Incorrect peak identification in TE-rich genome

I'm working with a very repeat-rich fungal genome, with expected haploid genome size around 70 - 80 Mb. Genoscope seems to be locking onto the second (repeat-associated) peak and is producing a much lower than expected genome size estimate.
Here are the kmer coverage counts from the jellyfish histo file, trimmed at 4 and with the manually identified peak at 8. A second peak occurs between counts ~30-110.
Jellyfish_K25.pdf
Genoscope is lumping the primary peak in with the low coverge "error" segment.

Histo file: 25mer_out.txt
Would it be possible to force Genoscope to fit a model around a user-specified peak?

Hi Adam,
Thanks for your note. We looked into this but are a little confused with
what we see. We agree with you that there does appear to be a local maximum
at coverage 8, but then the next clear peak is at around 68. If the
baseline coverage really is 8, that would imply most of the genome is
organized into ~8 copy nearly perfect repeats. We have never seen anything
like that before. I wonder if it could be something more straightforward --
the genomescope model reports haploid genome size, but I wonder if your
estimates are of the diploid genome size. For example in human, genomescope
would report the haploid genome size at about 3Gb, but the diploid genome
size is 6Gb. Could this explain it? Then I would expect the peak at 8x is
an artifact of sequencing error and the trimming you have used.
Good luck!
Mike
On Wed, May 2, 2018 at 6:00 PM Adam Taranto<EMAIL_ADDRESS>wrote:

I'm working with a very repeat-rich fungal genome, with expected haploid
genome size around 70 - 80 Mb. Genoscope seems to be locking onto the
second (repeat-associated) peak and is producing a much lower than expected
genome size estimate.
Here are the kmer coverage counts from the jellyfish histo file, trimmed
at 4 and with the manually identified peak at 8. A second peak occurs
between counts ~30-110.
Jellyfish_K25.pdf
https://github.com/schatzlab/genomescope/files/1968989/Jellyfish_K25.pdf
Genoscope is lumping the primary peak in with the low coverge "error"
segment.
[image: k25_genomescopea]
https://user-images.githubusercontent.com/2160099/39550585-a01f5646-4e16-11e8-8d9f-f48c5a54b5e6.png
[image: k25_genomescopeb]
https://user-images.githubusercontent.com/2160099/39550586-a0372bf4-4e16-11e8-8a30-f8528180dab6.png
Histo file: 25mer_out.txt
https://github.com/schatzlab/genomescope/files/1968988/25mer_out.txt
Would it be possible to force Genoscope to fit a model around a
user-specified peak?
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Hi Mike,
I've managed to get something more sensible by lowering the TYPICAL_ERROR to "2" and START_SHIFT to "1". This seems to prevent the peak at 8x from being ignored when looking for the homozygous peak. I confess that this is supposed to be a haploid species, though I was hoping the genoscope estimate would be ~ n/2. The new unique length is ~38.4 Mb which is indeed approx half the expected genome size.

Do you have any suggestions re modifying the nls() call to fit just two negative binomial distributions?(i.e. single copy peak , and repeat peak).
Thanks for writing a really great tool!

That explains it -- If you are certain the genome is haploid, I would would
just double the estimate from the default genomescope run that estimated
the genome length to be 31Mbp as the current model assumes the genome is
diploid.
Good luck!
Mike
On Fri, May 4, 2018 at 4:56 PM Adam Taranto<EMAIL_ADDRESS>wrote:

Hi Mike,
I've managed to get something more sensible by lowering the TYPICAL_ERROR
to "2" and START_SHIFT to "1". This seems to prevent the peak at 8x from
being ignored when looking for the homozygous peak. I confess that this is
supposed to be a haploid species, though I was hoping the genoscope
estimate would be ~ n/2. The new unique length is ~38.4 Mb which is indeed
approx half the expected genome size.
[image: plot]
https://user-images.githubusercontent.com/2160099/39651232-f1a13dec-4f9f-11e8-9897-55d36c79f989.png
Do you have any suggestions re modifying the nls() call to fit just two
negative binomial distributions?(i.e. single copy peak , and repeat peak).
Thanks for writing a really great tool!
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Hi Mike, can you tell me what does means the purple lines in my genome_scope graph?

It is supposed to highlight error kmers, meaning the kmers that are not
explained by the model fit.
We actually have a new version of genomescope that generally does a better
job with the fit. It works pretty much the same as before, although it now
has support for higher ploidy values (in addition to diploid samples). Can
you give it a try:
http://genomescope.org/genomescope2.0/
Good luck
Mike
On Tue, Sep 17, 2019 at 5:51 AM unalibun<EMAIL_ADDRESS>wrote:

Hi Mike, can you tell me what does means the purple lines in my
genome_scope graph?
[image: plot log]
https://user-images.githubusercontent.com/51210427/65031388-77f29900-d941-11e9-98a0-b9cccb30e1b1.png
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Thank you so much, I will work on it!

Hello Sir,
I hope you are doing well.

I am trying to use genome scope in order to know the repeat content of the genome. I am having a hard time understanding the output. Can you please please help me out with this. The results I obtained are attached below.
I ran the following command in order to get the results.

download jellyfish:

wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz

untar the file

tar -xvzf jellyfish-2.3.0.tar.gz

download the linux one too.

wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-linux

went to the jellyfish directory.

cd jellyfish-2.3.0/

ran count to find kmers:

./bin/jellyfish count - C  -m 21  -s<PHONE_NUMBER> -t 10 *.sra.fasta -o reads.jf
6.make histo file and dragged it to the site.
./jellyfish-2.3.0/bin/jellyfish histo -t 10 reads.jf > reads.histo
Your suggestion will really helpful.


Checkbox does not work with Redux Forms

Problem description
I can't seem to get the checkbox to work with this package. I'm following their example on Material UI integration. However, I get the following error:

Warning: Unknown prop onCheck on  tag. Remove this prop from the element.

I also can't check any of the checkboxes. However, if I change from the original example from this:
const renderCheckbox = ({ input, label }) =>
  <Checkbox
    label={label}
    checked={input.value ? true : false}
    onCheck={input.onChange}
  />

to this:
// remove the last 2 props
const renderCheckbox = ({ input, label }) =>
  <Checkbox
    label={label}
  />

I no longer get the warning and I can check the fields. However, when I submit the form, those checkbox fields are missing. All other text fields work.
Here is the full form:
const genres = ['sci-fi', 'fiction'];
...
<form onSubmit={this.props.handleSubmit}>
    <CardHeader title="Create Universe" color="contrast"/>

    <CardContent>

            <Field type="text"
                   name="name"
                   label="Name"
                   id="universe-create-name"
                   fullWidth={true}
                   component={renderTextField}
            />

            <Field type="text"
                   multiline={true}
                   name="description"
                   label="Description"
                   rows={4}
                   id="universe-create-description"
                   fullWidth={true}
                   component={renderTextField}
            />

            Genre
            <FormGroup row>
                {genres.map((genre) => (
                    <FormControlLabel
                        label={genre}
                        control={
                            <Field name="genres"
                                   label="Genre"
                                   id="universe-create-genres"
                                   value={genre}
                                   key={genre}
                                   component={renderCheckbox}
                            />
                        }
                    />
                ))}
            </FormGroup>

    </CardContent>

    <CardActions>
        <Button color="primary" type="submit">
            Primary
        </Button>
    </CardActions>
</form>

Steps to reproduce
See above.
Versions

Material-UI: 1.0.0-beta.5
React: 15.6.1
Browser: Chrome latest(?) on OSx

Have a look at the documentation, you need to use onChange over onCheck.

Thanks, that fixed it. However I am running into a different issue where the value of genres[] is something like
names[] = [
    NaN: true
]

What is the problem here?


cant get 0.58 acc

Hi, yumoxu.
great work about your paper, but i tried to reproduce the results you mentioned in your paper.
only 0.53 i can get.
Is there any tricks i should know to get 0.58?
Thanks

I got acc: 0.574405 without doing anything special.

@Chih-Ling-Hsu I wonder what things you did. I run the code with GTX 1080Ti and default config,yml, only get 0.435516 in the test set.

I also run the code with GTX 1080Ti and default config.yml, following the instructions in README file.
I have tried a second time and still get 0.57 acc so I guess it was not just a rare case.

@Chih-Ling-Hsu
Have you checked  the majority of the stock movement of the pre-processed data?

Hi, guys~ Questions about predicting y with posterior z. To predict the last T day, I think the gold label is leaked into z_post then g..

By the way, I implement code on pytorch with the posterior z to predict. The acc is 0.5564, and the mcc is 0.0949.

@Chih-Ling-Hsu I wonder what things you did. I run the code with GTX 1080Ti and default config,yml, only get 0.435516 in the test set.

Mine is 0.483135 not much different both in py27 and py36 with CUDA10

I also run the code with GTX 1080Ti and default config.yml, following the instructions in README file.
I have tried a second time and still get 0.57 acc so I guess it was not just a rare case.

I tried with Tesla P100 and got the same result with you by 30 epochs.

i have the same question

@Chih-Ling-Hsu I wonder what things you did. I run the code with GTX 1080Ti and default config,yml, only get 0.435516 in the test set.

Mine is 0.483135 not much different both in py27 and py36 with CUDA10

Hi, I'm running this repo with CUDA10. It takes a long time to finish one epoch. Did this happened in your test?

I got acc: 0.574405 without doing anything special.
Not 0.58 acc still, but I guess we can get 0.58 with more trials?

The test dataset has 1008 samples, 579 of which are positive.
0.574405=579/1008.
Maybe you should check your confusion matrix to see whether all samples in the testset were predicted to be positive.

不管怎么调，结果每次都是 0.5744。有问题！

请问vocab.txt是什么呢，怎么下载呀

Hi, yumoxu.
great work about your paper, but i tried to reproduce the results you mentioned in your paper.
only 0.53 i can get.
Is there any tricks i should know to get 0.58?
Thanks

Hi, could you plz tell me what the vocab.txt refer to? Where can I download it?

Running on cpu, with default config and exactly the same dependency versions as in README, on test set, mine is 0.42 for 15 epochs (loss = 1.06), and 0.45 for 30 epochs (loss = 1.54). Interestingly, it goes up to 0.53 for one epoch (loss = 2.35).


Make oauth_callback_confirmed optional

I'm working with an API (goodreads) that doesn't appear to be honouring it.
The check can be found here: https://github.com/thephpleague/oauth1-client/blob/4d4edd9b6014f882e319231a9b3351e3a1dfdc81/src/Client/Server/Server.php#L432
(Also worth noting is that the exception message being shown here could be a bit more descriptive.)

Thanks for the issue and the feedback! Two things:
If the good reads API is doing something a bit different, consider building or updating an existing provider to handle its use case. The core project is intended to cover the spec's implementation.
If you think the messaging could better for an error here, consider submitting a pull request to update. Prose updates are easy to update without fear of breaking functionality.
Also, it's worth noting that this project is in the midst of a refactor, so if you need the changes now feel free to build against or pull against current master, otherwise consider the changes that are currently in develop branch.

I'm working against develop in anticipation of the rewrite.  I require the newer guzzle support.

Anyway, I think there's still an issue with passing the response you get from any API to createFromResponse as that would require me to subclass TeporaryCredentials just to dodge the hard-requirement of oauth_callback_confirmed.
The only alternative to subclassing would be to somehow fake the presence of that value just to fake out the check.

@stevenmaguire
Sorry for the spam.  I took the time based on your suggestion to produce a provider/server implementation for goodreads.  The two quirks they have are:

oauth_callback_confirmed is never used
oauth_verifier is a bit of a flying dutchman

Gotta love oauth1 signatures...
<?php namespace App\Social\Oauth1Server;

use League\OAuth1\Client\Credentials\Credentials;
use League\OAuth1\Client\Server\GenericServer;
//
use GuzzleHttp\Exception\BadResponseException;
use League\OAuth1\Client\Credentials\TemporaryCredentials;
use League\OAuth1\Client\Credentials\TokenCredentials;
use League\OAuth1\Client\Exceptions\CredentialsException;

class Goodreads extends GenericServer {

	/**
	 * Gets temporary credentials by performing a request to
	 * the server.
	 *
	 * @return TemporaryCredentials
	 *
	 * @throws CredentialsException If the request failed
	 */
	public function getTemporaryCredentials() {

		$uri = $this->getBaseTemporaryCredentialsUrl();
		$header = $this->getTemporaryCredentialsProtocolHeader($uri);
		$authorizationHeader = array('Authorization' => $header);
		$headers = $this->buildHttpClientHeaders($authorizationHeader);

		try {
			$request = $this->getRequestFactory()->getRequest('POST', $uri, $headers);
			$response = $this->getHttpClient()->send($request);

		} catch (BadResponseException $e) {
			throw CredentialsException::temporaryCredentialsBadResponse($e);
		}

		// https://github.com/thephpleague/oauth1-client/issues/63
		parse_str($response->getBody(), $data);
		return new TemporaryCredentials($data['oauth_token'], $data['oauth_token_secret']);

	}

	/**
	 * Retrieves token credentials by passing in the temporary credentials,
	 * the temporary credentials identifier as passed back by the server
	 * and finally the verifier code.
	 *
	 * @param TemporaryCredentials $temporaryCredentials
	 * @param string               $temporaryIdentifier
	 * @param string               $verifier
	 *
	 * @return TokenCredentials
	 *
	 * @throws CredentialsException If the request failed
	 */
	public function getTokenCredentials(TemporaryCredentials $temporaryCredentials, $temporaryIdentifier, $verifier) {

		$temporaryCredentials->checkIdentifier($temporaryIdentifier);
		$uri = $this->getBaseTokenCredentialsUrl();

		// https://www.goodreads.com/topic/show/2043791-missing-oauth-verifier-parameter-on-user-auth-redirect#comment_149135628
		$bodyParameters = array('oauth_verifier' => 1);

		$headers = $this->getHeaders($temporaryCredentials, 'POST', $uri, $bodyParameters);
		$body = json_encode($bodyParameters);

		try {
			$request = $this->getRequestFactory()->getRequest('POST', $uri, $headers, $body);
			$response = $this->getHttpClient()->send($request);
		}
		catch (BadResponseException $e) {
			throw CredentialsException::tokenCredentialsBadResponse($e);
		}

		return TokenCredentials::createFromResponse($response);
	}

	//
	// Goodreads flying dutchman oauth_verifier
	// https://www.goodreads.com/topic/show/18053350-getting-invalid-oauth-request-with-signed-requests
	//

	/**
	 * Generates the OAuth protocol header for requests other than temporary
	 * credentials, based on the URI, method, given credentials & body query
	 * string.
	 *
	 * @param string      $method
	 * @param string      $uri
	 * @param Credentials $credentials
	 * @param array       $bodyParameters
	 *
	 * @return string
	 */
	protected function getProtocolHeader($method, $uri, Credentials $credentials, array $bodyParameters = array()) {

		$parameters = array_merge(
			$this->getBaseProtocolParameters(),
			$this->getAdditionalProtocolParameters(),
			[
				'oauth_token' => $credentials->getIdentifier(),
			]
		);

		if($verifier = static::getValueByKey($bodyParameters, 'oauth_verifier'))
			$parameters['oauth_verifier'] = $verifier;

		$this->signature->setCredentials($credentials);

		$parameters['oauth_signature'] = $this->signature->sign(
			$uri,
			array_merge($parameters, $bodyParameters),
			$method
		);

		return $this->normalizeProtocolParameters($parameters);

	}

}

Although of course subclassing works (thank goodness!) -- there's probably a worthwhile discussion here about what can be done to reduce the amount of boilerplate that needs to be reproduced when making a custom provider/server implementation.

Heya, so I agree with Steven here - the main aim when I originally wrote this package was to be the first fully-compliant package out there, and I don't want to deviate from that focus.
However, I'm also open to the suggestion of refactoring the Server class to maybe inject a "transport" object (or something of the like) in order to simplify boilerplate.
What are the others' views on this?

The more I think about this, the more I realise there could be any number of whacked oauth implementations out there.  Things are probably fine the way they are.

Yeah that's the tricky thing!
If Steven is okay, I'm happy to close this off then

Close away.


[T4A2][T15-B4] Lai Yingchen

Ready for review

@yingchen0505 Ensure calls to parseArgsAsDisplayedIndex use the class name and not an instance of class Parser.


EmptyEpsilon: use python3

Motivation for this change
https://github.com/NixOS/nixpkgs/issues/18185
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[x] Fits CONTRIBUTING.md.

cc @fpletz
Note that this was not tested.

Success on aarch64-linux (full log)
Attempted: EmptyEpsilon
Partial log (click to expand)
-- Installing: /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15/bin/EmptyEpsilon
-- Installing: /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15/./script_reference.html
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15
shrinking /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15/bin/EmptyEpsilon
strip is /nix/store/zrs21zqcchgyabjf4xfimncdq16njizc-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15/bin
patching script interpreter paths in /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15
checking for references to /build in /nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15...
/nix/store/bgg90r592j3idqc35zag93lqkgkh8q1d-empty-epsilon-2018.02.15

Success on x86_64-linux (full log)
Attempted: EmptyEpsilon
Partial log (click to expand)
-- Installing: /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15/bin/EmptyEpsilon
-- Installing: /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15/./script_reference.html
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15
shrinking /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15/bin/EmptyEpsilon
strip is /nix/store/1hi76hr87bd1y1q1qjk0lv8nmcjip1c8-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15/bin
patching script interpreter paths in /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15
checking for references to /build in /nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15...
/nix/store/yjar1jr63spf4z0wa5liwxx8cqx51hy0-empty-epsilon-2018.02.15


Follow up migration of solid auth to DPoP

Today's solid-team meeting has decided an action on this subject.
@ewingson I proposed you be part of this.
The purpose of this issue is to organise the follow up and support to migrate solid apps from legacy to DPoP authorization.
The main tasks could be

apps Inventory.

First basis from Aad Versteden https://bourgeoa.solidcommunity.net/public/todo/solid auth migration.html
should include https://solidproject.org/developers/tools/

prepare a small paper explaining the change and the motivation for migration

DPoP is replacing legacy
library https://github.com/inrupt/solid-client-authn-js

make a small list of examples

https://github.com/0dataapp/helloworld/solid/
mediakraken, penny, SolidOS webApp
getting a cookie see https://github.com/jeff-zucker/solid-node-client

contact the authors to explain the change (create issue with links to point 3. and 4.)
make the follow up (reminders)

Pod ressources
https://solidproject.solidcommunity.net could be used for the follow up
https://solidweb.me could be used to test the apps
As dog food

@jeff-zucker or @theRealImy could we have a ui-elements app for the follow up ?
The app will link : author - app - auth status - follow history
@timbl could the tracker pane be used for that kind of project

@bourgeoa - yes, for sure, if you have an RDF source for app information, I can make you a playground where you can experiment generating various different HTML outputs from it.

@bourgeoa
so a first step would be to synchronize https://bourgeoa.solidcommunity.net/public/todo/solid auth migration.html and https://solidproject.org/developers/tools/ ?
I just took the codebase and put it online on https://solidweb.me and https://solidweb.org and am not actively developing (as you all know).
I for sure 'd be glad to help, but a small action item would be helpful.
I have been just taking orders doing my job and have psychological experience which makes it hard to think in technical aims (seeing a target) for me.
what can I do ? how can I help ? how do we grow as a group and a community ?
is it correct NSS and CSS both support DPoP atm ?
I will update solidweb.me as soon as the 3.0 is out and know for sure penny is working with CSS.

@ewingson The first post in this issue lists the manual tasks to be done :

point 5. is the objective : a list of apps with an indication of status :

DPoP status --> yes/no/issue created/will not migrate/...
status date

actions :

create a model of issue the can be pasted in each github/gitlab repo
at the same time prepare a mardown table of apps : with 3 columns

| name/url  | DPoP status |  date |

then when the issue model is OK. create the issues

This is not a very high level work but useful.
@ewingson Are you part of it ? We can continue to discuss in private.

Project of issue to paste in each app repo
issue title : migrate legacy auth to DPoP
issue content :

purpose and motivation
examples and useful links

@bourgeoa
I'm perfectly well with speaking here.
yeah I'm part of it.
so to check are all apps in the Links of 1.
a) can we assume DPoP is working when able to log in with CSS ? are there cases DPoP on NSS is working and CSS not ?
b) https://solidproject.solidcommunity.net/Team/dpop-migration/applist.md gives a 401 when logging in with my solidweb account.
c) to summarize: how do I decide if DPoP status is yes or no ?
-- I'll help to create the table in a first step and THEN / in a second step we would create the issues ?
die I understand ?

p.s.: I as well could create the table either on my private pod or in my github repo and when done copy it over, case I get access... just an idea...

@ewingson Yes please do. Just give me the link and read/write access so that I can also come to help. My webId https://bourgeoa.solidcommunity.net/profile/card#me

@bourgeoa
and CSS login works means status yes.
what if NSS works, CSS not ? then would be a no ?
I've created an md-file, have to check the syntax https://testpro.solidweb.org/public/team/dpop.md

a) yes for CSS, for NSS you may not know easily
b) we are waiting for to @theRealImy
c) we can discuss it if you doubt.

https://testpro.solidweb.org/public/team/dpop.md can you give me write access.

would I modify the acl manually for that ?
with which of your accounts ?

@bourgeoa I've given you owner rights per drag and drop for your solidcommunity.net account

@bourgeoa
we could insert another column, so that we have two links for each app, one for the live-access and one for the github repo:
| name/URL | github repo | DPoP auth | date |
| | | | |
| solid-ide |  https://github.com/jeff-zucker/solid-ide | no? | 2022-01-15 |
What do you think ?

Usually the repo has a link to a live accès. So I would not generalize now.

good teamwork, @bourgeoa !
I've set all the links to the github repo, except for penny, that's on gitlab

@bourgeoa @theRealImy @timbl @jeff-zucker
our list (link above) is not yet fully populated, but I think I've covered a good start.
Although it's not my mother tongue I've created a small issue text (far from perfect, if any native speaker wants to take that part ?). I'll paste it below.

We on Solid recently had an update from legacy auth to the use of a DPoP Token.
We noticed that your app (URL to repo) still is using the old auth.
We'd like to encourage you to switch to the new auth using the Demonstrating Proof of Posession technology.
Our motivation for the update was using the standard OIDC-way.
The new library can be found at https://github.com/inrupt/solid-client-authn-js
An example of an app using the DPoP mechanism can be found here https://github.com/0dataapp/hello/tree/main/solid
On https://github.com/jeff-zucker/solid-node-client you'll find informations about getting a cookie.
Just let us know if we can assist you on switching your app at (link to gitter room/(which one?)/forum)
What do you think ?

I'd replace the lines from "The new library can be found... to the next blank line with this:
Javascript libraries using the new authentication methods include Inrupt's solid-client-authn-browser for the browser and solid-client-authn-node and solid-node-client for nodejs.  To obtain a token for nodejs app login, you will also need Inrupt's generate-oidc-token.
See also authentication libraries for other languages.

Also for future reference - please never link to the archived versions of Solid-Node-Client or Solid Rest in my repo.  Link instead to the live versions in the solid repo.

@ewingson I opened https://solidproject.solidcommunity.net/Team/dpop-migration/ with Read/Write to The team group, me and you
We shall continue there please.
You can log in with https://ewingson.solidcommunity.net/profile/card#me
There are 2 files :

dpop-status for list of apps (with a copy of the original from testpro
issue-proposal for a proposed text issue to the non DPoP apps (from your proposal and jeff's comments

@bourgeoa I've proposed two little changes...
marked with ori ... new ... end but the readability is not good therefor.
do you agree to the changes ?

@ewingson ok good job. Changes approved. You can also remove everything after end
If there are no more comments. We can raise the issues in the app repos.
Please update the app-status so we can follow the job advancement. Thanks 👍

@bourgeoa
issue text updated.
we have 32 apps of which 22 need to be addressed. shall we wait for @timbl / @theRealImy to approve (don't know though how to request review, this is an issue and not a PR, but when they're tagged, they will notice) or shall we proceed creating an issue ?
one more thing comes to my mind, what will the headline be ?
Request for updating your app to DPoP auth from the Solid Team ? does that sound good ?

You can proceed. I will not be available today.
Issue title : update to DPoP authentication. Legacy being deprecated
Greetings, I would prefer simply : From solid team
Simply remove:

request ... This is too much authoritative
for other languages .... We don't have anything to propose

@bourgeoa okay as perfectionist (I wanna do it right) "From the Solid Team" or "from solid team" (uppercase/lowercase, "the") ?

21 issues created. an example on github is https://github.com/jaxoncreed/o-edit/issues/13 and on gitlab is https://gitlab.com/vincenttunru/notepod/-/issues/7 . still not 100% convinced cause I've naturally copy/pasted them from the proposal and there are newlines between the sentences. but now they're out. can be closed.

Just out of curiosity - why did I get an issue on Solid File Cient?  Is it because the documentation is not updated?  The library works completely fine with the new auth and is, in fact, agnostic about the auth library.

then please excuse me, I thought I tested it with CSS. maybe was the mistake, that I wasn't aware that it's agnostic.

@jeff-zucker it relates to the demo https://jeff-zucker.github.io/solid-file-client/docs/examples/

Okay, no problem either way, you guys are doing a great job, thanks.

I can only agree with @jeff-zucker, it looks good to me!

@ewingson to have a follow-up we need to track the issue posted to the source app repo.
We may put something like issue#issueNumber in the comment in app-status row of the app.
What do you think ? If you have a better idea ?

yeah sounds good. will be the first I do in the morning.

I have left the issue numbers of the addressed apps in the comments.

I have updated the App list to include all Apps we found in different lists: see apps status v2.0.md
I also added 2 new columns which help us in preparing to move to CSS.


fix(TopologicalSpace/Basic): restore curly braces in continuous_def

These were placed on purpose; reverting them caused breakage downstream.

Follow-up to #9993.

I'm sorry for merging #9993 too soon.

bors d=Ruben-VandeVelde

I have incorporated the suggestion and merged master.

bors merge


Upgrade node version to fix semantic release version upgrade

:tada: This PR is included in version 1.15.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Receive complete resource on delete subscription notification

It would be really helpful to receive the complete resource on a delete subscription notification because we need to process some information from the deleted resource. Right now we would need to use call  _history method and fetch the version id before deletion which is rather costly. Would this possible to implement?

Would you accept a PR that would send at least the last version id with the resource delete notification? That would make it very easy to fetch it if needed.


Minor tweaks that show as hotspots when performance testing.

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@ryanjbaxter Having issues with that eclipse plugin - seems to be a disaster when formatting.
Would be nice if you used: https://github.com/spring-io/spring-javaformat

@ryanjbaxter Have you noticed that the import order on files for your own project is different depending if you or @spencergibb created the file.

We are planning to use that eventually. We can take care of the formatting while merging.

Closed with polish via 6deb7c872fa39ae6ea762b010a549e38f4e1967d

@dave-fl nope I have not noticed that


Update to React 17?

@ctxhou Do you have any plans to update this to be compatible with React ^17.0.0 / functional components & hooks? Thank you

hey @stevorr, thanks for asking. I don't have the plan to upgrade it to 17 in recent, but I will be able to review the change if you are interested in sending the PR


Throw better errors

Throw better errors / or successes with better details. Use cases where we don’t return a value (We should be able to return the actual response (and everything else) for external code to process)
This is probably a breaking change.

We just got hit by this in our CI at NBA - the rekeying and package signing via roku-deploy just timed out - it took some investigation to work out there was a compile error in our build; be great to get errors in surfaced that we can catch, in those situations.


Create a page listing all the available repositories

This comes directly from Docker Hub's "Explore" feature. So, for example, there would be a link on the top navigation bar that when clicked it will redirect the user to a page where all the repositories that are visible to the current user are listed.
Note that this would also apply for non logged-in users when the issue #279 gets implemented. For non-logged in users, only "open" repositories would be listed.

Closing since this has been recently implemented and I didn't double-check ...


docs(CODESPACES.md): add gemini

[!IMPORTANT]
Updates CODESPACES.md to include Google Gemini setup and usage as an alternative to OpenAI.

Documentation Update:

Renames title from "GitHub Codespaces support" to "Use Case: GitHub Codespaces" in CODESPACES.md.
Adds instructions for using Google Gemini as an alternative to OpenAI in CODESPACES.md.
Details prerequisites and setup for gemini-openai-proxy and usage limits for Gemini free tier.

References:

Adds links to Google AI Studio and Gemini API documentation.

This description was created by  for 39580947bf069e2d3fb0436443119e29869f07f3. It will automatically update as commits are pushed.

Related https://github.com/lloydchang/ipa-lab-hackingBuddyGPT/pull/3 https://github.com/lloydchang/ipa-lab-hackingBuddyGPT/pull/4 https://github.com/lloydchang/ipa-lab-hackingBuddyGPT/pull/5


Don't start ScopeThread's until UI is initialized

With high-latency instruments, there's contention between waveform downloading and all of the initial queries populating instrument settings from cache.
Would be best if the instrument were kept on hold until the GUI had fully loaded.

ngscopeclient does background loads of stuff as much as possible, so I think we're probably good. Can make tweaks to individual drivers in the future as needed.


feat: add more error kinds

The trait serde::de::Error allows reporting a type_mismatch,
length_mismatch and a custom message in syntax.
These errors are reported distinctly now.
This PR depends on https://github.com/serde-rs/serde/pull/165 or https://github.com/serde-rs/serde/pull/165 to use the extended de::value::Error.

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This message was auto-generated by https://gitcop.com

@homu: r+
looks great!

:pushpin: Commit a12d3c7 has been approved by erickt

:hourglass: Testing commit a12d3c7 with merge 318daba...

:broken_heart: Test failed - status

There were the following issues with your Pull Request

Commit: ac4d20a15148b7f1ca7fc2eb215f4ef947cacbea

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Commit: 2be6bbcad2cc6806d9d070633d1364f64e0d141f

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Commit: 7b89e839080ac1cd0e43f5a951936b76fea759a0

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Commit: 486a4dffff27b94c2e781fe4d7a45c4626011712

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@tomprogrammer: could you fix the test failures?

This PR depends on another PR in the serde repository. There is an open discussion there regarding the value::Error struct: https://github.com/serde-rs/serde/pull/166#discussion_r41864222 As soon as it is resolved and merged I will update this PR.

This PR is contained in #11 and thus superseded by it.


chore: automated PR to update ReleaseNotes for 202402.12.0 VHD

This is an automated PR to bump ReleaseNotes for the VHD release with image version 202402.12.0

Pull Request Test Coverage Report for Build<PHONE_NUMBER>
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No unchanged relevant lines lost coverage.
Overall coverage remained the same at 79.313%

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Covered Lines:
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poetry-exec-plugin isn't compatible with poetry 1.5.0

The newest release of poetry (1.5.0) makes it impossible to execute a command with poetry-exec-plugin:
poetry exec -vvv some-command
(...long stack trace...)
  AttributeError

  'PyProjectTOML' object has no attribute '_file'

  at ~/Library/Application Support/pypoetry/venv/lib/python3.9/site-packages/poetry_exec_plugin/plugin.py:39 in handle
       35│         ),
       36│     ]
       37│
       38│     def handle(self) -> Any:
    →  39│         pyproject_folder_path = self.poetry.pyproject._file.path.parent
       40│         pyproject_data = self.poetry.pyproject.data
       41│
       42│         cmd_name = self.argument("cmd")
       43│         cmd = (

I tested it out locally, and the fix seems to be very easy: Just change in line 39: self.poetry.pyproject.file.path.parent

@keattang Is there any hope that this will be fixed soon? Looking at how old the issues and PRs in this repo are, I'm a bit pessimistic about the future of poetry-exec-plugin...
I very much like poetry-exec-plugin - it would be sad if it slowly dies...

Hi all, a pull request is always appreciated. I also intend to take a look this weekend.

I created a branch locally, and the tests pass 😄 . But unfortunately I don't have permissions to push.
However, I spotted that in the GitHub CI, you test your plugin against a rather old version of poetry: https://github.com/keattang/poetry-exec-plugin/blob/main/.github/workflows/test.yaml#L27

This fix would be very much appreciated indeed! That's the only thing stopping my team from upgrading poetry to the latest version (1.5), and there're new features in it we're looking forward to. We could workaround it but it'd be nice if it came in as an official fix!

Thanks all for identifying the issue and @masuwo3 for his fix. This should now be fixed if you upgrade to 0.3.6


feat: Added ability to generate a log file

Added ability to update a change log file with the changes made.
I hope this PR conforms to your code style okay. Apologies for the failed builds in a test PR; it’s hard to test these things

@SamuelJohnsonMedia Hi, Thanks for the contribution
Correct me if I'm wrong, but I don't think the log file changes take effect unless they're committed.
Can you add the process to commit the log file changes as well?

Correct me if I'm wrong, but I don't think the log file changes take effect unless they're committed.
Yes; I didnt commit these files to git because there are other actions that can do that; but I would like to have only one action that does the two

Can you add the process to commit the log file changes as well?
Yeah sure, I will do that

Have now updated the PR to add the ability to commit the changelog or in fact any others like files updated with new version numbers

I have updated with your suggestions; let me know

I would like to use this action and having the ability to commit the changes would be great. No movement in 6 months, is this still being worked on?

@SamuelJohnsonMedia Sorry for not taking action on this PR for so long, if you're still willing, can you rebase and resolve the conflicts so that we can finalize and merge this feature?


Consider adding a license

Feel free to close if you are not interested, but in the modern world of open-source software it is useful for everyone involved to have a license in your code.  From below, "If you find software that doesn’t have a license, that generally means you have no permission from the creators of the software to use, modify, or share the software."
https://choosealicense.com/no-permission/

Done 27545621a6cf9df9f13a09344b119377411405b8


12/22/2020 Publish

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cant change character when pked

cant change character when pked, you have to reconnect to fix that, its bad please fix
if your dead and someone pks you then you cant change char

That's odd, for now to be safe I'd recommend you use Character bans, they're a lot cleaner anyways. Sorry about the inconvenience, we'll look into it.


[Discussion] ESM vs. CJS

Just curious why you decided to switch to CommonJS.
ESM is the agreed upon standard for modules in browsers, and already works in most modern browsers, whereas for CommonJS some build step is necessary to make it run in browsers.
I know that for node to work with ESM the file would need an .mjs extension, but in the current implementation this library works in browsers only anyway.
We could of course rename index.js to index.mjs with the caveat that some hosting solutions will serve the files with the wrong content-type.

What we could do is to use index.mjs as ESM and compile this to index.js as you previously did, defining them in package.json like this:
{
  ...
  "main": "index.js",
  "module": "index.mjs"
  ...
}

I did some testing myself and tooling support for .mjs files is still very limited and inconsistent. It might be better to use something like this instead, until there is a clear direction where .mjs is going:
{
  ...
  "main": "index.js",
  "module": "index.esm.js"
  ...
}


[BEAM-11693]  Update formatting. Fix email template

Adjust the formatting of the markdown in the release guide to be 1 sentence per line, rather than mix of that, 1 paragraph per line, and 80 char formatted. This makes reviewing later changes simpler, as new sentences appear as new lines, changes and removals as one would expect.
Also fixes the email template, which was broken by the explict more summary tag.

Thank you for your contribution! Follow this checklist to help us incorporate your contribution quickly and easily:

[ ] Choose reviewer(s) and mention them in a comment (R: @username).
[ ] Format the pull request title like [BEAM-XXX] Fixes bug in ApproximateQuantiles, where you replace BEAM-XXX with the appropriate JIRA issue, if applicable. This will automatically link the pull request to the issue.
[ ] Update CHANGES.md with noteworthy changes.
[ ] If this contribution is large, please file an Apache Individual Contributor License Agreement.

See the Contributor Guide for more tips on how to make review process smoother.

GitHub Actions Tests Status (on master branch)

See CI.md for more information about GitHub Actions CI.

R: @pabloem @chamikaramj
At time of review request, the precommits are still pending. I'll fix those (like whitespace) afterwards.

R: @pabloem @chamikaramj
At time of review request, the precommits are still pending. I'll fix those (like whitespace) afterwards.

Adjust the formatting of the markdown in the release guide to be 1 sentence per line, rather than mix of that, 1 paragraph per line, and 80 char formatted. This makes reviewing later changes simpler, as new sentences appear as new lines, changes and removals as one would expect.

The present inconsistency is annoying, but IMO putting each sentence on a new line decreases the readability of the source in many cases. I'd favor an 80 or 100 character limit since it keeps the paragraph structure visibly intact in the source, and most importantly a computer can enforce it.
In any case, there should be a website-wide consensus on this, and it should be checked automatically. Otherwise, it will take a Sisyphean effort to maintain without much benefit.

Adjust the formatting of the markdown in the release guide to be 1 sentence per line, rather than mix of that, 1 paragraph per line, and 80 char formatted. This makes reviewing later changes simpler, as new sentences appear as new lines, changes and removals as one would expect.

The present inconsistency is annoying, but IMO putting each sentence on a new line decreases the readability of the source in many cases. I'd favor an 80 or 100 character limit since it keeps the paragraph structure visibly intact in the source, and most importantly a computer can enforce it.
In any case, there should be a website-wide consensus on this, and it should be checked automatically. Otherwise, it will take a Sisyphean effort to maintain without much benefit.

While i agree in principle, I'm of the mind that since I'm going to be making the next half dozen changes to this one markdown file, that at the very least it should be more consistent than it is with itself.
A sentence per line is far less manual work than maintaining specific character counts per line. Otherwise each change means reflowing the rest of the paragraph.
Unless we can agree on a markdown formatter that we can just run from gradle. Given we have a whitepace lint that doesn't actually fix the problem, I'm inclined to believe we don't have one such thing at present.
Further, when i run the whitepace linter it operates even on the git submodules which we likely don't want to get in the habit of formatting.
Besides: the common case is not reading the source, it's reading the rendered site which handles the flows properly anyway. Qhen editing, one would commonly be in an editor which can handle the user's wrapping preference. Finally, if one is searching for a specific line to change, as long as your don't search on sentence breaks, you're easily able to Ctrl-F for the specific line. With arbitrarily broken up text (like max 80 char lines) to character counts, you don't know if you can't find a snippet due to a typo, or due to a line break in the text your looking for.
Your preference is noted but I strongly disagree with the sysyphean effort proposed by manually maintaining 80 char flows without automation.
That we don't currently impose a standard still means that imposing one consistently for this single file is a dramatic improvement over it's current state of 3-4 different approaches.

While i agree in principle, I'm of the mind that since I'm going to be making the next half dozen changes to this one markdown file, that at the very least it should be more consistent than it is with itself.
A sentence per line is far less manual work than maintaining specific character counts per line. Otherwise each change means reflowing the rest of the paragraph.
Unless we can agree on a markdown formatter that we can just run from gradle. Given we have a whitepace lint that doesn't actually fix the problem, I'm inclined to believe we don't have one such thing at present.
Further, when i run the whitepace linter it operates even on the git submodules which we likely don't want to get in the habit of formatting.
Besides: the common case is not reading the source, it's reading the rendered site which handles the flows properly anyway. Qhen editing, one would commonly be in an editor which can handle the user's wrapping preference. Finally, if one is searching for a specific line to change, as long as your don't search on sentence breaks, you're easily able to Ctrl-F for the specific line. With arbitrarily broken up text (like max 80 char lines) to character counts, you don't know if you can't find a snippet due to a typo, or due to a line break in the text your looking for.
Your preference is noted but I strongly disagree with the sysyphean effort proposed by manually maintaining 80 char flows without automation.
That we don't currently impose a standard still means that imposing one consistently for this single file is a dramatic improvement over it's current state of 3-4 different approaches.

Given we have a whitepace lint that doesn't actually fix the problem, I'm inclined to believe we don't have one such thing at present.

As far as I know, you're correct that there's no formatter right now. I agree that having a whitespace linter without an autoformatter is less than helpful since it adds to the manual maintenance burden without providing much benefit.

Your preference is noted but I strongly disagree with the sysyphean effort proposed by manually maintaining 80 char flows without automation.

To be clear, I'm proposing we don't set any standard until we can both enforce it with a precommit check and fix violations with an automatic formatter. This PR is fine, but I think we can agree that manual maintenance is unsustainable.

Given we have a whitepace lint that doesn't actually fix the problem, I'm inclined to believe we don't have one such thing at present.

As far as I know, you're correct that there's no formatter right now. I agree that having a whitespace linter without an autoformatter is less than helpful since it adds to the manual maintenance burden without providing much benefit.

Your preference is noted but I strongly disagree with the sysyphean effort proposed by manually maintaining 80 char flows without automation.

To be clear, I'm proposing we don't set any standard until we can both enforce it with a precommit check and fix violations with an automatic formatter. This PR is fine, but I think we can agree that manual maintenance is unsustainable.

To be clear, I'm proposing we don't set any standard until we can both enforce it with a precommit check and fix violations with an automatic formatter. This PR is fine, but I think we can agree that manual maintenance is unsustainable.

100% agree. Hence my preference to a sentence per line while there is no defined standard, or auto-formatter. Very minimal effort to maintain, among the other benefits I ranted about above.

To be clear, I'm proposing we don't set any standard until we can both enforce it with a precommit check and fix violations with an automatic formatter. This PR is fine, but I think we can agree that manual maintenance is unsustainable.

100% agree. Hence my preference to a sentence per line while there is no defined standard, or auto-formatter. Very minimal effort to maintain, among the other benefits I ranted about above.

Content LGTM. I'll let y'all resolve the discussion with regards to formatting.

Content LGTM. I'll let y'all resolve the discussion with regards to formatting.

Thanks! I'll get the next stage of this ready.


add SDL3 close code include

Fixes the nested inclusion error
error: Nested inclusion of SDL_begin_code.h

when including SDL library headers after this one e.g.
#define SDL_MAIN_USE_CALLBACKS 1
#include <SDL3/SDL.h>
#include <SDL3/SDL_main.h>
#include <SDL3_gpu_shadercross/SDL_gpu_shadercross.h>
#include <SDL3_image/SDL_image.h>

I didn't realize we were including begin_code... lgtm but if we can remove begin/end that'd be even better.

Guess it's a style thing. Looks like SDL_begin_code.h defines SDL_DECLSPEC which the header uses but the macro can be depended on transitively through SDL3/SDL.h and friends. Up to you guys.

Looks like this was added as part of #27:
https://github.com/libsdl-org/SDL_gpu_shadercross/commit/7d051302637e7c3ad06ff3701b437f8c12cef5c1#diff-2e60a45c03fef099e891f096d345c88bf5f932511d1f06186e2047c07346f364R26
@madebr, is this needed for the satellite libraries?

@madebr, is this needed for the satellite libraries?

I think so.
There was an issue about this, but it was decided to keep them.

Works for me - let's get this in then!


liquibase relative to changelog in folder reference broken

After updating to 2021.6.2-213 click through from the master changelog file to included files is broken:
Screen-shot:

These used to be green and would bring you to the actual file (with control-click).

Just ouside of the screenshot:
relativeToChangelog="true"
and the relative path is correct.

Hi Merijnv,
Thanks for using JPA Buddy and reporting issues.
But, this is a repository for documentation only, so I'll close it here and moved your ticket over into our internal issue tracker. Here is the link that you may use to follow its status.
We didn't expect to see the request in this repository :) That's why it's taken so long to answer. If in the future you see a bug or want to offer any feature that is missing, we will give you a response a lot quicker in the discord or email.


Flash MouseEvent stageX and stageY are read only

Hello,
I need to call a handler which handles a mouse event (followMe) and I want to do it by giving it explicitly the mouse coordinates from the current mouse position.
Because I couldn't find the coordinates of the mouse position outside of a triggered event I prototyped a solution where they are stored. I try to assign them to the MouseEvent object but I find that the code doesn't work on the flash target:
  Cannot access field or identifier stageX for writing

However the same code works in html5 and mobiles without major problems (I assume is the flash implementation of MouseEvent but I don't see any reason why this field can't be override).
Example:
        #if mobile
        var me = new MouseEvent(MouseEvent.MOUSE_MOVE);
        me.stageX = stored.x;
        me.stageY = stored.y;
        followMe(me);
        #end

A whole running example can be found here (you can change "Ngon" by rectangle).

Cause in flash MouseEvent stageX and stageY ARE read-only, there is nothing to do with OpenFL.
http://help.adobe.com/en_US/FlashPlatform/reference/actionscript/3/flash/events/MouseEvent.html#stageX

You could also use mouseX and mouseY for objects, or stage.mouseX and stage.mouseY for an absolute position :smile:

That still doesn't solve the fact that I can't dispatch a mouse event with custom coordinates. And that is still an inconsistency between platforms.
@pozirk That was not that obvious, especially since I only have read the openfl source code and it works for some platforms.
@jgranick that's nice to get the current position but those are still getters. I wanted to force the code that captured that event :(

Flash has security restrictions in place so that you can't make your own mouse events. You could hijack the user's mouse and click things, opening up links or saving files to their computer.

Thanks for the explanation @MSGhero, now everything makes sense (not a bug).


[NETBEANS-54] Module Review Apache License javafx2.project

Fixes #111
Due to note:
in the file javafx2.project/src/org/netbeans/modules/javafx2/project/templates/jfx-impl.xml_
So I just leave it without any change

Could you add the following files to rat excludes[1] after you undo the license headers. These files are used as templates when a user creates a new project.

FXSwingTemplate.html_
FXSwingTemplateApplet.jnlp_
FXSwingTemplateApplication.jnlp_

Then, *.template files should be also added there after you undo the license headers.
I don't know if project templates are visible for users.
see: https://github.com/emilianbold/incubator-netbeans/pull/282/files#diff-fa67ba03971f6d21c0ff2493bf5d922f
[1] https://github.com/bjansen/incubator-netbeans/blob/65de90b70575ba37044b533bf4e98a89851cdc8e/nbbuild/build.xml#L1949-L1974

Looks to me all that need to be done here is an exclude rule for javafx2.project/src/org/netbeans/modules/javafx2/project/templates/*

Done

@trantuyen1505: not sure if it was intentional but it was sneaky to add your change in the middle in order to make sure you don't get conflicts if somebody else appends an exception 👍


Amd ext to khr

Add the first steps to removing the AMD extension VK_AMD_shader_ballot.
Splitting up to make the PRs smaller.
Adding utilities to add capabilities and change the version of the
module.
Replaces the instructions:
OpGroupIAddNonUniformAMD = 5000
OpGroupFAddNonUniformAMD = 5001
OpGroupFMinNonUniformAMD = 5002
OpGroupUMinNonUniformAMD = 5003
OpGroupSMinNonUniformAMD = 5004
OpGroupFMaxNonUniformAMD = 5005
OpGroupUMaxNonUniformAMD = 5006
OpGroupSMaxNonUniformAMD = 5007
and extentend instructions
WriteInvocationAMD = 3
MbcntAMD = 4
Part of #2814

@dnovillo There is not document, but I added comments to the code describing the instruction sequence that is suppose to be generated.


Private kernel - enforce that non-transient reads are for the current contract address

See spike here for details: https://github.com/AztecProtocol/aztec-packages/issues/1354

Closed by #6310


Features dicussion for the API Python client

The objective of this issue is to discuss the functionalities that the Python client API should have. This library is oriented to insert in the database a large amount of information automatically using the python scripts.
possible features:

Check that you are not inserting duplicate information through the API from Python
Check that the file path really points to a file inside sct_testing / large

Also, I will place some use cases that occur to me if you have any more please comment
possible use case:

Add all the vertebral labeling files to the database.
Incorporate initial vertebra and final vertebra that appears in the image
Insert the spatial resolution of the image

where in this repos should we create those scripts? under "python/"? "api/"? "utils/"? other ideas?

also, what python should it be based on? SCT's python?

Francisco, please let me know if what I am saying is relevant/feasible.
Let's say I have 158 new subjects to add to the database (true story btw hehe).
From the same center
For these subjects I do not have the same contrasts available (ie {subj1: [t2_ax, t2_sag], subj2: [t1]})
For each 3D volume, I have *_seg_manual.nii.gz and *_lesion_manual.nii.gz.
Finally, in an excel I have the demographic info with the following columns: subject_id // gender // EDSS // DD // age // phenotype
Do you think that your API could help me? :)

Great use case @charleygros. Once that Python client is done I will make a use case code based on your needs. This code can be used like template for future.

@jcohenadad
where in this repos should we create those scripts? under "python/"? "api/"? "utils/"? other ideas?
A:/ I was thinking in "API_Python_client/" this is very descriptive and the user will understand  right away
also, what python should it be based on? SCT's python?
A:/ The API Python client doesn't need any SCT python environment dependencies, so don't think that is a good idea use it. Once that the client is finished I will say wich python libs are used, for sure os, requests to make HTML requests and JSON processing lib (not defined yet). Then the user can install these dependencies in the python environment that fit better her/his needs.
Allow better filtering for including folders like t2_sag, t2_ax #1763
A:/ Ok, I can do it but doesn't but this functionality will be only available in the python client not in the web UI.

May I add things? but please let me know if that's not appropriated.
Also know that there is no rush: all you will be able to offer us, I would see it as an unexpected gift :)
So:

It would be nice to add the initials of the rater automatically (e.g. FP) for the XX subjects we are adding at once in the DB
(Maybe already implemented but: ) would it be possible to output the list of the data for which no GT is available?
When we add a GT, could we add a test: check if data_shape and res and orientation is the same as the related image?

I will continue to think about it :)

@jcohenadad @charleygros @perone
In branch "API_Python_Client_by_Fco" you can see the code of the API Python client.
https://github.com/neuropoly/sct_testing_management/tree/API_Python_Client_by_Fco/API_Python_Client
The client is implemented on API_Python_client.py file.
A generic example is on the file example_insert_all_info.py
Could you please take a look at the code and give me some feedback.
Once that we decide that the API Python Client is released using in I can start to develop a code for the issue #32 wish depends on the current issue.

@fperdigon how about you open a PR? it will be easier to address point-by-point comments in the cord


Sunstone login not working for newly created user

Description
Users created via sunstone or via oneuser create can't login via sunstone interface.
To Reproduce
Install opennebula <IP_ADDRESS> with sunstone, node and sqlite3 backend on ubuntu 18.04.
Login example.org:9869 as oneadmin.
Create user with with public authentication.
oneadmin logout.
Login with newly created useraccount and given password.
"Invalid username or password"
Expected behavior
User should get authenticated. No error message.
Details

Affected Component: Sunstone
Hypervisor: n. a.
Version: <IP_ADDRESS>

Additional context
user is sometime created with clear text password, sometimes with hash, as seen in the sqlite3 db and oneuser show.
Ansible task:
- name: Distribution
  debug:
    msg: "{{ ansible_distribution }}"

- name: Distribution version
  debug:
    msg: "{{ ansible_distribution_version}}"

- name: Distribution major version
  debug:
    msg: "{{ ansible_distribution_major_version }}"

- name: Install Dependencies - Add Ubuntu standard repos
  shell: |
    add-apt-repository main
    add-apt-repository restricted
    add-apt-repository universe
    add-apt-repository multiverse

- name: Install Opennebula - Add repo key
  apt_key:
    url: "https://downloads.opennebula.org/repo/repo.key"
    state: present

- name: Install Opennebula - Add repo
  apt_repository:
    repo: "deb https://downloads.opennebula.io/repo/{{ one_version }}/{{ ansible_distribution }}/{{ ansible_distribution_version}} stable opennebula"
    state: present
    update_cache: yes

- name: Install Opennebula - Install packages
  package:
    name:
      - opennebula
      - opennebula-sunstone
      - opennebula-gate
      - opennebula-flow
    state: latest

Progress Status

[ ] Branch created
[ ] Code committed to development branch
[ ] Testing - QA
[ ] Documentation
[ ] Release notes - resolved issues, compatibility, known issues
[ ] Code committed to upstream release/hotfix branches
[ ] Documentation committed to upstream release/hotfix branches

can you send us your oned.log?

closing until further feedback


discovered pobably missing use of already set styles in Widgets\Table

Laravel Version: 5.7.22
PHP Version: 7.2
Laravel-admin: 1.6.9

Description:
when using the Table widget and use
$table->setStyle([]);
these styles are never applied
Steps To Reproduce:
just use the table widget and use setStyle()
used to fix:
public function render()
    {

        $this->attributes = array_merge(
            $this->getAttributes(),
            [
                'class' => implode(' ', $this->style)
            ]
        );

        $vars = [
            'headers'    => $this->headers,
            'rows'       => $this->rows,
            'attributes' => $this->formatAttributes(),
        ];

        return view($this->view, $vars)->render();
    }

seems that usage is different than expected - closing


(Practically) duplicate row in virus.csv

Was there an issue with the most recent data update?  It looks like row 64 and 63 in virus.csv are 82% identical.  As a comparison, rows 63 and 62 are only 15% identical.
Love this dashboard!

Actually, I think what I'm noticing is a duplicate of : https://github.com/jakobzhao/virus/issues/46, just from the data as opposed to from the image.

the csv file is keeping update. The raw data is stored in the database


/tp command is not currently working

When I run the /tp command without any arguments, I get the following:
[23:05:20] [Server thread/INFO] [essence]: dualspiral ran the command: /tp
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]: java.util.NoSuchElementException: No value present
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at java.util.Optional.get(Unknown Source)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at io.github.essencepowered.essence.commands.teleport.TeleportCommand.executeCommand(TeleportCommand.java:115)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at io.github.essencepowered.essence.internal.CommandBase.startExecute(CommandBase.java:317)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at io.github.essencepowered.essence.internal.CommandBase.execute(CommandBase.java:310)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at org.spongepowered.api.command.spec.CommandSpec.process(CommandSpec.java:332)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at org.spongepowered.api.command.dispatcher.SimpleDispatcher.process(SimpleDispatcher.java:331)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at org.spongepowered.common.command.SpongeCommandManager.process(SpongeCommandManager.java:252)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.command.ServerCommandManager.func_71556_a(SourceFile:83)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.network.NetHandlerPlayServer.func_147361_d(NetHandlerPlayServer.java:815)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.network.NetHandlerPlayServer.func_147354_a(NetHandlerPlayServer.java:794)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.network.play.client.C01PacketChatMessage.func_148833_a(SourceFile:37)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.network.play.client.C01PacketChatMessage.func_148833_a(SourceFile:9)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at org.spongepowered.common.network.PacketUtil.onProcessPacket(PacketUtil.java:106)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.network.PacketThreadUtil$1.redirect$onProcessPacket$0(SourceFile:51)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.network.PacketThreadUtil$1.run(SourceFile:13)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at java.util.concurrent.FutureTask.run(Unknown Source)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.util.Util.func_181617_a(SourceFile:44)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:660)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:344)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:605)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:481)
[23:05:21] [Server thread/INFO] [STDERR]: [io.github.essencepowered.essence.internal.CommandBase:startExecute:333]:     at java.lang.Thread.run(Unknown Source)

If I add arguments, it tells me there are too many. So, I'm thinking there is something wrong with the argument parsing, possibly the way I've used "firstParsing". I want /tp [-f] <player> to work with no extra permission check, whilst /tp [-f] <playerFrom> <player> should work only with the "others" permission. The NoCost and NoWarmup arguments can be removed for now if they make things harder to debug.

I have tested it and the issue appears to be with TwoPlayersArgument.

I removed that argument for two players, and it seems to still be broken for me...

OK, spotted the problem, but it's more due to the intracacies of Sponge.
The important line to consider is in Sponge - when we use GenericArguments.requiringPermission(...), if the permission check succeeds, we get to the following line:
https://github.com/SpongePowered/SpongeAPI/blob/master/src/main/java/org/spongepowered/api/command/args/GenericArguments.java#L1242
...that is, the generic parse method. This then calls parseValue...
https://github.com/SpongePowered/SpongeAPI/blob/master/src/main/java/org/spongepowered/api/command/args/GenericArguments.java#L1222
(which does a second, redundant, permission check unless you are checking for a second permission) and then calls parseValue on the child, NOT parse.
However, parseValue in my TwoPlayer argument and in GenericArguments.seq is null. Therefore, the command thinks it has succeeded, but it actually hasn't.
Honestly, I think this is actually a Sponge "bug", I think that the first highlighted line should call this.element.parse() which should hand off the full control to the enclosed argument. This might be a breaking change though - best to check with a Sponge dev. Any thoughts on who to ping?
I should be able to work around this for now.

If it is indeed a Sponge issue, you'll need to talk to zml. You can open an issue over on SpongeCommon.

It's a SpongeAPI issue, that's where the code is!
https://github.com/SpongePowered/SpongeAPI/issues/1123


handle potential travis service interruption

GitHub services are deprecated, and are being retired on January 31. This includes the Travis CI service that currently delivers test run information on PRs etc.
Travis is working on migrating to webhooks (https://changelog.travis-ci.com/migrating-from-github-services-to-webhooks-86328), which hopefully fixes this work without any interruptions. We'll keep an eye on the situation and file any needed work.
cc @cdata

Looks like Travis was able to migrate most people, and our builds are still working so I'll assume we're OK for now.
https://blog.travis-ci.com/2019-01-31-github-services-integration-deprecation


[admin] merge to live

Docs Build status updates of commit e4950a2:
:warning: Validation status: warnings

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outlook/Concepts/Creating-Form-Regions/add-a-form-region-to-an-existing-page-on-a-form.md
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This comment lists only the first 50 files in the pull request.

outlook/Concepts/Creating-Form-Regions/add-a-form-region-to-an-existing-page-on-a-form.md

Line 125, Column 1: [Warning-code-block-indented] Indented code blocks aren't allowed. Use a Markdown code block surrounded by triple backticks (```).

api/Access.Attachment.md

Line 80, Column 2: [Suggestion-column-header-missing] Column headers are required for tables. Add appropriate header text, or remove any extra table cells that cause an extra column.

api/Project.Application.TextStyles32Ex.md

Line 44, Column 2: [Suggestion-column-header-missing] Column headers are required for tables. Add appropriate header text, or remove any extra table cells that cause an extra column.
Line 59, Column 2: [Suggestion-column-header-missing] Column headers are required for tables. Add appropriate header text, or remove any extra table cells that cause an extra column.
Line 72, Column 2: [Suggestion-column-header-missing] Column headers are required for tables. Add appropriate header text, or remove any extra table cells that cause an extra column.
Line 84, Column 2: [Suggestion-column-header-missing] Column headers are required for tables. Add appropriate header text, or remove any extra table cells that cause an extra column.
Line 94, Column 2: [Suggestion-column-header-missing] Column headers are required for tables. Add appropriate header text, or remove any extra table cells that cause an extra column.

excel/Concepts/about-the-powerpivot-model-object-in-excel.md

Line 429, Column 4: [Suggestion-docs-link-absolute] Absolute link 'https://docs.microsoft.com/previous-versions/sql/sql-server-2012/gg413497(v=sql.110)' will be broken in isolated environments. Replace with a relative link.

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Support dark & light modes for accessibility

Discussed in https://github.com/neatnik/omg.lol/discussions/257

Originally posted by identithree October 16, 2022
There should be a light theme for the official omg.lol pages (homepage, dashboard, info center, etc.) to help out with accessibility. A friend of mine as trouble looking at the site for a while because of their astigmatism.

First pass of this is complete, with some refinement needed.

Closing this since we do technically have a functioning light/dark theme at this point. Will be working on https://lol.design and improving upon all of the accessibility issues that exist currently (contrast in particular).


{AKS} Update v2 managed cluster decorator - part 2

This checklist is used to make sure that common guidelines for a pull request are followed.

For new extensions:

[ ] My extension description/summary conforms to the Extension Summary Guidelines.

About Extension Publish
There is a pipeline to automatically build, upload and publish extension wheels.
Once your pull request is merged into main branch, a new pull request will be created to update src/index.json automatically.
The precondition is to put your code inside this repository and upgrade the version in the pull request but do not modify src/index.json.

AKS


Exposing Bluebird reference - Objections for pull request?

I'm trying to use this library in an Electron app with node.js integration disabled in the BrowserWindow context, in combination with Angular 1.x. In order to have Angular properly respond to promises coming from the node.js from within Electron itself, I have to call Bluebird.setScheduler in order to notify Angular about changes.
After trying lots of things, I eventually settled on modifying the rp.js-file from this library to include the following:
request.promise = function RP$promise() {
    return Bluebird;
}

I can then do something like this (where schedulerCallback comes from within the BrowserWindow context):
return rp.promise().setScheduler(schedulerCallback);

It's either this, or manually wrapping everything that goes into a promise inside a $scope.apply from Angular, which is simply annoying and code clutter.
I was wondering if there are any objections to adding these 3 lines to this project? If not, I'll happily make a pull request for it. Otherwise I'm curious to what another possible way to get the same thing done would be?

Since request-promise creates its own bluebird prototype and doesn’t expose it we would need to extend request-promise to allow your use case. The only other choices are that you build your own request-promise clone on top of request-promise-core or you use request-promise-any which allows you to inject your own bluebird prototype.
What is the current status of your project? Are you still looking for this solution?


[ximalaya] Fix and rework extractor due to the site and file format changed

… changed
Please follow the guide below

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Put an x into all the boxes [ ] relevant to your pull request (like that [x])
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Before submitting a pull request make sure you have:

[x] At least skimmed through adding new extractor tutorial and youtube-dl coding conventions sections
[x] Searched the bugtracker for similar pull requests
[x] Checked the code with flake8

In order to be accepted and merged into youtube-dl each piece of code must be in public domain or released under Unlicense. Check one of the following options:

[x] I am the original author of this code and I am willing to release it under Unlicense
[ ] I am not the original author of this code but it is in public domain or released under Unlicense (provide reliable evidence)

What is the purpose of your pull request?

[x] Bug fix
[x] Improvement
[ ] New extractor
[ ] New feature

Description of your pull request and other information
Explanation of your pull request in arbitrary form goes here. Please make sure the description explains the purpose and effect of your pull request and is worded well enough to be understood. Provide as much context and examples as possible.
Fix and rework the ximalaya extractor because during time www.ximalaya.com changed the page and method of the extractor.

Hey @svista, I've tested your branch with the following URL:
http://m.ximalaya.com/104781788/album/14518803
and it didn't work:
python2 ./__main__.py 'http://m.ximalaya.com/104781788/album/14518803'
[ximalaya:album_mobile] 14518803: Download album page for 14518803
[download] Downloading playlist: 60本金牌儿童故事乐园音频
[ximalaya:album_mobile] 14518803: Downloading JSON metadata
[ximalaya:album_mobile] playlist 60本金牌儿童故事乐园音频: Downloading 60 videos
[download] Downloading video 1 of 60
[ximalaya] 79080493: Downloading info json http://m.ximalaya.com/tracks/79080493.json
Traceback (most recent call last):
  File "./__main__.py", line 19, in <module>
    youtube_dl.main()
  File "/tmp/youtube-dl/youtube_dl/__init__.py", line 472, in main
    _real_main(argv)
  File "/tmp/youtube-dl/youtube_dl/__init__.py", line 462, in _real_main
    retcode = ydl.download(all_urls)
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 2002, in download
    url, force_generic_extractor=self.params.get('force_generic_extractor', False))
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 804, in extract_info
    return self.process_ie_result(ie_result, download, extra_info)
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 1003, in process_ie_result
    extra_info=extra)
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 865, in process_ie_result
    extra_info=extra_info)
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 804, in extract_info
    return self.process_ie_result(ie_result, download, extra_info)
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 858, in process_ie_result
    return self.process_video_result(ie_result, download=download)
  File "/tmp/youtube-dl/youtube_dl/YoutubeDL.py", line 1452, in process_video_result
    t['url'] = sanitize_url(t['url'])
  File "/tmp/youtube-dl/youtube_dl/utils.py", line 545, in sanitize_url
    if url.startswith('//'):
AttributeError: 'NoneType' object has no attribute 'startswith'


No extends not working with Sass Syntax

No Extends rule is currently not working with Sass syntax. The current method to check for nodes with the Extend type returns blank when using the Sass syntax.

Good catch, get #175 updated tomorrow and I'll merge it in.


MLX Evaluation / Roadmap?

My understanding is that MLX was invented to take advantage of the unified cpu-gpu architecture of the Apple Silicon chips in ways that PyTorch et al / MTS didn't (notably avoiding copying).  It is also open source, and so stands apart from the MacOS AI Frameworks.
A good deal of the focus seems to be on providing the infrastructure for building / training new AI models although it is perfectly possible to run them, as mlx-examples shows, although presumably that doesn't use quite as much of the mlx infrastructure as building and training.
Just as we are on the eve of the launch of a new MacOS, can I ask what are the evaluation plans for the MLX approach?  It can certainly perform faster than PyTorch on some tasks?  And llama.cpp?
If the benchmarks can show speed and memory (model size) benefits, there are costs in having to convert / adapt hugging face models, which might have more impact on some workflows.
Anyway, now the library is maturing, what are the plans for evaluating it and, perhaps and, perhaps, putting together a bit more of a roadmap based on the evaluation?

I generally agree. A clear roadmap would make people have more confidence in MLX and port/develop their projects.

Lot of models type cannot be validated due to missing or in development of equivalent functions (like scatter for Graphs), Should we also need to include list of missing equivalent functions in the roadmap to avoid devs to lose time for searching if what they need is already there ?

Can I ask what are the evaluation plans for the MLX approach? It can certainly perform faster than PyTorch on some tasks? And llama.cpp?

For the most part we don't intend to publish direct benchmarks comparing different frameworks. We'll provide examples and MLX benchmarks that you can run. But will look to more independent sources to benchmark e.g. MLX vs Llama.cpp or PyTorch. So you can certainly measure tokens-per-second using MLX LM for many different models, or image generation time with say FLUX + DiffusionKit, or Transformer training time with our example and then compare those to other frameworks as you like. We welcome the benchmarks if you publish them here or elsewhere.

Putting together a bit more of a roadmap

Not opposed to putting together a roadmap as a public artifact. But in the meantime if you have specific questions about whether or not we intend to work on something you can always ask in GH discussion.

Should we also need to include list of missing equivalent functions in the roadmap to avoid devs to lose time for searching if what they need is already there ?

@thegodone Please file an issue for any missing functions that you encounter. That would be super useful! For most common functions (e.g. ones you find in NumPy or the Python Array API, we intend to add them. In some cases we don't but the issue is still useful to discuss why and/or if we should reconsider. GH issues is the best place  for us to track missing features.

Thanks. The ad hoc approach to evaluation is fine, but does not really help me understand the tradeoffs between the potentially better speed / size performance versus cost of needing to use a similar but different interface, the need to convert models and the smaller ecosystem, etc.  I'd have thought that some more systematic evaluation might also help to guide the focus of future effort.  But it's good to understand your stance. Thanks again.


it's Me SaSuki

hey brudda i lost your telegram after i format my pc, send me your telegram, @SaSukiG

@IUserCast


Question pertaining to Level 5 of Task 1

Summary
Within the main.jsh file, it contains functions that directly call upon the Point and Circle classes' variables. Are we allowed to delete these functions?
Under Level 5 of the requirements, we were told to modify the method findMaxDiscCoverage, in this case, does the modification r meant ensure the conformity of the function to encapsulation and Tell-Don't-Ask principles?

Hi, I haven't tried the codecrunch autograder yet, but I believe that other than maxDiscCoverage, the rest are helper functions that you can remove, but using them would be extremely helpful for making your code more "human-readable". Our emphasis on design in CS2030 is also to ensure that you all write code that other developers (or your future self) can read and understand what is going on.
For maxDiscCoverage, you can try testing the original maxDiscCoverage with your Point and Circle class from task 1 - 4. I believe that it will not compile or run properly and your task is to fix maxDiscCoverage so it does work with your Point and Circle class.
Lastly, please don't post your solution to maxDiscCoverage or any part of the labs here on github. I have removed your code snippet above.

This issue is stale because it has been open for 30 days with no activity.

Hi, to add on to this, the test cases seem to suggest us to outsource the distanceBetween() and circleContainsPoint() methods to the Point and Circle classes respectively. CodeCrunch tests for a contains() method in Circle which is not specifically required in any of the levels. I think it might be better to move the methods out of main.jsh.


Cant Connect to MQTT home server

Using the code in the repository, I cant connect to my RPI hosted MQTT server. I just get the flashing blue LED and
mqtt_topic: 50:02:91:A0:6C:09
.Connectingreconnect mqtt
.Connecting....reconnect mqtt

did you have tried to use any MQTT client tools to test with your RPI server?  and it works, right?

Yes, every other device connects to the server and retrieves data

Ok different error here now
`ets Jun  8 2016 00:22:57
rst:0xc (SW_CPU_RESET),boot:0x13 (SPI_FAST_FLASH_BOOT)
configsip: 188777542, SPIWP:0xee
clk_drv:0x00,q_drv:0x00,d_drv:0x00,cs0_drv:0x00,hd_drv:0x00,wp_drv:0x00
mode:DIO, clock div:1
load:0x3fff0030,len:1184
load:0x40078000,len:13220
ho 0 tail 12 room 4
load:0x40080400,len:3028
entry 0x400805e4
M5Atom initializing...OK
HTTP server started`

Different message:
Get WIFI INFO From Preference
......WiFi Connected!
Get MQTT INFO From Preference
<IP_ADDRESS>
mqtt.m5stack.com
ConnectingMQTT Connected!
 success
subscribe: 50:02:91:A0:6C:09

Where is it calling mqtt.m5stack.com I cant find a reference to it anywhere?

in this line use the MQTT server config.
https://github.com/m5stack/ATOM-PRINTER/blob/master/examples/PRINTER_FW/PRINTER_FW.ino#L125

also.  we just update the example and fix some issues. you could test it again, thanks


Missing of vggsound_train_new.tsv and vggsound_test_new.tsv files

Thanks for sharing the helpful codebase.
When I downloaded the vggsound.zip and extracted it, I found there were no such two files for training and testing. Can you provide the two scripts or other useful resources for reproducing results on VGGSound?
Looking forward to your reply.

Hi, there should be two files in vggsound.zip: vggsound_train.tsv and vggsound_test.tsv. You can use these two files. The file name in the training script is incorrect, and we have just updated it.

Thank you for your reply. I have got it. Thanks again


[GHSA-pvc3-wvxr-7cmf] It was found that the smallrye health metrics UI...

Updates

Affected products
References
Source code location
Summary

Comments
There's not a ton of data on this one. I'm mostly working from the patch I tracked down and added to the references
We can see the fixed versions, looks like 3.2.1 and 3.3.1 picked this up
➜  smallrye-health git:(main) git branch --contains 01b25a038824887363cd413d8cd14052f5fc3541 | cat
dependabot/maven/io.smallrye.config-smallrye-config-3.4.4
jakarta

main
release-3.2.1
release-3.3.1
release-4.0.0
release-4.0.0-RC1
release-4.0.0-RC2
release-4.0.1
release-4.0.2
release-4.0.3
release-4.0.4

Hi @joshbressers, thanks for sharing your findings about GHSA-pvc3-wvxr-7cmf with us! This is interesting information to have. I agree that the purpose of the fix commit (health ui: validate input) is consistent with fixing the problem named in the description of GHSA-pvc3-wvxr-7cmf.
I'm surprised by the finding that the first version that contains the fix commit is 3.2.1. I see in the commit history of 3.2.0 and the commit history of 3.1.2 that the commit health ui: validate input is present in 3.2.0 and 3.1.2. The fix commit has s different hash in version 3.1.2 - 47a33f19f5bb1e4216a15f3aee6ca3b1e2ccba59 - what happens when you search for that hash?


localization .json file has wrong JSON schema URL

localization .json file has wrong JSON schema URL
It seems it should be MicrosoftTeams.Localization instead of MicrosoftTeams
Example localization .json file
{
  "$shema": "https://developer.microsoft.com/json-schemas/teams/v1.7/MicrosoftTeams.Localization.schema.json",
   ...
}

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

ID: 3f55e52a-5fc4-7fcb-0e1e-946bff5aaee4
Version Independent ID: b6c559fb-8512-575b-4fed-ebe1457e890e
Content: Localization for Team apps - Teams
Content Source: msteams-platform/concepts/build-and-test/apps-localization.md
Product: msteams
GitHub Login: @laujan
Microsoft Alias: lajanuar

@follower90 , Thank you for pointing it out. We will update the document.

Thanks for fixing documentation!
I am closing the issue


Add additional signposting, especially on mobile

Perhaps add some interstitial screens

The left navigation solves a lot of this problem. May wait for the UX audit to decide if this is actionable.


Items in Buffer ignored while requesting

Hey again!  I noticed that when I have items on arrival, I also have the same items in my buffer that can immediately be used, if I  select "Add to Inventory".
Shouldn't the plugin pull from the Buffered items first instead of requesting more from remote?  I end up with thousands of duplicate items otherwise.
Example with solar panels:

That makes more sense.  I kept spamming Return to Logistics thinking I was helping clear my buffer for new arrivals XD

Wow, this turned out to be a great bug report. I didn't realize it, but anything over 1k requested items were being generated out of thin air (oops). I didn't really notice it because I don't typically do that, but the plan all along was to have lower throughput than actual logistics stations (they can get up to 10x vessel capacity incoming at a time). The idea being that if you want to get a lot of items quickly, it's best to have them available on the local planet to draw from.
So, the fix I'm going with for now is to just hide any items that are in the buffer but that still have incoming requests. Before I landed on that, I tried to do something where buffered items were "locked" but it got to be too much to manage.
At any rate, I created a preview release here if you want to test it out. r2modman has an "Import local mod" option under Settings. Don't worry if you don't have time, I'm planning to release it later tonight after I've the nextrelease branch a last review


Error processing new user addition| Key type definition error

I have a sr25519 account
While trying to add it this account on a v0 dapp get this:

Guess the WRONG SEED PHRASE error also originates from the type mismatch, still, looks wierd
Meanwhile on the new dapp I get this:

THe account is for sure in RWS. Is this a false error description for a key type as well?

Based on ussie #118 this ussie should be converted to the problem:
DApp doesn't check or doesn't show that the user type account must be ED25519.

This issue occurred because "rws setup" was not previously added to the https://dapp.robonomics.network/#/rws-setups-list list.
For such a situation, a field for entering the address of the controller has been added.
Please check if it works now?


Fails in code workflows

Fails are in workflow because function is long, probably it'll need some refactor for "easy win", or it'd have to wait for full script refactor.
Sample:
```
long function rate 0.07692307692307693 is higher than maximum 0.0001
```

Even with moving helpers outside of function (no nesting) I get error with HIGHER points
```
INFO:code-inspector:long function rate 0.08333333333333333 is higher than maximum 0.0001
```
So it looks like the "file" is treated as a function. So there is a need to edit the workflow to work with that. I understand and agree that files should not be large, but this one is not that large. So I'll move workflow to the 0.1 threshold.