obvious wrong softmax dimension!

https://github.com/tonysy/CapsuleNet-Gluon/blob/39625d7a07d1da21e330d203b7b7448891a91942/CapsuleLayer.py#L109
axis = 2 is the output channel,  however your note hints to softmax on num_capsule dimension.
so is  softmax_prior = nd.softmax(priors, axis=1)  to be right?

read te paper again, what you done is right, but your note is quite confusing...


Change Tuya switch TS000x device type

Proposed change
Change device type of Switch_4G_GPP to be an actual switch, as the device consists of potential-free relais. Also the type switch is substitutable with other types using HA helpers, but not (or not easily) vice versa.
It would probably make sense to change this for other similar switches as well, but as I don't own any others, I don't want to change stuff blindy, potentially introducing unnecessary errors/misbehaviour.
I found no related tests to this device, so I didn't do anything in this regard as well, as I've got not enough time to read through your testframework (yet) :/
Checklist

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

The issue with this is that it'll break existing installations. Everyone who currently set it up will have the old entity become stale and get a new one. We've avoided changing the device type for new quirks because of this.
Please see this section on how to change the device type locally: https://www.home-assistant.io/integrations/zha/#modifying-the-device-type

I see. So this PR becomes obsolete?
While it is possible to work around this, I still see it at least somewhat inconvenient for new users setting up this (and potentialy any other wrongly specified device). Wouldn't it be possible to ensure somehow the original device type continues working by automatically generating a proper helper, just as "switch device type" in the UI does? The latter only seems to work when the "base" entity was a generic switch, but not when it is something specific like e.g. a lamp in this case.

@TheJulianJES sorry for the ping, I'd just close the PR if it really became irrelevant.

Wouldn't it be possible to ensure somehow the original device type continues working by automatically generating a proper helper, just as "change device type" in the UI does?

I know it's not ideal, but we can't really do this from quirks.

The latter only seems to work when the "base" entity was a generic switch, but not when it is something specific like e.g. a lamp in this case.

That's a limitation on HA Core side, as the integration responsible for that is called "Switch as X" and only allows you to "convert" switches.

So this PR becomes obsolete?

For now, probably yes. I'm aware the current situation isn't ideal (especially because you can't go from light to switch using HA UI and have to modify (ZHA) YAML configuration to fix this, but there's no "good" solution right now.)


Doc Review on PR checklist

Update PR checklist with an item to prompt contributors to think about the doc changes that will be required. We should list (possibly in the PR template comments) where the docs/videos all live that potentially need to be updated.
The intention is not to block the PR until the docs are updated, but we should at least be creating issues to track what doc updates are required as we merge PR's into main.

Implemented in this commit: https://github.com/github/gh-gei/commit/9508a02c937d7a8f7a62d8c293ae51e7ed1fea1a


Change UI

Overview:
This PR introduces several improvements and refactorings in the AddressBook application related to the display of person details and command handling. It focuses on better organization, enhanced functionality, and improvements to the user interface. Specifically, the following changes are included:
Changes Summary:

Person Details Panel Addition:

Added PersonDetails class and corresponding PersonDetails.fxml to display detailed information about a selected person.
Displays student ID, contact number, address, email, course, and enrolled modules with clear sectioning for improved readability.
Supports updating the details dynamically based on the selected person.
Refactored the MainWindow class to include the personDetailsPlaceholder StackPane to hold the person details UI component.

Person List Panel Improvements:

Updated PersonCard class and its FXML (PersonListCard.fxml) to better display person tags.
Added logic to differentiate between Student and Tutor roles by changing the styling of the tag label (i.e., student-pane for students and tutor-pane for tutors).
Improved display of the person's modules, ensuring they are neatly presented under the label Modules.

Command Result Enhancements:

Improved the feedback to the user by updating the CommandResult class, allowing feedback messages to be wrapped within the result display box when commands are executed.

UI Layout Refactor:

Adjusted the layout of the MainWindow.fxml to provide a more structured interface.
Refined the styles applied to various UI components, introducing custom classes  for a more polished and consistent look.

Things to Note:

UI for the PersonDetails is not entirely polished, a more aesthetic version will be updated.
CommandResult class will need to be slightly refactored after adding a new constructor to accommodate the new PersonDetails class.

Codecov failure is due to changes in UI in MainWindow.java, PersonCard.java and PersonDetails.java, which will not be unit tested.


Completed Donor Milk POC Labs Template

Signed-off-by: Marissa Iannarone<EMAIL_ADDRESS>

I hope you have everything you need to review our Labs proposal. Please let me know if you need anything else. Our full business case is here: https://wiki.hyperledger.org/groups/healthcare/donor_milk_transparency_and_traceability Thanks!

Hi, @MariLeigh. It looks like instead of copying proposal_template.md to a new file under the labs subdirectory, you overwrote the contents of proposal_template.md. Can you revert your changes to proposal_template.md and copy your changes into a new file under the labs directory with the name of your lab? Something like labs/milk-donor.md.

Sorry about that. Please confirm that I have done it correctly.
Marissa Iannarone
Associate with Forum Solutions LLC http://www.forumsolutionsllc.com/
phone number: +01<PHONE_NUMBER>
email<EMAIL_ADDRESS>On Tue, Jul 31, 2018 at 3:59 PM, Tracy Kuhrt<EMAIL_ADDRESS>wrote:

Hi, @MariLeigh https://github.com/MariLeigh. It looks like instead of
copying proposal_template.md to a new file under the labs subdirectory,
you overwrote the contents of proposal_template.md. Can you revert your
changes to proposal_template.md and copy your changes into a new file
under the labs directory with the name of your lab? Something like
labs/milk-donor.md.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/hyperledger-labs/hyperledger-labs.github.io/pull/35#issuecomment-409394944,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AhxRUYuyzy_5RyWNhxniIY6vSu17_lGQks5uMOFKgaJpZM4VnfGI
.

Yes, you're now on the right track. Closing this PR since you created a new one. FYI, you can update the one you already have rather than create a new one every time you make a change.

Thank you, Arnaud! Unfortunately, I wasn’t able to figure out how to revert via the Github browser, so I just created a new one. If you are aware an easy way, please let me know. You can tell I’m new to this functionality :-).
Thanks again,
Marissa

On Jul 31, 2018, at 10:14 PM, Arnaud J Le Hors<EMAIL_ADDRESS>wrote:
Yes, you're now on the right track. Closing this PR since you created a new one. FYI, you can update the one you already have rather than create a new one every time you make a change.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.


chore(master): release 0.59.0-alpha

:robot: I have created a release beep boop
0.59.0-alpha (2024-03-06)
Features

new (9fefa71)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/mafqla/yalis-blog/releases/tag/v0.59.0-alpha :sunflower:


Set REFF_T as 1.0 for all lenses

Motivation: the point mass model makes us lose ellipticity information of the lens.
Will have to modify analytical moment calculation to account for object that is sheared before convolution. Also consider generalizing calculation for a sheared PSF.

Setting REFF_T to zero for the vectorized source table function, but still can't accommodate shear.

Fixed as part of #32.


Display stack trace in Chrome DevTools console.

I would like to display stack trace in Chrome DevTools console, and the purpose itself is achieved with the change in this PR.
The problem of this approach is that the group cannot be filtered out.
https://stackoverflow.com/questions/38620729/google-chrome-console-filter-out-groups
Also, the output of console.trace is defaulted to expanded and cannot be defaulted to collapsed.
Moreover, there is no way to easily collapse all outputs. This means that I need to close the output of console.trace one by one manually.
In the end, the conclusion is that I will discard this PR.
The workaround is as follows:

Copy the console.info output for the target line.
Change console.info to console.trace
Rerun application.
Find the target line by filtering with the text copied in 1), and see the stack trace.
After the work is done, change console.trace to console.info

Reference:
https://stackoverflow.com/questions/52595559/how-to-log-js-stack-trace-with-console-trace-but-keep-it-collapsed


Azure SQL Database gateway IP addresses for Germany and other national clouds are missing

Do there exist a command to get the IP addresses from these national clouds, or is this place not even the right location?

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: e1a62365-4312-8aad-d2f1-bb5c4184adf1
Version Independent ID: 2ba5b809-8025-d7ee-c756-d6d1bab033fb
Content: Azure SQL Database connectivity architecture
Content Source: articles/sql-database/sql-database-connectivity-architecture.md
Service: sql-database
Product: unspecified
GitHub Login: @CarlRabeler
Microsoft Alias: carlrab

@DenWin Thanks for the feedback. We are actively investigating and it appears that, although, there is an Azure Government GitHub branch for documentation, the links from Azure Government Databases source links from the main MicrosoftDocs Azure repository. I believe the Azure SQL Gateway IP addresses would need to be reflected here: Azure SQL Database gateway IP addresses.
I have assigned the issue to the content author to evaluate and update as appropriate.
Regards,
Mike

Please assign to dhruv malik

@Mike-Ubezzi-MSFT please assign to oslake
@oslake per Joachim

article updated
#please-close


TaskDataset does not sub-type MLUtils.AbstractDataContainer

I would sub-type MLUtils.AbstractDataContainer to get some sensible defaults like Base.iterate defined on top of the MLUtils.jl interface.

That’s a good idea!

I like the package and was hoping to contribute. This one seems like a pretty easy place to start. As far as code goes I guess it's trivial? (I'm new to Julia, though not to programming so maybe I'm wrong here).
struct TaskDataset{TData, TTask <: LearningTask, TContext <: Context} <: MLUtils.AbstractDataContainer
    data::TData
    task::TTask
    context::TContext
end

But I was trying to figure out what tests I can add. I see MLUtils defines Base.size, Base.iterate, and Base.lastindex but I'm having a little trouble in FastAI.jl figuring out the right place to put the tests (seems like most of them are in the implementation file, but I didn't see any in taskdata.jl) and I was having a little trouble figuring out a quick and easy way to instantiate a test TaskDataset. If you're busy then no worries I'll just keep poking around until I figure it out but I'd glady take any tips too.

Yep, it should be a simple change. Happy to see contribution!


Text rendering engine

Use SharpFont to convert TTFs to texture atlases with character-to-rectangle mappings at runtime? Is this a terrible idea? Who knows!
https://github.com/Robmaister/SharpFont

Update, original lib is very old, have been told to use this one instead https://github.com/vonderborch/SharpFont

Scratch that, we're trying out https://github.com/FontStashSharp/FontStashSharp


Page List Filtering By Page Type and Show Aliases

When filtering the page list block by page type and also selecting the 'display page aliases' option aliases are not displayed. If I clear the page type filter, then the aliases are displayed properly.
However if I manually create an instance of a PageList objected and filter by the page type handle the logic appears to work. The only difference I see between how the page list block and my code is working is that the page list block is filtering based off of p.ptID while the other is using pt.ptHandle. I'm assuming that an aliased page doesn't have a ptID.
A quick fix may be to change the page list block to use $list->filterByPageTypeHandle() instead of $list->filterByPageTypeID() but that may be (marginally) slower in some cases.

Definitely good ratio of bug fix to code change in that commit. Thanks for the heads up – probably would have taken a lot longer to fix without knowing that filterByPageTypeHandle() worked and page type ID didn't.


tests: stable must_have_peer

Signed-off-by: Max<EMAIL_ADDRESS>What have you changed? (mandatory)
sleep longer
What are the type of the changes? (mandatory)

Improvement (non-breaking change which is an improvement to an existing feature)

How has this PR been tested? (mandatory)
unit test
Does this PR affect documentation (docs/docs-cn) update? (mandatory)
No
Does this PR affect tidb-ansible update? (mandatory)
No

PTAL @BusyJay


[Bug] Unrealised Currency Gains not reported

Is there an existing issue for this?

[X] I have searched the existing issues

Describe the issue
Xero reports unrealised currency gains, similar to quickbooks - but this transformation does not include the calcuation.
I noticed in the ReadMe history there was a mention about this but that mention was removed, can you confirm if unrealised gains/losses should be captured or not?
Relevant error log or model output
n.a

Expected behavior
Unrealsied gains should be available on the P&L
dbt Project configurations
Open invoices/bills should capture unrealised gains/losses in the transformation
Package versions
Using quickstart
What database are you using dbt with?
snowflake
dbt Version
Quickstart
Additional Context
No response
Are you willing to open a PR to help address this issue?

[X] Yes.
[ ] Yes, but I will need assistance and will schedule time during our office hours for guidance
[ ] No.

Hi @brandonrf94, at this moment we cannot capture unrealized currency gains, as we would need to know what the currency exchange rates are for each transaction. This is not something that is available within the Xero connector ERD. Without it, we can't work backward to understand what the gains or losses are. More details are here in the "Note about currency gains" section of the README.
I see you created a support ticket within Fivetran regarding this being a Transformations issue. This is actually a connector issue, as we would need those exchange rates available within the ERD schema to bring into our data models and then provide unrealized currency gains in the final models.
I'd recommend updating your Fivetran support request for an update in the Xero connector to include exchange rates, and once that's provided, we can work on adding support for unrealized gains.
Hope that helps!


Add a Consultation Form for Personalized Ayurvedic Advice or Feedback Form

Is your feature request related to a problem? Please describe.

The platform lacks a way for users to input symptoms for personalized Ayurvedic advice or provide feedback.
Users currently can't receive tailored suggestions or share their experience for improvements.

Describe the solution you'd like

Add a Consultation Form where users can input symptoms (e.g., health concerns, lifestyle habits) and receive personalized Ayurvedic advice.
Alternatively, implement a Feedback Form to collect user insights after interacting with the platform.

Describe alternatives you've considered

A static FAQ section, but it doesn't offer personalized guidance.
A chatbot interaction, though a form might be more user-friendly for structured inputs.

Additional context

The form could include fields like: Name, Age, Symptoms, Duration, Lifestyle Habits, etc.
This feature would improve user engagement and platform interaction.

If this feature fits in your project so you can assign this project to me so that i can start work on it.

@Mefisto04 You can proceed further with this and follow the README.md.


Hostname as fieldname not possible anymore

After I have updated the checkmk plugin from (I'm not sure exactly) version 2 to version 3.1.1 I can not set the fieldname to the hostname. On the old version I could set the label of each query to the hostname, f.e. with $host.

can you roll back to a 2.X version and show me some screenshots of your query configuration? i don't understand what you were doing.

can you roll back to a 2.X version and show me some screenshots of your query configuration? i don't understand what you were doing.
It's the 'label-format' there. I have also seen on the panel-json that there is something like this already set: "format": "$host",, but it doesn't work - it shows the service-name 'Uptime'.

Thanks for the additional information, I was not aware that we had a "Label Format" Field in the 2.X versions of this plugin.
In the meantime we released 3.2.2 which added a "Custom label" field to the query:

Can you update to 3.2.2 and give it a try?

Yes, it works now again. Thanks!


add subscription based cache refresh

add subscription based cache refresh.
The current design is optimisic and friendly, it assumes that nobody will spam cache_nft for invalid CIDs.
subscribe specifies the port and protocol used for a callback, the ip address is implied.
unsubscribe removed the ip address from the callback.
has_nft_cached returns true if a specific nft is already cached, based on a block hash.
cache_nft instructs the node to cache a specific nft. It looks up the send block that has the specific hash, converts the rep field to a cid, pulls the JSON from the CID, and validates the JSON. If it's valid, it caches the JSON and a url that links to the IPFS CID.

[ ] add subscribe {"action": "subscribe", "protocol":"^http|https$", "port":"^[0-9'+$"}
[ ] add unsubscribe {"action": "unsubscribe"}
[ ] add has_nft_cached {"action": "has_nft_cached", "hash", "<send-block-hash>"}
[ ] add cache_nft {"action": "cache_nft", "hash", "<send-block-hash>"}

Maybe it would make more sense for the node to simply cache all chains for a template. In most cases this will be called after announcing the template on the Banano ledger and might not even have any sends yet.
I suggest:
cache_assets {"action": "cache_assets", "ipfs_cid", "<nft-template-ipfs-cid>"}
has_assets_cached{"action": "has_assets_cached", "ipfs_cid", "<nft-template-ipfs-cid>"}


#11 - specify elasticsearch transport parameter and custom auth usera…

HI I have added my changes for review to specify a custom transport and ua class. We have a usecase where in instead of ES auth we are using something custom and ES is sitting behind a authentication proxy so queries should have some token added to them.
Users who are having similar requirements now can write their custom plugins and override.

@rfarley3 would you help here to move forward.


Add support for CRIU to the LXD snap

All that's needed for this in theory is to add criu to the stage-packages and have the criu binary included in the LXD snap.
Unfortunately because CRIU isn't available on all architectures and snapcraft doesn't know how to deal with that, we're a bit blocked right now.
We need https://github.com/snapcore/snapcraft/pull/876 to land before we can do this.

This has long been done.


31 training improvement

The following advancements have been made in branch 31_training_improvement:

Improved training procedure
Introduced 2 more classifier types (xgboost & fasttext)
Improved classifying performance
Created feature extraction classes for both audio and text
Created a utils script
Created config file
Created model_dict to store model information
Organized the output folder

Instructions

Text

Open the config file and go under the 'text_classifier' field. Choose the type of classifier you wish to use (i.e. svm, xgboost, fasttext), by setting True only this specifc classifier.
In case of the fasttext classifier, you must place the path to your pretrained embeddings vector at the field pretrained_embedding_vectors.
In case of SVM, set its parameters.
If you wish to reduce your dataset for debbuging reasons, use the hop_samples variable.
Run the script:

case 1: Using the whole embedding model:
python3 train_text.py -a "input" -p "wiki.en.bin" -o "svm_output_classifier_path"
case 2: Using an embeddings limit in order to avoid memory errors:
python3 train_text.py -a "input" -p "wiki.en.vec" -l embeddings_limit

Audio

Open the config file and go under the 'audio_classifier' field. Choose the type of classifier you wish to use (i.e. svm, xgboost), by setting True only this specifc classifier.
In case of SVM, set its parameters.
Set the parameters for the segment based feature extraction, using the field basic_features_params

Please add requirements file, sending some dependencies that I found necessary here:
nltk==3.5
fasttext==0.9.2
num2words==0.5.10
numpy==1.19.2
gensim==3.8.3
xgboost==1.3.3
glob2==0.7
pyAudioAnalysis==0.3.6
PyYAML==5.4.1

getting this error when I run test_audio. I've tried using the same sklearn version in train and test and that did not help. Any ideas @lobracost @sofiaele ?
models|31_training_improvement⚡ ⇒ python3 test_audio.py -i ~/Downloads/arousal_train_no_calls/weak/09F6VFFZWH_330.40999999999997_340.40999999999997.wav -c output_models/audio/audio_arousal.pt Traceback (most recent call last):   File "test_audio.py", line 65, in <module>     results = predict_audio_labels(args.input, args.classifier)   File "test_audio.py", line 24, in predict_audio_labels     model_dict = pickle.load(open(classifier_path, 'rb')) ValueError: unsupported pickle protocol: 5


feat: translator plugin with payload 3.0

Translator plugin works with payload 3.0

This PR is based on tag translator-1.3.0-pre.0
I added a new resolve: LibreTranslate
No unit test yet 😢

Thank you so much! I'm merging your PR as it is and going to clean up / see what I need to do before next release


Introduce bold theme.

Making life easier for bold font fanboys!

Thanks, Harish! I'll push an update soon.


Update to 1.21?

Is there any plans about updating this mod to newest version and if it is, how could we help with that?

See #9

See #9
MCEF needs to be updated first before im able to have this mod work on the newer versions.

I've released an updated MCEF for 1.21


Add high availability e2e tests

Add e2e tests that cover high-availability of Kueue webhooks and visibility extension API, as discussed in https://github.com/kubernetes-sigs/kueue/pull/1554#pullrequestreview-1818175088.
These tests should be as close as real-world use cases, and guarantee among other things:

The results return by the visibility API is correctly served by all replicas (eventually)
In case the current leading replica is terminated, reconciliation correctly fails over to the newly elected leader replica

/assign

/remove-lifecycle stale

/remove-lifecycle stale

/remove-lifecycle stale


Is there any way to upload application to the organization?

hello!
looks like original api https://support.hockeyapp.net/kb/api/api-apps supports owner_id, which, as i understand, is needed to upload directly to the organization.

Created a pull request.

#110


framework not found FirebaseDatabase

Xcode version: 13.3_
Firebase SDK version: 8.13.0_
Installation method: CocoaPods (select one)
Firebase Component: Firestore_
Target platform(s): macOS

[REQUIRED] Step 2: Describe the problem
I was using Firestore 8.13.0 and wanted to ensure my pods were all updated so I command-lined pod update. Cocoapods then downgraded all of my pods to pre-7.0 release to 6.34.0.
After finding issue 7195 and updating my podfile, deintegrating and the pod install all of the current versions were installed.
Installing Firebase 8.13.0 (was 6.34.0)
Installing FirebaseAuth 8.13.0 (was 6.9.2)
Installing FirebaseCore 8.13.0 (was 6.10.4)
Installing FirebaseCoreDiagnostics 8.13.0 (was 1.7.0)
Installing FirebaseFirestore 8.13.0 (was 1.19.0)
Installing FirebaseFirestoreSwift 8.13.0-beta (was 0.4.0)
Installing GoogleDataTransport 9.1.2 (was 7.5.1)
Installing GoogleUtilities 7.7.0 (was 6.7.2)
Installing PromisesObjC 2.0.0 (was 1.2.12)
Installing abseil 0.20200225.0
Installing nanopb 2.30908.0 (was 1.30906.0)

However, the project (it's about 10 lines of code) will no longer compile. The error is
framework not found FirebaseDatabase
Steps to reproduce:
hmmm... pod install and then build?
Relevant Code:
The podfile
project 'FirestoreTest.xcodeproj'

platform :osx, '10.15'

target 'FirestoreTest' do
  use_frameworks! :linkage => :static

  pod 'Firebase/Auth'
  pod 'Firebase/Firestore'
  pod 'FirebaseFirestoreSwift', '~> 8.0-beta'
end

Top of the project
import Cocoa
import Firebase
import FirebaseFirestore
import FirebaseFirestoreSwift

class ViewController: NSViewController {

The error

Looks like there is a reference to FirebaseDatabase in the Xcode project. pod deintegrate and another pod install might solve it. Otherwise you'll need to investigate where it's occurring in the project and remove it.  (or add pod 'FirebaseDatabase' to the Podfile.

Thanks @paulb777
No reference to FirebaseDatabase is in the project code. The only reference to it is in Google Firebase.h from the FirebaseCore Pod as shown in the below image, but I am not importing-ing anything like that.
Should the podfile include FirebaseDatabase? e.g. pod 'Firebase/Database' even though we are not using the Realtime Database at all?
I added that, deintegrated, pod install and then got a different error framework no found FirebaseStorage
So, I then added pod 'Firebase/Storage', deintegrated, pod install and it now seems to be working.
We are not using the Realtime Database nor Storage in any way so I am not sure what's causing the issue.
Here's my updated podfile which is working at this time.
project 'FirestoreTest.xcodeproj'

platform :osx, '10.15'

target 'FirestoreTest' do
  use_frameworks! :linkage => :static

  pod 'Firebase/Auth'
  pod 'Firebase/Database'
  pod 'Firebase/Firestore'
  pod 'Firebase/Storage'
  pod 'FirebaseFirestoreSwift', '~> 8.0-beta'
end

Weird. Try searching the project.pbx file in the Xcode project directory in a text editor or grep.

Hmm. I don't have a project.pbx file anywhere on my drive.
If you were referring to the project.pbxproj file that's inside the XCode app_name.xcodeproj package, I opened that and no references to FirebaseDatabase exist
I finally gave up and reconstructed the project from scratch using the podfile I outlined above, which is working correctly.. I will circle back around if I can find a way to consistently duplicate the issue.


Update README.md

Added https://github.com/Sematre/typst-letter
Repo URL:

Thanks for the awesome contribution, @basings !


Add dashboards for Alertmanager's mixin

Feature request
It would be lovely if Alertmanager's mixins could include two dashboards:

Alertmanager monitoring: To monitor Alertmanager itself, it would include metrics that are exposed by Alertmanager.
Alertmanager alerts: An informational dashboard that tells us what alerts are currently at the firing state, split by severity. For this one, I think it would be necessary to have Alertmanager's Grafana Datasource plugin, so I'm not sure how viable it could be.

Perhaps let's defer that to a possible native support for displaying alerts in Grafana.

Sounds good to me :)
Regarding the dashboard that monitors Alertmanager itself, could we start with a plain JSON? Or do you prefer that we should already start using jsonnet+grafonnet?

I've practiced a little bit with grafonnet-lib this last week. I think I'll have no problem creating the dashboard with jsonnet instead of plain JSON :)

One might argue if jsonnet is the right way to do that, but since the alerts are already provided in jsonnet, I would do the same with dashboards, at least for now.

Well, the mixin design document does suggest jsonnet above all other options, I don't see why not use jsonnet 🤷

As long as it is explained how someone not using jssonnet can also benefit from these dashboards, this is all good. (Not everyone uses it.)
I would also like to point out that there has not been a release of alertmanager in alsmot a year and the most useful feature "time based muting" has finaly been merged.
Is there something blocking release?


Incorrect usage of ${tld}

Unless I am using this wrong, if you configure dnsmasq to use something other than .dev, it fails to find the template file because obviously the template file isn't going to change it's name based on the tld specified.
This change will allow it to find the template file, and because the template file appears to have placeholders in it for correctly setting the tld, and it will be named correctly, I believe this should fix the issue.

This has been superseded by the work done in #17. Please let me know if anything has been missed.


sdk-release-1.4.1

Description
Enter a detailed description of the PR here, including the nature and purpose of the changes.
JIRA Ticket
Include a link to the JIRA Ticket linked to this PR.
Issue-0000
Additional Info (Test steps / Steps to reproduce etc.)
Details on how to test the feature

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.Anjali P M seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.

CLA issue


API management scalability is not "quick"

Hello,
In this document you say: "To support highly concurrent scenarios, turn on API Management autoscaling. Autoscaling quickly expands API Management capabilities in response to growing numbers of incoming requests".
By experience, API management takes roughly 2 hours to scale, therefore I wouldn't describe it as a way to support highly concurrent scenario if you expect it to "quickly" expand the capabilities.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: d61c0c47-bb1e-5bd4-55ed-92058c3c1e2b
Version Independent ID: 09757b3e-205b-4263-fada-4d0224048f6f
Content: Protect APIs with Azure Application Gateway and Azure API Management - Azure Reference Architectures
Content Source: docs/reference-architectures/apis/protect-apis.yml
Service: architecture-center
Sub-service: reference-architecture
GitHub Login: @fabriciosanchez
Microsoft Alias: fabriciosanchez

Thanks for reporting - this issue is under review. This is a Microsoft Internal DevOps Bug ID # 502301


Writer: initial implementation

This PR creates an implementation of io.Writer that can be passed to log.SetOutput in order to route log messages from the log package via github.com/apex/log.
Everything gets logged at Info level, I'm not sure there's a solution.
Fixes avct/birdseed#3047

Partially addressed avct/birdseed#3048


[5pt] Gaps in inundation with latest ras2inundation.py

Short description explaining the high-level reason for the new issue.
Current behavior
There appears to be a bug in the latest version (dev) of ras2inundation.py that results in missing inundation extents for some areas. We are testing the code against newly produced geocurve data from the USGS libraries. When running the original RAS2FIM script (the one that draws from precomputed geopackages via the filename field, there are no gaps. This is the version of ras2inundation.py that we are running. It has some minor changes, but the core logic is the same as the historically used version (it pulls from precomputed polygons via the filename field.
Ideally, the geometry column only could be used, as is designed in the dev version of the script, so hopefully this is a simple fix. It could also have to do with bad geometries, however we have confirmed that the geometries are using "is_valid".
Expected behavior
Inundation maps with no gaps.
Steps to replicate behavior (include URLs)
I would try testing to see if this behavior occurs on OWP's existing geocurve data to see if the issue can be reproduced.
Screenshots
The brown "out_new" (brown) represents the inundation map generated from the dev version of ras2inundation.py and the "ras_out" (gray) represents the historical approach where precomputed geopackages are referenced.

Carson and I researched this and we believe it has been fixed. We back fixed it into the V1 branch but is also in the new dev (v2) branch.  V2 version fix was added in PR 231 and V1 version fix was added as part of PR 230.   Any chance you were working with an older version of ras2inundation.py?  Let me know as I am currently making some minor tweaks to it (now in the tools folder) to give it  more re-ability and traceability.


Add fluent interface

Implements VRMManager.humanoidBone fluent interface
vrmManager.getBone('hips') // as Nullable<TransformNode>
// turns
vrmManager.humanoidBone.hips // as TransformNode or raise error

Implements VRMManager.rootMesh for Model Transformation
vrmManager.rootMesh.addRotation(0, 1, 0);

morphing will not throw error, ignored.
add vscode files

:tada: This PR is included in version 1.4.0 :tada:
The release is available on:

GitHub release
npm package (@latest dist-tag)

Your semantic-release bot :package::rocket:


Lab 02- Sort algorithm implementation

Implement bubble sort
Implement heap sort
Add test cases
Fix coverage issue

Fixes #
Changes proposed in this PR:

Codecov Report

Merging #111 into master will not change coverage.
The diff coverage is 100%.

@@          Coverage Diff          @@
##           master   #111   +/-   ##
=====================================
  Coverage     100%   100%
=====================================
  Files          35     36    +1
  Lines         475    520   +45
=====================================
+ Hits          475    520   +45

Impacted Files
Coverage Δ

02_bubble/jacklee/main.go
100% <100%> (ø)

Continue to review full report at Codecov.

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Why scraper add "checkpoint" into the address ?

Hi,
When I make a test with Donald Trump I have this result, can you help me ? :
INFO: Ignoring response <404 https://mbasic.facebook.com/checkpoint/DonaldTrump>: HTTP status code is not handled or not allowed
Why the scraper add /checkpoint/ into the link ?

Hi, sorry for my bad english.
I also encountered this problem a few days ago.
Try login facebook account on browser and goto this site https://mbasic.facebook.com/gettingstarted/.
Click all the setting make sure there is no more personal info setting page when you login and try the crawler again.

Thanks for your reply. I try your solution but now when scraper try to scrape, he make it on this kind of webadress : https://mbasic.facebook.com/login/*******
and i have a 404 error : <404 https://mbasic.facebook.com/login/*******
Another solution maybe ?

Try to go to https://mbasic.facebook.com/checkpoint and verify your account


speed benchmark

Initial draft for speed benchmark, using spaCy, stanza, flairNLP, HF transformers, etc.

TODO: define default corpus? Currently only works after dropping in .txt files in texts.
TODO: double-check whether some of the other libraries have better/faster capabilities for multi-doc processing

Also updated the readme and config files from other projects, according to the latest changes.

Ah, the CI fails because the updates to the configs etc are not yet reflected in a new spacy-nightly release. I think we can probably merge this anyway, and update pins & releases etc later.


Add custom function findMax()

Why user need to specify it? I think this method should be internal.

Give an example, please.

Do you ask @LAV45 or me?

You.

Seems like I overlooked the point of that.
This is kind of "sortable scope", but max is definetely redundant here.

Example
One product can have multiple images
Table Image

id
product_id
sort_order

1
1
1

2
1
2

3
1
3

4
2
4

5
2
5

When you add new pictures sort_order increases to max + 1
sort_order almost copies the id field
When sorting images in one product value fields sort_order just swapped while sort_order field is mandatory and must be filled

id
product_id
sort_order

1
1
3

2
1
2

3
1
1

4
2
5

5
2
4

because the items are sorted only within their product then there is no need to set a field sort_order huge value. In DB (mysql) for the field sort_order you can use tinyint (1)

id
product_id
sort_order

1
1
3

2
1
2

3
1
1

4
2
2

5
2
1

I made a string with maximum values sort_order in a separate method findMax, so you can add your own rules for getting the max sort_order

I think user should care only about setting sortable scope condition, and not about finding max. And you kind of mixing logic of setting sortable scope and finding max.

Also you are using different ways of storing order for different products.

That's why I gave the example of code in comments, because it is not mandatory. findMax you can customize as needed.
use himiklab\sortablegrid\SortableGridBehavior;

public function behaviors()
{
    return [
        [
            'class' => SortableGridBehavior::className(),
//            'sortableAttribute' => 'sortOrder'
//            'findMax' => function() {
//                return self::find()
//                    ->where(['product_id' => $this->product_id])
//                    ->max('sort_order');
//            },
        ],
    ];
}

Still doesn't make sense for me.

:+1: cool, offer your

You can see how I handle this in my similar extension.
https://github.com/arogachev/yii2-sortable

So the user shouldn't think about implementation details, finding maximums, etc.


Cryptsetup fails to open partition with TPM

Describe the bug
A clear and concise description of what the bug is.
Steps To Reproduce
Steps to reproduce the behavior:

Get a LUKS partition with a TPM key
Try to open said partition with only the TPM

Expected behavior
A clear and concise description of what you expected to happen.
The partition just opens when doing e.g. sudo cryptsetup open --token-only --debug --test-passphrase /dev/nvme0n1p3
Screenshots
If applicable, add screenshots to help explain your problem.
cryptsetup open

# cryptsetup 2.6.1 processing "cryptsetup open --token-only --debug --test-passphrase /dev/nvme0n1p3"
# Verifying parameters for command open.
# Running command open.
# Installing SIGINT/SIGTERM handler.
# Unblocking interruption on signal.
# Allocating context for crypt device /dev/nvme0n1p3.
# Trying to open and read device /dev/nvme0n1p3 with direct-io.
# Initialising device-mapper backend library.
# Trying to load any crypt type from device /dev/nvme0n1p3.
# Crypto backend (OpenSSL 3.0.12 24 Oct 2023 [default][legacy]) initialized in cryptsetup library version 2.6.1.
# Detected kernel Linux 6.1.69 x86_64.
# Loading LUKS2 header (repair disabled).
# Acquiring read lock for device /dev/nvme0n1p3.
# Opening lock resource file /run/cryptsetup/L_259:3
# Verifying lock handle for /dev/nvme0n1p3.
# Device /dev/nvme0n1p3 READ lock taken.
# Trying to read primary LUKS2 header at offset 0x0.
# Opening locked device /dev/nvme0n1p3
# Verifying locked device handle (bdev)
# LUKS2 header version 2 of size 16384 bytes, checksum sha256.
# Checksum:9ecc9337b52680b5a74c6a83e195e5451083e11b80e17592a2868413cdbe8c60 (on-disk)
# Checksum:9ecc9337b52680b5a74c6a83e195e5451083e11b80e17592a2868413cdbe8c60 (in-memory)
# Trying to read secondary LUKS2 header at offset 0x4000.
# Reusing open ro fd on device /dev/nvme0n1p3
# LUKS2 header version 2 of size 16384 bytes, checksum sha256.
# Checksum:71499ecb102c1c66aaa35851c49e70519f706d909b0e032c5d0f53db5cae7301 (on-disk)
# Checksum:71499ecb102c1c66aaa35851c49e70519f706d909b0e032c5d0f53db5cae7301 (in-memory)
# Device size<PHONE_NUMBER>024, offset 16777216.
# Device /dev/nvme0n1p3 READ lock released.
# PBKDF argon2id, time_ms 2000 (iterations 0), max_memory_kb 1048576, parallel_threads 4.
# Checking volume passphrase using token (any type) -1.
# Token 0 unusable for segment 0 with desired keyslot priority 2.
# Token 1 unusable for segment 0 with desired keyslot priority 2.
# Token 0 unusable for segment 0 with desired keyslot priority 1.
# Token 1 unusable for segment 0 with desired keyslot priority 1.
No usable token is available.
# Releasing crypt device /dev/nvme0n1p3 context.
# Releasing device-mapper backend.
# Closing read only fd for /dev/nvme0n1p3.
Command failed with code -1 (wrong or missing parameters).

cryptsetup luksDump

LUKS header information
Version:        2
Epoch:          12
Metadata area:  16384 [bytes]
Keyslots area:  16744448 [bytes]
UUID:           f1d7fec1-30f4-4a35-b9a8-8a5812adf3ff
Label:          (no label)
Subsystem:      (no subsystem)
Flags:          (no flags)

Data segments:
  0: crypt
        offset: 16777216 [bytes]
        length: (whole device)
        cipher: aes-xts-plain64
        sector: 512 [bytes]

Keyslots:
  0: luks2
        Key:        512 bits
        Priority:   normal
        Cipher:     aes-xts-plain64
        Cipher key: 512 bits
        PBKDF:      argon2id
        Time cost:  8
        Memory:     1048576
        Threads:    4
        Salt:       a5 7f 55 68 13 f6 b3 fc f9 4c 1c fc 09 95 c0 a5
                    8d c3 98 c4 87 5e a2 9a 70 6a 13 2b 62 50 10 e4
        AF stripes: 4000
        AF hash:    sha256
        Area offset:32768 [bytes]
        Area length:258048 [bytes]
        Digest ID:  0
  1: luks2
        Key:        512 bits
        Priority:   normal
        Cipher:     aes-xts-plain64
        Cipher key: 512 bits
        PBKDF:      argon2id
        Time cost:  8
        Memory:     1048576
        Threads:    4
        Salt:       f0 82 5a 60 7a fe 87 f5 48 15 e8 5b c7 d9 f2 0d
                    12 8d bb ee 01 c7 08 ed ac b0 46 3d 7d 43 bc ac
        AF stripes: 4000
        AF hash:    sha256
        Area offset:290816 [bytes]
        Area length:258048 [bytes]
        Digest ID:  0
Tokens:
  0: systemd-tpm2
  1: systemd-tpm2
Digests:
  0: pbkdf2
        Hash:       sha256
        Iterations: 330989
        Salt:       2a 28 1d e6 ef 4f fd fe 01 96 3b 61 fc 7a 1d 8b
                    41 b3 de 55 c3 e3 e6 db f5 39 3b 0c e0 b0 ed 92
        Digest:     1e 73 c1 bd b9 86 73 34 4e 94 b2 c6 7f d9 0f d1
                    a0 34 71 e3 71 d2 ac 82 f5 f4 81 d2 42 53 c3 20

Also how do I cleanup the multiple token entries?
I ideally should remove all tokens and enroll a new tpm key again.
This would also be good to know, if I ever decide/need to update secureboot dbs.
Another thing that I'm wondering is why systemd-cryptsetup does not exist in my path.
The arch wiki suggest trying systemd-cryptsetup attach mapping_name /dev/sdX - tpm2-device=auto, but that doesn't work for me, because the command itself cannot be found?
I heard, that it's as a binary maybe in the systemd nix-store somewhere? Having this command accessible makes about as much sense as having systemd-cryptenroll accssible in my eyes.
Additional context
Add any other context about the problem here.
Notify maintainers

Metadata
Please run nix-shell -p nix-info --run "nix-info -m" and paste the result.
[user@system:~]$ nix-shell -p nix-info --run "nix-info -m"
 - system: `"x86_64-linux"`
 - host os: `Linux 6.1.69, NixOS, 23.11 (Tapir), 23.11.20240101.2d2ea8e`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.18.1`
 - channels(root): `"nixos-23.11"`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixos`

Add a :+1: reaction to issues you find important.

Could be the same as https://github.com/NixOS/nixpkgs/issues/265366

I updated to 24.05 lately, and I get a similar message now:
sudo cryptsetup open --token-only --debug --test-passphrase /dev/nvme0n1p3:
[snip]
# Checking volume passphrase [keyslot -1] using token.
# Token 0 unusable for segment 0 with desired keyslot priority 2.
# Trying to load libcryptsetup-token-systemd-tpm2.so.
# libcryptsetup-token-systemd-tpm2.so: cannot open shared object file: No such file or directory
No usable token is available.


[no-unused-state] Ignore computed property keys for no unused state rule

For https://github.com/yannickcr/eslint-plugin-react/issues/1361.
This sets the no-unused-state rule to ignore computed property keys when the contents aren't literal.
I think it should cover all kinds of literals for checking unused state properties because it could happen in types other than string and could be checked. If that is undesirable, I could change it to only checking string literals.
Other than that, let me know what other improvements you have in mind.

 Look forward to doing more.


Add Resnet50 Retraining

Added code to retrain Resnet50.
Work in progress! Do not merge!

Current coverage is 93.45% (diff: 90.90%)

Merging #36 into master will decrease coverage by 0.10%

@@             master        #36   diff @@
==========================================
  Files            14         16     +2
  Lines           838        871    +33
  Methods           0          0
  Messages          0          0
  Branches        129        138     +9
==========================================
+ Hits            784        814    +30
- Misses           40         41     +1
- Partials         14         16     +2

Powered by Codecov. Last update ab2712f...a5ba737

Current coverage is 93.53% (diff: 93.22%)

Merging #36 into master will decrease coverage by 0.02%

@@             master        #36   diff @@
==========================================
  Files            14         16     +2
  Lines           838        897    +59
  Methods           0          0
  Messages          0          0
  Branches        129        133     +4
==========================================
+ Hits            784        839    +55
- Misses           40         44     +4
  Partials         14         14

Powered by Codecov. Last update ab2712f...b28b2ab

Current coverage is 94.00% (diff: 100%)

Merging #36 into master will increase coverage by 0.45%

@@             master        #36   diff @@
==========================================
  Files            14         16     +2
  Lines           838        901    +63
  Methods           0          0
  Messages          0          0
  Branches        129        133     +4
==========================================
+ Hits            784        847    +63
  Misses           40         40
  Partials         14         14

Powered by Codecov. Last update ab2712f...c623c84

Current coverage is 94.00% (diff: 100%)

Merging #36 into master will increase coverage by 0.45%

@@             master        #36   diff @@
==========================================
  Files            14         16     +2
  Lines           838        901    +63
  Methods           0          0
  Messages          0          0
  Branches        129        133     +4
==========================================
+ Hits            784        847    +63
  Misses           40         40
  Partials         14         14

Powered by Codecov. Last update ab2712f...6bc8fe2

I think this bit is ready for merging. @tiffapedia or @ymt123 could you review?

Current coverage is 94.38% (diff: 98.30%)

Merging #36 into master will increase coverage by 0.82%

@@             master        #36   diff @@
==========================================
  Files            14         16     +2
  Lines           838       1015   +177
  Methods           0          0
  Messages          0          0
  Branches        129        148    +19
==========================================
+ Hits            784        958   +174
- Misses           40         42     +2
- Partials         14         15     +1

Powered by Codecov. Last update ab2712f...0155618

Alright, the missing doc string is now fixed; ready for review. @tiffapedia


FR: Make Site variables available

Trying to do
@globalset('site', 'short_locale')

but getting the following error:
Call to a member function inCurrentSite() on null

Am I doing something wrong or is the site global not available?
Thanks for the great addon.

Is site an actual global? Like you created it?

Site is a global provided in antlers. https://statamic.dev/variables/site

Ah ya, that's not what this blade directive is for. This one is for actual GlobalSets, not global variables.

there you go @awcodes, added a new site directive for you in the latest release.

@edalzell Thank you so much. This is awesome. I really appreciate it.


Synchronize GitHub tags with composer.json keywords

What do you think about adding tool to synchronize composer.json keywords with GitHub repo tags?

@webimpress
Great idea! 👍
At the moment only the owners (@weierophinney and @ezimuel) can edit these tags. If we can write the keywords from the composer.json to the repository tags, then we can reduce the work for the repository owners.
Positive side effects:

consistency between composer.json keywords and repository tags
we can also update the repository tags 😉

@froschdesign not mine idea, @Xerkus suggest it to me on Slack :+1:
I'm working on the tool :smile:

@Xerkus
Great idea! 👍
@webimpress

I'm working on the tool

👍


Error: Module parse failed

Describe the bug
./node_modules/vue-next-select/dist/vue-next-select.es.prod.js 1:5557
Module parse failed: Unexpected token

Thank you for report this issue, could you provide more details like environments or reproduce steps?

Project was generated with vue-cli, it may be the problem?

Thank you again, no, It is because I didn't downgrade syntax. I will fix it.

@dragoonzx please try v2.0.1 again 😄 .


New logo/icon proposal

Good day sir. I am a graphic designer and i am interested in designing a logo for your good project. I will be doing it as a gift for free. I just need your permission first before I begin my design. Hoping for your positive feedback. Thanks

Hi @mansya ,
Thank you! I like the project's current logo developed by Hafiz Ahmed. I don't think that the project should change it:


fix: glob precedence in #263.

This doesn't work. The problem is that * should not be inserted by the user itself.


Set enable_fast_runtime_mode to True by default

Currently, enable_fast_runtime_mode is set to False in ttnn but we want the users to run at the full speed by default
Before it can be set to True, the following needs to be done:

allow_to_fallback_to_golden_function_on_failure flag should be deleted
failing tests should be updated to fallback to torch manually in the model/test code
Some unit tests need to be set to enable_fast_runtime_mode=False to test features like validation, logging, etc

in progress now


Can't authorize rclone with Dropbox

Failed to configure token: invalid character 'g' looking for beginning of value

What is your rclone version (eg output from rclone -V)

rclone v1.38
- os/arch: linux/amd64
- go version: go1.9

Which OS you are using and how many bits (eg Windows 7, 64 bit)

Ubuntu 14.04.5

Which cloud storage system are you using? (eg Google Drive)

Dropbox

The command you were trying to run (eg rclone copy /tmp remote:tmp)

rclone config

A log from the command with the -vv flag (eg output from rclone -vv copy /tmp remote:tmp)

Failed to configure token: invalid character 'g' looking for beginning of value

Seems like authorization method changed.

The auth method did change from v1 to V2 auth. Rclone is supposed to change it automatically for you but it looks like that didn't work for some reason. I assume that you used an older version of rclone and have upgraded?
Run through rclone config again and edit that remote. Don't change any values but do ask for the token again and it should start working.

I don't use rclone before. It is my first try.
Use auto config?
 * Say Y if not sure
 * Say N if you are working on a remote or headless machine
y) Yes
n) No
y/n> n
For this to work, you will need rclone available on a machine that has a web browser available.
Execute the following on your machine:
        rclone authorize "dropbox"
Then paste the result below:
result> g******-***********************
2017/11/01 09:53:31 Failed to configure token: invalid character 'g' looking for beginning of value
root@dcr01:~/rclone/rclone-v1.38-049-gd0b9baabβ-linux-amd64#

On remote machine when I press Apply on API Request Authorization it starts the endless process. I need remove redirect_uri field from request to receive auth code.
I also receive invalid character 'v' message for other Dropbox account.

Are you using the same versions of rclone at both ends?  From your log it looks like you are using a new version at the remote end and an old version at the local end?

I try version v1.38 on both ends with same results, same for Windows same for Linux. Version 1.38 beta only for Linux because it didn’t start on Windows.

When I run rclone authorize I get something like this
$ rclone authorize dropbox
If your browser doesn't open automatically go to the following link: http://<IP_ADDRESS>:53682/auth
Log in and authorize rclone for access
Waiting for code...
Got code
Paste the following into your remote machine --->
{"access_token":"XXXX","token_type":"bearer","expiry":"0001-01-01T00:00:00Z"}
<---End paste

So the thing you need to paste looks like
{"access_token":"XXXX","token_type":"bearer","expiry":"0001-01-01T00:00:00Z"}

Is that what you see?

Ok.
As I write early Waiting for code endless process. I get token “XXXX” form webpage and give to rclone.
Now I just replace XXXX to my token from you string and authorize rclone now. But it did’t work automatically.
Thank you. I can start testing it now.

Oh I see what you mean.

I need remove redirect_uri field from request to receive auth code.

You probably have a local firewall blocking rclone's web server it uses for receiving the token back. Rclone runs a web server on http://<IP_ADDRESS>:53682/ during the oauth process.

Hm. Maybe.
I can't reproduce that problem today. All works fine. Maybe it Dropbox temporary problem.
But I think better leave fully manual option.


Add more examples

Willing to accept examples on different datasets and models to demonstrate different parts of the Axon API and to demonstrate Axon's viability in the ecosystem. The TensorFlow guides are a great place to look for different datasets and problems. If you're blocked on any specific issue feel free to comment on the relevant issue with your use case :)

Hi @seanmor5 I am trying to create an example to predict diabetes with Axon and Nx, but I am still trying to understand how it works.
Currently I have an error:
X = #Nx.Tensor<
f32[615][8]
Y =  #Nx.Tensor<
s64[615]
This is the code I'm trying to create:
https://gist.github.com/tiagodavi/a905abeaf4d1f92c21f9df9043d196fe
StreamExecutor device (0): Host, Default Version
** (ArgumentError) expected input shapes to be equal, got {615} != {615, 1}
    (axon 0.1.0-dev) lib/axon/shared.ex:22: anonymous fn/1 in Axon.Shared."__defn:assert_shape!__"/2
    (nx 0.1.0) lib/nx/defn/compiler.ex:114: Nx.Defn.Compiler.__remote__/4
    (axon 0.1.0-dev) lib/axon/losses.ex:122: Axon.Losses."__defn:binary_cross_entropy__"/3
    (axon 0.1.0-dev) lib/axon/loop.ex:325: anonymous fn/5 in Axon.Loop.train_step/3
    (nx 0.1.0) lib/nx/defn/grad.ex:20: Nx.Defn.Grad.transform/3
    (axon 0.1.0-dev) lib/axon/loop.ex:332: anonymous fn/4 in Axon.Loop.train_step/3
    (axon 0.1.0-dev) lib/axon/loop.ex:1135: anonymous fn/4 in Axon.Loop.build_batch_fn/2
    (nx 0.1.0) lib/nx/defn/compiler.ex:101: Nx.Defn.Compiler.runtime_fun/4

Hi @tiagodavi! Axon's implementation of BCE expects y_true to have a last dimension of size 1 (there's an explicit check for shape equality between y_true and y_pred). If you add a new axis to your y_true: Nx.new_axis(y, -1) - then the error should go away.
We can probably relax the strictly equal shape constraint, feel free to open a PR otherwise I will open an issue to track.
Also, you might be interested in trying out [Explorer](https://github.com/elixir-nx/explorer) for easier Nx/Axon interop with structured data :)

Thank you @seanmor5 .
I was able to fix the error, but accuracy is quite bad. I am probably doing something wrong still.
model =
     input
     |> Axon.dense(features, activation: :relu)
     |> Axon.dense(features, activation: :relu)
     |> Axon.dense(1, activation: :sigmoid)

   trained_model =
     model
     |> Axon.Loop.trainer(:binary_cross_entropy, :adam)
     |> Axon.Loop.run([{x_train, y_train}], epochs: 10, compiler: EXLA)

   # trying to interpret sigmoid here
   result =
     model
     |> Axon.predict(trained_model, x_test, compiler: EXLA)
     |> Nx.map([type: {:s, 64}], fn x ->
       if x > 0.5, do: 1, else: 0
     end)

   IO.inspect Axon.Metrics.accuracy(y_test, result)

   #Nx.Tensor<
     f32
     0.3464052379131317
   >

Axon's accuracy should do that thresholding for you. What do you get if you just feed the result of Axon.predict(model, trained_model, x_test, compiler: EXLA) into Axon.Metrics.accuracy?

Something like that?
result =
      model
      |> Axon.predict(trained_model, x_test, compiler: EXLA)
      |> Axon.Metrics.accuracy(y_test)

    IO.inspect result

#Nx.Tensor<
f32
0.013071895577013493

I'll take this course to see if I can learn it better:
https://grox.io/language/nx/course

It is probably a bug, please send me the gist!

Sure, this is the most updated one:
https://gist.github.com/tiagodavi/a905abeaf4d1f92c21f9df9043d196fe


Can this be compiled to run on Windows 10, or Windows XP?

Assuming that a Windows 10 machine can run this code, can this run.c lllama2 be modified to be complied to run inference mode on a Windows 10 machine?
I asked Google Gemini 1.5 Pro this question and this is Gemini's response:
Compiling and Running the Code on Windows 10
While the provided code appears to be primarily written in C, it includes some POSIX-specific elements like mmap and munmap which are not directly available on Windows 10. Therefore, running this code directly on Windows 10 would require some modifications and additional libraries.
Here's a potential approach:

Replacing POSIX Functions:
Memory Mapping:
Use the Windows API functions CreateFileMapping, MapViewOfFile, and UnmapViewOfFile to achieve similar functionality as mmap and munmap.
Libraries like Boost.Interprocess could also provide cross-platform memory mapping solutions.
Other Functions:
Review the code for other potential POSIX-specific functions and find equivalent Windows API functions or libraries.
Compiler and Libraries:
Compiler:
Use a C compiler compatible with Windows, such as Microsoft Visual C++, MinGW, or Clang.
Libraries:
Ensure any required libraries (e.g., for linear algebra operations) have Windows versions or alternatives.
Code Structure:
Conditional Compilation:
The code already utilizes #if defined _WIN32 blocks. Adapt these sections to incorporate the necessary Windows-specific implementations.
Consider creating separate source files for platform-specific code to maintain clarity.
Building and Running:
Use the chosen compiler and build system to compile the code into an executable.
Run the executable from the command line, providing the required arguments (checkpoint path, options).
Additional Considerations:
OpenMP: The code utilizes OpenMP for parallelization. Ensure you have a compatible OpenMP library and compiler flags set up for Windows.
Testing: Thoroughly test the modified code on Windows 10 to ensure functionality and performance.
Tools and Libraries:
Microsoft Visual Studio
MinGW
Clang
Boost C++ Libraries
OpenMP library for Windows
Disclaimer:
Modifying the code to run on Windows 10 requires some C programming and Windows API knowledge. This response provides a general direction, and specific implementation details may vary.

lol.   yea absolutely. there is a small fix you need to compile it to run models over 4gig, like llama 7b. Just compile it with ming64 and run it first.

https://github.com/karpathy/llama2.c/pull/513

Hi. According to Google Gemini Pro, compiling a Llama2.c model on a Windows
10 machine is "difficult" also because of high RAM memory requirements.
And "Dependency Hell" due to "libraries optimized for Linux". I apprehend
that the windows-compile task is beyond my experience and practical
ability.   Can Windows run the Linux version of Llama2.c within a Windows
builtin Linux environment "MingW64 ~" prompt?  Is that the same method as
what you originally proposed?  Can you point to simple instructions printed
online?
On Sat, May 11, 2024, 12:03 AM James Delancey @.***>
wrote:

lol. yea absolutely. there is a small fix you need to compile it to run
models over 4gig, like llama 7b. Just compile it with ming64 and run it
first.
—
Reply to this email directly, view it on GitHub
https://github.com/karpathy/llama2.c/issues/516#issuecomment-2105527029,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/BHT6KT2R3CQSZGJRQKGVUEDZBWKAPAVCNFSM6AAAAABHJXVADWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBVGUZDOMBSHE
.
You are receiving this because you authored the thread.Message ID:
@.***>

Looking at the Makefile i see no compatibility issues with mingw. You can probably just clone the repo and run make in the root directory.


Windows on external main display overlay sketchybar

Hi there,
I have a multi-monitor setup where I use an external display as primary monitor. The MacOS menubar is configured to autohide. Windows that are on this external primary display are on top of sketchybar so that it isn't visible anymore. If I open an empty workspace I can see that it is there.
This does not happen on the main display, windows are sized in a way where sketchybar is visible.
Please let me know if there is anything I can provide that would help with understanding this and thank you for making aerospace!

You should setup something like this to use different gap for different monitor
[gaps]
outer.top = [
{ monitor."Built-in" = 4 },
{ monitor."DELL" = 32 },
32
]
execute aerospace list-monitors to see the monitor name.

@nohzafk thank you very much for the quick response, configuring the gap for the external display helped! What confuses me is that for the Built-In display it semms 0 is the correct config and this only has to be setup for the external display. Do you know if that is intended?

0 for built-in is fine. i set up 4 for some spaces to display the border


Goat goes wild

So running the goat... I did a gary sync-up... which touches everything...
The goat went crazy and ran around with it's horns out for about 10 mins... (broke the machine for about 10 minutes (100% on all cpu)).
It seems that the goat is watching any file changes in it's cwd and not just the configured locations? And / or the node_modules that are all touched by gary (even though they have not changed; just been felt up a bit by gary).

goat.config.json
{
  "name": "X",
  "version": "1.x",
  "browserSupport": [
    "> 1%",
    "last 2 versions"
  ],
  "locations": {
    "node_modules": "./node_modules",
    "styles": {
      "src": "components/",
      "dist": "css/"
    },
    "javascript": {
      "src": [
        "components"
      ],
      "dist": "dist"
    }
  },
  "styles": {
    "minify": true,
    "compass": false,
    "exclude": [],
    "sourceMaps": {
      "generate": true,
      "location": "/",
      "loadMaps": false,
      "identityMap": false,
      "debug": false,
      "addComment": true,
      "includeContent": true,
      "charset": "utf8",
      "destPath": "",
      "sourceMappingUrlPrefix": ""
    },
    "pxToRem": {
      "enabled": false,
      "settings": {
        "rootValue": 16,
        "replace": false
      }
    }
  },
  "bundler": {
    "js": {
      "output": {
        "filename": "[name].bundle.js",
        "publicpath": null
      }
    }
  }
}

Will close this for now as the problem is due to an external (gary sync-up)


vcl_msvc_warnings.h is not installed with ITK 5.0 RC1

I have built ITK 5.0 RC 1 on visual studio 2017 15.9.7. When I build a project against the installation of this build, it does not find vcl_msvc_warnings.h. The header is present in the source of ITK, but not in the installation folder. It is the same with master of ITK.
Version
5.0rc1, with RTK 2.0
Environment
Windows 10
Visual studio 2017 15.9.7
Compilation in 64 bits
Ninja
cmake command: cmake "D:/dev/library/source/ITK-5.0rc01" -G "Ninja" -DCMAKE_INSTALL_PREFIX:PATH=D:/dev/library/x86-64_msvc2017/itk/5.0_rc1 -DModule_RTK=ON -DRTK_BUILD_APPLICATIONS=OFF -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_DEBUG_POSTFIX=d -DBUILD_SHARED_LIBS=OFF -DBUILD_TESTING=OFF -DCUDA_TOOLKIT_ROOT_DIR=D:/dev/conan_c/Cuda/10.0/AI/extern/package/479e5c321685f6e20cbbf93c38ae334c54ade580

It seems equally that MetaIO is not installed. I am missing all the headers for this library.  On one of the cmake file associated with metaIO, I can find itk_module_target(ITKMetaIO NO_INSTALL). Is it normal ?

@Siron777 what is the header that depends on vcl_msvc_warnings.h? It may have been removed intentionally.
CC @hjmjohnson @dzenanz

This is vnl_vector.h, which is installed:
#ifdef _MSC_VER
#  include <vcl_msvc_warnings.h>
#endif

Maybe vnl_vector.h needs an update? @hjmjohnson touched it last, I think.


Don't ignore the Accumulo connector

Accumulo is the only connector that requires an actual instance of Accumulo and Zookeeper to be running. Start them in containers, maybe using Docker Compose.

Done in #5. Now annotations are extracted from compiled code, so starting up the dependencies is not required.


Deleteability should be removed for profilePhoto resource type

According to API reference, only GET and PUT are supported on the resource. As such, DELETE calls to the resource will fail with a "Method is not allowed".

As of today's announcement the DELETE method now works. Documentation doesn't reflect this, but finally can do this via Graph. Thanks!


Remove duplicate INSTALLER in RECORD

Summary
We write this a few lines down with a value passed in by the caller. I suspect I missed that this was already here (with a less accurate value) when adding INSTALLER.

This shouldn't really matter in practice but it is wrong.


Tap element2

Found a decent solution to tapping tabbed templates, and for tapping arbitrary elements. Not urgent, so leaving this in drafts until I can iterate on it for a bit longer.

I moved over some fixes from the accessibility branch that I had working on recently, but this should be ready for review. I'll make sure the tests are passing before pinging anyone there.

Test interview file in https://github.com/plocket/docassemble-ALAutomatedTestingTests/pull/187. Tested locally and passing 100%.

Future: I think one remaining improvement we could make in the future is to better handle when the tab doesn't exist. For example, for when the user has a typo.

How you you suggest handling it?

I think I'd try to detect the tab that has the actual ID. If it exists, can we assume its content exists too?

I suggest not using waitForSelector as that will slow everything down. Unless there's a reason you can think that the element would take a while to appear on the page.

Everything should be good (addressed the last comment, and added info to the changelog). The documentation is ready in https://github.com/SuffolkLITLab/docassemble-AssemblyLine-documentation/pull/244 and will be merged soon. I'll squash and merge now.


Incompatibility with Outliner plugin

My tasks from my daily note were not rolling over into the new daily note and I suspected it was due to the Outliner plugin installed and enabled.
I deleted the current day's daily note, disabled the Outliner plugin, recreated the Daily Note and saw that the previous day's tasks successfully rolled over.
This is on a Windows 11 PC.

I have it working fine with outliner and daily notes... it's been a while since you posted, so maybe fixed along the way.
Obsidian 1.0.3 and 1.1.0 of rollover (on windows 10)


[Suggestion] Add indicator for "current letter" when ordering alphabetically

:information_source: If you're interested in this feature, please leave comment or add a :+1:

Kind of issue

[x] Feature
[ ] Bug
[ ] Design
[ ] Other, namely:

Description
As per this comment, add an alphabetical indicator of where in the grid of icons you are - not present when ordering is by color or by relevance. For example. as seen in the mockup below :arrow_down:
An argument against this is that it is kind of redundant and may compete with the search functionality (i.e. users may try to search manually by scrolling to the right first letter and looking for an icon manually).

looks cool.
other than that it adds to the overall html and js size of the website, and it's only useful if the icons are alpha sorted (not sure if it should show on search results, since search results are significantly less in number and this may look bad in that case).
Too little usefulness for the HTML and js that needs to be added. I vote to close this one.

We could try a basic implementation to see if it looks bad when there are search results. Not to mention that it could just be hidden when there's a search query.
If size is a concern, this could still be added when we tackled that problem. In which case we could add a pending label for clarity.

size is always a concern with the way the icons are shown. The whole principle of serving the website as static HTML from the get go makes size a problem for... pretty much everything.
I would hide it on short search results. say, results <= 12 icons, so no scroll is needed.
again, I admit it looks very nice. But other than that... I'm going to focus more on the other tickets, for the time being.

Given a lack of interest in commenting or working on this issue, can we close it?

Up to you @jorgeamadosoria

Up to you @jorgeamadosoria

I wouldn't want to close tickets I didn't open, even if I really want to.


Get Error TwitterKit/TwitterKit.h file not found

URL: https://pub.dartlang.org/packages/flutter_twitter_login
Hi, when i using this package with setting ios platform is 9, then i will get the error "TwitterKit/TwitterKit.h file not found".
It loaded TwitterKit v3.0 but the code logic using api of TwitterKit v2.8

This issue was moved to roughike/flutter_twitter_login#12


No audio in the call with Quickstart example

I have followed all steps mentioned in the quickstart example with generating access tokens for device and simulator separately and installed app at both sides. When I call from my device to simulator, video works. I can see my video on simulator but audio does not come. I tried it many times but no audio. I checked speakers and everything but no success.
Please let me know if there is any quick solution. At least quickstart example should work.

@mobihunterz  Audio playout and recording does not work correctly on simulators is a known issue in Video SDK - https://www.twilio.com/docs/api/video/changelogs/ios#100-beta8-february-17-2017
I will let you know when this is fixed. I am sorry for the inconvenience.

Hi @mobihunterz and others,
I am pleased to say that our 1.2.0 release adds support for playback and recording on the iOS simulator.
There are however, some minor limitations. Firstly, you should set the sample rate of your computer's audio device to 48 khz. We tested the built-in audio device only.

After selecting 48 kHz I/O we had success with the following iOS simulator / Xcode combinations.
Xcode 9.0 Beta 2

Simulator
Operating System

iPhone 7 Plus
iOS 11, iOS 10.2

iPhone 7
iOS 11, iOS 10.2

iPhone 6s
iOS 11, iOS 10.2

iPhone 6s
iOS 11, iOS 10.2, iOS 10.0

iPhone 6 Plus
iOS 11, iOS 10.2

iPhone 6
iOS 11, iOS 10.2

iPhone 5s
iOS 11, iOS 10.2

iPhone 5
iOS 10.2

iPhone 4s
iOS 9.0

Xcode 8.3.3

Simulator
Operating System

iPhone 7 Plus
iOS 10.3, iOS 10.2

iPhone 7
iOS 10.3, iOS 10.2

iPhone 6s
iOS 10.3, iOS 10.2

iPhone 6s
iOS 10.3, iOS 10.2, iOS 10.0

iPhone 6 Plus
iOS 10.3, iOS 10.2

iPhone 6
iOS 10.3, iOS 10.2

iPhone 5s
iOS 10.3, iOS 10.2

iPhone 5
iOS 10.3

iPhone 4s
iOS 9.0

Best,
Chris Eagleston

Closing this issue since it's been resolved in our last release. We still plan to migrate this info to our docs pages.

Thanks for the info. I will check this.


fix: adding favicon

The path to icon is wrong somehow, I just referenced it manually and imported its src in herf
closes #626

Good job @rupali-codes!

@tobySolutions It's closed unmerged, and i can't see favicon on site stll

Why was this closed?

@krshkun I don't know, by mistake maybe

@krshkun i've made another PR


refreshed orthofinder support to latest generic version

OrthoFinder is used for orthology identification, which is essential for subsequent gene family tree building. However, this program only supports Python 2. Previously, a special version of OrthoFinder 0.4 which supports Python 3 was obtained from the developers. It is outdated however. In order to run up-to-date versions of OrthoFinder (now 1.1.4), a separate Python 2 conda environment is created, and is called from a new Bash script (like other external programs), instead of directly called from the Python scripts.
Note: OrthoFinder requires BLAST+ for homology search. Meanwhile, it has an option that allows the user to provide pre-computed BLAST results. Therefore, there is room for hacking this process by providing DIAMOND results. It is to be further explored.
Update: I did this hack. So now OrthoFinder is married to DIAMOND.
Note: This PR is NOT dependent on the last PR (#60).
PS: There really isn't any unit test added or removed. The coverage decrease is simply because some redundant codes are removed.
@ekopylova @wasade

Coverage decreased (-0.2%) to 94.135% when pulling 6142f78b883b8e03b90252cb51e546d1129750cc on qiyunzhu:orthofinder into d44189f5b0880a7d0056ecd80c65ea70a3182e37 on biocore:master.

Coverage decreased (-0.2%) to 94.135% when pulling 6142f78b883b8e03b90252cb51e546d1129750cc on qiyunzhu:orthofinder into d44189f5b0880a7d0056ecd80c65ea70a3182e37 on biocore:master.

PS: There really isn't any unit test added or removed. The coverage decrease is simply because some redundant codes are removed.

Are you planning on making this tool uninstallable?  If so, you'll need to make this either strictly Python 2 or Python 3.  Since we are in the process of making all of our tools Python 3 compatible, it'll make it difficult to directly interface with our tools in the lab.  So it is not recommended to go the Python 2 route.
If you decide to make everything Python 3 compatible, there are a few possible options

Copy over OrthoFinder to the WGS-HGT and make it Python 3.  Looks like there is very little code in the main repository, so it should be very fast to do that.  However, you'd have to kill the BSD license in favor of GPL, since you would be copying GPL code.
Push in a PR into OrthoFinder to make it Python 3 compatible.

Coverage decreased (-0.3%) to 93.732% when pulling 4c0dd7339f9ba28ec7b08069ce69aea6f7314ca2 on qiyunzhu:orthofinder into d5d7e164c60d9d5923b543143aa774b193bb1ba8 on biocore:master.

@mortonjt Thanks for your comments! To everyone else, Jamie and I discussed offline about the dependency issue. The reality is that WGS-HGT has whole loads of dependency issues. Python 2 is not the worst (see here for another example). Now that I managed to figure our an automated solution to run both Python 2 and 3 programs in the same pipeline, I think we can live with it. (Actually I figured out two solutions. If you want to know please leave message). There is a long way to go before making WGS-HGT user friendly.

Note that the IntervalMetadata is now merged into scikit-bio.  So we don't need to rely on my conda channel anymore.

@mortonjt Yes I noticed and already removed it.

@mortonjt @ekopylova @wasade Anyone would like to take a look? Thanks!

👍

Thank you bros! @mortonjt @RNAer @tkosciol


Paramedic & Security Crew Monitors

About the PR

Added Paramedic and Security crew monitors, renaming the base one to CMO's. The Paramedic one only shows crit/injured crew, and the Security one only shows Security and Command, crit or not.
Paramedics start with the paramedic one, and Wardens start with the sec one. CMO and HoS have an extra in their lockers as well.
https://github.com/space-wizards/space-station-14/assets/52761126/ac803b38-c556-481f-ad48-6d771c8e2d39
Why / Balance

Removing the paramedic monitor was understandable, but unfortunate, and I've always wanted a paramedic monitor that only shows crit/dead people for convenience anyway. I can remove the sec monitor from spawning with HoS/Warden if people think its bullshit; it's more there for brigmedic downstreams (of which I play on!) and just as an example of how to use the department/role controls, but having a monitor for prisoners might be really useful.
Technical details

I modified the crew monitor to take some extra parameters, allowing monitors to select who they want to see. Theoretically you could probably also use this to search in the UI of the full monitor (ie narrow down to just security), but I haven't touched UI stuff yet.
I messed around with adding a noise if someone's crit/dead, but it didn't work out so well, I'd have to learn more about the codebase to get something like that to work. (Needs a mute toggle. By god it needs a mute toggle.)
Media

[X] I have added screenshots/videos to this PR showcasing its changes ingame, or this PR does not require an ingame showcase

Changelog
:cl:

add: Added Paramedic and Security Handheld Crew Monitors with more limited functionality.

Perhaps sec also shows people with tracking implants?

(

normal crew monitor already does this

Perhaps sec also shows people with tracking implants?

if that was stored in SuitSensorStatus, i would filter it in right now, but the crew monitoring system is not privy to that data and i don't have time rn to look into it; could be a future PR.

Is there anyway to replace server not found with something like ‘no crew are currently dying’. It would be a good quality of life to see when the server is down versus it just saying no server because no one is dying

Is there anyway to replace server not found with something like ‘no crew are currently dying’. It would be a good quality of life to see when the server is down versus it just saying no server because no one is dying

i changed it to say 'no server found or no listings available', which i figured was vague enough to work. unfortunately, that is set just by having no data sent to the monitor, so the monitor literally does not know whether the server is down or no one is injured. like with the tracking implants, i would have to modify code further away from the functionality of this PR, which mostly relies on data that was already available to the system, so that could be a future PR if its too confusing (or i could just make the text more explicit)

Perhaps sec also shows people with tracking implants?

normal crew monitor already does this

I'm saying for the security monitor to show people with tracking implants.
"The Security one only shows Security and Command, crit or not."

I like the paramedic crew monitor but why would security need one?

I like the paramedic crew monitor but why would security need one?

In some ss13 forks, one of the warden's jobs is to check the health of the officers. It's useful for sec to know if and where their officers' dead bodies are. Might have some balance implications though.

I like the paramedic crew monitor but why would security need one?

crazily enough there is a Why / Balance section of the pr. that explains this

looks like you forgot to add to migration yml

ah, more like didn't know this was a thing, whoops. guess i'll remove that map change

i can remove the sec one if thats the main holdup for merging this

I thought a cool way to do this instead would be for paramedics to get a special pinpointer (not the nuke pinpointer), by default it would track nothing. The paramedic can go to a crew monitoring console and they can select the pinpointer to track someone. (i.e. if John Doe is crit w/ cords on, you use the crew monitor, track him, and then the pin pointer will point to him) The pinpointer will stop tracking if they turn their cords off, a jammer is active near them, or their jumpsuit/skirt is removed.

Sec having their own crew monitor just to bypass med isn't something we want. Paramedic having their own crew monitor makes the CMO's less unique as an item and kind of comes across like a way to revert the change.

Sec having their own crew monitor just to bypass med isn't something we want. Paramedic having their own crew monitor makes the CMO's less unique as an item and kind of comes across like a way to revert the change.

what about the code changes i did that allow them to exist, for downstreams? i know you guys 'dont do things for downstreams' but its impossible to do this with yml changes alone.


Using v1.10.0 of go-micro encountered "reading gopkg.in/fsnotify.v1/go.mod at revision v1.4.7: unknown revision v1.4.7"

When build the application on 07-Jun-2020 below error encountered:
go<EMAIL_ADDRESS>requires
<EMAIL_ADDRESS>requires
<EMAIL_ADDRESS>reading gopkg.in/fsnotify.v1/go.mod at revision v1.4.7: unknown revision v1.4.7
I didn't changed the version. it worked 10 days ago.
After pulling the<EMAIL_ADDRESS>manually it worked fine.

What are you trying to do?
compile the application on version v1.10.0 as per requirement.

What did you expect to happen?
it should be compiled seamlessly as happened 10 days ago.

What happens instead?
it gave error from another lib while pulling the same.
<EMAIL_ADDRESS>

Environment:
go version is 1.12

Sorry nut this is too old version. Try to upgrade to more recent version


Godot 4

Godot 4 port of addon, there are no new features

Hello :) !
I will not review 2646 files with +32,589 −31,687 updates.
Tell me files you want I see. Or if you are confident merge it :) !

I will not review 2646 files with +32,589 −31,687 updates.

Sorry about that most of this files/changes are made by importing graphics files to Godot 4.
Gihtub should have option to look up changes only in given commit in PR.
I'm confident is good to go, for merge I only need to update look of Nodes Icons a bit.


Update manage-compute-with-azure-functions.md

Scaling synapse requires a "c" at the end of the ServiceLevelObjective value. Without it, this code produces a JSON error when it is run. Image index-js.png should also be updated to reflect this.

@sql-chris-albert : Thanks for your contribution! The author(s) have been notified to review your proposed change.

@sql-chris-albert : Thanks for your contribution! The author(s) have been notified to review your proposed change.

#sign-off

Publishing in this repository is suspended until Tuesday, September 22. Merging will resume at 7 AM Pacific Tuesday.
This PR is ready to merge on 9/22.


Review names and document all output files and figures

A reviewer said:

Some of the names of the RiboViz2 output files are not intuitive. For example, a file labeled "3nt_periodicity.pdf" would indicate a plot showing the periodicity of reads. Instead, it appears to be a metagene plot which can indicate the periodicity but should include ‘metagene’ in the plot title as well. "pos_sp_rpf_norm_reads.pdf" appears to be a normalised metagene profile but the name here is very different. Consequently, clear explanations of the output files should be provided.

This is accurate and helpful, we need to respond to it:

[x] go through all output files (tsv and figures) and write a description of them, then consider renaming.
[x] new documentation file docs/user/riboviz_outputs.md that collects those descriptions of all the output files.
[ ] update output file names in docs/user/prep-riboviz-operation.md and link that to docs/user/riboviz_outputs.md
[ ] update prep_riboviz.nf and/or generate_stats.figs.R and the static html to account for new names. Be prepared to grep the repository.
[ ] update system tests to account for new file names.

The next step is to list the output files and make a checklist for all of them, further down this issue ticket.
Let's discuss with @FlicAnderson and @swinterbourne tomorrow.

So currently we have this documentation of the output files in prep-riboviz-operation.md.

I created branch output-docs-395 for this. About to start a new document in that branch, docs/user/riboviz_outputs.md.

Reviewing names, I think the ones that are okay as they are would be files like the bam and H5 files, which just have the sample name followed by the file type. I also think read_lengths.tsv and pdf is a pretty self explanatory name so probably doesn't need changed

Slightly related documentation table of contents issue ticket here (as if #400 is resolved soon, then the new documentation for #395 should be added to it)

The ones I can remember confusing me based on their name when I started were; 3nt_periodicity, pos_sp_nt_freq, pos_sp_rpf_norm_reads, codon_ribodens, and startcodon_ribogridbar

Checklist of output files. Let's tick them off as we rename or add to documentation

[ ]TPMs_collated.tsv
[ ]read_counts.tsv
[ ]<SAMPLE_ID>.bam
[ ]<SAMPLE_ID>.bam.bai
[ ]minus.bedgraph
[ ]plus.bedgraph
[ ]<SAMPLE_ID>.h5
[ ]3nt_periodicity.tsv
[ ]3nt_periodicity.pdf
[ ]read_lengths.tsv
[ ]read_lengths.pdf
[ ]pos_sp_nt_freq.tsv
[ ]pos_sp_rpf_norm_reads.pdf
[ ]pos_sp_rpf_norm_reads.tsv
[ ]features.pdf
[ ]tpms.tsv
[ ]codon_ribodens.tsv
[ ]codon_ribodens.pdf
[ ]startcodon_ribogridbar.pdf
[ ]startcodon_ribogrid.pdf
[ ]3ntframe_bygene.tsv
[ ]3ntframe_propbygene.pdf
[ ]<SAMPLE_ID>_output_report.html

I think the following could be improved in naming, mentioning metagene plots where that's what's happening:

3nt_periodicity
pos_sp_nt_freq  (expand)
pos_sp_rpf_norm_reads  (expand, perhaps doesn't need RPF in it, since we don't currently output rna-seq position specific normalised reads?)
features  (features of what could be clearer)
tpms  (is this sufficiently known as an acronym? Perhaps include if 'by sample' or 'per gene'?)
codon_ribodens  (ribodens is not particularly intuitive?)
startcodon_ribogridbar  (perhaps re-word to be more suggestive that this is a bar-chart of counts of reads for each in a specific set of read-lengths? Does 'startcodon' need to be included? @ewallace suggests yes, since this is a metagene of what's happening around the start codon, that should be included)
startcodon_ribogrid  (similar points as startcodon_ribogrid)
3ntframe_bygene  (could this be left as 'frame by gene'?)
3ntframe_propbygene  (expand to 'proportion_by_gene' perhaps? 'prop' isn't clear)
TPMs_collated   (collated between samples in the dataset, so perhaps could indicate this?)
read_counts (this is read counts at each stage of the riboviz workflow, for all samples)

@3mma-mack agreed to take a crack at this to write documentation and suggest new names where needed. Then we will discuss.

In terms of the tsv files - it could be useful for the documentation to contain a brief structure description (below) with a brief description of what each column contains (e.g explanation for abbreviations used) in addition to a general description of what the file is.
gene	       Ct_fr0	Ct_fr1	Ct_fr2	pval_fr0vs1	pval_fr0vs2	pval_fr0vsboth
YAL068C	          0	  0	  0	   1	              1	               1
YAL067W-A	  0       0	  0	   1	              1	               1

@swinterbourne agree. Also useful to mention the name of the function that produces it, where applicable?

I have added some first draft descriptions riboviz_outputs.md and have included tables showing the structure of tsv files. I still need to add descriptions for features.pdf, codon_ribodens.tsv, and codon_ribodens.pdf, as I am currently running the Brar dataset so I can see and properly describe these files.
I'm also planning on replacing the tables I have in the files at the moment with those produced by the Brar dataset so the tables have consistent genes which will hopefully minimise any confusion.
I also haven't added anything to Sample.bam, Sample.bam.bai, Minus.bedgraph, Plus.bedgraph yet as I was struggling to fund the py file that is actually used to create them and was not sure how to go about describing them.

.bam and .bam.bai are created by samtools. .bedgraph is created by bedtools.

I have added short descriptions on how .bam, .bam.bai and the .bedgraph files are created. Additionally I have added a 'potential new file name' section to each file description, feel free to add to it.
I plan to add descriptions for the final files, update the tables and add images of graphs once the Brar dataset has finished running

I have a first draft of riboviz_outputs, which includes a description, and either an image or a table depending on whether the file is a  pdf or a tsv file.
I plan to go through the documentation again to add more detailed descriptions on how each files is created.

https://github.com/riboviz/riboviz/blob/output-docs-395/docs/user/riboviz_outputs.md

I had a quick look. I think it is coming along nicely, main thing that I think could be added would be some information in terms of quality control checks (e.g. look at read_lengths.pdf, check peak to see if adapter has been removed correctly). Either its own little QC section listing which files to you should check and what to look for or a sentence within the relevant sections describing a QC for the relevant pdfs.

Current brainstorm for new file names:
TPMs_collated.tsv : TPMs_all_samples, TPMs_samples_collated, TPMs_genes_collated, TPMs_samples_genes_compared, TPMs_all_genes_all_samples
read_counts.tsv : reads_per_process, reads_per_stage, reads_stage_inputs
3nt_periodicity.tsv : meta_read_counts_start_stop, meta_reads_start_stop, all_reads_meta_transcript, reads_meta_feature_transcript
pos_sp_rpf_norm_reads.pdf : norm_reads_transcript, norm_reads_start_stop
pos_sp_rpf_norm_reads.tsv : norm_reads_transcript, norm_reads_start_stop
sequence_features.tsv : sequence_features_vs_tpms, tpms_feature_changes, feature_trends_tpms
features.pdf : sequence_features_vs_tpms, tpms_feature_changes, feature_trends_tpms
tpms.tsv : <SAMPLE_ID>_tmps
codon_ribodens.tsv : APE_codondens, APE_feature_codonden, APE_codondens_trend
codon_ribodens.pdf : APE_codondens, APE_feature_codonden, APE_codondens_trend
startcodon_ribogridbar.pdf : startcodon_gridbar, start_gridbar_readlen, readlen_gridbar_start
startcodon_ribogrid.pdf : startcodon_readlen_heatmap, heatmap_readlen_pos
These are just suggestions so feel free to add to the lists. I haven't come up with suggestions for 3ntframe_bygene.tsv, 3ntframe_bygene.pdf, read_lengths.tsv, read_lengths.pdf, <SAMPLE_ID>.h5, plus.bedgraph, minus.bedgraph, <SAMPLE_ID>.bam.bai, <SAMPLE_ID>.bam, or <SAMPLE_ID>_output_report.html as I feel they are well named already but if anyone feels differently then feel free to add suggestions.

Thinking about the features.pdf file, those are features of CDS or ORFs. So I think that CDS_features or CDS_tpms_vs_features might work?

The features are in ORFs so potentially ORF_features or ORF_tpms_vs_features

To add to the list of changes arising from changing file names:
[ ] Update Python constants, variables or Nextflow channel names and variables that represent these files to be consistent with the new file names.

I have edited the document to include a small paragraph at the top of the document describing features of read_lengths.pdf and 3nt_periodicity.pdf to look for as a quality control measure when first running the riboviz pipeline, as suggested by @swinterbourne
@ewallace would you be able to check the document when you have time. The document is at a point where I am not sure what to add, if I need to add anything else, or whether I should change the format so your input would be appreciated.

We have discussed some of the new names for files at the 11/08 developers meeting
The names we have decided on so far are:
TPMs_collated.tsv  -> TPMs_all_CDS_all_samples
read_counts.tsv  -> read_counts_per_file
3nt_periodicity.tsv -> metagene_start_stop_read_counts
pos_sp_rpf_norm_reads.pdf -> metagene_normalized_profile_start_stop
pos_sp_rpf_norm_reads.tsv -> metagene_normalized_profile_start_stop
sequence_features.tsv -> ORF_TPMs_vs_features
features.pdf  -> ORF_TPMs_vs_features
tpms.tsv  -> ORF_TPMs_and_counts
We are planning on coming back to: codon_ribodens.tsv , codon_ribodens.pdf , startcodon_ribogridbar.pdf, and startcodon_ribogrid.pdf
Any input is welcome.

Just thinking about it, things like 3ntframe_bygene.* ought to match our preference for 'ORF' over 'gene', and perhaps we can just drop '3nt' and use 'read_frame' instead?

Ah. Thanks for pointing that out, I'll have a look and add their descriptions to riboviz-outputs.md.

I have merged develop into output-docs-395 and then output-docs-395 into update-file-names-411 so that there is a copy of riboviz_outputs.md on branch update-file-names-411.
I plan to update riboviz_outputs.md so the names of files listed match the new file names where they have been changed

I plan to delete the branch and issue once file names have been decided for the following files:

codon_ribodens.tsv - suggestions include: APE_codondens, APE_feature_codonden, APE_codondens_trend
codon_ribodens.pdf - suggestions include: APE_codondens, APE_feature_codonden, APE_codondens_trend
startcodon_ribogridbar.pdf - suggestions include: startcodon_gridbar, start_gridbar_readlen, readlen_gridbar_start
startcodon_ribogrid.pdf - suggestions include: startcodon_readlen_heatmap, heatmap_readlen_pos
3ntframe_bygene.tsv - suggestions include: readframe_byORF
3ntframe_bygene.pdf - suggestions include: readframe_byORF

Once names have been decided then all of the next steps will be covered by issue #411 so this issue will be able to be closed

I plan to delete the branch and issue once file names have been decided for the following files:

codon_ribodens.tsv - suggestions include: APE_codondens, APE_feature_codonden, APE_codondens_trend
codon_ribodens.pdf - suggestions include: APE_codondens, APE_feature_codonden, APE_codondens_trend

I think 'ribodens' isn't particularly helpful, can we expand to 'ribosome_density_at_APE_sites' or similar?

startcodon_ribogridbar.pdf - suggestions include: startcodon_gridbar, start_gridbar_readlen, readlen_gridbar_start
What about something like start_codon_read_length_bar_chart?

startcodon_ribogrid.pdf - suggestions include: startcodon_readlen_heatmap, heatmap_readlen_pos
I think that this type of plot has been called a 'ribogrid' by the Lareau lab who I believe came up with this visualization? (correct me if I'm wrong  @lianafaye).  I think we can probably call it a ribogrid (with a bit in the name about what's plotted against what perhaps for extra clarity for the unfamilar?), if the documentation of outputs explains clearly that it's a type of heatmap plot and maybe includes a link to examples in @lianafaye 's paper?

3ntframe_bygene.tsv - suggestions include: readframe_byORF
3ntframe_bygene.pdf - suggestions include: readframe_byORF

I like the suggestion, but I think for consistency, we should probably snake_case_each_word? e.g: read_frame_by_ORF?

I agree with @FlicAnderson: read_frame_per_ORF or frame_proportions_per_ORF?
codon_ribodens.tsv : norm_density_APEsites_per_codon ?
startcodon_ribogridbar.pdf : metagene_start_read_counts_by_read_length ? Certainly this
startcodon_ribogrid.pdf : startcodon_readlen_heatmap, heatmap_readlen_pos
???

Current name suggestions following discussions at the meeting and on this issue ticket. Unless there are any objections to them raised here or at the meeting I plan to power through in the name changes in and aim to have all file names changed by the end of the week.

codon_ribodens.tsv - norm_density_APEsites_per_codon.tsv
codon_ribodens.pdf -  norm_density_APEsites_per_codon.pdf
codon_ribodens_gathered.tsv - norm_density_APEsites_per_codon_gathered.tsv
startcodon_ribogridbar.pdf - metagene_start_barplot_bylength.pdf
startcodon_ribogrid.pdf - metagene_start_ribogrid_bylength.pdf
3ntframe_bygene.tsv - read_frame_per_ORF.tsv
3ntframe_bygene_filtered.tsv - read_frame_per_ORF_filtered.pdf
3ntframe_propbygene.pdf - frame_proportions_per_ORF.tsv
read_lengths.pdf - read_counts_by_length.pdf
read_lengths.tsv - read_counts_by_length.tsv
pos_sp_nt_freq.tsv - nt_freq_per_read_length_pos.tsv

Current name suggestions following discussions at the meeting and on this issue ticket. Unless there are any objections to them raised here or at the meeting I plan to power through in the name changes in and aim to have all file names changed by the end of the week.

codon_ribodens.tsv - normalized_density_APEsites_per_codon.tsv
codon_ribodens.pdf -  normalized_density_APEsites_per_codon.pdf
codon_ribodens_gathered.tsv - normalized_density_APEsites_per_codon_long.tsv
startcodon_ribogridbar.pdf - metagene_start_barplot_by_length.pdf
startcodon_ribogrid.pdf - metagene_start_ribogrid_by_length.pdf
3ntframe_bygene.tsv - read_frame_per_ORF.tsv
3ntframe_bygene_filtered.tsv - read_frame_per_ORF_filtered.pdf
3ntframe_propbygene.pdf - frame_proportions_per_ORF.pdf
read_lengths.pdf - read_counts_by_length.pdf
read_lengths.tsv - read_counts_by_length.tsv
pos_sp_nt_freq.tsv - nt_freq_per_read_position.tsv

New names accepted, so review of names can close. The rest of the work changing the files will be documented on #411

This work was completed on issue ticket #411, merged as part of PR #422 and the contents of branch output-docs-395 are contained within develop via the 411 branch, so I'm deleting branch output-docs-395 to tidy up.


Chef Automate drop down needs refactoring

User Story
As per the latest UX recommendations, the drop down list in Chef Automate needs to be revamped and modified.
This requires us to modify the code to use the components from Chef-ui-library and also may require us to make some more CSS changes.
An example of it can be seen here in the constraints tab for create environment:
https://www.figma.com/file/JUyEFkapFuRuDnfGmoTx6y/Manage->-Automate-Environment?node-id=0%3A1
Definition of Done
Start automate
Go through all the tabs
All the drop downs should look similar to the one provided as an example.
Demo Script / Repro Steps

@jong-progress - are we animating this new dropdown?

@SEAjamieD - Good question! I will reach out to @ManishUX tomorrow, or he can comment here.

@jong-progress - cool!  no rush :)