Nested dynamic napespace problem (crash)

Let's have a config.ru defining a little API doing something with dates:
require 'grape'
require 'grape-swagger'

class API < Grape::API
  segment '/:year' do
    get do
      "Year #{params[:year]}"
    end

    segment '/:month' do
      get do
        "Month #{params[:year]}/#{params[:month]}"
      end

      get '/:day' do
        "Day #{params[:year]}-#{params[:month]}-#{params[:day]}"
      end
    end
  end

  add_swagger_documentation
end

run API

On startup add_swagger_documentation crashes:
/home/igneus/.rvm/gems/ruby-2.1.1/gems/grape-swagger-0.10.1/lib/grape-swagger.rb:70:in `block in combine_namespace_routes': undefined method `collect' for nil:NilClass (NoMethodError)
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/grape-swagger-0.10.1/lib/grape-swagger.rb:65:in `each'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/grape-swagger-0.10.1/lib/grape-swagger.rb:65:in `combine_namespace_routes'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/grape-swagger-0.10.1/lib/grape-swagger.rb:39:in `add_swagger_documentation'
        from /home/igneus/tmp/config.ru:21:in `<class:API>'
        from /home/igneus/tmp/config.ru:4:in `block in <main>'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/builder.rb:55:in `instance_eval'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/builder.rb:55:in `initialize'
        from /home/igneus/tmp/config.ru:in `new'
        from /home/igneus/tmp/config.ru:in `<main>'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/builder.rb:49:in `eval'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/builder.rb:49:in `new_from_string'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/builder.rb:40:in `parse_file'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/server.rb:299:in `build_app_and_options_from_config'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/server.rb:208:in `app'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/server.rb:336:in `wrapped_app'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/server.rb:272:in `start'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/lib/rack/server.rb:147:in `start'
        from /home/igneus/.rvm/gems/ruby-2.1.1/gems/rack-1.6.1/bin/rackup:4:in `<top (required)>'
        from /home/igneus/.rvm/gems/ruby-2.1.1/bin/rackup:23:in `load'
        from /home/igneus/.rvm/gems/ruby-2.1.1/bin/rackup:23:in `<main>'
        from /home/igneus/.rvm/gems/ruby-2.1.1/bin/ruby_executable_hooks:15:in `eval'
        from /home/igneus/.rvm/gems/ruby-2.1.1/bin/ruby_executable_hooks:15:in `<main>'

Tested with
ruby 2.1.1
grape 0.11.0
grape-swagger 0.10.1 as well as current master

+1,I have the error too.

+1
the same issue

I have been working on a fix, but I'm not sure if I will manage to complete it and make a pull request any soon.

I now encounter this error, too, although I'm doing something slightly different.
I have extracted all my endpoints into separate modules, like so:
      namespace 'courses' do
        mount Endpoint::ListCourses

        params do
          requires :course_id, type: String, desc: 'The course UUID'
        end
        route_param :course_id do
          namespace 'learning_rooms' do
            mount Endpoint::CreateLearningRoom
          end

          namespace 'quizzes' do
            params do
              requires :quiz_id, type: String, desc: 'The quiz UUID'
            end
            route_param :quiz_id do
              mount Endpoint::ViewQuiz

              namespace 'submissions' do
                mount Endpoint::ViewQuizSubmissions
              end
            end
          end
        end
      end

This worked fine, until I started further nesting these classes, like so:
Endpoint::Tables::ListTables
Endpoint::Tables::CreateTable

I don't know the code of this gem; can you point me to the root of this problem (the exception message doesn't say much) so that I can try to fix it?

A spec in this project would be helpful to start with.

For which issue exactly? The dynamic segments?

A minimal example that leads to this error.

No updates on this one?

I don't think anyone is actively working on a fix, please feel free to PR.

I get a similar, but slightly different error with the latest release:

C:/Ruby22-x64/lib/ruby/gems/2.2.0/gems/grape-swagger-0.20.0/lib/grape-swagger.rb:87:in `block in combine_namespace_routes': undefined method `reject' for nil:NilClass (NoMethodError)
        from C:/Ruby22-x64/lib/ruby/gems/2.2.0/gems/grape-swagger-0.20.0/lib/grape-swagger.rb:82:in `each'
        from C:/Ruby22-x64/lib/ruby/gems/2.2.0/gems/grape-swagger-0.20.0/lib/grape-swagger.rb:82:in `combine_namespace_routes'
        from C:/Ruby22-x64/lib/ruby/gems/2.2.0/gems/grape-swagger-0.20.0/lib/grape-swagger.rb:36:in `add_swagger_documentation'

I also facing kind of similar error
/home/faisal/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/grape-swagger-0.20.2/lib/grape-swagger.rb:66:in `combine_namespaces': undefined method `endpoints' for Kids:Module (NoMethodError)
	from /home/faisal/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/grape-swagger-0.20.2/lib/grape-swagger.rb:76:in `block in combine_namespaces'
	from /home/faisal/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/grape-swagger-0.20.2/lib/grape-swagger.rb:66:in `each'
	from /home/faisal/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/grape-swagger-0.20.2/lib/grape-swagger.rb:66:in `combine_namespaces'
	from /home/faisal/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/grape-swagger-0.20.2/lib/grape-swagger.rb:32:in `add_swagger_documentation'
	from /home/faisal/workspace/kidOrg/kidsapp-backend/app/api/api.rb:7:in `<class:API>'

I have also similar error.


Safari 14.1 and webm

I've had problems trying to use this package on a Mac in Safari in the past. I have everything working fine in Chrome and Firefox. When I try to run your example -
https://collab-project.github.io/videojs-record/demo/audio-video.html
then i get this in the browser console -

The file is then saved in mp4 format but the file size is many times larger (10x) than when I do it in Chrome which uses webm.
I understood the latest update from Apple this week for Big Sur and Safari meant that webm was now supported. Is there an update needed to your package or one of its dependencies still and if so then do you know when this might be fixed? Alternatively is there a way I can make the file size comparable to what I get using chrome as the file then needs to upload and this is fine with 3MB but not 30MB.
thanks for your help, Alistair

Hi @thijstriemstra I'm also struggling with record and playback cross browser and specially with safari.
I'm wondering what they mean with Supports VP9 codec used in WebRTC, does it mean Safari is supporting the video encoding in VP8/9 but not packing it in the webm container? I would apreciate some light on that.
For the playback you can have a look at OGV it helps a lot for IOS (both safari & chrome) and MacOS safari.

Playback also doesn't seem supported when testing this page in Safari 14.1: https://www.webmproject.org/detect/

Tested with Safari 15 and playback is still buggy. Sigh.

does it mean Safari is supporting the video encoding in VP8/9 but not packing it in the webm container?

No idea.


Any plans to suport debian buster (10)

Is your feature request related to a problem? Please describe.
We use the debian buster image for our java apps, but cannot because of azure sdk
Describe the solution you'd like
Dupport for debian buster
Describe alternatives you've considered
Debian 9, but its not as up to date

Hi, the official support is not planned yet. But based on some quick testing with  debian:stable from https://hub.docker.com/_/debian and our console sample app from https://github.com/Azure-Samples/cognitive-services-speech-sdk/tree/master/samples/java/jre/console, there should be no immediate problems with using the Speech SDK on Debian 10 either. Have you encountered any issues?
For Java, the same prerequisites apply as on Debian 9 except you can use newer versions of libssl and openjdk. So at least the following packages are required on Debian 10:

libasound2
libssl1.1
openjdk-11-jdk (or -jre if you need only the runtime)

If you want to use compressed audio for input, install also the following GStreamer packages:

libgstreamer1.0-0
gstreamer1.0-plugins-base
gstreamer1.0-plugins-good
gstreamer1.0-plugins-bad
gstreamer1.0-plugins-ugly

Thanks, i got a native exception from the jni carbon wrapper. But maybe i am just missing some libs, i assumed that it was because of buster, but i might be wrong. Nevertheless if it works it is still good to know that there is no official support planned, so we can make an informed decision about putting it live even if it works

As of now there is no schedule for official support, but most likely it will be considered at some point in the future. Currently Speech SDK releases are not tested on Debian 10, but if you can provide details of specific issues you are seeing, we can have a look at them as well.

Closed as answered, please reopen if you need further support.

I tried and it worked, now its more of a question of going to production on an unsupported platform

This is a late comment, but I've added a backlog work item for Debian 10 support (mainly verification and documentation) and we'll check if it can be prioritized for implementation in the coming months. This issue will be updated when the work is done and release information is available.


Gui system and prompt for querying prior

Closes #8
Closes #16

The main application will now be launched on its own thread with a main() function, while the GUI system is run on the main thread.

fixed small bug where arguments from window_initializer were not being spread into event_processor, which meant that all arguments accumulated in the first parameter.


File Type Associations incorrectly encode %1 to be %251 when setting the Verb handler's command line template.

Example of the incorrect template data in the registry: "C:\path\myApp.exe ----ms-protocol:ms-encodedlaunch://App/?ContractId=Windows.File&Verb=edit&File=%251"
This results in Unpackaged apps not getting a correct command line, and subsequently AppInstance::GetCurrent()::GetActivatedEventArgs() throws an exception.

Scott, what's the end impact of this? For example, what task/scenario can't be completed as a result of this? And do we have a workaround?

File Type association launches crash the app.  You can manually edit the registry value to be %1 instead as a partial workaround.  If the target file path has a space in it, then it will still fail and there is no workaround for that scenario.

I added more details to the issue that should answer your questions.  Let me know if I missed anything.
From: zaryaf @.>
Sent: Monday, October 4, 2021 11:45 AM
To: microsoft/WindowsAppSDK @.>
Cc: Scott Darnell @.>; Assign @.>
Subject: Re: [microsoft/WindowsAppSDK] File Type Associations incorrectly encode %1 to be %251 when setting the Verb handler's command line template. (#1524)
Scott, what's the end impact of this? For example, what task/scenario can't be completed as a result of this? And do we have a workaround?

You are receiving this because you were assigned.
Reply to this email directly, view it on GitHubhttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmicrosoft%2FWindowsAppSDK%2Fissues%2F1524%23issuecomment-933755569&data=04|01|scodar%40microsoft.com|42d38c7c0fa0456b4e4f08d9876707e9|72f988bf86f141af91ab2d7cd011db47|1|0|637689698992898292|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|1000&sdata=%2FcabhsPkRp9Jiv732TT%2FEQk9WpI7n1NfOdjNBovd3go%3D&reserved=0, or unsubscribehttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAE4I5UR5RAX5FXPNRPVRBM3UFHYZVANCNFSM5FFWFY6A&data=04|01|scodar%40microsoft.com|42d38c7c0fa0456b4e4f08d9876707e9|72f988bf86f141af91ab2d7cd011db47|1|0|637689698992908289|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|1000&sdata=tYb7Ls91JqL4oH7rfJZ%2FGNVXxYcCUzQnTd%2FZd0HT7D0%3D&reserved=0.
Triage notifications on the go with GitHub Mobile for iOShttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04|01|scodar%40microsoft.com|42d38c7c0fa0456b4e4f08d9876707e9|72f988bf86f141af91ab2d7cd011db47|1|0|637689698992918278|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|1000&sdata=NsRhu53QuIwj8lnxZX8m78Sm8FUzIeBLCZvZuduamFM%3D&reserved=0 or Androidhttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04|01|scodar%40microsoft.com|42d38c7c0fa0456b4e4f08d9876707e9|72f988bf86f141af91ab2d7cd011db47|1|0|637689698992918278|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|1000&sdata=8M17WhYXndfAS1QlA783hJZzvQPEDpud%2BMZR1k5DKxs%3D&reserved=0.


Set the worker restart policy to OnFailure

Try loading or unloading kernel modules until either:

the Module is deleted, or;
the Pod template has changed.

Remove the inProgress field of the NMC statuses.
Fixes #841
/cc @yevgeny-shnaidman

Codecov Report

Merging #842 (491fc3f) into main (5643c75) will decrease coverage by 0.29%.
Report is 1 commits behind head on main.
The diff coverage is 62.62%.

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
@@            Coverage Diff             @@
##             main     #842      +/-   ##
==========================================
- Coverage   76.44%   76.15%   -0.29%
==========================================
  Files          59       59
  Lines        5569     5611      +42
==========================================
+ Hits         4257     4273      +16
- Misses       1097     1116      +19
- Partials      215      222       +7

Files
Coverage Δ

api/v1beta1/nodemodulesconfig_types.go
100.00% <ø> (ø)

internal/controllers/nmc_reconciler.go
78.42% <62.62%> (-1.98%)
:arrow_down:

/lgtm

/cherry-pick release-2.0


Add sudo wrapper for allowing STDOUT configuration

This adds the sudo package to the squid proxy in order to allow the
main squid process to access STDOUT before it drops privileges when
forking.

@seanson does https://github.com/flaccid/docker-squid/blob/ca24e1ae8654e96f70db30a38ddd9eede1ab888c/Dockerfile provide a solution to save having to use sudo?


[utils] Fix some linter errors

Fixes 7 errors. 13 remaining

Great work!
Fix the remaining 13 errors when you get a chance.
Also change the lint script in package.json to run eslint
 "lint": "eslint -c ../../.eslintrc.json *.js tests/*.js src/*.js",

Now if there are any eslint errors at all, CircleCI will fail, and we shouldn't merge to master.


Revert "Manually track num_max_thread (#12380)"

This reverts commit 75410210e07a5fab5e044348aee276d578d5857e.
@azai91 @cjolivier01
Description
This fixes https://github.com/apache/incubator-mxnet/issues/13449 . Added more details in the issue.
Checklist
Essentials
Please feel free to remove inapplicable items for your PR.

[ ] The PR title starts with [MXNET-$JIRA_ID], where $JIRA_ID refers to the relevant JIRA issue created (except PRs with tiny changes)
[ ] Changes are complete (i.e. I finished coding on this PR)
[ ] All changes have test coverage:
Unit tests are added for small changes to verify correctness (e.g. adding a new operator)
Nightly tests are added for complicated/long-running ones (e.g. changing distributed kvstore)
Build tests will be added for build configuration changes (e.g. adding a new build option with NCCL)
[ ] Code is well-documented:
For user-facing API changes, API doc string has been updated.
For new C++ functions in header files, their functionalities and arguments are documented.
For new examples, README.md is added to explain the what the example does, the source of the dataset, expected performance on test set and reference to the original paper if applicable
Check the API doc at http://mxnet-ci-doc.s3-accelerate.dualstack.amazonaws.com/PR-$PR_ID/$BUILD_ID/index.html
[ ] To the my best knowledge, examples are either not affected by this change, or have been fixed to be compatible with this change

Changes

[ ] Feature1, tests, (and when applicable, API doc)
[ ] Feature2, tests, (and when applicable, API doc)

Comments

If this change is a backward incompatible change, why must this change be made.
Interesting edge cases to note here

@mxnet-label-bot add [pr-awaiting-review]


NO-ISSUE: [release-ocm-2.9] Use archived dnf repositories for centos8 as the current ones are no longer valid

Description

How was this code tested?
CentOS Linux 8 had reached the End Of Life (EOL) on December 31st, 2021. It means that CentOS 8 will no longer receive development resources from the official CentOS project. After Dec 31st, 2021, if you need to update your CentOS, you need to change the mirrors to vault.centos.org where they will be archived permanently. Alternatively, you may want to upgrade to CentOS Stream.
from - https://techglimpse.com/failed-metadata-repo-appstream-centos-8/

Assignees

/cc @gamli75
/cc @eifrach
Links

Checklist

[x] Title and description added to both, commit and PR
[x] Relevant issues have been associated
[x] Reviewers have been listed
[x] This change does not require a documentation update (docstring, docs, README, etc)
[ ] Does this change include unit tests (note that code changes require unit tests)

/retitle [release-ocm-2.9] NO-ISSUE: Use archived dnf repositories for centos8 as the current ones are no longer valid

/retitle [release-ocm-2.9] NO-ISSUE: Use archived dnf repositories for centos8 as the current ones are no longer valid


Inconsistency between Rearrangement and metadata field tables in docs

Sorry I didn't catch this earlier, but the field tables aren't consistent across the Rearrangement, metadata (Repertoire), and experimental schema (Alignment, Clone, Tree, Node, Cell).
Rearrangement and Alignment have columns:  Name, Type, Priority, Description. I changed "Priority" to "Level" in #389. Where Level is either required (in top level required) or optional (not in top level required).
Metadata objects and Clone, Tree, Node and Cell have "MiAIRR" instead of "Level".
The former also have a Download as TSV link and the latter do not.
I think these should be consistent. At the very least Clone, Tree, Node and Cell should follow whatever rules we use for Rearrangement and Alignment. I can see an argument for making the metadata field tables different. Though, I'm not certain "MiAIRR" is the right terminology to the convey the requirement levels. We can populated the column from the x-miairr tag, but I don't think the distinction between MiAIRR and not-MiAIRR is very useful.
Thoughts? I'm guessing this is partly due to us having some redundant code in docs/conf.py for building tables.

I agree that "MiAIRR" probably isn't the right terminology. I'd like the tables to provide the 4 main attributes for fields 1) MiAIRR level, 2) required, 3) nullable and 4) identifier. It's probably ok to pack them into a single column or we can consider splitting them out.

From the call:

Can link to the MiAIRR full table from the AIRR Data Model docs (https://docs.airr-community.org/en/latest/datarep/overview.html#airr-data-model).
Try one column with requirement level, nullable and identifier tags.

Working on this and a few other bits in the docs-tables  branch.  Should be done Soon(TM).


Expense Claims / Approval

[ ] US08.01.01
As an approver, I want to view a list of all the expense claims that were submitted for approval, which have their claim status as submitted, showing for each claim: the claimant name, the starting date of travel, the destination(s) of travel, the claim status, total currency amounts, and any approver name.

[ ] US08.02.01
As an approver, I want the list of submitted expense claims to be sorted by starting date of travel, in order from oldest to most recent, so that older claims are considered first.

[ ] US08.03.01
As an approver, I want to view all the details of a submitted expense claim.

[ ] US08.04.01
As an approver, I want to list all the expense items for a submitted claim, in order of entry, showing for each expense item: the date the expense was incurred, the category, the textual description, amount spent, unit of currency, and whether there is a photographic receipt.

[ ] US08.05.01
As an approver, I want to view any attached photographic receipt for an expense item.

[ ] US08.06.01
As an approver, I want to add a comment to a submitted expense claim, so that I can explain why the claim was returned or provide accounting details for a payment.

[ ] US08.07.01
As an approver, I want to return a submitted expense claim that was not approved, denoting the claim status as returned and setting my name as the approver for the expense claim.

[ ] US08.08.01
As an approver, I want to approve a submitted expense claim that was approved, denoting the claim status as approved and setting my name as the approver for the expense claim.

[ ] US08.09.01 added 2015-02-12
As an approver, I want to ensure I cannot return or approve an expense claim for which I am the claimant.

Do 	//US02.02.01 - list of expense claims to be sorted by starting date of travel, in order from most recent to oldest in ClaimListTests


Add a Web Dynpro ABAP App to Your Launchpad Site

Tutorials: https://developers.sap.com/tutorials/cp-portal-cloud-foundry-webdynpro-app.html
The final question might be wrong. I thought the answer is Role editor and Group editor and not Role, Group and App.
Which tools will you use to configure your Web Dynpro app so that users can see it and launch it from your launchpad site?
App editor
Provider Manager
Role editor
Group editor

Hi - thanks - you are correct and I've fixed it.  The app editor was also checked and I removed it.
Thanks
Lindsay

The problem is fixed


Firebase Crash on runtime APMDatabase insertBundle uploadData

Step 1: Describe your environment

Xcode version: 13.4.1
Firebase SDK version: 8.12.1
Installation method: Carthage (select one)
Firebase Component: Core, Messasing
Target platform(s): iOS

Step 2: Describe the problem
The application crashed in the foreground after a successful build without making any action. I think the crashed happened when the SDK send some data to the server periodical time.
Steps to reproduce:
I cannot say that I can produce all time. It happens without any indicator.
Relevant Code:
m 0 _pthread_kill
pthread_kill
2 abort
3 abort_message
3D 4 demangling_terminate_handler()
5 _objc_terminate()
6 std:: __terminate (void (*)())
<D> 7 std::terminate()
8 objc_terminate
) _dispatch_client_callout
10 _dispatch_lane_serial_drain
11 _dispatch_lane_invoke
m 12 _dispatch_workloop_worker_thread
mi 13 _pthread_wqthread
V Original Exception Backtrace
Thread
0 __exceptionPreprocess
1 objc_exception_throw
2 + [NSObject(NSObject) doesNotRecognizeSelector:]
3 _forwarding_
4 _CF_forwarding_prep_0
5 -[APMDatabase insertBundle:isRealtime: error: ]
8 41-[APMMeasurement (Bundle) bundleRawEvents]_block_invoke
8 7 - [APMSqliteStore performTransactionWithError: block: ]
E 8 - [APMDatabase performTransaction:]
8 9 -[APMMeasurement (Bundle) bundleRawEvents]
8 10 - [APMMeasurement uploadData]
E 11 - [APMMeasurement networkRemoteConfigFetchCompletionHandler...
8 12 35-[APMMeasurement fetchRemoteConfig]_block_invoke
m 13 _dispatch_call_block_and_release
I 14 _dispatch_client_callout
m 15 _dispatch_lane_serial_drain
mm 16 _dispatch_lane_invoke
``

Thanks for reaching out, @ttuygun. Could you provide the complete stack trace of your issue?

If you can repro the issue locally (even inconsistently), can you find the selector/receiver pair that's causing this crash? It should be part of the exception message printed to console.

2022-07-16 19:12:49.253095+0300 TestProject[50675:2249567] 8.12.1 - [Firebase/Analytics][I-ACS023105] Event is not subject to real-time event count daily limit. Marking an event as real-time. Event name, parameters: screen_view (_vs), {
ga_debug (_dbg) = 1;
ga_event_origin (_o) = auto;
ga_previous_class (_pc) = FirstViewController;
ga_previous_id (_pi) = -375749665399308660;
ga_realtime (_r) = 1;
ga_screen_class (_sc) = SecondViewController;
ga_screen_id (_si) = -375749665399308659;
}
2022-07-16 19:12:49.263800+0300 TestProject[50675:2249564] +[NSData gul_dataByGzippingData:error:]: unrecognized selector sent to class 0x1da864298
2022-07-16 19:12:49.268050+0300 TestProject[50675:2249564] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '+[NSData gul_dataByGzippingData:error:]: unrecognized selector sent to class 0x1da864298'
*** First throw call stack:
(0x1810b2d78 0x199d17734 0x181190ab8 0x181047988 0x181046a60 0x106242c24 0x10627a3d4 0x1062cf204 0x106240190 0x10627987c 0x1062723a0 0x106277ac4 0x106277570 0x10d74cc6c 0x10d74e7bc 0x10d7568a4 0x10d7575e0 0x10d764168 0x1f15860bc 0x1f1585e5c)
libc++abi: terminating with uncaught exception of type NSException
dyld4 config: DYLD_LIBRARY_PATH=/usr/lib/system/introspection DYLD_INSERT_LIBRARIES=/Developer/usr/lib/libBacktraceRecording.dylib:/Developer/usr/lib/libMainThreadChecker.dylib:/Developer/Library/PrivateFrameworks/GPUTools.framework/libglInterpose.dylib:/Developer/Library/PrivateFrameworks/DTDDISupport.framework/libViewDebuggerSupport.dylib
*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '+[NSData gul_dataByGzippingData:error:]: unrecognized selector sent to class 0x1da864298'
terminating with uncaught exception of type NSException
(lldb)

Please confirm that the GoogleUtilities.xcframework is linked and you followed the following step from the instructions:
Add $(OTHER_LDFLAGS) -ObjC flag to "Other Linker Flags" in "Build Settings".


login issue

I have a user with standard user role, user tried many times with incorrect password and later I reset his password still he is not able to login with new password, he is getting bad user or password error and captcha. I removed the user and re-added him (ofcourse all associated tasks were removed) to fix the login issue.
Is there a better way to fix such kind of login issue?
Thanks for your help.

As described here http://kanboard.net/documentation/bruteforce-protection, after 6 failures the account is locked down for a period of 15 minutes, you just need to wait.
At the moment there is no user interface to reset the failed login counter but that can be done manually in the database.

A user after 6 attempts is blocking access and is not releasing after 15 minutes. What to do? I need to set up some task in crontab? Something like ./kanboard -XXX unlock.
The current solution is to delete the user and grant all access again. But it loses all tasks already allocated.


cmd/compile: compiler hidden error is possible, that downgrade perfomance of binary search in array

What version of Go are you using (go version)?

go version go1.11.5 linux/amd64

Does this issue reproduce with the latest release?
yes
What operating system and processor architecture are you using (go env)?
go env Output
GOARCH="amd64"
GOOS="linux"

What did you do?
Create a binary search in an sorted array int32 without checking boundaries, using unsafe.
func unsafeBinSearch(a []uint32, x uint32) uint32 {
	p := (*[1 << 31]uint32)(unsafe.Pointer(&a[0]))
	n := uint32(len(a))
	i, j := uint32(0), n
	for i < j {
		h := (i + j) >> 1
		if p[h] < x {
			i = h + 1
		} else {
			j = h
		}
	}
	return i
}

What did you expect to see?
Maximum performance of compiled code without checking the boundaries inside the loop.
What did you see instead?
Compiler hidden error is possible, that downgrade perfomance, which may occur in other cases.
The result of compiling the above code:
0x001f 00031 (intunsafe.go:9)	XORL	BX, BX
0x0021 00033 (intunsafe.go:9)	CMPL	BX, AX
0x0023 00035 (intunsafe.go:9)	JCC	60

** 0x0025 00037 (intunsafe.go:11)	TESTB	AL, (DX) **

0x0027 00039 (intunsafe.go:10)	LEAL	(BX)(AX*1), SI
0x002a 00042 (intunsafe.go:10)	SHRL	$1, SI
0x002c 00044 (intunsafe.go:11)	MOVL	(DX)(SI*4), DI
0x002f 00047 (intunsafe.go:11)	CMPL	DI, CX
0x0031 00049 (intunsafe.go:11)	JCC	56
0x0033 00051 (intunsafe.go:12)	LEAL	1(SI), BX
0x0036 00054 (intunsafe.go:12)	JMP	33
0x0038 00056 (intunsafe.go:9)	MOVL	SI, AX
0x003a 00058 (intunsafe.go:14)	JMP	33

The compiler creates an additional instruction TESTB AL, (DX) for comparing two numbers, the result of which is not used further, because is replaced by the next CMPL DI, CX.

Just from looking at the assembly here on my phone, I’d say that that line is checking whether p is nil; it’d fault if so. It is thus not redundant.
If that’s right, of course, the nil check should be hoisted out of the loop. And I believe that @randall77 had plans to mark some manually constructed unsafe.Pointers as non-nil (which this one clearly is, as it points to the first element of a slice).

It is thus not redundant.
Yeah, this is probably true. But pay attention that there is no "complete" check, it's only TEST instruction. No jumps, no any other side effects which should follow after it.

If it faults, we’ll receive a segfault signal, which the runtime will catch and turn into a panic.

Why is this test inside the loop? Pointer is declared at the beginning of the function.

Yes, as I wrote:

the nil check should be hoisted out of the loop.

If it faults, we’ll receive a segfault signal, which the runtime will catch and turn into a panic.

This test is not for null pointer. This test check cap(a)==0, because 0x001a 00026 (intunsafe.go:9)	MOVQ	"".a+16(SP), DX, where a+16 is cap in slice struct (a+0 is pointer to data, a+8 is len).
Please see full asm code:
0x0000 00000 (intunsafe.go:5)	TEXT	"".unsafeBinSearch(SB), NOSPLIT, $8-40
0x0000 00000 (intunsafe.go:5)	SUBQ	$8, SP
0x0004 00004 (intunsafe.go:5)	MOVQ	BP, (SP)
0x0008 00008 (intunsafe.go:5)	LEAQ	(SP), BP
0x000c 00012 (intunsafe.go:5)	FUNCDATA	$0, gclocals·1a65e721a2ccc325b382662e7ffee780(SB)
0x000c 00012 (intunsafe.go:5)	FUNCDATA	$1, gclocals·69c1753bd5f81501d95132d08af04464(SB)
0x000c 00012 (intunsafe.go:5)	FUNCDATA	$3, gclocals·ebb0e8ce1793da18f0378b883cb3e122(SB)
0x000c 00012 (intunsafe.go:6)	PCDATA	$2, $0
0x000c 00012 (intunsafe.go:6)	PCDATA	$0, $0
0x000c 00012 (intunsafe.go:6)	MOVQ	"".a+24(SP), AX
0x0011 00017 (intunsafe.go:6)	TESTQ	AX, AX
0x0014 00020 (intunsafe.go:6)	JLS	73
0x0016 00022 (intunsafe.go:9)	MOVL	"".x+40(SP), CX
0x001a 00026 (intunsafe.go:9)	PCDATA	$2, $1
0x001a 00026 (intunsafe.go:9)	PCDATA	$0, $1
0x001a 00026 (intunsafe.go:9)	MOVQ	"".a+16(SP), DX
0x001f 00031 (intunsafe.go:9)	XORL	BX, BX
0x0021 00033 (intunsafe.go:9)	CMPL	BX, AX
0x0023 00035 (intunsafe.go:9)	JCC	60
0x0025 00037 (intunsafe.go:11)	TESTB	AL, (DX)
0x0027 00039 (intunsafe.go:10)	LEAL	(BX)(AX*1), SI
0x002a 00042 (intunsafe.go:10)	SHRL	$1, SI
0x002c 00044 (intunsafe.go:11)	MOVL	(DX)(SI*4), DI
0x002f 00047 (intunsafe.go:11)	CMPL	DI, CX
0x0031 00049 (intunsafe.go:11)	JCC	56
0x0033 00051 (intunsafe.go:12)	LEAL	1(SI), BX
0x0036 00054 (intunsafe.go:12)	JMP	33
0x0038 00056 (intunsafe.go:9)	MOVL	SI, AX
0x003a 00058 (intunsafe.go:14)	JMP	33
0x003c 00060 (intunsafe.go:17)	PCDATA	$2, $0
0x003c 00060 (intunsafe.go:17)	MOVL	BX, "".~r2+48(SP)
0x0040 00064 (intunsafe.go:17)	MOVQ	(SP), BP
0x0044 00068 (intunsafe.go:17)	ADDQ	$8, SP
0x0048 00072 (intunsafe.go:17)	RET
0x0049 00073 (intunsafe.go:6)	CALL	runtime.panicindex(SB)

I am wrong. MOVQ	"".a+16(SP), DX is a pointer to data, because MOVL	(DX)(SI*4), DI extract data at SI*4 byte.

In case it helps you understand, this is how the compiler views that code, step by step:
ssa.html.zip
(Generate with $ GOSSAFUNC=unsafeBinSearch go tool compile p.go.)

Thanks. Then, AX = j, SI = h, BX = i, DX = pointer to data.
If AX=j, why compiler test one low byte of 'j' (AL) by bitwise 'and' with byte '*p'?

We are found ssa.Op386LoweredNilCheck. Thanks for GOSSAFUNC :)

But we need to up this check outside from loop.

In case it helps you understand, this is how the compiler views that code, step by step:
ssa.html.zip
(Generate with $ GOSSAFUNC=unsafeBinSearch go tool compile p.go.)

I analyze this report and see:

On stage "start" compiler create this lines:

v30 (11) = Copy <*[2147483648]uint32> v55 (p[*[2147483648]uint32])
v31 (11) = Copy <mem> v53
v32 (11) = NilCheck <void> v30 v31

On stage "early copyelim" compiler reduce two lines:

v16 (6) = PtrIndex <*uint32> v15 v10 (p[*[2147483648]uint32])
...
-- v30 (11) = Copy <*[2147483648]uint32> v16
-- v31 (11) = Copy <mem> v1
v32 (+11) = NilCheck <void> v16 v1

At the "early copyelim" stage, v32 is not reduced.
It seems to me, a bug is here.
Another reason for remove this check: NilCheck does not add protection against a null pointer, since then there is "v38 (11) = PtrIndex <*uint32> v30 v33; v39 (11) = Copy  v31; v40 (11) = Load  v38 v39", which can also trigger SEGFAULT on invalid pointer.

CC @martisch

If that’s right, of course, the nil check should be hoisted out of the loop. And I believe that @randall77 had plans to mark some manually constructed unsafe.Pointers as non-nil (which this one clearly is, as it points to the first element of a slice).

My change only marks the results of unsafe pointer arithmetic as non-nil. It doesn't do so for simple casts.
We could mark the results of &a[x] as non-nil, though, that seems safe. That might fix this issue.


Colors inconsistency in stacked visuals with and without filters applied

I have a stacked bar chart that takes colors from the pbiColorNominal. What would be the best way to ensure that the same category gets the same color with and without (external) filters applied, similar to what standard Power BI stacked bar chart does?
Here is what I am getting without filters - colors in the native stacked bar chart and Deneb visuals are consistent:

And now with filters applied (BR and CA removed). Native visual keeps the same colors, while Deneb reassigns colors in the order defined in the spec (or default one):

You can find the pbix there: https://www.dropbox.com/s/2e5wciyb2ddhazv/FP.pbix?dl=0
The difficulty is that Deneb sees only data passed into it via the list of Values and doesn't get the rows with the categories that were filtered out (I am curious how native Power BI visuals deal with that).
The best I can come up with is to read the theme JSON file as a data file with Power Query, parse it (extract colors), build dimensions with <Category, Color> pairs, join it with original dataset and use those explicit colors within Vega-Light spec.
But I am not sure how to make it consistent with color assignments for other non-Deneb visuals on the page.
Any other ideas?

With conventional visuals that have data-bound properties (core or custom), the typical logic you would employ is to use the getColor method of the visual host to 'reserve' a specific colour by the data value. Any subsequent values get assigned the next available colour. Note that this will only work for the lifecycle of the visual, so will change if you navigate away from the current tab and back in, which will re-initalise it completely.
For categorical values (columns), these properties are bound by selector (which is a row pointer, and how interactivity works) rather than explicit values, so you can change a colour in the properties pane from the default assigned and this will stick, but only if the same categorical value occupies exactly the same pointer when the visual re-initialises (measures being an exception as their selectors are explicitly tied to the measure's query name and are therefore mor predictable).
Because Deneb doesn't have the same behaviour in that we cannot create dynamic properties in the pane and everything is declared as part of the specification, you have a couple of options as-is:

Declare the domain of all possible categorical values in the color scale, and then set up a corresponding range with the desired color value that corresponds with the index of that domain value. e.g. for range definition.
Define the colour for a category as a column or measure and pass this into the dataset. You can then bind the range to that field in the color encoding channel. This would be as functionally similar to the property binding approach detailed above, with the advantage that you could always guarantee colours are consistent for a specific value. However, I don't think that there's anything in DAX to extract the theme colours to automate this if you were looking to tie this together more simply than manually getting the values out of a theme's palette to populate them.

I currently don't have any further ideas as to how we could mimic the behaviour otherwise in the current state, but others might.
Going forward, it might be possible provide some kind of wrapper for getColor as a custom expression that can be used to reserve based on the specified datum.value that gets passed.

Daniel, thanks a lot for clarification. Option 2 looks better to me at risk of not matching colors used in non-Deneb visuals (as you mentioned as well).  Per my observations, Power BI sorts categories in the alphabetical order and then assigns colors from the theme to them. It's not guaranteed nor supported, but at least it works for now. Maintenance would be a bit messy too, but it's better than nothing :-)
Thanks again, appreciate your response!


Operational Insights: Broken link to example

Hi,
There is a broken link on this page under "Remarks" where it says "[Here] (/documentation/2-Using-the-API/Query)". Could this be fixed, I'd like to read the example. Thanks!

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

ID: 2463fe7f-e35e-9db5-3f8a-7a0c56236f02
Version Independent ID: 2b903fcd-9956-c2e8-0167-f4f2ea89270c
Content: OperationalInsightsDataClient.QueryWithHttpMessagesAsync(String, Nullable<TimeSpan>, IList<String>, Dictionary<String,List<String>>, CancellationToken) Method (Microsoft.Azure.OperationalInsights) - Azure for .NET Developers
Content Source: xml/Microsoft.Azure.OperationalInsights/OperationalInsightsDataClient.xml
Service: operational-insights
GitHub Login: @rloutlaw
Microsoft Alias: routlaw

Thank you for your feedback.  Tagging and routing to the team best able to assist.

@afratila Apologies for the late reply. Thanks for sharing the feedback. We have filed the above PR which is pending under review. In the meantime, if you have any queries please do let me know. Awaiting your reply.


Consider vulnerability report (be careful)

The internal Grafana metrics available under the /metrics endpoint is enabled by default for long time already. Not an issue for us especially considering that all the data are public (at least at this time).
Just in case I've disable it: https://benchmark.o1labs.org/metrics -> HTTP 404.


[FEATURE] Syntax for not stretching widget if contents are too big?

Description of the requested feature
Basically, whenever i make some content in eww too big for the box, eww streches the box to make it fit, is it possible to implement so that this does not happen? Just like polybar, it renders it, but outside of the visible area.
Proposed configuration syntax
<box strechable="false">?
Additional context
Just like polybar

yea i fear GTK makes this really hard. generally, i really want to provide this, but I haven't yet figured out a way how.

https://gitlab.gnome.org/GNOME/gtk/-/issues/3012
https://people.gnome.org/~ebassi/docs/_build/Gtk/4.0/property.Widget.overflow.html
Seems like GTK does support it, but programmatically & not with css.

Unfortunately not yet,
its hard to find a solution in GTK that works across every widget


Implement remark-lint

Do you have plans to integrate remark-lint?
If you need any help, I'd be glad to give a helping hand.

Hello, @TimonVS,
Yes, I'm going to make this plugin, but separately (because for linters I should use VS Code Language Server).
My personal queue of plugins that I'm going to create: https://github.com/mrmlnc/vscode-extensions-queue. Right now I'm working on autocompletion for Less.

Cool! Let me know if I can help.

@remarkjs you mean? 😉
How can I help?

Hi,
Unfortunately, now I don't have time to write new plugins and have a little time to support old ones. If you can do it on your own, then I am ready to help you in any way.


Assign Traffic Splitting

Description
As a user I want to be able to setup and assign traffic to different revisions.
Acceptance Criteria

It should set the traffic level for the revision
It should equal 100% across all the revisions of a service

I think we should always tag the split, it is convenient for a developer to be quickly reach to a revision.

Can you please elaborate?


Inconsistent type assumption for scratch variable

(I originally mentioned this in https://github.com/CesiumGS/cesium/issues/11665, but should probably be an own issue)
The scratchVariable in ModelAnimationChannel is initialized depending on the "path" of the channel: For "translation" animations, it is a Cartesian3, and for "rotation" animations, it is a Quaternion. But ... it is a global variable 😬 When initializing multiple channels, then there are cases where this should be a Quaternion, but it actually is a Cartesian3, meaning that some of the functions are just shoving some .w property into that poor Cartesian3. It happens to work (hooray to untyped languages), but ... feels wrong.
Would the preferred way of fixing this be to convert that scratchVariable an instance variable in the ModelAnimationChannel?

I think the preferred solution would be to have two scratch variables, one for each type.


Expose RollbarAppender(rollbar Rollbar) constructor overload, and make RollbarAppender#start() skip this.rollbar initialization if it's already non-null

Fixes #184

Released now in https://github.com/rollbar/rollbar-java/releases/tag/v1.5.2

thank you @ArturMoczulski!! much appreciated.


processMessage failed: Error: TypeError: undefined is not a function

processMessage failed: Error: TypeError: undefined is not a function cordova.js:1044
processMessage failed: Stack: TypeError: undefined is not a function
    at registrationHandler (http://localhost/app/settings.js:111:19)
    at Object.cordova.callbackFromNative (http://localhost/cordova.js:292:54)
    at processMessage (http://localhost/cordova.js:1039:21)
    at Function.androidExec.processMessages (http://localhost/cordova.js:1076:13)
    at pollOnce (http://localhost/cordova.js:944:17)
    at pollOnceFromOnlineEvent (http://localhost/cordova.js:939:5) cordova.js:1045
processMessage failed: Message: S01 PushPlugin1230508099 sAPA91bHIP6LrQF431LNbnyQURXHJnzVhShJVVwcf__ai3MeyDYc7MX6pO_S_RGt6UdSQzMxodtCgT68OCSqcI47QrnEn9iVXAtVnzkrn3NxnJj_jm3YMhHGBVgaKltXX7bijfigo6CJIx6L1Tedg-vUfUI7vSFFnsGq_0aglmLL9j9tIC_fgOGY cordova.js:1046

That line 111 of settings.js corresponds to the below, the pushNotification.onMessageInForeground( section
Its like the pushNotification js is not loading. Then when I reload the view in chrome debugger the error goes away, but I am getting zero output to the console when a push comes in, be it foreground or background
var pushNotification;

document.addEventListener("deviceready", function() {
  pushNotification = window.plugins.pushNotification;

  pushNotification.register(
		    registrationHandler,
		    errorHandler, {
		        //android options
		        "senderID":"xxxxxxxxxxxx",
		        //ios options
		        "badge":"true",
		        "sound":"true",
		        "alert":"true"
		        });
});

function errorHandler (error) {
    alert('error = ' + error);
}

function registrationHandler (deviceToken) {
	console.log('deviceToken = ' + deviceToken);
    //save the deviceToken / registration ID to your Push Notification Server

	pushNotification.onMessageInForeground(
	    messageInForegroundHandler,
	    errorHandler);

	pushNotification.onMessageInBackground(
	    messageInBackgroundHandler,
	    errorHandler);

}

function messageInForegroundHandler (notification) {

    //handle the contents of the notification
    console.log(notification.message || notification.alert);

    if ( event.sound ) {
        var snd = new Media(event.sound);
        snd.play();
    }

    if ( event.badge ) {

    }
    console.log(notification);
}

function messageInBackgroundHandler (notification) {
    if (notification.coldstart) {
        // ios, this is always true
        // the application was started by the user tapping on the notification
    }
    else {
        //this notification was delived while the app was in background
    }

    //handle the contents of the notification
    var message = notification.message || notification.alert;
    console.log(notification);

}

Can confirm this issue. Weird is that sometimes notification is being displayed on task bar but not on app (console output).
Where are you using your event listeners? Are these functions inside angular or other events?

I'm sorry, my mistake, right syntax is notification.aps.alert or notification.aps.sound for standard properties and notification.mycustomvar to access to custom variables.

It seems like an issue with the JS code, not push plugin. Not sure where it's going wonky – maybe the variables are not being exposed correctly and pushNotification is undefined? In any case, can't replicate any undefined errors when the push plugin API calls are made in the correct order, so closing this.


Recentering in 'phonopy --symmetry', and aperiodic systems

In some circumstances, phonopy applies some form of "recentering" before writing PPOSCAR.  Because phonopy also always reduces coordinates into the unit cell, this translation can present challenges for code working with aperiodic systems:
POSCAR
generated by phonopy
1.0
8.799999999999999 0.000000000000000 0.000000000000000
0.000000000000000 8.799999999999999 0.000000000000000
0.000000000000000 0.000000000000000 8.799999999999999
C H
1 4
direct
0.390000000000000 0.390000000000000 0.390000000000000 C
0.461705558018936 0.461705558018936 0.461705558018936 H
0.318294441981064 0.318294441981064 0.461705558018936 H
0.461705558018936 0.318294441981064 0.318294441981064 H
0.318294441981064 0.461705558018936 0.318294441981064 H

PPOSCAR
generated by phonopy
   1.0
     8.7999999999999989    0.0000000000000000    0.0000000000000000
     0.0000000000000000    8.7999999999999989    0.0000000000000000
     0.0000000000000000    0.0000000000000000    8.7999999999999989
C H
   1    4
Direct
  0.0000000000000000  0.0000000000000000  0.0000000000000000
  0.0717055580189361  0.0717055580189361  0.0717055580189361
  0.9282944419810639  0.9282944419810639  0.0717055580189361
  0.0717055580189361  0.9282944419810639  0.9282944419810639
  0.9282944419810639  0.0717055580189361  0.9282944419810639

In the PPOSCAR above, you can see that the atoms are no longer chosen from a single image of the molecule, which presents a challenge if somebody wants to read this file and e.g. create an ASE Atoms with pbc=False.  But, to my understanding, this translation is not necessary for the structure to be symmetrized, because each spacegroup operation (R, t) on the translated structure admits a spacegroup operation on the original structure by similarity transform.  (Basically, if the recentering is done by adding a vector c then you compose the operations (1, -c), (R, t), (1, +c))
So, could it be possible to add an option for phonopy --symmetry to not recenter PPOSCAR?  (by adjusting the printed spacegroup operators instead of the positions)
Alternatively, could the output of phonopy --symmetry possibly include the translation vector used for recentering, so that the user can easily undo the translation if desired?

To undo, not only the shift, but also rotation has to be given. But it's quite easily to include and I agree it should be done. I also think that users who can understand this detail can use spglib without any difficulty, and it is my recommendation.
There are a few options for creating the primitive cell in spglib, https://spglib.github.io/spglib/api.html#spg-standardize-cell. PPOSCAR is currently made with no_idealize=0, which can contain a rotation (https://spglib.github.io/spglib/definition.html#rotation-introduced-by-idealization), too. If we want to avoid those, we can use no_idealize=1. With this, basis vectors can not be fully standardised. The other possibility is to apply the full standardinzation and using transformation matrix and origin shift, we can return the cell approximately back to the orientation of the input one. The difficulty is that how can tell this to users.

Ah, thanks, I was unaware about the rotation.

I also think that users who can understand this detail can use spglib without any difficulty, and it is my recommendation.

Indeed, it looks like we can use spglib for our purposes.  I will note, the thing we are most interested in is actually not the symmetrized positions, but rather, the rotations & translations of the spacegroup operators that will be used by phonopy when it generates displacements.[^1]  To my understanding, phonopy does not apply these transformations to the structure when producing SPOSCAR, which is why it would be nice to have a way to obtain these spacegroup operators without these transformations.
For now though I will work on something that recovers the operations from spglib.

[^1]: We're trying to use a technique similar to phonopy to use symmetry to compute the derivative of some function with respect to atomic positions.  For this, we need the minimum displacements from phonopy as well as the spacegroup operators that can be used on these displacements to generate the rest of the data.

I see. Then probably the following might be more convenient for your,
import phonopy
ph = phonopy.load("phonopy_disp.yaml", produce_fc=False)
symmetry = ph.symmetry

(please have a look at phonopy.load docstring for more options.)
By this, you can get Symmetry instance of the supercell.
https://github.com/phonopy/phonopy/blob/develop/phonopy/structure/symmetry.py
Or rather, ph.symmetry.dataset will give you the spglib symmetry dataset, by which you see more symmetry details.
Note that, in phonopy, no symmetry search is performed for the input crystal structure, but only done for the supercell and the primitive cell (ph.primitive_symmetry).

Thanks!  Phonopy.symmetry does look like a reasonable solution, with usefully-defined rotations and translations.  And it makes sense that this should give data for the supercell, so this is no problem.  (I've just been working on 1x1x1 supercells lately so I didn't think of it)
Since this solves my use case I will close this for now.


Updates dependencies

ciao, happy new one, i hope you're a'ight.
this is just a head-ups for compatibility with the upcoming delb release. i'll finalize this pr once it is released.

Thanks for getting rid of Travis CI 👍 it was long overdue.

a'ight, this is ready for review.

now, it really is reviewable.


If inhreit from EmployeeListNotFoundException, do I need overwrite the three init method?

for example :
just do this:
class EmployeeListNotFoundDueToNetWorkException : EmployeeListNotFoundException{}

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ID: 041f6b4c-2b7e-5332-f24e-12af7a5b07aa
Version Independent ID: e9c2287f-1c4e-ee07-a1ff-77a3f07ce1a4
Content: How to: Create User-Defined Exceptions
Content Source: docs/standard/exceptions/how-to-create-user-defined-exceptions.md
Product: dotnet
Technology: dotnet-standard
GitHub Login: @tdykstra
Microsoft Alias: tdykstra

@naughtyGitCat Yes, you should create those three constructors.
If you don't the developers that want to use the new exception type you've created are going to be frustrated because that can't set the message, or set an inner exception to set the root cause.
I'll close this as an answered question.


Authentication not working

Currently the authentication flow for libby isn't working. We get this error:
[next-auth][error][session_error] TypeError: Cannot read property 'name' of null
at E:\libby\libby-web\node_modules\next-auth\dist\server\routes\session.js:99:26
at Generator.next ()
at asyncGeneratorStep (E:\libby\libby-web\node_modules\next-auth\dist\server\routes\session.js:22:103)
at _next (E:\libby\libby-web\node_modules\next-auth\dist\server\routes\session.js:24:194)
at runMicrotasks ()
at processTicksAndRejections (internal/process/task_queues.js:93:5)
https://next-auth.js.org/errors#session_error
This will be investigated until we find a fix.

I am getting this issue as well using Prisma.

I am getting this issue as well using Prisma.

I am getting this issue as well using next-auth and Prisma.

Yeah same here. Reference to this issue here: https://github.com/nextauthjs/next-auth/issues/1106#issuecomment-759970451
Hope NextAuth knows what's wrong. Otherwise I'm going to have to use a completely new database and new auth flow.

I am getting this issue as well using next-auth and Prisma.

Yeah same here. Reference to this issue here: https://github.com/nextauthjs/next-auth/issues/1106#issuecomment-759970451
Hope NextAuth knows what's wrong. Otherwise I'm going to have to use a completely new database and new auth flow.

Hope NextAuth knows what's wrong. Otherwise I'm going to have to use a completely new database and new auth flow.

Same. I'm debating on just writing my own authentication middleware but it's just so tedious to do.

Hope NextAuth knows what's wrong. Otherwise I'm going to have to use a completely new database and new auth flow.

Same. I'm debating on just writing my own authentication middleware but it's just so tedious to do.

We're probably going to migrate to a new authetincation and database infrastructure.
Closing this for now.

We're probably going to migrate to a new authetincation and database infrastructure.
Closing this for now.


Feature/selection history

Use the shortcuts 'a' and 'd' to traverse through your selection history.

Otherwise we should name it gate_selection_history_navigator?

Should we name it gate_selection_history_navigator otherwise?

You've got a point there. Currently only gates are saved in the history. I think we talked about only saving gates one time? Adding nets to the history should be a quick job. Or do you prefer only navigating between the gate history and renaming the class?

I would actually prefer to include nets. Is this a huge effort to add?

Shouldn't be. I'm sure I will find a solution. If you want I will get on it.
While we are at it: What do you think how many elements should be saved in the history by default? Last time we talked we mentioned a rather small numer around 20 or so.

@dertob I think a buffer of 20-50 entries should be Ok for the first implementation. Could we maybe set it via configuration variable? Otherwise please add the support for nets in the history. Thanks.

@dertob I'm closing this PR for now. We can reopen it, when you are ready.


Normalize CODEOWNERS entries to use -approvers

Are we sure that the approvers always contain the maintainers as well?

Actually, if it isn't the case, then the team rosters should be fix (IMHO).

if you checked a few then I hope we are safe here:-)

Yes, I cross-checked the following (so all those affected by this change), and the approvers include the maintainers via subteam inclusion:

cpp
java (main and instrumentation)
php
python
rust
operator
demo


[Face] Align with latest release version of Face API with million-scale features.

@huxuan feel free to share your comments on this. Will raise formal PR to Azure/azure-rest-api-specs after our internal review.

Supposed to review it tomorrow afternoon.


Improvements to attribute attack notebooks

Fix comments in attribute attack notebooks + add example of attacking a numerical feature.
Description
Updated notebooks to reflect latest functionality.
Type of change
Please check all relevant options.

[X] Improvement (non-breaking)
[ ] Bug fix (non-breaking)
[ ] New feature (non-breaking)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

Testing
Ran the notebooks.
Test Configuration:

OS: MacOS 12.6.8
Python version: 3.9

Checklist

[X] My code follows the style guidelines of this project
[ ] I have performed a self-review of my own code
[ ] I have commented my code
[ ] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes

Codecov Report

Merging #2269 (9ba2ec3) into dev_1.16.0 (cb4deda) will decrease coverage by 59.88%.
Report is 50 commits behind head on dev_1.16.0.
The diff coverage is n/a.

:exclamation: Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the GitHub App Integration for your organization. Read more.

@@               Coverage Diff               @@
##           dev_1.16.0    #2269       +/-   ##
===============================================
- Coverage       82.52%   22.65%   -59.88%
===============================================
  Files             313      313
  Lines           27782    27809       +27
  Branches         5082     4665      -417
===============================================
- Hits            22927     6300    -16627
- Misses           3603    21409    +17806
+ Partials         1252      100     -1152

see 248 files with indirect coverage changes


fix fixed loss of BetweenPredicate rewrite on reanalyze in legacy planner

pick from master https://github.com/apache/doris/pull/30328
Proposed changes
Issue Number: close #xxx

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

run buildall


Make the package installable via pip

Currently, you need to install the package by hand because of the native dependencies. We could make it installable via pip using either cibuildwheels or sdists.

cibuildwheels: May have problems with conda and the compilation of CGAL will be to expensive to use GitHubs free CI.
sdists: Seems easier but we would need to find a new way to trigger conan before build. This may be possible by driving conan from cmake (but I am not sure, if the cmake will not become unusable or at least ugly when also used for building pure C++-libraries).

An alternative is to also build and upload the package by hand for every update. However, there may still be problems with conda, as conda ships its own glibc, that can be incompatible to the one of the system.
The best option seems to me creating a sdist-package on PyPI and finding an elegant way to drive conan.

So I played around a little and we could simple trigger conan from cmake whenever SKBUILD is defined. This gets me much further, but for some reason not all dependencies will be installed (however, cgal will).
if(SKBUILD)
    execute_process(COMMAND "conan install . --build=missing -if cmake")
endif()

if(NOT EXISTS "${CMAKE_BINARY_DIR}/conan.cmake")
    message(STATUS "Downloading conan.cmake from https://github.com/conan-io/cmake-conan")
    file(DOWNLOAD "https://raw.githubusercontent.com/conan-io/cmake-conan/0.18.1/conan.cmake"
            "${CMAKE_BINARY_DIR}/conan.cmake"
            TLS_VERIFY ON)
endif()

include(${CMAKE_BINARY_DIR}/conan.cmake)

conan_cmake_configure()

conan_cmake_autodetect(settings)

conan_cmake_install(PATH_OR_REFERENCE .
        BUILD missing
        REMOTE conancenter
        SETTINGS ${settings})

Seems to work with fallback mode, producing  a lot of errors/warnings that could confuse the user.

Seems to work on the development branch by doing an ugly hack and adding a pyproject.toml. Needs further verification.

Should be fixed with v0.2.0


Add exprHole and typeHole

This PR fails as exprHole "?help" doesn't count as a valid Name Ident, and using exprHole "help" doesn't print the value with the question mark. Not sure what the best way forward is.

You will likely need to take the same approach I took for symbols.
https://github.com/natefaubion/purescript-tidy-codegen/blob/140c16ec2a30b674603f4d21923b1166ae32e3af/src/Tidy/Codegen/Types.purs#L12-L16
That is, specify an additional newtype, and hook into the conversion rules in Class.purs. The need for additional newtypes is arguably a bug in the CST.

This is also blocked by https://github.com/purescript/spago/issues/855


SessionContext from ExecutionEngine

Implement now function using SessionContext managed by the execution engine. Unlike #937 this implementation decouples the function definition from capturing query start time.
In addition, this declaration of Expression.valueOf allows for passing other metadata to function implementations.
Implementation overview
SessionContext is a class that stores query execution start time.
It is provided to now implementation through an argument to Expression.valueOf.
That is done by ProjectOperator while executing
ExecutionEngine provides an instance of SessionContext to each PhyiscalPlan by calling PhysicalPlan.open.
Remaining work
Ensure that SessionContext is passed in all instances where an expression can contain now() call.
Signed-off-by: MaxKsyunz<EMAIL_ADDRESS>By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.
For more information on following Developer Certificate of Origin and signing off your commits, please check here.

@penghuo what do you think of this implementation of query context (I called it SessionContext here). In this case, the value is provided at execution time, not function definition.

Will revisit this later.


Implement KNX dimming functionality

Description: Implement dimming functionality for KNX lights
Example entry for configuration.yaml (if applicable):
- platform: knx
  address: 1/220
  state_address: 1/221
  brightness_address: 1/223
  brightness_state_address: 1/224

Checklist:
If user exposed functionality or configuration variables are added/changed:

[ ] Documentation added/updated in home-assistant.github.io

If the code communicates with devices, web services, or third-party tools:

[ ] Local tests with tox run successfully. Your PR cannot be merged unless tests pass
[ ] New dependencies have been added to the REQUIREMENTS variable ([example][ex-requir]).
[ ] New dependencies are only imported inside functions that use them ([example][ex-import]).
[ ] New dependencies have been added to requirements_all.txt by running script/gen_requirements_all.py.
[ ] New files were added to .coveragerc.

If the code does not interact with devices:

[ ] Local tests with tox run successfully. Your PR cannot be merged unless tests pass
[ ] Tests have been added to verify that the new code works.

Thanks 🎉
I am planning on leveraging the new code owner functionality. Would you be interested to become code owner for KNX?


Adding in checks before chunks in case resource has no chunk_info

I encountered some situations where the resource returned from _get_resource was did not have chunks when we expected it to. In _get_chunks we would then try to get the "base_download_url" from a NoneType which would error out and cause the script to stop. I just added verification that the chunks exist before passing them to _get_chunks
Also some stray trailing space cleanup in search_series

Hey, thanks for this!
I haven't had a chance to check this, but is there a pattern to when the chunks aren't available? Because my gut feeling is that returning None instead of an error when something's gone wrong could cause more problems than this solves.

I don't recall. I'll keep an eye out if it comes up again.


#291 implement sortByMany

This PR aims to add support for sortByMany method asked in the issue #291
Corresponding Laravel implementation https://github.com/laravel/framework/blob/8.x/src/Illuminate/Collections/Collection.php#L1325

Thanks for the PR, @shafi-  🙏
I see I've made the mistake of thinking this was a public method that should be exposed to the user.
On a closer look, I see that sortByMany is called from the sortBy method, when the user passes an array or closure.
Could you please update you PR to reflect this?

@ecrmnn, Thanks for your response.
Updated it. Let me know if it is fine or not.


[WIP] Allow loose apply

See #1895 for high-level discussion

Implement loose keyword
pass it along dd.fillna
test loose fillna

Closing as it appears the proposal this PR implements was rejected


Simply importing notion into an Astro project doesn't work

Describe the bug
Adding this script tag to an Astro project, causes it to not run the script at all.
<script>
  import { Client } from "@notionhq/client";
  console.log("notion")
  const notion = new Client({ auth: "<secret>"});
</script>

And shows this error on the client
Uncaught SyntaxError: The requested module '/node_modules/@notionhq/client/node_modules/whatwg-url/lib/public-api.js?v=0c9a2969' does not provide an export named 'default' (at index.mjs?v=0c9a2969:4:8)

To Reproduce
Node version: v16.14.2
Notion JS library version: ^2.2.11
Steps to reproduce the behavior:
Import Client from library

It happens also when importing the library on a react component in Astro.


With latest React (15.5.4?) I get a warning:

Warning: Unknown prop `onCellDoubleClick` on <tbody> tag. Remove this prop from the element. For details, see https://fb.me/react-unknown-prop
    in tbody (created by DataTablesTableBody)
    in ClickAwayListener (created by DataTablesTableBody)
    in DataTablesTableBody (at DataTables.js:356)
    in table (created by DataTablesTable)
    in div (created by DataTablesTable)
    in div (created by DataTablesTable)
    in DataTablesTable (at DataTables.js:312)
    in div (at DataTables.js:310)
    in DataTables (at index.js:153)

(Line numbers might be a bit out of sync)

I've tried with React 15.5.4 and I got this warning, instead of above,
Warning: Accessing PropTypes via the main React package is deprecated. Use the prop-types package from npm instead.

I'm not sure but it seems like a problem with material-ui version compatibility. Can you make sure the module is using material-ui 0.16.4?

Yes, you also have to do:
import PropTypes from 'prop-types';

now, instead of the previous method.

Oh, and 0.15.4. I'll create a new PR soon.

@advance512 It's already fixed! :)
@Crecket Thanks!


rogue Uniprot ID in physical interactions data output file?

Dan and Giorgio have reported a rogue Uniprot ID in  this file:
In the file
http://curation.pombase.org/dumps/releases/pombase-chado-latest/exports/pombase-go-physical-interactions.tsv.gz
SPBC409.05	UniProtKB:O59671	PMID:15147268
any ideas where it comes from? I'll have a poke around....Very odd.....
Val

I checked in artemis as that's the only way it could have got into the manual annotation, its not there (could not be via canto).
I grepped for the  Uniprot ID in the current GO GAF  on the assumption that if all of the interaction data is generated form GO, if this exists it should be in this file. It isn't there.
I looked at the UniProt annotation to see if it was one of theirs that we were importing which had not had the "with" field converted to a PomBase systematic ID but I can't see any such interactions in UniProt for this SPBC409.05
Stumped!

Can you stick this  to the top of the pile?

We are getting this annotation from GOA:
UniProtKB   Q9Y709  skp1            GO:0005515      PMID:15147268   IPI     UniProtKB:O59671        F       Suppressor of kinetochore protein 1     SKP1_SCHPO|skp1|psh1|sph1|SPBC409.05    protein taxon:284812    20070103        UniProt
It's on this page:
https://www.ebi.ac.uk/QuickGO/GProtein?ac=Q9Y709
Does that explain things?

Yes and no ;)
On this page,
https://www.ebi.ac.uk/QuickGO/GProtein?ac=Q9Y709
there are lots of annotations of this type, but they do not end up with a UniProt ID in the output file. The ID at some point the thing in the "with" field should be converted to a pombase identifier?
There are other issues with duplication, I'll put that in a different ticket. The duplication might be part of the cause. In reality some of these annotations are triplicated in GOA. They are duplicated on our gene pages. We need to improve the filtering here so we only end up with each annotation once.
It is possible (although probably unlikely), that the reason we don't see this more than once in the file for EsyN is due to a weird combination of source/filtering getting rid of the other  ones like this. I can;t remember exactly how this works.

The ID at some point the thing in the "with" field should be converted to a pombase identifier?

We don't do any conversion when loading.  I'll dig deeper when I'm back.

No hurry I told Dan we'd let him know when ready.
I'll also have a look. I suspect that filtering removes most as duplicates and so the vast majority disappear. I can double check this first.
Already looked at the redundancy in these annotations so I have the info somewhere....

Its odd. The one in the file is describing skp1 biding to pof4. However there are other annotations which will have UniPRot IDs in the with field from this paper
See this ticket
https://github.com/pombase/curation/issues/859
Some interactions are curated by PomBAse unitpto and intact. Ideally you would filter the intace and the Uniprot ones. This might partly be happening, but on the skp1 page there are definitly some duplicates (but never any triplicates, even when all 3 , pombase/uniprot & intact) have made the annotations.
So i'm not sure why the only one which shows up with a uniprot ID in the with filed is this  particylar one?
There are others which we did not make at PomBase. But, I think  for these we might have made the reciprocal annotations. I think this is another reason why we want to do this:
https://github.com/pombase/pombase-chado/issues/433
Before any filtering the PomBase annotations need to be 'reciprocated' so that when imported annotations are filtered it is not dependant on the  directionality of  the curation.
Let me know if you need to chat about this. I think the first thing is for you to tell me what you think happens currently (I can't remember exactly)
val

Just so I can get this off my To Do list and onto a tracker
Note to self
"easyN  check updated, test metaphase anaphase transition chromosome segregation should update to show SPBC32H8.09 and gtb1"
Assign this ticket to me when this task is done.
Thanks
Val

We don't do any conversion when loading.

Sorry for the confusion, I was wrong about that.  I forgot that we map UniProt ID to pombe IDs using this file:
ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/PomBase2UniProt.tsv
It's downloaded for each Chado build.  That stray ID (O59671) isn't in the mapping.

Thanks. Mapping file issues are in progress.
Hang fire, I'll let you know when it's sorted.

We are waiting on
https://www.ebi.ac.uk/panda/jira/browse/PB-2408
but in the meantime maybe a check and report in logs if an entry  isn't mapping to UniProt correctly?

but in the meantime maybe a check and report in logs if an entry isn't mapping to UniProt correctly?

I've added a warning instead of exporting the interaction with a UniProt ID.

Hang fire, I'll let you know when it's sorted.

Is there more to do before I close this issue?

I need to open a new ticket about how we handle duplicate  annotations from uniprot generally. As this won't be needed until you are on to the filtering tasks, I wont get to it immediately.
Could you let me know when there is an update which picks up this change. I'll let Giorigio and Dan know to update EsyN
Thanks

Could you let me know when there is an update which picks up this change.

I wasn't planning to do any new loads for me because updating the ontologies is still a pain.  I can go ahead if needed.  It's probably quicker just to edit the file and remove the line that has a UniProt ID if that is holding up Dan and Giorgio.

We'll not worry about this until I get back.
Dan and Giorgio have both left the department now, they are babysitting this, but they don't want to do anything manually.
I want to check that everything is working as part of our release pipeline  so the update can wait until I can check it all properly.
There are still issues with the Uniprot file mapping.
https://www.ebi.ac.uk/panda/jira/browse/PB-2408
If we do have a chado update,  and the corrected file is in place I'll let them know, but we won't do anything as a temporary fix because they'll get annoyed if anything goes wrong.

If we do have a chado update, and the corrected file is in place I'll let them know

The file from the new load looks good - no UniProt IDs.
The links they use will be in place after we make a release.

These files look fine now. There is a blank line at the bottom of both files
pombase-go-substrates.tsv
and
pombase-go-physical-interactions.tsv
should you remove that?
Val

I can't see a blank line at the end of either file.

Seems to be, from here?
https://curation.pombase.org/dumps/releases/pombase-chado-v60-2016-05-12/exports/
I checked again

I've checked all the files there.  All have a new line at the end of each line and the last line isn't empty.  How are you viewing the files?

I'm downloading and opening in textedit. When I scroll down I see a blank line?

Double checking but files are currently empty.

When I scroll down I see a blank line?

In most editors if the last line of the file has a newline at the end, it shows a blank line at the end of file.  There are the same number of non-empty lines as there are newline characters.  If it doubt have a look at the file with "less" on the command line and then press capital G to go to end of file.

OK I never noticed that before!


[DOCFIX] Update configuration setting page for Spark and MR

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Loading indices to ES

Why:
To fix the error given by BF on Querying for the List of metrices.

@ChandraAddala You are right, but these files rarely change as they define schemas in ES and the other files are configs (blueflood.conf, properties), which people can adjust to taste.

@goru97 - let's have a quick chat today and see if we can reference some of hte existing scripts.

@ChandraAddala @usnavi Can I merge this for now. I will write a new dockerfile, which will be more according to the standards, very configurable and will also use the resources which are already there in ./blueflood-elasticsearch/src/main/resources. But people are using this repo and are saying it's broken!

Sure, you can merge it now....as long as you promise.... :-P

I keep my promises :smiley:


Upgrade yaml to 2.0.1 to remove deprecation warning

Motivation
To resolve #266
Approach

Upgraded yaml dependency
Fixed a small typescript error in loader.ts

TODOs

[ ] From<EMAIL_ADDRESS>they dropped support for node 10 and node 12 (see official release notes) so if we want to proceed with the yaml upgrade, the changes of this PR will need to be released as 8.0.0 to accommodate the breaking change
[ ] Also update the AppVeyor workflow to exclude node 10 and node 12

Switched to js-yaml in https://github.com/davidtheclark/cosmiconfig/pull/270. Releasing that soon.


chore(deps): update jasmine

This PR contains the following updates:

Package
Type
Update
Change

@types/jasmine
devDependencies
minor
~3.5.14 -> ~3.10.0

jasmine-core (source)
devDependencies
minor
~3.6.0 -> ~3.99.0

Release Notes

jasmine/jasmine
v3.99.0
Compare Source
Please see the release notes.
v3.10.1
Compare Source
Please see the release notes.
v3.10.0
Compare Source
Please see the release notes.
v3.9.0
Compare Source
Please see the release notes.
v3.8.0
Compare Source
Please see the release notes.
v3.7.1
Compare Source
Please see the release notes.
v3.7.0
Compare Source
Please see the release notes

Configuration
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♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.
👻 Immortal: This PR will be recreated if closed unmerged. Get config help if that's undesired.

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Mark v2.0.0 tag as latest release at GitHub Releases

https://github.com/nedbat/django_coverage_plugin/releases

Done.  I've never quite understood why GitHub releases are better than PyPI, but there it is.


Cannot resolve symbol 'Assertions'

Installed via Maven,
import static org.assertj.core.api.*;

works fine, but
import static org.assertj.core.api.Assertions.*;

raises a Cannot resolve symbol 'Assertions' error. Using Java 1.8 with version 3.2.0

Just tested, it runs fine, can you provide a full test case ?

What exactly do you mean test case?

A unit test to reproduce the problem along with the proper environment description.
it can be a simple maven project containing a single test.

Here is the github repo for my project. The java class in question is Problem_5_4.java at https://github.com/theluxury/epi-java/blob/master/src/main/java/Problem_5_4.java. It doesn't actually have any methods form your api since
import static org.assertj.core.api.Assertions.*;

raises the error. Please let me know if this is too much or not enough info.

what are you importing it if you don't use it ?
my guess is your IDE compiler settings raise an error for unused import.

Well I was tried using it but didn't since I couldn't import it, heh. I updated it with a version that has an
assertThat("aaa").contains('a');

and am getting the error
Cannot resolve method assertThat(java.lang.String)

You don't use maven properly, one can't use test dependencies in src/main/java, either move your tests to src/test/java or get rid of <scope>test</scope> when declaring assertj dependency.


TiGL Viewer always creates debugging breps on Linux

In the TiGL Viewer Settings, the debugging output can be switched on and off. On linux, this doesn't work. Debugging breps are always created.
The communication with TiGL is done using environment variables. The environment variable is "deleted" in TIGLViewerWindow.cpp:478
if (tiglViewerSettings->debugBooleanOperations()) {
    qputenv("TIGL_DEBUG_BOP", "1");
}
else {
    qputenv("TIGL_DEBUG_BOP", "");
}

The behaviour of qputenv is different between windows and linux. On windows, the line deletes the variable. On Linux, it's just set to an empty string.
Instead, use something like qunsetenv: https://qt.gitorious.org/qt/odysseus-qtbase/commit/574e5cf9c510fb28781c8006a1184ca158ee859f

Code has to be tested on windows

Now windows creates always debugging breps, if debugging output is once switched on. Only restarting TiGL Viewer helps.


Defining ggcyto aesthetics when calling ggcyto within a custom function.

Hi,
I've come up against a bug I seem incapable of resolving on my own.
I have defined a function which I will use to facilitate plotting while producing quality control reports for gating of my flow data. A simplified version which can be used to reproduce the problem is outlined below.
plot_cyto_2d <- function(gs, x, y, subset, bins = 256) {
  tryCatch({
    p1 <- ggcyto(gs[[1]], aes(x = x, y = y), subset = subset) +
      geom_hex(bins = bins)
  }, error = function(e) {
    # Print the error message or take any other appropriate action
    print(paste("Error:", e$message))
  })
}

When I pass this function my data
plot_cyto_2d(gs, x = "FSC-A", y = "SSC-A", subset = "cells", bins = 256

I get the error Error in getChannelMarker(frm, dim) : multiple markers matched: x.
The markers from my GS (colnames(gs)) do not contain duplicates of "FSC-A" or "SSC-A". They do however contain duplicates of "FSC" and "SSC" because of the area and height parameters.
The error appears to be arising during the call to getChannelMarkers() from the aes() argument to ggcyto(). Interestingly, though,
ggcyto(gs[[1]], aes(x = "FSC-A", y = "SSC-A"), subset = "cells") + geom_hex(bins = 256)

does not return an error, but plots the graph as desired.

x <- "FSC-A"
y <- "SSC-A"
subset <- "cells"
ggcyto(gs[[1]], aes(x = x, y = y), subset = subset) + geom_hex(bins = 256)

does return the error.
I'm unsure if this is something to do with the way ggcyto is interpreting x?
Any help is greatly appreciated. Thanks for your time!
K
gs_archive.zip
Session Info:
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8

time zone: Africa/Johannesburg
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ggcyto_1.30.2        ncdfFlow_2.48.0      BH_1.84.0-0          ggplot2_3.5.0
[5] openCyto_2.14.0      flowCore_2.14.1      flowWorkspace_4.14.2 CytoML_2.14.0

loaded via a namespace (and not attached):
 [1] utf8_1.2.4          generics_0.1.3      stringi_1.8.3       lattice_0.21-9
 [5] magrittr_2.0.3      grid_4.3.2          RColorBrewer_1.1-3  plyr_1.8.9
 [9] jsonlite_1.8.8      graph_1.80.0        gridExtra_2.3       fansi_1.0.6
[13] scales_1.3.0        XML_3.99-0.16.1     Rgraphviz_2.46.0    cli_3.6.1
[17] rlang_1.1.2         RProtoBufLib_2.14.0 Biobase_2.62.0      munsell_0.5.0
[21] withr_3.0.0         yaml_2.3.8          cytolib_2.14.1      parallel_4.3.2
[25] tools_4.3.2         dplyr_1.1.4         colorspace_2.1-0    BiocGenerics_0.48.1
[29] vctrs_0.6.5         R6_2.5.1            matrixStats_1.2.0   stats4_4.3.2
[33] lifecycle_1.0.4     stringr_1.5.1       zlibbioc_1.48.2     S4Vectors_0.40.2
[37] RBGL_1.78.0         pkgconfig_2.0.3     pillar_1.9.0        hexbin_1.28.3
[41] gtable_0.3.4        data.table_1.14.8   glue_1.7.0          Rcpp_1.0.12
[45] flowClust_3.40.0    xfun_0.41           tibble_3.2.1        tidyselect_1.2.1
[49] rstudioapi_0.15.0   knitr_1.45          farver_2.1.1        labeling_0.4.3
[53] compiler_4.3.2

This is a scoping issue.
It can be overcome using programmatic referencing from the rlang package.
For example:
library(rlang)
plot_cyto_2d <- function(gs, x, y, subset, bins = 256) {
  tryCatch({
    p1 <- ggcyto(gs[[1]], aes(x = !! sym(x), y = !! sym(y)), subset = subset) +
      geom_hex(bins = bins)
  }, error = function(e) {
    # Print the error message or take any other appropriate action
    print(paste("Error:", e$message))
  })
}

I am not convinced that this is a desirable or elegant solution, but it does work. It might be more appropriate to create a new environment.
If I find a tidier solution I will report back. Otherwise, I think this can be considered closed.
Thanks!