Switch to genomecov from nf-core (with separate sort)

Moving existing bedtools genomecov to use nf-core module.
PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

workflows/rnaseq/main.nf:
	653: Trailing whitespace


Tried anyone to install katex plugin?

Tried anyone to install katex plugin?
Because the mdPlugins and hastPlugins parameters work separately from each other, I can't understand in what order I need to install and connect such plugins as: remark, remark-math, remark-rehype, rehype-stringify, rehype-katex.
More information about those plugins you can find here.

You need to pass all your options in the same object like that:
https://github.com/pedronauck/docz/blob/master/packages/docz-core/src/config/mdx.ts#L7-L26
I don't like this pattern too, but is the way adopted by mdx 😕

Discussion already closed but don't know if it would help someone but I also had some problems using 'remark-math' and 'katex'. In my case, I get the katex rendering working but I am getting it rendered twice with the properly rendered and non-rendered text (e.g. $ a^2 $, I get both a2 and a^2 as the result.
Don't know why it works but including the 'katex' cdn in the index.html made it render properly. Still trying to figure out what's happening.
doczrc.js
import math from 'remark-math';
import katex from 'remark-html-katex';
import html from 'remark-html';
export default {
  indexHtml: './index.html',
  mdPlugins: [math, html, katex]
};

index.html
<!DOCTYPE html>
<html lang="{{ lang }}">

<head>
    <meta charset="UTF-8">
    <meta name="description" content="{{ description }}">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <meta http-equiv="X-UA-Compatible" content="ie=edge">
    <!-- <script src='https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML' async></script> -->
    <link rel="stylesheet"<EMAIL_ADDRESS>integrity="sha384-D+9gmBxUQogRLqvARvNLmA9hS2x//eK1FhVb9PiU86gmcrBrJAQT8okdJ4LMp2uv"
        crossorigin="anonymous">

    <!-- The loading of KaTeX is deferred to speed up page rendering -->
    <script defer<EMAIL_ADDRESS>integrity="sha384-483A6DwYfKeDa0Q52fJmxFXkcPCFfnXMoXblOkJ4JcA8zATN6Tm78UNL72AKk+0O"
        crossorigin="anonymous"></script>

    <!-- To automatically render math in text elements, include the auto-render extension: -->
    <script defer<EMAIL_ADDRESS>integrity="sha384-yACMu8JWxKzSp/C1YV86pzGiQ/l1YUfE8oPuahJQxzehAjEt2GiQuy/BIvl9KyeF"
        crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
    <title>{{ title }}</title>
    {{ head }}
</head>

<body>
    <div id="root" />
    {{ footer }}
</body>

</html>


Play song in current playlist, and continue through the playlist

If I'm playing a playlist in iTunes, is it possible to use this workflow to play a specific song from this playlist, and once that song is done, then cede control back to iTunes and continue playing the playlist like normal?
Because right now, this workflow creates a new playlist with just the song that I chose, therefore playing it indefinitely.

I can see how such a feature could be potentially implemented, however I will need to carefully consider the design as well. In other words, I will consider your feature request. :)

Thanks. If it helps, this workflow does the trick, but it hasn't been updated in two years and lacks almost all the features that your workflow has, except it is able to play from the current playlist.

@GaryKing, would you find it acceptable if I were to implement this feature such that holding down the Option key when selecting a result would do the following?

Stop playback of the workflow playlist
Immediately play the selected song/album/artist/etc.
Play the next song in the workflow playlist (the one after the interrupted song)

As I said, implementing this behavior should be rather straightforward.
@Tyilo, I would appreciate any input you have to offer on this proposed feature.

That wouldn't work for me, personally.
How I usually listen to my music is:

In Alfred, iTunes browser -> select a playlist (such as "instrumental music") and play it.
I want to jump to a specific song in that playlist, so I open Alfred and type "play ", which only selects from songs in the currently playing playlist, and once that song is done, iTunes simply continues from the same playlist.

With your suggestion, based on my understanding of your phrase "workflow playlist" (meaning the playlist created by your workflow in iTunes, with the name "Alfred playlist" or something similar, if I recall), this would first require I use the workflow to create the playlist. But in fact, I use my own playlists because they are all Smart Playlists with very specific criteria that I set, so of course I'd definitely prefer using them if possible.
My preferred method would essentially be the same as manually opening iTunes, typing in the search bar, and selecting a song, which would play that song immediately, then continue from the same playlist.

Hmm, that sounds to me a rather specific use case, and therefore isn't something I would adopt as a general feature of the workflow.
Caleb

Okay that's unfortunate. I don't think it's too specific. It basically boils down to:

Play a playlist in iTunes.
Want to play a specific song from that playlist, so open Alfred -> Type play <song name>, then when the song is done, continue playing that playlist.

This would basically be the same thing as selecting the song you want to play and clicking "Play Next". Unfortunately I don't think there is an easy way of adding songs to iTunes own queue using AppleScript.
The way we do it now we would have to determine all the songs that would be played after the song chosen and create a new playlist with the song you want to play and then add all the other songs in the current playlist to the new one. Then we would play the new playlist.
@GaryKing Say you were playing this playlist, were song2 is the current song:
song1
song2 <---
song3
song4
song5

You then want to play song4. I see 2 possible outcomes in the which songs is played:

song1
song2
song4
song3
song4
song5

song1
song2
song4
song5

Which of these were you thinking of? Or were you thinking of something different?

Based on your explanation, I think option 2 is the one I was thinking of.
But like I said, this has definitely been done before, because I'm currently using a workflow that does this, in my second post. When I choose a song to play, it doesn't add it to Up Next. It plays the song immediately, then it continues playing the playlist like before. The AppleScript they use is actually quite simple:
on run argv
    set itunes_item to item 1 in argv

    tell application "iTunes" to set playlist_list to the name of every user playlist

    if playlist_list does not contain itunes_item then
        tell application "iTunes" to play (first track of current playlist whose database ID is itunes_item)
    else
        tell application "iTunes" to play playlist itunes_item
    end if

end run

I would like this functionality too


Search folders in batches to avoid 413 entity too large from drive api

Description of Change
What it says on the tin - search folders in batches to avoid 413 entity too large from the Google Drive API.
Related Issue
Resolves #59
Motivation and Context
When we call drive.files.list() in fullSearch(), we pass all of the folderIds (if driveType === 'team').  When you have a lot of folders, the call to drive.files.list() returns 413 Entity too large because the query is too big.
In this PR I added a MAX_FOLDERS_TO_SEARCH parameter, and batched the folderIds to search into batches of that size or fewer, and then I search over the batches sequentially.
FWIW, we could search the batches simultaneously with a Promise.all().
In my testing with a 4-character search string, 128 folders worked, but 129 folders triggered the 413.  Because the querystring contains other data besides the parents, you may hit the 418 with fewer folders, so I set MAX_FOLDERS_TO_SEARCH to 100 to give us some headroom.
Checklist

[x] Ran npm run lint and updated code style accordingly
[ ] npm run test passes
[ ] PR has a description and all contributors/stakeholder are noted/cc'ed
[ ] tests are updated and/or added to cover new code
[ ] relevant documentation is changed and/or added

I ended up implementing the concurrent searching over the batches of folderIds


v1.0.0 DB misses some transactions!

I sent the same request to https://arweave.net/graphql and to my own v1.0.0 installation:
query {
  transactions(
    first: 2
    ids: [
      "qul1Elv7Xg6LtyTkPqDj0i5jNr38aOLvi9qsDMoO9Jg",
      "c3T92aWcYEt79uok96MkH6TyXuKageX-1cn1oW46v7s"
    ]
  ) {,
    edges {
      node {
        block {
          id
          height
        }
        id
      }
    }
  }
}

arweave.net replies:
{
  "data": {
    "transactions": {
      "edges": [
        {
          "node": {
            "block": {
              "id": "ImTHSwo1yrcUM35-Kd5UiZs5mCXebgHueroxWuXq_yaYLE3CU6_1agcv44aSOhCG",
              "height": 132702
            },
            "id": "c3T92aWcYEt79uok96MkH6TyXuKageX-1cn1oW46v7s"
          }
        },
        {
          "node": {
            "block": {
              "id": "xbBn0jc4zrqAXmDqczhkzypG0G1b_Nj0XqJZ73UETsQNb0lIc3WIXaVvvv0YtOJS",
              "height": 97283
            },
            "id": "qul1Elv7Xg6LtyTkPqDj0i5jNr38aOLvi9qsDMoO9Jg"
          }
        }
      ]
    }
  }
}

but my installation replies:
{
  "data": {
    "transactions": {
      "edges": [
        {
          "node": {
            "block": {
              "id": "ImTHSwo1yrcUM35-Kd5UiZs5mCXebgHueroxWuXq_yaYLE3CU6_1agcv44aSOhCG",
              "height": 132702
            },
            "id": "c3T92aWcYEt79uok96MkH6TyXuKageX-1cn1oW46v7s"
          }
        }
      ]
    }
  }
}

You see that the transaction qul1Elv7Xg6LtyTkPqDj0i5jNr38aOLvi9qsDMoO9Jg is missing in my server.
Moreover:
select count(*) from transactions where id='c3T92aWcYEt79uok96MkH6TyXuKageX-1cn1oW46v7s';

returns 1.
select count(*) from transactions where id='qul1Elv7Xg6LtyTkPqDj0i5jNr38aOLvi9qsDMoO9Jg';

returns 0.
It could be explained by my server being partially synchronized, but my server does show a transaction of a higher block height. So, there is a bug.

The same bug in v0.12.1.


Added Graph Representation

Description
I have added a graph for representing covid statistics of different countries using chart js. The graph can show statistics for about 203 countries.
Fixes:  #26

Type of change

[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)

Checklist:

[x] I have made this from my own
[x] I have taken help from some online resourses
[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] My changes generate no new warnings

ATTACH SCREEN-SHOTS / DEPLOYMENT LINK
67eb3219-b9d7-4b9f-a846-a1ee00e6df25.webm

@Sulagna-Dutta-Roy Please add labels to this PR.


Fix #164: serve ignores missing files

We log an error about the missing file, and skip building of that page.
The logging is simplified here, and should be updated along with #172

Merged in #317, Thanks!


Added support for testflight groups

Significant refactor, moved business logic to BoardingService
Moved most references to ENV[] into BoardingService and set at instantiation
Added startup checks to fail fast so you aren't left with an error'ing page if groups don't exist

This is a great refactor!!

🚀


3RI

3RI Details: https://docs.google.com/document/d/1iyV5bqL3Sm208Rfr2DlDs_EPv1asMnSIV_pZ7SYMmxg/edit?usp=sharing

[ ] 3RI MITs solutioning

[ ] Implementation to start from 27th May

Deprioritized for now


Switching doesn't load  the correct page position in  Story and commentary

In Bible stories and commentaries if scroll down to the end of the page and then do change the langauge, book, or story it fetches the last content, not from the beginning.
.(part of user experience) in the parellel mode -> commentary section -> scroll down to some mid positon and then change the chapter from the left pane (using prev/next button), the new commentary loaded is in some mid position instead of the start/beginning postion .

attaching video for reference
https://user-images.githubusercontent.com/102143707/168227227-6432244f-4e06-4cb0-a894-382b4e8bd84c.mp4

Testing completed the issue is fixed with the bible stories. But in commentary switching to different books doesnt load page from the begining. As discussed moving this issue back to in-progress.

Tesing completed and the issue is fixed . In commentary switching to different books loading the page as expected. As discussed moving this issue to done.


How to construct a carve::mesh::MeshSet<3> meshset if number of facet is zero?

Dear all,

Usually we can construct a meshset by the following lines:
...
  std::vector<carve::mesh::MeshSet<3>::vertex_t> verts;
  std::vector<carve::mesh::MeshSet<3>::face_t *> faces;
...
  carve::mesh::MeshSet<3> poly(faces);
...

Usually if all nodes are vertices of facets, all nodes and faces are included
in the meshset. However, if in this set the number of faces is zero, all the
sizes of verts and faces would be zero in poly. Furthermore, if there are only
one triangle (faces) but there are 4 nodes, if we construct the meshset as
above, the one node which are not the vertex of triangle is missed. How to do
to let all nodes are included in the meshset?

Thanks,
Tang Laoya

Original issue reported on code.google.com by<EMAIL_ADDRESS>on 19 Apr 2014 at 2:59

This problem is solved. The examples in geometry.cpp tell me how to do.

Thanks,
Tang Laoya

Original comment by<EMAIL_ADDRESS>on 21 Apr 2014 at 2:00


Prototype ADVI coverage model + germline HMM.

Following #1038 and in conjunction with #1039.  @asmirnov239, to start, could you make sure you can get the conda environment in https://github.com/broadinstitute/dsde-methods-prototyping/tree/sl_advi up and running?

Issue moved to broadinstitute/gatk #2986 via ZenHub


Build failure with -fno-common

GCC 10 is going to default to -fno-common. With the option, I see the following failure:
[  101s] /usr/lib64/gcc/x86_64-suse-linux/9/../../../../x86_64-suse-linux/bin/ld: test/run_tests-test-poll-closesocket.o (symbol from plugin): in function `run_test_poll_closesocket':
[  101s] (.text+0x0): multiple definition of `handle'; test/run_tests-test-poll-close-doesnt-corrupt-stack.o (symbol from plugin):(.text+0x0): first defined here
[  101s] /usr/lib64/gcc/x86_64-suse-linux/9/../../../../x86_64-suse-linux/bin/ld: test/run_tests-test-poll-closesocket.o (symbol from plugin): in function `run_test_poll_closesocket':
[  101s] (.text+0x0): multiple definition of `sock'; test/run_tests-test-poll-close-doesnt-corrupt-stack.o (symbol from plugin):(.text+0x0): first defined here

#2604 and thanks for the report.


Trusted Coin wizard stuck when restoring 2FA wallet from seed

I am trying to disable 2FA on my wallet by following some instructions that I have found here, so that I can send some BCH. When I choose New/Restore > Wallet with two-factor authentication > I already have a seed, the wizard hangs on a screen showing the Trusted Coin logo with a message saying Please wait....

go here: #41

My issue is not resolved by #41, but I have continued discussion there to keep all 2FA-related issues in one place.


onChange issue in CJK

Observed behaviour: Suggestions stay open
I'm using react-autosuggest with Korean language.
When I type Korean language and press up arrow key,
up event and type event occurs consecutively. (up event -> type evnet - up event)
It's same with the down arrow key.
It's okay when I type english letters.
Expected behaviour: Suggestions should be closed
A single up/down event should be fired.

This might be my fault.
It was an implementational issue.


Prevent some rebuilds for future Nix reformats

Description of changes
This is in preparation for https://github.com/NixOS/nixpkgs/pull/322537, which I'd like to get to 0 rebuilds. Now that it evaluated, the list of changed paths gives us all the info to do that. Well, almost, because this one can't be avoided.
This PR either avoids Nix files ending up in the build result (so that changing them won't cause rebuilds), or formats Nix files in advance, so that they don't need to be changed in the treewide reformat.
This is effectively part of https://github.com/NixOS/nixpkgs/issues/301014
Things done

[x] Built all the changed derivations

This work is sponsored by Antithesis :sparkles:
Add a :+1: reaction to pull requests you find important.

or formats Nix files in advance, so that they don't need to be changed in the treewide reformat.

This doesn't strike me as a great solution tbh. It just kicks the bucket down the road and will cause rebuilds again when the formatting rules are changed again in the future.

The cabalSdist test can be made to not depend on the formatting of the generated Nix file by using haskell.lib.compose.overrideSrc at the call site to use a filtered source. If this filtered source is also passed correctly to the other derivation that uses it (near the call site of generated.nix), all should be fine.
See #320572, #321246.

This doesn't strike me as a great solution tbh. It just kicks the bucket down the road and will cause rebuilds again when the formatting rules are changed again in the future.

Speaking for the formatting team, we don't expect to have to make any significant changes to the format in the foreseeable future. The only changes to expect soon are bug fixes, which won't change much. So I don't think we need to worry very much about it :)
@sternenseemann Thanks, done that in the last commit now!

Please also tag @NixOS/nix-formatting for PRs touching that topic.

@roberth Even if the formatting isn't perfect, having a standard enforced formatting is better than the current churn. Considering that these cases you highlighted are somewhat rare, I don't think we need to block on this. We can also improve the formatter and then do another reformatting pass later (which will then be much smaller in diff size!). If you have more feedback about the formatting, it would be best to open issues in https://github.com/NixOS/nixfmt instead btw :)

Even if the formatting isn't perfect, having a standard enforced formatting is better

As you've read, I agreed with this part.
However, considering that this aspect of the formatter is still subject to change, it seems that you have the priority inversed:

than the current churn.

Unnecessary formatter-induced churn is not ok. If the formatter doesn't behave correctly, or some aspects of it are still in development, don't both users with it.
I'm glad we've found this issue early, so that we can resolve it before bothering others with bad layouts and unnecessary churn.

I don't think we need to block on this.

So I think we should block on this, fix the formatter, and do another pass.

Considering that these cases you highlighted are somewhat rare

I assume you haven't run nixfmt on the whole repo.
There's two of them in this small PR, and I would expect more runCommand calls to be affected, because often it's just a single  nativeBuildInputs for simple tests.
But you're right, we should be doing more testing ;)

If the formatter doesn't behave correctly, or some aspects of it are still in development

I'd say we should distinguish between different levels of correctness:

Semantic correctness: That the AST isn't changed and that the formatter is idempotent. We have this verified on all Nixpkgs files since recently (and more recently also with nix-instantiate --parse).
Standard matching: That the formatter adheres to the established standard. This can be very fuzzy in certain edge cases, but as we progressed at establishing the initial standard in https://github.com/NixOS/rfcs/pull/166, @piegamesde did a great job keeping the implementation to match decently closely.
Standard correctness: That the standard doesn't have any inconsistencies in itself. We also tried this during RFC development.

So we have 1 now but probably not 2 or 3. These can arguably never be perfect and take more brainpower to resolve, so it's important to consider the cost/value tradeoff. (And in a twisted way, forcing something imperfect onto people might actually get us more help with improving it :P).
But okay, let's reconsider this and either improve this case or have a better justification for not needing to improve it now.

I assume you haven't run nixfmt on the whole repo.

Complete opposite! We've been automatically running nixfmt on the entirety of Nixpkgs already during development of the RFC to help us decide (e.g. see here), and we're continuing to run it on all PRs that change nixfmt (e.g. see here), and of course there's also the treewide reformatting PR that is being worked on recently :wink:

I assume you haven't run nixfmt on the whole repo.

Complete opposite!

Ah sorry, I was unclear. I meant to refer to this PR specifically, which I conclude is not tree-wide.

doesn't behave correctly

Oh, that was a bit harsh maybe, out of context at least. I meant to refer to your judgement that this may not be the desired behavior.
Anyway, I think we're on the same page now, and I'd really like to thank you for the effort you're putting into this!

@infinisil, any reason not to merge this?

@roberth's feedback in https://github.com/NixOS/nixpkgs/pull/326430#discussion_r1679889039 and https://github.com/NixOS/nixpkgs/pull/326430#discussion_r1679891836 is now addressed with https://github.com/NixOS/nixfmt/pull/224, force pushed to make use of it: diff


Add a fuzz test

Write a fuzz test for one of the validator types. You can see an example here that I previously worked on. You can take that and modify it our write your own. This will help improve our OpenSSF scorecard score.

@kehoecj I'm happy to take this on :)

Thank you @nadsella ! I assigned this task to you


Revert "Revert "[cxx-interop][SwiftCompilerSources] Use C++ enums directly from Swift""

The hosttools build issue is fixed in a recent trunk toolchain: swift-DEVELOPMENT-SNAPSHOT-2022-10-16-a.
The compiler bug that was causing it was fixed in https://github.com/apple/swift/pull/61540.
This reverts commit 69431f00

@swift-ci please smoke test

@swift-ci please smoke test macOS

@swift-ci please smoke test macOS

@swift-ci please smoke test macOS


JSONSplitter JAVA-165

So we can incorporate your pull request, please share the following:

What issue are you addressing with this pull request?  JAVA-165
Are you modifying the correct branch? (See CONTRIBUTING.md) yes
Have you run unit tests? (See CONTRIBUTING.md) yes
Version of MarkLogic Java Client API (see Readme.txt) 5.1
Version of MarkLogic Server (see admin gui on port 8001)
Java version (java -version) 11
OS and version macOS
What Changed: What happened before this change? What happens without this change?

Will merge changes in branch develop-165 #1197


fix(connector): avro logical type Duration parsing

Depends on #12562
https://github.com/risingwavelabs/risingwave/blob/e64543f9e5a8b080ddf8d8717846ccd4c68dac80/src/connector/src/sink/encoder/avro.rs#L528-L530

fixed by #13523


Replace resister with resistor in README

A resister is someone who resists, a resistor is the component.

Thanks! :)


include cyclic paths in graph via alignment

Basic cycles are supported in graphs, but there doesn't see to be a stable way to generate them from source sequences. Probably the path editing and handling are not right yet. Generating a few tests of this behavior should shake out the mistakes.
I can generate a cyclic alignment using banding. For instance, if I simulate a read from a cyclic graph I'll get something that traverses the cycles several times.
Here's the graph:
vg view -dpn cyclic/t_cyclic_path.vg

Here's a read:
vg sim -l 200 cyclic/t_cyclic_path.vg >cycle.read

TTAGTCCAGAAGCCCTTGAGGAGGGATGAGAATCTGACTCCCCGCACCTTTGTCCTTAGTCCACAGGAAACTTAAAATGGCCTGGGTAGCTTTGATGTGGAGTAGTTAGAAGCCCTTGAGGAGGGATGAGAATCTGACTCCCCGCACCTTTGTCCTTAGTCCACAGGAAACTTAAAATGGCCTGGGTAGCTTTGATGTGG
Now we can align it in banded mode by indexing and then mapping:
vg index -x c.xg -gd c.gcsa -k 11 cyclic/t_cyclic_path.vg
vg map -Q cyc -s $(cat cycle.read ) -B 20 -x c.xg -g c.gcsa -k 11 >c.gam

This works fine and generates a cyclic mapping (it's reversed in this case, thus the ordering):
vg view -a c.gam | jq '.path.mapping[].position.node_id' | uniq
5
1
5
4
3
2
1
5
4
3
2

The alignment viz is busy but explains that the expected thing is going on:
vg view -dA c.gam cyclic/t_cyclic_path.vg | dot -Tsvg -o x.svg  # open x.svg in your browser

But modifications of the graph with this alignment do not include the cyclic path correctly. MSGA also does not produce the correct result.
I think that an issue that @adamnovak pointed out about the default behavior of Paths::append_mapping is to blame. It works fine if the mapping ranks are already assigned. This is the case when we're reading from stdin, but never in the case that the ranks haven't been assigned.
There may be other issues.

#140 complicates things here. I'll resolve that first and then this.

Somewhat better.
echo TTAGTCCAGAAGCCCTTGAGGAGGGATGAGAATCTGACTCCCCGCACCTTTGTCCTTAGTCCACAGGAAACTTAAAATGGCCTGGGTAGCTTTGATGTGGAGTAGTTAGAAGCCCTTGAGGAGGGATGAGAATCTGACTCCCCGCACCTTTGTCCTTAGTCCACAGGAAACTTAAAATGGCCTGGGTAGCTTTGATGTGG >cycle.read
vg msga -f msgas/s.fa -b s2 -s $(cat cycle.read ) -B 25 -Nz

This is still very broken:
echo CCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGTCAGATTCTCATCCCTCCTCAAGGGCTTCTAACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGTCAGATTCTCATCCCTCCTCAAGGGCTTCTGGACTAA >cycle.read
vg msga -f msgas/s.fa -b s2 -s $(cat cycle.read ) -B 30 -Nz -D

x.pdf

It seems that certain cuts just aren't being made, and some jumps aren't being connected. I'm trying to make a simpler test case.

Path merging was borked due to the last commit, leading to the series of mappings against a single node that should have been merged.
Now I get:

It's working now.
The big challenge was to get normalization routines to respect paths when merging (unchopping) nodes.


Saving layout as img file

Hi Kale,
I tried to save a plate layout as an img file in the GUI and received the following error. I'm not sure if I'm missing a dependency or if my system config is not correct.
RED:[HTRF] -  wellmap HTRF.toml
RED:[HTRF] -  2021-02-01 16:44:21.088 python[18016:271852] +[NSXPCSharedListener endpointForReply:withListenerName:]: an error occurred while attempting to obtain endpoint for listener 'ClientCallsAuxiliary': Connection invalid
2021-02-01 16:44:23.829 python[18016:271850] Error received in message reply handler: Connection invalid
2021-02-01 16:44:23.829 python[18016:271852] Connection Invalid error for service com.apple.hiservices-xpcservice.
2021-02-01 16:44:31.326 python[18016:271851] Metal library creation failed: Error Domain=MTLLibraryErrorDomain Code=3 "Compiler encountered XPC_ERROR_CONNECTION_INVALID. Shutting down the connection permanently..." UserInfo={NSLocalizedDescription=Compiler encountered XPC_ERROR_CONNECTION_INVALID. Shutting down the connection permanently...}
2021-02-01 16:44:31.426 python[18016:271883] +[NSXPCSharedListener endpointForReply:withListenerName:]: an error occurred while attempting to obtain endpoint for listener 'HostCallsAuxiliary': Connection invalid
2021-02-01 16:44:31.429 python[18016:271883] +[NSXPCSharedListener endpointForReply:withListenerName:]: an error occurred while attempting to obtain endpoint for listener 'com.apple.view-bridge': Connection invalid

Hmmm, that error message doesn't really mean anything to me.  Can you try running wellmap with the -f option?  I seem to recall there being an issue with running the GUI in the background on Macs, but I don't remember what it was specifically (or if it was resolved).
Alternatively, you can use the -o option to save a layout as an image directly from the command line, but I know that it's sometimes more convenient to use the GUI.

Did you try wellmap -f HTRF.toml?  I'm curious if that would solve the problem with the GUI.

-f saved the visible portion of the plate layout from the GUI window. (see ‘HTRF.png’)
-o saved the entire layout, regardless of the FOV in the GUI. (see ‘img.png’)
[cid:8F575633-EA59-4D0C-B823-7C5047A1824D][cid:F80E2A23-F85C-4C53-96CA-9C9C9C736332]


Semantic Highlighting - basedpyright

Is there an existing issue for this?

[X] I have searched the existing issues.

What is your concern?
With the release of the new pyright fork basedpyright, semantic highlighting has now been enabled within Python. However, it looks like something might have to be updated in catppuccin as enabling semantic highlighting seems to change functions from peach to blue.
Please see my comments / screenshots on the below issue:-
https://github.com/DetachHead/basedpyright/issues/176

just been reminded issues can be transferred :)

Not read the full context of the issue but its worth saying that according to the style-guide, methods/functions should be blue.
afaik, Neovim still needs to get updated according to the revamped style guide so that might be part of the reason for the colour change?

Ah OK, so have methods / functions have now changed from peach to blue? There was just too much blue going on for my liking, hard to spot the differences.
Before:-

Afrer:-

You can try Overwriting highlight groups to adjust to your liking
require("catppuccin").setup {
  custom_highlights = function(C)
    return {
<EMAIL_ADDRESS>= { fg = C.peach },
    }
  end
}

Out of curiosity, why are my functions peach if they have been updated to blue under the below?
https://github.com/catppuccin/nvim/blob/main/lua/catppuccin/groups/syntax.lua
I am not currently overriding any colours and this is the same on both LazyVim and Lunarvim - peach from functions.


use TextChangeListener to invalidate regions with bounds check

Closes #19.
Adds the bounds checks before the existing checks. This bounds check (call to any) should return False in most cases, making it more efficient. That being said, I haven't measured this in any real scenario. WDYT?

Great, thank you!


Download failed with status 500 Internal Server Error

Hello,
Amazing work with this - I can see the potential and this is potentially exactly what I'm looking for... however I'm running into the above error. Here's my run log:
chad@ubnt-mdnld:~/unifi-protect-video-downloader$ python3 main.py --address=<IP_ADDRESS> --port=7443 --username="###########" --password="##########" --cameras="5db13a7802081a03e70003ef" --start="2020-04-05 00:00:00-0700" --end="2020-04-21 23:00:00-0700" --dest=./download --skip-existing-files --use-subfolders
Successfully authenticated as user chadohman
Successfully requested API Access Key
Successfully retrieved data from /api/bootstrap
Cameras found:
Front Yard (5db13a7802151a03e70003f0)
South Yard (5db13a7801db1a03e70003ed)
Car Park (5db13a7801f61a03e70003ee)
Back Yard (5db13a7802081a03e70003ef)
Downloading video files between 2020-04-05 00:00:00-07:00 and 2020-04-21 23:00:00-07:00 from 'https://<IP_ADDRESS>:7443/api/video/export'

Downloading footage for camera 'Back Yard' (5db13a7802081a03e70003ef)
Created path /home/chad/unifi-protect-video-downloader/download/2020/04/05/Back_Yard_03ef
Downloading video for time range 2020-04-05 00:00:00-07:00 - 2020-04-05 00:59:59-07:00 to /home/chad/unifi-protect-video-downloader/download/2020/04/05/Back_Yard_03ef/Back_Yard_03ef_2020-04-05--00-00-00-0700_2020-04-05--00-59-59-0700.mp4
Download failed with status 500 Internal Server Error

To skip failed downloads and continue with next file, add argument '--ignore-failed-downloads'
0 files downloaded, 0 files skipped, 0 files total

I'm running Ubuntu 18.04.04. What am I doing wrong? Thank you for any help you can provide.

Problem solved - I was going too far back.

Hi there,
thank you for opening (and closing 😄) this issue, and sorry for my delayed response.
Yes, if you go too far back or have cameras that are configured to only record motion, you can expect to get these status 500 errors. If you add the --ignore-failed-downloads flag to your command line, the software will skip these segments. This is especially useful when you don't really know at which date and time the first available recordings on the NVR's HDD start or, as mentioned earlier, you have motion-only recording enabled for some or all cameras.
Feel free to send me another message in case you need additional help getting things up and running or if you have questions or problems!

Yeah I should have thought of that off the start. I used the --ignore-failed-downloads flag after my first run, it seems corrupted video files are a common thing for Unifi Protect.
Appreciate all of the work you put into this! :)


[Bug]: "Clear" function also clear units

Contact Details
No response
What happened?
I wanted to change some numbers in a column in an already filled table. I used the "clear" function to delete the numbers. After adding new numbers the units disappeared.

What did you expect?
"Clear" function, should not clear units, if they are specified in the building block.
Host
ARCitect
Host Details
Windows 11
ARCitect v0.0.31
Swate version
v1.0.0-beta.03

This is currently intended behavior. It is intended to clear a full cell, plus the relevant reference cells.
What do you suggest, changing the name to clear up misunderstanding, or adding an additional function?

I'm not sure about that. It would be great to have a button to only delete numbers, but not the unit. Otherwise it's annoying to change sheets that have already been filled out.
An example use case would be that a user copies metadata sheets from one assay to another because there are only small changes in the experiment and it's too much work for the user to create a completely new Swate table.

I am trying to narrow down the use case. In your scenario would it also be feasible to update one cell and propagate it to all other cells?

This depends on the experiment. I think it would not be feasible for all experiments. If you change a parameter for e.g. temperature for all samples, it works fine. But sometimes you need individueal numbers per sample. So you have to change every entry individually e.g.

I think I may be missunderstood the clear button. In my example above, you have to change the numbers anyway. So changing the number isn't more difficult than entering a new number.
Maybe we can close the issue for now. But what was the purpose of the clear button? I haven't understood that yet.

The purpose of the clear button is to remove the information from the main and reference cells of one building block 👍 Will close for now, feel free to reopen 🙂


[Bug]: aws-sdk-js-codemod doesn't modify file when parser=ts is passed

Self-service

[ ] I'd be willing to implement a fix

Describe the bug
aws-sdk-js-codemod doesn't modify file when parser=ts is passed
Template name
v2-to-v3
Input code
// example.ts
import AWS from "aws-sdk";

const client = new AWS.DynamoDB();

Observed failure
No failure, but there's no modification when parser=ts is passed.
$ aws-sdk-js-codemod -t v2-to-v3 example.ts --parser=ts
Processing 1 files...
Spawning 1 workers...
Sending 1 files to free worker...
All done.
Results:
0 errors
1 unmodified
0 skipped
0 ok
Time elapsed: 0.926seconds

Expected output
import { DynamoDB } from "@aws-sdk/client-dynamodb";

const client = new DynamoDB();

Environment
aws-sdk-js-codemod: 0.4.2

jscodeshift: 0.13.1
 - babel: 7.17.5
 - babylon: 7.17.3
 - flow: 0.172.0
 - recast: 0.20.5

Additional context
This is likely an issue with jscodeshift. This was noticed when an attempt to pass parser=ts was made in tests in https://github.com/trivikr/aws-sdk-js-codemod/pull/83

Created a bug report with jscodeshift at https://github.com/facebook/jscodeshift/issues/489

It looks like this appears to happen as we check for Literal and parser=ts returns StringLiteral while we look for Literal
https://github.com/trivikr/aws-sdk-js-codemod/blob/ea497966812d6b59d98b5179b7362e549507b69a/src/transforms/v2-to-v3/utils/getImportIdentifierName.ts#L9-L11


Support for KV Storage

I've seen this article about new storage coming:
https://developers.google.com/web/updates/2019/03/kv-storage
Basically this is like localStorage but async and with better performance
It's currently not supported in browsers except Chrome 74+ but I'm curious if this should be supported too (maybe with a polyfill)

This would be awesome to add once widely supported. It's brand new, and still
even locked behind an experimental flag.
Note: The KV Storage module is currently available in Chrome 74 if you have
the experimental web platform features flag turned on:
(chrome://flags/#enable-experimental-web-platform-features).

If and when kv-storage is added and supported in browsers, support in ImmortalDB
would be awesome.

From further reading, kv-storage is built on top of IndexedDB

KV storage is layered on top of IndexedDB, storing its data in a specific
database, so the developer can fall back to using IndexedDB directly when
necessary.

https://www.chromestatus.com/feature/6428344899862528

and thus provides no additional redundancy beyond IndexedDbStore.
A separate kv-storage implementation could be built and added, but it's
redundant (and wastes space) on top of IndexedDbStore.
Closing. Please re-open this issue if you have a specific use case in mind where
you'd want kvStorageStore over IndexedDbStore.


Blinds support

Please, add support for blinds, contact sensor and battery status.

Thanks for the suggestion. I will try and add these when I get some spare time, PRs are welcome also.
Tagging meta issue and closing: https://github.com/oznu/homebridge-config-ui-x/issues/47


Change Monster Stat background color

This resolves #2123 with a tiny change to the monster stat block background color as suggested by @Kaiburr-kath-hound, for v3 only.
Sidenote, is there a good way to refresh phb css so that the changes go through quickly?  I thought i remember a configuration i could change that would quickly refresh the CSS after each change, but can't remember now.
Before:

After:

⭐ ⭐ ⭐ ⭐ ⭐ ⭐ ⭐


Variable selection should persist when editing a cell

When using variables in a dashboard, the variable selection should persist when you are editing a cell. currently, the values revert to the first selection.

Variable selection on dashboard is not persisted when going from dashboard->cell


Optimize validity buffer concat.

Close #2579

Please update the PR description. It will be displayed in the commit log. Simply saying "closes XXX" will just show that words, which is difficult to track the changes through commit log.

It will be displayed in the commit log

To be fair we do not have the automation (yet) of checking in PRs using the PR description. I follow the convention of copying the PR description as the commit message but it's not mandated and not followed widely in NVIDIA/spark* repos.

Could we copy by long instead of int?  We can avoid to use toIntExact and use Long.bitCount. This may be more fast.


assertion failed: mstate.c:896: 0 == ate->l_pages

Steps to reproduce
bdmprun -ns=16 -nr=1 -rm=910000 -sbma=default -wd=/scratch-ssd/bdmp bdmp_pr1d /scratch-ssd/uk2007.bcsr-shuff 5 1 0

This is due to the following line in vmm_swap_o:
/* Shortcut if there are no dirty pages. */
if (0 == ate->d_pages)
  goto RETURN;

It is possible to have a case where there are pages (resident+charged) whose flags should be updated by vmm_swap_o even if there are no dirty pages, and this shortcut skips those cases.


Error: Can't resolve 'async/eachSeries'

I'm trying to use the ipfs-api with vue/quasar. I think this is a webpack error but don't know how to solve it.

I'm not sure if I can help with this - I've double checked async is a dependency and with a fresh install of ipfs-api I can see node_modules/async/eachSeries.js. So, I don't think this is an issue with ipfs-api...have you tried removing your node_modules and package-lock.json and re-installing?


CARDS-1283: Export forms as text

To test:

create some forms
for each form, edit it's URL by removing content.html/ and appending .txt at the end, e.g. http://localhost:8080/Forms/94ac47cc-cb18-4d67-8459-e17c2a6de95a.txt
check that all the answers and notes are present in a human readable manner, e.g. units, vocabulary term labels instead of identifiers, Yes and No for booleans instead of numbers, Male instead of M
ideally labeled and recurrent sections should be tested as well, not sure if we have any sample questionnaires for that in the test runmode

Should pedigree be included in export?

Should pedigree be included in export?

Hm, good point. Is there an elegant way to output something like   [IMAGE] instead of the svg source for pedigree type questions?

Is there an elegant way to output something like [IMAGE] instead of the svg source for pedigree type questions?

Not right now, we could add a custom JSON processor that discards pedigree images. Something for the future?

I actually committed an improvement, I explicitly replaced pedigree answers with a simple "Pedigree provided" line. Is that OK @marta- ?

It looks much better now.


Rule request: unnecessary parenthesis after enumerate

With ruff==0.1.1:
for [_i, _hi] in enumerate(range(5)):
    pass
for (_i, _hi) in enumerate(range(5)):
    pass

It would be great to have an autofix to remove the extra parenthesis/bracket wrapping.
Testing pylint==3.0.1 and refurb==1.22.0, it doesn't seem either of these tools catch this possible improvement either.

Are you referring here to the parentheses around (_i, _hi)?

Yeah the parenthesis or brackets.  Sorry for the unclear OP!


Create pl.json

Polish translation added.

Thanks. Merged now, and will be included with the next release. Could you also have a look here and make a Polish file for the Beaufort and Wind Directions: https://github.com/briis/py-weatherbit/tree/master/weatherbitpypi/translations


Profiles in Magellan.json reverting to Default Browser Settings

Hello,
Given the following config:
"profiles": {
"tier-one-browsers": [
{
"browser": "chrome_latest_OS_X_10_11_Desktop",
"resolution": "1280x1024",
"executor": "seleniumgrid"
},
{
"browser": "firefox_latest_OS_X_10_11_Desktop",
"resolution": "1280x1024",
"executor": "seleniumgrid"
}
]
},
and the command:
./node_modules/.bin/magellan --profile tier-one-browsers --test tests/Account/accountSignInGmail.js --debug
I have been trying to run on multiple browsers through our selenium grid, but have been unsuccessful.  The grid config is working, because it hits the hub and distributes the tests correctly.  It is also correctly detecting the number of profiles, since the number of tests grows with each addition to the profile list.
However, there is no recognition of the different browsers attached here, every test reverts to the firefox default.  I've tried mirroring the nightwatch boilerplate as closely as my system allows and have had no luck.
At this point I've been trying to dig around in the node module to figure out if:
a. I'm missing some sort of config value
b. there is a bug preventing this from working under a set of circumstances.
I am able to run multiple browsers via the command line.  From the output of the failed attempts you can see the env is not being set (this value is set when we read from the command line):
[INFO] [Magellan] Running 2 tests with 3 workers with [env:undefined|executor:seleniumgrid, env:undefined|executor:seleniumgrid]
[INFO] [Magellan] --> Worker 2, port range: [12003, 12005], running test: tests/Account/accountSignInGmail.js @env:undefined|executor:seleniumgrid
[INFO] [Magellan] --> Worker 1, port range: [12000, 12002], running test: tests/Account/accountSignInGmail.js @env:undefined|executor:seleniumgrid
Note: it would also be helpful if in the documentation there were a guide to how to define the browsers in the config file.  Having to reverse engineer the structure of the string from examples left me in doubt as to whether I was constructing it correctly.
Thanks for the help,
Joe

can you let me know where you get this profile?
"profiles": {
"tier-one-browsers": [
{
"browser": "chrome_latest_OS_X_10_11_Desktop",
"resolution": "1280x1024",
"executor": "seleniumgrid"
},
{
"browser": "firefox_latest_OS_X_10_11_Desktop",
"resolution": "1280x1024",
"executor": "seleniumgrid"
}
]
},

this is not a valid profile for selenium grid. the browsers in the profile are for saucelabs, and these browsers cannot be picked up by seleniumgrid-executor. the browser you should use for selebiumgrid is the same as your local browser, please take a look at http://testarmada.io/#localBrowserPreresuisites.
magellan executor will convert the profile to a format it can understand. this chrome_latest_OS_X_10_11_Desktop format can only be understood by saucelabs-executor via guacamole.
to make things much easier, you can simply use the browsers defined in your nightwatch.json for seleniumgrid-executor by
--seleniumgrid_browser chrome,firefox,safari

The profile was pulled from the boilerplate project, then modified for my system.  It wasn't clear to me that it was meant for saucelabs only.
I tried using "chrome,firefox" in the profile block as well (it already works from the command line) but I got the same results--the environment variable comes up empty and it defaults to firefox.
It sounds like right now there is no way to set browsers in the profile for seleniumgrid -- is that right, or am I missing something?

You're right. seleniumgrid-executor doesn't support reading profile from magellan.json right now. We'll mark this as a feature request and implement it soon. For now to run massive tests on seleniumgrid you can use --seleniumgrid_browsers chrome,firefox.

i'm closing this one as magellan-seleniumgrid-executor is the right place to put the request in. https://github.com/TestArmada/magellan-seleniumgrid-executor/issues/3

Thanks, appreciate you taking the time to explain!


Add Separator Component

@radnan bhaia, I want to start working on this. I will update the issue with a summary of the API very soon. Can you please assign this issue to me if it is ok?


Connect and stop mode/do not use adb at all

Codecov Report

Merging #46 into master will increase coverage by 0.43%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #46      +/-   ##
==========================================
+ Coverage   74.08%   74.51%   +0.43%
==========================================
  Files           5        5
  Lines         409      416       +7
==========================================
+ Hits          303      310       +7
  Misses        106      106

Impacted Files
Coverage Δ

stf_utils/stf_connect/client.py
83.45% <100%> (+0.44%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
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GD wont load up

today every time the game will just not load or just crash will there be a fix soon?

use latest version of gdh and geometry dash


Keyword for supported sites

There should an api keyword (can be supported_sites) which would return the list of currently supported sites. This will make an user's life lot more easier!

@arijit4 yeah sure will add it asap.

@arijit4 done 42ce9b8bf9f1ded6afa32f983ba41134f3c37c63
endpoint - api/v1/sites


Chart specific labels for isuess in the repo

I think it is reasonable to add labels to be able to classify each issue to what chart it refers.

Closing in favor of issues template submitted here: https://github.com/kubernetes/charts/pull/1155

What issue request template have to with labels on the issue? Labels are very useful, it makes everything more visually observable, you can filter by labels, for example to get all issues related to partcular chart, how would you do this without lables? Labels usually assigned not by issue author, but by owners/collaborators, so users will not mess with them.
Not using labels for monorepos and complex project is a very big omission.


chore(turbo): rename 'pipeline' field to...

What does this PR do?
chore(turbo): rename 'pipeline' field to 'tasks' for turbo 2.2.3
Signed-off-by: Nick Boldt<EMAIL_ADDRESS>Screenshot/screencast of this PR
N/A
What issues does this PR fix or reference?
N/A (or see commit message above for issue number)
How to test this PR?
N/A
PR Checklist
As the author of this Pull Request I made sure that:

[x] Code produced is complete
[ ] Code builds without errors
[ ] Tests are covering the bugfix
[ ] Relevant user documentation updated
[ ] Relevant contributing documentation updated

Reviewers
Reviewers, please comment how you tested the PR when approving it.

/lgtm

So this won't work in CI:
  x Found an unknown key `tasks`.
   ,-[2:1]
 2 |   "$schema": "https://turbo.build/schema.json",
 3 |   "tasks": {
   :   ^^^^^^^
 4 |     "export-dynamic": {
   `----

But without it I can't use my local setup to update the release-1.3 branch now that I've got a newer version of turbo installed for 1.4 :(

Paul said:

I'd suggest looking at https://turbo.build/repo/docs/crafting-your-repository/upgrading to double check if we need to update any other config


gitdata.deleteReference failed with 404 error when use # sign in ref (branch name)

New versions of node-github (in ver 3.x.x was ok) gitdata.deleteReference is failed on # sign in "ref" with 404 (Error: "Not Found"). Other methods (creating and searching) with # sign is ok.
gitdata.deleteReference({
                owner: request.head.user.login,
                repo: request.head.repo.name,
                ref: `heads/some@another#other`
})

GitHub Enterprise 2.6

Deleting a reference with a hash in it is pretty dangerous since hash is treated as a fragment identifier.
Ex: https://api.github.com/repos/kaizensoze/test2/git/refs/heads/a#blah
Right now the ref param value isn't being encoded since it's a path, but the fix might be to specifically escape hashes. I'm not sure if there are any gotchas that would make this a bad idea.
Definitely looking for input on this.

Now you can do that:
git.getRef({
    owner: request.head.user.login,
    repo: request.head.repo.name,
    ref: `heads/some@another%23other`
})


NOOBS use?

Hello, I'm wondering if this works with the current versions of Windows IoT?
My goal is to make a NOOBS os image from a custom flash.ffu that can be used as a factory restore appliance for a Windows IoT running on RPi3.

I haven't tested it in quite some time - let me know your results.

Ah. Sorry. I saw your readme update from January this year that you were working on updating it to the current version of Windows IoT. I was wondering if you had verified that it works and maybe just not updated the repo yet.

Unfortunately not, it's still just an item on my to-do list.
On Oct 13, 2017 10:55, "mjmeans"<EMAIL_ADDRESS>wrote:

Ah. Sorry. I saw your readme update from January this year that you were
working on updating it to the current version of Windows IoT. I was
wondering if you had verified that it works and maybe just not updated the
repo yet.
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@t0x0 could you provide some clues as to what modifications are needed?
Some of us may be able to fork and start work on it for PRs.

As I recall, the original RPi FFU image didn't match the specification (https://docs.microsoft.com/en-us/windows-hardware/manufacture/mobile/ffu-image-format), and the code was written to successfully extract it anyway. I'm assuming that the future images actually conform to the spec, and so my code is broken. I apologize, but I won't be able to offer much more assistance until I can find time to dig into the details of the actual issues.

I've successfully followed this method using DISM for other non-RPi boards to flash the flash.ffu image:
https://docs.microsoft.com/en-us/windows/iot-core/connect-your-device/dism
So, perhaps if the flash.ffu file was created to the Microsoft "FFU specs", the above method using DISM will be fine.
(I instruct consumers not on Windows 10 to just install an evaluation of Windows 10 inside of a VM, and attach the USB device from there.  the ISO is freely downloadable from Microsoft.)

Dism isn't available to python under Raspbian. So that defeats the purpose of using a custom NOOBS under Raspbian or other Linux to handle the flash recovery.


When update index for model, got {:delete=>1}

Hello every body! I'm using Chewy 0.8.4 with Rails 4.2.1. I declare update_index in a model and when a record of that model is created, in log of Rails server it said something like:
ModelsIndex::TypeOfModel Import (2.6ms) {:delete=>1}

And there is no new document create for that record in Elastic search database. I don't know why it doesn't create new document and instead of {:index=>1}, it outputs {:delete=>1}. Do you know which case that Chewy/Elastic search doesn't create new document and output {:delete=>1} like that? Thank you very much!
(Sorry I can not show detail of the model because it is from a project of my company :bow: )

How did you define the type? Which scope did you use? Is the record included in this scope?

Thank you for your quickly response. I'm really sorry but I can's show the detail (I know that it is very uncomfortable when doing something without detail :bow: ). The record is included in the scope I use in define_type, I checked that. I set binding.pry inside the define_type's block and it goes to there. But after that block and when rails server done response, the server's log show that {:delete=>1} line. I just wonder which case that Chewy shows that {:delete=>1}, I will try to investigate my code to find out my bug with any clue about that case.
Thanks in advance and sorry for your inconvenience.

I've found the cause of that bug. In my scope, I find record by an array of ids return from a function (those ids are not fixed):
SELECT * FROM table WHERE id in (1, 2, 3)

and for some reasons, the id of new record (4, for instance) is not included in the array when execute the documenting process (when I check with the scope, it does include the new id). And when the function default_scope_where_ids_in in lib/chewy/type/adapter/orm.rb (line 128) is called in line 108, the query is:
SELECT * FROM table where id in (1, 2, 3) and id in (4)

So the new record is considered to not appear in the scope and it delete the document instead of create (output {:delete=>1}).

I know this was closed forever ago, but my company has been struggling with randomly failing specs for years due to this issue. I was able to track down and confirm we were running into the same bad query issue and I found a workaround:
define_type ModelName.unscoped do
...
end

Chaining .unscoped ensures stale bits of queries don't pollute subsequent imports.


PLFM-4614 (Subset of PLFM-2073)

Will break down into two separate pull requests for better separation of concerns. One PR to add the etag column and a second PR for the rest of the work.


Sound notification

Hey I love your plug-in it works perfect but would there be a possibility for you to add some sort of ping sound once a new tweet shows up after a refesh?

Hey @Lugicc!
Thank you for using my add-on and I'm glad it's working well for you! As far as playing a pinging sound goes, it is definitely something I could look into creating an optional setting for.
I've got a lot going on right now however and can't give you an estimated time for when I'll be able to get to it, but will do my best to look into it at the earliest convenience! :-)

Thanks for the quick reply! Great to hear you could make it work but no problem if not because it's already very usefull :D

I'll try to make it work at least, don't have much experience with playing audio through an add-on, haha. :-) But again, may take a little bit before I get the time to get started on it.
I'll ping you here when the feature is in place (or if it gets the better out of me).

I'm going to close this issue as I never got around to it and it's been several years. My apologies. If this is still something you really want, feel free to open up another issue and I'll revisit it.


Update workshops-and-tutorials.md

Updates for Ontology Tools and Workflows workshop.

@jamesaoverton Thanks for the update!


Always set tls-crypt instead of tls-auth

The install script always installs OpenVPN 2.4, even if it has to
install it from a third-party repository. In 2.4, tls-auth has been
replaced by tls-crypt and tls-crypt must be specified even if using
traditional RSA cryptography.
In short, RSA is currently broken and this patch is necessary to make it work again.

@alexhenrie I'm pretty sure the option to use tls-auth is to allow older (pre-2.4) clients to still function properly. Also, RSA's and OpenVPN's security is not affected by tls-auth or tls-crypt. tls-auth is mainly useful in preventing DoS attacks by signing every control channel packet with an HMAC signature, while tls-crypt is like tls-auth, but the OpenVPN control channel is encrypted using a key that all peers know, which prevents anybody without the key from viewing the TLS-secured control channel. tls-crypt has all of the benefits of tls-auth, and hides the certificates used in the TLS control channel by encrypting the control channel, and makes the traffic look less like OpenVPN traffic, but still not HTTPS traffic. If you haven't already, I suggest reading the OpenVPN manpage which has a lot of useful information on OpenVPN in TLS mode, tls-auth, and tls-crypt

Hi @Giraffe1966, the issue is that the OpenVPN server does not work at all if tls-auth is specified instead of tls-crypt. I don't know why exactly that is, but you can easily see the problem if you try it for yourself.

Not approving this, tls-auth still needs to be there and pre 2.4 still needs to be provided as an option.
https://github.com/pivpn/pivpn/issues/576


Push notifications triggered by the user's location?

Is it possible to trigger a push notification based on the user's location?

Sure it is but I don't think that this package will do it for you. You will have to build location trigger yourself and then use this package to send the notifications.


Windows 10 - Python3.7 - IndexError: tensors used as indices must be long, byte or bool tensors

After Executing the code from the first tutorial
sockeye-train -s data/train.source -t data/train.target -vs data/dev.source -vt data/dev.target --encoder transformer --decoder transformer --num-layers 1:1 --num-embed 32 --transformer-model-size 32 --transformer-feed-forward-num-hidden 64 --transformer-attention-heads 4 --max-num-checkpoint-not-improved 3 -o seqcopy_model
on my Windows 10 PC which runs a NVIDIA GeForce GTX960 2GB
Traceback (most recent call last):
  File "D:\Anaconda\envs\sockeye\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "D:\Anaconda\envs\sockeye\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "D:\Anaconda\envs\sockeye\Scripts\sockeye-train.exe\__main__.py", line 7, in <module>
    sys.exit(main())
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\train_pt.py", line 848, in main
    train(args)
  File "D:\Anaconda\envs\sockeye\lib\site-packages\torch\distributed\elastic\multiprocessing\errors\__init__.py", line 345, in wrapper
    return f(*args, **kwargs)
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\train_pt.py", line 924, in train
    output_folder=output_folder)
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\train_pt.py", line 400, in create_data_iters_and_vocabs
    batch_sentences_multiple_of=args.batch_sentences_multiple_of)
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\data_io_pt.py", line 974, in get_training_data_iters
    permute=permute)
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\data_io_pt.py", line 1812, in __init__
    self.reset()
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\data_io_pt.py", line 1832, in reset
    self.data_permutations, self.inverse_data_permutations = get_permutations(self.data.get_bucket_counts())
  File "D:\Anaconda\envs\sockeye\lib\site-packages\sockeye\data_io_pt.py", line 1501, in get_permutations
    inverse_data_permutation[data_permutation] = torch.arange(num_samples)
IndexError: tensors used as indices must be long, byte or bool tensors

According to pip3 freeze the following packages are installed:
certifi==2021.10.8
mkl-fft==1.3.1
mkl-random @ file:///C:/ci/mkl_random_1626186163140/work
mkl-service==2.4.0
numpy==1.21.4
olefile==0.46
Pillow==8.4.0
portalocker==2.3.2
pyaml==21.10.1
pywin32==302
PyYAML==6.0
sacrebleu==1.4.14
six @ file:///tmp/build/80754af9/six_1623709665295/work
sockeye==3.0.0
torch==1.10.0
torchaudio==0.10.0
torchvision==0.11.1
typing_extensions==4.0.1
wincertstore==0.2

We are not testing against Windows environments or officially supporting Windows. There seems to be some differences in how PyTorch handles dtype conversions on Windows, compared to Linux or MacOs (which are covered by our continuous integration tests).
You could try and change the code in the offending line to:
inverse_data_permutation[data_permutation.long()] = torch.arange(num_samples)
to see if this fixes the issue.

This works for me! Thanks!

We can't easily support Windows, but here is a PR that might fix this particular issue for Windows users: https://github.com/awslabs/sockeye/pull/990

Thanks for this pull request.
After editing the file data_io_pt.py you have to train as administrator.

if you re-install the latest version this should no longer be necessary.


Inconsistent code highlighting in many-to-many relations code snippet

In model Post field categoryIds should not be highlighted and instead data type string[] should be highlighted to make formatting consistent with other code examples/snippets.
Similarly In model Category field postIds should not be highlighted and data type string[] should be highlighted.

Here is a link to documentation section

We've ended up with a couple of duplicates of this issue, so I'll close this one and it can be tracked under #2476  - I've also added a comment asking if we can bump this one up the list a bit!


"add_list_member" with "list_id" parameter results in "twython.exceptions.TwythonError: Twitter API returned a 404 (Not Found), Sorry, that page does not exist."

Hi all, just thought I'd point out something that might be a bug. Here's the relevant code:
from queue import Queue

from twython import Twython
from twython import TwythonStreamer

consumer_key = 'xxx'
consumer_secret = 'xxx'
token = 'xxx'
token_secret = 'xxx'
twitter = Twython(consumer_key, consumer_secret, token, token_secret)

def process_tweets(tweets_queue):
    while True:
        tweet = tweets_queue.get()
        twitter.add_list_member(list_id=MY_LIST_ID, user_id=tweet['user']['id'])
        print(tweet['text'].encode('ascii','ignore'))

This produces:
Traceback (most recent call last):
  File "tweet_stream.py", line 60, in <module>
    process_tweets(tweet_queue)
  File "tweet_stream.py", line 52, in process_tweets
    twitter.add_list_member(list_id=MY_LIST_ID, user_id=tweet['user']['id'])
  File "C:\...\Anaconda3\lib\site-packages\twython\endpoints.py", line 794, in add_list_member
    return self.post('lists/members/create', params=params)
  File "C:\...\Anaconda3\lib\site-packages\twython\api.py", line 268, in post
    return self.request(endpoint, 'POST', params=params, version=version)
  File "C:\...\Anaconda3\lib\site-packages\twython\api.py", line 258, in request
    api_call=url)
  File "C:\...\Anaconda3\lib\site-packages\twython\api.py", line 194, in _request
    retry_after=response.headers.get('X-Rate-Limit-Reset'))
twython.exceptions.TwythonError: Twitter API returned a 404 (Not Found), Sorry, that page does not exist.

I noticed a similar issue opened in 2015. Possibly a regression?

Is MY_LIST_ID a valid list id?
Please see https://dev.twitter.com/rest/reference/post/lists/members/create for the API documentation.

Yes, it's valid.

Can you post the list id?

Or could you try using the list slug instead of list_id?

This worked for me
twitter.add_list_member(slug=listname, owner_screen_name=username, screen_name=tweet['user']['screen_name'])


[BUG] test_get_json_object_single_quotes failure

test_get_json_object_single_quotes failed in last night's Databricks 10.4 tests.
[2024-02-14T11:13:00.694Z] FAILED ../../src/main/python/get_json_test.py::test_get_json_object_single_quotes[DATAGEN_SEED=1707901022] - AssertionError: GPU and CPU are not both null at [1, 'sub_b']

Details
[2024-02-14T11:13:00.691Z] =================================== FAILURES ===================================

[2024-02-14T11:13:00.691Z] ______________________ test_get_json_object_single_quotes ______________________

[2024-02-14T11:13:00.691Z] [gw1] linux -- Python 3.8.10 /usr/bin/python

[2024-02-14T11:13:00.691Z]

[2024-02-14T11:13:00.691Z]     def test_get_json_object_single_quotes():

[2024-02-14T11:13:00.691Z]         schema = StructType([StructField("jsonStr", StringType())])

[2024-02-14T11:13:00.691Z]         data = [[r'''{'a':'A'}'''],

[2024-02-14T11:13:00.691Z]                 [r'''{'b':'"B'}'''],

[2024-02-14T11:13:00.691Z]                 [r'''{"c":"'C"}''']]

[2024-02-14T11:13:00.691Z]

[2024-02-14T11:13:00.691Z] >       assert_gpu_and_cpu_are_equal_collect(

[2024-02-14T11:13:00.691Z]             lambda spark: spark.createDataFrame(data,schema=schema).select(

[2024-02-14T11:13:00.691Z]             f.get_json_object('jsonStr',r'''$['a']''').alias('sub_a'),

[2024-02-14T11:13:00.691Z]             f.get_json_object('jsonStr',r'''$['b']''').alias('sub_b'),

[2024-02-14T11:13:00.691Z]             f.get_json_object('jsonStr',r'''$['c']''').alias('sub_c')),

[2024-02-14T11:13:00.691Z]             conf={'spark.rapids.sql.expression.GetJsonObject': 'true'})

[2024-02-14T11:13:00.691Z]

[2024-02-14T11:13:00.691Z] ../../src/main/python/get_json_test.py:59:

[2024-02-14T11:13:00.691Z] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

[2024-02-14T11:13:00.691Z] ../../src/main/python/asserts.py:595: in assert_gpu_and_cpu_are_equal_collect

[2024-02-14T11:13:00.691Z]     _assert_gpu_and_cpu_are_equal(func, 'COLLECT', conf=conf, is_cpu_first=is_cpu_first, result_canonicalize_func_before_compare=result_canonicalize_func_before_compare)

[2024-02-14T11:13:00.691Z] ../../src/main/python/asserts.py:517: in _assert_gpu_and_cpu_are_equal

[2024-02-14T11:13:00.691Z]     assert_equal(from_cpu, from_gpu)

[2024-02-14T11:13:00.691Z] ../../src/main/python/asserts.py:107: in assert_equal

[2024-02-14T11:13:00.691Z]     _assert_equal(cpu, gpu, float_check=get_float_check(), path=[])

[2024-02-14T11:13:00.691Z] ../../src/main/python/asserts.py:43: in _assert_equal

[2024-02-14T11:13:00.691Z]     _assert_equal(cpu[index], gpu[index], float_check, path + [index])

[2024-02-14T11:13:00.691Z] ../../src/main/python/asserts.py:36: in _assert_equal

[2024-02-14T11:13:00.691Z]     _assert_equal(cpu[field], gpu[field], float_check, path + [field])

[2024-02-14T11:13:00.691Z] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

[2024-02-14T11:13:00.691Z]

[2024-02-14T11:13:00.691Z] cpu = None, gpu = '"B'

[2024-02-14T11:13:00.691Z] float_check = <function get_float_check.<locals>.<lambda> at 0x7f9488165310>

[2024-02-14T11:13:00.691Z] path = [1, 'sub_b']

[2024-02-14T11:13:00.691Z]

[2024-02-14T11:13:00.691Z]     def _assert_equal(cpu, gpu, float_check, path):

[2024-02-14T11:13:00.692Z]         t = type(cpu)

[2024-02-14T11:13:00.692Z]         if (t is Row):

[2024-02-14T11:13:00.692Z]             assert len(cpu) == len(gpu), "CPU and GPU row have different lengths at {} CPU: {} GPU: {}".format(path, len(cpu), len(gpu))

[2024-02-14T11:13:00.692Z]             if hasattr(cpu, "__fields__") and hasattr(gpu, "__fields__"):

[2024-02-14T11:13:00.692Z]                 assert cpu.__fields__ == gpu.__fields__, "CPU and GPU row have different fields at {} CPU: {} GPU: {}".format(path, cpu.__fields__, gpu.__fields__)

[2024-02-14T11:13:00.692Z]                 for field in cpu.__fields__:

[2024-02-14T11:13:00.692Z]                     _assert_equal(cpu[field], gpu[field], float_check, path + [field])

[2024-02-14T11:13:00.692Z]             else:

[2024-02-14T11:13:00.692Z]                 for index in range(len(cpu)):

[2024-02-14T11:13:00.692Z]                     _assert_equal(cpu[index], gpu[index], float_check, path + [index])

[2024-02-14T11:13:00.692Z]         elif (t is list):

[2024-02-14T11:13:00.692Z]             assert len(cpu) == len(gpu), "CPU and GPU list have different lengths at {} CPU: {} GPU: {}".format(path, len(cpu), len(gpu))

[2024-02-14T11:13:00.692Z]             for index in range(len(cpu)):

[2024-02-14T11:13:00.692Z]                 _assert_equal(cpu[index], gpu[index], float_check, path + [index])

[2024-02-14T11:13:00.692Z]         elif (t is tuple):

[2024-02-14T11:13:00.692Z]             assert len(cpu) == len(gpu), "CPU and GPU list have different lengths at {} CPU: {} GPU: {}".format(path, len(cpu), len(gpu))

[2024-02-14T11:13:00.692Z]             for index in range(len(cpu)):

[2024-02-14T11:13:00.692Z]                 _assert_equal(cpu[index], gpu[index], float_check, path + [index])

[2024-02-14T11:13:00.692Z]         elif (t is pytypes.GeneratorType):

[2024-02-14T11:13:00.692Z]             index = 0

[2024-02-14T11:13:00.692Z]             # generator has no zip :( so we have to do this the hard way

[2024-02-14T11:13:00.692Z]             done = False

[2024-02-14T11:13:00.692Z]             while not done:

[2024-02-14T11:13:00.692Z]                 sub_cpu = None

[2024-02-14T11:13:00.692Z]                 sub_gpu = None

[2024-02-14T11:13:00.692Z]                 try:

[2024-02-14T11:13:00.692Z]                     sub_cpu = next(cpu)

[2024-02-14T11:13:00.692Z]                 except StopIteration:

[2024-02-14T11:13:00.692Z]                     done = True

[2024-02-14T11:13:00.692Z]

[2024-02-14T11:13:00.692Z]                 try:

[2024-02-14T11:13:00.692Z]                     sub_gpu = next(gpu)

[2024-02-14T11:13:00.692Z]                 except StopIteration:

[2024-02-14T11:13:00.692Z]                     done = True

[2024-02-14T11:13:00.692Z]

[2024-02-14T11:13:00.692Z]                 if done:

[2024-02-14T11:13:00.692Z]                     assert sub_cpu == sub_gpu and sub_cpu == None, "CPU and GPU generators have different lengths at {}".format(path)

[2024-02-14T11:13:00.692Z]                 else:

[2024-02-14T11:13:00.692Z]                     _assert_equal(sub_cpu, sub_gpu, float_check, path + [index])

[2024-02-14T11:13:00.692Z]

[2024-02-14T11:13:00.692Z]                 index = index + 1

[2024-02-14T11:13:00.692Z]         elif (t is dict):

[2024-02-14T11:13:00.692Z]             # The order of key/values is not guaranteed in python dicts, nor are they guaranteed by Spark

[2024-02-14T11:13:00.692Z]             # so sort the items to do our best with ignoring the order of dicts

[2024-02-14T11:13:00.692Z]             cpu_items = list(cpu.items()).sort(key=_RowCmp)

[2024-02-14T11:13:00.692Z]             gpu_items = list(gpu.items()).sort(key=_RowCmp)

[2024-02-14T11:13:00.692Z]             _assert_equal(cpu_items, gpu_items, float_check, path + ["map"])

[2024-02-14T11:13:00.692Z]         elif (t is int):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU int values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif (t is float):

[2024-02-14T11:13:00.692Z]             if (math.isnan(cpu)):

[2024-02-14T11:13:00.692Z]                 assert math.isnan(gpu), "GPU and CPU float values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]             else:

[2024-02-14T11:13:00.692Z]                 assert float_check(cpu, gpu), "GPU and CPU float values are different {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, str):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU string values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, datetime):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU timestamp values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, date):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU date values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, bool):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU boolean values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, Decimal):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU decimal values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, bytearray):

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU bytearray values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif isinstance(cpu, timedelta):

[2024-02-14T11:13:00.692Z]             # Used by interval type DayTimeInterval for Pyspark 3.3.0+

[2024-02-14T11:13:00.692Z]             assert cpu == gpu, "GPU and CPU timedelta values are different at {}".format(path)

[2024-02-14T11:13:00.692Z]         elif (cpu == None):

[2024-02-14T11:13:00.692Z] >           assert cpu == gpu, "GPU and CPU are not both null at {}".format(path)

[2024-02-14T11:13:00.692Z] E           AssertionError: GPU and CPU are not both null at [1, 'sub_b']

[2024-02-14T11:13:00.692Z]

[2024-02-14T11:13:00.692Z] ../../src/main/python/asserts.py:100: AssertionError

test_get_json_object_single_quotes is a new test introduced in PR 10407 case for verifying get_json_object with single quotes. I tested this on Databricks 10.4 Spark 3.2.1 against rapids-4-spark_2.12-23.12.2.jar. Turns out we don't match the CPU results.
from pyspark.sql import SparkSession
from pyspark.sql.functions import expr

spark = SparkSession.builder \
    .appName("Test get_json_object") \
    .getOrCreate()

spark.conf.set("spark.rapids.sql.enabled", "true")

json_data = [
    [r'''{'key':'A'}'''],
    [r'''{'key':'"B'}'''],
    [r'''{"key":"'C"}''']
]

df = spark.createDataFrame(json_data, ["json_str"])

result = df.select(
    expr("get_json_object(json_str, '$.key') AS key_value")
)

result.show()

| CPU | GPU 23.12 | GPU 24.04 |
|-----|-----------|-----------|
|  A  |    null   |     A     |
| null|    null   |    "B     |
| 'C  |     'C    |     'C    |

So databricks is different from Apache Spark when it comes to parsing JSON object values with single quotes? Because we match exactly with Apache Spark 3.4.2.

I think the issue is observed only in Databricks 10.4 since the IT tests have passed on other Databricks runtimes. It appears to be a bug in DB 10.4.


Ruff updates

Just dropping in to mention these changes all look sensible and good to me. I think I'm in favor of trying to move forward with getting this change adopted by the libraries.


Native E2E tests failing

I see native e2e tests failing throughout branches and PRs
https://github.com/apache/camel-k/actions/workflows/install.yml
From what I see in the logs the native build used in the e2e test is stuck in phase build running and the test finally hits validation timeouts (currently 10 mins). Maybe 3/10 times this tests is failing with timeouts. We need to investigate and see if this happens due to slow CI environment or how to improve the native e2e tests.

I remind some work on timeout was done by @tadayosi

Yes, if we are talking about this failure, I know why it sometimes happens.
📦 github.com/apache/camel-k/e2e/namespace/native
❌ TestNativeIntegrations (32m57.36s)
❌ TestNativeIntegrations/automatic_rollout_deployment_from_fast-jar_to_native_kit (30m54.21s)
✅ TestNativeIntegrations/unsupported_integration_source_language (1.03s)
✅ TestNativeIntegrations/warm_up_before_native_build_testing (1m41.61s)

The problem is that since Quarkus 2.11.3 a native build requires more memory whereas GitHub Actions only provide 7GB for the ubuntu GitHub runner. I tried to find the balance between successful build and avoiding OOME on the container and this was the result:
https://github.com/apache/camel-k/blob/main/e2e/namespace/native/native_test.go#L45-L49
Actually, recommendation for -Dquarkus.native.native-image-xmx is much higher in general, such as >=6g or even >=8g. And it's quite possible that upgrading to Quarkus 2.13.0 it becomes severer and the rate of success gets down further.
So ultimately unless GitHub gives us more memory for a GitHub runner in the future the problem won't be solved. Or we'd need to find a way to use a self-hosted runner for the upstream project. Or it's just a thought experiment, but GitHub-hosted macos runners have 14GB so running the native build e2e tests on a macos runner might possibly solve it?
https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources

As a simple workaround I just increased the build timeout from 30 to 40 mins with PR #3747:
📦 github.com/apache/camel-k/e2e/namespace/native
✅ TestNativeBinding (33m55.87s)
✅ TestNativeBinding/kamelet_binding_with_native_build (32m3.04s)
✅ TestNativeBinding/warm_up_before_native_build_testing (1m38.2s)
✅ TestNativeIntegrations (34m14.21s)
✅ TestNativeIntegrations/automatic_rollout_deployment_from_fast-jar_to_native_kit (32m24.14s)
✅ TestNativeIntegrations/unsupported_integration_source_language (1.05s)
✅ TestNativeIntegrations/warm_up_before_native_build_testing (1m34.08s)

So apparently native builds take 28~35 mins on GitHub workflows. At this moment, probably relaxing the timeout is the only way we can do to mitigate the problem.


FormMetadata type mismatch

Describe the bug and the expected behavior
I have a component that takes FormMetadata as a prop. The form metadata I get from useForm() is no longer compatible with the FormMetadata type.
The last working version was v1.0.0-rc.0. It looks like the problem was introduced in v1.0.0-rc.1.
Conform version
v1.0.0
Steps to Reproduce the Bug or Issue
https://stackblitz.com/edit/remix-run-remix-thrjv1?file=index.ts
Type 'FormMetadata<{ foo: string; }, string[]>' is not assignable to type 'FormMetadata'.
  Type 'FormMetadata<{ foo: string; }, string[]>' is not assignable to type '{ id: FormId<Record<string, unknown>, string[]>; context: Wrapped<FormContext<Record<string, unknown>, string[], Record<string, unknown>>>; status?: "success" | ... 1 more ... | undefined; getFieldset: () => { ...; }; onSubmit: (event: FormEvent<...>) => void; noValidate: boolean; }'.
    Types of property 'context' are incompatible.
      Type 'Wrapped<FormContext<{ foo: string; }, string[], { foo: string; }>>' is not assignable to type 'Wrapped<FormContext<Record<string, unknown>, string[], Record<string, unknown>>>'.
        Type 'FormContext<{ foo: string; }, string[], { foo: string; }>' is not assignable to type 'FormContext<Record<string, unknown>, string[], Record<string, unknown>>'.
          Type 'FormContext<{ foo: string; }, string[], { foo: string; }>' is not assignable to type '{ submit: (event: FormEvent<HTMLFormElement>) => void; onUpdate: (options: Partial<FormOptions<Record<string, unknown>, string[], Record<string, unknown>>>) => void; }'.
            Types of property 'onUpdate' are incompatible.
              Type '(options: Partial<FormOptions<{ foo: string; }, string[], { foo: string; }>>) => void' is not assignable to type '(options: Partial<FormOptions<Record<string, unknown>, string[], Record<string, unknown>>>) => void'.
                Types of parameters 'options' and 'options' are incompatible.
                  Type 'Partial<FormOptions<Record<string, unknown>, string[], Record<string, unknown>>>' is not assignable to type 'Partial<FormOptions<{ foo: string; }, string[], { foo: string; }>>'.
                    Types of property 'onValidate' are incompatible.
                      Type '((context: { form: HTMLFormElement; submitter: HTMLInputElement | HTMLButtonElement | null; formData: FormData; }) => import("stackblitz:/node_modules/@conform-to/dom/submission").Submission<...>) | undefined' is not assignable to type '((context: { form: HTMLFormElement; submitter: HTMLInputElement | HTMLButtonElement | null; formData: FormData; }) => import("stackblitz:/node_modules/@conform-to/dom/submission").Submission<...>) | undefined'. Two different types with this name exist, but they are unrelated. (2322)

What browsers are you seeing the problem on?
No response
Screenshots or Videos
No response
Additional context
I think it's possible something was missed in 465d1ba6193eb9aed3b2c9cc93e8b1e6dc33b20a, but so far I haven't found it.

It might be because we now have a basic FormContext type and a react version FormContext. Looked at the diff from rc.0 to rc.1 a bit but still unsure what's went wrong as well.
For now, I think you can just use FormMetadata<any> since that's what it really means when you don't specify the schema there.

I added "noErrorTruncation": true to the StackBlitz so we can see the full TypeScript error.
On this line:
Type 'FormMetadata<{ foo: string; }, string[]>' is not assignable to type 'FormMetadata'.
  Type 'FormMetadata<{ foo: string; }, string[]>' is not assignable to type '{ id: FormId<Record<string, unknown>, string[]>; context: Wrapped<FormContext<Record<string, unknown>, string[], Record<string, unknown>>>; status?: "success" | "error" | undefined; getFieldset: () => { [x: string]: FieldMetadata<unknown, Record<string, unknown>, string[]>; }; onSubmit: (event: FormEvent<HTMLFormElement>) => void; noValidate: boolean; }'.
    Types of property 'context' are incompatible.
      Type 'Wrapped<FormContext<{ foo: string; }, string[], { foo: string; }>>' is not assignable to type 'Wrapped<FormContext<Record<string, unknown>, string[], Record<string, unknown>>>'.
        Type 'FormContext<{ foo: string; }, string[], { foo: string; }>' is not assignable to type 'FormContext<Record<string, unknown>, string[], Record<string, unknown>>'.
          Type 'FormContext<{ foo: string; }, string[], { foo: string; }>' is not assignable to type '{ submit: (event: FormEvent<HTMLFormElement>) => void; onUpdate: (options: Partial<FormOptions<Record<string, unknown>, string[], Record<string, unknown>>>) => void; }'.
            Types of property 'onUpdate' are incompatible.
              Type '(options: Partial<FormOptions<{ foo: string; }, string[], { foo: string; }>>) => void' is not assignable to type '(options: Partial<FormOptions<Record<string, unknown>, string[], Record<string, unknown>>>) => void'.
>>              Types of parameters 'options' and 'options' are incompatible.
                  Type 'Partial<FormOptions<Record<string, unknown>, string[], Record<string, unknown>>>' is not assignable to type 'Partial<FormOptions<{ foo: string; }, string[], { foo: string; }>>'.
                    Types of property 'onValidate' are incompatible.
                      Type '((context: { form: HTMLFormElement; submitter: HTMLInputElement | HTMLButtonElement | null; formData: FormData; }) => Submission<Record<string, unknown>, string[], Record<string, unknown>>) | undefined' is not assignable to type '((context: { form: HTMLFormElement; submitter: HTMLInputElement | HTMLButtonElement | null; formData: FormData; }) => Submission<{ foo: string; }, string[], { foo: string; }>) | undefined'. (2322)

TypeScript starts to check whether type Record<string, unknown> satisfies type { foo: string; }, which will always fail.
I vaguely understand this is due to contravariance of function types, but I don't understand why it started happening when it did, nor do I know how to solve it.

Getting the same error with FieldMetadata, looping through an array of objects.
const Schema = z.object({
users: z.array(z.object({ name: z.string() })
})
const Component = () => {

	const list = fields.users.getFieldList();
	return (
		<div>{list.map(l => <ListItem config={l} key={l.key} />}</div>
	)
}
const ListItem = ({config}: {config: FieldMetadata<z.infer<typeof Schema>>}) => {
return null
}


withHttpConnectionOptions(configureHttpOptions: {(option) in usage?

Hi.!
The asp.net code is as follows.
.WithUrl($"chat?username={Globals.UserId}", option =>
{
option.AccessTokenProvider = () =>
{
return Task.FromResult(sToken);
};
}).Build();
How do I use the code above in swift?
In other words, I would like to know how to use the code below.
option.AccessTokenProvider = () =>
{
return Task.FromResult(sToken);
};
thank!

try likes this replacing you url and token.
hubConnection = HubConnectionBuilder(url: URL(string: API.shared.soketURL ?? "")!)
            .withLogging(minLogLevel: .debug)
            .withHttpConnectionOptions(configureHttpOptions: {val in
                val.skipNegotiation = true
                val.accessTokenProvider = {
                    return API.shared.socketToken ?? ""
                }
            })
            .build()

What @kjoe07 said. Closing.

Worked for me, Thanks @moozzyk


webpack-dev-server version needs bump

webpack-dev-server 3.x depends on selfsigned 1.x, which depends on node-forge^0.10.0, which has security vulnerabilities.
See the fix for selfsigned: https://github.com/jfromaniello/selfsigned/issues/55
Need top bump the webpack-dev-server version to get the fixed version of selfsigned.

Please take a look at this discussion thread regarding security vulnerabilities on our fork here: https://github.com/iTwin/itwinjs-core/discussions/3397
https://twitter.com/dan_abramov/status/1412376404738686984

Thank you @aruniverse. Closing this.


'static Lifetime of Filter for get_account_balances and get_account_transfers

It looks like the Filter arguments for get_account_balances and get_account_transfers require the 'static lifetime. The only way I can use these functions is to actually create a single static filter or create them dynamically (more realistic) and Box them and then Box::leak() them.
I'm not sure how the FFI works here, but would it be possible to have the filter args take a more reasonable lifetime?

Sorry, but relaxing lifetime there could lead to the use-after-free today:
use std::mem::forget;
let filters = [/* ... */];
let running_operation = client.get_account_balances(filters.as_slice());
forget(running_operation);
forget(client);
drop(filters); // client isn't deinitialized and can operate on `filters` memory, but `filters` array is freed here

This 'static bound wouldn't be needed in a possible synchronous (without async) version of the tigerbeetle-unofficial API, but I am not sure if anyone would be interested in it (let me know otherwise).
Also it should be possible to extend lifetime of the slice you give as an argument by using the scope-lock library and concurrently send batches of operations, but not without blocking the thread.
Anyway, you might find useful to take a look at the tigerbeetle-unofficial-core crate for a lower level approach.

The only way I can use these functions is to actually create a single static filter or create them dynamically (more realistic) and Box them and then Box::leak() them.

Sorry, I think you have misunderstood the API. You can pass as an argument anything Send + 'static from the implementors list, including things like Box<Filter>, Arc<Filter>.
Please never use Box::leak like this, it is absolutely not intended to be used like that.

Please never use Box::leak like this, it is absolutely not intended to be used like that.

😆  yeah I had no intent of shipping anything with Box::leak. It seemed at the time that just boxing it would cause "borrowed data escapes outside of closure" type error. Box::leak seemed like the only way to get it to compile.
However, now just Box::new seems to work, not sure what else I was doing wrong at the time.


Minor cleanups

Very minor cleanups to recently added modules.

Can one of the admins verify this patch? (see README)

ok to test


Update adyen-connector-troubleshoot.md

The current doc navigates us to old location and I've updated the event logs location for store commerce as from version 10.0.32+ store commerce logs are now logged under Windows logs with the event source as 'Microsoft Dynamics - Store Commerce'

@v-chgri the change looks good to me

Closing the PR. The changes were added using this PR in the private repo: https://github.com/MicrosoftDocs/Dynamics-365-Operations/pull/19263


Updating a DS w/ consistent hash query params creates unrelated change log message

I'm submitting a ...

bug report

Traffic Control components affected ...

Traffic Ops

Current behavior:
Create a new HTTP delivery service and give it one consistent hash query parameter. Now, update the delivery service (change the display name for example). For some reason, the following API change log message is being recorded.

Expected behavior:
Only if a delivery service consistent hash query parameter was actually deleted should that message be recorded. Actually, i think we decided that creating/updating/deleting ds consistent hash query parameters should never create a change log entry...period.
Minimal reproduction of the problem with instructions:
See current behavior.

Should already be fixed in https://github.com/apache/trafficcontrol/pull/5410

The Deleted N consistent hash query params changelog message is still an issue.


remove reference to 'this' builder in every AbstractConfig subclass

also fix some missing generics in InMemoryConfigSource and UrlConfigSource

@romain-grecourt
Yes. I sent email with filled scan of OCA.

Nice. @delabassee Can you let me know when you've received @wojtask9 's OCA ? Thanks.


Add a 36x36 OpenStreetMap logo for display on the login page, mention it in the README.

Thanks for creating this gem, @nabetaro, I found my server wouldn't start without an openstreetmap.svg in the asset pipeline and thought it might be useful to incorporate into your repo.

Thanks a lot!


Add timer module with initial support for STM32F412.

This goes together with https://github.com/therealprof/stm32f4xx-hal/pull/17.
Most of the implementation is taken from stm32f30x_hal.

https://github.com/therealprof/stm32f4xx-hal/pull/16 seems to do the same thing, maybe with some slight differences.  I wasn't aware of that PR when I made this branch.  Feel free to reject my PR if the existing one is better.

Yeah, plenty of PRs raised today. 👍 I think I'll take the other PR on the merit of both being first and looking a bit easier on the eye for me.
I'm sure there's still a lot todo so feel free to chime in any time.


redirect and error reform

Error has been made an opaque struct.
RedirectPolicy now makes use of RedirectAttempt and RedirectAction.

The problem with hiding the underlying error behind std::error::Error::cause() is that it's no longer possible to actually get to said underlying error and do something based on what kind of error it is.
With v0.5 I could have code that, say, retried the request on ConnectionAborted:
match send(url) {
    Err(::reqwest::Error::Http(::reqwest::HyperError::Io(ref io_err))) => match io_err.kind() {
        ::std::io::ErrorKind::ConnectionAborted => /* retry */,
        _ => /* abort */,
    },
}

but with v0.6 the result of reqwest_err.cause().unwrap() cannot be downcast to a concrete type.
Would it make sense to add as_http(&self) -> &::hyper::Error, as_serialization(&self) -> &::serde_urlencoded::ser::Error, etc methods to Error ?

I believe the cause can be downcast. This doesn't work?
if let Some(cause) = err.cause() {
    match cause.downcast_ref::<hyper::Error>() {
        Some(hyper::Error::Io(ref io)) => assert_eq!(io.kind(), ErrorKind::ConnectionAborted),
        _ => ()
    }
}

The ::<hyper::Error> may not even be needed, since it could be inferred by the match, I think.

std::error::Error::downcast_ref is just a wrapper around Any::downcast_ref and thus requires a 'static bound. It's a long-standing issue - https://github.com/rust-lang/rust/issues/35943

Oh what the...

Ok, so there could be a few solutions to this:

Add an inherent (so not impl Trait for Error) fn cause(&self) -> Option<&Error + 'static>, so that downcasting can work.
Add some TryFrom impls to allow static downcasting. Not stable yet, but will be stable in 1.18.
Add as_http() -> Option<&hyper::Error> and friends, as suggested.
Add some sort of is_io_kind(&self, std::io::ErrorKind) -> bool method.
Something else?

I was bitten by this too in 0.6, as I have code that does retries on ConnectionAborted. The first option seems to be the most straight-forward and flexible, although it could be confusing having two versions of  the cause fn. The is_io_kind is an interesting option, that would work for me, but I guess if others are matching on other Error variants it won't work for them.

I'm still not certain what would be the best thing to expose.
Tangentially, would there be benefit in reqwest retrying the requests itself, when the method is idempotent?

Oh, looking at std::io::Error, it has an inherent get_ref method that was added since cause wasn't usable. Perhaps reqwest::Error should get get_ref?

get_ref is a good idea.

I just published v0.6.1 that adds Error::get_ref that allows downcasting.

Works like a charm. Thanks!


Question about the design choice of the unified framework.

Thanks for the great work!
I had read the paper and raised a question about the choice of the unified framework. The author chose BART as a textual encoder and CLIP model as a visual encoder. I initially thought that that we could directly use CLIP textual and visual encoders. It could produce much better results since it was pre-trained on a cross-modal alignment task. Why is BART chosen instead?

This is a good question!
Our model design is motivated by this paper, which shows CLIP vision encoder can help vision-and-language models. There is another reason we use BART language model. While CLIP is good at image-text matching tasks (image classification), the tasks we focus on are conditional text generation tasks (QA, captioning), so using a generative model (BART) is a more straightforward way in this case.
You might also be interested in this paper, which combines both CLIP vision and text encoders to BART encoder-decoder model by distillation.


[Parsers] xsodata - Refactor xsk core services

Modules https://github.com/SAP/xsk/tree/main/modules/engines/engine-core/src/main/java/com/sap/xsk/xsodata
Depends on Issue: https://github.com/SAP/xsk/issues/30

refactor the old code

https://github.com/eclipse/dirigible/issues/814


Bookmarks removed after jsFormat(https://atom.io/packages/jsformat) formatting

Bookmarks created successfully with Ctrl+Alt+F2 but I am configured jsFormat on on save after formatting Bookmarks removed.

Hey @vinaymavi :wave:. We can't really debug other packages and look at what they're doing, but I'm guessing that the package is modifying the text in the editor somehow and that's causing the bookmark to be removed. If you can reproduce the problem in safe mode, then please report the issue on the Bookmarks package's repository: https://github.com/atom/bookmarks and provide steps to reproduce so that we can take a look. Thanks!


Make a finalised control scheme

This may have to wait until code is more settled but we are probably pretty close on that front already. Once a drive team has been selected, we should discuss with them how they want to control the robot and then implement those controls.

https://github.com/thedropbears/pycrescendo/pull/99


Append template-literal to template engine default list

Template Literal is fastest, smallest and simplest template engine, because it use JS's literal template feature,
You can find here a simple wrapper for Express templating engine system : https://github.com/Drulac/express-tl/
It's 910 times faster than edge,  55 times faster than EJS, 20 times faster than doT and 6 times faster than zup. So it may be better to use it in most of common cases 😀

I've added it to the Wiki for now. These lists will eventually move to expressjs.com


mongodb example connection string instructions

The instructions include this connection string:

mongodb+srv://mongodb:@serverlessinstance0.j9n6s.mongodb.net/myFirstDatabase?retryWrites=true&w=majority

But the example uses the database named 'demo', so the string should be either:

mongodb+srv://mongodb:(password)@serverlessinstance0.j9n6s.mongodb.net/demo?retryWrites=true&w=majority

or;

mongodb+srv://(username):(password)@serverlessinstance0.j9n6s.mongodb.net/demo?retryWrites=true&w=majority

...where (username) and (password) are provided by Mongo's admin interface for the serverless instance. Your user may be assigned the username 'mongodb' or some other username.

@jayair you looked at the Mongo example recently. Can you take a look at this?

This is fixed


'extract_url' function error

When tried with url it gives the following error:
Traceback (most recent call last):
  File "02 facebook_dl.py", line 65, in <module>
    main()
  File "02 facebook_dl.py", line 51, in main
    file_url = extract_url(r.text, args.resolution)
  File "02 facebook_dl.py", line 25, in extract_url
    url = re.search('sd_src:"(.+?)"', html)[0]
TypeError: 'NoneType' object is not subscriptable

I think Facebook has changed something which means I need to find where the new url is located. I will fix this soon :)

Any update on this?

@OrganicChem Im really sorry, I havent had much time to work on this, really busy with school at the moment.

@OrganicChem @UIlynn  It seems to be working now. I just tried downloading a video and it worked. Could you test again?

Seems to work just fine for me:

I'm still getting an error though.
muning-MacBook-Pro:facebook-dl muning$ python3 facebook-dl.py https://www.facebook.com/irwansamsuri.pg/videos/10216440231261658/
✔ Fetched source code
Traceback (most recent call last):
File "facebook-dl.py", line 64, in
main()
File "facebook-dl.py", line 49, in main
file_url = extract_url(request.text, args.resolution)
File "facebook-dl.py", line 28, in extract_url
url = re.findall('hd_src:"(.+?)"', html)[0]

@onoakino This tool only downloads videos from public groups at the moment. We would have to add way of logging into Facebook to download private posts, and I havent really figured out how to do that yet.