Update test_model.py

The unit test for the evaluation of Encoder, Decoder, and 2D attention module added.

@AshkanTaghipour could you please use explicit commit messages (unlike here), so it is easier to follow the git history of your commits? thanks

@AshkanTaghipour could you please use explicit commit messages (unlike here), so it is easier to follow the git history of your commits? thanks

Yes of course.

@AshkanTaghipour could you please use explicit commit messages (unlike here), so it is easier to follow the git history of your commits? thanks

Yes of course.

i see that your latest commit is more verbose https://github.com/ivadomed/ivadomed/pull/555/commits/1d1881b9555c11c3d962262942e2732d3c10b935, however please also use a more explicit commit message-- see: https://www.neuro.polymtl.ca/software/contributing#committing

@AshkanTaghipour could you please use explicit commit messages (unlike here), so it is easier to follow the git history of your commits? thanks

Yes of course.

i see that your latest commit is more verbose 1d1881b, however please also use a more explicit commit message-- see: https://www.neuro.polymtl.ca/software/contributing#committing

Thanks

dear @jcohenadad I had an assertion error in all encoder, decoder, and unet_att2d classes in the first commit, in the last commit, the error of the encoder class removed.
The remained error declared the unexpected keyword of "attention" which I think the testing is done on the Ivadomed models.py, not on the revised version which I added before,
should I change the current version of model.py  by my revised version in the master?

dear @jcohenadad I had an assertion error in all encoder, decoder, and unet_att2d classes in the first commit, in the last commit, the error of the encoder class removed.
The remained error declared the unexpected keyword of "attention" which I think the testing is done on the Ivadomed models.py, not on the revised version which I added before,
should I change the current version of model.py by my revised version in the master?

the unit test should be added directly in #552 — that’s the point of testing (ie make sure it passes before merging new code in master)

Pull Request Test Coverage Report for Build 406960155

1 of 1 (100.0%)  changed or added relevant line in 1 file are covered.
14 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.1%) to 90.506%

Files with Coverage Reduction
New Missed Lines
%

ivadomed/postprocessing.py
14
83.21%

Totals

Change from base Build 399931239:
-0.1%

Covered Lines:
5844

Relevant Lines:
6457

💛  - Coveralls

@AshkanTaghipour what is the status of this PR?

The changes related to the attention U-Net will be integrated in #552. As discussed internally during the meeting, this PR is not relevant and can be closed.


Add ability to change template elevation via keybinding

https://ptb.discord.com/channels/915186263609454632/1167221795103985764/1202268221793894410

Added in v0.7.4.


regenerate dlp v2 library

Are we not generating / creating any tests?

@tseaver, tests are generated but there aren't any changes.

@crwilcox That doesn't seem to bode well for our coverage story, given that not all the changes are docs-only.


Remove cleanup in toggle-group test code

Closes #1649
Description
There is a cleanup in the toggle-group test code. We think that cleanup should be removed since it is now in the library.
Is this a breaking change (Yes/No):
No.

Thanks!


uefi/fs: add path and pathbuf abstraction

I finally had time to work on the promised  (#472 / #747 ) path and pathbuf abstraction for the uefi::fs module.
Once this is merged and the other stuff in the tracking issue is solved, I think it would be a good time for a new release :)
Status

[x] path and pathbuf abstraction that works as good as possible with CStr16 and CString16 and are close to the API of std::path
[x] fix the open todo in code (just a small thingy)
[x] use the new abstractions in the FileSystem abstraction
[x] update the changelog

API Design
For simplicity, there are no . or .. components in a path allowed. However, if someone ever needs this, this can be part of a future MR. However, I don't see why one would ever want this. There is no present working directory in a UEFI environment..
Open Questions
Users will not be able to pass in str and String.. but they can do something like: fs::write(cstr16!("foo\\bar")) and I think this is sufficient and convenient enough. Do you agree?
Some other Remarks
The Cartesian product of all convenient trait implementations ({AsRef, Borrow, From} x {Path, PathBuf, CStr16, CString16, str, String}) is quite challenging. I decided that there is only a good interoperability between {Path, PathBuf} x {CStr16, CString16} and {str, String} x {CStr16, CString16}.
Checklist

[ ] Sensible git history (for example, squash "typo" or "fix" commits). See the Rewriting History guide for help.
[ ] Update the changelog (if necessary)

Are we good to go now?


Incomplete BrokerProperties DTO

The BrokerProperties DTO is missing several properties.  I specifically need the EnqueuedTimeUtc; I've created this pull request to add it.
Additionally the link to the spec here is dead.

the service bus client library is not in this repo anymore, so if this is still an issue, it should go there:
https://github.com/azure/azure-service-bus-java


Data conversion for 'magnetic' units

what conversions would we like to have?
can standard conversion tools do it already? (pint etc)
find solution

Arising in discussion at kick-off meeting.

We should consider using known tools such as Astropy. https://www.astropy.org/
This is a tutorial notebook that I wrote a little while ago that uses Astropy to convert CGS to Magnetic Units https://ubermag.github.io/getting-started/notebooks/unit-converter.html


Add a self-update command

Add a self-update command to the phar-composer.phar.
Possibly related:

fabpot/PHP-CS-Fixer
composer/composer
herrera-io/php-phar-update

:-1: #57 adds some simple installation and update instructions, so I see little point in implementing this and have little interest in maintaining this in the future.


Graphic bug

Type: Bug
Vscode has graphic bug, every element is surrounded by white line.  Unfortunately, it's hard for us to understand what issue you're seeing. Please help us out by providing a screen recording showing exactly what isn't working as expected. While we can work with most standard formats, .gif files are preferred as they are displayed inline on GitHub. You may find https://gifcap.dev helpful as a browser-based gif recording tool.
If the issue depends on keyboard input, you can help us by enabling screencast mode for the recording (Developer: Toggle Screencast Mode in the command palette). Lastly, please attach this file via the GitHub web interface as emailed responses will strip files out from the issue.
Happy coding!

it's the graphic bug, i try uninstall and reinstall but it doesn't work.

Can you see if it still reproduces when disabling the GPU support in VSCode? You can do that by running VSCode from the command line like this: code --disable-gpu
If that helps, you can permanently configure this option via:

Command Palette search for "Configure Runtime Arguments"
Set disable-hardware-acceleration: true
Restart

thanks you, it's solve, but do you have an idea of why there is the same problem on github desktop ?


Implementing a decentralised sorting mechanism?

I am trying to build an application where I have a lot of users and each user has a score. Every 5 minute the scores change for each one of them. These users are interested in seeing their relative ranking based on their scores.
How should I architect a solution using an append only log?
PS: Consider I have close to a million users and right now I am running this logic over at spark in a centralized manner.

It doesn't seem like an append only log is the right storage mechanism for a scoreboard. Do you need to rewind back through time to see scores at different times? Is there a trust aspect to the system that you gain from having previous scores stored? (i.e. p2p validation and verification)


example for how to train the network

thanks very much for your code and documents, I am really confused on pytorch ,so can you please share the code for train ,special what option should I need to input

and can you share the environment you installed? thanks in advance!


Pound symbol in project path breaks webpack

Bug report

What is the current behavior?
Running "yarn run dev" (or "npm run dev") on a Laravel project to build JS/CSS fails when the project path contains a # pound symbol. Removing the # pound symbol from the path allows it to run with no other changes.
If the current behavior is a bug, please provide the steps to reproduce.
Just add a # symbol to your project path and try to run webpack. Presumably it will fail for you too? This is the error;
PS E:\#test\repo> yarn run dev
yarn run v1.22.10
$ npm run development

> development
> mix

87% sealing module hashinginternal/crypto/hash.js:84
    throw new ERR_INVALID_ARG_TYPE(
    ^

TypeError [ERR_INVALID_ARG_TYPE]: The "data" argument must be of type string or an instance of Buffer, TypedArray, or DataView. Received undefined
    at Hash.update (internal/crypto/hash.js:84:11)
    at BulkUpdateDecorator.update (E:\#test\repo\node_modules\webpack\lib\util\createHash.js:51:14)
    at NormalModule.updateHash (E:\#test\repo\node_modules\webpack\lib\NormalModule.js:1120:8)
    at Compilation._createModuleHash (E:\#test\repo\node_modules\webpack\lib\Compilation.js:3085:10)
    at Compilation.createModuleHashes (E:\#test\repo\node_modules\webpack\lib\Compilation.js:3057:10)
    at E:\#test\repo\node_modules\webpack\lib\Compilation.js:2334:11
    at Hook.eval [as callAsync] (eval at create (E:\#test\repo\node_modules\tapable\lib\HookCodeFactory.js:33:10), <anonymous>:10:1)
    at Hook.CALL_ASYNC_DELEGATE [as _callAsync] (E:\#test\repo\node_modules\tapable\lib\Hook.js:18:14)
    at E:\#test\repo\node_modules\webpack\lib\Compilation.js:2294:36
    at Hook.eval [as callAsync] (eval at create (E:\#test\repo\node_modules\tapable\lib\HookCodeFactory.js:33:10), <anonymous>:10:1)
    at Hook.CALL_ASYNC_DELEGATE [as _callAsync] (E:\#test\repo\node_modules\tapable\lib\Hook.js:18:14)
    at Compilation.seal (E:\#test\repo\node_modules\webpack\lib\Compilation.js:2285:27)
    at E:\#test\repo\node_modules\webpack\lib\Compiler.js:1056:20
    at E:\#test\repo\node_modules\webpack\lib\Compilation.js:2104:4
    at eval (eval at create (E:\#test\repo\node_modules\tapable\lib\HookCodeFactory.js:33:10), <anonymous>:42:1)
    at E:\#test\repo\node_modules\webpack\lib\FlagDependencyExportsPlugin.js:332:11 {
  code: 'ERR_INVALID_ARG_TYPE'
}
npm ERR! code 1
npm ERR! path E:\#test\repo
npm ERR! command failed
npm ERR! command C:\WINDOWS\system32\cmd.exe /d /s /c webpack --progress --config=node_modules\\laravel-mix\\setup\\webpack.config.js

npm ERR!      C:\Users\username\AppData\Local\npm-cache\_logs\2021-02-03T03_18_26_556Z-debug.log
npm ERR! code 1
npm ERR! path E:\#test\repo
npm ERR! command failed
npm ERR! command C:\WINDOWS\system32\cmd.exe /d /s /c mix

npm ERR!      C:\Users\username\AppData\Local\npm-cache\_logs\2021-02-03T03_18_26_612Z-debug.log
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

What is the expected behavior?
I assume that legal characters in path names should not fail, so having a # pound symbol in the project path should run the build without issue.

Other relevant information:
webpack version:  5.20.0
Node.js version: 14.15.4
Operating System: Windows 10
Additional tools:
Here is my package.json
{
    "private": true,
    "scripts": {
        "dev": "npm run development",
        "development": "mix",
        "watch": "mix watch",
        "watch-poll": "mix watch -- --watch-options-poll=1000",
        "hot": "mix watch --hot",
        "prod": "npm run production",
        "production": "mix --production"
    },
    "devDependencies": {
        "autoprefixer": "^10.2.4",
        "axios": "^0.21",
        "laravel-mix": "^6.0.6",
        "lodash": "^4.17.19",
        "postcss": "^8.1.14",
        "postcss-import": "^14.0.0",
        "resolve-url-loader": "^3.1.2",
        "sass-loader": "^10.1.1",
        "tailwindcss": "^2.0.2",
        "vue": "^2.6.12",
        "vue-loader": "^15.9.5",
        "vue-template-compiler": "^2.6.12"
    },
    "dependencies": {
        "webpack": "^5.20.0"
    }
}

Here is my webpack.mix.js
const mix = require('laravel-mix');

mix.js('resources/js/app.js', 'public/js')
    .vue()
    .postCss('resources/css/app.css', 'public/css', [
        require('postcss-import'),
        require('tailwindcss')('tailwind.config.js'),
    ]);

Just noticed issue #12156, which seems similar but the error messages are different and I'm not having the issue of a space inserted in the path. Not sure if they are related or separate issues.

@benderbr22 Can you provide minimum reproducible test repo

Well it happens for me on a default Laravel install. I don't have to do anything at all to make it happen, it doesn't even require any code or modifications to happen. Sequence of commands to reproduce in Windows 10, from a PowerShell;
e:
mkdir e:\#test
cd e:\#test
composer create-project laravel/laravel test
cd test
npm install
npm run dev

That's it. I then get the above error. No code changes done at all, nothing beyond the commands I typed above, just a plain default Laravel install. I can copy/paste the above commands one at a time in to a PowerShell and it's the same outcome every time. Then if I do this;
cd ..
cd ..
Rename-Item e:\#test e:\test
cd test
cd test
npm run dev

Now it runs fine. No difference at all except the renamed folder to remove the # pound symbol. I'll paste some other info from the e:\test\test folder in case it helps;
PS E:\test\test> node --version
v14.15.4

PS E:\test\test> npm ls -g
C:\Users\username\AppData\Roaming\npm
+--<EMAIL_ADDRESS>`--<EMAIL_ADDRESS>
PS E:\test\test> npm ls
test@ E:\test\test
+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>`--<EMAIL_ADDRESS>
PS E:\test\test> composer --version
Composer version 2.0.9 2021-01-27 16:09:27

PS E:\test\test> composer global show
Changed current directory to C:/Users/username/AppData/Roaming/Composer

PS E:\test\test> composer show
asm89/stack-cors                   v2.0.2  Cross-origin resource sharing library and stack middleware
brick/math                         0.9.2   Arbitrary-precision arithmetic library
dnoegel/php-xdg-base-dir           v0.1.1  implementation of xdg base directory specification for php
doctrine/inflector                 2.0.3   PHP Doctrine Inflector is a small library that can perform string manipulations with regard to upper/lowercase and singular/plural forms of words.
doctrine/instantiator              1.4.0   A small, lightweight utility to instantiate objects in PHP without invoking their constructors
doctrine/lexer                     1.2.1   PHP Doctrine Lexer parser library that can be used in Top-Down, Recursive Descent Parsers.
dragonmantank/cron-expression      v3.1.0  CRON for PHP: Calculate the next or previous run date and determine if a CRON expression is due
egulias/email-validator            2.1.25  A library for validating emails against several RFCs
facade/flare-client-php            1.3.7   Send PHP errors to Flare
facade/ignition                    2.5.10  A beautiful error page for Laravel applications.
facade/ignition-contracts          1.0.2   Solution contracts for Ignition
fakerphp/faker                     v1.13.0 Faker is a PHP library that generates fake data for you.
fideloper/proxy                    4.4.1   Set trusted proxies for Laravel
filp/whoops                        2.9.2   php error handling for cool kids
fruitcake/laravel-cors             v2.0.3  Adds CORS (Cross-Origin Resource Sharing) headers support in your Laravel application
graham-campbell/result-type        v1.0.1  An Implementation Of The Result Type
guzzlehttp/guzzle                  7.2.0   Guzzle is a PHP HTTP client library
guzzlehttp/promises                1.4.0   Guzzle promises library
guzzlehttp/psr7                    1.7.0   PSR-7 message implementation that also provides common utility methods
hamcrest/hamcrest-php              v2.0.1  This is the PHP port of Hamcrest Matchers
laravel/framework                  v8.26.1 The Laravel Framework.
laravel/sail                       v1.3.0  Docker files for running a basic Laravel application.
laravel/tinker                     v2.6.0  Powerful REPL for the Laravel framework.
league/commonmark                  1.5.7   Highly-extensible PHP Markdown parser which fully supports the CommonMark spec and Github-Flavored Markdown (GFM)
league/flysystem                   1.1.3   Filesystem abstraction: Many filesystems, one API.
league/mime-type-detection         1.7.0   Mime-type detection for Flysystem
mockery/mockery                    1.4.2   Mockery is a simple yet flexible PHP mock object framework
monolog/monolog                    2.2.0   Sends your logs to files, sockets, inboxes, databases and various web services
myclabs/deep-copy                  1.10.2  Create deep copies (clones) of your objects
nesbot/carbon                      2.44.0  An API extension for DateTime that supports 281 different languages.
nikic/php-parser                   v4.10.4 A PHP parser written in PHP
nunomaduro/collision               v5.3.0  Cli error handling for console/command-line PHP applications.
opis/closure                       3.6.1   A library that can be used to serialize closures (anonymous functions) and arbitrary objects.
phar-io/manifest                   2.0.1   Component for reading phar.io manifest information from a PHP Archive (PHAR)
phar-io/version                    3.0.4   Library for handling version information and constraints
phpdocumentor/reflection-common    2.2.0   Common reflection classes used by phpdocumentor to reflect the code structure
phpdocumentor/reflection-docblock  5.2.2   With this component, a library can provide support for annotations via DocBlocks or otherwise retrieve information that is embedded in a DocBlock.
phpdocumentor/type-resolver        1.4.0   A PSR-5 based resolver of Class names, Types and Structural Element Names
phpoption/phpoption                1.7.5   Option Type for PHP
phpspec/prophecy                   1.12.2  Highly opinionated mocking framework for PHP 5.3+
phpunit/php-code-coverage          9.2.5   Library that provides collection, processing, and rendering functionality for PHP code coverage information.
phpunit/php-file-iterator          3.0.5   FilterIterator implementation that filters files based on a list of suffixes.
phpunit/php-invoker                3.1.1   Invoke callables with a timeout
phpunit/php-text-template          2.0.4   Simple template engine.
phpunit/php-timer                  5.0.3   Utility class for timing
phpunit/phpunit                    9.5.2   The PHP Unit Testing framework.
psr/container                      1.0.0   Common Container Interface (PHP FIG PSR-11)
psr/event-dispatcher               1.0.0   Standard interfaces for event handling.
psr/http-client                    1.0.1   Common interface for HTTP clients
psr/http-message                   1.0.1   Common interface for HTTP messages
psr/log                            1.1.3   Common interface for logging libraries
psr/simple-cache                   1.0.1   Common interfaces for simple caching
psy/psysh                          v0.10.6 An interactive shell for modern PHP.
ralouphie/getallheaders            3.0.3   A polyfill for getallheaders.
ramsey/collection                  1.1.3   A PHP 7.2+ library for representing and manipulating collections.
ramsey/uuid                        4.1.1   A PHP library for generating and working with universally unique identifiers (UUIDs).
sebastian/cli-parser               1.0.1   Library for parsing CLI options
sebastian/code-unit                1.0.8   Collection of value objects that represent the PHP code units
sebastian/code-unit-reverse-lookup 2.0.3   Looks up which function or method a line of code belongs to
sebastian/comparator               4.0.6   Provides the functionality to compare PHP values for equality
sebastian/complexity               2.0.2   Library for calculating the complexity of PHP code units
sebastian/diff                     4.0.4   Diff implementation
sebastian/environment              5.1.3   Provides functionality to handle HHVM/PHP environments
sebastian/exporter                 4.0.3   Provides the functionality to export PHP variables for visualization
sebastian/global-state             5.0.2   Snapshotting of global state
sebastian/lines-of-code            1.0.3   Library for counting the lines of code in PHP source code
sebastian/object-enumerator        4.0.4   Traverses array structures and object graphs to enumerate all referenced objects
sebastian/object-reflector         2.0.4   Allows reflection of object attributes, including inherited and non-public ones
sebastian/recursion-context        4.0.4   Provides functionality to recursively process PHP variables
sebastian/resource-operations      3.0.3   Provides a list of PHP built-in functions that operate on resources
sebastian/type                     2.3.1   Collection of value objects that represent the types of the PHP type system
sebastian/version                  3.0.2   Library that helps with managing the version number of Git-hosted PHP projects
swiftmailer/swiftmailer            v6.2.5  Swiftmailer, free feature-rich PHP mailer
symfony/console                    v5.2.3  Eases the creation of beautiful and testable command line interfaces
symfony/css-selector               v5.2.3  Converts CSS selectors to XPath expressions
symfony/deprecation-contracts      v2.2.0  A generic function and convention to trigger deprecation notices
symfony/error-handler              v5.2.3  Provides tools to manage errors and ease debugging PHP code
symfony/event-dispatcher           v5.2.3  Provides tools that allow your application components to communicate with each other by dispatching events and listening to them
symfony/event-dispatcher-contracts v2.2.0  Generic abstractions related to dispatching event
symfony/finder                     v5.2.3  Finds files and directories via an intuitive fluent interface
symfony/http-client-contracts      v2.3.1  Generic abstractions related to HTTP clients
symfony/http-foundation            v5.2.3  Defines an object-oriented layer for the HTTP specification
symfony/http-kernel                v5.2.3  Provides a structured process for converting a Request into a Response
symfony/mime                       v5.2.3  Allows manipulating MIME messages
symfony/polyfill-ctype             v1.22.0 Symfony polyfill for ctype functions
symfony/polyfill-iconv             v1.22.0 Symfony polyfill for the Iconv extension
symfony/polyfill-intl-grapheme     v1.22.0 Symfony polyfill for intl's grapheme_* functions
symfony/polyfill-intl-idn          v1.22.0 Symfony polyfill for intl's idn_to_ascii and idn_to_utf8 functions
symfony/polyfill-intl-normalizer   v1.22.0 Symfony polyfill for intl's Normalizer class and related functions
symfony/polyfill-mbstring          v1.22.0 Symfony polyfill for the Mbstring extension
symfony/polyfill-php72             v1.22.0 Symfony polyfill backporting some PHP 7.2+ features to lower PHP versions
symfony/polyfill-php73             v1.22.0 Symfony polyfill backporting some PHP 7.3+ features to lower PHP versions
symfony/polyfill-php80             v1.22.0 Symfony polyfill backporting some PHP 8.0+ features to lower PHP versions
symfony/process                    v5.2.3  Executes commands in sub-processes
symfony/routing                    v5.2.3  Maps an HTTP request to a set of configuration variables
symfony/service-contracts          v2.2.0  Generic abstractions related to writing services
symfony/string                     v5.2.3  Provides an object-oriented API to strings and deals with bytes, UTF-8 code points and grapheme clusters in a unified way
symfony/translation                v5.2.3  Provides tools to internationalize your application
symfony/translation-contracts      v2.3.0  Generic abstractions related to translation
symfony/var-dumper                 v5.2.3  Provides mechanisms for walking through any arbitrary PHP variable
theseer/tokenizer                  1.2.0   A small library for converting tokenized PHP source code into XML and potentially other formats
tijsverkoyen/css-to-inline-styles  2.2.3   CssToInlineStyles is a class that enables you to convert HTML-pages/files into HTML-pages/files with inline styles. This is very useful when you're sending emails.
vlucas/phpdotenv                   v5.3.0  Loads environment variables from `.env` to `getenv()`, `$_ENV` and `$_SERVER` automagically.
voku/portable-ascii                1.5.6   Portable ASCII library - performance optimized (ascii) string functions for php.
webmozart/assert                   1.9.1   Assertions to validate method input/output with nice error messages.

Without # all works fine?

Yes, in the example above I showed a series of command to rename the e:#test folder to just e:\test, then run "npm run dev" again and it works. With the only difference that I renamed e:#test to e:\test. After doing that it runs fine.
   Laravel Mix v6.0.11

✔ Compiled Successfully in 1085ms
┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬─────────┐
│                                                                                File │ Size    │
├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼─────────┤
│                                                                                /js/app.js │ 596 KiB │
│                                                                                css/app.css │ 1 bytes │
└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴─────────┘
PS E:\test\test>

Yep, bug, thanks

Let's close in favor https://github.com/webpack/webpack/issues/12156 (I have changed title), yes, we have problems with #


As an efficient user, I want to be able to clear the meal planner immediately.

So that I can save time.

Completed


Found an ExtendTemplate node inside a SyntaxTree. Extend nodes must be the root of a tree.

Perhaps I am missing how to do this from the documentation, but I'm trying to render an ASP.NET page with a master layout.
My page view (TempGeneralContentPage) is as follows:
{{< TempMaster }}
some body text...
{{ Content.CreatorName }}

My master layout (TempMaster) is as follows:
<!DOCTYPE html>
<html lang="en">
<head>
    <title>hello!</title>
</head>
<body>
    {{ body }}
</body>
</html>

Stack trace excerpt:
[VeilCompilerException: Found an ExtendTemplate node inside a SyntaxTree. Extend nodes must be the root of a tree.]
   Veil.VeilEngine.CompileNonGeneric(String templateId, ITemplateParser parser, TextReader templateContents, Type modelType) +677
   NitroNet.ViewEngine.ViewEngines.VeilViewEngine.CreateNonGenericView(String templateId, String content, IVeilEngine viewEngine) +113
   NitroNet.ViewEngine.ViewEngines.<CreateViewAsync>d__4.MoveNext() +807
   System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw() +31
   System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +62
   NitroNet.Mvc.<GetViewResult>d__8.MoveNext() +1429

[AggregateException: One or more errors occurred.]
   System.Threading.Tasks.Task`1.GetResultCore(Boolean waitCompletionNotification) +4719080
   NitroNet.Mvc.NitroNetViewEngine.FindView(ControllerContext controllerContext, String viewName, String masterName, Boolean useCache) +117
   System.Web.Mvc.<>c__DisplayClass6.<FindView>b__4(IViewEngine e) +45
   System.Web.Mvc.ViewEngineCollection.Find(Func`2 lookup, Boolean trackSearchedPaths) +114
   System.Web.Mvc.ViewEngineCollection.FindView(ControllerContext controllerContext, String viewName, String masterName) +220

As you can see I'm using NitroNet, and I'm not sure from the stack trace whether this is a misunderstanding on my part, or a bug in Veil or NitroNet. I have cross-posted this issue in the Veil project as well - https://github.com/csainty/Veil/issues/23.
Could you help please? This is my last blocker in getting the engine to work with Umbraco :)

This exception should mean the reference to the master page was not the first node in the template.
Is there any whitespace coming before it?

No, there is no whitespace before the reference to the master page - the templates are exactly as I entered them above.

This might start to fall in to the extensions made to Veil in this project then.
I'll probably look at Veil a little in the coming weeks for Core 2.0 stuff, so I can try these templates out then and make sure the tests are covering this case.

Thank you for registering this issue.
We have investigated the issue and it turned out that with our modified version of Veil it is not possible to use the master page feature. This is because we made some major changes to the class VeilEngine and thus we are not passing the VeilContext here.
One of our big goals respectively task in the near future is to make the underlying handlebars parser updatable (i.e. the parser stays unmodified). To achieve this we will have to get in contact with Chris Sainty and we will have to see if and how we possibly can transfer some of our changes back to Veil and how we can make possible modifications of our own work with the parser.
Concerning your issue, a possible way to mitigate the absence of master templates is to extract all the common parts into partials or components (e.g. head element). If you want to use partials you need to keep in mind to use the "with" expression to pass the right context.
We are sorry for this missing feature and hope that the suggested workaround suits your needs.


Allow products with no category

See here:
https://github.com/Flagbit/Magento-FACTFinder/issues/146


fixes flaky GeoJSONUtil test by not randomizing it

Otherwise the default locale changes randomly and will break expected
results. Geometry uses DecimalFormat at its toString methods which uses
always the current set locale.
Follow up commit of 71640ee7f5aa956f9c49d21150357246082627d3.

Codecov Report

Merging #5119 into master will decrease coverage by 0.09%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##             master    #5119     +/-   ##
===========================================
- Coverage     82.54%   82.44%   -0.1%
+ Complexity    11015    11001     -14
===========================================
  Files          1331     1331
  Lines         45047    45047
  Branches       5660     5660
===========================================
- Hits          37184    37139     -45
- Misses         5221     5263     +42
- Partials       2642     2645      +3

Impacted Files
Coverage Δ
Complexity Δ

...t/executionphases/FailureOnlyResponseListener.java
40% <0%> (-33.34%)
2% <0%> (-2%)

...exceptions/GroupByOnArrayUnsupportedException.java
66.66% <0%> (-33.34%)
1% <0%> (-1%)

...rc/main/java/io/crate/analyze/UnboundAnalyzer.java
65% <0%> (-20%)
2% <0%> (ø)

...ration/collect/collectors/OrderedDocCollector.java
90% <0%> (-10%)
5% <0%> (-1%)

...transport/executionphases/ExecutionPhasesTask.java
83.33% <0%> (-9.26%)
21% <0%> (-3%)

...io/crate/protocols/postgres/types/VarCharType.java
91.66% <0%> (-8.34%)
10% <0%> (-1%)

...src/main/java/io/crate/jobs/UpsertByIdContext.java
77.5% <0%> (-7.5%)
8% <0%> (ø)

.../java/io/crate/analyze/symbol/ParameterSymbol.java
87.5% <0%> (-6.25%)
6% <0%> (-1%)

.../collect/collectors/LuceneOrderedDocCollector.java
90.12% <0%> (-3.71%)
25% <0%> (-1%)

...nce/sys/check/node/DiskWatermarkNodesSysCheck.java
66.66% <0%> (-3.71%)
7% <0%> (-1%)

... and 17 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Fix Navigation Issue: 'Make an Appointment' Button Not Redirecting to Appointment Page

Currently, upon clicking 'Make an Appointment' in the doctor's section, the screen fails to redirect to the appointment page as intended. I'll investigate and rectify this navigation glitch to ensure a smooth user experience. Please assign this task to me for GSSoC contribution

Hello @Anishkagupta04  I am Gargi! I work with html,css,js,react.js and so on and am eager to learn more. I'd appreciate being assigned this task for GSSoC 24.

Hello @Anishkagupta04 I am Gargi! I work with html,css,js,react.js and so on and am eager to learn more. I'd appreciate being assigned this task for GSSoC 24.

hey can you please find issues by your own please it takes time to search for one-

@Pratik2401 continue doing

please assign me

@varshith257 can you pls assign these issue to me as it was raised by me

@Pratik2401 Assigned!

@Pratik2401 this issue was made by me #20 and it has been resolved
Kindly check past issues before creating new one
@varshith257 kindly look into this

I am talking about these ones @CS251000

ANY UPDATES?


Implement super_squash_history in HfApi

Resolve #1636.
This PR adds support for the /super-squash endpoint in HfApi. This endpoint squashes all the commits on a specified branch. The goal is to avoid bad user experience when repos have thousands of commits. The squash operation is non-revertible and should be used with care.
Will be useful for recurrent commits cc @thomwolf. I added a squash_history argument to the CommitScheduler that squashes the history after each commit.
(cc @Pierrci FYI)

cc @severo might be useful for datasets-server as well to clean the refs/convert/parquet branch?

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

cc @severo might be useful for datasets-server as well to clean the refs/convert/parquet branch?

Thanks. I created an issue here: https://github.com/huggingface/datasets-server/issues/1774


Dx improvments

PR Checklist
Please check if your PR fulfills the following requirements:

[x] The commit message follows our guidelines: https://github.com/analogjs/analog/blob/main/CONTRIBUTING.md#-commit-message-guidelines
[ ] Tests for the changes have been added (for bug fixes / features)
[ ] Docs have been added / updated (for bug fixes / features)

PR Type
What kind of change does this PR introduce?

[ ] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[X] CI related changes
[ ] Documentation content changes
[ ] Other... Please describe:

Which package are you modifying?

[ ] vite-plugin-angular
[ ] vite-plugin-nitro
[ ] astro-angular
[ ] create-analog
[ ] router
[ ] platform
[ ] content
[ ] nx-plugin
[ ] trpc

What is the current behavior?

Closes #
What is the new behavior?
Does this PR introduce a breaking change?

[ ] Yes
[ ] No

Other information
[optional] What gif best describes this PR or how it makes you feel?

I've noticed that prettier rules are not enforced on all files. Perhaps we should format all of them them in one commit?
It's pretty easy to run, but I haven't done it yet.
Thats also the reason the prettier ci job fails.
pnpm exec prettier --write .

Formatting them all in one commit is fine

@allcontributors add @Dafnik for infra


I wanted to remove 1 pomodoro today

I wanted to remove 1 Pomodoro today. Because I forgot to stop the timer when there's an urgent happened in the house

Potential duplicate of #277.

Thanks for the redirect.


[BACKLOG-17138] Add KETTLE_HADOOP_CLUSTER_GATEWAY_CONNECTION variable.

New property to hide knox gateway.

Build Completed
:fire: This pull request has some issues. It would be preferable to fix them in order for it to be just perfect. See below for more details. Some links are also available below for further assistance in addressing those issues.
Build Commands
ant -Dtestreports.dir=bin/reports/unit-test -f engine/build.xml clean-all resolve jacoco && ant -f engine/build.xml checkstyle publish-local

Cleanup Commands
rm -r ~/.ivy2/local || echo no publish local to remove

Changed files
  engine/src/kettle-variables.xml

Unit test coverage change
These statistics help you identify how your changes have affected the coverage of the following files. If a file is not in this list, then its coverage was not affected by your changes. To get some help interpreting these metrics, please refer to Jacoco's documentation.
org.pentaho.di.core.auth.core.impl.DefaultAuthenticationConsumerFactory

Branch Change:  + 7.14%
Complexity Change:  + 7.69%

org.pentaho.di.job.entries.evaluatetablecontent.JobEntryEvalTableContent

Branch Change:  + 1.01%
Complexity Change:  + 1.06%
Instruction Change:  + .17%

org.pentaho.di.job.entries.getpop.MailConnectionMeta

Branch Change: -1.00%:small_red_triangle_down:
Complexity Change: -1.41%:small_red_triangle_down:
Instruction Change: -.30%:small_red_triangle_down:

org.pentaho.di.job.entries.sql.JobEntrySQL

Instruction Change:  + 3.28%
Line Change:  + 3.87%

org.pentaho.di.trans.step.StepMeta

Branch Change: -.68%:small_red_triangle_down:
Complexity Change: -.58%:small_red_triangle_down:
Instruction Change: -.19%:small_red_triangle_down:
Line Change: -.26%:small_red_triangle_down:

org.pentaho.di.trans.steps.calculator.CalculatorMetaFunction

Branch Change:  + 8.70%
Complexity Change:  + 3.03%
Instruction Change:  + .75%
Line Change:  + .89%

org.pentaho.di.trans.steps.combinationlookup.CombinationLookupMeta

Instruction Change: -.04%:small_red_triangle_down:

org.pentaho.di.trans.steps.constant.ConstantMeta

Instruction Change:  + .10%

org.pentaho.di.trans.steps.dbproc.DBProcMeta

Instruction Change: -.11%:small_red_triangle_down:

org.pentaho.di.trans.steps.dimensionlookup.DimensionLookupMeta

Branch Change:  + .31%
Instruction Change:  + .06%
Line Change: -.23%:small_red_triangle_down:
Method Change: -1.02%:small_red_triangle_down:

org.pentaho.di.trans.steps.groupby.GroupByMeta

Branch Change:  + 2.08%
Complexity Change:  + 2.11%
Instruction Change:  + .28%
Line Change:  + .74%

org.pentaho.di.trans.steps.ldapinput.LDAPInputMeta

Branch Change:  + 1.61%
Complexity Change:  + .97%
Instruction Change:  + .09%

org.pentaho.di.trans.steps.sort.SortRowsMeta

Instruction Change:  + .08%

org.pentaho.di.trans.steps.textfileinput.TextFileInputMeta

Branch Change: -.53%:small_red_triangle_down:

org.pentaho.di.trans.steps.uniquerows.UniqueRowsMeta

Instruction Change:  + .18%

org.pentaho.di.trans.steps.webservices.WebServiceMeta

Branch Change: -1.79%:small_red_triangle_down:
Complexity Change: -1.19%:small_red_triangle_down:
Instruction Change: -.07%:small_red_triangle_down:

org.pentaho.di.www.TransformationMap

Branch Change: -9.09%:small_red_triangle_down:
Complexity Change: -6.15%:small_red_triangle_down:
Instruction Change: -10.03%:small_red_triangle_down:
Line Change: -10.00%:small_red_triangle_down:

@rmansoor Could you review please?


Pressure

Changed the method SingleVessel::updatePressure(). This method is called by AbstractObjectCCOTree::computePressure(AbstractVascularElement *) which in turn is called by StagedFRROTreeGenerator::generate() and associate methods by the end of the optimization proccess. Perhaps we should consider ditching  computePressure and let updateTreeViscositiesBeta deal with pressure computation.


Mail plugin form should have autocomplete set as off

Because chrome (or other password  managers) save credentials, those credentials get automatically filled into the username and password fields of the SMTP section of the Mail plugin. So, anytime I go in to any plugin settings, I have to remember to clear these fields, otherwise I receive an error.
Adding autocomplete="off" to the form or to the individual fields would prevent this issue.
`
…

Thank you, works great, I merged and published a new version.


FS.File.copy should allow modifying objects before saving

It should be possible to pass Mongo Modifier as a parameter of FS.File.copy function to alter object just before saving it. The other solution could be one proposed by @aldeed that it could by just function that will be invoked before saving.

Hi folks, just wondering if there was any progress on this?
If it's not possible to change the meta data before the copy, what's the best approach to modify it afterwards, pls? ie do I do the copy and then call some update function or just a straight mongodb update?

@adamgins I know this is kind of a late response, but I just encountered this and figured I would say what I was doing, figuring if anyone sees this and lets me know I did it wrong, it could help out people in the future.
My code looks a bit like this:
let newFile = original.copy();

newFile.update({
  '$set': {
    'owner': Meteor.userId()
  }
});

I am doing this on the server, and it appears to work as intended.

@CoolestNerdIII cheers. I am not using CollectionFS any longer.. especially as it now has the "deprecated" tag

Yeah I have been looking for another solution to migrate to. What do you use now if you don''t mind my asking?

I ended going commercial filestack.com , I use it for www.buzzy.buzz
I did look at Slingshot https://github.com/CulturalMe/meteor-slingshot/ but needs some features that were not available.

Thanks I will check those out. Kinda wish this wasn't deprecated. Oh well

yeah, I wish Meteor JS has had a set of core services for files, editors etc as part of the platform/framework. I know this is highly dependent on the UX approach chosen by each developer, but would be nice to have some core services that almost every app needs.

I agree 100%.


extend secret TTL to 24hour, add grace period for secret refresh

https://github.com/istio/istio/issues/9035
address meeting feedback -
extend secret TTL from 1 hour to 24hour, add grace period for secret refresh.

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About dataset

Thank you for the great work!
Is there any color mismatching or different intensity issue, during the collection of the dataset?
I think there might be some issues that come from the scattering of light or the refractive index of the beam splitter.
Thank you in advance!

There is a little bit of color mismatching. It can be solved by offline calibration. ISP auto white balance can also be an option to solve this problem.
For more details, please contact Prof. Zheng (yqzheng@ai.u-tokyo.ac.jp).


Map.publish() issue

Environment Information

geemap version:0.11.4
Python version: 3.7
Operating System: MacOS

Description
The datapane package has been updated. the visibility has been changed to DEFAULT/  PORTFOLIO /PRIVATE
On line #960 of eefolium.py   should be changed to  =>    visibility = dp.Visibility.DEFAULT or visibility = dp.Visibility.PORTFOLIO
On line #964 of eefolium.py   should be changed to  =>    dp.Report(dp.Plot(self)).upload(
What I Did
Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

Thank you for reporting. Would you like to submit a pull request so that you can get credits for this?

Thank you for reporting. Would you like to submit a pull request so that you can get credits for this?

Ok, I'll try to do that.

I believe leafmap has the same issue. Contributions are welcome.

Pull request submitted.


[CI] Welcome bot not firing. PR Labeler issue?

@kushthedude is the PR labeler getting in the way of the Welcome bot again?
Originally posted by @leecalcote in https://github.com/layer5io/meshery/issues/2027#issuecomment-737718609

@ramrodo FYI... there has been weird behavior with two bots conflicting in the past. The PR labeler's configuration has been removed.


cannot modify/merge eloquent relations.

Laravel Version
10.10
PHP Version
8.2.17
Database Driver & Version
mariadb:10
Description
wanted to merged eloquent relations collection, but keeps being reset to the original value.
$entity->load('deliveries');
$deliveries = $entity->deliveries;

$deliveryNumbers = $deliveries->pluck('deliveryNumber');

$otherDels = $this->getOtherDeliveries($deliveryNumbers);

//bug : deliveries is always reset to the original value
$entity->deliveries = $deliveries->merge($otherDels); //even used ->toArray() is still the same

//but delivs is work as expected
$entity->delivs = $entity->deliveries;

$entity->deliveries contains 1 item, merge expected to contains 2 items
i debug it in the controller, it is still containing expected value.
but in the the resulted http response , deliveries keeps being reset to the original value (1 item).
also checked in the DiagnosticMiddleware (after middleware), it is already reset to the original.
$response = $next($request);
dd($response->getContent()); (deliveries: 1 item)

but delivs works fine, contains 2 items.
middleware in the kernel
protected $middleware = [
        \App\Http\Middleware\TrustProxies::class,
        \App\Http\Middleware\HeadMiddleware::class,
        \Illuminate\Http\Middleware\HandleCors::class,
        \App\Http\Middleware\PreventRequestsDuringMaintenance::class,
        \Illuminate\Foundation\Http\Middleware\ValidatePostSize::class,
        \App\Http\Middleware\TrimStrings::class,
        \Illuminate\Foundation\Http\Middleware\ConvertEmptyStringsToNull::class,
        \App\Http\Middleware\DiagnosticMiddleware::class,
        \App\Http\Middleware\PrometheusMetricsMiddleware::class
    ];

Steps To Reproduce

setup eloquent relations

public function deliveries(): HasMany
    {
        return $this->hasMany(Delivery::class, 'docReference', 'orderNumber');
   }

lazy eager load
merge the relation collection
return entity

Hi there,
Thanks for reporting the problem you are encountering, but it looks like this is a question which may be better suited for a support channel. We only use this issue tracker for reporting bugs with the library itself. If you have a question on how to use functionality provided by this repository you can try one of the following channels:

Laracasts Forums
Laravel.io Forums
StackOverflow
Discord
Larachat
IRC

However, this issue will not be locked and everyone is still free to discuss solutions to your problem!
Thanks.

i thought it is a bug, because i couldn't find the solution. will try to ask in discord.


fix(payment): INT-5153 added card code validation

INT-5153
What?
Fix error while paying with a saved card (Mollie)
Why?
Every time there was a third payment with a previously save card this attempt failed.
Testing / Proof

Proceed to make a payment with a 3DS enrolled cart, opt to save the car on file.
Checkout again and pay with the card saved from previous step.
Checkout again and attempt to pay once more with previously saved card (step 1)

ping @bigcommerce/apex-integrations @bigcommerce/checkout

:green_heart: tested
QA Details: Payments with saved cards and 3DS validation work as expected


OBO Core Disease

Documenting in this ticket 'disease' term history, usage

Below,  I have outlined how 'disease' has been defined in the DO since 2006,
then revised in 2010-2012, to be orthogonal with OGMS.
I have included links to the source documents: google docs, archives of files.
I also had a look at BioPortal,
to get a view of how the term - URI - definition has been re-used for new ontologies.
Cheers,
Lynn
Under the Disease Ontology Project:
archived in SF: http://sourceforge.net/p/diseaseontology/
2005: DiseaseOntology2 release
-- prior to upper level re-structuring
2007 DiseaseOntology3 release
2006-08-28.    DO3v30.obo 2006-08-28
DOID:4 Disease --> root of DO tree, upper level branches defined
2006-11-05   Revision 20
DOID:4 Disease, defined:
A disease is an enduring pattern of abnormal functioning, or abnormal localization of normal functioning, and / or abnormal localization of constituents of the human body, or a normal physiological response to an environmental insult, which without intervention, would lead to an evolving set of signs and symptoms.
In 2008: The DO received an R01 (Warren Kibbe and Lynn Schriml), formed an advisory board.
The definition of disease in the DO, was discussed with the advisory board
and (see notes from  2010, 2011 and 2012, below)
These discussions included Barry Smith and Alan Ruttenburg (DO Advisory board
members).
         These discussions are documented in the following Google docs

Discussion of Definition of Disease
  as we came to consensus, the outcome of the discussions was recorded in this google doc:
      [Definition of Disease(https://docs.google.com/document/d/1N_A6kJb3UmrYwzRIwj99Bzb-YGY7OpaGzM9AxP8dptk/edit)

DO 'disease' definition in 2011-2012: A disease is a pattern of abnormal functioning, or abnormal localization of normal functioning, and / or abnormal localization of constituents when compared to other members of that species.
Barry created OGMS, OBO Foundry page
and defined disease as:
A disposition to undergo pathological bodily processes that exists in an organism because of one or more disorders in that organism.
The initial versions of OGMS are found in the archived Google code ohms directory
OGMS (OBO) v0.1 darted Jul 27, 2009
with disease defined as:
[Term]
id: ID:0000031
name: disease
def: "A disposition (i) to undergo pathological processes that (ii) exist in an organism because of one or more disorders in that organism." [http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf]
comment: Examples: Epilepsy as a disease that disposes to the occurence of seizures (pathological process) due to an underlying abnormality in the neuronal circuitry of the brain (phyisical basis).
is_a: ID:0000009 ! disposition
created_by: agoldfain
creation_date: 2009-06-23T11:21:20Z
--> This definition was published in
Toward an Ontological Treatment of Disease and Diagnosis (2009) [PDF(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/pdf/amia-s2009-116.pdf)]
Barry suggested aligning the DO 'disease' definition with the OGMS definition.
--> During these discussions, Barry, in OGMS had devised a new disease definition, which the DO
The four of us, Warren, Barry, Alan and myself, upon further discussion, revised the DO definition of disease, to be orthogonal with the new OGMS definition of disease.
The DO definition of disease became:
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Reference:
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
Use - Re-Use of 'term', URI, definitions:
I thought it would be informative to take a look at how these have been implemented:
Querying BioPortal, query results
-- there is quite a bit of variation in how the term 'disease' is represented.
In some cases the URI has been re-used with the DO or OGMS definition, in other cases
there is a new URI, with the same definition.
the purl the term disease, the DO - OGMS definitions, showing the diversity of 'disease' usage/definition across ontologies.
Google doc

Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it.  They look the same to me.
Since they are the same, it seems like we need to merge them into one term with a single ID.

Hello Ramona,
The DO originally had a different definition for ‘disease’, we worked with Barry and others (documented in the GitHub ticket), to make a new DO definition that all were happy with. This was before OGMS. This definition was then subsequently used by OGMS.
Cheers,
Lynn
Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls<EMAIL_ADDRESS>wrote:
Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it. They look the same to me.
Since they are the same, it seems like we need to merge them into one term with a single ID.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.

I think Ramona was just picking up on the word 'orthogonal', which would
imply that DO and OGMS have fundamentally different definitions of disease.
As Lynn goes on to explain, that does not seem to be the case, so the use
of the word in the first email was likely just an oversight by Lynn (which
happens to me all the time, so no judgement)
On Sun, Jul 28, 2019 at 6:34 PM lschriml<EMAIL_ADDRESS>wrote:

Hello Ramona,
The DO originally had a different definition for ‘disease’, we worked with
Barry and others (documented in the GitHub ticket), to make a new DO
definition that all were happy with. This was before OGMS. This definition
was then subsequently used by OGMS.
Cheers,
Lynn
Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls<EMAIL_ADDRESS>wrote:
Hi @lschriml. I think maybe when you say that the DO definition was
revised to be orthogonal with the OGMS definition, you mean that it was
revised to be consistent with it. They look the same to me.
Since they are the same, it seems like we need to merge them into one
term with a single ID.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/OBOFoundry/Experimental-OBO-Core/issues/19?email_source=notifications&email_token=ADJX2ITFWW2DW6GHVOTMFDTQBYNGJA5CNFSM4HH3SSVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27H62Y#issuecomment-515800939,
or mute the thread
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.

--
Bjoern Peters
Professor
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

Good point.
Synergy is good :)
Sent from my iPhone

On Jul 28, 2019, at 6:53 PM, bpeters42<EMAIL_ADDRESS>wrote:
I think Ramona was just picking up on the word 'orthogonal', which would
imply that DO and OGMS have fundamentally different definitions of disease.
As Lynn goes on to explain, that does not seem to be the case, so the use
of the word in the first email was likely just an oversight by Lynn (which
happens to me all the time, so no judgement)
On Sun, Jul 28, 2019 at 6:34 PM lschriml<EMAIL_ADDRESS>wrote:

Hello Ramona,
The DO originally had a different definition for ‘disease’, we worked with
Barry and others (documented in the GitHub ticket), to make a new DO
definition that all were happy with. This was before OGMS. This definition
was then subsequently used by OGMS.
Cheers,
Lynn
Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls<EMAIL_ADDRESS>wrote:
Hi @lschriml. I think maybe when you say that the DO definition was
revised to be orthogonal with the OGMS definition, you mean that it was
revised to be consistent with it. They look the same to me.
Since they are the same, it seems like we need to merge them into one
term with a single ID.
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Thanks, Lynn and exactly, Bjoern. I just wanted to make sure I wasn’t missing something in my sleep deprived state following and early morning flight.
Enviado de Buffalo

On Jul 28, 2019, at 6:54 PM, lschriml<EMAIL_ADDRESS>wrote:
Good point.
Synergy is good :)
Sent from my iPhone

On Jul 28, 2019, at 6:53 PM, bpeters42<EMAIL_ADDRESS>wrote:
I think Ramona was just picking up on the word 'orthogonal', which would
imply that DO and OGMS have fundamentally different definitions of disease.
As Lynn goes on to explain, that does not seem to be the case, so the use
of the word in the first email was likely just an oversight by Lynn (which
happens to me all the time, so no judgement)
On Sun, Jul 28, 2019 at 6:34 PM lschriml<EMAIL_ADDRESS>wrote:

Hello Ramona,
The DO originally had a different definition for ‘disease’, we worked with
Barry and others (documented in the GitHub ticket), to make a new DO
definition that all were happy with. This was before OGMS. This definition
was then subsequently used by OGMS.
Cheers,
Lynn
Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls<EMAIL_ADDRESS>wrote:
Hi @lschriml. I think maybe when you say that the DO definition was
revised to be orthogonal with the OGMS definition, you mean that it was
revised to be consistent with it. They look the same to me.
Since they are the same, it seems like we need to merge them into one
term with a single ID.
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La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
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🐛 [Bug Report]: Trinity core, master branch not supported

BlizzCMS Version
v2.0.0-beta3
Emulator
TrinityCore
PHP Version
PHP 8.1
Operating system
Linux, Windows
Web server
Apache
Database
MySQL 8.0.31
What happened?
The newly created and registered accounts during installation are unable to log in to the game properly, and the data in the table seems to be inconsistent with the account information registered on the trinitycore console

How can the issue be reproduced?
全新的trinitycore,master分支
Screenshots
No response

New trinity core, master branch

Duplicate issue #140


QUAL 0

I used freebayes to call variants and a lot of them have a QUAL 0 but they have a good depth. And when I used samtools mpileup, the same variants have quality greater than 100. I am really confused what QUAL means in the .vcf file I got after using freebayes?
And also is it possible to use any parameter that gives an idea about the confidence with which the variant is called.

In my understanding the QUAL in freebayes stand for the genotype qualities. So QUAL increases with higher allele frequencies and depth.
I assume that the variants with QUAL 0 are variants with a low allele frequency?
For you second question I think you should look at the QR, QA and GQ fields.
GQ can be obtained with --genotype-qualities

##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">

Thanks for the clarification, I was looking at SNP's with low allele frequencies in some viral strains.

QUAL is the confidence that the locus is polymorphic under the model that is specified. If you're looking for allele frequency estimates, use the AO and RO fields to calculate them. If you're looking for frequency in a pool there isn't much that we can do model wise to differentiate high and low quality candidates that doesn't reduce to something approximating allele frequency and observation quality sum.


build and push action v2

use new docker/build-push-action@v2 - fixes https://github.com/IDunion/indy-node-container/issues/4

LGTM !


Mapping / metadata refactoring

[x] Split AttributeLoader in SerializerMetadataLoader, ReflectionLoader and AttributeMetadataFactory
[x] Typehint against the interface instead of the implementation
[x] Make ClassMetadata and AttributeMetadata immutable
[x] wip add unit tests

I've refactored the AttributeLoader class and the alternative identifier system. Btw I fixed a bug with attributes included that shouldn't be.
@MLKiiwy can you take a look?

And the hard work is done. ClassMetadata and AttributeMetadata are now immutable.
I've also heavily refactored the identifier metadata system. Can you take a look @MLKiiwy?

@dunglas I like the idea of the immutable AttributeMetadata, but it's still not the case as the properties are still public, so in the AttributeMetadataInterface I'd put only getters.
The other point is: why these with methods in the interface ? Are the metadatas supposed to be updated outside of the factory and the loaders ?

Public properties are mandatory for the cache system (serialization) but they are explicitly marked with @internal so anyone using them directly know it will cause wrong sides. And they are not part of the interface.
with* methods in interfaces are mandatory for 2 reasons:

allowing external loaders (custom loaders in custom projects)
allowing to typehint loaders with loadClassMetadata(...) with interfaces and not implementations

Btw it's the same design than in PSR-7.


[stable/memcached] - Add .Release.Namespace

Signed-off-by: Lord-Y<EMAIL_ADDRESS>What this PR does / why we need it:
Add .Release.Namespace in all yaml files as it's required when deploying with Spinnaker. Without this, the deployment will be done in default namespace instead of the one you are targetting.
Checklist
[Place an '[x]' (no spaces) in all applicable fields. Please remove unrelated fields.]

[x] DCO signed
[x] Chart Version bumped
[x] Variables are documented in the README.md
[x] Title of the PR starts with chart name (e.g. [stable/mychartname])

@gtaylor @olemarkus Can you guys please have a look on my PR :) ?

/lgtm


🐛 [Bug] Share Table has no functionality

🐛 Bug

Share Table has no functionality

Which link do we want to share here?
If we want to share the guest link (with #1948), we can do that only with tables with active meetings. But in this list are also tables without an active meeting.
If we share the internal dreammall link like /table/23, does that make sense? What would be the use case?

Gebe ich so an @Hardy-Hart-am-Start weiter

Closing in favor of solution decided for: https://github.com/dreammall-earth/dreammall.earth/issues/2222


⚠ Bofrost.at has degraded performance

In 81078d8, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1223 ms

Resolved: Bofrost.at performance has improved in 6021bc8.