text:
build: add image signing for all release images

Description
What this PR does / why we need it:
This PR adds release image signing using Notation and Cosign for all release images: ghcr.io/ratify-project/ratify, ghcr.io/ratify-project/ratify-crds, ghcr.io/ratify-project/ratify-base. The next minor version release v1.4.0 will utilize the new signing workflow.
Doc update PR: https://github.com/ratify-project/ratify-web/pull/129/files
Sample workflow showing release flow successful: https://github.com/akashsinghal/ratify/actions/runs/11963756788/job/33354797232
Cosign signature attached:

Notary Project signature attached:

Which issue(s) this PR fixes (optional, using fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when the PR gets merged):
Fixes #1437
Type of change
Please delete options that are not relevant.

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] Helm Chart Change (any edit/addition/update that is necessary for changes merged to the main branch)
[ ] This change requires a documentation update

How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Please also list any relevant details for your test configuration

[ ] Test A
[ ] Test B

Checklist:

[ ] Does the affected code have corresponding tests?
[ ] Are the changes documented, not just with inline documentation, but also with conceptual documentation such as an overview of a new feature, or task-based documentation like a tutorial? Consider if this change should be announced on your project blog.
[ ] Does this introduce breaking changes that would require an announcement or bumping the major version?
[ ] Do all new files have appropriate license header?

Post Merge Requirements

[ ] MAINTAINERS: manually trigger the "Publish Package" workflow after merging any PR that indicates Helm Chart Change

interesting that cosign signs with the command vs notation we use the action. Curious if both are available, is it better to use the command or the action?

yeah good point. It seems that cosign github action is only for installation. recommended way is to use cosign cli directly once installed on runner.

repo: ratify-project/ratify


text:
[Bug] No config shown, plugins don't load

Describe the Bug
Plugins don't load, no configuration options shown in Discord settings
To Reproduce

Install BBD
Launch, check settings

Expected Behavior
Plugins do load, I can customize BBD
Screenshots

Discord Version
Stable
Additional Context
On Linux, using this to install https://github.com/bb010g/betterdiscordctl

Can you check console for errors?

[FAST CONNECT] wss://gateway.discord.gg/?encoding=etf&v=6&compress=zlib-stream, encoding: etf, version: 6 9833a7395829bb4e2d56.js:49 Initializing voice engine with audio subsystem: standard 9833a7395829bb4e2d56.js:49 [BUILD INFO] Release Channel: stable, Build Number: 38950, Version Hash: 4483a2c7d8be95c80b8555ec0c25c778fc221af0 9833a7395829bb4e2d56.js:49 [NATIVE INFO] host 0.0.9, modules: discord_desktop_core: 1, discord_erlpack: 1, discord_spellcheck: 1, discord_utils: 1, discord_voice: 1, discord_game_utils: 1, discord_rpc: 2, discord_contact_import: 1, discord_zstd: 1 9833a7395829bb4e2d56.js:49 unsupported locale en-GB e.(anonymous function) @ 9833a7395829bb4e2d56.js:49 9833a7395829bb4e2d56.js:49 unsupported locale en e.(anonymous function) @ 9833a7395829bb4e2d56.js:49 9833a7395829bb4e2d56.js:49 [FAST CONNECT] connected in 565ms 9833a7395829bb4e2d56.js:49 CloudSync is not supported on this platform e.(anonymous function) @ 9833a7395829bb4e2d56.js:49 9833a7395829bb4e2d56.js:49 [GatewayDiscovery] [STICKY] wss://gateway.discord.gg 9833a7395829bb4e2d56.js:49 [GatewaySocket] [CONNECT] wss://gateway.discord.gg, encoding: etf, version: 6, compression: zlib-stream 9833a7395829bb4e2d56.js:49 [GatewaySocket] [CONNECTED] wss://gateway.discord.gg/?encoding=etf&v=6&compress=zlib-stream in 0 ms 9833a7395829bb4e2d56.js:49 [GatewaySocket] [IDENTIFY] 9833a7395829bb4e2d56.js:49 [GatewaySocket] [HELLO] via gateway-prd-main-8w26, heartbeat interval: 41250, took 5 ms 9833a7395829bb4e2d56.js:49 [RPCServer:WSS] Starting on 6463 9833a7395829bb4e2d56.js:49 [RPCServer:IPC] Starting on /run/user/1000/discord-ipc-0 9833a7395829bb4e2d56.js:49 [BandagedBD] [Startup] Initializing Settings 9833a7395829bb4e2d56.js:49 [BandagedBD] [Startup] Initializing EmoteModule 9833a7395829bb4e2d56.js:49 [Deprecation] Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user's experience. For more help, check https://xhr.spec.whatwg.org/. (anonymous) @ 9833a7395829bb4e2d56.js:49 9833a7395829bb4e2d56.js:49 [BandagedBD] [Emotes] Loading emotes from local cache. 9833a7395829bb4e2d56.js:49 [GatewaySocket] [READY] via gateway-prd-main-8w26 -> discord-sessions-prd-1-24 as 097a5c5db377ecf1a1454966ec18935e, took 980 ms 9833a7395829bb4e2d56.js:49 [GuildAvailabilityStore] 4 guilds are unavailable on connection open: 86004744966914048,227543998590353408,280806472928198656,327892735963037696 e.(anonymous function) @ 9833a7395829bb4e2d56.js:49 9833a7395829bb4e2d56.js:49 Tried getting Dispatch instance before instantiated e.(anonymous function) @ 9833a7395829bb4e2d56.js:49 9833a7395829bb4e2d56.js:49 patch render of TabBar 9833a7395829bb4e2d56.js:49 patch default of Object 9833a7395829bb4e2d56.js:49 patch render of Guild 9833a7395829bb4e2d56.js:49 patch render of Guilds 9833a7395829bb4e2d56.js:49 [BandagedBD] [Startup] Updating Settings 9833a7395829bb4e2d56.js:49 [BandagedBD] [Emotes] Emotes loaded from cache. 9833a7395829bb4e2d56.js:49 patch render of MessageContent 9833a7395829bb4e2d56.js:49 [BandagedBD] [Startup] Initializing QuickEmoteMenu 9833a7395829bb4e2d56.js:49 Uncaught TypeError: Cannot read property 'remove' of null     at setTimeout (cdn.staticaly.com/gh/rauenzi/BetterDiscordApp/c268371144a5ac3dbeaa6b2af0aebcba055d10b5/js/main.min.js:55)     at i (9833a7395829bb4e2d56.js:49) 9833a7395829bb4e2d56.js:49 [GuildAvailabilityStore] Guild has become available: 227543998590353408 9833a7395829bb4e2d56.js:45 [Deprecation] Using unescaped '#' characters in a data URI body is deprecated and will be removed in M71, around December 2018. Please use '%23' instead. See https://www.chromestatus.com/features/5656049583390720 for more details. n.setFullScrollerState @ 9833a7395829bb4e2d56.js:45 my_god_v3.2.png:1 Failed to load resource: the server responded with a status of 504 () 9833a7395829bb4e2d56.js:49 Hold Up! 9833a7395829bb4e2d56.js:49 If someone told you to copy/paste something here you have an 11/10 chance you're being scammed. 9833a7395829bb4e2d56.js:49 Pasting anything in here could give attackers access to your Discord account. 9833a7395829bb4e2d56.js:49 Unless you understand exactly what you are doing, close this window and stay safe. 9833a7395829bb4e2d56.js:49 If you do understand exactly what you are doing, you should come work with us https://discordapp.com/jobs

Nothing pops up when going to settings?

Nope. in the first screenshot that's basically it. BBD logo in bottom right, credits link at the bottom, nothing changed. The emoji picker is changed in the way of the background color and borders

Not sure why it's not loading properly. Are you sure your installation is up to date and the local config is pointing to the right branch?

Yes. I already checked that and have done a clean install as of today. Is it possible the Linux injector is broken?

It's possible your version is out of date, but the Linux installer and the injection was just updated and redone very recently

It's not possible since this is the first time I've installed BBD on this machine.

Resolved after a full X session restart, it might be useful to pin this or add to faq

If I quit BBD, and reopen it again, I have the same issue. You have to restart your pc or even just X in order to fix it

I cannot personally recreate this. Perhaps another Linux user has seen something similar? @ObserverOfTime

I can't reproduce it either but @JeremyStepp's issue might be related.

What do your setups look like?
Ubuntu 18.10 (switching to 04 soon)
AwesomeWM

I am still having issues after upgrading to 1.6.0 and installing/reinstalling, it now doesn't give even a popup or the loading gif now.

Version 1.6.0 of what?

Betterdiscordctl

@Meizwe You're using snap, right? Please post the output of:
snap info discord
betterdiscordctl reinstall -v -v --snap
betterdiscordctl update -v -v --snap

I get the same issue, but the emotes loaded message will show up. I'm on Linux Mint 19 using the flatpak Discord and the ppa for betterdiscordctl. The error I get after betterdiscord starts up is
(node:4) UnhandledPromiseRejectionWarning: Error: ENOSPC: no space left on device, watch '/home/jeremy/.var/app/com.discordapp.Discord/config/BetterDiscord/plugins'
    at FSWatcher.start (internal/fs/watchers.js:164:26)
    at Object.watch (fs.js:1232:11)
    at Object.watchContent (https://cdn.staticaly.com/gh/rauenzi/BetterDiscordApp/c268371144a5ac3dbeaa6b2af0aebcba055d10b5/js/main.min.js:55:18798)
    at V2_SettingsPanel.initializeSettings (https://cdn.staticaly.com/gh/rauenzi/BetterDiscordApp/c268371144a5ac3dbeaa6b2af0aebcba055d10b5/js/main.min.js:55:79707)
    at Core.init (https://cdn.staticaly.com/gh/rauenzi/BetterDiscordApp/c268371144a5ac3dbeaa6b2af0aebcba055d10b5/js/main.min.js:4:580)
(node:4) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1)
(node:4) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.
/app/bin/discord: line 9: kill: (3) - No such process

@JeremyStepp That seems like a Flatpak issue and thus unrelated to BBD. Move your comment to a new issue in betterdiscordctl and I'll look into it.

miw@q8D-AX370-K7:~$ betterdiscordctl reinstall -v -v --snap
VV: Checking /snap/discord/93/usr/share/discord
V: Using Discord at /snap/discord/93/usr/share/discord
V: Found modules in /home/miw/snap/discord/93/.config/discord/0.0.9/modules
Killing Discord processes...
No active processes found.
V: Removing old injector folder.
V: Copying BetterDiscord injector...
Reinstalled.
miw@q8D-AX370-K7:~$ betterdiscordctl update -v -v --snap
VV: Checking /snap/discord/93/usr/share/discord
V: Using Discord at /snap/discord/93/usr/share/discord
V: Found modules in /home/miw/snap/discord/93/.config/discord/0.0.9/modules
Updating Git repository...
remote: Enumerating objects: 62, done.
remote: Counting objects: 100% (62/62), done.
remote: Compressing objects: 100% (31/31), done.
remote: Total 58 (delta 28), reused 49 (delta 26), pack-reused 0
Unpacking objects: 100% (58/58), done.
From https://github.com/rauenzi/BetterDiscordApp

branch            injector   -> FETCH_HEAD
HEAD is now at 1c2e6f6 update for linux
``

`miw@q8D-AX370-K7:~$ snap info discord
name:      discord
summary:   All-in-one voice and text chat for gamers
publisher: Snapcrafters
contact:   https://github.com/snapcrafters/discord/issues
license:   unset
description: |
All-in-one voice and text chat for gamers that's free, secure, and
works on both your desktop and phone.
This snap is maintained by the Snapcrafters community, and is not necessarily endorsed or
officially maintained by the upstream developers.
commands:

discord
snap-id:      qHVefGEBezeuCeSfTND40uoUD6GRw8BO
tracking:     stable
refresh-date: 2019-03-12
channels:
stable:    0.0.9 2019-03-12 (93) 69MB -
candidate: ↑
beta:      ↑
edge:      0.0.9 2019-05-31 (94) 69MB -
installed:   0.0.9            (93) 69MB -
`

After update and reinstall this issue doesn't seem to persist, I can reliably close and reopen and BBD loads each time.
Discord: /usr/share/discord
Modules: /home/usr/.config/discord/0.0.9/modules
Index modified: yes
Linked injector directory: /home/usr/.local/share/betterdiscordctl/bd/0
Linked injector repository: ssh://git@github.com/rauenzi/BetterDiscordApp

source: gharchive/issue

authors: JeremyStepp Meizwe ObserverOfTime S-B99 rauenzi

repo: rauenzi/BetterDiscordApp

license_type: permissive

license_source: github-api


text:
number of differentiations

Thank you for your quick help.
I allude to 2dim-data: N1 samples in dim1-space., N2 samples in dim2-space.
This amounts to Na=N1xN2 samples (datapoints): product, huge.
It seems not necessary to compute that many derivatives.
In my opinion,  Nb = N1+N2 derivatives suffice: sum, limited size.
The Jacobian size needs to be  Na x Npar, though, where Npar is the total number of parameters.
I wish to build this Jacobian from the Nb derivatives with GADfit.
I can do this with my own simple-minded f90 program (no Levenberg-Marquardt, no coarrays, no OOP,
derivatives analytically obtained from computer algebra).
Tomorrow, 5 April, I am absent. Dirk.

The number of derivatives calculated is (N1+N2) times a number which is on the order of the number of parameters. For example, with one global and one local fitting parameter, the number of derivatives would be roughly 2*(N1+N2). I don't quite see where N1xN2 comes from. Note that even though there are many more elements in the Jacobian, most of them are set to zero. Any linear algebra that is done on the Jacobian is generally fast anyway and so the extra zeros do not pose a significant problem.
Minor note: it's better to follow the same thread when making new posts. Each Github issue should in principle describe a separate technical question and not be spread over several issues.

Dear Raul,
for_GADfit.pdf
jacobian.pdf
This is a new attempt to make my point without wasting too much of your precious time. My arguments are in jacobian.pdf'. This file in turn refers to for_GADfit.pdf' which I presented two years ago (under different name) in an MR group that applies hyperpolarisation. Sorry for asking your time. Thank you in advance. Should you have no time, could you please nonetheless acknowledge receipt of this email to a weird address? Best regards, Dirk.

repo: raullaasner/gadfit

license_source: bigquery


text:
🛑 Cuchilloco is down

In 28a6016, Cuchilloco (http://cuchilloco.funsadu.ar:60080) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Cuchilloco is back up in 71bff68.

repo: raulredes/funsadu

license: MIT


text:
Update UCXShuffleTransport.scala

build1

build1

source: gharchive/pull-request

repo: ravitestgit/spark-rapids


text:
Use reconnect_uri

Slack now provides a uri to reconnect the websocket without doing a full rtm.start. we should use it.

Is this the reason WeeChat won't reconnect to Slack after I wake up my Mac from sleep?  If not, should I open a different issue for that?

This behavior has been fixed in #257

authors: cro rawdigits

repo: rawdigits/wee-slack

license: mit


text:
Add FAQ page

Why are these changes needed?
Adding FAQs to assist Users with Troubleshooting.
Related issue number
Closes #1130

This PR only updates documentation and has no relationship with the CI failure.

repo: ray-project/kuberay


text:
[API Server] Add Ray Job output - start/end time and ray cluster name

Why are these changes needed?
Adding the starttime, endtime, and the rayclustername fields to the api server output to match the status fields on the rayjob CRD.
These fields are useful for displaying the job start/end time information and easily pulling the cluster information. For us, they are also useful for generating the grafana links to show the Prometheus metrics collected during the job's run.
Checks

[x] I've made sure the tests are passing.
Testing Strategy

[x] Unit tests
[x] Manual tests
[ ] This PR is not tested :(

/assign @YQ-Wang

LGTM

cc @kevin85421 @andrewsykim

We are currently in KubeCon. I have already approved the CI. I will merge it if CI passes because @YQ-Wang has already approved this API server PR.

@han-steve would you mind taking a look at the lint error? Thanks!

Yep!

@han-steve would you mind fixing the conflict? Thanks!

Done :)

authors: YQ-Wang han-steve kevin85421


text:
[ChatGPT] Unable to automatically synchronize OpenAI newest official models

Extension
https://www.raycast.com/abielzulio/chatgpt
Description
The OpenAI model has been updated to 0125, the extension only has 1106.
Can the user enter a Model ID?
Or is it possible to synchronize official updates?
Steps To Reproduce

Latest Raycast and ChatGPT extension
Call Model by selecting the model in Edit Model
GPT-3.5 and GPT-4 only have 1106 version

Current Behaviour
No response
Expected Behaviour
No response

I would like to propose, that the model value can be freely overwritten with any value. Not only does it allow to change to new or less popular OpenAI models, it would also enable to use other LLMs which have a compatible API (for example, Perplexity).

@renehuber @AeonWorks the latest version can customize the model's name

authors: AeonWorks bxb100 renehuber

repo: raycast/extensions


text:
OAuth - Raycast button “Open Raycast” doesn’t work

Hi team,
I’m following the guides at [1] and [2] to implement OAuth for Notion. Since I cannot store CLIENT_SECRET in Raycast, I also use a proxy server [3] for to keep it for me.
Problem
After Notion redirect to https://raycast.com/redirect?packageName=Extension with code, I see the web page below. The issue is clicking “Open Raycast” doesn’t do anything. Which prevent my extension to continue since promise is not fulfilled.

My OAuth flow:

In Raycast extension, send an authorize request to Notion using PKCEClient
Notion redirects to Raycast with code <— I’m having problem after this step
In Raycast extension, after the promise is fulfilled, I make a request containging code to myproxy.com/notion/access-token
Notion returns access_token to proxy
Proxy returns access_token to my Raycast extension

Any suggestions on how to do this is welcome. Thank you so much in advance!

Hi! The link to the screenshot is not accessible.
Could you also share the full redirect URL from the Raycast page? (safe to share since only you have the code challenge.)
We already have an extension using OAuth with Notion in the store, maybe that helps to double check your implementation:
https://github.com/raycast/extensions/blob/main/extensions/notion/src/utils/notion.ts

hi @fe9lix I have updated the image. Yup I also consult the code from that extension and learn about the oauth-proxy approach. It’s very helpful haha.
However, back to the topic, I followed the oauth flow (like the extension) and got stuck at the step mentioned above.

I have a suspicion that only approved extension can be open from the web browser.
When testing with the other Notion extension, immediately after Notion redirect to raycast website with this url:
https://www.raycast.com/redirect?packageName=Extension&code=<…>&state=<…>
Browser shows a popup to ask me to allow opening Raycast.
My redirect url is similar, just different code and state, but the browser never shows that popup.

hi @fe9lix , thanks for your support, I have figured out what is the issue.
My redirect url is actually:
https://www.raycast.com/redirect?packageName=Extension&?code=aaa&state=bbb
Notice the 2 question marks 🥲


text:
[Todoist] Can't add a date to task

Extension
https://www.raycast.com/doist/todoist
Description
When I try to use the Create Task command, all fields work except the Date one, which allows me to select a date but doesn't register the input
https://github.com/raycast/extensions/assets/85531625/e335aaf9-c9a7-45c8-a2fe-aa50aa948f66
Steps To Reproduce

Open Create Task
Try to add date to a task

Current Behaviour
Creates task without selected date
Expected Behaviour
Should add the date

Fixed as part of v1.58.1.

authors: brunocbreis thomaslombart


text:
feat(spotify-player): add quicklink to add playing song to a specific playlist

Description

adds a command to the Add Playing Song to Playlist command to create a quicklink so that users can easily add a song to a specific playlist, rather than having to go through the List view every single time.
Screencast

Checklist

[x] I read the extension guidelines
[x] I read the documentation about publishing
[x] I ran npm run build and tested this distribution build in Raycast
[x] I checked that files in the assets folder are used by the extension itself
[x] I checked that assets used by the README are placed outside of the metadata folder

It seems to be only adding songs once for me. The useEffect should've made sure that the logic is only added once.

Not for me 😕
https://github.com/user-attachments/assets/e9c43c41-885d-43f2-8a41-3c2e1f077906

Weird, not sure what could be causing this.

Reopen

@thomaslombart Could you reopen this PR and if possible, take a look as to what might be causing this? I really don't know what could be the bug. Thanks!

I just gave it a spin and for me it also just adds the song once 🤔

That's pretty weird. Could it be that before, an older version of the branch was used, without the proper useEffect fix?

I've tested it again and I can't reproduce the error anymore, which is weird.

Let me know if it's good for you @pernielsentikaer

authors: erics118 pernielsentikaer thomaslombart


text:
Laravel Livewire documentation extension

Description
Adds Laravel Livewire Documentation to Raycast

New extension

Screencast
Included within extension's readme
Checklist

[ Done ] I read the extension guidelines
[ Done ] I read the documentation about publishing

Hello @pernielsentikaer 🤙
Thank you so much!
I have already made two changes:

Added versions via json files which get pulled by selected preference

Replaced current icon with a new icon without transparent

Please, let me know if you propose further changes and/or addons!

Hey @pernielsentikaer
I think we are READY 🤩


text:
.write() doesn't write to already created file

I used .write method on a file i previously created. But it doesn't give errors or write to that file.
when i console log the write function. I get "true" but i don't see anything being written
On the other hand. When i try that with non-existent file. It works. It creates the file and read inside it
But on previously created file it doesn't change the file..

Umm. lol just realized that it writes inside a console.log. sorry 😅


text:
childAspectRatio

how can i set childAspectRatio in LiveGrid?

@MahdiPishguy
LiveGrid(
              padding: EdgeInsets.all(16)),
              showItemInterval: Duration(milliseconds: 100),
              showItemDuration: Duration(milliseconds: 250),
              gridDelegate: SliverGridDelegateWithFixedCrossAxisCount( // gridDelegate from default grid
                crossAxisCount: 3,
                childAspectRatio: 0.55, // <------------ here
                crossAxisSpacing: 16,
                mainAxisSpacing: 16,
              ),
              itemBuilder: (BuildContext context, int index, animation) =>
                  FadeTransition(
                opacity: Tween<double>(
                  begin: 0,
                  end: 1,
                ).animate(animation),
                child: SlideTransition(
                  position: Tween<Offset>(
                    begin: Offset(0, -0.025),
                    end: Offset.zero,
                  ).animate(animation),
                  child: _buildIssue(state.issues[index]),
                ),
              ),
              itemCount: state.issues.length,
            )

authors: MahdiPishguy SergeShkurko


text:
Unable to serve app ruby 2.5.3?

Not sure if anyone else has encountered this already with serving ruby 2.5.3 app. I am trying to serve an app that uses ruby 2.5.3. I get the following from terminal
$ rails server
Traceback (most recent call last):
	4: from bin/rails:3:in `<main>'
	3: from bin/rails:3:in `load'
	2: from /Users/tiffanylo/CHAYN/SoulMedicine/soulmedicine/bin/spring:8:in `<top (required)>'
	1: from /Users/tiffanylo/.rbenv/versions/2.5.3/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
/Users/tiffanylo/.rbenv/versions/2.5.3/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require': cannot load such file -- bundler (LoadError)

I am also having issues with Rails Server. Are you using raspbian? Ubuntu?

Hi @missamii and @ultrasam, how is it going?
According to your logFile, your ruby version compiled is 2.5.3, while your bundle is trying to use ruby version 2.5.0. Taking a little close to the beggining of the rbenv official documentation (how rbenv works), there is a priority in searching the versions path, first local and after global.
It's seems your bundle is searching the global path instead of the local one. Try remove (uninstalling) the global one to avoid bundle to find this path.
Checking your ruby versions:
rbenv local - this will say the first path reached.
rbenv global this may say system, meaning the global ruby version.

This issue tracker is for a Ruby version manager. Please ask questions about general Ruby usage elsewhere, in more appropriate support forums. Thank you!

authors: Pauloparakleto mislav missamii ultrasam

repo: rbenv/rbenv


text:
Route 53

Create Route 53 module for better reusability.

Added the basic config to pull data from Route53

repo: rc-oss/terraform-static-website


text:
RE-360 Include Reno notes in release notes

This changes updates the release notes that will be generated by the
rpc-gating generate_release_notes hook to include those managed by Reno.
The result of this change is that the release notes now returned will be
any Reno notes followed by those produced by rpc-differ. If there are no
Reno notes for the release that will be explicitly stated in the release
notes.
The code was restructured so that the code for generating the different
types of notes could be kept separate. A wrapper script is used to
create a single set of notes from the separate files.
(cherry picked from commit 773413d94a6df65576c27fe8f68733e43f4c4b8a)
Issue: RE-360

recheck_cit_trusty_swift_deploy
recheck_cit_xenial_swift_deploy

recheck_cit_trusty_swift_deploy
recheck_cit_xenial_swift_deploy

repo: rcbops/rpc-openstack


text:
add decorate tag to prowjobs

Issue #, if available:
Description of changes:
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repo: rcrozean/eks-distro-prow-jobs


text:
Kekulization failure on round tripped SMILES through RDKit

Logging this problem here before I forget about it on vacation.
Came across this SMILES string as an output from MolVS, chased it down to RDKit. RDKit is failing to read back in a SMILES it generated due to a kekulization failure.
In [5]: rdkit.__version__
Out[5]: '2018.03.1.dev1'
In [14]: mol = Chem.MolFromSmiles('CN\N=C1/C(=N)C2=C3C4=C1C1=CC=CC5=C1C1=C6C7=C8C(=CC=C57)C=C(C)C=C8C5=CC(C)=C7C8=C(C)C=C9C%10=CC(C)=CC%11=C%10C%10=C(C=C%11)C%11=CC=CC2=C%11C2=C3C(=C8C9=C%102)C(C7=C65)=C41')

In [15]: Chem.MolFromSmiles(Chem.MolToSmiles(mol, True))
[11:32:38] Can't kekulize mol.  Unkekulized atoms: 6 7 8 9 10 11 12 13 14 15 16 17 19 20 21 22 23 25 26 27 29 30 31 32 33 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65

This looks fun... (highlights are the kekulization issues)

Yeah, I’m “looking forward” to tracking this one down.

Some additional info.
There's an order dependence here:
In [19]: mol = Chem.MolFromSmiles('CN=C1C(=N)C2=C3C4=C1C1=CC=CC5=C1C1=C6C7=C8C(=CC=C57)C=C(C)C=C8C5=CC(C)=C7C8=C(C)C=C9C%10=CC(C)=CC%11=C%10C%10=C(C=C%11)C%1
    ...: 1=CC=CC2=C%11C2=C3C(=C8C9=C%102)C(C7=C65)=C41')

In [20]: Chem.MolToSmiles(mol)
Out[20]: 'CN=c1c(=N)c2c3cccc4c5ccc6cc(C)cc7c8cc(C)c9c%10c(C)cc%11c%12cc(C)cc%13ccc%14c%15cccc%16c1c1c2c2c(c43)c(c5c67)c8c9c2c2c%10c%11c(c%14c%13%12)c(c%15%16)c12'

In [21]: Chem.MolFromSmiles(Chem.MolToSmiles(mol))
[04:49:56] Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11 12 13 14 15 16 18 19 20 21 22 24 25 26 28 29 30 31 32 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64

In [22]: mol = Chem.MolFromSmiles('ClN=C1C(=N)C2=C3C4=C1C1=CC=CC5=C1C1=C6C7=C8C(=CC=C57)C=C(C)C=C8C5=CC(C)=C7C8=C(C)C=C9C%10=CC(C)=CC%11=C%10C%10=C(C=C%11)C%
    ...: 11=CC=CC2=C%11C2=C3C(=C8C9=C%102)C(C7=C65)=C41')

In [23]: Chem.MolToSmiles(mol)
Out[23]: 'Cc1cc2ccc3c4cccc5c6c(=N)c(=NCl)c7c8cccc9c%10ccc%11cc(C)cc%12c%13cc(C)c%14c%15c(C)cc%16c(c1)c2c3c1c%16c%15c2c3c%14c%13c(c%10c%11%12)c(c98)c3c7c6c2c1c45'

In [24]: Chem.MolFromSmiles(Chem.MolToSmiles(mol))
Out[24]: <rdkit.Chem.rdchem.Mol at 0x7f6de0949300>

I guess the problem did not get resolved?
I am still having this problem when I re-try the above example.
In fact, I have a lot of large molecules like that, and I am having trouble kekulizing them...
It would be great to know if there is any plan on fixing the issue...

authors: bp-kelley coleb greglandrum stewu5

repo: rdkit/rdkit


text:
yaehmop external git clone by cmake fails on ubuntu 16.04

Description:
rdkit version: current master branch
platform: ubuntu 16.04
fails to build a docker image from ubuntu 16.04 on osx 10.14.2.

RDKit Version: build from source, current master branch
Platform: ubuntu 16.04

Git clone fails only for yaehmop in cmake, especially 'tight bind', thus installation fails.
Git clone for other repos are fine. And git clone in cmd works fine.

FAIL (current default, yaehmop support is on):
RUN cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 \
-DRDK_BUILD_AVALON_SUPPORT=ON \
-DRDK_BUILD_INCHI_SUPPORT=ON ..
RUN make -j3 .. install

PASSED (turned off yaehmop support):
RUN cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 \
-DRDK_BUILD_AVALON_SUPPORT=ON \
-DRDK_BUILD_INCHI_SUPPORT=ON \
-DRDK_BUILD_YAEHMOP_SUPPORT=OFF ..
RUN make -j3 .. install

Full dockerfile for building rdkit image is as follows:
FROM tensorflow/tensorflow:latest-py3-jupyter

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get upgrade -y && apt install -y \
  tzdata \
  curl \
  wget \
  libboost-all-dev \
  cmake \
  git \
  g++ \
  libeigen3-dev \
  python3 \
  libpython3-all-dev \
  python3-numpy \
  python3-pip \
  python3-pil \
  python3-six \
  python3-pandas \
  locales

ENV LANG C

#
RUN mkdir /src
WORKDIR /src
ENV RDBASE=/src/rdkit
ARG RDKIT_BRANCH
RUN git clone https://github.com/rdkit/rdkit.git
WORKDIR $RDBASE
RUN git checkout $RDKIT_BRANCH

ENV PYTHONPATH=$RDBASE
ENV LD_LIBRARY_PATH=$RDBASE/lib
WORKDIR $RDBASE
RUN mkdir build
WORKDIR build

# following command fails until -DRDK_BUILD_YAEHMOP_SUPPORT=OFF is set.
RUN cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 \
-DRDK_BUILD_AVALON_SUPPORT=ON \
-DRDK_BUILD_INCHI_SUPPORT=ON ..

RUN make -j3 .. install
RUN ctest -j3
RUN mkdir /home/DeployedProjects/
WORKDIR /home

# Set the locale
RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
    locale-gen
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8

Thanks for reporting this. The YAeHMOP integration should not have been enabled by default, and I've now fixed that on master.
I will still take a look into reproducing what you're observing.

authors: greglandrum grinnnnnn


text:
Bond removal and readdition changes isomer

Description:

RDKit Version: 2018.09.1
Platform: Pop OS 18.04 LTS (Ubuntu 18.04 LTS)

When removing and adding the same bond the chirality sometimes changes if the new bond has a higher idx than before.
I am not a chemist but from my understand rdkit is using the order of the bonds to determine order in which different R groups added to the chiral center. Perhaps due to this when I remove a bond to make fragments, and later need to combine then, the same isomer is not created. Any help is appreciated.
(Code from python API)

from rdkit import Chem

Initmol = Chem.MolFromSmiles("[4*][C@H](c1cccs1)[C@H]([4*])C")
smiles = Chem.MolToSmiles(Initmol, isomericSmiles=True)
print(smiles)
mol = Chem.MolFromSmiles(smiles)
# C[C@H](c1cccs1)[C@H](C)C
emol = Chem.EditableMol(mol)
emol.RemoveBond(1, 2)

emol.AddBond(1, 2, Chem.rdchem.BondType.SINGLE)
mol2 = emol.GetMol()
new_smiles = Chem.MolToSmiles(mol2, isomericSmiles=True)
print(new_smiles)

# Outputs:
# [4*][C@H](c1cccs1)[C@H]([4*])C
# [4*][C@@H](c1cccs1)[C@H]([4*])C

This does not make sense as I should be recreating the original molecule, not a isomer of it.

If there was a way to change Bond Index or ordering of bonds on an atom then it would allow developers to create the isomer they want.

This is exactly what is happening.  You are changing the order of the bonds around the atom.
>>> mol = Chem.MolFromSmiles(smiles)
>>> emol = Chem.RWMol(mol)
>>> order = [bond.GetIdx() for bond in emol.GetAtomWithIdx(1).GetBonds()]
>>> order
[0, 1, 6]
>>> emol.RemoveBond(1, 2)
>>> emol.AddBond(1, 2, Chem.rdchem.BondType.SINGLE)
10
>>> order = [bond.GetIdx() for bond in emol.GetAtomWithIdx(1).GetBonds()]
# note atom #6 has become #5
>>> order
[0, 5, 9]

In this case as you've changed the clockwise/counter clockwise ordering, you need to invert chirality:
>>> Chem.MolToSmiles(emol)
'[4*][C@@H](c1cccs1)[C@H]([4*])C'

>>> emol.GetAtomWithIdx(1).InvertChirality()
>>> Chem.MolToSmiles(emol)
'[4*][C@H](c1cccs1)[C@H]([4*])C'

Thank you for your response.
Right, however there are times where I do not need to invert chirality.
I trying breaking and reconnecting thousands of bonds around hundreds of molecules, and I cannot tell which one needs their chirality inverted to make it the same as the original molecule.
Would there be any good way to track this chirality issue and only invert as needed?

Currently, I store the chiralTag of the molecule where I break the bond and restore it when I recombine it, however because fragments are rendered different than the original molecule, I may be running into some issues there. When I added the tracking of the chiralTag less False Fragments were generated.

To clarify I want to order the bonds for a given atom, so the chirality is exactly as I want it to be.
Any help would be appreciated.

There's probably a way to do this, but I want to understand what exactly you're trying to do.
You say "I want to order the bonds for a given atom, so the chirality is exactly as I want it to be"
Given that the RDKit understands atomic chirality based on the order of the bonds I'm not quite sure what that means or how you would tell the RDKit what chirality you want so that it can either give you the appropriate order of the bonds or, more likely, the correct chiral tag.
Do you want to replace a bond in an molecule without changing the stereochemistry?

Sorry for the lack of clarity, its my first time doing chemistry related coding.
Do you want to replace a bond in an molecule without changing the stereochemistry?
Yes, but I cannot use the replace substruct or replace bond methods as I want both the broken parts and later on rebuild some of these broken bonds.
I break molecules into fragments (replacing the brokes ends of both new ends with 0 atomic number, and different isotopes as IDs). The breakdown works fine, I get only valid sub fragments.
Valid: being a proper substructure of the original molecule.
However when I rebuild the fragments into different substructures, I need to remove that placeholder atomic number 0 on both fragments and reattach them. Here is where the issue happens.
example:
CCC(NO)CC breaks into CCC([1*])CC and [2*]NO
When I recombine them potentially get CCC(CC)NO.
The ordering of the R groups around C is changed, making the rebuild not the same as the original.
I was wondering if there was anyway for me to indicate, when adding a bond, that NO should be ordered before CC.

ok, I think I'm starting to get it.

Original mol: COc1ccc(N2CCN([C@H](c3cccs3)[C@@H](C)NC(=O)C(=O)NCc3ccco3)CC2)cc1
frag 1: [106*][C@H]([116*])[C@H]([112*])C
frag 2: [117*]c1cccs1
frag 1 and 2 from BRICS.Decompose and from my code(i'ved just changed the isotope on the pseudo atoms)
desired: [4*][C@H](c1cccs1)[C@H]([4*])C (from BRICS.Decompose())
Getting: [4*][C@H](C)[C@@H]([4*])c1cccs1 (from my code)
I'm trying to build up different sub structures as opposed to breaking down to them.
Subfragments from BRICS.Decompose() I do cannot build. (2nd one is the given example)

Subfragments BRICS.Decompose() cannot built, but I can, some have this bond order issue. (4th column, 5th row is given example)

@harsh6646 did the gist help out?

To carry on for @harsh6646  here (I am now also working on this issue a little bit), unfortunately the gist does not help (or I am misunderstanding it).
Specifically there is one bond being deleted (a-b), two atoms being added (x,y), and then two new bonds being added ((a-x), (y-b)).
So originally the bonds for atom a might look like this:
[(2, 3), (3, 4), (3, 5)]
then afterwards they look like this:
[(3, 4), (3, 5), (3, 30)]
What I need is to have them look like this:
[(3, 30), (3, 4), (3, 5)]
Similarly, for atom b:
old b bonds: [(1, 2), (2, 3)]
new b bonds: [(1, 2), (2, 31)]
In this case there is no issue (but not always.)
However, as far as I can tell, adding a bond to an atom always adds it at the end of this list, and the order of this list is being used to define the chirality? If I delete those other bonds and add all of them back in the correct order, this error propagates to all the atoms that were connected to those atoms as well, ending only when we get to atoms with only one bond or where the removed bond was last in the list of bonds.
the eMol.ReplaceBond() function is also not going to work here, as even if I replace one bond, I will still need to add another for the other atom.

The gist doesn’t preserve ordering, it preserves chirality, I.e. it knows when to flip the chirality in the output molecule.

Does it flip the chirality of all stereocenters? Or only the incorrect ones?

The incorrect ones.  The “trick” here is that the attachment points in all fragments need to be dummy atoms so we know the original bond orders.

Brian Kelley

On Oct 8, 2019, at 5:41 PM, Andrew E Brereton notifications@github.com wrote:

Does it flip the chirality of all stereocenters? Or only the incorrect ones?
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or mute the thread.

I do have dummy atoms, and I am storing the chiral tags, but I'm not sure I understand how to apply this gist to this issue.
The issue is not just with zipping molecules together, but also in breaking them down. In the process of breaking apart a molecule we’re destroying one bond and adding two. This sometimes borks the stereochemistry, long before we attach molecule fragments back together.
Ideally we should see that even just the frag_a -> dummy_atom_a bond and the frag_b -> dummy_atom_b bond should have the same stereochemistry as before fragmentation. However, upon adding the bond to the dummy atom, the stereochemistry often changes (because the bond order changes).

@bp-kelley Okay so we have managed to get something working by sidestepping this entirely, and simply creating a different non rdchem.Mol object, editing the bonds in that object, and then using that object to build each fragment from scratch as an editableMol object.
Thanks all for your help and feel free to close this issue if you want. Though I still think it would be really nice to add a feature to the editableMol class that allows you to reorder the bonds for a given atom.

The main idea of Brian's code snippet is to look at the parity of the permutation order of the bonds, which is either even or odd. If it's changed, then swap the chirality from CW to CCW or back.
He mentioned some writings I did on the topic. The most specific is at http://www.dalkescientific.com/writings/diary/archive/2016/08/14/fragment_chiral_molecules.html .
The work I did then lead to some fixes in the RDKit, which should have improved some of the errors I found.
My general view these days is to manipulate things as SMILES strings, rather than as molecule objects, because getting chirality (and double-bond stereochemistry) correct, while editing a molecule object, ended up being difficult and confusing.

Wow! Thanks for sharing the link, that’s a remarkably clear analysis of this issue! Since the consensus seems to be that it’s better to deal with this outside of the Chem.Mol format anyway, I feel a little better about the approach we ended up taking, which only converts back to Mol at the end, when finished.

authors: adalke atomoton bp-kelley greglandrum harsh6646


text:
Some naphthalene SMARTS lead to a central bond with single bond order

Configuration:

RDKit Version: 2020.03.1
Operating system: Linux
Python version (if relevant): 3.6.2
Are you using conda? No
If you are not using conda: how did you install the RDKit? Schrodinger build.

Description:
When parsing a SMARTS for naphthalene, I'm surprised that one of the bonds is a single bond according to GetBondType():
In [71]: mol = Chem.MolFromSmarts('c1cccc(c12)cccc2')

In [72]: [b.GetBondType() for b in mol.GetBonds()]
Out[72]:
[rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.SINGLE,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC]

But note that the query still works, because the bond in question still matches single or aromatic:
In [73]: [b.DescribeQuery() for b in mol.GetBonds()]
Out[73]:
['SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'BondOr\n  BondOrder 1 = val\n  BondOrder 12 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n',
 'SingleOrAromaticBond 1 = val\n']

It is curious that for this one bond, instead of using the SingleOrAromaticBond check, we use BondOrder 1 OR BondOrder 12 (where 12 means aromatic, so it works anyway).
With a different SMARTS representation without branching, the issue does not occur:
In [75]: [b.GetBondType() for b in Chem.MolFromSmarts('c1cccc2c1cccc2').GetBonds()]
Out[75]:
[rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC,
 rdkit.Chem.rdchem.BondType.AROMATIC]

This is not the worst thing in the world since, like I said, the query still works, but we had a program that was inspecting the bond orders from a SMARTS and this was confusing (we are only using simple bonds, nothing fancy like "single or double" or "double and not ring" or anything like that).

Hi Ivan,
There is a single bond in naphthalene- it’s the fusion bond. The 10 atom
envelope ring Is aromatic but the two 6 atom rings aren’t.
I don’t have a pen and paper to hand to check, but I don’t think your
second SMARTS is correct for naphthalene. I would write it (I think, I
haven’t checked) as c12ccccc2cccc1.
Dave
On Thu, 4 Jun 2020 at 20:06, Ivan Tubert-Brohman notifications@github.com
wrote:

Configuration:

RDKit Version: 2020.03.1
Operating system: Linux
Python version (if relevant): 3.6.2
Are you using conda? No
If you are not using conda: how did you install the RDKit?
Schrodinger build.

Description:
When parsing a SMARTS for naphthalene, I'm surprised that one of the bonds
is a single bond according to GetBondType():
In [71]: mol = Chem.MolFromSmarts('c1cccc(c12)cccc2')
In [72]: [b.GetBondType() for b in mol.GetBonds()]
Out[72]:
[rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.SINGLE,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC]
But note that the query still works, because the bond in question still
matches single or aromatic:
In [73]: [b.DescribeQuery() for b in mol.GetBonds()]
Out[73]:
['SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'BondOr\n  BondOrder 1 = val\n  BondOrder 12 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n',
'SingleOrAromaticBond 1 = val\n']
It is curious that for this one bond, instead of using the
SingleOrAromaticBond check, we use BondOrder 1 OR BondOrder 12 (where 12
means aromatic, so it works anyway).
With a different SMARTS representation without branching, the issue does
not occur:
In [75]: [b.GetBondType() for b in Chem.MolFromSmarts('c1cccc2c1cccc2').GetBonds()]
Out[75]:
[rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC,
rdkit.Chem.rdchem.BondType.AROMATIC]
This is not the worst thing in the world since, like I said, the query
still works, but we had a program that was inspecting the bond orders from
a SMARTS and this was confusing (we are only using simple bonds, nothing
fancy like "single or double" or "double and not ring" or anything like
that).
—
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--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk

The bond orders in molecules constructed from SMARTS are not always set to what you expect (I hesitate to use the word "correctly" since there's not really any such thing for these query molecules). It's kind of a "best guess" approach that we do in the hopes that you will be able to generate a SMILES for a molecule generated from SMARTS and get something sensible.
In this particular case that algorithm isn't doing the right thing.
Interestingly, if you use the SMARTS c1ccc2ccccc2c1 for napthalene everything works fine.
Marking this as a bug since we should be handling this case better.

authors: DavidACosgrove greglandrum i-tub


text:
EnumerateStereoisomers Runtime error when enumerate guanidine derivatives on rdkit 2024.03.4

Describe the bug
EnumerateStereoisomers() fails to enumerate guanidine derivatives
To Reproduce
from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions

mol = Chem.MolFromSmiles('N=C(N1CCC1)NCCOc2ccc(C(F)(F)F)cc2')

opts = StereoEnumerationOptions(tryEmbedding=True, unique=True, maxIsomers=0)
isomers = list(EnumerateStereoisomers(mol, options=opts))```

RuntimeError: Range Error
	idx2
	Violation occurred on line 352 in file Code/GraphMol/ROMol.cpp
	Failed Expression: 4294967295 < 20
	RDKIT: 2024.03.4
	BOOST: 1_84

Update:
The bug is general to other N=C(C)N-containing structures as well, such as:
CS(=O)(CCC(NOCc1c(Cl)cccc1F)=N)=O
N=C(N)NS(=O)(=O)c1ccc(NC(=O)CCCc2ccc(Br)s2)cc1

**Expected behavior**
The script should return the mol as is if it could not enumerate the stereoisomers, otherwise enumerate the possible stereoisomers.

**Configuration :**
 - RDKit version: 2024.03.4
 - OS: WSL Ubuntu 20.04 on Windows 11
 - Python version (if relevant): 3.11
 - Are you using conda? yes
 - If you are using conda, which channel did you install the rdkit from? conda-forge
 - If you are not using conda: how did you install the RDKit?

Hi @greglandrum, hope that you can check if this is a bug on the newest version (2024.03.4) as when I downgraded to 03.3, the script worked completely fine.


text:
Question Mark Drawn In Molecule

Describe the bug
When rendering a MDL Molfile with an explicitly drawn hydrogen, if you set the mergeQueryHs flag to true when creating the molecule, rdkit outputs a ? in the resulting svg image.
To Reproduce
Navigate to https://www.rdkitjs.com/#drawing-molecules-svg
Input the following code into the code editor under Drawing molecules:
  var molfile = `
  Mrv2114 11212416242D

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 7 7 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -5.1742 -0.0084 0 0
M  V30 2 C -5.1764 -1.5529 0 0
M  V30 3 C -3.8419 -2.3235 0 0
M  V30 4 C -2.5046 -1.5519 0 0
M  V30 5 C -3.8452 0.7622 0 0
M  V30 6 H -1.1792 0.7734 0 0
M  V30 7 C -2.51 -0.0016 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 5 1
M  V30 2 2 1 2
M  V30 3 2 3 4
M  V30 4 1 2 3
M  V30 5 1 6 7
M  V30 6 2 7 5
M  V30 7 1 4 7
M  V30 END BOND
M  V30 END CTAB
M  END
`;
  var mol = RDKitModule.get_mol(molfile, JSON.stringify({ mergeQueryHs: true }));
  var dest = document.getElementById("example-1-output");
  var svg = mol.get_svg();
  dest.innerHTML = "
" + svg + "
";

Observe question mark in the resulting image:

Expected behavior
I would not expect to see a question mark ? rendered there. I would expect to see either an attached or detached hydrogen.
Screenshots

Configuration (please complete the following information):

RDKit version: @rdkit/rdkit 2024.3.5-1.0.0
OS: [e.g. Ubuntu 20.04]: OSX/Chrome

Thanks for the info. The reason we are merging the query Hs when rendering is because if we do not, we have many cases where highlighting and aligning do not work if some structures have the explicit hydrogens and others do not.

Do you have a case where the hydrogens are not being suppressed?

Ok, I confirmed that the hydrogens are not suppressed in get_mol, this seems wrong.

removeHs is what you want, but it does appear not to work for mol files.

I've tracked down the issue to this call
MolFromMolBlock(mb, sanitize=False, removeHs=True, strictParsing=False)

When sanitize is False, Hydrogens are not removed.

@ptosco @greglandrum This is a real bug where removeHs isn't removing Hs with mol blocks in some circumstances.

@bp-kelley Yes, I have just carried out your same investigation and got to the same conclusion. This is indeed a real bug; I'll commit a fix later.
@lounsbrough In the meantime, you may call mol.remove_hs_in_place() before generating your SVG.

Thank you both for the quick response and analysis.

authors: bp-kelley lounsbrough ptosco


text:
Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams()

calcImplicitValence() and setNumExplicitHs() are now called after all aromaticity flags have been set
ChemicalForceFields.MMFFHasAllMoleculeParams() now operates on a copy of the molecule such that atom and bond aromaticity are not altered by the check
test11 was added to GraphMol/ForceFieldHelpers/Wrap/testHelpers.py to check for the two bugs fixed by this PR

Not sure why the Travis CI build failed - when I click on "Details" I cannot see anything.. It builds fine on my machine, and the AppVeyor Windows build succeded.

Thanks Paolo.

authors: greglandrum ptosco


text:
Fixes #4281

Made the pyridine N-oxide pattern more specific and added a test.

The Ubuntu_16_04  build has failed with a weird linker error on libxml2.so.2.

The Ubuntu_16_04 build has failed with a weird linker error on libxml2.so.2.

I restarted that build. Hopefully it was just a temporary thing.
I need to create a ToDo item to get rid of those Ubuntu16.04 builds anyway... that OS is now EOL so there's no real reason to still be testing on it. I'll add some tests on 20.04 instead.


text:
Configuration to show pagination buttons above table rather than below the table.

Is there any configuration which allows displaying pagination buttons above table rather than below the table.

HI @karanbajaj2209 right now, we don't have this kind of configuration, will implement it, thanks

can we add more custom options such as the container css class?

check this example and document https://react-bootstrap-table.github.io/react-bootstrap-table2/docs/basic-pagination.html#advance-customization

authors: AllenFang cbfrank karanbajaj2209


text:
Currently, starting a new project throws the error "Error: Invalid sdkVersion."

Description
Following the instructions in the read.me gives the error "Invalid sdkVersion"
Expected Behavior
If someone is following instructions from the readme shouldn't it work?
Observed Behavior
I had to change the sdkversion of expo and react-native. I also had to clear the watchman cache and delete node_modules and reinstall packages. This could have been avoided if the sdk version was set to version that worked.
Error: Invalid sdkVersion. Valid options are 10.0.0, 11.0.0, 12.0.0, 13.0.0, 14.0.0, 15.0.0, 16.0.0, 17.0.0, 18.0.0, 19.0.0, 20.0.0, 21.0.0, 22.0.0, 23.0.0, 24.0.0, 25.0.0, 7.0.0, 8.0.0, 9.0.0

Environment
Please run these commands in the project folder and fill in their results:

npm ls react-native-scripts: 1.13.1
npm ls react-native: 0.54.0
npm ls expo:  26.0.0
node -v: 9.8.0
npm -v: 5.6.0
yarn --version: 1.5.1
watchman version:  4.9.0

Also specify:

Operating system: Mac high sierra 10.13
Phone/emulator/simulator & version: iOS sim v10

Changing expo to v25 and react-native to v52 fixed this error. Just wondering why it's set to an unsupported sdk version.
Reproducible Demo
Just follow the readme.
create-react-native-app my-app
cd my-app
npm run start

Can you share the results of running the following in the terminal: exp -V, mine is 51.4.0 and it works fine... 0.0

Mine is ‘50.0.5’

Updated exp to 51.4.0 and still get the following error.
Error: Invalid sdkVersion. Valid options are 10.0.0, 11.0.0, 12.0.0, 13.0.0, 14.0.0, 15.0.0, 16.0.0, 17.0.0, 18.0.0, 19.0.0, 20.0.0, 21.0.0, 22.0.0, 23.0.0, 24.0.0, 25.0.0, 7.0.0, 8.0.0, 9.0.0

try rm -rf ~/.expo/cache

Doing that in addition to also reseting and reinstalling the expo app on the ios sim made it work. Thanks for the quick reply.

authors: Devhound EvanBacon brentvatne

repo: react-community/create-react-native-app


text:
markers not rendering

I am having a problem, no marker is rendering.
here is my package.json
"react": "16.3.1",
"react-native": "0.55.2",
"react-native-maps": "https://github.com/react-community/react-native-maps.git",

this is my map screen:
import MapView from 'react-native-maps';
import { Marker } from 'react-native-maps';

export default class HomeStudent extends Component {
      constructor(props) {
    super(props);
    this.state={
      //default location
      location: {
        latitude: 31.11452,
        longitude: 32.236515,
        latitudeDelta: 0.3,
        longitudeDelta: 0.3,
      },

      markers: [
        {
          latlng: {
            latitude: 31.957866,
            longitude: 35.857494,
          },
          title: "habiba",
          description: "none at the moment"
        },
        {
          latlng: {
            latitude: 31.957866,
            longitude: 35.857494,
          },
          title: "7th circle",
          description: "none at the moment"
        },
      ],
      id: "",
    };
  }

  render() {
    return (
      <View style={styles.container}>
        <MapView
            showsUserLocation={true}
            showsMyLocationButton={true}
            followsUserLocation={true}
            enableHighAccuracy={true}
            style={styles.map}
            region={this.state.location}
        >

        {this.state.markers.map(marker => (
          <MapView.Marker
            coordinate={{latitude: marker.latlng.latitude, longitude: marker.latlng.longitude}}
            title={marker.title}
            description={marker.description}>
          </MapView.Marker>
          ))}

        </MapView>
      </View>
    );
  }
}

when i run use react-native run-android not markers is rendered, but the maps renders without issue.
is there something wrong with my code?

sorry guys, i was rendering different screen, which was the reason i thought markers are not being rendered.
will have to double check next time.

repo: react-community/react-native-maps


text:
tabs renders nothing sometimes

Environment
react-native
Reproduction link
Steps to reproduce
code

import React, { PureComponent } from 'react';
import {ListView,Text} from 'react-native'
import {Tabs,Button,List} from 'antd-mobile'
import {StackNavigator,TabNavigator} from 'react-navigation'

const ds = new ListView.DataSource({rowHasChanged: (r1, r2) => r1 !== r2});

class Test extends PureComponent {

    constructor(props) {
        super(props);
        this.state={
            tabs:[{title:'一',index:0},{title:'二',index:1},{title:'三',index:2},{title:'四',index:3},{title:'五',index:4}]
        }
    }

    renderContent = (tab, index) => {
        let arr=[];
        for(let i=0;i<100;i  ){
            arr.push(1)
        }
        return <ListView    dataSource={ds.cloneWithRows(arr)}
                            renderRow={(rowData) => <Text>{rowData}</Text>}/>
    };

    render() {
        return (
            <Tabs

                tabs={this.state.tabs}
                initialPage={0}
            >
                {this.renderContent}
            </Tabs>
        )
    }
}

const Tabs2 = TabNavigator({
    Home: {
        screen: Test,
        navigationOptions: {
            tabBarLabel: '1',

        }
    },
    Video:{
        screen:Test,
        navigationOptions:{
            tabBarLabel:"2",

        }
    },
    Mine:{
        screen:Test,
        navigationOptions: {
            tabBarLabel: "3",
        }
    }

}, {
    initialRouteName:"Home",
    tabBarPosition: 'bottom',
});

const AppNavigator = StackNavigator({
    Tabs2: { screen: Tabs2,
    }
},{
    initialRouteName: 'Tabs2'});

export default AppNavigator;

this bug about react-navigation?
https://github.com/ant-design/ant-design-mobile/issues/2048
What is expected?
no white screen
What is actually happening?
white screen

Change RCTView.m
if (!CGRectContainsRect(testView.bounds, testRect)) {
  clipView = testView;
  clipRect = CGRectIntersection(testView.bounds, testRect);
}

To
if (!CGRectContainsRect(testView.bounds, testRect) && !CGRectIsEmpty(CGRectIntersection(testView.bounds, testRect))) {
          clipView = testView;
          clipRect = CGRectIntersection(testView.bounds, testRect);
}

Without properly following the issue template, it's nearly impossible to understand & investigate the issue. Please answer/explain these questions:

have you tried updating to the latest release?
does it happen only on Android/iOS?
does it happen on both Debug and Release modes?
does it happen with Debugger On or Off? Both?
Can you provide a repo or a snack to reproduce this issue?

And write down your dependencies.

@apsbtn works fine,thank you.
@kelset
1.have you tried updating to the latest release?
my navigation version is git+https://github.com/react-community/react-navigation.git#ed2fc9a09e2f562ae9d3fc7f5df17c593989db0a.
2.does it happen only on Android/iOS?
only ios.
3.does it happen on both Debug and Release modes?
may be,i have no try
4.does it happen with Debugger On or Off? Both?
does
5.Can you provide a repo or a snack to reproduce this issue?
sorry,i can't

@shi1hh you mean that the suggestion provided by @apsbtn fixed the issue?
Moreover, I'll say it again: without properly following the issue template, it's nearly impossible to understand & investigate the issue. And you not answering my follow up questions leaves the situation unchanged.

Closing in favor of https://github.com/react-community/react-navigation/issues/3035

authors: apsbtn kelset shi1hh

repo: react-community/react-navigation


text:
header Hidden changes top of ScrollViews to -20 on iOS11

react native 0.46.4
simulator ios 11
ScrollView top -20:
react-navigation:1.0.0-beta.15
please help me! how to fix it?

Closing because you haven't followed the issue template; please open a new one that follows the template.
Without that, it's nearly impossible to understand & investigate the issue. I suggest you also try (in the new issue) to answer/explain in a way that fits these questions:

have you tried updating to the latest release?
does it happen only on Android/iOS?
does it happen on both Debug and Release modes?
does it happen with Debugger On or Off? Both?
Can you provide a GIF or a repo or a snack to reproduce this issue?

authors: chenweigh kelset


text:
Add headerLeftOnPress to change the default behavior of the back button

This PR adds the option headerLeftOnPress to NavigationStackScreenOptions to allow overwriting the onPress property without having to replace the whole component using headerLeft.

To customize this behavior you can just import the HeaderBackButton and set the headerLeft option with an instance of it which has your custom press handler.
Something like this;
import { HeaderBackButton } from 'react-navigation';

// ...

navigationOptions: ({ navigation }) => ({
  headerLeft: (
    <HeaderBackButton onPress={navigation.navigate('MyScreen')} />
  ),
}

But since it is called a back button, you probably shouldn't use it for anything else than going back. Just use a normal button, or some other component instead.

Sure, that's possible. But I had to somehow duplicate the code in https://github.com/react-community/react-navigation/blob/master/src/views/Header.js#L115-L143 to get the same style. This PR would allow me to just replace the functionality while keeping the rest.

That I understand, but I doubt that you need that code when not using it as a back button

I'd still be using it as a back button.
I just encountered the second case where I would like to be able to overwrite the onPress function, so I writing again ;-)
My first use case is to skip one route when going back (also requested in #1213). The second usecase is to make a tracking call when the button is tapped.
Both cases can be implemented differently, but overwriting the onPress-handler seems the simplest way to me.

Thanks @Koblaid . I have a similar use-case where I just want to add a secondary call to reset some stuff while keeping the rest of the button behaviour the same.

#2712 is a similar PR

A PR which allows to customize the back button behaviour was recently merged: #2712
Since the mentioned PR covers the use cases mentioned here, I will close this PR as being redundant. With that being said, thank you for your efforts, @Koblaid  !

authors: Koblaid ixje koenpunt vonovak


text:
optimize clearedFieldMetaCache

resetFields will reset clearedFieldMetaCache now.
The time to get clearedFieldMetaCache is getFieldProps now (saveRef before).

seem the code in saveRef can't be deleted. I'm thinking about the reason.......

In the original code, if use clearedFieldMetaCache in saveRef, will not call forceUpdate. So it will not rerender.

learn a lot because of this PR...

Can you try to add a test case for this?

Let me try. I haven't written the unit test of jest before.

sad to find resetFields is still a problem.

update resetFields and add two test cases.
The test cases is not passed with the previous code.

先 pending，等讨论清楚了再做决定。

首先，reset fields这部分的修改应该是没有疑问的。
然后，现在因为saveRef中读取cache之后不进行forceUpdate，导致有间隔的remount会在下一次render时发生闪烁。这个情况在Form和Modal同时使用的时候，极其容易触发。因此我认为有必要先防止这种情况的发生。@benjycui 提到的场景，由于当前版本定义field时并不指定类型，所以唯一的解决方案就是此处继续采用1.x版本的方案。
最后，关于解决这个问题的方案。

1.x版本中，一个组件remount会清空value和error，只要在文档中说明这个情况的话，其实也算是一个解决方案。
我PR中这个版本，则是组件unmount之后会暂时隐藏，然后在组件remount或者不绑定组件单独使用getFieldDecorator/Props，会将隐藏的部分重新暴露。（在官网demo中不定项表单例子中，有单独使用getFieldDecorator不绑定组件的场景）。这个方案还有一个需要讨论的点，就是field被暂时隐藏的这个时间段，setFields系列函数能否使用，如果可以使用，那么这些函数均需要recoverClearedField。目前来看，应该是所有方案里面，兼顾的最好的方案。
在使用当前getFieldDecorator的逻辑的基础上，另一个不容易出现歧义的方案，是永远不要去自动隐藏field，让用户通过option.hidden来自动隐藏。但是这个方案在不定项Form中，又存在无法自动删除rerender后消失的fields，且使用起来极为不便，不如上一个方案。
还有一个方案，就是将field的定义和getFieldDecorator/Props函数分开。但实际应用中，一个field的定义可能与另一个field的value有关，这个方案不够灵活。

Shall I repeat a PR with only resetFields?

我看看。

先改成只有 resetFields 的 PR 吧，另一个问题需要提供具体的问题再看看。

先改成只有 resetFields 的 PR 吧，另一个问题需要提供具体的问题再看看。

除了上面提到的重现
官网demo 中 situation 3 存在一模一样的问题。

👌，我晚点再看看 modal 这个问题。

销毁组件的时候还是直接干掉对应的表单值比较合理。对于 https://codesandbox.io/s/o4nwr2x7z 我找到一个更合理的解决方案，我先合并了这个再发一个 PR。

authors: HunDunDM afc163 benjycui

repo: react-component/form


text:
[Question] a lot of @DragSource elements

Can you perform fast work React-dnd, if on page 100 + DragSource?
I want to make a map and display a lot of svg elements.
And for everyone hangs a DragSource from React-dnd.
Is this a good idea?

This demo may be helpful:
http://react-dnd.github.io/react-dnd/examples/sortable/stress-test

repo: react-dnd/react-dnd


text:
Fix code example in Controller docs

Fixes a typo on the code example. props isn't available as everything is destructured.

Thank you @msutkowski !

repo: react-hook-form/documentation


text:
Fix typo in README

Summary
Fix typo in README by changing "libray" to "library."

Test Plan
Nothing else changed

What's required for testing (prerequisites)?
N/A
What are the steps to reproduce (after prerequisites)?
N/A
Compatibility
N/A

OS
Implemented

iOS
✅❌

Android
✅❌

Checklist
N/A

[ ] I have tested this on a device and a simulator
[ ] I added the documentation in README.md
[ ] I mentioned this change in CHANGELOG.md
[ ] I updated the typed files (TS and Flow)
[ ] I added a sample use of the API in the example project (example/App.js)

Thanks!

authors: davidpwu luancurti

repo: react-native-community/datetimepicker


text:
iOS Audio Playback Category

Summary
Allow configuring iOS audio session category rather than being forced to use AVAudioSessionCategoryPlayback.
Test Plan
Put phone on silent, set new playback option category to PlaybackCategories.Ambient and sounds will no longer play.
What's required for testing (prerequisites)?
What are the steps to reproduce (after prerequisites)?
Compatibility

OS
Implemented

iOS
✅

Android
❌

Checklist

[x] I have tested this on a device and a simulator
[x] I added the documentation in README.md
[x] I mentioned this change in CHANGELOG.md
[x] I updated the typed files (TS and Flow)
[ ] I added a sample use of the API in the example project (example/App.js)

Thank you for your contribution

authors: sbeca ssg-luke


text:
A segment is necessary

maybe it is simple to use icon button to do segment?

@zhangruinian When you say segment.. are you thinking about something like UISegmentedControl on iOS?

@zhangruinian any updates on this?

For now consider using https://github.com/lelandrichardson/react-native-segmented-view
We might add this to RNE in the future.