could not compile thaw_utils 0.1.0-beta4

   Compiling thaw_utils v0.1.0-beta4
error[E0119]: conflicting implementations of trait `class_list::IntoClass` for type `MaybeProp<std::string::String>`
   --> C:\Users\micross\scoop\persist\rustup\.cargo\registry\src\rsproxy.cn-0dccff568467c15b\thaw_utils-0.1.0-beta4\src\class_list.rs:338:1
    |
313 | / impl<T, U> IntoClass for T
314 | | where
315 | |     T: Fn() -> U + 'static,
316 | |     U: IntoClassValue,
    | |______________________- first implementation here
...
338 |   impl IntoClass for MaybeProp<String> {
    |   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ conflicting implementation for `MaybeProp<std::string::String>`

error[E0119]: conflicting implementations of trait `class_list::IntoClass` for type `(&'static str, leptos::prelude::Memo<bool>)`
   --> C:\Users\micross\scoop\persist\rustup\.cargo\registry\src\rsproxy.cn-0dccff568467c15b\thaw_utils-0.1.0-beta4\src\class_list.rs:364:1
    |
344 | / impl<T> IntoClass for (&'static str, T)
345 | | where
346 | |     T: Fn() -> bool + 'static,
    | |______________________________- first implementation here
...
364 |   impl IntoClass for (&'static str, Memo<bool>) {
    |   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ conflicting implementation for `(&'static str, leptos::prelude::Memo<bool>)`

For more information about this error, try `rustc --explain E0119`.
error: could not compile `thaw_utils` (lib) due to 2 previous errors

I ran into this issue a couple days ago. I was using Leptos with the "nightly" feature enabled, but hadn't enabled the "nightly" feature for thaw.
As soon as I enabled the "nightly" feature for thaw as well, it compiled fine.

@TheToddmeister Can you post your error log?

error[E0046]: not all trait items implemented, missing: reset
--> C:\Users\Tormo.cargo\git\checkouts\thaw-057be4168b51a04a\2c2ae8d\thaw_utils\src\class_list.rs:162:1
|
162 | impl leptos::tachys::html::class::IntoClass for ClassList {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing reset in implementation
|
= help: implement the missing item: fn reset(_: &mut <Self as leptos::tachys::html::class::IntoClass>::State) { todo!() }
I have tried removing nightly and adding nightly

Apologies, but i think a cargo update solved my problems @luoxiaozero
My bad

@sssilver Currently leptos 0.7.0-rc1 can only match Thaw(git). You can change it to:
[package]
name = "reel"
version = "0.1.0"
edition = "2021"

[lib]
crate-type = ["cdylib", "rlib"]

[dependencies]
axum = { version = "0.7", features = ["macros"], optional = true }
console_error_panic_hook = "0.1"
dotenvy = "0.15"
futures = "0.3"
getrandom = { version = "0.2", features = ["js"] }
http = { version = "1.1" }
leptos = "0.7.0-rc1"
leptos_axum = { version = "0.7.0-rc1", optional = true }
leptos_integration_utils = { version = "0.7.0-rc1", optional = true }
leptos_meta = "0.7.0-rc1"
leptos_router = "0.7.0-rc1"
serde = { version = "1.0", features = ["derive"] }
sqlx = { version = "0.8", features = [ "postgres", "runtime-tokio" ], optional = true }
- thaw = { version = "0.4.0-beta4", features = ["csr"] }
+ thaw = { git = "https://github.com/thaw-ui/thaw" }
thiserror = "2.0"
tokio = { version = "1.39", features = ["full"], optional = true }
tower = { version = "0.5", features = ["util"], optional = true }
tower-http = { version = "0.6", features = ["fs"], optional = true }
uuid = {version = "1.10", features = ["serde", "v4", "fast-rng", "macro-diagnostics"] }
wasm-bindgen = "0.2"

[features]
hydrate = [
    "leptos/hydrate",
+   "thaw/hydrate"
]
ssr = [
    "dep:axum",
    "dep:tokio",
    "dep:tower",
    "dep:tower-http",
    "dep:leptos_axum",
    "leptos/ssr",
    "leptos_meta/ssr",
    "leptos_router/ssr",
    "dep:tracing",
+   "thaw/ssr",
]


threshold moving in ktrain

hello, is there any way to apply threshold moving in ktrain on predictions, it would help greatly on umbalanced data but I cannot find examples in documentation, can you provide me with one example:
here's tensorflow example from a course:
sample_example = ['Why is it that European food is so terrible', 'Are you ashamed of being Indian?']
test_data = tf.data.Dataset.from_tensor_slices((sample_example, [1]*len(sample_example)))
test_data = test_data.map(to_feature_map).batch(1)
preds = model.predict(test_data)
threshold = 0.4
['Insincere' if pred >= threshold else 'Sincere' for pred in preds]
or
from sklearn.tree import DecisionTreeClassifier
clf = DecisionTreeClassifier(random_state = 2)
clf.fit(X_train,y_train)
y_pred = (clf.predict_proba(X_test)[:,1] >= 0.3).astype(bool)
any help with a working code for ktrain would be greatly appreciated, I am trying to predict sentences in column and output to a file
but I would also need a threshold, I tried to apply this threshold and the prediction itself works but its capped at 0.5, ie the threshold does not work:
preds = predictor.predict(df['Text'].values.tolist())
threshold = 0.9
['Neutral' if pred >= threshold else 'Negative' for pred in preds]
df['Text'] = preds
on the whole Internet I have not seen 1 person using threshold moving in ktrain that would share a code

Please see this FAQ entry.  Getting prediction probabilities is also discussed in the text classification tutorial


Rich Edit bug fixes

:tada: This PR is included in version 0.300.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


[Bar Chart] Y axis labels are cutoff from the edge when they are long enough

Description:
Y axis labels in the horizontal bar chart are cutoff if they are long enough. Label must have a maximum length to avoid this.
Affected Product Version:
SP 4.3-M1
Steps to reproduce:
Create a horizontal bar chart with long enough labels to see they are cutoff at the end of the widget boundary

you can add a length limit so that it will and some ... to the text
can you try with that ?

Sure ayya I will


Update layout.ts

Description
Fix for input values treatment, they should not be mutated
Related links, issue #, if available: n/a
How has this been tested?
Modified tests to ensure that input objects are frozen. Fails before the fix and passes afterwards

Review checklist
The following items are to be evaluated by the author(s) and the reviewer(s).
Correctness

Changes include appropriate documentation updates.
Changes are backward-compatible if not indicated, see CONTRIBUTING.md.
Changes do not include unsupported browser features, see CONTRIBUTING.md.
Changes were manually tested for accessibility, see accessibility guidelines.

Security

If the code handles URLs: all URLs are validated through the checkSafeUrl function.

Testing

Changes are covered with new/existing unit tests?
Changes are covered with new/existing integration tests?

By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

No questions to the fix itself. There is a change in a snapshot, though. Flaky?

Tested locally, cannot reproduce. I will count this as flakiness


Added Liberty Financial to the list

I work at Liberty Financial, hopefully the tweet I've referenced is a good enough source. :)

Thanks!


enrichment plot is giving small values

The plot generated by tests/performance_tests/algorithm_performance_tests_transitionscenario.py https://github.com/ergs/d3ploy/pull/174/files, gives a really small value at time = 0. This issue can be closed when this is fixed

timeseriesdemandsourceout:

At timestep 1,2, etc some enrichment facilities demand 1.72476340700596e-316 ...

If the inital_feed for the enrichment facility is 0 we get those values. In my input file I changed the initial feed to 1e10 and those values are gone.

Now, why does that happen? Why an initial feed of 0 kg of Natural Uranium to the enrichment facility produces a demand of very small amount of Natural Uranium? Is this a bug in the archetype?
Should this open a new issue?

We can just make sure to keep the initial feed at a finite amount so that this error doesn't occur?

Probably best to look closely at https://github.com/cyclus/cycamore/blob/master/src/enrichment.cc to figure out what's happening in the demand.

@gwenchee if the initial feed is different to 0 then this doesn't happen.
@katyhuff I looked at it briefly and it exceeds a lot my current knowledge of cycamore. I will look at it in detail and try to find a bug.
Anyway, I re run the input without d3ploy and the demand at t=0 is in that order of magnitude. The initial feed is again 0.

@robfairh Right -- I described the reason and solution above. Repeated below:
start here: https://github.com/cyclus/cycamore/blob/master/src/enrichment.cc#L341
You can see that it requests the max between 0.0 and inventory.capacity() - inventory.quantity()).. so if inventory capacity is anything but zero... it seems it would make a request no matter what..
This genenerally makes sense, in the context of the way cyclus usually works. The enrichment facility, if it's running, should seek out natural uranium and start enriching it to the best of its ability, immediately. Of course, this perhaps doesn't work well with the way d3ploy works. In the context of d3ploy, and the way you've designed this problem, then it seems you're expecting the enrichment facility to only enrich uranium if some other facility requests enriched uranium... if that's the case then there will need to be an if/then comparison with the requests coming into the facility...

Okay, it makes sense. So can we close this issue? and set always an initial feed different to 0.

The demand of sourceout is usually very small for timestep 0. As we are plotting in log scale for the axis y, we get this 10^-200 values. Going back to linear scale will solve the issue.

closed with https://github.com/arfc/d3ploy/pull/201


Component shutdown fails if docker id file doesn't exist

This can be fixed by ensuring that the docker id file is only deleted if it actually exists.

This was actually a bit more of a problem around the reading of the container id file. Regardless, both were fixed in f56b714.


Support cal::date_duration

fixes https://github.com/edgedb/edgedb-go/issues/230

depends on https://github.com/edgedb/edgedb-go/pull/221

@elprans when you have a moment would you review this?


⚠ Bofrost.at has degraded performance

In 088591c, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1596 ms

Resolved: Bofrost.at performance has improved in 91e84de.


CHAOS hotfix: Removes FF note

This is for the chaos 0.14.0 release

Please check the Execution Link of the Pipeline for the Website Draft URL. This is located in the Preview Step and also is available in #hdh_alerts. E.g Website Draft URL: https://unique-id--harness-developer.netlify.app

This change will part of a different PR.


The operator tries to contact unrelated pods

When the ActiveMQArtemisAddress CR is created before ActiveMQArtemis CR, the operator tries to contact unrelated pods:
Steps:

Deploy cluster wide operator
Create AMQAddress ex-aao-address
See logs for following message:

2023-08-21T13:25:08.338Z	ERROR	Pod IsNotFound	{"Request.Namespace": "71149", "Request.Name": "ex-aaoaddress", "Namespace": "71149", "Name": "ex-aaoaddress", "error": "Pod \"alertmanager-main-0\" not found"}

When the pod doesn't exist the Controller Runtime Client return an error that points to an unrelated pod, see https://github.com/artemiscloud/activemq-artemis-operator/blob/v1.0.15/pkg/utils/jolokia_client/jolokia_client.go#L85

The fix will be included in 1.0.16


[QUERY] Storage: Exception while copying blob

Library name and version
Azure.Storage.Blobs 12.10.0
Query/Question
I have the requirement to copy the file from an URI to my azure storage account. The file can be in another azure storage account or can be anywhere, i just have the link to it and no other information.
I am trying to use StartCopyFromUriAsync function from BlobClient object to upload a file to my azure storage account.
I have noticed that randomly my copy operation will fail.
Mostly whenever i get an error it is below(8 out of 10 times)
Error: System.InvalidOperationException: The operation has not completed yet.
Some times I get this error also(2 out of 10 times)
Error: Azure.RequestFailedException: Forbidden ErrorCode: CannotVerifyCopySource
Here is my code
CopyFromUriOperation operation = await this.blobServiceClient.GetBlobContainerClient("Container").GetBlobClient("fileName").StartCopyFromUriAsync("urlOfTheNewBlob");

await operation.WaitForCompletionAsync();

if (operation.HasCompleted)
{
    //do stuff
}

The weird thing is that if I try, sometime it succeeds. Sometimes I have to retry 2-3 times.
Environment
I am using azure function v3. Azure sdk version is azurefunctions: <IP_ADDRESS>

Thank you @Shivam60 ,We are checking on this error if this is intermittent or not, we will keep you posted.

As per the offline conversation the below error looks like related to access issue.
Error: Azure.RequestFailedException: Forbidden RequestId: Time:2022-01-12T19:00:05.1483054Z Status: 403 (Forbidden) ErrorCode: CannotVerifyCopySource
I was able to reproduce the issue due to public access not being enabled on the source container.
[2022-01-12T19:42:26.131Z] Executed 'Function1' (Failed, Id=ac3f4d1e-bb29-430d-b4cc-33bb016d1bbb, Duration=2109ms)
[2022-01-12T19:42:26.134Z] System.Private.CoreLib: Exception while executing: Azure.Storage.Blobs: Public access is not permitted on this storage account.
RequestId:5b0b8a03-c01e-002b-46ec-075b69000000
Time:2022-01-12T19:42:24.9424324Z
[2022-01-12T19:42:26.137Z] Status: 409 (Public access is not permitted on this storage account.)
[2022-01-12T19:42:26.138Z] ErrorCode: CannotVerifyCopySource
[2022-01-12T19:42:26.139Z]
Once the public access was given, I was able to run the command! May be we should try with Storage account which has public access enabled, please do let us know if the issue still exists when trying with another storage account? would be able to help further!

Thanks @SatishBoddu-MSFT
This is indeed an issue at my end. Thanks for helping me


WIP:  Modified test infra to run integration test in helm3

Modify ItUsabilityOperatorHelmChart
a) to support Helm 3.0. Few use cases were failing as the Exception description is different in Helm 2.0 and Helm 3.0. Need to change the expected exception String to a common string to support both Helm2/Helm3
b) Removed Duplicate Usecase
c) Removed commented Tests which can not be run on the parallel mode
Modified setupenv.sh to exclude tiller set up in case of Helm 3.0
Modified  sample/charts/util/setup.sh to modify logic verify pre-existing Chart
Modified LoadBalancer.java to check the logic to check helm version and added --debug option
External Jenkin ( quicktest cluster )  All passed
https://build.weblogick8s.org:8443/job/weblogic-kubernetes-operator-quicktest/1318/
Cluster 6 ( with helm 3 )
https://build.weblogick8s.org:8443/job/weblogic-kubernetes-operator-integration-test-cluster-6/125/

Comment on the PR description... I still don't want to support Helm 2 & 3.  The description mentions a common set of exception strings so that we can support both versions of Helm.  We are explicitly dropping support for Helm 2 with the 3.0.0 operator version because the industry now regards the use of a "Tiller" pod as unsafe.

This PR is so much better... Just a few questions.  I think the only substantive item is that I'd like to not assert on particular error messages as this is likely brittle.


Chart does not show (clear)(sync) buttons - 1.5.48

Difficult to reproduce. After problem occurs its difficult to get buttons back!
Watching very carefully when switching from details then back to chart the buttons appear briefly but then seem to be over rotten by graphs.
Only 2 sensors known (others removed earlier)

Most likely this happens when you use this sensor in iOS app with Keep the Connection toggle on. While iPhone is keeping connection we can't get history from sensor.
This video illustrates this behavior:
https://user-images.githubusercontent.com/24788772/142232630-031ce851-8e64-4fb7-bdfa-020ddcea5f9e.mp4


Update DeadlyReentry netkan to point at currently-active fork

Well, currently active not-a-fork, since it's actually the head repo. :D

Ugh I shoulda branched, you should squash this on merge I guess, sorry!

Thanks for the update!

Apparently the previous fork wasn't actually abandoned. Lovely.
https://forum.kerbalspaceprogram.com/index.php?/topic/50296-112-deadly-reentry-v782-the-barbie-edition-aug-5th-2021/&do=findComment&comment=4015220

I will be interested to see whether any actual development occurs.

Well there's already a new release:
https://github.com/Starwaster/DeadlyReentry/releases/tag/v7.8.2

Oh dear. This is what I get for working PST hours, I have not been following.


frame rates

Hi,
What frame rates are you experiencing with deeplabV3 using a webcam on a coral edge tpu?

With PiCamera + Raspberry Pi 4 + Edge TPU, it is about 5.5 FPS.
The following sample.

https://github.com/NobuoTsukamoto/edge_tpu/tree/master/deeplab/cpp/transparent
Youtube link: https://www.youtube.com/watch?v=gZxDs8-sA8c

For your reference.
I posted a benchmark on Raspberry Pi 3 + Edge TPU on my blog.(It's in Japanese)
https://nextremer-nbo.blogspot.com/2019/10/edge-tpudeeplabv3september-2019-updates.html

Close the issue. If you have any problems, please open it again.

Close the issue. If you have any problems, please open it again.


Multi-GPU training

Hi Kevin,
Thanks for the great work and releasing the codes/models. Was wondering if you have tried multi-GPU training for ELECTRA-base and ELECTRA-large (does your current codes support multi-GPU)? And if you have stats for multi-GPU experiments as well?
Also the stats for single GPU training of ELECTRA-base and ELECTRA-large (how many days needed till they converge to a descent performance?).
Thanks!
-Hamid

I've tried the current starter's code for pretraining a small network. It seems like the model is trained on a single GPU.

Yes. It is working on a single GPU. Looking for multi-gpu support.

Gentle follow up Kevin, any thoughts?
Thanks,
-Hamid

Is there any plans for multi-gpu support @clarkkev

Hope to support multiple GPU and provide detailed configuration. @clarkkev

@008karan @Palang2014 How are you getting the model to run on a GPU? Even with a GPU available, I'm only able to run on CPU. Mostly interested in running the fine-tuning, not the pre-training.

@008karan @Palang2014 How are you getting the model to run on a GPU? Even with a GPU available, I'm only able to run on CPU. Mostly interested in running the fine-tuning, not the pre-training.

I had the same issue and I realised it was because the program could not find the cuda libraries. Check if you get messages like
"Successfully opened dynamic library libcudnn.so.7"
If not, or if you see errors saying it couldn't find some cuda libraries, maybe you have the same problem?


Where are the Scheme communities and enthusiasts?

As we move towards the launch of the new version of Exercism we are going to be ramping up on actively recruiting people to help provide feedback.
Our goal is to get to 100%: everyone who submits a solution and wants feedback should get feedback. Good feedback. You can read more about this aspect of the new site here: http://mentoring.exercism.io/
To do this, we're going to need a lot more information about where we can find language enthusiasts.

Is Scheme supported by one or more large organizations?
Does Scheme have an official community manager?
Do you know of specific communities (online or offline) that are enthusiastic about Scheme? (Chat communities, forums, meetups, student clubs, etc)
Are there popular conferences for Scheme? (If so, what are some examples?)
Are there any organizations who are targeted specifically at getting certain subgroups or demographics interested in Scheme? (e.g. kids, teenagers, career changers, people belonging to various groups that are typically underrepresented in tech?)
Are there specific groups or programs dedicated to mentoring people in Scheme?
Are there popular newsletters for Scheme?
Is Scheme taught at programming bootcamps? (If so, what are some examples?)
Is Scheme taught at universities? (If so, what are some examples?)

In other words: where do people care a lot and/or know a lot about Scheme?
This is part of the project being tracked in https://github.com/exercism/meta/issues/103

Is Scheme supported by one or more large organizations?
It depends on what you mean by "support".
Some time ago, Cisco purchased Cadence, the developer of the top quality Scheme implementation called Chez. Since then, they released the compiler to the open source.
Microsoft recently also released a low footprint implementation of Scheme for the .NET platform called Schemy.
Does Scheme have an official community manager?
It's a complex issue. The Scheme community isn't just a community of language users, but also a community of language implementors. The development of Scheme proceeds in a highly democratic fashion. The development of the subsequent Scheme standards is entirely community-driven, and the extension proposals (Scheme Request for Implementation or SRFI need to pass a formal review process.
The current role of SRFI editor is played by Arthur Gleckler, and the person who has been driving the most recent Scheme standard (R7RS) is John Cowan.
Note however, that the people who play these roles have been changing historically.
Do you know of specific communities (online or offline) that are enthusiastic about Scheme? (Chat communities, forums, meetups, student clubs, etc)
schemers.org is probably the most centralized resource for the diverse Scheme community. There are also vivid communities around various particular implementations such as Racket, Chicken, Guile, Gambit and many others.
There is also comp.lang.scheme news group on usenet and a reddit room.
Some meetups are pointed to by schemers.org, but I don't think that the list is updated very often.
Are there popular conferences for Scheme? (If so, what are some examples?)
The most important one is Scheme Workshop, which is held annually with ICFP. Note however, that the word "intimate" describes it better than "popular", especially if you compare it with conferences devoted to languages like Python or C++.
Are there any organizations who are targeted specifically at getting certain subgroups or demographics interested in Scheme? (e.g. kids, teenagers, career changers, people belonging to various groups that are typically underrepresented in tech?)
There is Bootstrap which is targeted mainly at kids.
Are there specific groups or programs dedicated to mentoring people in Scheme?
Not that I know of. But most Schemers I know are really kind and helpful. I've seen some people devoting their time to answer Scheme-related questions on Stack Overflow.
Are there popular newsletters for Scheme?
I don't think so.
Is Scheme taught at programming bootcamps? (If so, what are some examples?)
All the bootcamps I'm familiar with focus on teaching technologies that are useful for jobs for which there is a high demand on the market - which in my experience mainly means web-related things like JavaScript, HTML, CSS or SQL, and frameworks like ReactJS. While JavaScript is a cluttered derivative of Scheme, it seems that teaching Scheme in such short-sighted contexts would be an expensive luxury.
Is Scheme taught at universities? (If so, what are some examples?)
Yes. Scheme has been used for many years by MIT in their introductory Computer Science course.
Currently it is also a significant part of the curricula of Northeastern, Brown, Indiana and WPI, among others.

@panicz Thank you so much, this is incredibly helpful!
I'm going to close this, as I think we've got what we need. 💙

There are also some Scheme fans on Quora and Twitter.
It's easy to find them on Quora in particular:
https://www.quora.com/topic/Scheme-programming-language-1/writers
As to Twitter, I can recommend the following accounts:
https://twitter.com/racketlang
https://twitter.com/guilelang
https://twitter.com/alamajesse
https://twitter.com/ShriramKMurthi
https://twitter.com/lambda_calculus
https://twitter.com/mattmight
https://twitter.com/webyrd
https://twitter.com/schemeworkshop
https://twitter.com/nadamin
https://twitter.com/sperbsen
https://twitter.com/andywingo
https://twitter.com/dustyweb
https://twitter.com/dfried00
https://twitter.com/mwand
https://twitter.com/lexi_lambda
https://twitter.com/samth

That's a great find, thank you.


Can't access network drives

Describe the bug
The app crashes when trying to open network drives.
To Reproduce
Steps to reproduce the behavior:

Open a new tab
Change the path from 'Home' to a network drive path

Expected behavior
As in the default file explorer, the network drive should be opened and its contents should be visible.
Desktop (please complete the following information):

OS: Windows 10 1909
App version: <IP_ADDRESS>

Log file
2020-11-08 16:39:51.6526|ERROR|Files.App|Invalid URI: The format of the URI could not be determined.|System.UriFormatException: Invalid URI: The format of the URI could not be determined.
   at SharedLibrary!<BaseAddress>+0xafcaa0
   at System.Uri..ctor(String) + 0x17
   at Files.Helpers.PathNormalization.NormalizePath(String) + 0xea
   at Files.UserControls.HorizontalMultitaskingControl.<SetSelectedTabInfo>d__10.MoveNext() + 0x65b

@Steve01010 thanks for this report! Could you post here the path you were trying to open?

for example, on windows file explorer, i see a network pane on the left sidebar... and i can click on any of the network drives
i can also type in the name of a network volume, for example, //HOME_NAS, and it will open and display the contents
the same behavior crashes this application and throws the invalid path error, which i believe may be due to a lack of implementation of a feature to detect network drives and network drive paths

Thanks @Steve01010 a fix for this issue will be included in version 0.20.0
The fix will allow you to navigate to path like \\DESKTOP-XXXX\Shared\SomePath


Fix redirects

Describe the bug
https://techqueria.netlify.com and https://beta.techqueria.org do not redirect to https://techqueria.org right now
Additional Context
This may because of how the domain is set up right now but I'm not 100% sure

This is being fixed in #202

Looks like that didn't work, we can move to managed DNS at netlify on a low visiting weekend that we decide on.

Gracias @dvidsilva for verifying this - how about this upcoming weekend or next weekend? I have bandwidth to help with this migration. Let me know what you think here or in Slack! 🙇♀

@fvcproductions  The migration takes a second on the config side, but it might take down the website, email, and any service for a bit. Anything from 1 hour to 48. I can get it done whenever; but is better if done in a time where we don't expect a lot of visits or emails or so.

@dvidsilva Does November 21st work?

@fvcproductions sure


update the tone service URL value

for watson tone URL... had to debug to realize https:// is a must else the analyzer will fail.

@beemarie PTAL
cc @duglin @rvennam

LGTM

@beemarie copy works for me too.  I don't know how the kubecon content will be merged back that is why i submitted it here first.


Dockerfile update to accommodate new use cases

The following docker file updates are in preparation for https://github.com/lasp/adamant/pull/38 merge and upcoming VSCode support.

Updates look good to me. I have verified the user mod works well with VS Code.


Create basecamp3applesilicon.sh

This label is for Basecamp 3 for Apple Silicon systems. The current label "basecamp3" is the intel installer.

Connected to bc3-desktop.s3.amazonaws.com (<IP_ADDRESS>) port 443
ALPN: curl offers h2,http/1.1
(304) (OUT), TLS handshake, Client hello (1):
} [333 bytes data]
CAfile: /etc/ssl/cert.pem
CApath: none
(304) (IN), TLS handshake, Server hello (2):
{ [106 bytes data]
TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4969 bytes data]
TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
TLSv1.2 (OUT), TLS change cipher, Change cipher spec (1):
} [1 bytes data]
TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
TLSv1.2 (IN), TLS change cipher, Change cipher spec (1):
{ [1 bytes data]
TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
ALPN: server accepted http/1.1
Server certificate:
subject: CN=*.s3.amazonaws.com
start date: Oct 10 00:00:00 2023 GMT
expire date: Jul  3 23:59:59 2024 GMT
subjectAltName: host "bc3-desktop.s3.amazonaws.com" matched cert's "*.s3.amazonaws.com"
issuer: C=US; O=Amazon; CN=Amazon RSA 2048 M01
SSL certificate verify ok.
using HTTP/1.1

GET /mac_arm64/basecamp3_arm64.dmg HTTP/1.1
Host: bc3-desktop.s3.amazonaws.com
User-Agent: curl/8.4.0
Accept: /

< HTTP/1.1 200 OK
< x-amz-id-2: 5XBq0eknPu+KLpX31wAlc8UXmEnetiU4PeYD82dg7cfdghfiXm5y4/GwHVCoXH+RJ2GAkY21R1Vi+eEikguxRQ== < x-amz-request-id: 6E4FFQNTAFMG4QVN
< Date: Mon, 25 Mar 2024 14:46:19 GMT
< Last-Modified: Fri, 22 Sep 2023 13:04:24 GMT
< ETag: "08ff7fc079f73017775ac746fa196b34"
< x-amz-server-side-encryption: AES256
< x-amz-version-id: 0kJiLS4xpTxpZsuGnbRfN3_qxccsMFaK < Accept-Ranges: bytes
< Content-Type: application/x-apple-diskimage
< Server: AmazonS3
< Content-Length: 91727114
<
{ [15791 bytes data]

Connection #0 to host bc3-desktop.s3.amazonaws.com left intact

2024-03-25 09:46:28 : REQ   : basecamp3applesilicon : no more blocking processes, continue with update
2024-03-25 09:46:28 : REQ   : basecamp3applesilicon : Installing Basecamp 3
2024-03-25 09:46:28 : INFO  : basecamp3applesilicon : Mounting /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.K5sA0FEiFx/Basecamp 3.dmg
2024-03-25 09:46:34 : DEBUG : basecamp3applesilicon : Debugging enabled, dmgmount output was:
Checksumming Protective Master Boot Record (MBR : 0)…
Protective Master Boot Record (MBR :: verified   CRC32 $C34A8150
Checksumming GPT Header (Primary GPT Header : 1)…
GPT Header (Primary GPT Header : 1): verified   CRC32 $C9462BE1
Checksumming GPT Partition Data (Primary GPT Table : 2)…
GPT Partition Data (Primary GPT Tabl: verified   CRC32 $FE424713
Checksumming  (Apple_Free : 3)…
(Apple_Free : 3): verified   CRC32 $00000000
Checksumming disk image (Apple_HFS : 4)…
disk image (Apple_HFS : 4): verified   CRC32 $E395E400
Checksumming  (Apple_Free : 5)…
(Apple_Free : 5): verified   CRC32 $00000000
Checksumming GPT Partition Data (Backup GPT Table : 6)…
GPT Partition Data (Backup GPT Table: verified   CRC32 $FE424713
Checksumming GPT Header (Backup GPT Header : 7)…
GPT Header (Backup GPT Header : 7): verified   CRC32 $0DE1FF3B
verified   CRC32 $B161226F
/dev/disk4          	GUID_partition_scheme
/dev/disk4s1        	Apple_HFS                      	/Volumes/Basecamp 3
2024-03-25 09:46:34 : INFO  : basecamp3applesilicon : Mounted: /Volumes/Basecamp 3 2024-03-25 09:46:34 : INFO  : basecamp3applesilicon : Verifying: /Volumes/Basecamp 3/Basecamp 3.app 2024-03-25 09:46:34 : DEBUG : basecamp3applesilicon : App size: 214M	/Volumes/Basecamp 3/Basecamp 3.app 2024-03-25 09:46:35 : DEBUG : basecamp3applesilicon : Debugging enabled, App Verification output was: /Volumes/Basecamp 3/Basecamp 3.app: accepted
source=Notarized Developer ID
origin=Developer ID Application: Basecamp, LLC (2WNYUYRS7G)
2024-03-25 09:46:35 : INFO  : basecamp3applesilicon : Team ID matching: 2WNYUYRS7G (expected: 2WNYUYRS7G ) 2024-03-25 09:46:35 : INFO  : basecamp3applesilicon : Installing Basecamp 3 version 2.3.14 on versionKey CFBundleShortVersionString. 2024-03-25 09:46:35 : INFO  : basecamp3applesilicon : App has LSMinimumSystemVersion: 10.13 2024-03-25 09:46:35 : INFO  : basecamp3applesilicon : Copy /Volumes/Basecamp 3/Basecamp 3.app to /Applications 2024-03-25 09:46:36 : DEBUG : basecamp3applesilicon : Debugging enabled, App copy output was: Copying /Volumes/Basecamp 3/Basecamp 3.app
2024-03-25 09:46:36 : WARN  : basecamp3applesilicon : Changing owner to danny 2024-03-25 09:46:36 : INFO  : basecamp3applesilicon : Finishing... 2024-03-25 09:46:39 : INFO  : basecamp3applesilicon : App(s) found: /Applications/Basecamp 3.app 2024-03-25 09:46:39 : INFO  : basecamp3applesilicon : found app at /Applications/Basecamp 3.app, version 2.3.14, on versionKey CFBundleShortVersionString
2024-03-25 09:46:39 : REQ   : basecamp3applesilicon : Installed Basecamp 3, version 2.3.14
2024-03-25 09:46:39 : INFO  : basecamp3applesilicon : notifying
ERROR: Notifications are not allowed for this application
2024-03-25 09:46:39 : DEBUG : basecamp3applesilicon : Unmounting /Volumes/Basecamp 3
2024-03-25 09:46:40 : DEBUG : basecamp3applesilicon : Debugging enabled, Unmounting output was:
"disk4" ejected.
2024-03-25 09:46:40 : DEBUG : basecamp3applesilicon : Deleting /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.K5sA0FEiFx
2024-03-25 09:46:40 : DEBUG : basecamp3applesilicon : Debugging enabled, Deleting tmpDir output was:
/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.K5sA0FEiFx/Basecamp 3.dmg
2024-03-25 09:46:40 : DEBUG : basecamp3applesilicon : /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.K5sA0FEiFx
2024-03-25 09:46:40 : INFO  : basecamp3applesilicon : Installomator did not close any apps, so no need to reopen any apps.
2024-03-25 09:46:40 : REQ   : basecamp3applesilicon : All done!
2024-03-25 09:46:40 : REQ   : basecamp3applesilicon : ################## End Installomator, exit code 0

Is there a reason you did not put the apple silicon installer in the same label as the intel one?
There are plenty of examples of labels that download a different version depending on architecture

Hey Armin,
My bad there, didn’t realize there are dynamic labels- I’ll fix and re-submit.
Thanks!
Danny Rosenthal
Jr. Systems Administrator
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On Mar 25, 2024, at 10:46 AM, Armin Briegel @.***> wrote:
Is there a reason you did not put the apple silicon installer in the same label as the intel one?
There are plenty of examples of labels that download a different version depending on architecture
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replaced by #1565


Dependency graph: Dependency submission API (Public Beta)

The dependency graph today uses manifest parsing to understand the set of dependencies in a repository. This approach has some shortcomings: we can't easily support complex dependency systems which use executable code in the build to resolve dependencies (like Gradle), and users of an ecosystem need to wait for GitHub to add support for it.
The dependency submission API will allow users to upload details of their dependencies directly, via an API request. It will be designed to work with the output of build tools and package managers. The dependency graph will store this data and, if an ecosystem is supported in the advisory database, GitHub will send alerts if/when a vulnerable dependency is present.
This release will be a public beta.

🚢 This has shipped: https://github.blog/changelog/2022-06-17-dependency-graph-has-a-rest-api-for-submitting-dependencies-detected-at-build-time/


fix: updating python package version and CI improvements

:tada: This PR is included in version 5.0.16 :tada:
The release is available on:

v5.0.16
GitHub release

Your semantic-release bot :package::rocket:


Update transifex CLI version

Transifex has deprecated its old CLI, this PR install the new CLI  into the docker image

Tests seems failing, i need to check the new arguments.


swagger link and related updates

swagger link added to the template
version added to the model and related tests are updated

@dontseyit I've added a temporary fix for the tags, I'm not sure when we'll actually conclude this discussion - also, the old tags will remain on dockerhub I guess.


tensorboard 执行中没有载入

执行中没有载入，无法测试训练的模型是不是符合自己的要求，
跑到20000了出来的结果还是让人失望，还有继续程序执行，但也不知道是训练过头了还是还要继续执行训练！
还有日志信息显示错误是由于多进程训练时日志模块试图向已经关闭的管道写入日志，导致报错，这个问题如何解决？

Without knowing what the quantity or quality of dataset is used it is hard to tell what quality of results should be expected. I cannot provide very much guidance on this as I personally have not completed any training using the Colab notebook. It would be helpful if you could provide the full log and traceback for the problem you encounter


How to develop against VirtualDesktop-OpenXR (i.e. connect an IDE launched application to it)

When I'm developing against SteamVR my workflow is as follows:

Connect to virtual desktop
Start SteamVR from the virtual desktop. It launches into a waiting state (void with mountains)
Start my application from within the IDE (it connects to the already running SteamVR runtime; my application takes over and replaces the waiting state).

What would be the equivalent of that with VirtualDesktop-OpenXR? In particular how do I get it in a running and waiting state? I think the instructions imply it will be launched along with the application when the OpenXR Runtime is set to VDXR but I don't think that will work when Virtual Desktop is unaware my application exists and I'm going to be launching it separately.
(I don't think it matters but my application is a Java OpenXR application launched from IntelliJ)

but I don't think that will work when Virtual Desktop is unaware my application exists

That won't matter actually. If you choose VDXR as OpenXR runtime the Virtual Desktop settings (or using the OpenXR runtime picker  of your choice), the runtime will be set system-wide. Any OpenXR application run in any way (even outside of the Virtual Desktop Games tab) will use it.

Hmm, I now realise it does actually behave differently when Virtual Desktop is connected in VDXR mode and not connected at all, so it is trying to talk to VDXR just an error occurs. Thanks!
OpenXR.log
When in VDXR mode the call XR10.xrEndFrame returns a nice super generic XR_ERROR_RUNTIME_FAILURE but the virtual desktop OpenXR logs are slightly more helpful
2024-03-12 17:57:33 +0000: VirtualDesktopXR - v1.0.2 (C:\Program Files\Virtual Desktop Streamer\OpenXR)
2024-03-12 17:57:33 +0000: Application: Tamarin OpenXR Example (java.exe); Engine:
2024-03-12 17:57:33 +0000: Requested extension: XR_KHR_opengl_enable
2024-03-12 17:57:33 +0000: Requested extension: XR_EXT_hand_tracking
2024-03-12 17:57:33 +0000: Using Virtual Desktop runtime
2024-03-12 17:57:33 +0000: Streamer: 1.30.1
2024-03-12 17:57:33 +0000: OVR: 1.64.0
2024-03-12 17:57:33 +0000: Device is: Oculus Quest2 (20)
2024-03-12 17:57:33 +0000: Using OpenGL on adapter: NVIDIA GeForce RTX 3070 Laptop GPU
2024-03-12 17:57:33 +0000: Recommended resolution: 2016x2112
2024-03-12 17:57:34 +0000: xrEndFrame: OpenGL error: 0x502
    Origin: error == GL_NO_ERROR
    Source: D:\a\VirtualDesktop-OpenXR\VirtualDesktop-OpenXR\virtualdesktop-openxr\utils.h:350
2024-03-12 17:57:34 +0000: xrEndFrame failed with XR_ERROR_RUNTIME_FAILURE

Not really sure what that means although I have had problems before with SteamVR being more permissive of technically wrong things than other runtimes.
This is the call (in the Tamarin library) that upsets it
        checkResponseCode(XR10.xrEndFrame(
                xrSession,
                XrFrameEndInfo.malloc(stack)
                        .type$Default()
                        .next(NULL)
                        .displayTime(continuation.getPredictedDisplayTime())
                        .environmentBlendMode(xrSettings.getXrVrMode().getXrValue())
                        .layers(didRender ? layers : null)
                        .layerCount(didRender ? layers.remaining() : 0)
        ));

OpenGL support isn't very well tested. 0x502 is GL_INVALID_OPERATION, which could be a few things. It's probably easier to send me the app (even compiled) to investigate.

Actually - could you try using Virtual Desktop Beta (1.30.3)? It has a fix for an OpenGL issue that might be the same you are having. You can find instructions in the Virtual Desktop Discord.

Nice! The 1.30.3 beta boots up correctly! Thank you
(Although I notice that the hand bone positions aren't quite right; not wildly wrong, just different to what steamVR produces; although I realise I'm assuming that SteamVR is correct here maybe I should just say different, not wrong. Is that a known difference)
The app I'm using to test is https://github.com/oneMillionWorlds/TamarinTestBed incidentally, a basic test application for Tamarin & jMonkeyEngine based VR. Although I suspect it won't matter now the openGL issue is sorted

Incidentally I really like the lightweightness of VDXR. The way SteamVR would boot into home (which seems to be really resource intensive and revs up my fans to maximum) was really annoying for development.  I think VDXR's hands off approach is much better.


"could not normalize versions"

We're moving from many SBT projects to a single monorepo with Bazel. I'm in the midst of trying to figure out our dependencies.
We have versionConflictPolicy: fixed.
I'm getting the following message:
[ERROR] could not normalize versions:
io.netty:netty: Version(3.6.6.Final), Version(3.7.0.Final), Version(3.10.1.Final)
(snip)

I've tried fixing the netty version with
dependencies:
  (snip)
  "io.netty":
    "netty":
      version: "3.10.1.Final"
      lang: "java"
  (snip)

However, I keep getting the version conflict.
I've made sure that there are no other io.netty dependencies declared anywhere else in dependencies.yaml.
Is this a bug or am I simply missing something?

It may just be a bug. Sorry I didn't see this till now. Can you share a minimal dependencies.yaml that shows the problem?

Sorry for not updating. The issue was simply that not all version conflicts listed was solved.
I.e. if three conflicts (A, B, C) are listed by the tool, and you fix A, the tool will still list (A, B, C) as unresolved.
I solved by adding some debugging so that I could see what transitive dependencies were not fixed. I also attempted to improve the error message, but I didn't find a clean way to transport that context to the right place.
--- a/src/scala/com/github/johnynek/bazel_deps/Normalizer.scala
+++ b/src/scala/com/github/johnynek/bazel_deps/Normalizer.scala
@@ -154,9 +154,13 @@ object Normalizer {
     unversioned: UnversionedCoordinate,
     rootVersion: Option[Version],
     duplicates: Set[Version],
-    opts: Options): Either[String, MavenCoordinate] =
+    opts: Options): Either[String, MavenCoordinate] = {
+      println(unversioned)
+      println("-" + rootVersion.toString)
+      println("-" + duplicates.toString)
       opts.getVersionConflictPolicy
         .resolve(rootVersion, duplicates)
         .right
         .map { v => MavenCoordinate(unversioned, v) }
+    }
 }

Does that answer your question or would you still like me to submit a repro?

Huh, I don't see how this applies to your example. You seem to have fixed to 3.10.1.Final which if you use the fixed I expect this to not give an error:
https://github.com/johnynek/bazel-deps/blob/master/src/scala/com/github/johnynek/bazel_deps/DepsModel.scala#L425
So, I would have thought in your example root was Some(3.10.1.Final) so why did you get any error at all?
We need more tests, sadly, I have skimpted because you generally know if the build is broken, but adding more tests is on the todo-list.

Yes, in my debug output rootVersion for netty would be `Some(3.10.1.Final)´, but it would still end up in the list of not normalized dependencies (the error message).
For other (also on the list) I would see rootVersion being None which meant I had to fixate that dependency then etc. One no dependencies needs fixing, the error message would disappear completely :)
I'll see if I can fix this properly in my fork. I'll submit a PR in that case.
For now, feel free to close this issue if you want to.

okay, yeah, I see it here it think: https://github.com/johnynek/bazel-deps/blob/master/src/scala/com/github/johnynek/bazel_deps/Normalizer.scala#L19
when we errorize a Table we stop where we are (we don't try to minimize, and we discard the error message). Then, we either totally normalize, or completely fail to normalize printing all duplicates:
https://github.com/johnynek/bazel-deps/blob/master/src/scala/com/github/johnynek/bazel_deps/MakeDeps.scala#L23
So, we need to not return an Option but something like Either[List[Conflicts], T] and give a better error message.


StatsD metric exporter

Is your feature request related to a problem? Please describe.
I want to export metrics via StatsD, a common protocol used for many backends including Graphite.
Describe the solution you'd like
StatsD exporter.
Describe alternatives you've considered

Additional context

https://github.com/open-telemetry/opentelemetry-specification/issues/374 should be of interest:

The reason we can't do this is that statsd (and dogstatsd) do not have a formal specification.

We will not pursue a statsd implementation until there is a specification to follow. Let's revisit this discussion when there is a specification to follow.

It's still true that there's no statsd spec, although at least one document in the OTel org describes it now:
https://github.com/open-telemetry/opentelemetry-collector-contrib/blob/master/receiver/statsdreceiver/README.md
Most systems that support statsd also support other formats, which is part of the reason that we haven't included statsd in the OTel specification.
That said, it's a very useful protocol that can be implemented with few dependencies and people like it for that reason. I am supportive of including statsd exporters, e.g., https://github.com/open-telemetry/opentelemetry-go-contrib/tree/master/exporters/metric/dogstatsd

I think we should add it to the contrib repo. It can be upgraded to main repo when the spec includes it.

And FYI, there is already a Node.js StatsD client (node-statsd).

And FYI, there is already a mature Node.js StatsD client (node-statsd).

FWIW https://github.com/brightcove/hot-shots is also a good one

Any updates on this issue?


Refactored the DoublyLinkedList script

Generalized it to be non specific to rooms
Improved nomenclature
Relocated to the 'Utilities' folder

closed #78
closed #79

This looks really good. Kind of hard to test since it's not used anywhere in the codebase, but might be nice to have in our back pocket. Good job on this. :smile:


Numpy2 Support

Issue Description
The last merge to master failed due to numpy2 being installed and we have a lot of dependencies that cannot deal with it.
These are the packages that pinned the numpy version below 2 (reproducible by installing numpy2 on a venv where one installed shap before):
tensorflow 2.16.1 requires numpy<2.0.0,>=1.23.5; python_version <= "3.11", but you have numpy 2.0.0 which is incompatible.
scipy 1.12.0 requires numpy<1.29.0,>=1.22.4, but you have numpy 2.0.0 which is incompatible.
scikit-learn 1.4.1.post1 requires numpy<2.0,>=1.19.5, but you have numpy 2.0.0 which is incompatible.
pandas 2.2.1 requires numpy<2,>=1.22.4; python_version < "3.11", but you have numpy 2.0.0 which is incompatible.
numba 0.59.0 requires numpy<1.27,>=1.22, but you have numpy 2.0.0 which is incompatible.

So this is a tracker of all packages we'll wait for in order to support numpy2:

[ ] tensorflow
[x] scipy
[x] sklearn
[x] pandas
[x] numba

see this pipeline: https://github.com/shap/shap/actions/runs/9619331932/job/26535218641
EDIT: Our problems might be bigger than I first thought. It's not just the dependencies but two more things:

[x] merge PR #3704 (check that the newly used function exists on previous numpy version before)
[ ] It seems like the <numpy/arrayobject.h> is no longer there, see: https://github.com/shap/shap/actions/runs/9602964617/job/26556244608?pr=3704#step:8:381. We potentially need to rewrite the c code

EDIT2: as a first step I would restrict shap to numpy < 2, so:

[ ] merge #3708

Thanks for looking at this - agreed, it looks like a show-stopper at the moment.
I saw numpy created a migration guide which could be useful, including things like a new Ruff linter rule to help compatibility.
https://numpy.org/doc/stable/numpy_2_0_migration_guide.html#numpy-2-migration-guide
The C ABI compatibility break looks like a bigger deal though, so yes let's stabilise the current CI by pinning numpy. It might help to make a release that contains the new version pin to numpy 1.X, to avoid broken downstream builds?

There's an overview page of which libraries already support NumPy 2.0: https://github.com/numpy/numpy/issues/26191
According to this, scipy>=1.13.0, pandas >= 2.2.2 and numba >= 0.6.0 are already updated, while tensorflow might take a while. sklearn isn't listed there, but they started to build against the NumPy nightlies in November 2023, so current versions should work fine.

Just about to comment the same actually:
Numpy has a tracker here which shows the broader ecosystem compatibility with numpy 2.0.
https://github.com/numpy/numpy/issues/26191
I noticed that most of the libraries above (scipy, scikit-learn, pandas, numba) do support numpy 2.0 on recent releases.

I created a PR for the purpose of running tests against numpy 2.0. This might help us track down any other incompatibilities:
#3712

I noticed that we sometimes resolve incompatible versions of numpy and tensorflow, as older versions of tensorflow are missing the required upper bound pin on numpy.
Tensorflow doesn't yet support numpy 2.x, pending https://github.com/tensorflow/tensorflow/issues/67291 .
However, tensorflow only introduced an upper bound on numpy<2 in tensorflow 2.15. tensorflow 2.14
misses that upper bound, so we get a broken install with tensorflow 2.14 , numpy 2.
This is not really an issue with shap, but it can lead to broken builds in our CI pipeline.

Tensorflow has added support for numpy 2. However, we're still waiting for catboost and ngboost, as tracked on #3922.


Charts updates to add global labels

This PR updates the following charts to add global labels to the resources deployed within the chart

charts/snowplow-iglu-server
charts/priority-class
charts/daemonset
charts/cron-job
charts/cluster-warmer

Good call @jparavisini . I've made some updates to account for trailing whitespace Have run them through helm template with and without passing labels
Example with priority-class
➜ helm template priority-class priority-class
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: critical
  labels:
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: Critical priority pods that preempt all other priority classes.
globalDefault: false
preemptionPolicy: PreemptLowerPriority
value: 1e+06
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: high
  labels:
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: High priority pods that preempt medium and low tier priority classes.
globalDefault: false
preemptionPolicy: PreemptLowerPriority
value: 900000
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: medium
  labels:
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: Medium priority pods that preempt low tier priority classes. The default for services.
globalDefault: true
preemptionPolicy: PreemptLowerPriority
value: 500000
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: low
  labels:
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: Low priority pods.
globalDefault: false
preemptionPolicy: Never
value: 100000

and with setting labels
➜ helm template priority-class priority-class --set labels.app=my-app --set labels.environment=production
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: critical
  labels:
    app: my-app
    environment: production
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: Critical priority pods that preempt all other priority classes.
globalDefault: false
preemptionPolicy: PreemptLowerPriority
value: 1e+06
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: high
  labels:
    app: my-app
    environment: production
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: High priority pods that preempt medium and low tier priority classes.
globalDefault: false
preemptionPolicy: PreemptLowerPriority
value: 900000
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: medium
  labels:
    app: my-app
    environment: production
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: Medium priority pods that preempt low tier priority classes. The default for services.
globalDefault: true
preemptionPolicy: PreemptLowerPriority
value: 500000
---
# Source: priority-class/templates/priority-class.yaml
apiVersion: scheduling.k8s.io/v1
kind: PriorityClass
metadata:
  name: low
  labels:
    app: my-app
    environment: production
    helm.sh/chart: priority-class-0.2.0
    app.kubernetes.io/name: priority-class
    app.kubernetes.io/instance: priority-class
    app.kubernetes.io/managed-by: Helm
description: Low priority pods.
globalDefault: false
preemptionPolicy: Never
value: 100000


fMRIPrep preprocessing problem

What happened?
Hi, I'm very new to fmriprep. I followed a tutorial to have it installed with docker and then after running in my BIDS data, but I got errors, even if I have tried many times. Thank you!
What command did you use?
fmriprep-docker ./Nifiti ./Nifiti/derivatives participant --dummy-scans 1 --fs-no-reconall --fs-license-file ./license.txt -w .
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=26.1.4 -it -v /mnt/e/VerbalFluenc/license.txt:/opt/freesurfer/license.txt:ro -v /mnt/e/VerbalFluenc/Nifiti:/data:ro -v /mnt/e/VerbalFluenc/Nifiti/derivatives:/out -v /mnt/e/VerbalFluenc:/scratch nipreps/fmriprep:24.0.0 /data /out participant --dummy-scans 1 --fs-no-reconall -w /scratch

What version of fMRIPrep are you running?
24.0.0
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
[Node] Finished "conf_plot", elapsed time 2.935544s.
240705-08:24:24,889 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_04_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,908 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_01_wf.anat_fit_wf.fast
240705-08:24:24,921 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_05_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,925 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_06_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,929 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_08_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,933 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_07_wf.anat_fit_wf.fast
240705-08:24:24,937 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_02_wf.anat_fit_wf.fast
240705-08:24:24,941 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_10_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,945 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_03_wf.anat_fit_wf.fast
240705-08:24:24,950 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_12_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,954 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_11_wf.anat_fit_wf.fast
240705-08:24:24,958 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_14_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,962 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_09_wf.anat_fit_wf.fast
240705-08:24:24,966 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_15_wf.anat_fit_wf.fast
240705-08:24:24,970 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_18_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,974 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_13_wf.anat_fit_wf.fast
240705-08:24:24,978 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_20_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,982 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_21_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,986 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_16_wf.anat_fit_wf.fast
240705-08:24:24,991 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_19_wf.anat_fit_wf.fast
240705-08:24:24,995 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_23_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
         could not run node: fmriprep_24_0_wf.sub_17_wf.anat_fit_wf.fast
240705-08:24:25,3 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_26_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:25,7 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_22_wf.anat_fit_wf.fast
240705-08:24:26,724 nipype.workflow CRITICAL:
         fMRIPrep failed: 24 raised. Re-raising first.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

Additional information / screenshots
No response

Unfortunately, there are no errors shown here. Can you provide the full logs?


BACKEND: create account page properly creates account

-create account page makes an new account
-create account page tells user if account already exists
-create account page will redirect to the login page if user is created successfully

chd63- I finished creating a new account and redirecting to the login page if user is successfully created
TODO: we need to let the user know if an account with that username already exists


flex/06-flex-layout: Improvement to mobile layout in solution

Complete the following REQUIRED checkboxes:

[x] I have thoroughly read and understand The Odin Project Contributing Guide
[x] The title of this issue follows the location for request: brief description of request format, e.g. Foundations exercises: Add exercise for XYZ

The following checkbox is OPTIONAL:

[x] I would like to be assigned this issue to work on it

1. Description of the Feature Request:

I would like to make things a little prettier in mobile view with a few lines of code change.
Current predefined CSS in solution.css (before solution portion) will yield a UI like this.

After CSS changes:

2. Acceptance Criteria:

@TheOdinProject/html-css
Can someone take a look please

@jwsoh07 it depends greatly on what your changes are.  Can you share what you're proposing?

@codyloyd hey again!
I only wanted to change 2 things.

The logo image to resize smaller in mobile view.
The text / search field to resize smaller in mobile view.

If you compare the 2 images above, you can see the size of the 2 mentioned items smaller in the 2nd image which looks a tad prettier.

We don't want to introduce media queries yet.. so I don't think we should worry about that on this one.

I actually did it using a min-width property like so (in the image).

I still think this is too advanced for students at this point.. almost none of them will come up with it on their own, and then they will be frustrated when they see it in the solution.

@codyloyd okay, I got you. We can close this 🙂


Create stale.yml

⚡ Deploying PR Preview c4c5a8f8a775286ed24c2478f043cd74f48d449a to surge.sh ... Build logs

🤖 By surge-preview


Locale/currency pair BG/USD crashes.

When the view is editing and the locale is set to "bg" Bulgarian and the currency is set to USD, the application crashes. This is because the currency code "щ.д." is interpreted as two dots, which is invalid, then the result is force unwrapped.
Thoughts 1: This is isolated to the “value -> number -> value” section in the commit(value:) method. One solution is therefore to always use the plain number format style in that section. No formatting asymmetry would be introduced with this solution.
Thoughts 2: It is not quite so simple, actually, because doing this results not in a crash but in a state where changes are invalid—also because of those two dots.

BG/USD should work as expected (without crashes) with: 4bbb9a330085aeb2a787c62685e71fcb1ee094ea.


Add Code4z as an option to the labs

Signed-off-by: Zeibura Kathau<EMAIL_ADDRESS>This is related to issue #119. I have added info on using Code4z to the beginning of the second lab.

cc @MikeBauerCA - can't add you as a reviewer.


CI doesn't find unused function args

CI does not seem to pick up unused function arguments.
I had two unused arguments to circuit_knitting.forging.efknitter._estimate_expvals in #307, and the style checks passed. The unused args have since been removed, but this should have been caught in CI.

I think ruff should catch this but checking now

I think ruff should catch this but checking now

If not, #146 should.


Show tutorial dialog for first-time players

When a player first plays the game, display a pop-up telling the user how to play the game. Use localStorage to determine the first time.
Also add a button or menu option that allows the user to see the tutorial dialog again after the "first time" display.

Refactor Dialog component for reusability. Props include:

body
positive (confirm) action and text
negative (cancel) action and text

Dialog component has been generalized here: https://github.com/johneastman/circles/commit/dbb6fad7d00c2c821f2137895c8cb7e5a52b162a.


add_top_1_dp

(Put an X inside the [ ] to denote check mark [X].)

[ ] If creating a new file :

[ ] added links to it in the README files ?
[ ] included tests with it ?
[ ] added description (overview of algorithm, time and space compleixty, and possible edge case) in docstrings ?

[ ] if done some changes :

[ ] wrote short description in the PR explaining what the changes do ?
[ ] Fixes #[issue number] if related to any issue

[ ] other

Pull Request Test Coverage Report for Build 743

1 of 12 (8.33%)  changed or added relevant lines in 1 file are covered.
1 unchanged line in 1 file lost coverage.
Overall coverage decreased (-0.1%) to 71.426%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

algorithms/arrays/top_1.py
1
12
8.33%

Files with Coverage Reduction
New Missed Lines
%

algorithms/linkedlist/is_palindrome.py
1
93.33%

Totals

Change from base Build 742:
-0.1%

Covered Lines:
4307

Relevant Lines:
6030

💛  - Coveralls

Hi! Sorry for late response. Can you please explain what your algorithm is doing and also rename it and save as some descriptive name with explainations? Thanks.

Hi, my algorithm is another solution to the arrays problem top 1, which
counting elements and updating the result during once iteration. Comparing with the available solution, I think it will be more efficient.

@edwardw1987 why did you close this PR?

Hi, Keno
It's superised to catch your message!
The project you launched is really cool and awesome.
I am a python developer who has been interested in algorithm, but I didn't find a right way to contribute code snippets. (my first pull request)
Sorry for the closing!


Remove hardcoded repo checkout for the repo opensearch-build

We have noticed a few places where the build repo link is hardcoded for checkout. E.g
https://github.com/opensearch-project/opensearch-build/blob/ff40ffba5e96836eaf8a3d70f0b4444bf6d2ef2b/vars/buildDockerImage.groovy
https://github.com/opensearch-project/opensearch-build/blob/9a82a23231cfa6f07bc4fa677b43795fbe8f49ff/vars/detectDockerAgent.groovy
Developers need to modify these values to their folked repo name and branch which is lowering the development efficient. These values shall read from the local workspace or as params.

cc @peterzhuamazon

[triage] We can take in the repository url and the branch as parameters and default to main if not provided for places where we checkout opensearch-build within libraries.

Apparently jenkins would pull git repo when pulling the jenkinsfile, so we can delete these git url calls once we confirm not needing them anymore.
Thanks.

This is nearly done except @zelinh whitesource scan, but that one is ok as it does not need to specify other versions.
@zelinh can decide whether want to change it or not.
Thanks.


Query rows should have 'display: flex'

I'm using a custom component for the valueEditor (a autocomplete from material ui)

And its causing a line break
The row component should be flex

Simply by changing to display: flex in the page i get this result

@Luifr have you tried using the code in the demo for Material UI components?  The components are here and you can see how they're used in the main.tsx file.  The demo doesn't have the line wrapping problem so it should be a good example.


Bug: The drag bar will always exist after the selected text is dragged and inserted in the windows 11

Step 1 Select the text and click the selected text to drag

Step 2: Put the text in another line and drag the bar will always

How to solve this problem

Hello!
Unfortunately they (@acywatson specifically) either no answer or straight away close the issues related to UI, even if it is about reference UI implementation right from the official docs.
I may help you but please note that there is some text was lost in your post after "Step 2: Put the text in another line and drag the bar will always (guess something was here) ".  so it hard to understand what was meant, so please correct the text

Hi @SGDS666! Could you please record a quick video? I'm having trouble reproducing the issue on my Mac and I'm not sure if it's a Windows-only bug. Thanks!

Unfortunately they (@acywatson specifically) either no answer or straight away close the issues related to UI, even if it is about reference UI implementation right from the official docs.

Please understand that they may not be comfortable interacting with someone who engages in personal attacks (@Alex-Github-Account specifically). Let's try to keep the discussion respectful and productive. Thank you. :)

Please understand that they may not be comfortable interacting with someone who engages in personal attacks (@Alex-Github-Account specifically). Let's try to keep the discussion respectful and productive. Thank you. :)

You imply that @acywatson is offended that when he send me to 'build you own text editor first' he got response that I've actually built, and first? thus he ditching the issues I am opening about (not even his) product?
FYI, I don't care. I usually have bugs already fixed (in my forks) by the time I open issues about them, so I could not care less.
Note I offered help here for somehone here because I already fixed floating-panel UI bug that seems related to this.
Thanks you for starting this interaction with me, but I don't see interest in interacting with you until it is offtopic, no offense.

你好@SGDS666！你能录制一个快速视频吗？我在我的 Mac 上重现该问题时遇到问题，我不确定它是否是仅限 Windows 的错误。谢谢！

I can be sure that this is a problem with Windows, because this is a problem tested by my colleague, and I also use the mac logic. The mac cannot drag the selected text after the selected text is boxed. Windows can, so it needs to be tested with Windows


Beautiful API

The current API can be improved. The version 2 should have something closer to the Leaflet API.

[ ] Sanitize user inputs
[ ] GeoJSON support
[ ] Separate documentation examples and unit tests

I think we should start by writing the documentation. If the documentation is hard to write, the API should be improved.
Feel free to edit the wiki page. However the page is currently empty. I will fill it slowly in the next months.

If you can put an example up on the wiki of how you would like the docs to be, I'd be glad to help fill them in.

:+1:

I'm thinking about an API providing input streams where the user can push GeoJson documents. I don't know if it's a good idea, but at least it's something :D


Add support for metrics collection and evaluation

Kraken-hub needs to support the metrics collection and evaluation features in Kraken to be able to capture metrics of interest from in-cluster prometheus and also evaluate them to determine pass/fail: https://github.com/cloud-bulldozer/kraken#scraping-and-storing-metrics-long-term and https://github.com/cloud-bulldozer/kraken#alerts.

Fixed by #34.


blast_orthofinder error

Hi,
when running zDB on 105 genomes like this:
zdb run --input="$(basename ${INPUT_TABLE})" \
        --name="<name>" \
        --out="${OUTPUT_DIR}" \
        --ref_dir="${ZDB_REF_DIR}" \
        --cpu="${THREADS}" \
        --mem=200GB \
        --ko --cog --pfam --vfdb --swissprot --amr \
        --singularity_dir="/dev/shm" \
        --resume &> "${LOG_DIR}/zdb_run.log"

, I end up getting the following error:
...
ERROR ~ Error executing process > 'blast_orthofinder (263)'

Caused by:

  Process `blast_orthofinder (263)` terminated with an error exit status (2)

Command executed:

  blastp -outfmt 6 -evalue 0.001 -query /.../work/59/7ac0b48e8598b3b7868cabf102bc27/OrthoFinder/Results_output/WorkingDirectory/Species51.fa -db /.../work/59/7ac0b48e8598b3b7868cabf102bc27/OrthoFinder/Results_output/WorkingDirectory/BlastDBSpecies10 -num_threads 1 > Results_output/WorkingDirectory/Blast51_10.txt

Command exit status:

  2

Command output:

  (empty)

Command error:

  INFO:    Converting SIF file to temporary sandbox...

  WARNING: Skipping mount /.../singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container

  BLAST Database error: CSeqDBAtlas::MapMmap: While mapping file [/.../work/59/7ac0b48e8598b3b7868cabf102bc27/OrthoFinder/Results_output/WorkingDirectory/BlastDBSpecies10.pin] with 0 bytes allocated, caught exception:

  NCBI C++ Exception:

      T0 "/opt/conda/conda-bld/blast_1537407096784/work/c++/src/corelib/ncbifile.cpp", line 5503: Error: ncbi::CMemoryFileMap::CMemoryFileMap() - To be memory mapped the file must exist: /.../work/59/7ac0b48e8598b3b7868cabf102bc27/OrthoFinder/Results_output/WorkingDirectory/BlastDBSpecies10.pin

  INFO:    Cleaning up image...

Work dir:

  /.../work/d9/2e161667c4c3a453af57bc5315350c

Container:

  /.../singularity/quay.io-biocontainers-orthofinder-2.5.2--0.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

I am unsure how do debug since the pin file is there and not empty after manually checking.
Also, even when using --resume it seems to rerun most of the steps, especially all the ~11k blast_orthofinder steps. Is this expected behavior?
Let me know if you need any more info.
Best
Oskar

The file is there but it does not get mounted into the singularity container. Did you by any chance set nextflow's workDir yourself to /.../work? Apptainer needs absolute paths to mount the files if I remember well, so here /.../work/59/7ac0b48e8598b3b7868cabf102bc27/OrthoFinder/Results_output/WorkingDirectory/BlastDBSpecies10.pin was not mounted.

Ah ok, I was confused. In that case I do not have any a priori idea why it's failing. I'll need to see whether I can reproduce the issue. Can you attache the .nextflow.log file (it might be one of the older ones .nextflow.log.1 or so)?
As to your question about the --resume option, this is passed directly to nextflow (as -resume) and that usually works well. I've just seen that for blast_orthifinder we use the each qualifier in the inputs of the process and I do not know whether that might break the resume. I'll need to test as well.

Ok.  I attached .nextflow.log, the stdout and the specific error log created. Not sure if the java error is a result of me killing the process.
I restarted again, but unfortunately, it seems to basically rerun everything again, as before. I attached the current log state.
hs_err_pid3314236.zip
zdb_run.zip
nextflow.log.zip
zdb_run_resume.zip
nextflow.log1.zip

I got it to run by adding:
singularity.runOptions = "-B $baseDir:$baseDir"
singularity.envWhitelist = "PYTHONPATH"

to nextflow.config. I am running it all in RAM disk (work dir + nextflow scratch) to avoid IO/network problems. I was consistently getting this error before adding the singularity params:
<rest of log>
Plus 2 more processes waiting for tasks…

Annotation pipeline completed

You may now start the web server with the zdb webapp command

WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException

ERROR ~ Error executing process > 'load_base_db (1)'

Caused by:

  Process `load_base_db (1)` terminated with an error exit status (1)

Command executed:

  #!/usr/bin/env python

  import setup_chlamdb

  kwargs = "<long_list_was_here"

  gbk_list  ="<long_list_was_here"

  alignments_lst = "<long_list_was_here"

  print("Loading gbks", flush=True)

  setup_chlamdb.load_gbk(gbk_list, kwargs, "gigantic_linnaeus")

  print("Loading groups", flush=True)

  setup_chlamdb.load_groups("zdb_input.csv", kwargs, "gigantic_linnaeus")

  # kept for now, need to check whether this is really necessary to keep the hash

  print("Loading seq hashes", flush=True)

  setup_chlamdb.load_seq_hashes(kwargs, "nr_mapping.tab", "gigantic_linnaeus")

  print("Loading orthofinder results", flush=True)

  setup_chlamdb.load_orthofinder_results("Orthogroups.txt", kwargs, "gigantic_linnaeus")

  print("Loading alignments", flush=True)

  setup_chlamdb.load_alignments_results(kwargs, alignments_lst, "gigantic_linnaeus")

  print("Loading checkm results", flush=True)

  setup_chlamdb.load_genomes_info(kwargs, gbk_list, "checkm_results.tab", "gigantic_linnaeus")

  print("Loading phylogenies")

  gene_list = "<long_list_was_here"

  setup_chlamdb.load_reference_phylogeny(kwargs, "core_genome_phylogeny.nwk", "gigantic_linnaeus")

  setup_chlamdb.load_gene_phylogenies(kwargs, "orthogroups_summary_info.tsv", gene_list, "gigantic_linnaeus")

Command exit status:

  1

Command output:

  (empty)

Command error:

  INFO:    Converting SIF file to temporary sandbox...

  Traceback (most recent call last):

    File ".command.sh", line 3, in <module>

      import setup_chlamdb

    File "/.../micromamba/envs/zdb/share/zdb-1.3.4/bin/setup_chlamdb.py", line 9, in <module>

      from lib import KO_module, search_bar

  ModuleNotFoundError: No module named 'lib'

  INFO:    Cleaning up image...

Work dir:

  /dev/shm/ohickl_zdb_work/work/3b/ee0756b9753a55a7e65afa9606cc80

Container:

  /dev/shm/registry.hub.docker.com-metagenlab-annotation-pipeline-1.4.1.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Could not finish the analysis

Try to rerun the same command with the --resume flag set to rerun the analysis

The problem i have now is that there are no annotations (e.g. COG entries) available in the UI on the webserver.
I ran it like this, skipping amrfinder, since there was always one job stuck indefinitely:
zdb run --input="$(basename ${INPUT_TABLE})" \
        --name="A_muciniphila" \
        --out="${OUTPUT_DIR}" \
        --ref_dir="${ZDB_REF_DIR}" \
        --cpu="${THREADS}" \
        --mem=200GB \
        --singularity_dir="/dev/shm" \
        --ko --cog --pfam --vfdb --swissprot \
        --resume &> "${LOG_DIR}/zdb_run.log"

Here the log of that run:
zdb_run_v2.zip

It's hard to know what is going from from the logs. But here a few points/suggestions:

I have no experience with RAM disks, but if I understand well, data is copied back and forth between the RAM disk and your HD. Nextflow's resume uses hashes composed from various information, plus the files present in the work directory to decide whether a job has to be repeated or not. That hash notably contains the modification date of the files, so moving/copying a file will break the resume. That might be your issue there.
I have just run zDB from scratch on an example dataset and did not encounter any issues, including running AMRFinderPlus. Did you check the log file of AMRFinderPlus process which was hanging? Each nextflow process has a corresponding log file in the work directory. Did you maybe run out of memory or something alike?
As far as I know there should be no need to add any singularity options.
When you start the webapp, make sure to that you are opening the correct run. So in your case zdb webapp --name=compassionate_mendel --dir="${OUTPUT_DIR}".
If you point the webapp to the correct run and it does not display the expected data, that would be very strange. You could have a look at what is in the database, or send it to me (it's in $OUTPUTDIR/zdb/results/db)

I could also advise to first make sure everything works using a small example dataset, and maybe simplifying things by not running on a RAM disk. As a test dataset you can for example use the one from the zDB tests (https://github.com/metagenlab/zDB/tree/master/testing/pipelines/assets), you will just need to modify the paths to the files in the test_input.csv file.
I hope that helps...

Ok, thanks!

The RAM disk runs cannot be resumed of course. Those are always fresh runs. I am doing this do speed things up and also to avoid crashes because my file write quota is consumed. With the 1.5K genomes, it writes hundreds of thousands of files.
On a small subset (16 genomes) it does work fine, and also all annotations are displayed correctly in the webserver.
I checked both the small and the large runs outputs in the webapp, the large one does correctly show e.g. the phylogeny etc, just all the functional annotations are missing. they seem to be in the db though:

> sqlite3 zdb_output_v2/zdb/results/db/compassionate_mendel
SQLite version 3.46.0 2024-05-23 13:25:27
Enter ".help" for usage hints.
sqlite> .tables
biodatabase                 location
biodb_config                location_qualifier_value
bioentry                    og_hits
bioentry_dbxref             ontology
bioentry_path               orthology_identity
bioentry_qualifier_value    reference
bioentry_reference          reference_phylogeny
bioentry_relationship       seqfeature
biosequence                 seqfeature_dbxref
cog_functions               seqfeature_path
cog_names                   seqfeature_qualifier_value
comment                     seqfeature_relationship
dbxref                      sequence_hash_dictionnary
dbxref_qualifier_value      taxon
filenames                   taxon_in_group
gene_phylogeny              taxon_name
genome_summary              term
groups                      term_dbxref
ko_class                    term_path
ko_def                      term_relationship
ko_module_def               term_relationship_term
ko_pathway_def              term_synonym
ko_to_module                versions
ko_to_pathway
sqlite> PRAGMA integrity_check;
ok

here also some lines from the contained tables:
db_inspection_results.zip
could it be a memory issue? i am also running through WSL on windows. but then again, with the same setup, the small output seems just fine.
what is the largest dataset you tried? i was also planning on running on an order of magnitude larger number of genomes later, if the issues can be resolved.

Ok I did not realize your dataset was that large. Are the genomes particularly small? Wasn't the orthofinder excessively slow? This is currently all against all, so scales as n**2, and is the clear bottleneck in the annotation pipeline. We were planing on replacing it with pirates, but haven't done that yet. zDB is typically used for datasets for up to 150 genomes.
As for the webapp, what to you mean by "functional annotations are missing"?  You have the menu points on the left hand side right? And if you navigate to index_comp/ko you see the available comparisons? But nothing is displayed when you go to entry_list_ko? zDB does the table rendering front end side, which does not work well for large tables (backend returns the whole table and the frontend sorts it and displays only the first page). So while the backend sends the data pretty quickly, then the frontend can take ages to display the data. You can verify this in the network tab of the web inspection tool (right-click in the browser and choose "inspect", which opens the inspection tools, and there choose the "network tab". reload the page and you'll see the requests. I expect the request to entry_list_ko to return normally, but then the data is not displayed).
If instead in the webapp you go for example to /extract_ko/, i.e. the extraction form, and perform a complex search (present in a few strains and absent from a few others), does that get displayed?
So basically I think this is a performance issue. We are planing on working on the support of larger datasets, replacing orthofinder and improving table rendering by letting the backend only return the data that will be displayed, using ajax requests. So that should all happen at some point in the coming year, but it's not quite top priority just now...


Milestone 2: Create app

In this milestone, the following features were added:

When the page loads, the webapp shows the list of categories that could be filtered out by some parameter, for example by the category name.
The project is a single-page application (SPA) built with React and Redux.
The data retrieved from the API is stored in the Redux store.
It filters the data that you retrieve from the API using a Filter stateless component.
Every page (the main page and the pages for each item) has a unique route within the SPA.
Along with the category name, it will display some numeric values per category that come from the API.
When the user clicks (or taps) on a category item, the application navigates to the details page.
In the details page, the webapp retrieves data from the API to show detailed data in the category.
When the user clicks on the "Back" button (<), the user navigates to the home page.
Create unit tests for pure functions in your Redux code.
Create integration tests for your application using the React Testing Library

Thanks


Parsing JSON Reports to allow Ignored Warnings to be displayed

Sorry for this taking so long, but this ended up being a fairly large PR. This PR is in reference to #8 about reading JSON reports and displaying ignored warnings (while remaining backwards compatible to read the tabs reports as well). My strategy to accomplish this was to check the report file content and check if it matches a JSONObject. If it does, it will scan the file with the JSON strategy, if not it will scan the file based on the tabs strategy.
I also had to make sure that these new ignored warnings that can be added would not affect the status of a build (ex. a build won't fail if a threshold is set for 0 warnings, and a brakeman report includes 1 ignored warning). This would've probably made a lot of developers mad if their builds started failing because of this; so I made evaluateStatus only factor for non-ignored annotations/warnings.
Everything is working fine for me in two different local Jenkins instances!
Here are some more details about what this PR includes:

Ability to use JSON reports (as well as tabs)
Can read ignored warnings in JSON reports
Annotations with category "Ignored" don't factor into threshold evaluations
Ignored Warnings Total on build status page
Ignored Warnings added to Reports screens and Trend Graphs
Error handling for invalid JSON reports

This closes #8.
Feel free to let me know if there are any suggestions or concerns!

I'll review this [hopefully] sometime this weekend.

@ConstantineXVI sounds good, thanks!

Ok all issues with this PR should be resolved now. Here's a summary of the changes:

Removed org.json dependency from pom, not needed because net.sf.json is available to you
Changed org.json imports to net.sf.json, and refactored a little bit of the JSON parsing code to use this library's [net.sf.json] code
Switched a couple methods to return an enum, per suggestion

Let me know if there's anything else that is needed.

@ConstantineXVI any progress on this?

Sorry, I've been swamped lately. I'm hoping to finish this up over the holiday.

@ConstantineXVI no worries, I was just curious. Thanks!

@ConstantineXVI thanks! 👍


Enforce unique constraints on space names

Currently we allow spaces to:

Have duplicate names (all spaces have unique ids)
Contain any unicode character

In light of the zapi cli we have seen that it useful to have a human readable, unique handle for spaceIDs. As such change space name so that:

They are unique among all spaces in a zqd instances
Containing only characters a-zA-Z0-9_

This will also have to include some undocumented endpoint for migrating old space name/ids to this new format (i.e. old brim spaces).

Reopening this as there's a need to discuss the name character restriction impact on the Brim UI.

 See https://github.com/brimsec/zq/issues/937#issuecomment-650311707.
Thanks @mattnibs and @alfred-landrum!


docs(readme.md): update latest version

ref #305
I changed cdn link.
Description

Compatibility

Caveats

:tada: This PR is included in version 2.1.1 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


feat(vmi): add SetHostnameAsFQDN option

What this PR does / why we need it: Support pod option setHostnameAsFQDN in vmi.
Which issue(s) this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when PR gets merged):
Fixes #6371
Release note:
Add SetHostnameAsFQDN option to VirtualMachineInstanceSpec.

/ok-to-test

/retest


Adding RDS Instance/Cluster Auditors and tests.

Auditors specifically look for internet-accessible databases by checking attached security groups.

Coverage increased (+0.2%) to 71.621% when pulling 87ffc59775fa6194cf315f9d98e592912ef962d3 on rds_auditor into 889cb67b8f93a3fb22fd6325a353c44970385c82 on develop.

Coverage increased (+0.2%) to 71.625% when pulling a5f74f0c093314c2700f9ce51d44b0574474b4b3 on rds_auditor into 889cb67b8f93a3fb22fd6325a353c44970385c82 on develop.

Ended up discovering that linked issues would not get marked as fixed when the original issue was fixed.
I have corrected this bug in this PR.

In the future, it may make sense to have a foreign key relationship between an issue and any linked issues.
It would also be nice if the notes field was present in linked issues.  This would help with the d3 cross account dashboard initiative.


python3Packages.pre-commit: 2.14.0 -> 2.15.0

Motivation for this change
Update to latest upstream release 2.15.0
Change log: https://github.com/pre-commit/pre-commit/releases/tag/v2.15.0
Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
21.11 Release Notes (or backporting 21.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 137288 run on x86_64-linux 1

3 packages built:

pre-commit (python39Packages.pre-commit)
python38Packages.pre-commit
wlc


Prevent mobile browsers from sleeping during transfer

Ref: https://github.com/LeastAuthority/winden/issues/120

I have tested on iOS (16.2), but it didn't work, phone still went sleep.
Seems repo https://github.com/richtr/NoSleep.js abandoned by owner and a lot of PR hanging without merge.
However, I see there is PR which is fixing iOS problem: https://github.com/richtr/NoSleep.js/pull/138, I will try with it.
Alternatively, we need to search for another package.

I have tested on iOS (16.2), but it didn't work, phone still went sleep.
However, I see there is PR which is fixing iOS problem: richtr/NoSleep.js#138, I will try with it. Tried with replace package<EMAIL_ADDRESS>Still not working with. JS error:
NotAllowedError
The request is not allowed by the user agent or the platform in the current context, possibly because the user denied permission.

Seems repo https://github.com/richtr/NoSleep.js abandoned by owner and a lot of PR hanging without merge.

Seems Safari (webkit) requires allowsInlineMediaPlayback="true" https://github.com/react-native-webview/react-native-webview/issues/1251, https://developer.apple.com/documentation/webkit/wkwebviewconfiguration/1614793-allowsinlinemediaplayback?language=objc
@JustusFT can we add?

I have tested on iOS (16.2), but it didn't work, phone still went sleep.
However, I see there is PR which is fixing iOS problem: richtr/NoSleep.js#138, I will try with it. Tried with replace package<EMAIL_ADDRESS>Still not working with. JS error:
NotAllowedError
The request is not allowed by the user agent or the platform in the current context, possibly because the user denied permission.

Seems repo https://github.com/richtr/NoSleep.js abandoned by owner and a lot of PR hanging without merge.

Seems Safari (webkit) requires allowsInlineMediaPlayback="true" react-native-webview/react-native-webview#1251, https://developer.apple.com/documentation/webkit/wkwebviewconfiguration/1614793-allowsinlinemediaplayback?language=objc @JustusFT can we add?

Seems plugin example works on iOS: https://richtr.github.io/NoSleep.js/example. So maybe issue on our side?

@donpui I'm unable to check the problem since I don't own any ios device. It works on my android device though.
All I can guess is that video playback is being blocked, but I can't test it

We can pair and experiment together. In NoSleep.js documentation, there is saying:
NOTE: This function call must be wrapped in a user input event handler e.g. a mouse or touch handler

@donpui Since ios blocks video playback if not tied to user input, I have changed nosleep so that it activates on button presses.
I tested the following scenarios on android and it works, hopefully it works on ios as well.

activates when sender clicks the + button
deactivates if upload fails (file too large or multiple files)
activates when receiver clicks "Next"
activates when receiver submits code by hitting the enter key
deactivates if submitted code is invalid
activates when receiver accepts a file (clicks "Download")

unfortunately in cases where the user uses a link like https://winden.app/#7-guitarist-revenge , this is the earliest moment to get a user input. This scenario doesn't work if they don't click the download button before the screen locks.

deactivates on transfer completion and cancellation.

Tested on iOS device with Safari, Chrome, Firefox:

Waiting for code accepted, sending from iPhone to workstation (note: manage to send 1gb file from phone to workstation)
Waiting to accept file on iPhone;
Receiving file to iPhone (note: large file receive still fails);

NoSleeps works for mobile devices, should check mobile browsers/device and do not enable/disable wakelock. Or do we leave for nosleep package to take care?

Several concerns, which we might need to think:

nosleep.js main repo doesn't have active maintenance, however community quite big and there are PRs and forks, which solves one or other issue. Not sure if we should use this or move to one of forks.
such functionalities, require error logging, as we will not be aware if it works properly on users side or spams JS/TS errors.
not sure if we can have somekind of tests for this feature (for E2E, we would need device with short screen time, fore integration tests, maybe we can just check wake status)

Since our testing seems to show that it works on the common mobile os (Android, iOS) and browsers (Safari, Chrome, Firefox), I think this pr is ok to merge, maybe after adding some tests. If we find any issues, we can review the existing forks to use or make our own if needed.
We don't have any setup for automated e2e for mobile devices, but I can add integration tests that can check the NoSleep state

We don't have any setup for automated e2e for mobile devices, but I can add integration tests that can check the NoSleep state

Lets add at least integration test.

Copying my message here (TL;DR we'll hold off adding the tests for now: https://github.com/LeastAuthority/winden/issues/128)

I encountered some problems. The code isn't really testable in the desired layer (integration tests with react-testing-library)
The best way to test nosleep deactivation is by

mocking nosleep,
mounting the whole app with react-testing-library,
simulate a cancelled or completed transfer.
then we can verify that the mock was called at the right times.

But to do this, we have to stub out go, wasm, the webworker, some of the react context providers, etc. And I'm having trouble getting them all stubbed.
I'm currently refactoring the code so these parts could be easily be stubbed out, but it's taking me a while...
What is possible right now is to just mount as little of the ui as needed (instead of the whole app), and check for the mock calls like that, but I would say such tests would be too fragile and not that useful. (for example, the test would break every time a nosleep call moved somewhere else, even though it still works. I would have to re-do the test setup)
We can also make nosleep global and check the value through e2e, but that isn't ideal situation because we should avoid testing implementation details at the e2e layer.
(also, one thing that would help is to finally add state management because state is quite scattered at the moment. I ended up spending quite some time yesterday and today looking into solutions for that as well. I know we were gonna hold off any changes related to the worker until dilation and multiple file transfer since these parts would need to be rewritten by then anyway, but now I'm thinking it's a good idea if we refactor now, just so testing could be easier.)

Adding to this, we would very much also need E2E running on real devices, issue: #106. As even if we test states and activation, we are not fully sure if it works for end users. For example WakeLock API is very differently supported via different browsers and in some case workarounds are implemented inside library.


[Feature] Add a help prompt to the start.sh

Purpose
Add a help prompt to the startup.sh
Tests

API and Format

Documentation

close #405


Changing terms content in QR Code app as outlined in github issue #629

Summary | Résumé
Making content changes as outlined in github issue #629

I am closing this pull request since Dorian already made the changes due to the fact that they were duplicated on 2 tickets.


Clicking multiple times in target while dismiss animation is running restarts animation

[X] I have verified the issue exists on the latest version
[X] I am able to reproduce it

Whenever the TapTargetView is clicked, onTargetClick is triggered, which calls view.dismiss(true); - that will kick off the dismiss animation. If the user repeatedly clicks the target while the animation is running, that listener method will be called again, which restarts the dismiss animation, allowing the whole cycle to be executed indefinitely.
Version used:
1.5.1
Stack trace:
None.
Android version:
API 25

Thank you for the quick fix, @xiphirx. I'll try the new version asap and come back with results :+1:


Documentation 3.0 issues

Next.js setup topic -  the json data in the screenshots in the guide does not match the actual json data (displayName, dataAsJson)

Live deployment  topic - Create a new route  should be replaced with create new Ingress:

Would be nice if you could include actual json data @sgauruseu


[REQUEST] 1.19.3 Support

Mixin errors when using 1.19.3 fabric server/api versions.
Probably not a huge update, but would be appreciated! Thanks

I haven't managed to reproduce any mixin errors, could you provide a log file?

I had version 2.4.1 and updated to 2.4.4 and there are no error logs.
I would say that it is fixed now and if anyone has this issue, update your mod file.