Python3 copy

Same code as in https://github.com/tmm1/pygments.rb/pull/192/files
re-opening so travis will re-run

Okay PR is ready. Python3 support!
Credit goes to @terceiro for getting this started and @slonopotamus for figuring our the fix for the windows issue https://github.com/tmm1/pygments.rb/issues/152#issuecomment-680304941
@tmm1 Please take a look and push our a new gem if you think this makes sense (Python 3 much more widely supported now, and in fact default version on most OSs).

It not only fails on MacOS, see this.
Looks like 8s is not enough to initialize pygments Python process. Either this needs to be fixed (why it needs so much time?) or time limit needs to be increased.

Increasing default timeout to 16 seconds makes it pass, but it feels like a hack. I vote for timeout removal (at least by default). Something like "timeout < 0 means no timeout and default is -1".

@ivanistheone thanks for pushing this forward. I closed my PR in favor or yours.

I could also suggest a half-good solution: only apply timeout when highlighting files, not when doing internal interaction (like getting list of lexers) with python process.

@slonopotamus Thx for figuring this out.  I found this other PR https://github.com/tmm1/pygments.rb/pull/123 that adds configurable :timeout option.
I copied over this :timeout option to current PR and set :timeout = for the lexers!/get_all_lexers call (I first tried with 16 but it was still timing out sporadically). I also added a 1 sec sleep on startup to avoid sending commands to Python "too fast" before it can read them.
Green green green!

This build has 8s between ruby cache-lexers.rb and undefined method inject' for nil:NilClass (NoMethodError)` error even though you've bumped timeout to 40s.

"mega tolerant" also failed after 8s. I think :timeout param is not working as you expect it to.
You can enable timestamps in GitHub Actions:

@gfx ping. Maybe you could review/merge/release this?

@ivanistheone you may want to add "resolves #152" text to PR drscription so that #152 will close automatically when this is merged.

@tmm1 @gfx ping?

Looking 👀

Great PR. I'll check it, and merge after review.
Generally: goal is for a few proper semantic releases over the next months to help you all out. Would like to see this lib continue to work for those who need it.


Add support for axis keyword arg to numpy.argmax()

This adds support for the axis keyword argument to np.argmax and np.ndarray.argmax.
~I could not get arbitrary dimensions working, because np.transpose() only works (as far as I can tell) with literals. Suggestions are welcome.~

Any chance someone can look at this? I have more functions I'd like to implement, but don't want to get ahead of myself if e.g. I'm doing it wrong.

Many thanks, I will try to address comments next week.

Addressed most comments, the dimension-limitation one I am not sure how to approach, the error is mysterious to me.

Thanks to @stuartarchibald this now supports more than 3 dimensions, should be able to remove "Waiting for author" label.

@stuartarchibald I reviewed 858498 and can confirm, that it looks good!

@stuartarchibald I reviewed 858498 and can confirm, that it looks good!

Presume c858498 is meant? thanks for checking @esc .

I applied the minor fixes, so assuming everything passes, sounds like this is ready to merge?

@itamarst Congratulations on your first contribution to Numba!

Thanks for the help! Next up on my list is adding axis to argmin, and then escalating difficulty until the final boss, "it'd be nice if Numba did einsum", which is frankly terrifying.

Thanks for the patch!


Fix code highlighting

CC @isoos

Deployed at https://kevmoo-better-highlighting-dot-dartlang-pub.appspot.com/packages/built_mirrors

Seems like it's breaking more lines now. Maybe you could update it so it fits 80 characters on one line inside the <code> block?
Otherwise looks fine.

@mkustermann LGTY?


Eko-lan / HA integration

Hi, is there a way to integrate it with eko-lan (G927) and take the payload from there in home assistant?
I've tried to run the script and connect to eko-lan by changing the values of ip/port in
serial.serial_for_url('socket://ip:port')
unfortunately- no luck.
Do i need to have separate device (rs485 -> lan) to make it work or eko-lan module should be enough?

Hi,
i don't think, that you can use the G927 with code in this repository. AFAIK, the G927 is connecting to the hewalex cloud.
You need a simple RS485/USB or RS485/LAN converter for our code & for direct communication.

Thanks, a lot for Your replay :)
I will try to get some converter and test that, if you have any that you can recommend please let me know.


[5.7] Make httpOnly CSRF cookie optional

This httpOnly Cookie is added by default, to enable automatic passing of the CSRF token to frameworks like Angular. But this is not the case for many other Http libraries (eg. for jQuery and Axios, Laravel just sets the headers directly).
While this cookie does not have any security implications (that I'm aware of), I've had multiple security audits flag this as an issue. While they may be (and probably indeed are) incorrect, it can be difficult to explain, especially if you don't actually use libraries that require this.
This adds a flag to toggle the cookie more easily. It should be accompanied by adding the same property to the laravel/laravel framework and/or a note in the docs.
This is breaking, so it warrants an upgrade guide notice. But we could also change the default to true to avoid the break.
See also https://github.com/laravel/ideas/issues/873

Defaulted it to true.

Ok cool, I've added it to laravel/laravel the same as your new text in https://github.com/laravel/laravel/pull/4692

@barryvdh I've also seen this issue being raised in a security audit. Although it's questionable to leave it as true by default, I understand Taylor's decision to avoid the breaking change.
In my case, I simply solved it by replacing the middleware with a version that short-circuits the addCookieToResponse method:
class VerifyCsrfToken extends \Illuminate\Foundation\Http\Middleware\VerifyCsrfToken
{
    protected function addCookieToResponse($request, $response)
    {
        return $response; // Don't add CSRF token to the response cookies.
    }
}

Your change is a step in the right direction but what would be really convenient is a config value, because your $addHttpCookie still forces users to swap out the middleware class.

It does not require to swap the middleware, you already have it in your local Middleware by default, see https://github.com/laravel/laravel/blob/develop/app/Http/Middleware/VerifyCsrfToken.php

Although it could be changed in laravel/laravel to have it set to false by default for new projects, without breaking anything for existing projects.

My bad, you're absolutely right; in that particular project the local VerifyCsrfToken middleware had been deleted.

I came across this issue after a security audit. They asked for XSRF-TOKEN cookie to be set with HttpOnly = true.
I have set  'http_only' => true, in sessions.php config but it does not apply to this cookie.
Looking into \Illuminate\Foundation\Http\Middleware\VerifyCsrfToken.php@addCookieToResponse method I realized this parameter is hardcoded with false.
$response->headers->setCookie(
            new Cookie(
                'XSRF-TOKEN', $request->session()->token(), $this->availableAt(60 * $config['lifetime']),
                $config['path'], $config['domain'], $config['secure'], false, false, $config['same_site'] ?? null
            )
        );

I was expecting this to be $config['http_only'] instead of false.
Is there a reason why this is hardcoded with false?
I am using Laravel v6.5.1
Thank you!

Yes because the point of that cookie is to be able to read if with Javascript (Axios etc). If you don't use it, just set addHttpCookie to false.


pass unregistered user id to caused by

hi ,
when i log my users activity i want to pass some unregistered user id to causedBy and thats because we are working on a microservice and i am getting the user id from some other service and i dont save them in my database but i want to know which user id have done what actions in my database so i get the user id in my controller but i dont know how to pass the id thruogh the causedBy because it gives the unidentified user error and dont log the action .

Hey,
the problem is much larger. The causer columns are a polymorphic relation with the corresponding causer method.
We also load the causer to format the message to replace placeholders like :causer.name. So if you really want to do this I recommend to use the custom properties to add this value. Otherwise you will have to replace a lot of logic.
What do you want to do with the ID in your system? Do you want to load data via API sometimes? Or is it just for completion to allow an admin to search for the causer manually?

actually it should shows the user name and other stuff but i  think my co worker can write some api to get the id from my property api and show user name so i think the solution is to do it with costum property so thanks this problem is solved i think :)

Ok, just another hint: logs shouldn't really depend on other systems . in best case even not other tables.
So if you need the name you should put it into the custom properties also. This will save you from requesting it all the time via API and also prevents you from handling error responses if the foreign user is deleted and you can still display the name.

@Gummibeer excuse me for not being clear enough we are not depending on any other services we just have a gateway that manages the user and the authentication of it so we just deal with the user_id that we get from gateway and for any kind of user name we send the id to gateway and get the username so we save the userid and when even we need to show that then we send request to gateway for name !!!


npm test fails

Sails version (sails): 1.0

npm test fails for newly generated Sails v1.0 application:
Warning: truncate.less: line 5, col 2, finalNewline: Files should end with a newline.
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR<EMAIL_ADDRESS>lint: `./node_modules/eslint/bin/eslint.js . --max-warnings=0 --report-unused-disable-directives && echo '✔  Your .js files look so good.' &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/*.ejs &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/**/*.ejs &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/**/**/*.ejs &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/**/**/**/*.ejs &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/**/**/**/**/*.ejs &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/**/**/**/**/**/*.ejs &&
./node_modules/htmlhint/bin/htmlhint -c ./.htmlhintrc views/**/**/**/**/**/**/*.ejs && echo
'✔  So do your .ejs files.' && ./node_modules/lesshint/bin/lesshint assets/styles/ --max-warnings=0 && echo '✔  Your .less files look good, too.'`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the<EMAIL_ADDRESS>lint script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.
npm ERR!  Test failed.  See above for more details.

The file assets/styles/styleguide/truncate.less needs to be generated with a trailing newline for the test to pass correctly.

@accuser Thanks for bringing this to attention - I'm also getting that warning for a new app in the latest Sails v1.2.2.  I'll bring it up to the team for an update. 👍

@accuser We got this fixed in<EMAIL_ADDRESS>which should be automatically installed as part of the global sails install if you run npm install sails@latest -g.  Error should be resolved now 👍

@johnabrams7 have done - all working now. 👍


[SPARK-15324] [SQL] Add the takeSample function to the Dataset

What changes were proposed in this pull request?
In this pr, I add the takeSample function with the Dataset which is to sampling with the specify num instead of the fraction in sample function.
How was this patch tested?
add a test in DatasetSuite

Can one of the admins verify this patch?

@burness thanks for working on this. The PR in its current state has some serious potential memory and performance problems (see the comments). What is the usecase for this? If you do want to press ahead you will need to take a look at the physical SampleExec operator and somekind of limit to that.

@hvanhovell  Thank you for code review. In my project, I want to sample by the specify num but in DataFrame or Dataset, there is only the sample by fraction. And I have take these days , but it's not easy for me to resolve the serious potential memory and performance problems(only add the line to require that the sample num shouldn't bigger than the dataset's size).

@burness that is no problem. I have taken a look at the current implementation of the RDD's takeSample; it is very similar to your implementation. I do still think that implementation has problems, and I am not sure we should add to the Dataset/Dataframe API.
You can always use the datasets 's RDD use its takeSample method, i.e.: spark.createDataset(dataset.rdd.takeSample(...)).

@hvanhovell yeah, I agree with your opinion！ Thanks

Hi @burness, what's the state of this PR?

@HyukjinKwon  It is too hard to solve the OOM, I'm so sorry

Ah, that's fine. I just wondered if this is on a progress and we maybe close this for now.

@HyukjinKwon  Ok, I will close this now 😆


Allow for moving mail from the Unified Inbox

Checklist

[X] I have used the search function to see if someone else has already submitted the same bug report.
[X] I will describe the problem with as much detail as possible.

App version
8.0b
Where did you get the app from?
Google Play
Android version
14
Device model
P8P
Steps to reproduce

Open Thunderbird
Scroll through mail
Go to move mail to relevant folders

Expected behavior
Should be simple
Actual behavior
Option is missing as you're in unified inbox mode
Logs
No response

Duplicate of #5709


fix: use globalThis i/o window

I'm making some progress with a generic solution for SSR.
Got it working in a plain Node app and Cloudflare worker, working on Next.js now...
https://github.com/luwes/wesc
The worker is pretty cool, it can take any URL with Media Chrome components and add DSD to it
https://wesc.luwes.workers.dev/?url=https%3A%2F%2Fmedia-chrome.mux.dev%2Fexamples%2Fvanilla%2Fadvanced.html
https://wesc.luwes.workers.dev/?url=https://www.media-chrome.org/
There is a limit on CPU time for cloudflare workers so it might time out but I haven't seen it yet.
SSR'ing 3 Media Chrome players took like 35ms locally.

one of the things that came up is that some frameworks like Next.js recommend server checks with typeof window === 'undefined' https://stackoverflow.com/questions/49411796/how-do-i-detect-whether-i-am-on-server-on-client-in-next-js
so we don't want to be shimming window but globalThis with a DOM shim otherwise we are making the server / build look like a client environment.

Got a Next.js example running! https://wesc-nextjs.vercel.app/
In the new Next.js app router it's really minimal what you need to add because it supports async components

DOM shim: https://github.com/luwes/wesc/blob/main/examples/nextjs/app/page.js#L1
WeSC container: https://github.com/luwes/wesc/blob/main/examples/nextjs/components/player.js#L26

so we don't want to be shimming window but globalThis with a DOM shim otherwise we are making the server / build look like a client environment.

Have you actually run into this problem? We're not setting window globally, just locally to the project, so any typeof window check shouldn't be affected by our local usage of a variable named window right?
globalThis is already "server safe", so it feels backwards to then create a "server safe shim" for it. It also doesn't have a consistent API across platforms, so how do you shim it? We're intentionally shimming the window API, not globalThis so
components expecting window functions don't blow up on the server.

@heff I haven't run into any issues but I think it would break that typeof window === 'undefined' check though.
I know the window export variable is local to Media Chrome but the DOM API's have to be shimmed on a global object right, either window or globalThis.
In the window scenario this will happen.
// This will be true if JSDOM or Linkedom shimmed window with equivalent API's.
const isShimmed = Object.keys(windowShim)
  .every(key => key in window);

// If we keep using window the `window` in the ternary else has to be shimmed with equivalent API's for SSG / SSR to work
export const Window = isServer && !isShimmed ? windowShim : window;

// => typeof window === 'undefined' won't be true anymore

but the DOM API's have to be shimmed on a global object right, either window or globalThis.

No? We've shimmed all the DOM APIs we've needed on windowShim. As long as we continue to import our internal version of window whenever a window API is needed, no shim has to go on a global object.
I'm not clear on if what you're doing here requires a bunch of additional window APIs though. I think I need you to walk me through this feature in general to get caught up.


HtmlEditorConfig in 3.x is very difficult to work with as-is

Hi, I'm encountering a lot of difficulty in dealing with HtmlEditorConfig in 3.x since I'm noticing that it's not injected in this version at all (i.e. instantiates itself via new keyword) and doesn't provide adequate getters to access properties so that I can at least workaround some of the built in limitations of SilverStripe at it's core (namely dynamically creating config's for custom toolbars configured in->getCMSFields() which don't work with PJAX). In my case, an innate limitation that prevents me from initializing ssTinyMceConfig since that's set once on initial page load and isn't updated. It looks like this has thankfully been overcome in SS4 with a relatively eloquent solution, but so far the SS3 API isn't sufficient in exposing private/protected properties so I can do this  mostly in PHP with a Requirements::customScript() (but this is just an example where I'm hitting a wall).
I can probably still hack around this in my own custom JavaScript using data- attributes (similar to SS), but is it worthwhile in SS3 to add the following getters that are alreadin SS4? These would be new methods that should still hopefully be semver as it's an addition of new methods to an API and not modification of existing and would be both backward/forward compatible.

->getSettings()
->getButtons()
->getPlugins()

These methods alone I'm sure would be super helpful to tide us all over until we get upgraded to SS3. Please let me know your thoughts!

Hey Patrick, can you check if this is any better in SS4 now?

I'll close this for now. If you think this issue still applies to SS4, let us know  and I can reopen.


CameraRoll.getAlbums() broken in Android API Level 29

Summary
CameraRoll.getAlbums() has 2 issues with API Level 29:

Exception thrown: java.lang.IllegalArgumentException: Invalid column COUNT(*) as count.
Exception get swallowed and doesn't return the promise here https://github.com/react-native-community/react-native-cameraroll/blob/master/android/src/main/java/com/reactnativecommunity/cameraroll/CameraRollModule.java#L430 so the function called CameraRoll.getAlbums() never get into the then or the catch part from client perspective

For the issue #1, it looks like GROUP BY support is removed from Android Q, that's why is not working.
see here:

https://stackoverflow.com/questions/60623594/replacement-for-group-by-in-contentresolver-query-in-android-q-android-10-a
https://stackoverflow.com/questions/468211/how-do-i-get-the-count-in-my-content-provider

Environment info
Android with API Level 29
Library version: 1.6.2
Steps to reproduce
Try to use CameraRoll.getAlbums() on Android with API Level 29. No callback is never been called.
Reproducible sample code
CameraRoll.getAlbums()
.then( (res) => console.log(res))
.catch( (err) => console.error(err))

No console statement is going to happen as there is an exception and has being swallowed without calling the reject callback.

neither GROUP BY or DISTINCT would work on Android Q, the only way that I can think of to achieve this behaviour is having a cursor to scroll all MediaStore.Images.ImageColumns.BUCKET_DISPLAY_NAME and found the set of this values, then for each of them create a cursor with filter that will return the size using getCount.
I don't know how would look like performance-wise.

Just did some research. It seems the current solution doesn't works if you targeting api level 29 and above.
Found 2 keys in ContentResolver that are looks promising but they are added in Android R
QUERY_ARG_GROUP_COLUMNS
Specifies the list of columns (stored as a String[]) against which to group results.

QUERY_ARG_SQL_GROUP_BY
Key for an SQL style GROUP BY string that may be present in the query Bundle argument passed to ContentProvider#query(Uri, String[], Bundle, CancellationSignal).

So, the solution could be your suggestion above. But I think you just need 1 query for all media items in device, then iterate and group it by BUCKET_DISPLAY_NAME. Finally, count all items in each group.
You can also get the first item for thumbnail image for each album.
For now I don't have much time to work on it. Will check it when having free time. In the mean times, PR are welcome :D

@r0b0t3d yep I am working to get together this PR hopefully today

Created a PR here: https://github.com/react-native-community/react-native-cameraroll/pull/176

fixed by #176
(unrelated, @dokkis you can let Github and semantic-release know that a PR fixes a particular issue by putting
fixes #174

on a line in the description of the first commit. Then this issue would be auto closed and a comment that it is included in release x is added)

@bartolkaruza thanks for the tip! I didn't knew that :)


Replace name with event name on login

Replace the name field with name of event on login to know which event this version referring.

solved by pull request


GPT: Create an Ansible Playbook and push to repo

Goal
Details to follow
What problem does this solve?
Details to follow
Use cases
Details to follow
Acceptance criteria
Details to follow
Issues in Epic

https://github.com/janus-idp/software-templates/issues/147
https://github.com/janus-idp/software-templates/issues/173 [ENG]
https://github.com/janus-idp/software-templates/issues/157 [DOC]
https://github.com/janus-idp/software-templates/issues/156 [QE]

@jasperchui assigning to you as the engineering work is being done by Ryan Cook. Once the PR is approved and merged, this will satisfy the engineering work required for this one and we would just need to track Doc and QE work.

As discussed during the triage call, this can be shipped independently from Milestone 3 or Milestone 4.
There is also the outstanding question of how this is different from #127 (what is the difference between launching and creating an ansible playbook in the context of the Backstage template?)

No longer needed according to https://github.com/janus-idp/software-templates/issues/193


openvpn and protonmail

Hello !
Ahm, first, i am not an expert. But we have encountered a problem. On Mageia 9 ProtonVPN is only usable with openvpn due to discontinued support / openresolv fedora packages do not match and openresolv is needed. I have filed a bug to the Mageia bug list.
So, here is my noob question: I don´t know, how this works in here, but, can we have a openresolv rpm for Mageia 9 ?
Regards
Sielwall

Hi!
I only supply sources, not per distro packages.
Take that up with Mageia I guess.

Could you give me a hint, how to compile this tarball to a rpm ? configure make ... did not go.
I will search the procedure and learn then.


Support for Internationalisation

This feature implemented. for more details, checkout the documentation: https://hyva-themes.github.io/magento2-hyva-checkout/i18n/


Send a message to 'content-script@' but only to a frame

The page I'm working on has several frames (iframes), so I would like to send a message to just one specific frame, something like:
const returnData = await sendMessage('bar', { /* ... */ }<EMAIL_ADDRESS>// tab 175, frameId: 1

Is it possible right now? If not, I can happily help with a PR for that :)

Not sure. How could you specify the id of the iframe? If you can find a solution, PR will be greatly welcome :)

@antfu I opened this one long ago, but now I'm more confident with web extension APIs so I created a PR for this specific problem. https://github.com/antfu/webext-bridge/pull/13
LMK what you think!


[HELP]

error: process didn't exit successfully: target\debug\main.exe (exit code: 0xc0000139, STATUS_ENTRYPOINT_NOT_FOUND)
This happens with gtk4 only, gtk worked perfectly.
I installed gtk4 with MSYS2 and also witth vcpkg for the stable-msvc toolchain.
Getting the same error both with gnu and msvc.
All path directories included, ran dependecy walker and couldn't manage to find what's wrong.

Put the bin and everything with gtk in (env path) to the very top.


EKS Refactor - Determine if "controllerManager" &  "scheduler" cluster log types are needed

cloudwatch_log_group_retention_in_days = 30
cluster_enabled_log_types = [
"api",
"audit",
"authenticator",
"controllerManager",
"scheduler",
]
https://docs.aws.amazon.com/eks/latest/userguide/control-plane-logs.html

Determine if controllerManager and/or scheduler logs are useful. If one of both are useful / might possibly be needed, then add them to the EKS config; otherwise close the issue stating log types not needed.


PoC: Simplified PTQ API

Changes

Reason for changes

Related tickets

Tests

I would suggest moving it to the PR to the main repo and refining it there.


Updated the repos.

This guide will help learners to prepare and equip themself with the knowledge and skills necessary to answer the toughest of interview questions.

@letscode-17 We don't have an "Articles" section. Open an issue or a Feature Request instead.


Make oxidized_navigation generic over Parry3d colliders instead of requiring bevy_rapier3d

This adds support for bevy_xpbd_3d, and should allow end users to easily use their own (Parry3d compatible) colliders.
This changes plugin creation to OxidizedNavigationPlugin::<Collider>::new(NavMeshSettings { ... }),, as OxidizedNavigationPlugin now stores a PhantomData<C>, where C: Collider + Component.
In order for users to implement their own Parry3d wrapper components, they just need to implement the Collider trait (should probably should be renamed to OxidizedCollider or something) from /src/colliders/mod.rs.
Todo:

[ ] Update docs
[x] Test with bare Parry3d colliders wrapped in components

I like this solution. 👍 Very nice stuff.

Xpbd (currently) only uses bevy's transform for the initial collider creation, and not for if it moves: https://github.com/Jondolf/bevy_xpbd/pull/96
Xpbd and my parry example also don't automatically scale the collider based on bevy's transform scale. Xpbd will probably add that eventually, but I'm not sure if it's worth adding that complexity to the parry example.
I still haven't gotten around to fixing the docs or commenting the parry example.
I'm not sure if we want to add a builtin parry3d wrapper component?

Xpbd (currently) only uses bevy's transform for the initial collider creation, and not for if it moves: Jondolf/bevy_xpbd#96

Already merged by the time I read this :P Wonderful.

Xpbd and my parry example also don't automatically scale the collider based on bevy's transform scale. Xpbd will probably add that eventually, but I'm not sure if it's worth adding that complexity to the parry example.

The current expectation (because this is how it's worked with Rapier) is that the collider is scaled. The transform scale is ignored when building the nav-mesh. It's possible this is not ideal.

I'm not sure if we want to add a builtin parry3d wrapper component?

This may be a good idea.
Could then possibly generate from a parry collider without needing a rapier or Xpbd, which would allow fewer dependencies when generating from just meshes. Although even that is possibly too much.
What I would be interested in though is a private placeholder component for when you aren't using any collision & just meshes. Though that may be out of scope for this as it ties more into meshes in #9

I'm not sure if we want to add a builtin parry3d wrapper component?

This may be a good idea.

I figure anyone who's using raw parry3d colliders probably has additional data associated with them for eg. spatial queries and if/when transform propagation takes place for them (eg. FixedUpdate vs PostUpdate vs PreUpdate), and the basic implementation is trivial.

Could then possibly generate from a parry collider without needing a rapier or Xpbd, which would allow fewer dependencies when generating from just meshes. Although even that is possibly too much.

This PR already works like that. If you don't enable the xpbd or rapier features then it won't compile either of them and you just need to pass in your own parry3d wrapper component. (see the parry example).
On a related note, I originally made rapier a default feature, but I think it might be better to have no default features so users don't end up accidentally enabling both rapier and xpbd by adding the xpbd feature and not disabling default features (having them both enabled won't break anything it'll just slow down compiles, though you can't use both rapier and xpbd colliders (or parry3d + rapier/xpbd colliders) without having to make a custom wrapper component that can be either of them).

What I would be interested in though is a private placeholder component for when you aren't using any collision & just meshes. Though that may be out of scope for this as it ties more into meshes in https://github.com/TheGrimsey/oxidized_navigation/issues/9

I think that'll need some much larger changes that's beyond the scope of what I was hoping to do for this.

I think this is ready now?

Looks great. Thank you for another fantastic PR! 👍


Specify which provider you want to publish

I've appended the service provider to the vendor:publish line. In my projects i want as few config files as possible. This way you only publish the config for this package, not for other packages where the default config is fine as it is.

That's probably better. Thank you :)


SUP-995: Changelog updates, v0.18.0 release prep

Bumping and aligning versions to the changelog with past history. Also prepping for the v0.18.0 release

[x] CHANGELOG.md updated
[x] README.md version examples updated
[x] docs/ updated

@james2791 docs/ updated is checked, is that missing from the commit or was it not required? If the latter then it doesn't need to be checked.

@james2791 docs/ updated is checked, is that missing from the commit or was it not required? If the latter then it doesn't need to be checked.

Copypasta from the to-be-coming PR template - un-needed, check now 👍


Threshold Argument Added

Threshold Added as Argument

DeepFace.py

verify function
find function

Subject: Add Parameterized Threshold
Hi Sir,
I appreciate the awesome deep face package! 🚀 While using it for my project, I found that the hardcoded threshold values in distances.py didn't suit my needs. For my contribution, I've added a parameter to make the threshold customizable. This marks my first-ever open-source contribution.
Thanks,
Rohit Vilas Ingole (DataRohit)


Enable clients to pass the free-risk interest rate

Decide on which is the best way for the input — CLI vs. file (CSV) vs. others.

PR dealing with this issue https://github.com/Waifod/quant_finance_models/pull/61.

This is done, thank you! Closing.


adding grumphp, fixing style, narrowing namespace, fixing tests

Tests were failing on this because it depends on the partial view helper, which was removed from zf1-view after this component was extracted.

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@21bd95f). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master       #1   +/-   ##
=========================================
  Coverage          ?   84.37%
  Complexity        ?       14
=========================================
  Files             ?        1
  Lines             ?       32
  Branches          ?        0
=========================================
  Hits              ?       27
  Misses            ?        5
  Partials          ?        0

Impacted Files
Coverage Δ
Complexity Δ

src/Zend/View/Helper/PaginationControl.php
84.37% <ø> (ø)
14 <0> (?)

Continue to review full report at Codecov.

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[DEPENDENCIES] Update Gonum and UUID version

There is newer version of Gonum - https://github.com/gonum/gonum/releases/tag/v0.14.0
There is newer version of UUID - https://github.com/google/uuid/releases/tag/v1.4.0

via #2


Remove Composer dev dependencies from package output

When a Composer based build is packaged, development dependencies in composer.json should be excluded from the vendor resources included in the package output.
Follow up from #284.

We should also regenerate the autoload files so they don't include the dev dependencies. This may be automatically done depending on how we remove them (otherwise composer dump-autoload --no-dev would do it).

If we end up running dump-autoload for a package, should we also run with --optimize?
This still leads to pushing the dev dependencies, I found composer remove --update-no-dev as a possibility, though I haven't tested to see if that's frustratingly slow.

In manual testing, running composer install --no-dev works, and is super fast. We could run this after packaging so as not to change the local install.

This is merged now.


Case-related bugfix

On a case sensitive OS, including "Diacritics.js" while the file is named "diacritics.js" fails.
Hence the fix + release (note that the version number in bower.json wasn't up to date in 0.0.2).

Thanks :)


Remove PRINT macro and replace by LOG.  Simplify PrintVar.h.

Remove OutputDebugStringA from Linux build, replace by LOG
Fix compilation error due to not including Windows.h in OrbitBase/Loggins.h

Original PR: https://github.com/google/orbit/pull/383


Setting keeps reverting to Celsius

After changing setting from Celsius to Farenheit in Homekit app, anytime you adjust the temperature or go to the settings screen, it reverts back to Celsius.
Could we add a config setting for preferred temperature type (C or F)?

Hi!
Which of this plugin version are you using?
The target temperature setter always expects a celsius temperature so i can't preferred temperature type on config.

I am using the latest 1.4.4 build.   Also it changes the LED display on the AC unit from F to C anytime I adjust the temp in homekit.

I am also on 1.4.4 and can confirm I have the same issue as ryannowlin. Other than that this plugin works great.

Second this, keeps reverting back to C.

I'm using OSK-102 with two units and it's work perfect. I think that the commands is a little bit different with the new models.

@hillaliy - here's the debug mode output when I try to update from "Celsius" to "Fahrenheit" in the Hardware Display -> Unit Home config option. No matter what I do, useFahrenheit is always set to: false, so that seems to be the crux of the issue.
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] useFahrenheit is set to: false
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Target Temperature: 21.5˚C
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Indoor Temperature is: 20.5˚C
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Outdoor Temperature is: 23.5˚C
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Power State is set to: 1
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Operational Mode is set to: 2
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Fan Speed is set to: 102
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Swing Mode is set to: 12
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Eco Mode is set to: true
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Turbo Mode is set to: false
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] Full data is: 11000000,1,1010101,1100110,0,0,0,111100,0,10000,100,1011011,1100001,100000,1110000,0,0,0,0,0,0,0,0,11,11101010,100110,0,0,0,0,0,0,0,0,0,0,0,0,0,0
[5/12/2022, 3:47:15 PM] [homebridge-midea-air] [updateValues] Sent update command to: Master Bedroom<PHONE_NUMBER>3404)

---

[5/12/2022, 3:47:53 PM] [homebridge-midea-air] Updating accessory: Master Bedroom<PHONE_NUMBER>3404)
[5/12/2022, 3:47:53 PM] [homebridge-midea-air] [updateValues] Header + Command: 90,90,1,16,89,0,32,0,80,0,0,0,169,65,48,9,14,5,20,20,213,50,1,0,0,17,0,0,0,4,2,0,0,1,0,0,0,0,0,0,170,32,172,0,0,0,0,0,0,3,65,129,0,255,3,255,0,2,0,0,0,0,0,0,0,0,0,0,0,0,3,205,156,16,184,113,186,162,129,39,12,160,157,100,102,118,15,154,166

This is for OSK-103 Midea U Inverter AC units in my case.

+1 for all the same. I have the OSK-103 Midea U Inverter AC as well, showing this same Celsius-only display. Still troubleshooting my horizontal oscillate also not working.

This is for OSK-103 Midea U Inverter AC units in my case.

+1 for all the same. I have the OSK-103 Midea U Inverter AC as well, showing this same Celsius-only display. Still troubleshooting my horizontal oscillate also not working.

Good news is that I can help you with the second problem, the Midea U oscillates vertically (up and down), not horizontally, so you just need to enable the other in the config and disable horizontal to resolve the issue. I wrote a quick fork that sends the “change to f” command after a temp change call is made, but I’d love to get it working without the additional call!

+1 for all the same. I have the OSK-103 Midea U Inverter AC as well, showing this same Celsius-only display. Still troubleshooting my horizontal oscillate also not working.

Good news is that I can help you with the second problem, the Midea U oscillates vertically (up and down), not horizontally, so you just need to enable the other in the config and disable horizontal to resolve the issue. I wrote a quick fork that sends the “change to f” command after a temp change call is made, but I’d love to get it working without the additional call!

I thought the same and have tried both, but neither are working from my HomeKit app control. The Midea App GUI states "horizontal swing" so I figured that would be the terminology, but yeah I tried both and neither are working at this point. I'm also trying to find out how to have Eco Mode turned OFF when first powering on the unit.
Also, is the "Change to F" command something easy to implement? I'm interested in trying that.
Thanks for the help already!

@taylorwilsdon how could I install that fork to get my plug-in to work?

@taylorwilsdon how could I install that fork to get my plug-in to work?

I installed it by cloning the repository to my Homebridge server and then using npm to install it.
git clone https://github.com/taylorwilsdon/homebridge-midea-air-osk103
npm install ./homebridge-midea-air-osk103

@LampeMW Did you already have the Midea-air plug-in installed, If so, how did you configure it to pull from the osk103 fork?
Version 1.5.0

@hillaliy - if seems to still be reverting to Celsius


⚠ Bofrost.at has degraded performance

In b53edb1, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1043 ms

Resolved: Bofrost.at performance has improved in 2272901 after 6 minutes.


Add subscribe link at the beginning of the article content

Related: https://github.com/RSSNext/Follow/issues/805
If Follow will take long to ship this feature, this extension should implement it first.

Closed by #23


RFC0510: updates

presentation_definitions -> presentation_definition
add options object
add option for BbsBlsSigantureProof2020

TODO

should the Verifier require VPs with proof containing VCs with BbsBlsSignatureProof2020?

followup: if VCs have BBS+ proofs, does the VP proof need to be BBS+ as well?

Not required I think. You could issue a Bbs credential with a credentialSubject.id that is an ed25519 did:key. In that case the VP proof would be of type Ed25519Signature2018

answer: yes - VP needs a proof because the proof derivation is done with the Issuer's public key

Not necessarily right. If I issue a BBS+ credential without credentialSubject.id then you could just create a derived VC and not include a proof on the VP right?

Not required I think. You could issue a Bbs credential with a credentialSubject.id that is an ed25519 did:key. In that case the VP proof would be of type Ed25519Signature2018

Correct. The VP proof is of the type of the holder key. Eg, Could be  BbsBlsSignature2020 or Ed25519Signature2018 or JsonWebSignature2020.

Not necessarily right. If I issue a BBS+ credential without credentialSubject.id then you could just create a derived VC and not include a proof on the VP right?

I would assume that typical use cases want some form of holder authentication along with the credential.
Including the VP proof needs to be possible.

Including the VP proof needs to be possible.

Definitely! I just meant that not including a proof is also possible

Note: This still does not have passing DCO.

Updates pushed.
@troyronda @TimoGlastra please check


Change IsAjaxRequest in IsApiRequest in CookieAuthenticationEvents

It would be ideal to have a way of overwriting the IsAjaxRequest method in order to cover API only implementations
Describe the solution you'd like
I would propose renaming IsAjaxRequest into IsApiRequest and use the same function body as we currently have.
Describe alternatives you've considered
Overwriting each event individually.

Why would this be ideal? If you're calling APIs you really ought to consider switching to bearer tokens, unless you're stuck in the browser, in which case it is an Ajax request.
What are you trying to achieve?

I am doing web requests with a JWT token (mostly experimenting with an api only backend to a vuejs spa). Unless I am overwriting the methods I am getting an unwanted http response code (since technically it returns the 302 for the to login page redirect).

Unfortunately this would be a breaking change to gain minimal value, so we are closing this issue.
Also, it seems like cookies and JWT are being mixed, though they shouldn't be used together. If you're having some other issue, please log a new issue with details.

@Eilon just to clarify for anybody else that might have this issue. If the cookie auth is on, and you also have JWT , it doesn't matter that JWT works, the cookie technically has precedence on the redirect . Am i reading this correct ?

Thanks, makes sense. Will try updating the documentation this week to explain it since it's a bit confusing initially since both the token works and the redirect 'happens' based on the http code


Tree view initialization and opening / closing branches is slow

I'm using the develop branch of HyperGrid to display a tree with a few thousand rows and a depth of about 10. It initializes very slowly and opening or closing branches is slow (about half a second delay between clicking and the tree updating).
It seems that some hash table is not working because this function gets called 152876097 times at init and 22493829 times when opening or closing any branch (regardless of whether it's at the root, or deeper with only two leaves as children).
The tree is initialized with:
import Hypergrid from 'fin-hypergrid';
import TreeView from 'fin-hypergrid/add-ons/tree-view';
import DrillDown from 'fin-hypergrid/add-ons/drill-down';
import RowById from 'fin-hypergrid/add-ons/row-by-id';
import analytics from 'hyper-analytics';

// ...

		const grid = new Hypergrid(this.node, {
			data: [{ID: null, parentID: null, key: '', value: ''}]
		});

		grid.installPlugins([
			DrillDown,
			RowById,
			['treeviewAPI', TreeView, {
				treeColumn: 'key',
				hideIdColumns: true
			}]
		]);

		grid.addProperties({
			showRowNumbers: false,
			showFilterRow: false
		});

		grid.behavior.setColumnProperties(grid.behavior.columnEnum.VALUE, {
			halign: 'left'
		});

		(window as any).fin = {
			Hypergrid: {analytics: analytics}
		};

		grid.plugins.treeviewAPI.setRelation(true);

All data is occasionally replaced like this (works very slowly):
		grid.plugins.treeviewAPI.setRelation(false);

		grid.setData(data);
		grid.behavior.reindex();
		grid.behaviorShapeChanged();
		grid.repaint();

		grid.plugins.treeviewAPI.setRelation(true);

Looking at the findRow API makes me sad:
     * @param {object|null|undefined} [replacement] - One of:
     * * _omitted_ - Ignored.
     * * _object_ - Replacement for the data row if found.
     * * `null` - Flag to delete the data row if found. The found data row is nonetheless returned.
     * * `undefined` - Flag to return index of found row instead of row object itself.

Therefore:
findRow(column, value, null) and findRow(column, value, undefined) and findRow(column, value) all have different behaviour: delete the row, return its index or its contents. Reading code making such calls is depressing.

Hey @jjrv Thank you for your concerns, but I have to advise you to remain off the develop branch and test on alpha or the master branch. Alpha and develop may be mirrored now, but that won't always be the case (so its a future notice kind of thing). That being said, thanks for point these errors out, They shouldn't behave that way
Elaborating on my response in https://github.com/openfin/fin-hypergrid/issues/483
We will look into addressing your these bugs but also note that treeview will not be apart of core and future maintenance of it will be dropped very shortly. Abstracting it to a generic interface is the current goal in mind and fixing the bugs you pointed out would make having a general hierarchy view useful.
I'll keep you posted as I look into each of the problems mentioned

The speed issue is also present in master, where the function that gets called millions of times is here.
I also have the triangle issue with the master branch (not yet sure why).

I wonder what abstracting to a generic interface will mean... If I have hierarchical data like a directory tree, will showing it in a tree-like way still be supported by default, or require 3rd party add-ons?

Well viewing the hierarchy will be fully supported. However the restructure of the underlying data before its bound to the grid will need to be done at the application layer

@jjrv I'll provide an update for you this week

I fixed my data so the numbers are now 10070423 calls for init and 720265 for toggling any branch. The lack of speed is no longer a blocker for my use case, but still not ideal either.

@jjrv
Everyone can take a look at an review this example on the alpha branch for how to use tree-column.html to build your own tree-view. Hypergrid's implementation of tree-view is of course going away
Please also take a look at the notes in https://github.com/openfin/fin-hypergrid/issues/569. Any feedback is appreciated.


yarn create docz-app my-docz-app --example typescript error,TypeError: e.destroy is not a function

Bug Report
Describe the bug
TypeError: e.destroy is not a function.
To Reproduce
yarn create docz-app my-docz-app --example typescript
Expected behavior
run yarn create docz-app my-docz-app --example typescript error
Environment

docz version: [e.g. 2.0.0-rc.x or 1.3.2]
OS: [ OSX 11.5.2]
Node/npm version: [Node v14.15.4/npm 6.14.10]

Additional context/Screenshots

duplicated by #1452
Additionally, we're still thinking how much makes sense to have a create-docz-app, once it's not the official way to use docz, even because it's not come from docz properly. However, you're still able to install docz directly in your codebae, which in case you don't have, you can use create-react-app, and then, install it afterward. How it does sound to you?

I have the same problem with create-react-app，I am looking for a working example

Which version did you try it? Probably is your node version.


npm install fail

Hi,
it seems that npm install of milsymbol fail (on windows) with this error :
194 error enoent ENOENT: no such file or directory, chmod '\node_modules\mil-symbol\MilSymbol.js'
Thanks.

Hi,
There has been a lot of changes in the new version of milsymbol, and you should now be able to install it using npm milsymbol.
I forgot to update the npm regrestry when I released the new version this week, but hopefully everything should be up and running now. I have been kind in of a rush since I’m going to present the library to US/NATO representatives next week.
Please check out the new API documentation located in the library or at http://spatialillusions.com/milsymbol/
I hope that this hasn’t caused you any major problems.
Regards
Måns Beckman
www.spatialillusions.com

On 24 Jul 2015, at 18:14 , Arnaud Marant<EMAIL_ADDRESS>wrote:
Hi,
it seems that npm install of milsymbol fail (on windows) with this error :
194 error enoent ENOENT: no such file or directory, chmod '\node_modules\mil-symbol\MilSymbol.js'
Thanks.
—
Reply to this email directly or view it on GitHub.

So I tried the milsymbol package (why change the name from mil-symbol ?) and it still doesn't work, with the same error. I looked into it and the bin entry create the error, in the latest pull request I removed it and it works now.

Hi,
Sorry my fault, but it’s working now.
The name change was to create consistancy, before the library was named MilSymbol, camel case, the file was named milsymbol, all lower case, and the npm was named mil-symbol with a dash in it. Now it is all just milsymbol, I understand that this might cause some troubles at the moment, but I think it is a change that makes things more future proof. I decided to do all this at the same time as I developed the new API, I didn’t like to break the API either, but I had a lot of request that I couldn’t make with the old API.
It is quite easy to port old code the new API, and the new API gives you so much more flexibility and consistency. (And all code behind is so much cleaner now, before I was kind of confused by it my self, it was a conglomerate showing how I added code to my base that I developed when I started building milsymbol for a basic demo, now it’s much cleaner code and it’s possible to manage the code in a much better way.)
Regards
Måns

On 24 Jul 2015, at 20:16 , Arnaud Marant<EMAIL_ADDRESS>wrote:
So I tried the milsymbol package (why change the name from mil-symbol ?) and it still doesn't work, with the same error. I looked into it and the bin entry create the error, in the latest pull request I removed it and it works now.
—
Reply to this email directly or view it on GitHub.

ok, thanks.


Deptrac fails on invalid PHP8 code

running deptrac on my codebase fails due to some code which is invalid in PHP 8 (see https://github.com/nikic/PHP-Parser/issues/715).
This is due to the fact that PhpParser is created with option PREFER_PHP7, which actually tries to parse the code as if it was PHP 8.
Could it be better to use ONLY_PHP7 directly? Or even to expose as a configuration parameter the choice of the parser version to use?

Thanks for reporting.
The issue is not about using PREFER_PHP7 but using an emulative lexer which has become the default one in php-parser.
The fix might be passing a non emulative lexer as a second parameter here https://github.com/sensiolabs-de/deptrac/blob/master/src/AstRunner/AstParser/NikicPhpParser/ParserFactory.php#L13

Right!
I'd like to do a PR for this. What do you suggest? Having a fixed lexer or making it configurable, with PHP_7_4 as the default option?

Can you try this approach?
$phpVersion = Lexer\Emulative::PHP_7_3;
if (PHP_VERSION_ID >= 80000) {
    $phpVersion = Lexer\Emulative::PHP_8_0;
} elseif (PHP_VERSION_ID >= 70400) {
    $phpVersion = Lexer\Emulative::PHP_7_4;
}

return (new ParserFactory())->create(ParserFactory::ONLY_PHP7, new Lexer\Emulative(['phpVersion' => $phpVersion]));

I added a fixed Lexer in #417

nice, thank you!


Update enforcing-ssl.md

Edit #28028
Instructions are a bit dated, .NET 3.1
cc @omarerc

@tmds is this link worth adding?

@tmds is this link worth adding?


upgrade k8s-deployer image

for https://github.com/SeldonIO/seldon-core/issues/505
linked pr - https://github.com/SeldonIO/seldon-core/pull/517

Ping @gsunner


Workload events command

Description of problem
Logs and events are helpful for seeing what is happening on a system, and troubleshooting when things go awry.
Today it is not easy to see events from the different resources associated with building and running a workload.
Proposed solution
The CLI could bring together the events from the different resources associated with a workload, in the same way we do with tail to bring together the logs.
Example
$ tanzu apps workload events <WORKLOAD NAME>

LAST SEEN   TYPE     REASON                         OBJECT                      MESSAGE
20m         Normal   StampedObjectApplied           workload/where-for-dinner   Created object [gitrepositories.source.toolkit.fluxcd.io/where-for-dinner]
20m         Normal   ResourceHealthyStatusChanged   workload/where-for-dinner   [app-config] found healthy status in [<nil>] changed to [True]
20m         Normal   ResourceHealthyStatusChanged   workload/where-for-dinner   [service-bindings] found healthy status in [<nil>] changed to [True]
20m         Normal   ResourceHealthyStatusChanged   workload/where-for-dinner   [api-descriptors] found healthy status in [<nil>] changed to [True]
20m         Normal   StampedObjectApplied           workload/where-for-dinner   Created object [deliverables.carto.run/where-for-dinner]

Describe alternatives you've considered
Event flag

considered using $tanzu apps workload get NAME --events
This would be inconsistant with tail, which is it's own subcommand
If we want to add additional control to the events command (filtering for example) it would be nice to associate them with the events command rather than adding more flags to the get command.

App events
The apps abstraction would benefit from being able to list/get apps, as well as see the aggregated logs and events from a set of associated workloads.
$ tanzu apps events <APP NAME>

LAST SEEN   TYPE     REASON                         OBJECT                      MESSAGE
20m         Normal   StampedObjectApplied           workload/where-for-UI     Created object [gitrepositories.source.toolkit.fluxcd.io/where-for-dinner]
20m         Normal   ResourceHealthyStatusChanged   workload/where-for-data   [app-config] found healthy status in [<nil>] changed to [True]
20m         Normal   ResourceHealthyStatusChanged   workload/where-for-data   [service-bindings] found healthy status in [<nil>] changed to [True]
20m         Normal   ResourceHealthyStatusChanged   workload/where-for-UI

Color
Warning event types could be presented in color to make them more discoverable when reviewing long lists
Pagination / limit output
The example workloads I saw only had a few events saved, so the lists were short. If it turns out to be common to have very long lists it may be worth exploring a flag to limit the length of the output.
Filtering / field-selector
If event lists run long it would be helpful to be able to cherry-pick or filter, for example returning non-normal event types, or events associated with a particular resource.
Additional context
Add any other context or screenshots about the feature request here.

The most recent events should be on the top of the output. i.e. order the events in ascending order. This matches the behavior that kubectl has.

The workload events command should also include the events associated with the resources that are stamped out by the supply chain and delivery for that workload.

Visibility into events will be covered as part of our application inspector spike and I'm going to close this issue.
If we pivot away from the apps inspector based on the spike, we can consider reopening this issue for implementation.


Pond - Ebola Sudan Fasta

Choose any of these SRRs from the FDA Argos Project for Ebola sudan (attached). Complete reference guided assembly, whole genome + BCO:
EbolaSudan_FDABioProject.csv
REF:
Sudan ebolavirus, Strain: Gulu – Complete Genome – 2004
https://www.ncbi.nlm.nih.gov/assembly/GCF_000855585.1/
GenBank assembly accession: GCA_000855585.1
RefSeq assembly accession: GCF_000855585.1
BioProject: PRJNA485481
GenBank sequence: AY729654.1
NCBI Reference Sequence: NC_006432.1

[ ] @stephenshank add steps consecutively, here:

My preliminary comments are as follows:
Picked two SRA accessions at random. Reference-guided approach was not promising, perhaps because the reference was out of date and there is a long time variability in the dataset (at least 1970s-2010s). De novo appeared more promising...found one contig that was about the length of an Ebola genome. It aligns nicely with the Genbank sequence that corresponds to that SRA.
Right now I can deliver an associated BCO up to the contig file. The contig was picked out manually and will take a non-negligible amount of work to automate.
This is a fantastic opportunity to benchmark assembly approaches. Future work can include:

explore different references (easy)
explore other accessions (easy)
flashy viz with our alignment viewer (medium): http://alignment.hyphy.org/sam-scaffold
development functionality in Galaxy for mapping to multiple references in batches (medium)
automate contig picking (hard)
extend to viruses with multiple segments (hard)
deliver full BCO (hard)

and more. Further expertise in assembly is appreciated. Questions/comments are welcome.

Great! Send the fasta sequence for the assembly. Even incomplete BCO is
fine for now. Are you using megahit or metagenomicSPAdes?
On Wed, Oct 26, 2022, 12:56 PM Stephen Shank @.***>
wrote:

My preliminary comments are as follows:
Picked two SRA accessions at random. Reference-guided approach was not
promising, perhaps because the reference was out of date and there is a
long time variability in the dataset (at least 1970s-2010s). De novo
appeared more promising...found one contig
https://data.hyphy.org/web/argos/ebola-reassembly/contig.fasta that was
about the length of an Ebola genome. It aligns nicely
https://data.hyphy.org/web/argos/ebola-reassembly/aligned.fasta with the
Genbank sequence https://www.ncbi.nlm.nih.gov/nuccore/MH121161.1/ that
corresponds to that SRA.
Right now I can deliver an associated BCO up to the contig file. The
contig was picked out manually and will take a non-negligible amount of
work to automate.
This is a fantastic opportunity to benchmark assembly approaches. Future
work can include:

explore different references (easy)
explore other accessions (easy)
flashy viz with our alignment viewer (medium):
http://alignment.hyphy.org/sam-scaffold
development functionality in Galaxy for mapping to multiple
references in batches (medium)
automate contig picking (hard)
extend to viruses with multiple segments (hard)
deliver full BCO (hard)

and more. Further expertise in assembly is appreciated. Questions/comments
are welcome.
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ID: @.***>

FASTA is here: https://data.hyphy.org/web/argos/ebola-reassembly/contig.fasta

BCO up to contig is here: https://data.hyphy.org/web/argos/ebola-reassembly/bco_bf60fd5f5f7f44bf.json

Jingyue or Emily, can you please add these to data.argosdb.org and send me
the link?
On Wed, Oct 26, 2022, 1:17 PM Stephen Shank @.***>
wrote:

BCO up to contig is here:
https://data.hyphy.org/web/argos/ebola-reassembly/bco_bf60fd5f5f7f44bf.json
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@.***>

https://biocomputeobject.org/builder/https/biocomputeobject.org/ARG_000002/DRAFT

@JingyueWu

Mostly for my own usage... Galaxy/BCO integration, @HadleyKing feel free to add/modify:
Usability - annotate workflow and history
Contributors - add to a workflow (ORCID)
Description domain/steps - toolshed/(test toolshed?) entry

I queued up my (de novo) assembly pipeline for all 98 accessions in about 1 minute last night without writing a single line of code (what I will refer to henceforth as "no code", and can be performed by undergraduates on up). I copied and pasted accessions from the above CSV (thank you for that!) into Galaxy and executed the associated workflow. This results in a single BCO and 98 contig files, one for each SRA accession. It completed overnight and has an associated history and an incomplete assemblyQC table.
There are three non-negligible efforts that would make this work more complete:

automated extraction of contigs to assemblies, which are currently being done by hand
batch mapping of (re)assemblies back to existing assemblies for comparison (currently somewhat clunky in Galaxy)
more quantification of comparisons (essentially, complete my assemblyQC table) and associated visualizations

Happy to discuss further tomorrow.

@rajamazumder Any Ebola assemblies to compare/FASTAs to share? I also tried an ivar based reference-guided approach that seemed less promising than de novo. It was an eye opening experience for me.

Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***> wrote:

@rajamazumder https://github.com/rajamazumder Any Ebola assemblies to
compare/FASTAs to share? I also tried an ivar
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
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https://github.com/FDA-ARGOS/data.argosdb/issues/113#issuecomment-1299089602,
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You are receiving this because you were mentioned.Message ID:
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Yes - @rajamazumder  I have been watching all of our task and conversations. I will send the ngs read to Thomas, but Stephen already has what we want him to have, and we still have not finish this initial task, so I will not pile more on to @stephenshank - Also Thomas is not in this project so he can't see what you are messaging.
@JingyueWu is following up on all the tasks to complete this.

@stephenshank
Argos_FDA_BioProject_List.xlsx
Two tabs in this excel File:
Tab 1 (ArgosFDABioProject) - all entries in the BioProject, for Reference
Tab 2 (EbolaSudan_FDABioProject) - Sudan Ebolavirus ONLY. Highlighted yellow entries are preferred, as they are WGS. Use this second list to guide your task.

Cursory thoughts:

I'm going to run all Sudan Ebola in the list you shared because if I understand correctly this should facilitate comparisons with previous assemblies (thanks for the updated list). Time permitting I can hunt for accessions during the last highly publicized outbreak by looking at news articles and filtering on date ranges in SRA (just thinking out loud)
See above
Will do, I will update the workflow to auto-populate previously requested fields and try to make my own draft in the portal
Will do, I can use some direction on a proper header as commented in #114
It's possible that this gets wrapped up by our Monday meeting, but depends on some elements that are slightly outside of my control/understanding. I have a Galaxy friendly strategy for the partial contig issue I raised today that I need to test, if it fails it may necessitate further development

Great catch with the Zaire accession today @steph-sing!

Hi Stephen,
Attached is an alignment of assemblies of the SARS-CoV-2 Wuhan-Hu genome
that Millicent (cc'd) and I did using different software available on
either HIVE or Galaxy. All assemblies were done using SRR10971381 from SRA
using software available either on HIVE or Galaxy. I have included the NCBI
reference genome (NC_045512) in the alignment and indicated in the name of
each sequence which software was used and the operator's initials.
I also found a paper (
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5)
that provides a good comparison of the performances of several different
assemblers for viral genomes.
Let me know if you have any questions or concerns.
Best,
Tommy Voigt
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder @.***> wrote:

Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***>
wrote:

@rajamazumder https://github.com/rajamazumder Any Ebola assemblies to
compare/FASTAs to share? I also tried an ivar
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
Reply to this email directly, view it on GitHub
https://github.com/FDA-ARGOS/data.argosdb/issues/113#issuecomment-1299089602,
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You are receiving this because you were mentioned.Message ID:
@.***>

Dear Thomas,
Thanks so much for this, this looks great! My first question is whether there are BCOs or workflows (files and/or URLS) associated to the Galaxy based assemblies. The paper looks awesome too!
My next thought is that I'd love to install some of the tools/workflows on our instance and get an integration with ObservableHQ going. I have an alignment viewer:
http://alignment.hyphy.org/fasta-viewer
that (so far) has barely made it to our preferred, aforementioned notebook platform:
@.***/assembly-qc?payload_id=59db80eee3e3e18f&base_url=galaxy.hyphy.org
Note that the above notebook is pulling live from an existing Galaxy history:
https://galaxy.hyphy.org/u/stephenshank/h/assemblyqc---92622
due to a software integration between the two platforms that is being developed by our lab for this project. Here's some eye candy that Professor Mazumder asked for, since it is way flashier than a table:
@.***/selection-analysis-on-spike-antibody-complex-for-sars-cov-2?payload_id=17702c03e6f9b734&base_url=galaxy.hyphy.org
I will do a deeper dive, but again this looks fantastic. Thanks again for sharing, I would greatly enjoy further correspondence with you on this topic.
Regards,
Stephen

From: Thomas Voigt @.>
Sent: Wednesday, November 2, 2022 6:22 PM
To: Stephen D. Shank @.>; Mention @.>
Cc: FDA-ARGOS/data.argosdb @.>; FDA-ARGOS/data.argosdb @.>; Stephanie Singleton @.>; @.*** @.>; Quartey, Millicent @.>
Subject: [External] Re: [FDA-ARGOS/data.argosdb] Ebola Sudan Fasta (Issue #113)
Hi Stephen,
Attached is an alignment of assemblies of the SARS-CoV-2 Wuhan-Hu genome that Millicent (cc'd) and I did using different software available on either HIVE or Galaxy. All assemblies were done using SRR10971381 from SRA using software available either on HIVE or Galaxy. I have included the NCBI reference genome (NC_045512) in the alignment and indicated in the name of each sequence which software was used and the operator's initials.
I also found a paper (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicrobiomejournal.biomedcentral.com%2Farticles%2F10.1186%2Fs40168-019-0626-5&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=5RWt2d99219zhiUx5nJCNbVFrdQ%2BwZpV9ELJAHEK9bQ%3D&reserved=0) that provides a good comparison of the performances of several different assemblers for viral genomes.
Let me know if you have any questions or concerns.
Best,
Tommy Voigt
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder<EMAIL_ADDRESS>wrote:
Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank<EMAIL_ADDRESS>wrote:
@rajamazumderhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frajamazumder&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=gk1OSU9Io2HOW9fTKLo%2Ba2%2FgsWPuDVfLxVQrvP3E%2Fgo%3D&reserved=0 Any Ebola assemblies to compare/FASTAs to share? I also tried an ivarhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticles%2F10.1186%2Fs13059-018-1618-7&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=xzxrVRIFHavr%2F40PktrOe7UVtZlSbJf8%2FshJ3cAkKSg%3D&reserved=0 based reference-guided approach that seemed less promising than de novo. It was an eye opening experience for me.
—
Reply to this email directly, view it on GitHubhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFDA-ARGOS%2Fdata.argosdb%2Fissues%2F113%23issuecomment-1299089602&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365843684|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=%2Bag7iPsngULuh1FVLWkeuC56UkjuODQzfmXE%2B6WslXo%3D&reserved=0, or unsubscribehttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAE3GISLDUP7YFDRF6K7SPR3WGF3NXANCNFSM6AAAAAARNHLWJE&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365843684|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=qTv0gZh0y73wU9AExSKwB7QeeRoVTT0cCg0dorDZFYY%3D&reserved=0.
You are receiving this because you were mentioned.Message ID: @.***>

Yes, Raja, I set up the ticket.
Thomas,
I've attached a file to guide your assembly process:
Two tabs in this excel file:
Tab 1 (ArgosFDABioProject) - all entries in the Argos BioProject, for
reference
Tab 2 (EbolaSudan_FDABioProject) - Sudan Ebolavirus ONLY. Highlighted
yellow entries are preferred, as they are WGS. If you have different or
have additional selection criteria, please note those reasons to me via
email. Use this second list to guide your task.
Please let me know if you have any questions! Thanks
*Stephanie Singleton, MS *
Senior Bioinformatics Research Associate
Microbial Computational Biologist & Scientific Project Lead - FDA-ARGOS
Scientific Coordination Team Member
Department of Biochemistry and Molecular Medicine, HIVE Lab
School of Medicine & Health Sciences
The George Washington University
2300 I St NW, Washington, DC 20052
Office 543B
Phone:<PHONE_NUMBER>
Check Us Out! HIVE Lab https://hive.biochemistry.gwu.edu/home
*My LinkedIn http://www.linkedin.com/in/stephanie-singleton-ms-2788b078 *
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder @.***> wrote:

Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***>
wrote:

@rajamazumder https://github.com/rajamazumder Any Ebola assemblies to
compare/FASTAs to share? I also tried an ivar
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
Reply to this email directly, view it on GitHub
https://github.com/FDA-ARGOS/data.argosdb/issues/113#issuecomment-1299089602,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AE3GISLDUP7YFDRF6K7SPR3WGF3NXANCNFSM6AAAAAARNHLWJE
.
You are receiving this because you were mentioned.Message ID:
@.***>

Thanks, Stephanie!
I will get started on this ASAP and should be able to get this back to you
by Monday, but will make sure to let you know if anything comes up that
delays the process.
Best,
Tommy Voigt
On Thu, Nov 3, 2022 at 9:19 AM Singleton, Stephanie <
@.***> wrote:

Yes, Raja, I set up the ticket.
Thomas,
I've attached a file to guide your assembly process:
Two tabs in this excel file:
Tab 1 (ArgosFDABioProject) - all entries in the Argos BioProject, for
reference
Tab 2 (EbolaSudan_FDABioProject) - Sudan Ebolavirus ONLY. Highlighted
yellow entries are preferred, as they are WGS. If you have different or
have additional selection criteria, please note those reasons to me via
email. Use this second list to guide your task.
Please let me know if you have any questions! Thanks
*Stephanie Singleton, MS *
Senior Bioinformatics Research Associate
Microbial Computational Biologist & Scientific Project Lead - FDA-ARGOS
Scientific Coordination Team Member
Department of Biochemistry and Molecular Medicine, HIVE Lab
School of Medicine & Health Sciences
The George Washington University
2300 I St NW, Washington, DC 20052
Office 543B
Phone:<PHONE_NUMBER>
Check Us Out! HIVE Lab https://hive.biochemistry.gwu.edu/home
*My LinkedIn http://www.linkedin.com/in/stephanie-singleton-ms-2788b078 *
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder @.***> wrote:

Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***>
wrote:

@rajamazumder https://github.com/rajamazumder Any Ebola assemblies to
compare/FASTAs to share? I also tried an ivar
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
Reply to this email directly, view it on GitHub
https://github.com/FDA-ARGOS/data.argosdb/issues/113#issuecomment-1299089602,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AE3GISLDUP7YFDRF6K7SPR3WGF3NXANCNFSM6AAAAAARNHLWJE
.
You are receiving this because you were mentioned.Message ID:
@.***>

Stephen,
Thanks for sharing, those all look great!
Regarding my specific parameters, files, etc, I made my history on Galaxy
accessible for this project through the link below:
https://usegalaxy.org.au/u/tvoigt/h/sars-cov-2-wuhan-hu1-assembly
I will coordinate with Millicent to get a link to her assemblies. Let me
know if you have any questions or concerns.
Best,
Tommy Voigt
On Wed, Nov 2, 2022 at 6:45 PM Stephen D. Shank @.***>
wrote:

Dear Thomas,
Thanks so much for this, this looks great! My first question is whether
there are BCOs or workflows (files and/or URLS) associated to the Galaxy
based assemblies. The paper looks awesome too!
My next thought is that I'd love to install some of the tools/workflows on
our instance and get an integration with ObservableHQ going. I have an
alignment viewer:
http://alignment.hyphy.org/fasta-viewer
that (so far) has barely made it to our preferred, aforementioned notebook
platform:
@.***/assembly-qc?payload_id=59db80eee3e3e18f&base_url=galaxy.hyphy.org
Note that the above notebook is pulling live from an existing Galaxy
history:
https://galaxy.hyphy.org/u/stephenshank/h/assemblyqc---92622
due to a software integration between the two platforms that is being
developed by our lab for this project. Here's some eye candy that Professor
Mazumder asked for, since it is way flashier than a table:
@.***/selection-analysis-on-spike-antibody-complex-for-sars-cov-2?payload_id=17702c03e6f9b734&base_url=galaxy.hyphy.org
I will do a deeper dive, but again this looks fantastic. Thanks again for
sharing, I would greatly enjoy further correspondence with you on this
topic.
Regards,
Stephen
From: Thomas Voigt @.>
Sent: Wednesday, November 2, 2022 6:22 PM
To: Stephen D. Shank @.>; Mention <
@.>
Cc: FDA-ARGOS/data.argosdb <
@.>;
FDA-ARGOS/data.argosdb @.>; Stephanie
Singleton @.>; @.*** @.>;
Quartey, Millicent @.>
Subject: [External] Re: [FDA-ARGOS/data.argosdb] Ebola Sudan Fasta
(Issue #113)
Hi Stephen,
Attached is an alignment of assemblies of the SARS-CoV-2 Wuhan-Hu genome
that Millicent (cc'd) and I did using different software available on
either HIVE or Galaxy. All assemblies were done using SRR10971381 from SRA
using software available either on HIVE or Galaxy. I have included the NCBI
reference genome (NC_045512) in the alignment and indicated in the name
of each sequence which software was used and the operator's initials.
I also found a paper (
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicrobiomejournal.biomedcentral.com%2Farticles%2F10.1186%2Fs40168-019-0626-5&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=5RWt2d99219zhiUx5nJCNbVFrdQ%2BwZpV9ELJAHEK9bQ%3D&reserved=0)
that provides a good comparison of the performances of several different
assemblers for viral genomes.
Let me know if you have any questions or concerns.
Best,
Tommy Voigt
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder @.***> wrote:
Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***>
wrote:
@rajamazumder
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frajamazumder&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=gk1OSU9Io2HOW9fTKLo%2Ba2%2FgsWPuDVfLxVQrvP3E%2Fgo%3D&reserved=0
Any Ebola assemblies to compare/FASTAs to share? I also tried an ivar
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticles%2F10.1186%2Fs13059-018-1618-7&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=xzxrVRIFHavr%2F40PktrOe7UVtZlSbJf8%2FshJ3cAkKSg%3D&reserved=0
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
Reply to this email directly, view it on GitHub
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFDA-ARGOS%2Fdata.argosdb%2Fissues%2F113%23issuecomment-1299089602&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365843684|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=%2Bag7iPsngULuh1FVLWkeuC56UkjuODQzfmXE%2B6WslXo%3D&reserved=0,
or unsubscribe
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.
You are receiving this because you were mentioned.Message ID:
@.***>

Stephen- Just to make sure we are all on the same page. Thomas is a
rotating PhD student who is just helping out with this side project so that
we had another pair of eyes looking at the assemblies because others in the
Argos team at our end have been busy with other things. Millicent also is
helping out with some HIVE assembly tools and she works for the HIVE
platform.
--
Raja Mazumder, Ph.D.
Professor
Department of Biochemistry and Molecular Medicine
School of Medicine & Health Sciences
The George Washington University
Ross Hall, Room 540
2300 Eye Street N.W.
Washington, DC 20037
Phone office:<PHONE_NUMBER>
Phone lab:<PHONE_NUMBER>
Phone dept:<PHONE_NUMBER>
Fax:<PHONE_NUMBER>
On Thu, Nov 3, 2022 at 9:34 AM Thomas Voigt @.***> wrote:

Stephen,
Thanks for sharing, those all look great!
Regarding my specific parameters, files, etc, I made my history on Galaxy
accessible for this project through the link below:
https://usegalaxy.org.au/u/tvoigt/h/sars-cov-2-wuhan-hu1-assembly
I will coordinate with Millicent to get a link to her assemblies. Let me
know if you have any questions or concerns.
Best,
Tommy Voigt
On Wed, Nov 2, 2022 at 6:45 PM Stephen D. Shank @.***>
wrote:

Dear Thomas,
Thanks so much for this, this looks great! My first question is whether
there are BCOs or workflows (files and/or URLS) associated to the Galaxy
based assemblies. The paper looks awesome too!
My next thought is that I'd love to install some of the tools/workflows
on our instance and get an integration with ObservableHQ going. I have an
alignment viewer:
http://alignment.hyphy.org/fasta-viewer
that (so far) has barely made it to our preferred, aforementioned
notebook platform:
@.***/assembly-qc?payload_id=59db80eee3e3e18f&base_url=galaxy.hyphy.org
Note that the above notebook is pulling live from an existing Galaxy
history:
https://galaxy.hyphy.org/u/stephenshank/h/assemblyqc---92622
due to a software integration between the two platforms that is being
developed by our lab for this project. Here's some eye candy that Professor
Mazumder asked for, since it is way flashier than a table:
@.***/selection-analysis-on-spike-antibody-complex-for-sars-cov-2?payload_id=17702c03e6f9b734&base_url=galaxy.hyphy.org
I will do a deeper dive, but again this looks fantastic. Thanks again for
sharing, I would greatly enjoy further correspondence with you on this
topic.
Regards,
Stephen
From: Thomas Voigt @.>
Sent: Wednesday, November 2, 2022 6:22 PM
To: Stephen D. Shank @.>; Mention <
@.>
Cc: FDA-ARGOS/data.argosdb <
@.>;
FDA-ARGOS/data.argosdb @.>; Stephanie
Singleton @.>; @.*** @.>;
Quartey, Millicent @.>
Subject: [External] Re: [FDA-ARGOS/data.argosdb] Ebola Sudan Fasta
(Issue #113)
Hi Stephen,
Attached is an alignment of assemblies of the SARS-CoV-2 Wuhan-Hu genome
that Millicent (cc'd) and I did using different software available on
either HIVE or Galaxy. All assemblies were done using SRR10971381 from SRA
using software available either on HIVE or Galaxy. I have included the NCBI
reference genome (NC_045512) in the alignment and indicated in the name
of each sequence which software was used and the operator's initials.
I also found a paper (
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicrobiomejournal.biomedcentral.com%2Farticles%2F10.1186%2Fs40168-019-0626-5&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=5RWt2d99219zhiUx5nJCNbVFrdQ%2BwZpV9ELJAHEK9bQ%3D&reserved=0)
that provides a good comparison of the performances of several different
assemblers for viral genomes.
Let me know if you have any questions or concerns.
Best,
Tommy Voigt
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder @.***> wrote:
Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***>
wrote:
@rajamazumder
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frajamazumder&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=gk1OSU9Io2HOW9fTKLo%2Ba2%2FgsWPuDVfLxVQrvP3E%2Fgo%3D&reserved=0
Any Ebola assemblies to compare/FASTAs to share? I also tried an ivar
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticles%2F10.1186%2Fs13059-018-1618-7&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=xzxrVRIFHavr%2F40PktrOe7UVtZlSbJf8%2FshJ3cAkKSg%3D&reserved=0
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
Reply to this email directly, view it on GitHub
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFDA-ARGOS%2Fdata.argosdb%2Fissues%2F113%23issuecomment-1299089602&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365843684|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=%2Bag7iPsngULuh1FVLWkeuC56UkjuODQzfmXE%2B6WslXo%3D&reserved=0,
or unsubscribe
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAE3GISLDUP7YFDRF6K7SPR3WGF3NXANCNFSM6AAAAAARNHLWJE&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365843684|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=qTv0gZh0y73wU9AExSKwB7QeeRoVTT0cCg0dorDZFYY%3D&reserved=0
.
You are receiving this because you were mentioned.Message ID:
@.***>

Stephen,
Millicent's history on Galaxy can be accessed with the link below:
https://usegalaxy.org.au/u/milli_q/h/sars-cov-2-assembly---millicent
Let me know if you have any questions.
Best,
Tommy Voigt
On Thu, Nov 3, 2022 at 9:34 AM Thomas Voigt @.***> wrote:

Stephen,
Thanks for sharing, those all look great!
Regarding my specific parameters, files, etc, I made my history on Galaxy
accessible for this project through the link below:
https://usegalaxy.org.au/u/tvoigt/h/sars-cov-2-wuhan-hu1-assembly
I will coordinate with Millicent to get a link to her assemblies. Let me
know if you have any questions or concerns.
Best,
Tommy Voigt
On Wed, Nov 2, 2022 at 6:45 PM Stephen D. Shank @.***>
wrote:

Dear Thomas,
Thanks so much for this, this looks great! My first question is whether
there are BCOs or workflows (files and/or URLS) associated to the Galaxy
based assemblies. The paper looks awesome too!
My next thought is that I'd love to install some of the tools/workflows
on our instance and get an integration with ObservableHQ going. I have an
alignment viewer:
http://alignment.hyphy.org/fasta-viewer
that (so far) has barely made it to our preferred, aforementioned
notebook platform:
@.***/assembly-qc?payload_id=59db80eee3e3e18f&base_url=galaxy.hyphy.org
Note that the above notebook is pulling live from an existing Galaxy
history:
https://galaxy.hyphy.org/u/stephenshank/h/assemblyqc---92622
due to a software integration between the two platforms that is being
developed by our lab for this project. Here's some eye candy that Professor
Mazumder asked for, since it is way flashier than a table:
@.***/selection-analysis-on-spike-antibody-complex-for-sars-cov-2?payload_id=17702c03e6f9b734&base_url=galaxy.hyphy.org
I will do a deeper dive, but again this looks fantastic. Thanks again for
sharing, I would greatly enjoy further correspondence with you on this
topic.
Regards,
Stephen
From: Thomas Voigt @.>
Sent: Wednesday, November 2, 2022 6:22 PM
To: Stephen D. Shank @.>; Mention <
@.>
Cc: FDA-ARGOS/data.argosdb <
@.>;
FDA-ARGOS/data.argosdb @.>; Stephanie
Singleton @.>; @.*** @.>;
Quartey, Millicent @.>
Subject: [External] Re: [FDA-ARGOS/data.argosdb] Ebola Sudan Fasta
(Issue #113)
Hi Stephen,
Attached is an alignment of assemblies of the SARS-CoV-2 Wuhan-Hu genome
that Millicent (cc'd) and I did using different software available on
either HIVE or Galaxy. All assemblies were done using SRR10971381 from SRA
using software available either on HIVE or Galaxy. I have included the NCBI
reference genome (NC_045512) in the alignment and indicated in the name
of each sequence which software was used and the operator's initials.
I also found a paper (
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicrobiomejournal.biomedcentral.com%2Farticles%2F10.1186%2Fs40168-019-0626-5&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=5RWt2d99219zhiUx5nJCNbVFrdQ%2BwZpV9ELJAHEK9bQ%3D&reserved=0)
that provides a good comparison of the performances of several different
assemblers for viral genomes.
Let me know if you have any questions or concerns.
Best,
Tommy Voigt
On Tue, Nov 1, 2022 at 6:59 PM Raja Mazumder @.***> wrote:
Stephanie,
Are you a watcher on this? Can you please send Ebola ngs accession to
assemble. Also, Thomas can you please send your assembly to Stephen?
On Tue, Nov 1, 2022, 4:19 PM Stephen Shank @.***>
wrote:
@rajamazumder
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frajamazumder&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=gk1OSU9Io2HOW9fTKLo%2Ba2%2FgsWPuDVfLxVQrvP3E%2Fgo%3D&reserved=0
Any Ebola assemblies to compare/FASTAs to share? I also tried an ivar
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticles%2F10.1186%2Fs13059-018-1618-7&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365687475|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=xzxrVRIFHavr%2F40PktrOe7UVtZlSbJf8%2FshJ3cAkKSg%3D&reserved=0
based reference-guided approach that seemed less promising than de novo. It
was an eye opening experience for me.
—
Reply to this email directly, view it on GitHub
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFDA-ARGOS%2Fdata.argosdb%2Fissues%2F113%23issuecomment-1299089602&data=05|01|stephen.shank%40temple.edu|19f31131f2814ea74b8d08dabd20b00f|716e81efb52244738e3110bd02ccf6e5|0|0|638030245365843684|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=%2Bag7iPsngULuh1FVLWkeuC56UkjuODQzfmXE%2B6WslXo%3D&reserved=0,
or unsubscribe
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.
You are receiving this because you were mentioned.Message ID:
@.***>

hi @stephenshank please attached the Ebola Sudan fasta here. @JingyueWu will take care of the header for you. If the protocol has been updated, please send and updated link for your BCO here as well, we will push it through the backend.
Otherwise, please provide a general status update.

https://data.hyphy.org/web/argos/ebola-reassembly/

Status: BCO issue is being fixed by @HadleyKing

FASTA file is here, still needs appropriate header: http://data.hyphy.org/web/argos/ebola-reassembly/reassembled.fasta

@HadleyKing I'll try converter on the BCO.

@stephenshank do you have a status update on this task?

I have a much better approach that is essentially described here. It uses a tool called VAPOR to a select a reference from several candidates based on kmer distributions between reads and reference genomes. This approach yielded the highest fidely to published ARGOS assemblies yet, only off by a single nucleotide.
I unfortunately encountered some last minute hiccups with the BCO. Will give a FASTA/BCO early next week and then discuss scaling.

I now have 8 out of 10 assemblies that look great, ranging from 99-99.99% accuracy, each with a BCO.
Among the two failures, on one the VAPOR tool failed, and required rerunning with a less stringent parameter.
On another, everything ran, but the BAM is of low quality (large stretches where no reads mapped resulting in large stretches of Ns). This is the case for more than one mapper. I suspect that VAPOR may have either picked a poor reference, or no suitable reference was found.
I'll send the 8 decent FASTAs + BCOs ASAP and investigate the above issues for this month. It should not be that much extra work to assemble all Sudan Ebola SRAs.

will include in the April Data push on the 5th and April Tasks.

FASTA is here: https://data.hyphy.org/web/argos/ebola-reassembly/sudanese_ebola_PL.fasta
biocomputeobject.org appears to be down right now.


PATCH /session/account/profile -> 409 "data.id must be '{id}'" error

This is a starter issue. It’s part of https://github.com/hoodiehq/hoodie-server-account/issues/83
:octocat:  Your First Pull Request?
We would like to take the opportunity to invite someone who did not yet contribute to Hoodie to work on this issue. Follow @YourFirstPR on Twitter for more of these issues across many open source projects :)
:bug: The Bug
To change a profile, user send a PATCH /session/account request with the changed attributes. The JSON API Spec which we comply with requires an update request to send data.id. So in theory a user could send a data.id of a profile which is not theirs.
:dart: The goal
Compare the data.id from request payload with the profile id of the current user. If they diverge, return a 409 Conflict error with the message "data.id must be '{id}'", where {id} is the current user’s profile id
:clipboard: Step by Step

[ ] claim this issue (comment below or assign yourself)
[ ] Setup repository locally and make sure that all tests pass
[ ] Uncomment tests here
[ ] Make sure tests fail when you run npm test
[ ] Commit with test(routes): PATCH /session/account/profile -> 409 "data.id must be '{id}'" error
[ ] Start a Pull Request.
(If this is your first, welcome :tada: :smile: Here is a great tutorial on how to send a pull request)
[ ] Implement :)
[ ] Make sure tests pass when you run npm test. Commit with fix(routes): PATCH /session/account/profile -> 409 "data.id must be '{id}'" error
[ ] Done :+1: Ask in comments for a review :)

Ping us in the Hoodie Chat or on Twitter if you have any questions :)

I'd love to tackle this if possible (I'm completely new to the hoodie project).

@tnguyen14 welcome Tri :) The issue is all yours

merged via #121, released as v2.6.17.
Congratulations and thank’s a lot :bouquet: for your first PR to Hoodie :) We have invited you to the contributors team. If you like you can accept the invitation at https://github.com/hoodiehq. As Hoodie Team member you can push directly to our main repositories, no need to do forks. That makes it simpler to collaborate.  We love giving new contributors a shout out with our @hoodiehq twitter account, if you like?

Many thanks @gr2m! this is honestly the best contributing experience to an open source project I've had (not that I've had many to compare to). Really appreciate your patience and guidance throughout. I am on twitter @tridnguyen.


Transformation idea: vector access like .x to [0]

Hi
i want to solve this good first issue
please guide me through

Sure.
OpaqueExpressionGenerator.java has a field:
private final List expressionIdentities;
An ExpressionIdentity is a class that knows how to turn an expression e into an equivalent expression e'.  In this case we want to turn "v.x", where "v" is a vector, into "v[0]" (and similarly for other components).
Lines 72 onwards in OpaqueExpressionGenerator feature statements like:
    expressionIdentities.add(new IdentityAddSubZero());
    expressionIdentities.add(new IdentityMulDivOne());
    expressionIdentities.add(new IdentityAndTrue());
    expressionIdentities.add(new IdentityOrFalse());
    expressionIdentities.add(new IdentityLogicalNotNot());
    expressionIdentities.add(new IdentityTernary());

You would want to add something like:
    expressionIdentities.add(new IdentityVectorComponent());

Then, lower in the class, you would need to write the IdentityVectorComponent class.
Have a look at other classes in the file, such as IdentityOrFalse, for inspiration.
In your case you will need to override preconditionHolds to check that the expression being considered for transformation is a MemberLookupExpr. Then, in apply, you'll need to inspect which field of the vector is being accessed, and replace the expression with an ArrayIndexExpr that uses the appropriate index.
Hope this helps you get started.

Hey,
I read this code
May, I contribute?

shivani please let me work on this code .....
this is my first time ever
a little experience will help me :))

shivani please let me work on this code .....
this is my first time ever
a little experience will help me :))

Okay , No problem 🙂

how to proceed from start ??
please help

@shubhav99 Can you explain in detail what the problem is that you are facing? What did you try and what error messages are you getting?

sir i want to work on this issue , from where can i start?

sir i am stuck in the return statement of this issue , can you help me out?

sir in the return statement i need to return ArrayIndexExpr ?? like this
return  ArrayIndexExpr(Expr array, Expr index) {
    // vec2 v;
    // v[0]; // fine
    // v + vec2(0.0)[0]; // not fine - the following was probably intended:
    // (v + vec2(0.0))[0]; // fine

    if (array instanceof BinaryExpr) {
      throw new IllegalArgumentException("Array index into binary expression "
          + array.getText() + " not allowed.");
    }
    this.array = array;
    this.index = index;
  }

Hello sir, Can I work on this issue?

hello i am a beginner in this issue,could you please tell me how to get started


Could you update to 3D deformable convolution?

I can't find a suitable 3d version of DCN/DCNv2 on the Internet. Could you update this PyTorch version with a 3D DCN with support for large images?
For example: (N, 3, 128, 128, 128)

Maybe this repo can help you :)
D3Dnet

Maybe this repo can help you :)
D3Dnet
Thanks, I've tried it before. The "core dumped" error would occur if the image size is too big.