seem fit?

It's a bit easier to keep my fork in sync when you merge PR. Besides v2-api branch is a huge WIP so we're not breaking anything by merging. Just my two cents.

Looking at v2 docs they changed from using user address to fid in many places. Think we need FIR support in Registry ASAP. Will try to work on this.
As for the v2 functionality i think we're getting close. The only major thing left is to rewrite using v2 endpoints and auth headers. Apart from this some v2 struct might need adjusting.

kk, will merge & merge all future PR's instantly
also i'll look into FIR support tonight
and will look into endpoints


Redstone Lamp (Breeding)

Redstone lamps are only showing lit as if they were unlit, so instead of 3 on breeding, they get one point per lit lamp

Can you confirm this in SP? If so, can you report it to Pixelmon?

Closing the ticket since Pixelmon is reworking their breeding mechanics.
https://pixelmonmod.com/tracker.php?p=2&t=18082


Fix error in javadoc @see

Fixed an error in javadoc.
Check List:

Fixes #??? (ignore if not applicable)
Unit tests : NA
Javadoc with a code example (on API only) : YES
PR meets the contributing guidelines

Following the contributing guidelines will make it easier for us to review and accept your PR.

Thanks, @uc4w6c!


Handling Text Input

The page at https://facebook.github.io/react-native/docs/handling-text-input.html is rendering the majority of the documentation twice beginning with the phrase "For example." The markdown document seems fine though, so I'm not sure what's going on.

Nice catch!
Looks like some recent changes introduced this weird behavior.

Thanks for the reporting, Hector just fixed this and it should be deployed in a few minutes.