fix: social links use inline svg

currently supported:

GitHub
GitLab
Twitter

icons key off name
see https://github.com/daKmoR/rocket/pull/23/files#diff-c6b1e7591049df1b35a8e60808d254c9R33

nice 👌


Error message appears when clicking into the IOU thread of send money

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Version Number:
Reproducible in staging?: needs reproduction
Reproducible in production?: Needs reproduction
If this was caught during regression testing, add the test name, ID and link from TestRail:
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Expensify/Expensify Issue URL:
Issue reported by: @davidcardoza
Slack conversation: https://expensify.slack.com/archives/C049HHMV9SM/p1713482155608439
Action Performed:

Send money > input amount > email > pay with Expensify
Tap into IOU thread
Click back in the browser
Tap into IOU thread again

Expected Result:
The thread should should show the IOU details
Actual Result:
Consistently errors out
Workaround:
Can the user still use Expensify without this being fixed? Have you informed them of the workaround?
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android: Native
[ ] Android: mWeb Chrome
[ ] iOS: Native
[ ] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[ ] MacOS: Desktop

Screenshots/Videos
Add any screenshot/video evidence
https://github.com/Expensify/App/assets/38435837/0b80335e-c75f-4d6e-8eed-8c6e928c1b2f
https://github.com/Expensify/App/assets/38435837/50c21a00-bedc-4211-9c4c-dbcf6736a3a8

View all open jobs on GitHub

This has been labelled "Needs Reproduction". Follow the steps here: https://stackoverflowteams.com/c/expensify/questions/16989

@m-natarajan  Please ensure to open console / network tab about to understand apis/app bugs....
I added screenshots

This has been labelled "Needs Reproduction". Follow the steps here: https://stackoverflowteams.com/c/expensify/questions/16989

@MelvinBot Could you send me Slack/stackoverflow invite at<EMAIL_ADDRESS>

@saifelance - the StackOverflow is internal, it's just a process for Expensify employees to request retesting.
@m-natarajan is not reporting the bug, they merely triage bugs reported in Slack to filter out duplicates and format them nicely for my triage. I will test this tomorrow, with all of the console logging available.

Send money > input amount > email > pay with Expensify

Damn, I literally can't replicate this because I don't have a wallet or that option.

Unable to repro.  @davidcardoza can you try again on staging.new.expensify.com? Send money is now. "Pay Someone" so I'm wondering if that might be playing a part.
https://github.com/Expensify/App/assets/22508304/7aa352d7-0d34-49f4-8aa6-893047a24e74

@davidcardoza , can you see if you can repro? Thx

Yep, I can still reproduce it...
https://github.com/Expensify/App/assets/6643649/e4231e1a-fc1e-48ad-a8df-09b6debad263

@saifelance , please check CONTRIBUTING.md for details about how to join.
Going to throw retest on this to see if QA is able to reproduce.  If not, I'll open it up next week to see if others can repro

Waiting for retest

Still waiting for retest.

Issue not reproducible during KI retests. (First week)
https://github.com/Expensify/App/assets/43995119/bbebfd99-0595-40ba-ae46-6d8e667176d3

Issue not reproducible during KI retests. (Second week)

Bumped to weekly, increased price to $250 to see if we can get repro steps.

Issue not reproducible during KI retests. (First week)

@davidcardoza , the error appears once you click on the receipt graphic, right?  I tried to repro with two different accounts and, when i click on the receipt image, nothing happens.

Issue not reproducible during KI retests. (Fourth week)

Leaving this open and at $250 to document reproducible steps.

I am getting an unexpected error now when I test on staging
https://github.com/Expensify/App/assets/6643649/2fe4ae2b-414a-4e2e-a596-86ed9ab0621e

Issue not reproducible during KI retests. (Fifth week)

@davidcardoza can you see if you can open your chat with<EMAIL_ADDRESS> If so,

Please send a screenshot of what you see
Can you try to send money once you have the chat open and see if it works?

I ran into a couple issues while trying to test, trying to suss out if my bugs are related to yours, or not.

My chat with<EMAIL_ADDRESS>doesn't load. I've tried refreshing several times.

@mallenexpensify Anything else I can provide?

I tried with a new gmail address and didn't run into any issues. My hunch is this is because it's your expensify.com account (and/or an email you used for testing previously where something broke and now there are issues).
I think it's best to close this unless you can reproduce with a non-expensify.com email.

Sounds good.


Players can use /sethome and /tpahere while in spectator mode

Would there be any way to add a player to a different perms group or some other way to block commands like /sethome and /tpahere which effectively bypasses the  'teleporting back' feature.

This has now been added in the latest version of 1.3.10. Thanks for the idea!


[Event Request] - OnBeforeValidateBaseExcludedAmount in Table 12137 "Purch. Withh. Contribution"

Hello, please consider adding the following event to Table 12137 "Purch. Withh. Contribution"
    [IntegrationEvent(false, false)]
    local procedure OnBeforeValidateBaseExcludedAmount(var PurchWithhContr: Record "Purch. Withh. Contribution"; var xPurchWithhContr: Record "Purch. Withh. Contribution"; var IsHandled: Boolean)
    begin
    end;

and call it accordingly inside "OnValidate" trigger of field 6 "Base - Excluded Amount":
            trigger OnValidate()
            var
                **IsHandled: Boolean;**
            begin
                **OnBeforeValidateBaseExcludedAmount(Rec, xRec, isHandled);
                if not IsHandled then begin**

                    if "Base - Excluded Amount" > ("Total Amount" - "Non Taxable Amount By Treaty") then
                        Error(InvalidBaseExcludedAmountErr, "Total Amount" - "Non Taxable Amount By Treaty");
                    if "Base - Excluded Amount" > "Total Amount" then
                        Error(BaseExcludedAmtGreaterThanTotalErr);

                **end;**

                GetHeader;

                ValorizzaRitenute;
...
...

Thank you!

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. Please do not reply to this, as we do not monitor closed issues. If you have follow-up questions or requests, please create a new issue where you reference this one.
Build ID: 49479.


Rename authHost setting in order to fix ambiguity

Problem/Motivation
I noticed that many people (e.g this case) including myself had issues with Laravel Echo Server configuration caused by some ambiguity of the "authHost" setting name.
It is not clear that we should set the absolute url of our Laravel app in the "authHost" setting, especially if the "host" requires us a hostname.
Proposed Resolution
Fix this ambiguity by renaming "authHost" to something like "authAppUrl" to refer to the app.url Laravel setting. You may come up with a better name.

I agree it's confusing, changed the default values in init to indicate that here,; https://github.com/tlaverdure/laravel-echo-server/pull/110
We could also verify the options on boot and give proper messages.

Thanks @barryvdh. I think it's a step in the right direction.

I'm also not sure, should authHost usually fall back to host? Do we even need the host at all? In most examples it's just omitted, it just listens for local connections; http://socket.io/get-started/chat/

https://nodejs.org/api/http.html#http_server_listen_port_hostname_backlog_callback

Begin accepting connections on the specified port and hostname. If the hostname is omitted, the server will accept connections on any IPv6 address (::) when IPv6 is available, or any IPv4 address (<IP_ADDRESS>) otherwise.

Isn't that what you would usually want?

Do we even need the host at all?

I believe we do. The Laravel Echo Server host should be accessible from the outside and it should not be localhost, especially when the polling transport is used. I guess it can be the server IP address but a browser, as an external client, should be able to communicate with it from the outside. Please correct me if I'm wrong here.

https://nodejs.org/api/http.html#http_server_listen_port_hostname_backlog_callback
Isn't that what you would usually want?

When an application grew to a point when it needs to be scaleled, we would want to separate Laravel Echo Server from the Laravel application, in other words move it to another VPS, for example. Thus, such default wouldn't probably work.

Yeah but it says any IPv4 address (<IP_ADDRESS>) otherwise, so it will still be available for all..
If I set my host option to null, it will still listen connections from outside.

But I do agree that that might not be the issue here, but it adds to confusion adding 2 'hosts', which can be different en have a different format.
perhaps appUrl? In reference to the APP_URL value?

Yeah but it says any IPv4 address (<IP_ADDRESS>) otherwise, so it will still be available for all..
Interesting. If it works this way, I would remove host option completely or make it optional (only for cases where the network structure is complex).

perhaps appUrl? In reference to the APP_URL value?
Yes. Some more ideas:
laravelAppUrl
authAppUrl (to correspond with authEndpoint)
Or even better - include authHost into authEndpoint, so that it would be http://example.com/broadcasting/auth
and then remove authEndpoint. It depends on how the authHost is used inside (I didn't check it out).

This is the only actual place it's used: https://github.com/tlaverdure/laravel-echo-server/blob/6d83f1817749082b3514bf17c0d4ab4ca3194aec/src/channels/private-channel.ts#L29
So you don't need to extract it.
But broadcasting/auth is probably always the url, so might not be really needed to always configure that.

It's great news. We don't need authHost and we can get server IP address on the fly (or use <IP_ADDRESS>) and concatenate it with "broadcasting/auth" ourselves in the echo server code, so that the authEndpoint becomes a totally optional setting, which is a great usability improvement. More like convention over configuration.

Huh, you would still need the authHost option, right? Or should we just use the referrer from the application?

Huh, you would still need the authHost option, right? Or should we just use the referrer from the application?

If we can be sure that the referrer is always set properly then we can remove authHost setting and obtain it from referrer. On the other hand, we need to be prepared for a custom auth route.

So not the referrer, but the Origins header is set for cross-origin (which is usually the case).
We could also include it client-side, when we update laravel-echo

Yeah, there can be a few ways to achieve what we need. It's up to you and other commiters/maintainers. The good thing is that the Laravel Echo Server is improving. Thanks for listening to users' feedback.

You do realise that I'm also just a contributor, not a maintainer? ;)
I think @tlaverdure is the only maintainer.

@barryvdh your help has been very appreciated! I'm listening in on this issue and see where the improvements can be made. I'll check out that PR when I get a chance.

You do realise that I'm also just a contributor, not a maintainer?  Anyway, thank you for helping me.

I'm listening in on this issue and see where the improvements can be made. I'll check out that PR when I get a chance.

@tlaverdure Thanks.

@tlaverdure what do you think about this:

in laravel/echo, as window.location.origin to the data here, https://github.com/laravel/echo/blob/861ebea42121500b73300c4487d2167f4cdbd529/src/channel/socketio-channel.ts#L68

subscribe(): any {
	this.socket.emit('subscribe', {
		channel: this.name,
		auth: this.options.auth || {},
		authEndpoint: this.options.authEndpoint,
		origin: window.location.origin
	});
}

(Note that authEndpoint already exists in laravel/echo, with default '/broadcasting/auth`; https://github.com/laravel/echo/blob/b618e53d1c98fcf4cd68819a2aaf960b47350dde/src/connector/connector.ts#L14 )
We could now default our authHost + authEndpoint options to null and instead use the options from subscribe when null (but allow override).
let options = {
	url: (this.options.authHost || data.origin) + (this.options.authEndpoint || data.authEndpoint),
	form: { channel_name: data.channel },
	headers: (data.auth && data.auth.headers) ? data.auth.headers : {},
	rejectUnauthorized: false
};

This would:

Allow zero-config for auth endpoint by default
Allow client-side endpoint changes
Allow server-side override options when needed.

Wait, nevermind. You can't allow the client to set the auth directly, because then they can use their own server to validate it :P

I guess Pusher solves this by returning a signature in the authentication process, which the echo-server can validate, which seems like a good idea. But wouldn't be zero config.

I think we that we may just need to clarify when authHost should be used.
The initial intent was to allow you to set a different location for authentication if the domain where you are are running the server as in host is different than the domain used to authenticate users, as in authHost. That being said, if everything were kept as is, and we removed the prompt to set the authHost during init, I think it would clear up confusion.
Here is a good place to see where that logic is followed.
https://github.com/tlaverdure/laravel-echo-server/blob/891e006e62a3a645fe1147f7222332afb39e74e7/src/channels/private-channel.ts#L43
authHost is not necessary.

But the host is usually the local IP-address of the server, right? And authHost should be the full host, including http/https.
It might be my setup, but I can't start the server with the full address. I CAN on my local valet server, as the host just maps back to <IP_ADDRESS>.
What do you think about removing host instead, and defaulting that to null?

Besides, I think we should make sure that if we use "protocol": "https" it will also request the auth host through https by default.

So I did some more reading, pretty sure you usually want to bind on all addresses, so <IP_ADDRESS> (when host is null); http://stackoverflow.com/questions/2919068/what-host-do-i-have-to-bind-a-listening-socket-to
So just authHost is the only host you want to configure most of the time.

@barryvdh I've not been able to reply to this for a few weeks due being away.
Thank you for helping to clarify the issue I've been having for ages https://github.com/tlaverdure/laravel-echo-server/issues/33
When the echo-server binds to <IP_ADDRESS> it's a disaster! We absolutely want to bind on all addresses (<IP_ADDRESS>) but there was definitely a change from around version 0.9 --> 1.0 where the echo-server went from defaulting to <IP_ADDRESS> to <IP_ADDRESS> which caused me hours of debugging work!
Anything you do to negate the confusion/messing about is a big thumbs up from me.

I'm not sure if this is still an issue but I'm going to close.


New landing pages

Bugs noticed:

[] "Fetching data" spinner never disappears on http://staging.openprescribing.net/ccg/10Y/measures/
[] Add some intro text to alert email sample
[] Form fields not appearing on measures page
[] Check only signing up for newsletter doesn't also sign up for alerts (when testing I did get "Thanks, you're now subscribed to monthly alerts" message - pretty sure didn't get a bookmark though)
[] Write a test that includes the PPU total

Graphs for practice landing pages don't appear, e.g. http://staging.openprescribing.net/practice/Y02847/
Looks fine for CCGs

Graphs not showing on practice landing page?

Otherwise - I like!

There are discrepancies in PPU savings - this example is 09X:

versus:

Is it possible to zoom in a bit on the maps? They are so zoomed out it's difficult to see which area is highlighted - I think it was clearer when we had the big marker as in previous version. Don't get me wrong, the area maps are better overall, just harder to see when zoomed out so far. After double clicking on the map once or twice it's better.
On a related note, with the circular crop of the map, the controls aren't visible so it's not possible to zoom out again!

It would probably be useful to add a "Looking for something else?" note at the bottom of the dashboards to link to the other features such as the Analyse and Trends pages.


Issue with Multiple Attachments (First Attachment OK, Second Attachment Corrupted)

I've run into a problem when attempting to attach two files (pdf and csv) into an e-mail.  Whichever file I attach first is OK, but the next attachment is corrupted.  I've tested/confirmed both single attachments can be sent correctly; the issue only occurs when both files are attached to the same e-mail.  Here's a simplified example of my code.
        $attachment_csv = \Swift_Attachment::newInstance()
            ->setFilename('file.csv')
            ->setContentType('text/csv')
            ->setBody($this->renderView('file.csv.twig'));

        $attachment_pdf = \Swift_Attachment::newInstance()
            ->setFilename('file.pdf')
            ->setContentType('application/pdf')
            ->setBody($this->get('spraed.pdf.generator')->generatePDF($this->renderView('file.pdf.twig')));

        $message = \Swift_Message::newInstance()
            ->setSubject('Message Subject')
<EMAIL_ADDRESS><EMAIL_ADDRESS>            ->setBody($this->renderView('message.html.twig'),'text/html' )
            ->attach($attachment_pdf)
            ->attach($attachment_csv);

        $this->get('mailer')->send($message);

Documentation refers to multiple attaching files from disk, wondered I'm using the attachment instance incorrectly or whether there is an issue.
Assistance appreciated, thanks.

I don't know exactly, but in this example "fromPath()" is used?! https://github.com/suzuki/swiftmailer-samples/blob/master/src/120-message-attach.php

Thanks Voku, you are correct - to add attachments from disk you can use the fromPath method.  I tested the example and unfortunately it generates the same error.
In my case both attachments are derived from a HTML query report (one is converted to PDF) - so I would prefer not to store them to disk before attaching.
    $attachment_csv = \Swift_Attachment::fromPath(
            '/assets/report.csv',
            'text/csv'
        );

    $attachment_pdf = \Swift_Attachment::fromPath(
            '/assets/report.pdf',
            'application/pdf'
        );

    $message = \Swift_Message::newInstance()
        ->setSubject('Message Subject')
<EMAIL_ADDRESS><EMAIL_ADDRESS>        ->setBody($this->renderView('message.html.twig'),'text/html' )
        ->attach($attachment_pdf)
        ->attach($attachment_csv);

    $this->get('mailer')->send($message);

Another thing I have just noticed is that attachments are the same size and should not be.  i.e. the PDF file should be larger than the CSV.  I checked the contents and it looks like the second file is just a duplicate of the first.
So I'm guessing that the way that I'm attaching multiple files is not correct.  Maybe it's not possible with Swiftmailer as there are no examples of multiple attachments in the documentation. :-(

As a painful workaround for this I ended up sending two separate emails with single attachments.
I wonder if anyone else has been successful in sending multiple attachments?
I'm suspicious that the second attachment is a copy of the first, so maybe the second Swift_Attachment instance was not created correctly.

@dahomz I have added a test, but it didn't work as expected ... maybe you can take a look at the test, there is something still missing in the reg-ex ... :/

Test: https://github.com/voku/swiftmailer/commit/88da230db1bc161e5015798bd5de666ba411a414#diff-4927cf89a98d1b7b62691864add38c15
Result: https://travis-ci.org/voku/swiftmailer/jobs/83845356

It's a problem on Windows os.
The quick fix for that is to disable the cache before attach the files.
Swift_Preferences::getInstance()->setCacheType('null');

I have the problem, but could identify the issue. If the messages are spooled, the message will be cloned. And during cloning a new _cacheKey is generated. BUT the key is generated in another way than inside the constructor.
inside Swift_Mime_SimpleMimeEntity:__construct():
$this->_cacheKey = md5(uniqid(getmypid().mt_rand(), true));

inside Swift_Mime_SimpleMimeEntity:__clone():
$this->_cacheKey = uniqid();

which resulted for me to:
string(37) "old: 777fbc62960334c26b67eed702aa93ad"
string(18) "new: 57347b49dcdf8"

string(37) "old: 7ac80fd2f64f313dc4acc10bf087d728"
string(18) "new: 57347b49dcdf8"

string(37) "old: 92f1ae6836c5049d68d6bf56ea7f90c9"
string(18) "new: 57347b49dcdf8"

string(37) "old: 86d0cd18a8fbeec0ede400b3e9d34b74"
string(18) "new: 57347b49dcdf8"

string(37) "old: 39cad7f3564ddd34076bbb3837eead4f"
string(18) "new: 57347b49dcdf8"

string(37) "old: 316a631354da94049dcfc6f2295bfc52"
string(18) "new: 57347b49dcdf8"

As you can see the same ID is generated, so the first image or attachment will be ok and the data of all other attachments and images are linked to the first rendered one.

It has been fixed in bf40b5635c09e09eaad9c48bcb245ca4a6961401


[REEF-643] Remove APIs deprecated since 0.12 from reef-common: AllocatedEvaluator

This removes deprecated setType methods and related process factories.
JIRA:
REEF-643
Pull Request:
Closes #

I will test and merge.


Deploy successully on github pages.

Add Jekyll configuration to make this work.
This workflow pulls the repo, configured the git global configuration to avoid error in future, runs the php command and commit changes to repo.
 steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Setup Pages
        uses: actions/configure-pages@v3
      - name: Set Git user name
        run: git config --global user.name "Github Actions Bot"
      - name: Set Git user email
        run: git config --global user.email<EMAIL_ADDRESS>      - name: Generate index.html from portable.php
        run: php portable.php > index.html
      - name: Add index.html, style.css, and new markdown files to git
        run: git add -A
      - name: Commit changes
        run: git commit -m "Generated new artifacts"

This is great, thank you very much.

This is great, thank you very much.

Your welcome.


Import Function App in APIM doesn't work even for Anonymous HttpTriggered functions

[Enter feedback here]
Point 1:
Under the section "Import an Azure Function App as a new API", bullet 4 has an image "Click on the Function App section to choose from the list of available Function Apps". This image shows an arrow to the right hand to select the function. In reality, there's a 'Select' button.
Point 2:
Though I have created multiple Function Apps some with Anonymous Auth and some with Function Auth levels for HttpTrigger functions, I cannot see those functions when I click on the 'Select' button. Note, I was able to import one HttpTrigger after clicking twice on Select. But I am unable to import another function.
In the past I have been able to import functions using Open API, but since I am trying to follow the Learn article, I decided to do exactly what's given in there. But it doesn't help.

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

ID: a0b38af1-81e7-341a-d7bf-e471ea7585e5
Version Independent ID: 6d16fd43-249e-5afc-062a-2e019eade30e
Content: Import an Azure Function App as an API in API Management - Azure API Management
Content Source: articles/api-management/import-function-app-as-api.md
Service: api-management
GitHub Login: @dlepow
Microsoft Alias: danlep

@yogeshrc
Thanks for your feedback! We will investigate and update as appropriate.

@yogeshrc I am able to import Function API following the tutorial. If you face issues with the import, I suggest you create a ticket with azure support team to investigate and mitigate the issue since it might be due to a specific environment.
#point-1 we will update the doc with the new screenshot.

I created a doc work item to address this article update in an upcoming doc sprint. According to our usual process, I will now proceed to close this issue. Thanks for raising it!
#please-close


ESP32 crashes when reading bytes from file on FAT partition using fgetc (IDFGH-11052)

Answers checklist.

[X] I have read the documentation ESP-IDF Programming Guide and the issue is not addressed there.
[X] I have updated my IDF branch (master or release) to the latest version and checked that the issue is present there.
[X] I have searched the issue tracker for a similar issue and not found a similar issue.

IDF version.
5.1.1
Operating System used.
Windows
How did you build your project?
VS Code IDE
If you are using Windows, please specify command line type.
None
Development Kit.
ESP32 DEVKIT V1
Power Supply used.
USB
What is the expected behavior?
I built a FAT partition inside the ESP32 flash using the "wear-leveling" as starting point. I created a custom partition csv file as well as modified the CMakeLists.txt file to create the image. The FAT FS API can open the files, and once opened, I expected to read the files bytes using fgtc() and store the bytes in a char array (I'm reading text files) without problems.
What is the actual behavior?
When reading the files bytes using fgtc I get a crash (see debug log).
Steps to reproduce.
#include "fatfs.h"
#include "webservice.h"
#include <stdlib.h>
#include <stdio.h>
#include "esp_vfs.h"
#include "esp_vfs_fat.h"
#include "esp_system.h"
#include "nvmem/nvmem.h"
#include "string.h"

//module name
const char *fatfs_mod_name = "FAT-FS MGMT";

//root directory name
const char *base_path = "/root";

//files paths
const char home_path[] = "/root/pages/home.htm";
const char reg_path[] = "/root/pages/reg.htm";
const char cmds_path[] = "/root/pages/cmds.htm";
const char meas_path[] = "/root/pages/meas.htm";
const char log_path[] = "/root/pages/log.htm";

char *file_paths[5]={&home_path,&reg_path,&cmds_path,&meas_path,&log_path};

//Handle of the wear levelling library instance when unlocked for file writing...
//static wl_handle_t s_wl_handle = WL_INVALID_HANDLE;

FILE *home_page = NULL;
FILE *reg_page = NULL;
FILE *cmds_page = NULL;
FILE *meas_page = NULL;
FILE *log_page = NULL;

FILE *file_list[5];

char home_page_buff[MAX_FILE_SZ];
char reg_page_buff[MAX_FILE_SZ];
char cmds_page_buff[MAX_FILE_SZ];
char meas_page_buff[MAX_FILE_SZ];
char log_page_buff[MAX_FILE_SZ];

char *html_pages_list[5]={&home_page_buff,&reg_page_buff,&cmds_page_buff,&meas_page_buff,&log_page_buff};

uint32_t home_sz, reg_sz, cmds_sz, meas_sz, log_sz;
uint32_t *file_sz_list[5]={&home_sz,&reg_sz,&cmds_sz,&meas_sz,&log_sz};

void FileSystem_Init() {

    ESP_LOGI(fatfs_mod_name, "Mounting FAT filesystem");

    const esp_vfs_fat_mount_config_t mount_config = {
            .max_files = 10,
            .format_if_mount_failed = false,
            .allocation_unit_size = CONFIG_WL_SECTOR_SIZE
    };

    esp_err_t err;
    err = esp_vfs_fat_spiflash_mount_ro(base_path, FATFS_PARTITION_NAME, &mount_config);
    if (err != ESP_OK) {
        ESP_LOGE(fatfs_mod_name, "Failed to mount FATFS (%s)", esp_err_to_name(err));
        return;
    }

    //Load files contents
    int c = 0;
    uint_fast32_t i = 0;
    for(uint_fast8_t k=0; k<5; k++) {
        file_list[k] = fopen(file_paths[k],"r");

        if(file_list[k] == NULL) {
            ESP_LOGE(fatfs_mod_name, "Failed to open file %u for reading",k);
            continue;
        }

        while(c != EOF) {
            c = fgetc(file_list[k]);
            if(c != EOF) html_pages_list[k][i++] = c;
        }
        html_pages_list[k][i] = '\0';
        *file_sz_list[k] = i;
        c = 0;
        i = 0;

        fclose(file_list[k]);
    }

    esp_vfs_fat_spiflash_unmount_ro(base_path, FATFS_PARTITION_NAME);

    //Point webservice page pointers to buffers, these pointers are declared in "webservice.h"
    p_home_page_buff = home_page_buff;
    p_reg_page_buff = reg_page_buff;
    p_cmds_page_buff = cmds_page_buff;
    p_meas_page_buff = meas_page_buff;
    p_log_page_buff = log_page_buff;
}

Debug Logs.
I (622) main_task: Calling app_main()
I (647) FAT-FS MGMT: Mounting FAT filesystem
Guru Meditation Error: Core 0 panic'ed (LoadProhibited). Exception was unhandled.

Core 0 register dump:
PC : 0x4008aec9 PS : 0x00060730 A0 : 0x800830ec A1 : 0x3ffbcbd0
0x4008aec9: xQueueTakeMutexRecursive at C:/Espressif/frameworks/esp-idf/components/freertos/FreeRTOS-Kernel/queue.c:776

A2 : 0x01000000 A3 : 0xffffffff A4 : 0x3ffcaf88 A5 : 0x00000080
A6 : 0x00000000 A7 : 0x00000100 A8 : 0x8008c3fd A9 : 0x3ffbcbc0
A10 : 0x00000003 A11 : 0x00060723 A12 : 0x00060720 A13 : 0x00000000
A14 : 0x00000000 A15 : 0xb33fffff SAR : 0x00000018 EXCCAUSE: 0x0000001c
EXCVADDR: 0x01000008 LBEG : 0x4000c2e0 LEND : 0x4000c2f6 LCOUNT : 0x00000000
0x4000c2e0: memcpy in ROM

0x4000c2f6: memcpy in ROM

Backtrace: 0x4008aec6:0x3ffbcbd0 0x400830e9:0x3ffbcbf0 0x400831f1:0x3ffbcc20 0x4008327e:0x3ffbcc40 0x401585a6:0x3ffbcc70 0x401585ff:0x3ffbcca0 0x400d993f:0x3ffbccc0 0x400d8b1c:0x3ffbccf0 0x401706cf:0x3ffbcd10 0x4008cf6d:0x3ffbcd40
0x4008aec6: xQueueTakeMutexRecursive at C:/Espressif/frameworks/esp-idf/components/freertos/FreeRTOS-Kernel/queue.c:769 (discriminator 1)

0x400830e9: lock_acquire_generic at C:/Espressif/frameworks/esp-idf/components/newlib/locks.c:144

0x400831f1: _lock_acquire_recursive at C:/Espressif/frameworks/esp-idf/components/newlib/locks.c:158

0x4008327e: __retarget_lock_acquire_recursive at C:/Espressif/frameworks/esp-idf/components/newlib/locks.c:314

0x401585a6: _fgetc_r at /builds/idf/crosstool-NG/.build/HOST-x86_64-w64-mingw32/xtensa-esp32-elf/src/newlib/newlib/libc/stdio/fgetc.c:93 (discriminator 2)

0x401585ff: fgetc at /builds/idf/crosstool-NG/.build/HOST-x86_64-w64-mingw32/xtensa-esp32-elf/src/newlib/newlib/libc/stdio/fgetc.c:114

0x400d993f: FileSystem_Init at C:/Users/XXX/Documents/Repo/XXXXXXX/FW/main/nvmem/fatfs.c:122

0x400d8b1c: app_main at C:/Users/XXX/Documents/Repo/XXXXXXX/FW/main/main.cpp:21

0x401706cf: main_task at C:/Espressif/frameworks/esp-idf/components/freertos/app_startup.c:208 (discriminator 13)

0x4008cf6d: vPortTaskWrapper at C:/Espressif/frameworks/esp-idf/components/freertos/FreeRTOS-Kernel/portable/xtensa/port.c:162

More Information.
If I modify the wear-leveling example to read bytes using fgetc instead of reading lines using fgets, I also get a crash, but with a different backtrace. I suspect it has something to do with the "string.h" functions not being placed on IRAM, but I can't do it without enabling external flash in menuconfig; if I do so, I get another crash because I have no external flash.

I found the problem, it was an overflow in the buffer of the homepage, the file was larges than the char buffer. I found the backtrace a bit misleading, so it took me some time to realize this.


Parallel/Dual Dialog in Atom Plug-in Doesn't Appear to Render

Using the following example text directly from the fountain page, in both PDF generation and PDF preview, the carot char is basically ignored.
The men look at each other.

BRICK ^
Screw retirement.

I tried this several months back and it seemed to work fine.  Unfortunately, I do not recall which version of the plug-in it worked in.

@jrbostic, any thoughts on this, since I think you set up the defaults?

@superlou Definitely!  I don't see any issue with updating the project defaults other than how it behaves with local defaults that users have already set up.  I'd want to make sure that we don't wipe their changes on version updates.  I seem to remember this coming up in another thread...
We just need to ensure that there's a local config on the users machine and a package config to fallback on.  Maybe?

I would be fine closing this issue if the default configuration is set to "On" going forward.  I'll leave it up to the community, as it works fine once I change the default locally.


add_inverse_permutation

This might not be the ideal long term solution but this allows SumOfSquares to implement a quick-and-dirty ScaledPerm

Superseeded by https://github.com/kalmarek/SymbolicWedderburn.jl/pull/32


Builder pattern shows warning message.

Consider the following struct:
function foo_builder() constructor
{
    do_bar = function()
    {
        return self;
    }
}

Using the function like this shows a warning message:
var foo = new foo_builder()
    .do_bar();

Current work around is:
var foo = new foo_builder();
foo.do_bar();


"Feed Url" label overlaps input on the add feed screen

see screenshot.

it looks ok before you try putting any content in it

I sanity checked that this wasn't just a large font size issue. It's not.
The short width of the box is controlled by this css:
.setup .control-group input {
  width: 210px;
}

which, in addition to not being wide enough, is problematic in that it is defined as i fixed pixel size and thus doesn't expand with the size of a user's font setting. Should be switched to rem instead of px
the problem with the "Feed URL" text is caused by this CSS
.setup .field-label {
  display: block;
  color: #BFC9CA;
  position: absolute;
  left: 13px;
  top: 10px;
  -webkit-transition: 0.25s;
  -moz-transition: 0.25s;
  -o-transition: 0.25s;
  transition: 0.25s;
}

This is using an absolute pixel based positioning (again a problem as font sizes - and thus line height- grow).  It's interacting negatively with the input which has NO absolute positioning. The small height forces it to be over (or under) the input. if you remove the top: 10px it drops down to below the input which makes sense given the HTML that's creating these 2 elements and it looks like this.

Given the top: 10px I'm unsure if it's supposed to be above or below the input.
(tested using Firefox)

@masukomi I think the label should be moved above the field. They appear to have been designed to be inside the field, but I may have broken it with other updates. Would you be up for making a PR?

@mockdeep fixed it here: https://github.com/stringer-rss/stringer/pull/1229


Error: object has no attribute 'num_train_imgs' in version master, but not 0.6.0

I am running on Ubuntu 18, and trying to run the vq_vae.yaml config from this package:
https://github.com/AntixK/PyTorch-VAE
It runs fine under version 0.6.0 with python 3.7 but when I update to lighting-master (0.6.1)  I get this error:
AttributeError: 'VAEXperiment' object has no attribute 'num_train_imgs'
The relevant .py file is attached:
experiment.zip
Is there a change-log that would tell me what might be wrong since AntixK wrote this package for 0.6.0 and I'd like to use it with Apex, which isn't supported on 0.6.0

🐛 Bug

To Reproduce
Steps to reproduce the behavior:

Go to '...'
Run '....'
Scroll down to '....'
See error

Code sample

Expected behavior

Environment
Please copy and paste the output from our
environment collection script
(or fill out the checklist below manually).
You can get the script and run it with:
wget https://raw.githubusercontent.com/pytorch/pytorch/master/torch/utils/collect_env.py
# For security purposes, please check the contents of collect_env.py before running it.
python collect_env.py

PyTorch Version (e.g., 1.0):
OS (e.g., Linux):
How you installed PyTorch (conda, pip, source):
Build command you used (if compiling from source):
Python version:
CUDA/cuDNN version:
GPU models and configuration:
Any other relevant information:

Additional context

try running from master again?

Hrm. I get the same error with the new master. If you are curious to know
more about my base, here is my pip freeze and I'm using Python version 3.7
when this happens.
When I use python 3.6, I get this error whether I am using lightning 060 or
070.
Thanks for working so hard on Lightning.  I really like the idea.  I've
created a similar package for systematizing  psychophysics experiments and
it's been tremendously useful.  Getting the right balance of customization
vs structure is hard to do and I think you've done it very well.
On Fri, Mar 6, 2020 at 7:16 AM William Falcon<EMAIL_ADDRESS>wrote:

try running from master again?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/PyTorchLightning/pytorch-lightning/issues/1053?email_source=notifications&email_token=ABEWS5A3DO6MGSZ2AAA277DRGDSSNA5CNFSM4LCOXZQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEOBFCSI#issuecomment-595743049,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABEWS5GZCHTF6KDJURPR5A3RGDSSNANCNFSM4LCOXZQA
.

  It seems that the way antixk had
structured his base experiment file was to assume that train_dataloader
would be called prior to validation.  However in 0.7.0, maybe you don't do
this anymore?
Here's what allowed the code to run:
https://github.com/AntixK/PyTorch-VAE/issues/2#issuecomment-597175324
On Fri, Mar 6, 2020 at 11:26 AM Brad Wyble<EMAIL_ADDRESS>wrote:

Hrm. I get the same error with the new master. If you are curious to know
more about my base, here is my pip freeze and I'm using Python version 3.7
when this happens.
When I use python 3.6, I get this error whether I am using lightning 060
or 070.
Thanks for working so hard on Lightning.  I really like the idea.  I've
created a similar package for systematizing  psychophysics experiments and
it's been tremendously useful.  Getting the right balance of customization
vs structure is hard to do and I think you've done it very well.
On Fri, Mar 6, 2020 at 7:16 AM William Falcon<EMAIL_ADDRESS>wrote:

try running from master again?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/PyTorchLightning/pytorch-lightning/issues/1053?email_source=notifications&email_token=ABEWS5A3DO6MGSZ2AAA277DRGDSSNA5CNFSM4LCOXZQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEOBFCSI#issuecomment-595743049,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABEWS5GZCHTF6KDJURPR5A3RGDSSNANCNFSM4LCOXZQA
.

--
Brad Wyble
Associate Professor
Psychology Department
Penn State University
http://wyblelab.com

--
Brad Wyble
Associate Professor
Psychology Department
Penn State University
http://wyblelab.com


train for fcn by caffe-windows-cudnn

The  caffe-windows-cudnn can test the fcn8 well. But the big problem is how to train for the fcn8 model. The layer of input is datalayer, then it could not build lmdb file in the windows for many times. So, is there a codes for inputting images directly and successful training?

You can follow the comments from https://github.com/BVLC/caffe/issues/1698 and convert the data and label lmdb.

@northchert , how did you test the fcn8? in the downloaded zip file, there is only one folder (example/fcn) related to fcn. Or did you follow the instruction from the model zoo?


Added the ui parameter and removed ui_* ones

Hi, I did some changes that break backward compatibility but work with UI from Consul >v0.9.0

Does this address https://github.com/solarkennedy/puppet-consul/issues/384 ?
Or https://github.com/solarkennedy/puppet-consul/issues/246 ?

Actually I thought about #358, but these issues suit too.

Ok. I'll merge this in, but I expect some complaints :)
Can you comment on each of those issues please with the current state of the art on how to deal with the UI after I merge?


No type declarations found in package

Hi, thanks for this project.
Just wanted to point out that the type declarations seem to be missing in the npm package. (v0.5.1)
TS yields Cannot find module 'wili' or its corresponding type declarations.
when trying to import { WienerLinien } from 'wili'
The folder types/ is not present after intalling via npm.

Hopefully fixed in v0.6.0


Client Side Request Diagnostics

Currently NodeJS doesn't have client side request diagnostics. It is very important to have diagnostics for all the operations to cover the tracks of a slow request or high latency.

Attendees: @kirankumarkolli , @kushagraThapar , @sajeetharan , @JericHunter , @simorenoh
Azure Cosmos JS V4 SDK is built on azure core pipeline which are already observable as dependency by anyone like AI (Application Insights). Its practically the way other azure libraries are also instrumented and supported.
Next steps forward:

Push AI guidance forward. @sajeetharan will try a sample E2E and publish the guidance and also circle back with CX & collect feedback.
ReqeustDiagnostics (as in .NET & JAVA) SDK's will be followed-up if it's still a requirement. @sajeetharan to define/close if its a requirement further.

@kirankumarkolli @kushagraThapar  Here is the E2E sample that i built with JS and added AppInsights to generate some metrics. https://github.com/sajeetharan/cosmos-js-appInsights
I am adding some sample metrics produced for the insert and query operations :
QueryMetrics information is available in the customDimensions
query_data.csv
we don't have a sample or documentation available for this right now, I will take this as a next step to publish the same.
Whereas if we compare the Client Diagnostics generated via the JAVA SDK, it has much more useful information's in order to debug the issues. https://raw.githubusercontent.com/abinav2307/cosmosdb-java-v4-sdk-request-diagnostics/main/diagnostics-successful-request.json

@sajeetharan what's your take on request diagnostics?
WE could do similar to JAVA/.NET OR we can start with OpenTelemetry integration which mean means the same you have will done in no-code way.
Personally I would like to start with OpenTelemetry as first step and enrich it fully and then later if needed include API level like JAVA/.NET. It has a big assumption that existing CX want OpenTelemetry and suffice as first step.

@kirankumarkolli Based on the analysis of support requests related to Latency issues, having request diagnostics enabled on client is very useful to troubleshoot issues. These are actionable metrics for us but certainly not for customers.

Is this done? There is no associated PR?

This issue is only targeting the spec and documentation of Client Side request diagnostics. @jay-most is working with @ealsur on the documentation. Once the documentation is approved, then we will close this issue.
For code complete and implementation of client side request diagnostics in NodeJS, we will be tracking the work here - https://github.com/Azure/azure-sdk-for-js/issues/21177

Reopening as we need to review the documentation @kirankumarkolli  @jay-most @kushagraThapar


Enhancement: Refactor Art mappings to use the built in v12 function

In v12, there is a built in way of mapping artwork in compendiums. Investigate removing system built in and converting legacy mapping flags over to the new format. Existing mapping files appear compatible with the new build in method. Artwork mappings will then be managed in the core settings.
new module flags
"compendiumArtMappings": {
   "shadowdark": {
      "mapping": "modules/art-module/mapping-system-id.json",
      "credit": "Portrait and token artwork by Art Module."
    }
}

In v12, there is a built in way of mapping artwork in compendiums.

Interesting.  I was not aware they added that.


Fix #1438

Motivation
I'm on run
Test plan
Added test from issue

Fixes #1438

Checked on pay-server that this doesn't introduce new errors go/kgKtkfF2


Add WeightedSamplerPDB

Introduced a sampler that implements the algorithm described in Section 2.5.1 of the AlphaFold 3 supplement. In the current version, iterating on this object will return a list of strings, referencing IDs to PDB items (e.g., ['6lr1', '2v33', '3bs1', ..., '2ktf']). These can then be used to load the corresponding .cif files during training.
The __iter__() function of the sampler uses the sample() method, but since I was not entirely sure what the original paper was describing, I implemented a secondary cluster_based_sample() function to handle a slightly different approach. This method first samples a number of unique cluster_ids, and then samples one molecule from each according to the normalized in-cluster weights. However, this function is noticeably slower than the simpler sample() (avg. 19.78 ms/it vs 445.75 ms/it). This could be optimized further by calculating the in-cluster weights beforehand, but I wanted to see what everyone else thinks before making optimizations.
One other issue that should be discussed for the default sampling approach is whether we should indicate which chain is the target, in case it is part of an interface. There is a chance that a molecule will be sampled multiple times in a batch, since a pdb_id can reference both an interface, and multiple chains. This is also not really mitigated with the cluster_based_sample() approach, as we can still sample the same pdb_id (max. 2 times) from the chain and interface mappings. I could probably indicate this by appending the chain IDs to the PDB ID (e.g., 121d_A_B for an interface, 121d_A for the chain).
Finally, I already rewrote the code in the repository to use Polars instead of Pandas, and I could push those changes after I have tested them. I could also rewrite this code to implement Pandas instead to avoid having both, if it is required for other libraries you are using. Otherwise, I would suggest we make use of the improved parallelization that Polars offers for training.

@vandrw this looks good Andrei! would you like to try moving the code you have under the "is main" condition to a pytest function?

Great effort, @vandrw. Perhaps we can also rename the file to weighted_pdb_dataset.py to better describe the main class within this script?

I implemented the changes, plus pushed the changes to change from Pandas to Polars. I tried testing the changes, but the cluster IDs for interfaces fluctuate from run to run, which made it a bit hard to determine if it is a correct implementation. Can @amorehead check it out?

Hey, @vandrw. Can you clarify where you are seeing interface cluster IDs fluctuate? Are you referring to the new WeightedPDBDataset you pushed? Or is this in the cluster_pdb_dataset.py instead?

Yes, it's in the cluster_pdb_dataset.py. If I run the original code multiple times and save each interface_cluster_mapping.csv, I can observe that the maximum value for the interface_cluster_id keeps changing. Same thing with the Polars implementation.

OK. To debug, are you also clearing out the *_chain_clusters.csv files each run, which would have MMseqs2 rerun each time?

Yes. I've been deleting all *_cluster_mapping.csv files and reruning with mmseq. I will try again in a few hours, once I am back home, to debug further. But just to have a starting point, could the cluster_ids be differing because of the parallelization?

Have you been deleting the data/pdb_data/data_caches/clusterings/all_chain_sequences.json and data/pdb_data/data_caches/clusterings/interface_chain_ids.json files each run as well? If not, I suspect MMseqs2 may be assigning some chains different chain cluster IDs each run, which may then impact how many interface clusters are found by the script. Otherwise, off the top of my head, I can't think of anything in the clustering script that would be non-deterministic run-to-run (unless someone else can find something).

If it's the chain and interface extraction code that's causing this non-determinism in clustering, one solution is for everyone to use the all_chain_sequences.json and interface_chain_ids.json files uploaded to OneDrive so we don't encounter this issue repeatedly. If it's MMseqs2 that's causing the stochasticity, then we can have folks also use the chain cluster mapping CSVs uploaded to OneDrive (and just redo the interface clustering as desired).

Thanks for the suggestions! I did not delete the .json files. Looking at it a bit deeper, the *_chain files have the same number of clusters, albeit with different cluster IDs assigned to each molecule. Running the original code with Pandas resulted in 84716 interfaces the first time, and 84734 the second time. There was also a small difference in the number of nucleic acid clusters, resulting in 10147 the first time and 10146 the second time. The Polars implementation showed very similar results, so I suspect that the new code does the same thing, and the difference is due to MMseqs2. The original cluster_pdb_mmcifs.py script with Pandas took ~1m 35s to recreate all the *_cluster_mapping.csv files, while the Polars implementation took ~1m 3s. The overall speed up on my machine seems to be around 30s. It's not a big improvement, but we can skip the pandas dependency :)
What I also should double check is whether the datetime conversion works correctly in the new filter_pdb_mmcifs.py. I tried to test it out, but I couldn't easily find any examples in the PDB data that had a header containing a release_date. Do you happen to know any such entires in the dataset? If not, how would the format for the date look like (e.g., %Y-%m-%d)?
Finally, going back to the main point, I might have made a mistake with the sampler. Are the cluster_ids for ligands, proteins, nucleic acids, peptides and proteins different from each other? For example, items in cluster 0 for proteins should not be associated with items in cluster 0 for peptides. I'll correct this quickly if that is the case.

@vandrw, on this line of the filtering script, what should happen is that two versions of the same PDB complex should be loaded into memory at the same time (i.e., the assembly1 version and the asym unit version). The assembly1 versions of each PDB complex mmCIF file sadly (and for some odd reason) do not include a large portion of metadata (such as release date headers) that the corresponding asym unit mmCIF files do. In which case, we have to load both versions into memory at once and "impute" the header metadata (and a few other important pieces of information only available in the asym unit file) into the original assembly1 MmcifObject (which we ultimately want to parse the sequence and structure from for filtering and clustering).
Regarding clustering, this is a great point. It's important to note that the cluster_idsfor the protein, nucleic acid, peptide, and ligand clusters will overlap with each other by design, since they are essentiallyaranges. However, the cluster IDs within these chain_mapping` CSV files should be distinguished from one another based on which file they were loaded from. In other words, even though protein chain cluster 0 and ligand chain cluster 0 share the same index, they represent different clusters entirely (since these represent different "chains" or segments within the original PDB complex).

@vandrw, I just went through all your weighted sampling code, and it looks great! Regarding needing to distinguish cluster IDs for different molecule types, I just created a PR (that looks bigger than it actually is) to address this concern. The sampler now returns a tuple of three strings: a PDB ID, a first chain ID, and (for interfaces only) a second chain ID (left as an empty string for single chains that were sampled).

@amorehead Really sorry for the oversight, it seems that I was using the unfiltered data when loading them. I think everything is good on that front! I initially used the date_parser from dateutil to infer the format automatically, but I see now that the format is Year-Month-Day, so I will change it to dateutil.strptime(str_date, "%Y-%m-%d) to avoid surprises (i.e., inferring it as Year-Day-Month). It shouldn't matter much, as the cut-off point is mainly the year.
Also, thanks for letting me know about the cluster_ids. ~I will make another pull request with the correct cluster ID arrangement.~ It seems I was not fast enough, haha! I will look at what changes you made now :)


Multiple vispy visualisations in one notebook

Hi folks,
I was trying to get multiple visualizations in the same notebook, for example as one would do with matplotlib where one has multiple plots.
Is this expected to work? In the simple examples that I have here, it seems like creating a new vispy canvas/visualization affects the previous one too.
I've taken one of the vispy examples and just split it into two different visualizations:
from vispy import scene
from vispy.geometry.torusknot import TorusKnot

import numpy as np

canvas = scene.SceneCanvas(keys='interactive')
view = canvas.central_widget.add_view()

points1 = TorusKnot(5, 3).first_component[:-1]
points1[:, 0] -= 20.
points1[:, 2] -= 15.

points2 = points1.copy()
points2[:, 2] += 30.

l1 = scene.visuals.Tube(points1,
                        shading='flat',
                        color='red',
                        tube_points=8)

l2 = scene.visuals.Tube(points2,
                        color=['red', 'green', 'blue'],
                        shading='smooth',
                        tube_points=8)

view.add(l1)
view.add(l2)
view.camera = scene.TurntableCamera()
# tube does not expose its limits yet
view.camera.set_range((-20, 20), (-20, 20), (-20, 20))
canvas

and
newcanvas = scene.SceneCanvas(keys='interactive')
newview = newcanvas.central_widget.add_view()

points3 = points1.copy()
points3[:, 0] += 41.
points3[:, 2] += 30

points4 = points1.copy()
points4[:, 0] += 41.

points5 = points1.copy()
points5[:, 0] += 20.4
points5[:, 2] += 15

l3 = scene.visuals.Tube(points3,
                        color='green',
                        shading='flat',
                        tube_points=8,
                        closed=True)

l4 = scene.visuals.Tube(points4,
                        color='blue',
                        shading='smooth',
                        tube_points=8,
                        mode='lines')

# generate sine wave radii
radii = np.sin(2 * np.pi * 440 * np.arange(points5.shape[0]) / 44000)
radii = (radii + 1.5) / 2

l5 = scene.visuals.Tube(points5,
                        radius=radii,
                        color='white',
                        shading='smooth',
                        closed=True,
                        tube_points=8)

newview.add(l3)
newview.add(l4)
newview.add(l5)
newview.camera = scene.TurntableCamera()
# tube does not expose its limits yet
newview.camera.set_range((-20, 20), (-20, 20), (-20, 20))
newcanvas

Until i run the third cell, the second cell works fine.
Once I run the third cell, the second cell is also modified. Video attached:
https://github.com/user-attachments/assets/ade109e9-9c10-4b00-88c6-7e0d1291be72
I tried it with vispy outside of a jupyter notebook, and it does work. I get two windows with the expected outputs and they're independent of each other. Here's that script:
#!/usr/bin/env python3

from vispy import scene
from vispy.geometry.torusknot import TorusKnot

import numpy as np

canvas = scene.SceneCanvas(keys='interactive')
view = canvas.central_widget.add_view()

points1 = TorusKnot(5, 3).first_component[:-1]
points1[:, 0] -= 20.
points1[:, 2] -= 15.

points2 = points1.copy()
points2[:, 2] += 30.

l1 = scene.visuals.Tube(points1,
                        shading='flat',
                        color='red',
                        tube_points=8)

l2 = scene.visuals.Tube(points2,
                        color=['red', 'green', 'blue'],
                        shading='smooth',
                        tube_points=8)

view.add(l1)
view.add(l2)
view.camera = scene.TurntableCamera()
# tube does not expose its limits yet
view.camera.set_range((-20, 20), (-20, 20), (-20, 20))
canvas.show()

newcanvas = scene.SceneCanvas(keys='interactive')
newview = newcanvas.central_widget.add_view()

points3 = points1.copy()
points3[:, 0] += 41.
points3[:, 2] += 30

points4 = points1.copy()
points4[:, 0] += 41.

points5 = points1.copy()
points5[:, 0] += 20.4
points5[:, 2] += 15

l3 = scene.visuals.Tube(points3,
                        color='green',
                        shading='flat',
                        tube_points=8,
                        closed=True)

l4 = scene.visuals.Tube(points4,
                        color='blue',
                        shading='smooth',
                        tube_points=8,
                        mode='lines')

# generate sine wave radii
radii = np.sin(2 * np.pi * 440 * np.arange(points5.shape[0]) / 44000)
radii = (radii + 1.5) / 2

l5 = scene.visuals.Tube(points5,
                        radius=radii,
                        color='white',
                        shading='smooth',
                        closed=True,
                        tube_points=8)

newview.add(l3)
newview.add(l4)
newview.add(l5)
newview.camera = scene.TurntableCamera()
# tube does not expose its limits yet
newview.camera.set_range((-20, 20), (-20, 20), (-20, 20))
newcanvas.show()

canvas.app.run()

It's the same as the notebook, but uses canvas.show() and then has the app.run() call at the end.

CC: @lej0hn

This is supposed to work. For some reason the first canvas now takes the content of the second. Not sure whether this is related to jupyter_rfb or vispy. Will have to look into this.

Thanks @almarklein . Please do let me know if there's any more information I can provide. Also happy to help with any testing etc.


Update multivariate-testing.md

Just a missing "d", past participle.

Thanks for the correction! I'll publish it now.


When the file changes, the event is dispatched 4 times.

Version 0.2.4, windows amd64
When the file changes, the event is dispatched 4 times.
.\xnotify.exe --verbose --client <IP_ADDRESS>:8090 -i . -e "(vendor|.git)$"
output:
......
[xnotify] Watching: C:\localhost\laravel\xnotify.exe
write rsync.sh
write rsync.sh
write rsync.sh
write rsync.sh

What's writing the file? Some text editors make multiple writes when you save. You can try modifying the file via cli to see if it still happens.

Netbeans, Notepad++

I've not used those before. But have you tried writing to a file via cli? If that only trigger once then it's probably the editor that's writing multiple times.

Try  Vim:
[xnotify] Watching: C:\localhost\laravel\xnotify.exe
write rsync.sh
write rsync.sh~
write rsync.sh
write rsync.sh~
write rsync.sh
write .rsync.sh.swp

Yeah look like it's working fine since the .swp file is triggering only once. It'll be better if you can do something like echo 123 > file.txt to be sure.

Yes, 1 line:
Write file.txt

👍 There's nothing much I can do about editors triggering multiple write events. You can try using the --batch option. I'll close the issue.


warnings cause system exit unless --ignore-warnings are passed.

Description
Warnings now cause a system exit unless --ignore-warnings is passed to the CLI.
GitHub Issues

#423

Coverage decreased (-0.6%) to 77.722% when pulling 68865eb882a7a80d71cbcc4b40a85b5d59cc0296 on mcrowson:feature/ignore-warnings into 7fef0fa0c4fdf078236e542cd1835b97fa40ded8 on Miserlou:master.

Coverage decreased (-0.6%) to 77.722% when pulling 0599fde4ce0f79ce560edf3325dd0fd0d1e77efd on mcrowson:feature/ignore-warnings into 7fef0fa0c4fdf078236e542cd1835b97fa40ded8 on Miserlou:master.

@mcrowson Can you check what the situation is with the tests, please?


[YUNIKORN-178] Remove call to get config from the admission controller

hard code the scheduler name to yunikorn

Codecov Report

Merging #127 into master will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #127   +/-   ##
=======================================
  Coverage   53.13%   53.13%
=======================================
  Files          32       32
  Lines        3002     3002
=======================================
  Hits         1595     1595
  Misses       1347     1347
  Partials       60       60

Impacted Files
Coverage Δ

...missioncontrollers/webhook/admission_controller.go
27.84% <100.00%> (ø)

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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Wisdom Modal Updates

https://issues.redhat.com/browse/AAH-2220

Looks good, adding a name update as per AAP-11237,
TODO(me): test in community mode


feat(vscode-extension): add varlet documentation and  varlet playground  btns

Checklist

[ ] Fix linting errors
[x] Tests have been added / updated (or snapshots)

Change information

close #955

Codecov Report

Merging #962 (2a4be1f) into dev (c054e21) will not change coverage.
The diff coverage is n/a.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@           Coverage Diff           @@
##              dev     #962   +/-   ##
=======================================
  Coverage   91.33%   91.33%
=======================================
  Files         278      278
  Lines        5909     5909
  Branches     1332     1332
=======================================
  Hits         5397     5397
  Misses        467      467
  Partials       45       45

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disable darwin on ci cause unbox doesn't have a darwin agent

And that's why I wasn't happy about this whole monkey business, not at all


Pa refactor 2

@jepidoptera can you remind me if there are tests that are currently failing, and if so, what they are?

All tests are passing as of now


stacked bar plots wrong?

mwe_data = DataFrame(animal = rand(["cat", "mouse"], 1000), location = rand(["inside", "outside"], 1000))
draw(data(mwe_data) * frequency() * mapping(:location; color = :animal, stacked=:animal))

draw(data(mwe_data) * frequency() * mapping(:location; color = :animal, dodge=:animal))

Looks like super different distributions! am I doing something wrong?
AlgebraOfGraphics v0.4.5
CairoMakie v0.6.1

The keyword argument is stack, not stacked.

Oh! Thank you. I guess then the issue here is the Makie.jl thing of not erroring on extraneous keyword arguments, which is probably not an AoG issue.


Add support for yaml

Would be really useful to supporto also yaml files for openapi specification, other than json

added js-yaml to parse yaml file, now you can pass your yaml file as swagger input, details can refer to changelog and readme


ENH: initial contents and tests

This contains all of the types defined in the q2-feature-table and q2-diversity plugins, so is a first pass at centralizing common types.
Types were not explicitly tested in those packages, so we need to decide how we want to handle testing. The current PR contains a tests/data directory with example artifacts. I have defined two tests based on these data:

Load/save/re-load each example artifact. This ensures that those methods of the type of that artifact work as expected.
All types defined by this system must be imported by at least one of the example artifacts. This ensures that the first test is run for all types.

The downside of this approach is that our data directory is going to grow, but we're going to need some test data to test the load and save methods.

Thanks!


Evaluate performance returns non-positive ranks

Description
Evaluate performance returns non-positive ranks.
Actual Behavior
Six ranks out of ten thousand are non-positive in the attached example.
Expected Behavior
Ranks should always be positive.
Steps to Reproduce
Run attached notebook script: https://gist.github.com/tabacof/42c72b6e7b15df66584a4fd8ab770d06
Dataset: http://pages.cs.wisc.edu/~anhai/data/784_data/movies5.tar.gz
Image

Can you please confirm if the x_filter had duplicate triples?

I just verified. Actually there are 3 triples in X_valid that have duplicates in X_filter. Hence the ranks are <=0 for those 3 triples.
print(X_valid[np.logical_or(r[:,0]<=0, r[:,1]<=0),:])

Similarly in the entire dataset, there are 37 duplicates
uniq_triples, counts = np.unique(filter_triples,
                                 return_counts=True,
                                 axis=0)
duplicate_triples = np.concatenate([uniq_triples[counts>1],
                                    np.expand_dims(counts[counts>1],1)], 1)
print('Duplicates :', duplicate_triples.shape[0])
print(duplicate_triples)

It is because of the duplicates you are getting this issue. Ideally there should not be any duplicate statements in the graph. Since we do not have checks in place to verify the presence of duplicates, the rank computation logic gets affected.

I have modified the logic which subtracts the ranks of False Negatives that are generated by corruption generation in eval (when there are duplicate triples in the filter_triples).
This fix assumes that the user may want to have duplicate triples in order to weigh a particular edge more than others in the graph. In such scenarios, the input may contain duplicate triples. But while evaluating, such duplicates must be treated as one triple (if the filter_triples contain such cases).


Plugin fails on iOS, when media play is called

Using:
de.appplant.cordova.plugin.background-mode 0.6.3 "BackgroundMode"
org.apache.cordova.media 0.2.15 "Media"
On iOS: when in background mode, calling working code:
var media = new Media(src);
media.play();
will end background mode, without any event fired, and make the application stop running.

@GwenWing, I tried it out but plugin does not stop as you describe.
Please reopen the issue if still existing for you. Thanks!


Fix/cron jobs run more than once

@marcelolx
Thank you for maintaining a great gem.
I made this PR with reference to your PR. (https://github.com/sidekiq-scheduler/sidekiq-scheduler/pull/396)
In your idea you were trying to calculate the scheduled time for cron, but I noticed that the jobs in rufus-scheduler already have that information. That is the previous_time.
I rewrote it to use previous_time for cron jobs and added a test. I would be happy to have it merged if there is no problem.

@muk-ai I am not sure this solves the issue, we already use the previous_time PR as well https://github.com/sidekiq-scheduler/sidekiq-scheduler/pull/396/files#diff-0ddd2bcc9bd29aac261acdd76530920c85887c269cc29e3f054e465b4ac8699eR355, but don't rely solely on it...
I added this to my TODO list and will take a better look when I have more time and see if just this solves the problem or not. Thanks for opening the PR, though. Any help is always welcome!

Oops, you were already using previous_time and trying to take some further care of it.
I will wait for your PR. You can refer to my test code if you like.

@marcelolx
Sorry, I did not understand how busy you were.
Let me explain about my motivation.
To completely prevent the sidekiq scheduler from running multiple cron jobs, the server must be configured as follows.

I would like to do that as follows.

There are three advantages to doing this.

The scheduler becomes redundant.
No longer have to run two differently configured sidekiqs.
It prevents the users from unknowingly having multiple job runs.

So I would like you to check my PR again when you have the time, of course.
If you are unsure whether it will work well, you can make it an optional experimental feature. Then you can release it and we can try it out to see if it works in our production.

Thanks @muk-ai! Would you have some time to look at #463? I see you just used previous_time, but that might not work if Rufus runs the jobs precisely at the time it is supposed to run — i.e. run every minute, if it runs exactly at 12:00:00 we would return 11:59:00 even though it could have already run previously at this time
Let me know what you think (feel free to continue the discussion in #463) and then we can work together to get this finally in the library 🙏

Closing in favor of #463

https://github.com/sidekiq-scheduler/sidekiq-scheduler/pull/463 This code is better. thanks!


Activate travis for running tests under several platforms

Would be nice if you could setup travis to run tests,
so we know that they work across platforms.
(as I don't have windows…)

I'll see what I can do to set it up. In the meantime, I can run test on Windows.

Seems to be running: https://travis-ci.org/sharneng/gm4java


Debian 12 - Build-ui Fail

Same error here.

I'm don't fix this error, then I came back to Debian 11.
But now there a new bug, Hyperglass cann't connect do FRRouting to run the queries.
The vtysh works properly when I call it on terminal, but not when hyperglass do it.


Assignment 5

⚠It is important to note that submitting pull requests after the deadline is not allowed. Late submissions will not be accepted and will not be eligible for grading. Ensure your academic success by submitting your work on time.

Hi Kiran, I have already completed it on time but while checking my commit on the following day found that I missed to upload it. Can you please consider it for this time and I will ensure that I'll commit my changes before the deadline.


How to check secret validity

Hello,
how can I check if secret stored in keychain is not expired or its still valid ?

Hey @khaliddd,
Instagram authentication cookies never actually expire: they timeout client side but they're still just as valid for requesting.
So the approach for dealing with Secret's invalidation should always be "try fetching your request" and be ready to deal with failures, instead of directly questioning whether your Secret is still valid or not 😊
Hope it helps.


Using this project on Windows OS without docker

I'm using the Windows OS, and I don't like using docker for build and test this project.
So when I ran it showed me an error with ffmpeg path.
I fixed it with the way:

Add package @ffmpeg-installer/ffmpeg with npm i -D @ffmpeg-installer/ffmpeg
Add it to youtube.js like this

I think it may help someone who is don't like the docker like me :v

const ffmpegInstaller = require('@ffmpeg-installer/ffmpeg');

ffmpeg.setFfmpegPath(ffmpegInstaller.path);


Update prettier to 2.0.4

This updates prettier to 2.0.4. Note that the new version comes with several minor style updates as well, which requires code changes in the same commit (which is why #164 failed).
This also removes Node.js 8 from the GitHub Actions test matrix. @keithamus - If you require Node.js 8 compatibility, please close this PR (as well as #164). Node.js 8 is no longer supported, and Prettier 2 seems to be incompatible with it
Supersedes and closes #164

@friederbluemle You don't have to remove Node.js@8, just skip eslint by if.

@fisker That's even better. Thanks for the suggestion! :+1:

Haha, FYI: you can still set  arrowParens to avoid

They are giving some additional details on this decision in their docs:

At first glance, avoiding parentheses may look like a better choice because of less visual noise. However, when Prettier removes parentheses, it becomes harder to add type annotations, extra arguments or default values as well as making other changes. Consistent use of parentheses provides a better developer experience when editing real codebases, which justifies the default value for the option.

Personally, in this specific case I don't have a strong preference for or against the parens. However, most of the time it's easier to go with the defaults instead of against them (convention over configuration).


Any examples or better documenation on updateToast and how to use it?

Is this correct? :)
https://codesandbox.io/s/toastupdate-h0fm6


filter users by custom_data

is there a way to filter users by custom data?
here you have an example of my request and i always get '422 (Unprocessable Entity)'
What i am doing bad?

response:
Incorrect search field - "custom_data" for filter string "string custom_data eq 000001"

and i have user on connectycube with custom_data

Hi @daniel-track, it is not allowed to search by custom_data

If you want to use some id, you can use external_user_id field

Hi @daniel-track, it is not allowed to search by custom_data

but the documentation says that all fields are allowed

Hi @daniel-track, it is not allowed to search by custom_data

@banshiAnton and can i use my login(my external id) as my occupant_id or last_message_user_id instead the connecty-cube user id?
Thanks for your quick response

No you can't
Maybe you need to use https://developers.connectycube.com/js/authentication-and-users?id=authentication-via-external-identity-provider
About custom_data - this is docs issue

No activity


Defect, or missing docs?

The default styling was missing when using the module as documented. I had to:
import 'react-dat-gui/dist/index.css';
in my main component to get the default styling to work.

I also ran into this issue, but found that the example code provided used the @tim-soft/react-dat-gui npm package, which worked as expected. I'm not sure if it's an intentional change, but I opted to use that version of the package to import the least amount of additional code.

Any update on this one @rohan-deshpande?

I'll get this done in #47

Resolved by #51

Met the same problem at "react-dat-gui": "^4.0.3", , 2020.11.15

Same problem, Feb 2021

any update on this? . June 2021, same problem :(

Same problem, Feb 2022

Kind of worked the problem around by taking this css file and importing it at the root component (next.js, react-dat-gui ^4.1.1)


token not changing

when I try to use the macro (either wild shape or spell shape), everay values change to the right one (as far as I can tell anyways), but the token does not change, neither the image or the size.
I have the images I'm using to test the macro in the same folder as the original image for the token, and have tried with the gm and the trusted permission.
Is there something I'm not doing right ?

Would you mind navigating to the developer console (that's hitting F12 in the Foundry window/Chrome if you use Windows) and letting me know if you see any errors? And if you do, what do they say?

There is an error message that says :
Uncaught (in promise) TypeError: Cannot read property 'totalModifier' of undefined
at transform (eval at callScriptMacroFunction (Macros.js:176), :1097:96)

A couple questions:

Under the Actions tab of your character sheet, do you have the "Fist" option? Did you change its name or any details?
Are you using Handwraps of Mighty Blows? Did you change its name or any details?

Would you mind exporting the character you're testing on and sending me the file via Discord? (Some Knucklehead#4725). Thanks!

I got a translation module that renamed it, I'll try renaming it

It's working when i deactivate my translation module, so that's fixed.

I'm glad to hear it! Out of curiosity, what module is it? I just want to see if I can find a workaround for you.

https://gitlab.com/pathfinder-fr/foundryvtt-pathfinder2-fr
It's this one. I changed the line in your code that checked the "Fist" bonus by "Poing" (the french word) and it worked perfectly.

Perfect! And if you ever get Handwraps of Mighty Blows, you just need to make sure a similar change and you should be golden.


SNMPV3 AES192/256 privacy does not work with Cisco IOS.

Pysnmp SNMPV3 AES192/AES256 privacy options does not work for Cisco devices
(test this with any Cisco device running an IOS that suppports AES192/AES256).
This is because Cisco devices (ie, IOS that supports AES192/AES256) do not use
https://tools.ietf.org/html/draft-blumenthal-aes-usm-04 for key localization/short key extension.
Instead, they use the procedure for 3DES key localization specified in
https://tools.ietf.org/html/draft-reeder-snmpv3-usm-3desede-00 which
specifies the 3DES key localization/short key extension.
I believe Cisco did this because they view the reeder mechanism as an improvement
over the bluementhal mechanism.
Please see the pull request that fixes this issue. However, the pull breaks
SNMPV3 AES192/AES256 privacy for any device that uses the key localization in
https://tools.ietf.org/html/draft-blumenthal-aes-usm-04

I have an update to this. At our research center, I was able to test against an Extreme Networks switch runnning ExtremeXOS (X440G2-48p-10G4) version <IP_ADDRESS> <IP_ADDRESS>-patch1-5.
This implemented AES192/AES256 in exactly the same was as Cisco (this means my pull request solves this problem for Extreme network devices as well).
I believe that Cisco has now establish a 'de facto' standard for AES192/256 privacy, and that everybody else is following with this, so there is no reason to support multiple key localization methods for AES192/256.  Just do it how Cisco does it (i.e, via my pull request that implements the 3DES localization method) and that should be good enough.

Sorry, did not mean to close this issue.

Thank you for solving this mess!
Could you please take a look at PRs to resolve my uncertainties?

I made commits to both of my pull requests that cleaned up the code as per your comments, and left some other comments that hopefully cleared up things.
Thank you for looking at this.

Both schemes were implemented in master since 6eed8eff24910727316a25b6a180822174d2bcab. Your verification and further changes are very welcome. Thank you for your efforts!

Public SNMP simulator is now running  pysnmp master. You are welcome to test its agent-side 3DES/AES192/256 implementation with your MIB browsing tools.

On August 22/2016, pulled latest PySNMP source and tested 3DES/AES192/256 SNMPV3 privacy credentials against Cisco IOS 15.4, 800 Series Router -- all passed!
I am closing this issue.


Feature Request: Underscore prefix for meta keys

What
I'd like to see underscore prefixes for the meta keys like activitypub_user_id (to be _activitypub_user_id instead).
Why
Meta keys without underscore prefixes show up in the Custom Fields UI, which clogs up the select/dropdown menu.

How
No response

🤔 wasn't aware of that.
I will see how we could possibly migrate!


Network: Bridge forkdns return empty AAAA record response when equivalent A record exists

Fixes compatibility with nslookup that looks up A and AAAA records and returns with non-zero exit status if AAAA is returned as NXDOMAIN.
Fixes #8389
Tested in Alpine 3.13:
Before
c2:~# nslookup c1; echo $?
Server:		<IP_ADDRESS>
Address:	<IP_ADDRESS>#53

Name:	c1.lxd
Address: <IP_ADDRESS>
** server can't find c1.lxd: NXDOMAIN

1

After:
c2:~# nslookup c1; echo $?
Server:		<IP_ADDRESS>
Address:	<IP_ADDRESS>#53

Name:	c1.lxd
Address: <IP_ADDRESS>

0

Testsuite passed

Testsuite passed


Gateway discovery mode is the only one supported by KIC

Is there an existing issue for this?

[X] I have searched the existing issues

Problem Statement
Currently, Helm chart installs KIC in the following mode - every pod has one instance of Kong Gateway and the respective instance of KIC.
To use newer and more scalable and cost-efficient mode - gateway discovery
ingressController.gatewayDiscovery.enabled=true

has to be configured.
It should be enabled by default, other modes should be deprecated.
Proposed Solution
No response
Additional information
Requires update in Helm chart that will become the default way of deploying KIC

https://github.com/Kong/kubernetes-ingress-controller/issues/4712

Obsoletes

https://github.com/Kong/kubernetes-ingress-controller/issues/4598

Acceptance Criteria

[ ] gateway discovery is the only supported mode
[ ] documentation properly describes how it works
[ ] KIC tests and supported deployment (Helm) should test/provide it

Blocked by https://github.com/Kong/kubernetes-ingress-controller/issues/4671

In fact, #4751 and #4671 satisfy 100% of the scope of what's to be done. Closing this.


Added a Hold-To-Play option

I've added an option to change the bind to a "hold-to-play" style using aliases.
If HoldToPlay.Checked Then
     slam_cfg.WriteLine("alias +slam_hold_play slam_play_on")
     slam_cfg.WriteLine("alias -slam_hold_play slam_play_off")
     slam_cfg.WriteLine("bind {0} +slam_hold_play", My.Settings.PlayKey)
Else
     slam_cfg.WriteLine("bind {0} slam_play", My.Settings.PlayKey)
End If

With this, the sound will be played for as long as the user is holding the play key.
The current design requires 2 key presses, one to start playing and another one to stop. That's one key press too many IMO.
Regards

Sweet. I prefer to use the two presses so I can handsfree songs while I play/dance w/o having to hold the key in but I'm sure many users will love it :thumbsup:


[ZEPPELIN-3726] Fix NPE for resourceList function "getAllResourcesExcept".

What is this PR for?
Trivial fix for exclude NPE in org.apache.zeppelin.interpreter.InterpreterSettingManager#getAllResourcesExcept
What type of PR is it?
Bug Fix
What is the Jira issue?
[ZEPPELIN-3726]
Questions:

Does the licenses files need update? no
Is there breaking changes for older versions? no
Does this needs documentation? no

CI is green https://travis-ci.org/TinkoffCreditSystems/zeppelin/builds/416710567

LGTM


Utility functions for PMap

Depending on #561

I can't update this PR.

I'll make a new PR from my fork. Liqwid-Labs fork seems to have problem with permission


VEP error

When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule annotate_variants:
input: results/R22025/variants/somatic.snvs.vcf.gz, results/R22025/variants/somatic.snvs.vcf.gz.tbi, resources/refs/genome.fasta, resources/vep/cache, resources/vep/plugins
```
output: results/R22025/annotation/somatic.snvs.vcf, results/R22025/annotation/somatic.snvs.html
log: logs/vep/R22025_somatic.snvs_annotate.log
jobid: 2
reason: Missing output files: results/R22025/annotation/somatic.snvs.vcf; Input files updated by another job: results/R22025/variants/somatic.snvs.vcf.gz.tbi, results/R22025/variants/somatic.snvs.vcf.gz
wildcards: sample=R22025, vartype=somatic.snvs
threads: 4
resources: tmpdir=/tmp
Traceback (most recent call last):
File "/mnt/work/zhumc/software/ScanNeo2/ScanNeo2/.snakemake/scripts/tmp_6vhvqtx.wrapper.py", line 68, in
shell(
File "/home/zhumc/.conda/envs/scanneo2/lib/python3.12/site-packages/snakemake/shell.py", line 297, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  (bcftools view 'results/R22025/variants/somatic.snvs.vcf.gz' | vep --everything --fork 4 --format vcf --vcf --offline --cache --dir_cache resources/vep/cache --cache_version 111 --species homo_sapiens --assembly GRCh38  --fasta resources/refs/genome.fasta --dir_plugins resources/vep/plugins --plugin NMD, --plugin Wildtype, --plugin Downstream, --output_file STDOUT --stats_file results/R22025/annotation/somatic.snvs.html | bcftools view -Ov > results/R22025/annotation/somatic.snvs.vcf)  2> logs/vep/R22025_somatic.snvs_annotate.log' returned non-zero exit status 255.
RuleException:
CalledProcessError in file /mnt/work/zhumc/software/ScanNeo2/ScanNeo2/workflow/rules/annotation.smk, line 70:
Command 'set -euo pipefail;  /home/zhumc/.conda/envs/scanneo2/bin/python3.12 /mnt/work/zhumc/software/ScanNeo2/ScanNeo2/.snakemake/scripts/tmp_6vhvqtx.wrapper.py' returned non-zero exit status 1.
Could you please provide some assistance?

Hi, thanks for reporting this. Could you please provide me with the logs/vep/R22025_somatic.snvs_annotate.log file? It should give us more information about what went wrong.
Thanks

Unfortunately, there are no entries in the log file.
R22025_somatic.snvs_annotate.log

Ok, thanks.
Could you please verify that the plugins for VEP have been downloaded? And print the content of the folder resources/vep/plugins. It looks like these have not been downloaded correctly. These should contain: Downstream.pm, NMD.pm, and Wildtype.pm
Could you also check if the SNV Vcf file is correct (e.g., bcftools view 'results/R22025/variants/somatic.snvs.vcf.gz') as this is getting piped to VEP. Could be that this causes some issues already. As I understand this happens to multiple samples?

Thank you for your suggestion. The SNV VCF file format is correct, I have tested it. The contents of the resources/vep/plugins folder are complete, and my SNV VCF contains only one sample.

I encounter the following error when executing the command below:
bcftools view 'results/R22031/variants/somatic.snvs.vcf.gz' | vep --everything --fork 4 --format vcf --vcf --offline --cache --dir_cache resources/vep/cache --cache_version 111 --species homo_sapiens --assembly GRCh38  --fasta resources/refs/genome.fasta --dir_plugins resources/vep/plugins --plugin NMD, --plugin Wildtype, --plugin Downstream, --output_file STDOUT --stats_file results/R22031/annotation/somatic.snvs.html | bcftools view -Ov > results/R22031/annotation/somatic.snvs.vcf  2> logs/vep/R22031_somatic.snvs_annotate.log
ERROR：
Can't use an undefined value as an ARRAY reference at /home/zhumc/.conda/envs/scanneo2/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Funcgen/BindingMatrix.pm line 501.

Hello,
I can't reproduce this error.. could you maybe provide me the SNV file (or part of it)? Thanks

I tried removing the parameter --everything  and then the exception doesn't appear

Ok thanks for reporting this. It runs through without --everything? Need to test this. Thanks

Unfortunately，my SNV file is too large and can not be uploaded.


Create Max Hit sound effect plugin

Created a plugin that plays a sound effect when you hit your max hit

Superior version Hit Sounds already exists


PNG saving issue

when I run images in the GUI (or in the command line) cellpose is able to correctly identify cells. however, when i try and save the masks as a png, it always saves as a completely black image. why would this be?
thanks in advance.

it is an int16 image so you may not be able to see the masks in your standard image viewer, I'd recommend opening them in imageJ or python

it is an int16 image so you may not be able to see the masks in your standard image viewer, I'd recommend opening them in imageJ or python


Create yuwapatschool.txt

@63warittochi Please provide us with:

the school official website URL
the school street address, including city.

@63warittochi You might miss my previous comment. Please react.

@63warittochi I am sorry, this request remains unanswered for a while. I have to close it without merging. Please reopen and comment if you have an update regarding the aforementioned issue. Thank you for your understanding!


Clean up logging output

The logging output is currently very messy and partly wrong. let's fix it.

@linki was this issue already addressed ? if not, please include some examples

definitely not.
for example, services that aren't type LoadBalancer generate a log.Warn() which was useful in the beginning but is just wrong now.


Research Byzantine Cycle Mode

Announcement and feedbacks on Bitcointalk: https://bitcointalk.org/index.php?topic=752260.0
Documentation on GitHub: https://github.com/sundance30203/dubmix

Anonymity set is low and the scheme is expensive. For decentralized mixing it's interesting idea, though. It basically coordinates users to make many small mixes with each other.


Make HttpCompletionOption configurable

See this discussion for more details: https://github.com/basdijkstra/rest-assured-net/discussions/125

@RothAndrew tagging you so you can follow the progress in here.

@RothAndrew could you upgrade to https://www.nuget.org/packages/RestAssured.Net/4.3.0-beta.1 and test whether setting the HttpCompletionOption works as intended for you? Example:
Given()
    .UseHttpCompletionOption(HttpCompletionOption.ResponseHeadersRead)

The value defaults to HttpCompletionOption.ResponseContentRead, so if that's the value you need, you don't have to change anything.
In this release, you can only set the HttpCompletionOption value for individual requests, not yet in the RequestSpecification or global config. I'll add that as soon as I know this is what you were looking for.

Yep! Will give it a show now.

It's working great! Thanks! 😁

If you can think of a better name for the UseHttpCompletionOption method I'm open to suggestions ;)

I've always been a fan of using descriptive names over short and cryptic so I love it.
I suppose if you really wanted something different I could potentially see the argument being
// Wait for all the content. Equivalent to using HttpCompletionOption.ResponseContentRead
Given()
  .WaitForContent(true)

// Don't wait for content. Equivalent to using HttpCompletionOption.ResponseHeadersRead
Given()
  .WaitForContent(false)

with the default being true to preserve backward compatibility

Thanks so much for the feedback! Happy to hear it works. I’ll add the options to the RequestSpecification and the config options and will release a proper 4.3.0 soon.

@RothAndrew RestAssured.Net 4.3.0 is live: https://www.nuget.org/packages/RestAssured.Net/4.3.0
You can now also specify the HttpCompletionOption in a RequestSpecification and in the global config. Feel free to install and test it.
Please let me know if all still works OK, so I can close the issue. Cheers!

Any more feedback, @RothAndrew? If not I’ll close this issue.

Nope, everything's great. thanks!


Plot HR(exp(coefficients)) for CoxPHFitter

I am using lifelines to run a Cox’s proportional hazard model.
And now I have a little confusing about the plot function of model’s coefficients, I read the Docs and find that the packages could only plot log(HR) (in fact they are model’s coefficients)directly, but in medical research, reporting HR(also means exp(coefficients)) in plot and result are more acceptable.
So, I wonder if they are some ways to get the HR plot directly? I have search in google but couldn’t find any solution about my idea.
If the packages have  built-in way to plot HR will make the packages more useful for medical researcher.
Here is an example about HR plotting. We campare HR with 1 to find whether they are any effection about the factors.

Thank you for your attention!

👍 seems easy enough to add as a kwarg to plot in the next release.

This is now possible in v0.21.3. Try cph.plot(..., hazard_ratios=True)


RapierPhysicsPlugin requires generics

Trying to add the plugin the way that most Bevy plugins are added fails:
fn main() {
    App::new()
        .add_plugins((DefaultPlugins, RapierPhysicsPlugin::default()))
        .run();
}

It fails because Rust cannot infer the type for PhysicsHooks. Instead, you need to do something like this:
RapierPhysicsPlugin::<()>::default()

or:
RapierPhysicsPlugin::<NoUserData>::default()

This isn't obvious for new users, and is especially confusing because the plugin has no documentation example (outside the website's general usage guides). The use of NoUserData or the concept of physics hooks isn't even explained on the website before the "Advanced collision-detection" section, even though the plugin initialization is essentially the first thing that a user has to do. It shouldn't be necessary to use generics here.
Additionally, limiting the user to a single PhysicsHooks type feels rather limiting and annoying from a composability standpoint. But that's another issue.

I'm not too familiar with this part of the code, but I agree with the struggle.


shift enter

Shift enter should insert a new line after the cursor

fwiw the default system behavior for me is that shift enter works the same way as just enter on linux, though I think what you're suggesting is better

How are you coming about that? Would like to try myself

after the cursor as in, at the end of the cursor's line?

No just after the cursor.


ability to add contributors to the model

Describe what problem your feature request solves
At the moment the UI does not provide for adding contributors
Describe the solution you'd like
Provide similar functionality to version 1.x
Additional context

This is not a bug - the form does allow the addition of contributors, you just need to start typing
Commit dfd68b9 makes this need to start typing more obvious, and closing this issue


Do not allow AMP version

Greetings.
The website i'm currently working on has AMP version of it.
Basically most of the URLs have a second version with striped HTML and they go to https://www.example.com/music/amp (...)
The documentation says that there is no need for including AMP pages in the sitemap, but also i can't disallow them in robots.txt.
What can i do in this situation?

Hi! Those pages should not be added then of course. I can add a filter on either the URL or depending on the content of the pages. First option would be better as it's faster.
Is there any standard on how the URL for AMP should look like?

Hi again.
I've actually implemented it myself by editing /src/discoverResources.js file, adding
// exclude AMP
if (/amp/i.test(href)) {       return null; }
Unfortunately, there is no actual standard about how the AMP URL can be structures (i.g. amp.domain.com or domain.com/amp).
The issue for me is currently solved :)

@Cool-Programmer Indeed there is no URL standard format. That being said, proper ways to detect if a webpage is using AMP is (you have to visit the page first):

Detect if its <html> tag has the amp attributes (such as <html ⚡> or <html amp>, see markup of https://www.ampproject.org/docs/getting_started/create/basic_markup).
Detect if the page has a canonical link to a non-amp version (https://www.ampproject.org/docs/fundamentals/discovery).
Dunno if these properties is ever useful in your case... (I am actually working with the AMP team recently so I can also ask them for alt ways)

@kevinkassimo Thank you for your answer! In this specific case, when i can be sure that the /amp part in the URL can never be changed, the solution is quite simple. As far as i know, if the website has 2 versions (1 amp and 1 common), they can be differentiated by url, but if it has only one amp version, then it gets harder to implement.

Actually we have the content of the page available and can ignore such cases. As I'm reading @kevinkassimo's suggestions I'm thinking about adding both. Pages with canonical links shouldn't be added event if it's not AMP I think.
BTW @Cool-Programmer: For now you can ignore AMP pages without adjusting the source code.
const crawler = generator.getCrawler();
crawler.addFetchCondition((queueItem, referrerQueueItem, callback) => {
  callback(!queueItem.path.match(/\/amp\//));
});

Hopefully I can add the AMP changes today.

I created a feature branch (feature/ignore-amp) with the discussed functionality. @Cool-Programmer would you mind testing if it works with your site?

@lgraubner Worked perfectly, great!

Published a new version containing this feature.


feat: ProgressBar component

Codecov Report
Base: 64.61% // Head: 64.69% // Increases project coverage by +0.08% :tada:

Coverage data is based on head (1eb46ad) compared to base (ad9e733).
Patch coverage: 69.23% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #14      +/-   ##
==========================================
+ Coverage   64.61%   64.69%   +0.08%
==========================================
  Files          43       44       +1
  Lines        4052     4130      +78
  Branches      195      195
==========================================
+ Hits         2618     2672      +54
- Misses       1433     1458      +25
+ Partials        1        0       -1

Impacted Files
Coverage Δ

packages/core/src/components/ProgressBar.ts
68.83% <68.83%> (ø)

packages/core/src/components/index.ts
100.00% <100.00%> (ø)

packages/core/src/renderer/render.ts
72.72% <0.00%> (ø)

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Python3 only

Fixes the bug https://github.com/lneuhaus/pyrpl/issues/469 (module 'qtpy.QtCore' has no attribute 'pyqtBoundSignal')
Adds a folder with all notebook examples for the paper to be published.
I checked that all unittests are fine at this stage

--> We need this to be in master to put the proper link in the paper if possible !

Merged it into master @SamuelDeleglise. I also took the opportunity to rename master into main, which is the default now. Should we keep the python3-only branch or rather delete it?

Well, the only problem is that we don't have direct push authorization on main so we somehow need a working branch...