Fix dead links

I found that there are a lot of dead links, which I think should be corrected asap.
Here is a report generated by Broken link checker

Error
URL
Anchor Text
Linked From

404 Not Found
https://coderefinery.org/workshops/about/

https://coderefinery.org/

404 Not Found
https://www.nordforsk.org/en
NordForsk [301 from http://www.nordforsk.org/en]
https://coderefinery.org/

404 Not Found
https://coderefinery.org/blog/2020/11/13/carpentry-community-discussion-nordic/coderefinery.org
CodeRefinery
https://coderefinery.org/blog/2020/11/13/carpentry-community-discussion-nordic/

404 Not Found
<EMAIL_ADDRESS>get in touch
https://coderefinery.org/blog/2020/04/24/nordic-rse-conference/

404 Not Found
https://coderefinery.org/privacy-policy/github.com/coderefinery
GitHub
https://coderefinery.org/privacy-policy/

404 Not Found
https://coderefinery.org/privacy-policy/coderefinery.zulipchat.com
Zulipchat
https://coderefinery.org/privacy-policy/

404 Not Found
https://coderefinery.org/privacy-policy/hackmd.io/@coderefinery
HackMD
https://coderefinery.org/privacy-policy/

404 Not Found
https://coderefinery.org/privacy-policy/twitch.tv/coderefinery
Twitch
https://coderefinery.org/privacy-policy/

404 Not Found
https://coderefinery.org/privacy-policy/[youtube.com/](https://www.youtube.com/channel/UC47aupE7HKGduAjXKt1Gwrg)
YouTube
https://coderefinery.org/privacy-policy/

404 Not Found
https://coderefinery.org/privacy-policy/neic.no
neic
https://coderefinery.org/privacy-policy/

404 Not Found
https://coderefinery.org/get-involved/
get in touch
https://coderefinery.org/about/project/

-1 Not found: The date in the certificate is invalid or has expired
https://rse.ac.uk/conf2017/workshop-and-tutorial-abstracts/
Workshop: Interfacing Fortran, C, C++, and Python (Manchester)
https://coderefinery.org/about/statistics/

-1 Not found: A connection with the server could not be established
https://bssw.io/
Better Scientific Software (BSSw)
https://coderefinery.org/lessons/other-projects/

Too many redirections
https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3
Graf-Vlachy, L., Buhtz, K. & König, 2018 [302 from https://doi.org/10.1007/s11301-017-0133-3] [301 from http://link.springer.com/10.1007/s11301-017-0133-3] [301 from https://link.springer.com/10.1007/s11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3]
https://coderefinery.org/blog/2020/07/31/mega-coderefinery/

Too many redirections
https://www.nature.com/articles/s41567-019-0624-3
Nature Physics 15, 728–730 (2019) [302 from https://doi.org/10.1038/s41567-019-0624-3] [301 from http://www.nature.com/articles/s41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3]
https://coderefinery.org/about/reports/

Error	URL	Anchor Text	Linked From
404 Not Found https://coderefinery.org/workshops/about/ https://coderefinery.org/
404 Not Found https://www.nordforsk.org/en	NordForsk [301 from http://www.nordforsk.org/en]	https://coderefinery.org/
404 Not Found https://coderefinery.org/blog/2020/11/13/carpentry-community-discussion-nordic/coderefinery.org	CodeRefinery	https://coderefinery.org/blog/2020/11/13/carpentry-community-discussion-nordic/
404 Not Found<EMAIL_ADDRESS>get in touch	https://coderefinery.org/blog/2020/04/24/nordic-rse-conference/
404 Not Found https://coderefinery.org/privacy-policy/github.com/coderefinery	GitHub	https://coderefinery.org/privacy-policy/
404 Not Found https://coderefinery.org/privacy-policy/coderefinery.zulipchat.com	Zulipchat	https://coderefinery.org/privacy-policy/
404 Not Found https://coderefinery.org/privacy-policy/hackmd.io/@coderefinery	HackMD	https://coderefinery.org/privacy-policy/
404 Not Found https://coderefinery.org/privacy-policy/twitch.tv/coderefinery	Twitch	https://coderefinery.org/privacy-policy/
404 Not Found	[https://coderefinery.org/privacy-policy/youtube.com/](https://coderefinery.org/privacy-policy/[youtube.com/](https://www.youtube.com/channel/UC47aupE7HKGduAjXKt1Gwrg))	YouTube	https://coderefinery.org/privacy-policy/
404 Not Found https://coderefinery.org/privacy-policy/neic.no	neic	https://coderefinery.org/privacy-policy/
404 Not Found https://coderefinery.org/get-involved/	get in touch	https://coderefinery.org/about/project/
-1 Not found: The date in the certificate is invalid or has expired	https://rse.ac.uk/conf2017/workshop-and-tutorial-abstracts/	Workshop: Interfacing Fortran, C, C++, and Python (Manchester)	https://coderefinery.org/about/statistics/
-1 Not found: A connection with the server could not be established	https://bssw.io/	Better Scientific Software (BSSw)	https://coderefinery.org/lessons/other-projects/
Too many redirections https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3	Graf-Vlachy, L., Buhtz, K. & König, 2018 [302 from https://doi.org/10.1007/s11301-017-0133-3] [301 from http://link.springer.com/10.1007/s11301-017-0133-3] [301 from https://link.springer.com/10.1007/s11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3] [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3]	https://coderefinery.org/blog/2020/07/31/mega-coderefinery/
Too many redirections https://www.nature.com/articles/s41567-019-0624-3	Nature Physics 15, 728–730 (2019) [302 from https://doi.org/10.1038/s41567-019-0624-3] [301 from http://www.nature.com/articles/s41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3] [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3]	https://coderefinery.org/about/reports/

Looks like only four broken links now!  Two server errors, two of the articles which seem to redirect forever when accessed without a browser.  I think this could be closed for now...
Would be nice if Zola could do internal link checking.  There is a zola check which checks external links, but many of these were internal.  (Makes me wonder abou sphinx's strategy of document-based references for internal and different syntax for external - seems nice and continuously warns of broken internal links.)

Error
URL
Anchor Text
Linked From

-1 Not found: The date in the certificate is invalid or has expired
https://rse.ac.uk/conf2017/workshop-and-tutorial-abstracts/
Workshop: Interfacing Fortran, C, C++, and Python (Manchester)
https://coderefinery.org/workshops/past/

-1 Not found: A connection with the server could not be established
https://bssw.io/
Better Scientific Software (BSSw)
https://coderefinery.org/lessons/other-projects/

Too many redirections
https://www.nature.com/articles/s41567-019-0624-3
Nature  Physics 15, 728–730 (2019) [302 from  https://doi.org/10.1038/s41567-019-0624-3] [301 from  http://www.nature.com/articles/s41567-019-0624-3] [303 from  https://www.nature.com/articles/s41567-019-0624-3] [302 from  https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3]  [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from  https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3]  [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from  https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3]  [303 from https://www.nature.com/articles/s41567-019-0624-3] [302 from  https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41567-019-0624-3]
https://coderefinery.org/about/reports/

Too many redirections
https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3
Graf-Vlachy,  L., Buhtz, K. & König, 2018 [302 from  https://doi.org/10.1007/s11301-017-0133-3] [301 from  http://link.springer.com/10.1007/s11301-017-0133-3] [301 from  https://link.springer.com/10.1007/s11301-017-0133-3] [303 from  https://link.springer.com/article/10.1007/s11301-017-0133-3] [302 from  https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3]  [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3]  [302 from  https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3]  [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3]  [302 from  https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11301-017-0133-3]  [303 from https://link.springer.com/article/10.1007/s11301-017-0133-3]
https://coderefinery.org/blog/2020/07/31/mega-coderefinery/

Thanks, @rkdarst !!


[Request] Invert feature

I would like to have an option where I could have the keys disabled by default and activate them when I choose to. The reason is that I often listen to spotify but the media keys don't work until I disable them in chrome from every tab, chrome seems to have a higher priority...

Duplicate #166

Any plans to see this feature implemented in the store version? I'm currently using it sideloaded with the edit @MuhsinFatih suggested and it's working fine, but I'd like to have it installed normally.

There are several problems affecting tab management but I think this particular issue can now be closed since Chrome can be set up to provide requested behavior


TypeError: glslify is not a function

I'm getting an error when trying to add it as a plugin.
TypeError: glslify is not a function
// vite.config.mts
import glslify from 'vite-plugin-glslify';

// https://vitejs.dev/config/
export default defineConfig({
  base: '/',
  plugins: [react(), svgr(), glslify()],
  ....

// package.json
  "devDependencies": {
    "vite-plugin-glslify": "^2.1.0",
    ...

Appreciate any help, thanks!

No worries on this, ended up using vite-plugin-glslify-inject. Thanks!


Problem..

Hello comunity , Where is the agar.io client ? for use with own hosting ? Thanks.

you can use agar.io/?ip=YOUR-IP:PORT

It's a server project, not client.


Change the color of the folder icon

I can't change the color of the directory icon. I didn't find a parameter in the file highlights.lua that would be responsible for this.
Previously , it was possible to implement this through:
api.nvim_set_hl(0, "NvimTreeFolderIcon", {
    fg = "#eeeeee",
})

But now that doesn't work either.

You should put custom highlights in setup

It turned out to do this:
highlights = {
    NvimTreeFolderIcon = {
        fg = "#eeeeee"
    },
}

This parameter should probably be added to the highlights.lua file?


i get this sometimes when exploring the end with latest 1.18 version

[21:15:18] [Worker-Main-29/INFO]: [STDOUT]: Negative index in crash report handler (0/19)
[21:15:18] [Server thread/FATAL]: Error executing task on Chunk source main thread executor for minecraft:the_end
net.minecraft.class_148: Feature placement
at Not Enough Crashes deobfuscated stack trace.(1.18.1+build.12) ~[?:?]
at net.minecraft.server.world.ThreadedAnvilChunkStorage.method_39934(ThreadedAnvilChunkStorage:619) ~[?:?]
at net.minecraft.util.thread.ThreadExecutor.executeTask(ThreadExecutor:151) ~[?:?]
at net.minecraft.server.world.ServerChunkManager$MainThreadExecutor.executeTask(ServerChunkManager:552) ~[?:?]
at net.minecraft.util.thread.ThreadExecutor.runTask(ThreadExecutor:125) ~[?:?]
at net.minecraft.server.world.ServerChunkManager$MainThreadExecutor.runTask(ServerChunkManager:561) ~[?:?]
at net.minecraft.server.world.ServerChunkManager.executeQueuedTasks(ServerChunkManager:282) ~[?:?]
at net.minecraft.server.MinecraftServer.runOneTask(MinecraftServer:768) ~[client-intermediary.jar:?]
at net.minecraft.server.MinecraftServer.runTask(MinecraftServer:756) ~[client-intermediary.jar:?]
at net.minecraft.util.thread.ThreadExecutor.runTasks(ThreadExecutor:134) ~[?:?]
at net.minecraft.server.MinecraftServer.runTasksTillTickEnd(MinecraftServer:741) ~[client-intermediary.jar:?]
at net.minecraft.server.MinecraftServer.runServer(MinecraftServer:688) ~[client-intermediary.jar:?]
at net.minecraft.server.MinecraftServer.method_29739(MinecraftServer:270) ~[client-intermediary.jar:?]
at java.lang.Thread.run(Thread.java:833) [?:?]

Can you please post full logs?


Introduce an option to terminal options to be visible all the time.

Can terminal options be visible all the time with option in settings? It's right now shows when mouse hover.

Do you mean only the active terminal, not all of them? Note that it's on hover of keyboard focus. This was a change compared to other lists but I think we should do it there too. See https://github.com/microsoft/vscode/issues/122016

If you can add both as an option it 'll fit more users preferences.

@Tyriar If you can add both as an option it 'll fit more users preferences. But I personally prefer all of them available.

Sorry I don't think we will do this because of the additional visual noise is will cause, and I don't believe the amount of usage this will see is worth the cost of another setting.


Detect marker dragend

Hello,
There is anyway I can detect the drag-end event in gmap-maker, the move event is good but it's too sensitive, I only need the lat lng when the drag is stop and that all

I have just release v0.6.2 and added drag, dragstart, and dragend events to the marker.
I can't get it to work in the online demo though but seems to be working on other environments. Can you please test it for me?

yeah the event is working fine now, thanks @xon52 <3


[Bug]: cards not working anymore after HA Update  2023.2.5

Requirements

[X] I have updated Mushroom to the latest available version
[X] I did a search to see if there is a similar issue or if a pull request is open.

Current Behavior
Hi, After update to HA 2023.2.5 my Dashboard looks like this:

What can I do to fix this?
Thanks
Hyper
Expected Behavior
No response
Steps To Reproduce
No response
Context
YAML state

Environment
- Browser: Android App
- HA Version: 2023.2.5
- Mushroom: v2.6.0

Anything else?
No response

I had to download it again 😵💫


Make IDs unique per label?

I'm finding that it's easy to create conflicting IDs in my application code. To manage that, I started prefixing the IDs by the vertex/edge type (label). That gives me peace of mind, but now I'm getting areas in my code where the ID hasn't been properly prefixed, so the vertex is (silently) not found.
I think it would be great if the database handled all this for me. Unique IDs per table/document type seems like a normal concept, so this feels like a reasonable feature.

Although, I guess that changes the meaning of V()

This feels like a pretty fundamental change to the data model, with the potential for a bunch of potential weird implications.
Can we mark this as considered, and closed for the moment. And bring it back if there becomes a major argument for it?


Finalize vue3 update

Ideally closes #83 some day
It builds/serves the frontend fine (haven't checked the backend integration because yolo 💩 ), pretty sure vue-meta is currently broken though. Looking forward to feedback

I don't get the CI failure, it complains about an audit of a dependency I'm updating (to the version that doesn't have the vulnerability anymore) 🙄


Add mode attribute to Aqara T1 relay

Proposed change

Add the mode attribute to the aqara T1 relay
TODO:

[ ] change mode to an enum?
[ ] add config entities to ZHA

Additional information

Checklist

[ ] The changes are tested and work correctly
[ ] pre-commit checks pass / the code has been formatted using Black
[ ] Tests have been added to verify that the new code works

change mode to an enum?

This mode/0x0009 attribute is only 0 ("ZCL mode") or 1 ("Aqara/Xiaomi hub mode"), so not like the mode attribute from your T2 relay PR (which should probably be renamed to switch_mode there).
Since this attribute isn't really meant to be user-accessible (ideally, it should auto-set to 1), I don't think we need to change it to an enum. If we do, we should probably change it in all quirks though.
It might make sense to change switch_type to an enum though (maybe that's also what you meant?). Just like done in opple_switch.py (scroll in code field below):
https://github.com/zigpy/zha-device-handlers/blob/529112195dcdc3c8108df05e3a838478ee75ac6e/zhaquirks/xiaomi/aqara/opple_switch.py#L63-L106
Maybe that implementation/enum can be used/shared if it's the same for this T1 relay.

Also, regarding "auto-setting" mode:
Although mode is likely only needed for old firmware versions of this relay, we could probably try to set it to 1 every time (when binding the cluster), since Z2M does it too. Like this:
https://github.com/zigpy/zha-device-handlers/blob/aeca76da0ea81ecba5b17e0f7314620cd686faae/zhaquirks/xiaomi/aqara/opple_remote.py#L142
https://github.com/zigpy/zha-device-handlers/blob/aeca76da0ea81ecba5b17e0f7314620cd686faae/zhaquirks/xiaomi/aqara/opple_remote.py#L149-L153
If that request errors out (when changing from 0 to 1), this might be needed instead zhaquirks/xiaomi/aqara/plug_eu.py#L65-L76, as it seems like that particular device briefly reboots (or something) and doesn't send back a response.

Also, regarding "auto-setting" mode:
Although mode is likely only needed for old firmware versions of this relay, we could probably try to set it to 1 every time (when binding the cluster), since Z2M does it too. Like this:
https://github.com/zigpy/zha-device-handlers/blob/aeca76da0ea81ecba5b17e0f7314620cd686faae/zhaquirks/xiaomi/aqara/opple_remote.py#L142
https://github.com/zigpy/zha-device-handlers/blob/aeca76da0ea81ecba5b17e0f7314620cd686faae/zhaquirks/xiaomi/aqara/opple_remote.py#L149-L153
If that request errors out (when changing from 0 to 1), this might be needed instead zhaquirks/xiaomi/aqara/plug_eu.py#L65-L76, as it seems like that particular device briefly reboots (or something) and doesn't send back a response.

I debated doing this initially... the quirks work for multiple models and multiple fw differences... I didn't want to add this without more information. The goal was just to get the attribute there so we can set it from the UI and collect more info from users. thoughts?

I debated doing this initially... the quirks work for multiple models and multiple fw differences... I didn't want to add this without more information. The goal was just to get the attribute there so we can set it from the UI and collect more info from users. thoughts?

Yeah, let's not set it automatically for now then. I can't recall seeing any issues regarding this, so maybe everyone just uses a new firmware version on these.


Integration Test

In this milestone, we(@jugosack and @djo1975 :
Fixed N+1 problem when fetching all posts and their comments for a user.
before the fix:

After the fix

Used Capybara to write integration tests for:

User index page
user show page
User post index page
Post show page

Fixed linter errors


How to seed data with monorepo workspace in nestjs

I use monorepo to build the applications. I've some apps and libs
My code folder is below. How to write typeorm config file in my case for seeding data.

ormconfig.ts

package json seeding script

Error

The codebuild only has the main.js file. It doesn't have some file like .entity.js. So I think my ormconfig.ts file is wrong. Please help. Thanks you guys a lot.

Hum

@Sotatek-PhuongNguyen4 we are having the same issue that the lib import doesn't resolve right. Have you figured it out yet?

@weilinzung I resolved this problem by creating SeederModule and run it as application context to initialize database. In each module, I run service to insert data directly to database. I hop It's helpful for you.

@Sotatek-PhuongNguyen4 any update on this one? Have you found a solution that works together with Nest.js? Thank you!

@Sotatek-PhuongNguyen4 any update on this one? Have you found a solution that works together with Nest.js? Thank you!

@davidhoeck As I commented above, I seeded data manually by using standalone application feature. Read more:
https://docs.nestjs.com/faq/serverless#using-standalone-application-feature
The main idea here is call directly to database to insert datas.


[Feature] Support 2-channel Audio

Description
On opening of a two channel audio file, wave.py's read_wav method generates a MultiChannelError.  Per earlier offline discussion, multi-channel audio files should create a MultiTrack object, consisting of separate tracks for each channel.
What I Did
Load a two channel audio file.
Traceback (most recent call last):
  File "/Users/ognyan/Developer/fred/src/main/python/fred/views/TableView.py", line 85, in currentChanged
    self.mainWindow._controller.selectFile(current)
  File "/Users/ognyan/Developer/fred/src/main/python/fred/controllers/controller.py", line 78, in selectFile
    track = self.getTrack(pathObj)
  File "/Users/ognyan/Developer/fred/src/main/python/fred/controllers/controller.py", line 86, in getTrack
    return Track.read(pathObj)
  File "/Users/ognyan/Developer/fred/.venv/lib/python3.7/site-packages/signalworks/tracking/tracking.py", line 155, in read
    return Wave.wav_read(path, channels, mmap)
  File "/Users/ognyan/Developer/fred/.venv/lib/python3.7/site-packages/signalworks/tracking/wave.py", line 269, in read_wav
    f"must select channel when loading file {path} with {value.shape[1]} channels"
signalworks.tracking.error.MultiChannelError: must select channel when loading file /Users/ognyan/Developer/fred/.venv/lib/python3.7/site-packages/scipy/io/tests/data/test-44100Hz-2ch-32bit-float-le.wav with 2 channels

We can either change this so that all channels are loaded simultaneously, or have an additional GUI interaction that clarifies which channel(s) should be loaded. The latter will certainly be required for EDF and XDF support in the future.

I would say we should load both channels simultaneously, if we already used all the disk in to access the file to begin with... Also I think the code to exclude a channel may be more complicated as well.

Since this is signal works and not a GUI, how about by default we read everything, but optionally the user can specify a channel.
Do we return a Wave with a N-D array, or a MultiTrack with N Waves?

I would think a multitrack with a wave object for each channel would be preferred, having a 2D wave object may introduce unnecessary complexity

my preference as well

I'm having a circular import problem :)
Wave imports MultiTrack and MultiTrack imports Wave.
We want Wave.read_wav() return MultiTrack. The MultiTrack need Wave in reading read_xdf(), read_edf()

@tuanad121 and I discussed this, we should likely incorporate a signalworks.read() method that can return either a Track or MultiTrack.

I am closing this issue because more recent conversations of this are in #24


client: do cleanup after UT stop mock server

Remove /tmp/agentserver.socker when test case is done and output firendly error message when remove the file failed.
Fixes #418
Signed-off-by: NingBo<EMAIL_ADDRESS>

Good catch! And we like friendly messages :smile:
lgtm
/test

Thanks @BetaXOi!
lgtm
/test

Re-started the 16.04 CI which got wedged on what looks like an external net connectivity issue:
not ok 1 Verify nginx connectivity between pods
# (from function `setup' in test file nginx.bats, line 19)
#   `sudo -E crictl pull "$nginx_image"' failed
# Image is up to date for docker.io/library/busybox@sha256:915f390a8912e16d4beb8689720a17348f3f6d1a7b659697df850ab625ea29d5
# time="2018-11-30T02:38:08Z" level=fatal msg="pulling image failed: rpc error: code = Unknown desc = Error writing blob: error storing blob to file \"/var/tmp/storage826968591/2\": read tcp <IP_ADDRESS>:47454-><IP_ADDRESS>:443: read: connection reset by peer"
# Error from server (NotFound): deployments.extensions "nginx-deployment" not found
# Error from server (NotFound): services "nginx-deployment" not found
# error: resource name may not be empty
Makefile:69: recipe for target 'kubernetes' failed

lgtm, thanks @BetaXOi !


[Azure] OpenShift console operator not present in some installations

Hi,
the day before yesterday I had twice the problem, that during an installation of OKD 4.4 (Beta Version!) I came in a situation that there was no openshift-console-operator or openshift-console present, not even the namespace existed.
The assumption was, that it has something to do with the CVO (may be).
Could this also be related to this PR here: https://github.com/openshift/machine-config-operator/pull/1603 ?
I recreated (deleted and created) the cluster again yesterday and everything worked as expected.
I only saw this effect on Azure up to now but this could only be bad luck.
Thanks and greetings,
Josef

console operator is always included in the payload and is required for cluster install to complete.
We're gonna need CVO logs (check pods in openshift-cluster-version namespace) and preferably must-gather archive

I never saw this again. Maybe ist was a problem with the Beta1 release that occurred in parallel at that time.


You set USE_PYTHON2 to make CMake find python2 libs only, but CMake found   python3 libs instead.

Explain the problem here ...
I want to compile ycm server with python3.5 which I installed via pyenv. I installed the cmake and downloaded the newest llvm+clang from official site. However, I was stuck when I run the following command:
cmake -G "Unix Makefiles" -DPYTHON_INCLUDE_DIR=~/.pyenv/versions/3.5.1/include/python3.5m -DPYTHON_LIBRARY=~/.pyenv/versions/3.5.1/lib/libpython3.5m.so -DPATH_TO_LLVM_ROOT=~/ycm_temp/llvm_root_dir . ~/.dot/nvim/plugged/YouCompleteMe/third_party/ycmd/cpp

It reported：
-- The C compiler identification is GNU 4.8.4

-- The CXX compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
Your C++ compiler supports C++11, compiling in that mode.
-- Found PythonLibs: /home/doug/.pyenv/versions/3.5.1/lib/libpython3.5m.so (found suitable version "3.5.1", minimum required is "2.6")
CMake Error at CMakeLists.txt:207 (message):
You set USE_PYTHON2 to make CMake find python2 libs only, but CMake found
python3 libs instead.  Either don't set USE_PYTHON2 or install the
necessary python2 headers & libraries.

NVIM v0.1.3
Build type: Debug
Compilation: /usr/bin/cc -Wconversion -g -Wall -Wextra -pedantic -Wno-unused-parameter -Wstrict-prototypes -std=gnu99 -Wvla -fstack-protector
--param ssp-buffer-size=4 -DINCLUDE_GENERATED_DECLARATIONS -DHAVE_CONFIG_H -D_GNU_SOURCE -I/home/doug/Git/repositories/neovim/build/config -I/
home/doug/Git/repositories/neovim/src -I/home/doug/Git/repositories/neovim/.deps/usr/include -I/home/doug/Git/repositories/neovim/.deps/usr/in
clude -I/home/doug/Git/repositories/neovim/.deps/usr/include/luajit-2.0 -I/home/doug/Git/repositories/neovim/.deps/usr/include -I/home/doug/Gi
t/repositories/neovim/.deps/usr/include -I/home/doug/Git/repositories/neovim/.deps/usr/include -I/home/doug/Git/repositories/neovim/.deps/usr/
include -I/usr/include -I/home/doug/Git/repositories/neovim/build/src/nvim/auto -I/home/doug/Git/repositories/neovim/build/include
Compiled by doug@Trident-Linux

Optional features included (+) or not (-): +acl   +iconv    +jemalloc
For differences from Vim, see :help vim-differences

   system vimrc file: "$VIM/sysinit.vim"
  fall-back for $VIM: "/home/doug/Applications/neovim/share/nvim"

Type:

[ ] Bug
[ ] Enhancement
[ ] Feature Request
[x] Question

OS:

[ ] All/Other
[x] Linux
[ ] OS X
[ ] Windows

Vim:

[ ] Terminal Vim
[ ] GVim
[x] Neovim

Is this relevant to vim-plug?
Shouldn't you be reporting this to https://github.com/Valloric/YouCompleteMe/issues instead?
/ping @vheon

Sorry, I posted this issue wrong place....


Update BoringSSL to 25773430c07075a368416c3646fa4b07daf4968a

CC: @tomerd
This is going to break SPM builds on non-macOS targets.  This update pulls in https://boringssl-review.googlesource.com/c/boringssl/+/48985 which makes a number of structs completely opaque typedefs, which I believe are not imported into Swift via the clang importer.

Thanks @compnerd. SwiftPM is still on swift-crypto 1.x so it should be fine for now, but we will definitely need to change the code when SwiftPM upgrades to swift-crypto 2.x.


fix: searchbar

Your checklist for this pull request
🚨Please review the guidelines for contributing to this repository.

[ ] Make sure you are requesting to pull a topic/feature/bugfix branch (right side). Don't request your default branch!
[ ] Make sure you are making a pull request against the default branch (left side). Also you should start your branch off default branch.
[ ] Check the commit's or even all commits' message styles matches our requested structure.
[ ] Check your code additions will fail neither code linting checks nor unit test.
[ ] I have added necessary documentation (if appropriate)

Linked Issues
#465
Description
Please describe your pull request.
❤Thank you!
Post merge checklist

[ ] Follow steps from the guidelines for contributing to this repository.
[ ] If you are a new contributor, ping in the thread and one of the maintainers will add you to all-contributors list.

@SUNNYKUMAR1232 resolve conflicts in case of issue reach out to @120EE0692 .


Problems with using useraccounts:flow-routing

Hi guys,
just ran into a problem when combining this with useraccounts:flow-routing (https://github.com/meteor-useraccounts/flow-routing) and I am getting the error:
 "Exception in template helper: Error: Unknown component 'fullPageAtForm'"

The error is thrown right here https://github.com/peerlibrary/blaze-layout-component/blob/085155cfb9b4294cc4a2dc416e11352477f9b9b3/layout.coffee#L46, probably because the useraccounts:core "{{>fullPageAtForm}}" is NOT a BlazeComponent.
This is my config
AccountsTemplates.configure({
  defaultLayout: 'LayoutComponent',  // BlazeLayoutComponent (`return this._renderRegion('content', parentComponent)`)
  defaultLayoutRegions: {},
  defaultContentRegion: 'content',
})

AccountsTemplates.configureRoute('signIn')

@mitar: Do you have a quick fix for this?

I am using flow-routing in this app: https://github.com/peer/mind/blob/master/packages/peermind/package.js#L40
And pass a component in: https://github.com/peer/mind/blob/master/packages/peermind/account/config.coffee#L31
So not sure exactly where your code is different.

This is my account form: https://github.com/peer/mind/blob/master/packages/peermind/account/form.html


ElementHandle.Type types with the different speed time in v1.12.2

Hello, everyone, I really hope that someone will be able to help me with this issue:
Well, I'm having troubles with elementHandle.type because it types string variables in Input sides all the time with the diffrent speed and I'm really do not know why it works like this. The text can be typed into the input as fast as it only could be, but then text typed into this input one character by one character and it lasts for 3-4 seconds.
I'm using this code:
await page.type(inputSelector, text);
There is no slowMo, there is no global delay, so I'm realy confused about this.

@anDDDy we'd need to debug this locally to see what's going on. Can you share a small script that reproduces the issue?

If you are typing a large amount of text, like a few kilobytes, it could take that amount of time.
If you don't care about actual key presses, you can use page.keyboard.sendCharacter(text) to do something akin to pasting in the text. That will be almost instantaneous.

If you are typing a large amount of text, like a few kilobytes, it could take that amount of time.
If you don't care about actual key presses, you can use page.keyboard.sendCharacter(text) to do something akin to pasting in the text. That will be almost instantaneous.

Thanks a lot! That is exactly what I'm looking for.


bus status should be changed when bus socket disconnect

bus is still active when unexpectedly a bus socket is disconnected

@manav402 @Vatsal-S-Patel seems like a backend issue

issue resolved


bug: GitHub Discrepancies

Describe the bug
The GitHub issue template's "Device" section contains inconsistencies. The "OS" field contains a colon but the others do not.
To Reproduce
Steps to reproduce the behavior:

Create a new issue or go to .github/ISSUE_TEMPLATE/bug_report.md
See the inconsistencies

Expected behavior
Consistent formatting.
Screenshots

Device:

OS: [e.g. iOS]
Browser [e.g. chrome, safari]
Version [e.g. 22]

By looking into the template more, the "Device" heading as a whole does not fit the correct formatting. 😂


Windows support

In windows, ANSYS Mechanical APDL command window opens up as a separate window and hence pexpect is not able to send keys to that window natively. It is however possible to read the output of ANSYS.
One thought of solving this is using win32api; Finding out the window id of the newly opened MAPDL window and then sending keystrokes to it. But it wont be a robust solution.

Not sure if this is still an issue, but you might want to checkout pyansys.

Hey, thanks for the comment. Welldone with pyansys! I saw that you have solved the windows issue with pyansys. I just couldnt make time to adopt something similar in this module. Personally, I didnt want to use corba and that's why I've been a little reluctant :)

At the moment (until probably 2020R1 or 2020R2), ANSYS won't support additional interfaces.  I agree that CORBA isn't great, but it works reasonably well and I've already built up the CORBA interfaces in ansys_corba.


Update SQL schema: Add json data to account

What is this pull request?
Add json data to account and update sql schema
Why do you implement it? Why do we need this pull request?
To allow storage of account personal info we need add JSONb field in account table.
How to use the features provided in the pull request?

Add new test in wsv_command_query

Details/Features

By default account is created with empty JSON data

Codecov Report

Merging #658 into develop will decrease coverage by 0.08%.
The diff coverage is 6.25%.

@@             Coverage Diff             @@
##           develop     #658      +/-   ##
===========================================
- Coverage    43.31%   43.23%   -0.09%
===========================================
  Files          298      298
  Lines        12068    12093      +25
  Branches      6645     6669      +24
===========================================
+ Hits          5227     5228       +1
  Misses         724      724
- Partials      6117     6141      +24

Impacted Files
Coverage Δ

irohad/model/account.hpp
50% <ø> (ø)
:arrow_up:

irohad/ametsuchi/impl/storage_impl.hpp
85.71% <ø> (ø)
:arrow_up:

irohad/model/execution/impl/command_executor.cpp
40.33% <0%> (-0.14%)
:arrow_down:

irohad/model/commands/create_account.hpp
25% <0%> (ø)
:arrow_up:

irohad/ametsuchi/impl/postgres_wsv_command.cpp
34.93% <0%> (-1.09%)
:arrow_down:

irohad/model/generators/impl/command_generator.cpp
22.22% <0%> (ø)
:arrow_up:

irohad/ametsuchi/impl/postgres_wsv_query.cpp
27.45% <0%> (-0.19%)
:arrow_down:

test/module/irohad/ametsuchi/ametsuchi_test.cpp
16.34% <0%> (-0.21%)
:arrow_down:

...module/irohad/ametsuchi/wsv_query_command_test.cpp
16.82% <18.18%> (+0.15%)
:arrow_up:

...odule/irohad/model/converters/pb_commands_test.cpp
6.84% <0%> (-0.69%)
:arrow_down:

Continue to review full report at Codecov.

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UnknownError: OpenQA.Selenium.WebDriverException: OpenQA.Selenium.WebDriverException: Package was not found.

Hi all, I got a weird issue "OpenQA.Selenium.WebDriverException: OpenQA.Selenium.WebDriverException: Package was not found." when running Calculator example. I ran the test project on Windows Server 2022 Standard Edition.
Appium.WebDriver, version : 4.4.0
Appium version : 1.22.3
[TestClass]
public class CalculatorSession
{ // Note: append /wd/hub to the URL if you're directing the test at Appium
private const string WindowsApplicationDriverUrl = "http://<IP_ADDRESS>:4723/wd/hub";
private const string CalculatorAppId = "Microsoft.WindowsCalculator_8wekyb3d8bbwe!App";
    protected static WindowsDriver<WindowsElement> session;

    public static void Setup(TestContext context)
    {
        // Launch Calculator application if it is not yet launched
        if (session == null)
        {
            // Create a new session to bring up an instance of the Calculator application
            // Note: Multiple calculator windows (instances) share the same process Id
            AppiumOptions options = new AppiumOptions();
            options.AddAdditionalCapability("deviceName", "WindowsPC");
            options.AddAdditionalCapability("app", CalculatorAppId);
            Uri url = new Uri("http://<IP_ADDRESS>:4723/wd/hub");
            session = new WindowsDriver<WindowsElement>(url, options);
            Assert.IsNotNull(session);

            // Set implicit timeout to 1.5 seconds to make element search to retry every 500 ms for at most three times
            session.Manage().Timeouts().ImplicitWait = TimeSpan.FromSeconds(1.5);
        }
    }

    public static void TearDown()
    {
        // Close the application and delete the session
        if (session != null)
        {
            session.Quit();
            session = null;
        }
    }
}

}
The issue happened on this line session = new WindowsDriver(url, options);
I'm a new beginner for WinAppDriver,  I tried several methods and still could not resolve this problem.
If someone knows the solution, could you please tell me, thank you!!

It will not work, you need to downgrade to windows server 2016.

Thanks for replying me, I still would like to ask whether changing server system is the only resolution to fix the issue?

Yes.

OK. Got it. Thanks again.


filestore: directionality fix backported to 7

Ticket
Redmine ticket: https://redmine.openinfosecfoundation.org/issues/6622
#1560 backport

Merged in #1651, thanks!


seems grpc name has collision

What did you do?
2022/05/24 03:25:35 proto: duplicate proto type registered: pb.WorkerInfo
https://github.com/pingcap/tiflow/runs/6566411247?check_suite_focus=true
What did you expect to see?
no error
What did you see instead?
2022/05/24 03:25:35 proto: duplicate proto type registered: pb.WorkerInfo
Versions of the cluster
master

Yep,
https://github.com/pingcap/tiflow/blob/12317f4139996245d238fcaff7c15d18308607da/dm/dm/proto/dmmaster.proto#L349
https://github.com/pingcap/tiflow/blob/12317f4139996245d238fcaff7c15d18308607da/engine/proto/master.proto#L92
WorkerInfo defined in dataflow engine should be renamed.


Add support for rounded timestamps on environment metrics (#6396)

Pull request opened by the merge tool on behalf of #6396

Merged into branches iso6 in bc85cf0391bb8f3465bc0e9fd41c820daa4fcc63


policy-testdrive: remove confusing panic message

Since the introduction of context-aware policies, the policy-testdrive can produce confusing message when there's no connection available to the k8s cluster defined inside of ~/.kube/config.
For example, this is the output produced on my machine when my minikube server is down:
policy-testdrive --policy module.wasm --request-file pod-req-no-specific-apparmor-profile.json
thread '<unnamed>' panicked at 'could not initialize Kubernetes client: Error loading kubeconfig: Failed to infer config.. cluster env: (Error loading kubeconfig: Unable to load in cluster config, KUBERNETES_SERVICE_HOST and KUBERNETES_SERVICE_PORT must be defined), kubeconfig: (Error loading kubeconfig: Unable to load current context: )', crates/policy-evaluator/src/cluster_context.rs:74:31
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Settings validation result: SettingsValidationResponse { valid: true, message: None }
Policy evaluation results:
ValidationResponse { uid: "", allowed: true, patch_type: None, patch: None, status: None }

Acceptance criteria
No panic message is printed, instead a nicer warning message should be shown. Something that tells:

cannot reach the Kubernetes cluster defined inside of your configuration
context-aware policies are not going to be working

To add more information to this while reproducing. There are different behaviors that can happen with invalid configurations.

A syntactically valid kubeconfig file, with unreachable Kubernetes cluster does not panic but does not inform the user that contextual policies might not work as expected.

A syntactically invalid kubeconfig file does not panic, but does not inform the user.

A completely missing kubeconfig file makes the testdrive panic.

Handle all these cases so we inform the user about the situation WRT to contextual policies as the acceptance criteria describes.,


Unrecognized commanderjs CLI options

I just tested the latest stable version of nexe against a tiny CLI-configurable HTTP server (commander: 2.8.1, express: 4.13.3).
I cannot specify any command line parameters to the generated binary. Any known workaround or fix for this?

Hi! Have you tried adding -f true to your command line with nexe?
That's normally the cause, this enables command line opts being passed to the node.js script instead of node.

Nice, it works perfectly! Thanks a lot!


PALINDROME STRING CHECK USING STACK IN C (GSSoC'21)

🚀 Feature
Have you read the Contributing Guidelines on Pull Requests?
Yes !
AIM :: PALINDROME STRING CHECK USING STACK IN C
Motivation
As i didn't found PALINDROME STRING CHECK USING STACK IN C, So i am willing to contribute it...
Pitch
Hi I am GSSoC'21 participant,
"I am looking to work on the PALINDROME STRING CHECK USING STACK IN C"
I will write the clean and optimized code , by keeping best case time and space complexity in mind and
with  brief commenting and algorithm.
I will use C language.

/assign


Refactor CI workflows

Issue

N/A

Overview (Required)

Refactor CI workflows.
In my forked repository, the modified workflow is successful.

https://github.com/hkusu/conference-app-2021/actions/runs/653045758
https://github.com/hkusu/conference-app-2021/actions/runs/653045757

Links

Screenshot
Screen not changed.

👀

🆒


Versions

This mod is awesome, but it is lacking 1.18 support.

hold on im updating it rn

it should be done in 5 minutes


Recording timeout traffic

Hi guys,
I have been using your tool for a couple months now, and so far, I think it is an amazing tool. It has a very good interface and is easy to use and set up. However, I have encountered a case in which mitmproxy does not provide the functionality I need.
I am working on a use case in which I want to be able to view all traffic and connection attempts sent by the client whether the server responds or not. At one point the client makes a connect attempt the a server that results in a connection timed out error (netliberror [error 110]). This gets recorded as an error in the event log but does not show up in the traffic recorded by mitmdump. Would it be possible to have an attempt at a connection that ends up timing out get recorded with the rest of the traffic?
Thanks for all the work. Your tool is really awesome.

Hi there,
thanks for the report! Unfortunately, @cortesi and I are fairly busy right now. We'll certainly get back to your issue, but it may take a bit - sorry for that.
Cheers,
Max

Hi @nvanbalen,
I believe this is a duplicate of #108.
Cheers,
Max


don't crash if start_index is not found, just return an empty list

My project mainly looks up English words but, since it processes dynamic web content, it occasionally looks up a word from another language but has no way of knowing in advance which language it is.  I ran into a case where WiktionaryParser looked up "Ramos" (Spanish) but did not find any <span class="toctext"> tags matching English, causing this exception:
TypeError: startswith first arg must be str or a tuple of str, not NoneType
I think it's better to return no results than to crash.

https://github.com/Suyash458/WiktionaryParser/issues/31
This looks to be a fix for the issue I opened here.


Add RELEASE note about config versioning

Closes #3196
Signed-off-by: Michael Crosby<EMAIL_ADDRESS>

Codecov Report

Merging #3398 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #3398   +/-   ##
=======================================
  Coverage   45.05%   45.05%
=======================================
  Files         113      113
  Lines       12563    12563
=======================================
  Hits         5660     5660
  Misses       6049     6049
  Partials      854      854

Flag
Coverage Δ

#linux
48.98% <ø> (ø)
:arrow_up:

#windows
40.27% <ø> (ø)
:arrow_up:

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Consistent links based on cleanUrl setting

💥 Proposal
When cleanUrl setting is used, it works great but if this option is not enabled, every page shows ".html" at the end of the url. But, the "home" link (near the top-left corner of navigation bar) still points to the site url as "http://example.com/". Can it be made as "http://example.com/index.html" to be consistent? There might be similar links in the footer.
Have you read the Contributing Guidelines on issues?
Yes

There was a similar issue and fix brought up here - #1146. Many sites that do not have clean URLs still have their logo link as the clean version. Example:

https://reactjs.org/docs/getting-started.html
http://docs.vulcanjs.org/nutshell.html

So we prefer to stick with this convention.

Thank you for your reply. I'm sorry I cannot yet follow the logic behind sticking with this convention.
Since there is a configuration for clean url, in my opinion its usage should be consistent. Also, as it was already explained in #1146, this is needed for the situations where directory listing/indexing is not supported or does not automatically redirect to /index.html. Here's my current issue.
I'm hosting the static site built using docusaurus, in aws s3 bucket. However, I needed to host it in a subdirectory of the bucket instead of at the root. If I enable website hosting option for the bucket, everything is okay but I cannot use ssl. I needed to use aws cloudfront cdn for effecient distribution and also ssl. Because the site is hosted in a subdirectory of the s3  bucket, automatic redirection to the index.html file of the site's root has been challenging (with and without the website hosting option at s3 bucket). As you know, aws s3 is not a traditional web server. So, currently in my doc site hosted in aws s3 and served by aws cloudfront, clicking on the site logo/title fails.
Anyways, besides my current issue, I believe current functuonality is somewhat inconcsistent with regards to the configuration option of the site.

Many sites that do not have clean URLs still have their logo link as the clean version.

I just understood now what you meant here and why you want to stick with this convention.
I do see your point. I personally prefer to use the clean url but unfortunately I haven't been able to use it in my case because of the issues I encountered in aws s3. I believe this is one of the many popular choices for hosting static site.

Thought I'd add some updates here. I have been trying to add some work-around in aws based deployment. Just for clarification, this is not an issue if you deploy to the root of the s3 bucket. Aws Cloudfront (used as a cdn for s3 bucket as source) has a setting to default to index.html if the client requested a url without specifying it. But, this only works if you deploy/upload built static files to the root of your s3 bucket.
In my case, since I needed to deploy to subdirectories, I'm adding Lamda@Edge function to the cloudfront to handle this issue. So incoming requests are intercepted and redirected to /index.html file.
Thinking about this whole issue, even if you add /index.html to the logo href as I had suggested, it would solve or help avoid broken link when browsing within the site but there will still be an issue in another case. What if users point to the site without ending in /.
For example: http://example.com/docusaurus-site
In this case, 'docusaurus-site' is the subdirectory in s3 bucket that holds the static site. In this case, aws cloudfront will fail unless I take care of redirecting to following url using lamda function.
http://example.com/docusaurus-site/index.html

This just caught my attention. Just read #1146 as well
I implemented the cleanUrl feature so I might be able to give more context on that. The backstory of cleanUrl setting is that we don't want to see any .html extension anymore. I think the convention here is slightly different.

We will stick with current convention :)


bug: Intermittent visual artifacts

Looks like something in the vertex shader is getting confused.
Seems to happen randomly. At the very least, I have not found a way to reliably reproduce this.
Happens a lot more often when using post processing effects.
Seems to happen only with textured particles.
Confirmed in: Chrome, Firefox

https://user-images.githubusercontent.com/1061/174601164-dc976adb-1e99-4e6a-9f2e-0538597c222e.mov
(Video recorded in Chrome for macOS on a M1 Mini runing OS X Monterey.)

This is fixed in the VFX Composer reimplementation.


Memory consumption explodes on advisor and evaluator

When trying to analyse Eclipse Jemo, the advisor, and then evaluator come to fail. The error message displayed with the reporter run is:
00:44:03.955 [main] INFO  org.ossreviewtoolkit.utils.scripting.ScriptRunner - Evaluating the script took 7m 2.842815630s.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
	at java.base/java.util.HashSet.<init>(HashSet.java:163)
	at java.base/java.util.LinkedHashSet.<init>(LinkedHashSet.java:155)
	at kotlin.collections.SetsKt___SetsKt.minus(_Sets.kt:52)
	at org.ossreviewtoolkit.model.utils.FindingsMatcher.match(FindingsMatcher.kt:151)
	at org.ossreviewtoolkit.model.licenses.LicenseInfoResolver.resolveLocations(LicenseInfoResolver.kt:197)
	at org.ossreviewtoolkit.model.licenses.LicenseInfoResolver.createLicenseInfo(LicenseInfoResolver.kt:129)
	at org.ossreviewtoolkit.model.licenses.LicenseInfoResolver.resolveLicenseInfo(LicenseInfoResolver.kt:61)
	at org.ossreviewtoolkit.evaluator.RuleSet.packageRule(RuleSet.kt:79)
	at Script_rules$ruleSet$1.invoke(script.rules.kts:15)
	at Script_rules$ruleSet$1.invoke(script.rules.kts:8)
	at org.ossreviewtoolkit.evaluator.RuleSetKt.ruleSet(RuleSet.kt:165)
	at org.ossreviewtoolkit.evaluator.RuleSetKt.ruleSet$default(RuleSet.kt:160)
	at Script_rules.<init>(script.rules.kts:8)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
	at kotlin.script.experimental.jvm.BasicJvmScriptEvaluator.evalWithConfigAndOtherScriptsResults(BasicJvmScriptEvaluator.kt:105)
	at kotlin.script.experimental.jvm.BasicJvmScriptEvaluator.invoke$suspendImpl(BasicJvmScriptEvaluator.kt:47)
	at kotlin.script.experimental.jvm.BasicJvmScriptEvaluator.invoke(BasicJvmScriptEvaluator.kt)
	at kotlin.script.experimental.host.BasicScriptingHost$eval$1.invokeSuspend(BasicScriptingHost.kt:48)
	at kotlin.script.experimental.host.BasicScriptingHost$eval$1.invoke(BasicScriptingHost.kt)
	at kotlin.script.experimental.host.BasicScriptingHost$eval$1.invoke(BasicScriptingHost.kt)
	at kotlin.script.experimental.host.BasicScriptingHost$runInCoroutineContext$1.invokeSuspend(BasicScriptingHost.kt:36)
	at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
	at kotlin.coroutines.ContinuationKt.startCoroutine(Continuation.kt:115)
	at kotlin.script.experimental.impl.RunSuspendKt.internalScriptingRunSuspend(runSuspend.kt:19)
	at kotlin.script.experimental.host.BasicScriptingHost.runInCoroutineContext(BasicScriptingHost.kt:36)
	at kotlin.script.experimental.host.BasicScriptingHost.eval(BasicScriptingHost.kt:46)
	at org.ossreviewtoolkit.utils.scripting.ScriptRunner.runScript(ScriptRunner.kt:71)
	at org.ossreviewtoolkit.evaluator.Evaluator.run(Evaluator.kt:56)

I could make it pass by adding JAVA_OPTS="-Xmx10g", and then JAVA_OPTS="-Xmx14g" env var to the docker runs.
What is concerning is that the "analyzer" and "scanner" runs went well, and I see no reason for it to fail on the advisor if the previous steps went well.
We use the docker images for the runs, and our full process can be seen in our GitLab project for more information.
The full log of the failed execution can be found on our Jenkins instance.

See this run as an example.

It looks like the advisor silently fails because it should print a summary of the findings and the next step can't find the advisor result.

The analyzer finds 5 Maven and 2 NPM projects which is not an unusual number, I'm a bit surprised that this scan takes so much memory, the projects probably have a lot of dependencies. As a workaround you could try to run two separate scans for the Maven and NPM projects.

Update: this kind of silent stop happened again on another project [1]. When looking deeper into it, I could correlate it with oom-kills showing up in /var/log/messages. So the silent fail is not on ORT. Still, this is a project code I've been analysing for months without any issue and the fact it now generates an oom-kill is.. strange, and concerning.
[1] https://github.com/eclipse/che
/cc @sschuberth The more I think about it, the more I come to agree with your initial though of a memory leak..

FYI This is the memory consumption during the last failed execution. The run started around 1:22 and the oom-kill occurred at 4:28, as you can see.

Which command is causing these OOMs, is it always the advisor or different commands?

This one (shown on the graph) occurred during the scanner phase.
Log can be seen here if it helps.

So, to sum it up, and looking further at our memory consumption, we can indeed see the memory peaks and oom kills are all related to the silent failures:

technology.jemo crashed on 11 at 11.55 in the advisor phase [jenkins].
ecd.che crashed on 11 at 13:56 in the scanner phase [jenkins].
ecd.che crashed on 12 at 4:28 in the scanner phase [jenkins].

I've rebooted the server, just in case, and started other runs. Will let you know asap.

I've rebooted the server, just in case, and started other runs. Will let you know asap.

Any update here @borisbaldassari?

Hi @sschuberth We doubled the memory on the production server (from 16 GB to 32 GB) and ooms no longer happen there. On the staging server however (which still has 16 GB of memory) ooms still happen.
I have a strong feeling that the resources (memory, time to run) required to analyse a sample project have dramatically increased over the last 6 months -- but it's hard to tell as a lot has changed on our setup: we now use the Docker setup, with OSADL matrix computation / lists of licences, and upgraded ORT regularly. So, I'm not sure which step exactly made the setup significantly more resources-hungry. But as a matter of facts, I could analyse any of our projects 6 months ago on our servers, and now it takes 1.5 times longer and roughly 1.5 times the memory it used to.
So this issue was solved by adding more memory, and can be closed from my side. If you want to keep it to track resources please feel free to reopen it. Thank you!

So this issue was solved by adding more memory, and can be closed from my side. If you want to keep it to track resources please feel free to reopen it.

I'm indeed going to close this for now as we're not anymore in a position to reproduce this.


Deaths Data automation

Hi, Firstly this is an amazing tool you've made and I've made some adaptions for it for work.
I've added some additional code to make the deaths import from ons more automated please see below:
library(rvest)
library(stringr)
tmp <- tempfile(fileext = ".xlsx")
##Takes first xlsx file
page <- html("https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/causesofdeath/datasets/deathregistrationsandoccurrencesbylocalauthorityandhealthboard")
ext<-page %>%
html_nodes("a") %>%       # find all links
html_attr("href") %>%     # get the url
str_subset("\.xlsx") %>% # find those that end in xlsx
.[[1]]                    # look at the first one
URL<-paste("https://www.ons.gov.uk",ext,sep="")
this would be used in pre-processing.R for row 99-101.
I hope this helps.
Kind regards,
Louis

Thanks Louis - this is a great idea. I have adapted your code and incorporated it into the pre-processing script.


App Crashes on Selective MacOS Groups

When selecting the Computer Groups Smart & Statiic.
The app will crash when loading the view of groups.
Tested and works fine in Version 4.1.0 (1)
Fails on 4.1.2

Thanks for the heads up @rickgmac - issue should be resolved in v4.1.3.


dhcp in vmware/virtualbox guests fails to hear DHCP server response

I have an Ubuntu 14.04 physical host..  pipework works great to configure the network on containers using dhcpd (using udhcpc of course)..  I can start as many as I have resources for..
now to move this to my company network, where the systems I will use are actually virtual machines.
the same scripts and containers time out getting the dhcp assigned address.
the guest systems are setup in bridged mode, and get their ip addressed form the same DHCP server without issue.
using dhcpdump on the host (primary interface etho and in the guest (eth0)
sees the dhcp request from the container as expected, and the dhcp offer response.
except the container doesn't see the response. and times out.
I 'suspect' that the bridged vmware/virtualbox  driver doesn't KNOW about the container mac address and so, doesn't listen for responses there.
to test, I made a small container
docker build -t foo .
Dockerfile
from ubuntu
cmd tail -f /var/log/bootstrap.log
the start the container with no networking
docker run -d --name=test --net=none --privileged  foo
docker exec test ip addr
shows only the lo adapter..
bash -x pipework eth0 -i eth1 test dhcp
run on the host works great,
now load up a vmware player image for Ubuntu 14.04
then use the same Dockerfile and steps..
no dhcp response., timeout, fails.
docker exec test ip addr shows eth1 was created as expected.
add dhcpdump -i eth0 to the host, and to the guest -i eth0
then run again.
you will see the request (in both host and guest) and offer (only in host),
docker exec test ip addr to get the mac address, and you will see that it matches
the request, and offer response packet data, but the guest doesn't see it.
selinux is off, ufw disable to turn of any filters.
edit: I don't need the host machine to talk to the docker containers over IP, so a bridge is not required.
help.. trying to move my stuff to work environment.

Doah.. promiscuous mode.. right there in the doc..  not a network guy, so that word didn't mean anything to me..   does now!
working great on vmware and virtualbox.

Cool, thanks for following-up!


Cannot switch between PHP versions

Describe the bug
When trying to switch between versions I only get PHP 7.4
php -v gives me:
➜  ~ php -v
PHP 7.4.27 (cli) (built: Dec 17 2021 00:35:51) ( NTS )
Copyright (c) The PHP Group
Zend Engine v3.4.0, Copyright (c) Zend Technologies
    with Zend OPcache v7.4.27, Copyright (c), by Zend Technologies

If I do:
brew link --force --overwrite<EMAIL_ADDRESS>
I get:
➜  ~ brew link --force --overwrite<EMAIL_ADDRESS>Warning: Already linked<EMAIL_ADDRESS>To relink, run:
  brew unlink<EMAIL_ADDRESS>&& brew link --force<EMAIL_ADDRESS>
If I run (as per the README):
➜  ~ brew unlink<EMAIL_ADDRESS>Unlinking<EMAIL_ADDRESS>25 symlinks removed.
➜  ~ brew link --overwrite --force<EMAIL_ADDRESS>Linking<EMAIL_ADDRESS>25 symlinks created.

If you need to have this software first in your PATH instead consider running:
  echo 'export PATH="/usr/local/opt/php@8.0/bin:$PATH"' >> ~/.zshrc
  echo 'export PATH="/usr/local/opt/php@8.0/sbin:$PATH"' >> ~/.zshrc

And then restart the shell, I still get PHP 7.4 ...
Funny enough, if I do:
valet use<EMAIL_ADDRESS>
and then do phpinfo() I see that the webserver is running PHP 8.0
CLI version is still 7.4 though ...

What is the output when you run this echo $PATH

➜  ~ echo $PATH
/usr/local/sbin:/usr/local/opt/php<EMAIL_ADDRESS>[ ---- ]

@shivammathur thanks for the help: turns out I had the version hard-coded in the .zshrc file. Once I commented that out, and ran php -v it shown the expected version.
Thanks for the valuable input and for your efforts in keeping the project alive.
Cheers.


Transaction getList fix

The current transaction getList function ensure that the cursor is a valid UUID but the zabo api now returns transaction id in many forms such as:

0x54e431ef4dede09910b00b1cd9bc10f4c87ea7981b775a03f0bb1dc283d57d8b-555703935
Internal transfer<PHONE_NUMBER>4

which does not follow the uuid format.
This PR removes any check on the cursor parameter in the transaction resource.

Thanks for the input, it's indeed simpler that way.


Add support for Git LFS

@naglepuff We don't want larger binary files to get committed directly to Git history, as this will permanently bloat our repo sizes (even if the files are later deleted) and slow down initial checkouts for everyone.
To verify that this works, could you rebase #19 on top of this branch, and redo the commit the adds the data file? You should observe that the file will be included in git lfs ls-files --all afterwards.


Fix Getting Started Guide link in READMEs

Hi @joshuadavidthomas and thanks for the PR and well spotted.
Sadly I cannot accept this PR as you are branching from the main branch, this project uses git flow so any PR should branch from the develop branch instead.

Fixed in https://github.com/Frojd/Wagtail-Pipit/commit/7871c2ec474ec58e437f8f67c53fb561ab13f04d


Fire on hover?

Hello.
Is it possible to fire the animation when hovering a div? I tired this but it's not working:
 $('document').ready(function() {     var path1 = new ProgressBar.Path(document.getElementById('circle1'), {         duration: 1000,         easing: 'easeOut'     });     $('#svglink-1').hover(function() {         path1.animate(1);         path1.animate(0);     }); });
and the html:

                     <svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" x="0px" y="0px"                          viewBox="0 0 224.10257 224.10257">                         <path fill-opacity="0" stroke-width="10" stroke="#fff" d="M5,112.05128C5,52.92849,52.92849,5,112.05128,5s107.05128,47.92849,107.05128,107.05128 	s-47.9285,107.05128-107.05128,107.05128"/>                         <path id="circle1" class="toprogress" fill-opacity="0" stroke-width="10" stroke="#197dbe" d="M5,112.05128C5,52.92849,52.92849,5,112.05128,5s107.05128,47.92849,107.05128,107.05128 	s-47.9285,107.05128-107.05128,107.05128"/> </svg>

It's not working. Note that if I use path1.animate(1) without the hover function, the animation shows when loading the page

One problem is this: path1.animate(1); path1.animate(0); You cannot call animate(0) immediately after animate(1) like that. You need to do it via callbacks
path1.animate(1, function() {
  path1.animate(0);
});

Oh yeah, I was tired yesterday, in fact with the "hover" jquery function, the right spelling is:
$('#svglink-1').hover(function() {path1.animate(1);},function() {path1.animate(0);});
Now it's working great! :)


Consider decoupling navigator and PageTransitionsTheme

Currently the PageTransitionsTheme returns the builder that builds transition around Route. This forces the customer to use navigator if they want to use platform adaptive transition.
We should consider refactoring this theme to provide builder that does not rely on Route

@xster Can you help prioritize this issue?


[SPARK-35281][SQL] StaticInvoke should not apply boxing if return type is primitive

What changes were proposed in this pull request?

In StaticInvoke, when result is nullable, don't box the return value if its type is primitive.
Why are the changes needed?

It is unnecessary to apply boxing when the method return value is of primitive type, and it would hurt performance a lot if the method is simple. The check is done in Invoke but not in StaticInvoke.
Does this PR introduce any user-facing change?

No
How was this patch tested?

Added a UT.

Test build #138141 has started for PR 32416 at commit 7c687d0.

Kubernetes integration test unable to build dist.
exiting with code: 1
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/42662/

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder-K8s/42662/

Test build #138141 has finished for PR 32416 at commit 7c687d0.

This patch fails from timeout after a configured wait of 500m.
This patch merges cleanly.
This patch adds no public classes.

retest this please

retest this please

Merged to master.


No LoadData method for image classification

Image classification doesn't have a sample load method for IDataView.

@beccamc to provide code for this scenario.

Does the image has loadData Method  only Tabular data sources

Nope, I need to provide the source code!

public static IDataView LoadImagesFromFolder(MLContext context, string folder)
        {
            var res = new List<ModelInput>();
            var allowedImageExtensions = new[] { ".png", ".jpg", ".jpeg", ".gif" };
            DirectoryInfo rootDirectoryInfo = new DirectoryInfo(folder);
            DirectoryInfo[] subDirectories = rootDirectoryInfo.GetDirectories();

            if (subDirectories.Length == 0)
            {
                throw new Exception("fail to find subdirectories");
            }

            foreach (DirectoryInfo directory in subDirectories)
            {
                var imageList = directory.EnumerateFiles().Where(f => allowedImageExtensions.Contains(f.Extension.ToLower()));

                if (imageList.Count() > 0)
                {
                    res.AddRange(imageList.Select(i => new ModelInput
                    {
                        Label = directory.Name,
                        ImageSource = File.ReadAllBytes(i.FullName),
                    }));
                }
            }

            return context.Data.LoadFromEnumerable(res);
        }

for Azure, it should be CreateFromFile instead of LoadFromFile.
Is that right ?@LittleLittleCloud


github for public repository type (#8)

Description
for rebase develop on main
Related Issue (Optional)

N/A
Changes
for public
Screenshots (Optional)
N/A
Additional Comments (Optional)
N/A

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


NTRs: 'toll-like receptor TLR4:TLR6 signaling pathway'-related and 'cellular response to oxidised low-density lipoprotein particle stimulus'.

Hello,
I am currently annotating PMID:20037584 where Figure 1 demonstrates cooperative signalling of TLR4 and TLR6, which depends on TRIF as well as MyD88.
Atm we have relevant terms in the ontology that are specific to TLR4:
GO:0035667 TRIF-dependent toll-like receptor 4 signaling pathway
GO:0035660 MyD88-dependent toll-like receptor 4 signaling pathway
So I wondered whether corresponding terms should be created for TLR4 and TLR6 working together? These would be:
NTR1: 'TRIF-dependent toll-like receptor TLR4:TLR6 signaling pathway';
NTR2: 'MyD88-dependent toll-like receptor TLR4:TLR6 signaling pathway'.
If these get created I suppose I also ought to request:
NTR3: 'toll-like receptor TLR4:TLR6 signaling pathway'
Because corresponding GO terms for other toll-like receptors currently exist, e.g.
GO:0038123 toll-like receptor TLR1:TLR2 signaling pathway
If the new terms get created please use the DbxRef: ARUK-UCL and GOC:bc.
Or are the existing toll-like receptor gene product-specific terms going to be removed, and so I should use the parent terms for annotations?
GO:0035666 TRIF-dependent toll-like receptor signaling pathway; and
GO:0002755 MyD88-dependent toll-like receptor signaling pathway.
The experiments (in Figure 1 and in the following figure) also show that the TLR4/6 signalling is triggered by oxidised LDL. Consequently could I request a new term:
NTR4: 'cellular response to oxidised low-density lipoprotein particle stimulus'
This would be a child of:
GO:0071404 cellular response to low-density lipoprotein particle stimulus
Thanks,
Barbara
@RLovering
DbxRef: ARUK-UCL
GOC:bc

Hi @BarbaraCzub
I am finally getting around to this. I am a little worried to add the different combinations of TLR because that might be a lot of terms. Did you try making a Noctua model with this ? It may give some insight into how to annotate in a more pre-composed way.
Pascale

Hi @pgaudet
No, I have not tried making a Noctua model. These annotations are a part of the Alzheimer's Research UK (ARUK)-funded project, and so they need to be attributed to ARUK in bioinformatic resource databases.
Creating models in Noctua currently results in attributing them generally to Noctua (this is how they are displayed in AmiGO2) rather than specific project/funding bodies. Therefore, I have been using Protein2GO to annotate papers for the ARUK-funded project; these annotations are subsequently displayed as ARUK-UCL in QuickGO and AmiGO2.
I suppose whether or not the specific TLR-related GO terms get created depends on decisions wrt whether or not GO terms specific to gene products should get created.
@RLovering do you know whether this was discussed (and hopefully decided) at the GO meeting?
Barbara

Hi @BarbaraCzub
Why are Noctua models attributed to Noctua? Your ORCID is saved in the model, it should be completely traceable. Perhaps this is an issue with the GAF export from Noctua that doesn't export that information?
Pascale

Hi @pgaudet
It is certainly possible for GOC members to trace models to specific ORCIDs by using the Noctua annotation tool. But publicly all annotations created using Noctua are displayed as contributed by 'GO_Noctua', e.g. screenshot below:

So an external user has no option to trace an annotation to the project that it originated from. Because we rely on grants from funding bodies, we need to be able to acknowledge them in the annotations made with their help.
The attribution of Noctua models to specific projects/funding bodies was discussed during the Noctua training at the EBI in Hinxton last year, but I am not aware what decisions have been made with regard to this.
Barbara

Hello @BarbaraCzub ,
Thanks for bringing up the problem to our attention. We have now added your group to the yaml file, so when you log into Noctua there should be a small arrow at the right of your name, that provides a pull down with the list of groups you belong to. This should give the right attribution.
Can you please give that a try?
Pascale

Hi @pgaudet
I have just logged into Noctua and I found the arrow with the dropdown menu in the model view after clicking on 'create Noctua model'. Thank you for bringing this to my attention. So, if I select, e.g. 'ARUK-UCL', how will annotations created as a part of this model be displayed in AmiGO2? Will they be displayed as ARUK-UCL? Or Noctua-ARUK-UCL?
Thanks,
Barbara
CC @RLovering

@kltm can you please answer @BarbaraCzub ?

Hi @pgaudet
To follow up from the above, I think I am now able to answer my own question. I did a little test, I ticked 'SynGO-UCL' in the drop-down menu, which you indicated; then I saved the model and I downloaded the GPAD file (screenshot below). In GPAD the annotation source is still displayed as GO_Noctua.
So although you can select a project, when you are working on a model, this selection does not appear to be linked to the GPAD. In addition the project, which I originally selected for this model, did not remain saved with it. When I went back to the model after viewing the GPAD file, and clicked on the drop-down menu again, the project, which was ticked was 'BHF-UCL' (this was the top one on the list, so I suppose the top one is the 'default' one). (When I downloaded the GPAD, it opened in the same window, and the I used the 'go back' arrow in my browser to return to the model view). So, although these functions are available for initial selection, they do not stay selected after you stop viewing a model (even when you save it before moving on), and they are not exported in the GPAD files.

@kltm is this the expected behavior?

Hi @BarbaraCzub
My understanding is that you need to save a new annotation (or re-save an old annotation, you probably need to change something to be able to save it). Just changing the group will not attribute all the existing annotations.
Can you try that ?
Thanks for your patience !
Pascale

Hi @pgaudet
I tried what you suggested. I used a test model, which I created earlier today:

This model was originally created with the default BHF-UCL attribution, which I confirmed when I opened the drop-down menu:

I then changed the 'heart process' to another process, changed the attribution to ARUK-UCL, and saved:

I then went back to the Noctua landing page, and from there I selected this test model again and checked the attribution in the drop-down menu. BHF-UCL was ticked:

So, although I have made a significant change to the model and re-saved, the attribution did not get saved with it.
I am not sure what else I can do. @RLovering wanted to try this in her account, but she does not even have the drop-down menu options to choose from, so we were not able to do that test.
I will look forward to receiving further instructions.
Thanks,
Barbara

Let me clarify the part about what is seen in AmiGO, which is a separate issue from group-level attribution.
Currently it's up to individual groups to take the GPAD output from Noctua and incorporate into their database. So far, only MGI does this. In the future, when people are happy with the GPAD export, we can look at doing this in GO Central.
Btw, we in future it's better to open Noctua issues in the noctua tracker, but let's keep this discussion here for now.

One more issue: I get no annotations from this model at all, when I click 'Export GPAD':

@BarbaraCzub - you need to add evidence to get annotations. In future @dougli1sqrd's checks will inform if there are assertions lacking evidence, for now this is something you just have to know

Re:

I am not so sure this is a correct inference about the tool. The tick merely indicates what hat(s) you are wearing, it does not reflect current attribution of either the whole model or the assertions within it (@kltm can confirm). To see model-level attribution go to model->edit annotations and look for "provided by"

Thank you @cmungall for explaining this. So do I understand correctly that once I'm happy with a model and would like it to be attributed to ARUK-UCL, I should just download the GPAD and forward it to @tonysawfordebi ? Or what is the procedure?
As this is a test model it did not occur to me that I was missing the evidence. Thanks @cmungall for pointing this out.
This was originally a new term request, but it has turned into a Noctua issue...

So do I understand correctly that once I'm happy with a model and would like it to be attributed to ARUK-UCL, I should just download the GPAD and forward it to @tonysawfordebi ? Or what is the procedure?

I guess you could but that would be a pretty rubbish pipeline! No, this is all meant to be more intuitive.. I have to get into work now will reply in more detail later

This was originally a new term request, but it has turned into a Noctua issue...

Yes, it's easy for these to blend together

Ok, I checked "provided by" and it links to our UCL websites (both the one associated with BHF and ARUK annotation projects). So the tool 'memorised' both ticked attributions.

Thank you @cmungall you've already clarified a lot! This was very helpful. Have a good day! (It's almost the weekend here!).

Should we close this then ?

Note Barbara has opended as separate github request for https://github.com/geneontology/go-ontology/issues/13712

Closing this and starting work on #13712
@BarbaraCzub @RLovering , please reopen if this is not resolved.
Thanks, Pascale


Sonar test

Codecov Report

Merging #565 (a973dfc) into release-sonartest (b243fa6) will increase coverage by 14.79%.
The diff coverage is 100.00%.

:exclamation: Current head a973dfc differs from pull request most recent head d431183. Consider uploading reports for the commit d431183 to get more accurate results

@@                  Coverage Diff                   @@
##           release-sonartest     #565       +/-   ##
======================================================
+ Coverage              67.56%   82.35%   +14.79%
======================================================
  Files                    258       12      -246
  Lines                  17678     1009    -16669
  Branches                3999      213     -3786
======================================================
- Hits                   11944      831    -11113
+ Misses                  5695      177     -5518
+ Partials                  39        1       -38

Impacted Files
Coverage Δ

...server-core-integration/src/lib/corePeripherals.ts
100.00% <100.00%> (ø)

meteor/server/api/blueprints/http.ts

meteor/lib/collections/BucketAdlibActions.ts

...eor/server/migration/deprecatedDatabases/0_25_0.ts

meteor/lib/collections/lib.ts

meteor/lib/collections/ExpectedPlayoutItems.ts

...eor/lib/collections/ExpectedPackageWorkStatuses.ts

meteor/server/cache/ActivationCache.ts

meteor/server/cronjobs.ts

meteor/server/systemStatus/api.ts

... and 233 more

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[Autocomplete] Clear TomSelect input on LiveProp refresh

Hey, I'm using Autocomplete UX in a LiveComponent.
Here, with my own options :
<select
          name="school_class_course"
           {{ stimulus_controller('symfony/ux-autocomplete/autocomplete') }}
           class="form-select"
           data-action="live#action"
           data-action-name="resetPage"
            data-model="debounce(300)|filterSchoolClassCourseId"
                    >
                        <option value=""></option>
                        {% for school_class_course_item in schoolClassCourses %}
                            <option {% if schoolClassCourses|length == 1 %}selected{% endif%} value="{{ school_class_course_item.id }}">{{ school_class_course_item.createShortLabel }}</option>
                        {% endfor %}
</select>

Or here with a real Autocomplete route to fill options :
                    <select
                            name="employer"
                            {{ stimulus_controller('symfony/ux-autocomplete/autocomplete', {
                                url: path('ux_entity_autocomplete', { alias: 'listing_employer' }),
                            }) }}
                            class="form-select"
                            data-action="live#action"
                            data-action-name="resetPage"
                            data-model="debounce(300)|filterEmployerId"
                    >
                    </select>

In both cases, I've a LiveProp(writable: true) associated to the select autocomplete :
#[LiveProp(writable: true)]
public ?string $filterEmployerId = null;

#[LiveProp(writable: true)]
public ?string $filterSchoolClassCourseId = null;

I've a Live Action which reset the filterEmployerId and filterSchoolClassCourseId values to null.
The "real select" is resetted, the table is reloaded without the filter.
The problem is that the TomSelect is keeping the previous value as the selected value.
https://user-images.githubusercontent.com/53140475/227525713-4ad46422-8029-4c5b-9d65-fbc7630da43f.mp4
If I use a traditionnal select (not autocomplete), it works.
Do I must to add a parameter, an option, or do something to remove the TomSelect selected value ?

I think this was likely fixed by #1290, which will be released soon


Cannot calculate tf.gradients wrt embedding_matrix

Please go to Stack Overflow for help and support:
https://stackoverflow.com/questions/tagged/tensorflow
If you open a GitHub issue, here is our policy:

It must be a bug, a feature request, or a significant problem with documentation (for small docs fixes please send a PR instead).
The form below must be filled out.
It shouldn't be a TensorBoard issue. Those go here.

Here's why we have that policy: TensorFlow developers respond to issues. We want to focus on work that benefits the whole community, e.g., fixing bugs and adding features. Support only helps individuals. GitHub also notifies thousands of people when issues are filed. We want them to see you communicating an interesting problem, rather than being redirected to Stack Overflow.

System information

Have I written custom code (as opposed to using a stock example script provided in TensorFlow): yes
OS Platform and Distribution (e.g., Linux Ubuntu 16.04): Debian 8.1
Mobile device (e.g. iPhone 8, Pixel 2, Samsung Galaxy) if the issue happens on mobile device:
TensorFlow installed from (source or binary): binary
TensorFlow version (use command below): v1.3.0-rc2-20-g0787eee 1.3.0
Python version: 3.6.3
Bazel version (if compiling from source):
GCC/Compiler version (if compiling from source):
CUDA/cuDNN version:  8/6.0.21
GPU model and memory: Titan Xp
Exact command to reproduce:

You can collect some of this information using our environment capture script:
https://github.com/tensorflow/tensorflow/tree/master/tools/tf_env_collect.sh
You can obtain the TensorFlow version with:
python -c "import tensorflow as tf; print(tf.GIT_VERSION, tf.VERSION)"

Describe the problem
Describe the problem clearly here. Be sure to convey here why it's a bug in TensorFlow or a feature request.
I used tensorflow to implement an end-to-end lambdaRank retrieval model. There are 3 modules: rep_module, inter_module, and L2R_module. The embeddings (emb_mat) was defined in L2R_module, and pass as params to rep_module and inter_module: So the aggregating L2R module will have:
self.emb_mat = tf.get_variable("emb_mat",
shape=[self.vocab_size, self.emb_dim], dtype=tf.float32)
self.rep_mod = RepModule(...., emb_mat=self.emb_mat)
self.inter_mod = InterModule(..., emb_mat=self.emb_mat)
The goal is to let the emb_mat shared by both rep and inter modules, and learn it jointly with those 2 modules. This L2R module will output a batch of scores: score=(Batch_size, 1)
Then I have a another higher-level lambdaRank module to calculate the gradients by hand (I cannot use built-in off the self optimizer, since I have to get the grads and multiply that with the things in lambda rank). I have a _jacobian(y, x) function as follows:
def _jacobian(self, y_flat, x):
"""
https://github.com/tensorflow/tensorflow/issues/675
for ranknet and lambdarank
"""
loop_vars = [
    tf.constant(0, tf.int32),
    tf.TensorArray(tf.float32, size=self.batch_size),
]

_, jacobian = tf.while_loop(
    lambda j, _: j < self.batch_size,
    lambda j, result: (j + 1, result.write(j, tf.gradients(y_flat[j], x))),
    loop_vars)

return jacobian.stack()

which will calculate the grad of each element of y wrt x, and reassemble them together. I can get Jacobians of all score wrt all other variables(model parameters, if I use a fixed embedding, so emb_mat is no longer in trainable_variables()) except the emb_mat. My other variables are like tf.layers.. variables like
tf.Variable 'conv1/conv1d/kernel:0' shape=(3, 300, 256) dtype=float32_ref,
but it cannot calculate the gradients wrt the emb_mat. It returned something like : TypeError: Failed to convert object of type <class 'list'> to Tensor. Contents: [<tensorflow.python.framework.ops.IndexedSlices object at 0x7f025e161f28>] and TypeError: Expected binary or unicode string, got <tensorflow.python.framework.ops.IndexedSlices object at 0x7f025e161f28>
The whole traceback is attached in logs section
Source code / logs
Include any logs or source code that would be helpful to diagnose the problem. If including tracebacks, please include the full traceback. Large logs and files should be attached. Try to provide a reproducible test case that is the bare minimum necessary to generate the problem.
Class L2R_Model(object):
.....
self.emb_mat = tf.get_variable("emb_mat",
shape=[self.vocab_size, self.emb_dim], dtype=tf.float32,
initializer=tf.orthogonal_initializer(1.0))
self.rep_mod = RepModule(...., emb_mat=self.emb_mat)
self.inter_mod = InterModule(..., emb_mat=self.emb_mat)
def _jacobian(self, y_flat, x):
"""
https://github.com/tensorflow/tensorflow/issues/675
for ranknet and lambdarank
"""
    loop_vars = [
        tf.constant(0, tf.int32),
        tf.TensorArray(tf.float32, size=self.batch_size),
    ]

    _, jacobian = tf.while_loop(
        lambda j, _: j < self.batch_size,
        lambda j, result: (j + 1, result.write(j, tf.gradients(y_flat[j], x))),
        loop_vars)

    return jacobian.stack()

Traceback (most recent call last):
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/tensor_util.py", line 460, in make_tensor_proto
str_values = [compat.as_bytes(x) for x in proto_values]
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/tensor_util.py", line 460, in
str_values = [compat.as_bytes(x) for x in proto_values]
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/util/compat.py", line 65, in as_bytes
(bytes_or_text,))
TypeError: Expected binary or unicode string, got <tensorflow.python.framework.ops.IndexedSlices object at 0x7f025e161f28>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "main_lambda.py", line 234, in
debug()
File "main_lambda.py", line 230, in debug
inter_param_dict=inter_param_dict, resume=r_flag)
File "/u/nieyifan/projects/L2R_RM/L2R_LambdaRank.py", line 25, in init
self.loss, self.num_pairs, self.score, self.train_op = self._build_model()
File "/u/nieyifan/projects/L2R_RM/L2R_LambdaRank.py", line 215, in _build_model
grads = [self._get_derivative(score, Wk, lambda_ij) for Wk in vars]
File "/u/nieyifan/projects/L2R_RM/L2R_LambdaRank.py", line 215, in
grads = [self._get_derivative(score, Wk, lambda_ij) for Wk in vars]
File "/u/nieyifan/projects/L2R_RM/L2R_LambdaRank.py", line 112, in _get_derivative
dsi_dWk = self._jacobian(score, Wk)  # (BS, )
File "/u/nieyifan/projects/L2R_RM/L2R_LambdaRank.py", line 98, in _jacobian
loop_vars)
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2775, in while_loop
result = context.BuildLoop(cond, body, loop_vars, shape_invariants)
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2604, in BuildLoop
pred, body, original_loop_vars, loop_vars, shape_invariants)
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2554, in _BuildLoop
body_result = body(*packed_vars_for_body)
File "/u/nieyifan/projects/L2R_RM/L2R_LambdaRank.py", line 97, in
lambda j, result: (j + 1, result.write(j, tf.gradients(y_flat[j], x))),
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/util/tf_should_use.py", line 175, in wrapped
return _add_should_use_warning(fn(*args, **kwargs))
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/ops/tensor_array_ops.py", line 302, in write
value = ops.convert_to_tensor(value, name="value")
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/ops.py", line 611, in convert_to_tensor
as_ref=False)
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/ops.py", line 676, in internal_convert_to_tensor
ret = conversion_func(value, dtype=dtype, name=name, as_ref=as_ref)
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/constant_op.py", line 121, in _constant_tensor_conversion_function
return constant(v, dtype=dtype, name=name)
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/constant_op.py", line 102, in constant
tensor_util.make_tensor_proto(value, dtype=dtype, shape=shape, verify_shape=verify_shape))
File "/u/nieyifan/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/tensor_util.py", line 464, in make_tensor_proto
"supported type." % (type(values), values))
TypeError: Failed to convert object of type <class 'list'> to Tensor. Contents: [<tensorflow.python.framework.ops.IndexedSlices object at 0x7f025e161f28>]. Consider casting elements to a supported type.

@yifannieudem You can probably use tf.gradients(loss, embeddings) for your case which will give a tf.IndexedSlices object corresponding to the gradients of embeddings. You can also use optimizer.apply_gradients to aggregate gradients for repeating word units.
Manually calculation using jacobian is another way of doing it, make sure that all the types match.


rpc: Bump yargs to 15.3.1

<EMAIL_ADDRESS>(from<EMAIL_ADDRESS>is vulnerable to prototype pollution. This PR bumps yargs to 15.3.1 which resolves audit pipelines that may be reporting a vulnerability in @jest-runner/rpc. This could be a breaking change since it drops support for Node 6.

Hi @aaronabramov , would you be able to review this when you get a chance?

hey @rajivshah3
looks good! thank you!


Not able to run the repo

Hi @christian-bromann,
It's a wonderful idea to communicate with dev-tools and analyze the performance of the web applications using v5. I am really excited to see how this works. But the sad part is that I am not able to run any of the spec files.
Checked selenium-standalone module as well, but concatenation of the url is not broken at that point. Not sure from where exactly wdio is trying to phrase the url and hit. Please advise.
Attaching the log files here. The only issue I could see as of now is sending the POST request to the invalid url. I mean http://<IP_ADDRESS>/:4444E/wd/hub/session
wdio-0-0.log
wdio-0-1.log
wdio.log

It looks like chromedriver is not started where the request are send to. Please open a bug ticket in the selenium-standalone package as this seems to be clearly a mis-function when running stuff in Windows.
For the time being you can run Chromedriver manually and set host and port in your wdio.conf.js.

I have started the chromedriver like this..
java -Dwebdriver.chrome.driver=chromedriver.exe -jar selenium-server-standalone-3.14.0.jar
The above started by default on 4444 port. The changes I have made to config part is
//runner: 'local',
    host: '<IP_ADDRESS>',
    port: 4444,

Then selenium-standalone logs like this

16:28:09.351 ERROR [SeleniumServer.boot] - Port 4444 is busy, please choose a free port and specify it using -port option

Now I removed selenium-standalone from services and manually started it on 4444 port with chromedriver. Still no luck. The error message remains the same and the test fails. Any comments?


[FEEDBACK] Make mod mail threads close after 24 hours of inactivity

Version
0.6.2-pre.5
Feedback
Make mod mail threads close after 24 hours of inactivity
Submitter Information
Discord Tag: Karma's Guide#6864
Discord ID:<PHONE_NUMBER>69041665
Date/Time Submitted: 8/27/2020, 9:30:06 AM
Disclaimer: PLEASE READ
This issue was NOT written by the author of the repository OR the account that posted this issue. This issue was submitted through the program hosted in this repository, via Github's API, by someone that uses the program ("user"). The user can be found above.

This will be considered.


Navigate to event on notification tap

Realized this is called a notification. not notice. oh well

Fixed Navigator.push to event


render text within li if no child tag is present

I am not sure if anyone still cares about this project, but here would be a fix for this bug: https://github.com/thlorenz/hermit/issues/2
I didn't go crazy deep into the internals of this project, but the main changes I made are that I check in parse.js in the function parser.ontext if the li tag has "real text" meaning other text than blanks and line breaks, if that is the case I add the text to currentItem.
in layout.js in the function processNode
I check if the li tag has text, if it does, I add it back after the indention.
I am not sure if this breaks anything else since I didn't go deep into the internals, but I added a test case and all the other tests still pass.
Sorry for the reformatting, if it bothers you and anybody still cares about the project I can start a new pull request without the reformatting.

Hey thanks for your contribution. There are tons of white space changes added in the commits.
I know I can ignore them when reviewing, but would like to only pull in the actual changes to keep the diff clean.
Could you please remove those? Maybe you need to setup you IDE to not add them automatically.
Thanks!


[Req] navigating with XPath

XPath uses path expressions to select nodes or node-sets.
brief introduction:
http://www.w3schools.com/xsl/xpath_syntax.asp
EBNF-like grammar:
http://www.w3.org/TR/xquery-xpath-parsing/#id-grammar
.net class library contains a set of classes and interfaces which automates that.
(starting from System.Xml.XPath, IXPathNavigable )
I propose to implement such access to the tree of Match-es, which are returned as result of parsing

good idea

http://stackoverflow.com/questions/2324432/using-an-xpath-style-query-with-reflection

http://goessner.net/articles/JsonPath/
 XPath  JSONPath  Description
 /  $ the root object/element
 .  @ the current object/element
 /  . or [] child operator
 ..  n/a parent operator
 //  .. recursive descent. JSONPath borrows this syntax from E4X.
 *  * wildcard. All objects/elements regardless their names.
 @  n/a attribute access. JSON structures don't have attributes.
 []  [] subscript operator. XPath uses it to iterate over element collections and for predicates. In Javascript and JSON it is the native array operator.
 |  [,] Union operator in XPath results in a combination of node sets. JSONPath allows alternate names or array indices as a set.
 n/a  [start:end:step] array slice operator borrowed from ES4.
 []  ?() applies a filter (script) expression.
 n/a  () script expression, using the underlying script engine.
 ()  n/a grouping in Xpath

https://www.sitepen.com/blog/2010/11/02/resource-query-language-a-query-language-for-the-web-nosql/
RQL is designed to be URI friendly, leveraging URI encoding and designated delimiters for syntax that works perfectly in web requests.
RQL is designed to be extensible.


Implement changelog generation

I've added instructions on how to generate a changelog in docs/changelog/README.md and some rules about tags and releases in the general README.md
This will close #125 and #126

I've added a few lines in the general README specifying when to generate the changelog file, but you can modify it of course if you think more frequent generation is needed.