Fatal Error: Uncaught Logic Exception -- twig 3.10 deprecation @ timber/src/Twig.php

with
composer show timber/timber
	name     : timber/timber
	descrip. : Create WordPress themes with beautiful OOP code and the Twig Template Engine
	keywords : templating, themes, timber, twig, wordpress
	versions : * 2.x-dev
	released : 2024-05-07, this week
	type     : library

and update to just-released Twig 3.10
composer show twig/twig
	name     : twig/twig
	descrip. : Twig, the flexible, fast, and secure template language for PHP
	keywords : templating
	versions : * v3.10.0
	released : 2024-05-11, today
	type     : library
	...

access to my site front-page, fires a new fatal error; e.g.,
( ! ) Fatal error: Uncaught LogicException: You must call "setEnvironment()" before calling "Twig\Extension\EscaperExtension::setEscaper()". in /srv/www/wp.app/web/app/themes/test-flynt/vendor/twig/twig/src/Extension/EscaperExtension.php on line 127

( ! ) LogicException: You must call "setEnvironment()" before calling "Twig\Extension\EscaperExtension::setEscaper()". in /srv/www/wp.app/web/app/themes/test-flynt/vendor/twig/twig/src/Extension/EscaperExtension.php on line 127

the call stack identifies,
.../Twig.php:558

	Twig\Extension\EscaperExtension->setEscaper( $strategy = 'esc_url', $callable = class Closure { } )

checking Timber src,
cat  ./vendor/timber/timber/src/Twig.php

	        if (\class_exists('Twig\Extension\EscaperExtension')) {
	            $escaper_extension = $twig->getExtension('Twig\Extension\EscaperExtension');
558	            $escaper_extension->setEscaper('esc_url', $esc_url);
	            $escaper_extension->setEscaper('wp_kses_post', $wp_kses_post);
	            $escaper_extension->setEscaper('esc_html', $esc_html);
	            $escaper_extension->setEscaper('esc_js', $esc_js);
	        }
	        return $twig;
	    }

and @ twig src,
https://github.com/twigphp/Twig/blob/3.x/src/Extension/EscaperExtension.php#L127

the deprecation causing the error,
	...
114	    /**
	     * Defines a new escaper to be used via the escape filter.
	     *
	     * @param string                        $strategy The strategy name that should be used as a strategy in the escape call
	     * @param callable(Environment, string) $callable A valid PHP callable
	     *
	     * @deprecated since Twig 3.10
	     */
	    public function setEscaper($strategy, callable $callable)
	    {
	        trigger_deprecation('twig/twig', '3.10', 'The "%s()" method is deprecated, use the "Twig\Runtime\EscaperRuntime::setEscaper()" method instead (be warned that Environment is not passed anymore to the callable).', __METHOD__);

	        if (!isset($this->environment)) {
127	            throw new \LogicException(sprintf('You must call "setEnvironment()" before calling "%s()".', __METHOD__));
	        }
	        if (!isset($this->escaper)) {
	            throw new \LogicException(sprintf('You must call "setEscaperRuntime()" before calling "%s()".', __METHOD__));
	        }

	        $this->escapers[$strategy] = $callable;
	        $callable = function ($string, $charset) use ($callable) {
	            return $callable($this->environment, $string);
	        };

	        $this->escaper->setEscaper($strategy, $callable);
	    }
	...

Just opened the same issue a few minutes earlier with a temporary fix https://github.com/timber/timber/issues/2993

Duplicate of #2993. We'll track in that ticket if any upgrades are needed in our codebase.


⚠ SceneTime has degraded performance

In 8548df7, SceneTime ($ST) experienced degraded performance:

HTTP code: 200
Response time: 13104 ms

Resolved: SceneTime performance has improved in 3019ab4.


insert snippet picker list show where the snippet from

Snippets may from extension or builtin, it would be helpful if display where the snippet from.

@jrieken Hi, a partner (@DavidJRWang) and I are interested in taking on this issue, could this be reassigned to us? Thanks!

...this issue, could this be reassigned to us?

We can only assign issues to team members but you now have your stick in the ground for this one

This extension maybe be help https://github.com/robole/vscode-snippets-ranger @jrieken  @wengj9

i tried

This is an early preview of what the snippet picker would look like:

Would you prefer any changes to the current look/feel of it?

The message should be shorter, for example: extension: C/C++ Language Basics be enough, if is built in extension, should be builtin extension: C/C++ Language Basics? @wengj9

Also using the group label on the right for each and every entry seems a bit heavy. Today it's "User Snippets", "Workspace Snippets", and "Extension Snippets". I would suggest to remove the last group and have than one group per extension, not per snippet

+1 to only having a single category/group at the end as we do the same thing in the remote picker:

We've made the requested changes and here's what the snippet picker looks like now:
.
We also changed the sorting of the snippets to group extensions together to minimize the category/groups in the picker.

Do we really need to add the version info? I think having it as Angular Snippets (Extension) or even Angular Snippets would be a cleaner look

Right, the version number seems to be part of the extension name so I'm not sure there's much we can easily do about it right now. So you're suggesting, for example in the screenshot, instead of "Extension: Angular Snippets..." for it to just say "Angular Snippets"?

Yes just to simplify it as many snippet extension names are long:

I omitted the "Extension: " and here's what it looks like now:

Are there any other changes you'd like to the picker?

Looks good to me, thanks for taking the feedback!

PR merged. Thanks everyone!

@wengj9 @jrieken @misolori

The workspace snippets should be front of user snippets.

The VSCode snippet picker in the current stable version also lists user snippets before workspace snippets:

Not sure if you mean to open another issue about this?

maybe it should be another issue. @wengj9

I have create another issue: https://github.com/microsoft/vscode/issues/139103

looks good!


Incomplete eip verification in layer2 or vip mode

When the eip configured in layer2 or vip mode and the specified NIC are not in the same network segment, an error should be reported instead of being created successfully.
root@node1:~/openelb# ip a | grep eth0
2: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc mq state UP group default qlen 1000
    inet <IP_ADDRESS>/24 brd <IP_ADDRESS> scope global dynamic noprefixroute eth0

apiVersion: network.kubesphere.io/v1alpha2
kind: Eip
metadata:
  name: layer-eip
spec:
  address: <IP_ADDRESS>-<IP_ADDRESS>
  interface: eth0
  protocol: layer2

When the address is set to the network segment <IP_ADDRESS>/24, the creation is successful.
apiVersion: network.kubesphere.io/v1alpha2
kind: Eip
metadata:
  name: layer-eip
spec:
  address: <IP_ADDRESS>-<IP_ADDRESS>
  interface: eth0
  protocol: layer2

When the address is set to the network segment <IP_ADDRESS>/24, the creation should fail.
/kind bug

A fix addressing this was adopted on May 28, 2022, but likely should not have been. See #456


Designed Contact Us#534

Description
Please include a summary of the change and which issue is fixed.
Fixes # (issue)
List any dependencies that are required for this change
Type of change
Added map to contact us section and made it responsive.

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

How Has This Been Tested?
UI /UX changes
Attach gif or screenshot for changes.

Before :
- After :

Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes

@harikesh409 pls review and assign issue #534

Already contact page is present.


Navbar Title and menu element alignment

Hi!
is it just my OCD or is it true that the navbar title and the following menu items are not aligned (but probably are aligned to the center of both texts)

Is it possible to align the elements to the bottom of the letters?
best regards,
Ruud

Could be if we play with the flexbox alignment and try out the baseline option instead of center.

@ruudvddries It honestly looked good to me when I first saw your screenshot.

Closing as a won't fix.


Added playground action

Fixes #1893
"playground block air and bat"

Checklist

[x] I have added tests
[/] I have updated the docs and cheatsheet
[/] I have not broken the cheatsheet

Andreas gave me a live demo. This is super slick; I'm excited to use it.
I wonder whether the spoken form should be syntax tree or treesitter or even inspect/dump/show syntax tree rather than playground.

@josharian Updated the image with the changes we talked about

@pokey @josharian scm query added

@pokey updated


feat(GUI): add uuid to flash events

Change-Type: patch

Let me take over this PR. ImageWriterService is on the angular world, and that point we can emit the flash event with access to the flash uuid, so I'll move the flash analytics over there (which is the correct place to have those anyway), and move the uuid generation to the unset flashing flag step.

Done!

@stefan-mihaila @Shou @jhermsmeier @lurch Can anybody review my changes here?

@jviotti what did you change? There aren't any changes showing up here for me after you reviewed this... or am I missing something?

@jviotti what did you change?

Looks like @jviotti made his changes between his "Let me take over this PR." and "Done!" comments, and then squashed everything down to a single commit.

@jviotti If you've taken over this PR, do you want to remove your approval? ;)

Yeah, sorry about the confusion. I'm too used to amend and force push :(

I'll merge this so we can release today. I'm happy to address any comments afterwards!


Feature request: Cachebusting assets referenced in XML file

Windows 8.1 and IE 11 rely on tile pictures (aka favicons) specified in an XML file called browserconfig.xml that sits at a website's root. We therefore need to cachebust assets referenced in XML. (Thanks, Microsoft!)
I looked through the code and this functionality doesn't appear to exist -- please consider this a feature request.
If you'd like to take a crack at implementing asset path scraping from XML, here's an example browserconfig.xml:
<?xml version="1.0" encoding="utf-8"?>
<browserconfig>
  <msapplication>
    <tile>
      <square70x70logo src="/mstile-70x70.png"/>
      <square150x150logo src="/mstile-150x150.png"/>
      <square310x310logo src="/mstile-310x310.png"/>
      <wide310x150logo src="/mstile-310x150.png"/>
      <TileColor>#2b5797</TileColor>
    </tile>
  </msapplication>
</browserconfig>

Happy to include this. Marked as an enhancement. Will try to get round to it soon. Thanks.

Completed in #118

Looks great, thank you for implementing!


Is there a way to solve the noise caused by camera disturbance?

Due to the motion of the camera, a large number of false target information will be introduced into the video frame. Is there a way to solve the noise caused by camera disturbance?

This algorithm does make errors and we have no specific ways of mitigating this type of error.


Create Connect Us and Review

done the task of creating Contact Us and Review

Work is checked and ready to be merged into main.


Improve layout

Regions and other compound nodes sometimes overlap on top of other structures and there are various other ways in which these look "bad".
For example minimizing regions for some reason often ends up causing one of the worst layouts, where things get spread very far apart vertically.
Some ideas for improvements:

The bad layouts are largely due to the graphs being too complex, which is due to too many nodes and edges.  To resolve this, we could allow more filtering, and make that easier to do.  Also compress nodes in the initial layout.
We are using a compound layout to allow nodes (ex. EC2's) to have parent nodes (ex. EC2's are in subnets, which are in AZ's, etc.).  We could allow for non-compound layouts, which would allow us to use algorithms other than cose-bilkent, which may look better.
Improve cose-bilkent to score and hill climb.  cose-bilkent works by randomly laying out the diagram and then applying spring and gravity forces over iterations to bring things to a state that matches those forces.  This could be improved by making multiple layout attempts and choosing the "best" where a scoring algorithm would need to be created to decide on the "best" layout.  This would need to do things like counting the number of over-lapping edges and nodes, and find the area of the layout (ex. to avoid the layout being too spread out).  Ideally, this scoring would be incorporated into the forces that are applied to bring them toward better states.  Additionally, I think the "final" states are sometimes local maxima and could benefit from some hill climbing techniques to "shake" the state a little on each iteration.

Nodes can be compressed on the initial layout as shown in this demo: https://rawgit.com/iVis-at-Bilkent/cytoscape.js-expand-collapse/master/demo-compounds-collapsed.html

I also found that for very complex diagrams, where on init - resources are spread across the screen in an exaggerated manner,  clicking the hammer icon aka redraw with randomized layout sanitizes the layout to some extent.

Attempted at a different visualization made in #368
At this point I believe the best way to improve the layouts is to continue adding ways to reduce the number of nodes shown, such as by filtering by tags that was recently done. I'm therefore closing this.


Turbo restoration visit displays wrong AJAX

When visiting a specific page by clicking a link and then going back to previous page everything is fine. However, when this is repeated, after going back to previous page the icon on "Symfony Web Debug Toolbar" which represents AJAX request is flashing and shows:

1	[7e31b1]  GET	fetch	200	https://some.site/login	76 ms
2	n/a       GET	fetch	n/a	https://some.site/login	n/a

Which means it is either performing or showing the wrong AJAX call.
Used versions:
Symfony 7.0.3
symfony/ux-turbo v2.14.0
NPM:
├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>-> ./vendor/symfony/ux-turbo/assets

It's possible some ajax call is being cancelled... or perhaps the web debug toolbar is getting confused by this. You could look to see what Ajax calls are really happening and when to see if the web debug toolbar is reporting accurately...

After checking the real network activity in Firefox's dev tools, it's evident that there is no additional AJAX call triggered when going back in history for the second time. Therefore, the web debug toolbar must be confused in some way.

Don't know. Can't test it now.

After further testing, I confirm that it still happens.


MediaElch: Versioning format has changed

The versioning format has changed for MediaElch requiring an update script change to grab the correct release for Windows 10 and above.

@bugwelle Latest version has been published after the fix.
https://community.chocolatey.org/packages/MediaElch/2.10.0

@sumo300 Thank you very much! :-)


Improved script-reference

Added links to each API.
Added midi/hid docs.
Added basic examples.

I do, but it's kind of a circular problem for me at this point, I cannot write docs for it, since there are no .. docs for it.
The current list of methods taken from the refs, is not really explaining how to use it, I've tried to use this in tutorial code and I never managed to get something that worked reliably so I cannot document it. I'd say, until we have a study that demonstrates how to use it, I'd not include it in the script-reference. Once we have that, I would add it here as well.

fair enough! and this rationale prods it higher on my priority list, thanks.

I'm actually really anxious to get started messing with softcut!
✊

tomorrow then!


convert to immutable for CUDA tests

Converts NonlinearProblem to ImmutableNonlinearProblem for CUDA compatibility (SciML/NonlinearSolve.jl#439)

Tests are failing due to this methoderror. I'm not sure why given the constructor in the new ImmutableNonlinearProblem struct
 MethodError: no method matching SimpleNonlinearSolve.ImmutableNonlinearProblem(::SciMLBase.NonlinearFunction{false, SciMLBase.FullSpecialize, typeof(Main.var"##CUDA Kernel Launch Test#1070".f), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing}, ::StaticArraysCore.SVector{2, Float32}, ::SciMLBase.NullParameters, ::SciMLBase.StandardNonlinearProblem)

I will review it in detail later, but tagging @Vaibhavdixit02 because it will very likely break GPUPSO. Maybe we tag a breaking release just for safety

Since that package wasn't released, you should be fine on that end.

GPUPSO should be fine if this is done right? We just need to make sure the kernels use everything immutable.

Left a few comments. If those two things are done this should be quick to finish.

I made changes according to your comments. The simple adjoint test is failing with this error:
  Cannot determine ordering of Dual tags Nothing and ForwardDiff.Tag{Base.Fix2{SciMLBase.NonlinearFunction{false, SciMLBase.FullSpecialize, typeof(Main.var"##Simple Adjoint Test#264".ff), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing}, Vector{Float64}}, Float64}
Any thoughts on the fix for that?

These tests are also failing: https://github.com/SciML/SimpleNonlinearSolve.jl/blob/40958d2c2fdff0986d113ea1f5ed1ffa96316e89/test/gpu/cuda_tests.jl#L40C1-L40C107
Doesn't the kernel_function need to change given that the conversion to an Immutable struct happens within the solve call? I'm not sure how that test should be restructured.

They kernel function needs to be the immutable form. And this would need an FAQ entry.

Any thoughts on the fix for that?

Add the immutable stuff to the AD dispatches?


Improve Alexa interface selection for binary sensors

Description:
This allows the sensor to work correctly as a contact or motion sensor in alexa, if the user overrides its display category as such.
Without this, if the user sets a binary sensor display category to CONTACT_SENSOR, for example, Alexa will show an error for that device, unless the binary sensor HA display_class is door.
Checklist:

[x] The code change is tested and works locally.
[x] Local tests pass with tox. Your PR cannot be merged unless tests pass
[x] There is no commented out code in this PR.
[x] I have followed the development checklist

If user exposed functionality or configuration variables are added/changed:

[ ] Documentation added/updated in home-assistant.io

If the code communicates with devices, web services, or third-party tools:

[ ] The manifest file has all fields filled out correctly. Update and include derived files by running python3 -m script.hassfest.
[ ] New or updated dependencies have been added to requirements_all.txt by running python3 -m script.gen_requirements_all.
[ ] Untested files have been added to .coveragerc.

If the code does not interact with devices:

[ ] Tests have been added to verify that the new code works.

In what scenario does the entity not have the right device class? That seems like a bug in the integration.

@balloob Lets say you have a leak sensor, that has the correct device class. If I want to be able to use it in Alexa I would need to force it into the CONTACT_SENSOR or MOTION_SENSOR display_category.

I see. that's fine for now. Ok to merge when docs PR linked.

@balloob what docs? The display categories were already documented previously, they were just not working properly (the sensor would appear with the correct type in alexa, but with an error).

ok


Python DateTime Error For Blob Events In Event Grid Azure Function

Issue Description
The Azure Event Grid Trigger function in python throws an error on receiving a blob event. The error is related to DateTime format. The date returned by the blob event to the python function cannot be parsed by python as the millisecond value has seven digits. E.g. the date '2018-12-09T23:47:03.285137Z'  cannot be parsed by python as the millisecond value has seven digits which is not recognized in python.
Result: Failure
Exception: ValueError: time data '2018-12-12T03:16:34.2191989Z' does not match format '%Y-%m-%dT%H:%M:%S.%fZ'
Stack:   File "/home/site/wwwroot/.python_packages/lib/python3.6/site-packages/azure/functions_worker/dispatcher.py", line 250, in _handle__invocation_request
    pytype=pb_type_info.pytype)
  File "/home/site/wwwroot/.python_packages/lib/python3.6/site-packages/azure/functions_worker/bindings/meta.py", line 285, in from_incoming_proto
    trigger_metadata=trigger_metadata)
  File "/home/site/wwwroot/.python_packages/lib/python3.6/site-packages/azure/functions_worker/bindings/eventgrid.py", line 94, in from_proto
    event_time=cls._parse_datetime(body.get('eventTime')),
  File "/home/site/wwwroot/.python_packages/lib/python3.6/site-packages/azure/functions_worker/bindings/meta.py", line 181, in _parse_datetime
    raise last_error
  File "/home/site/wwwroot/.python_packages/lib/python3.6/site-packages/azure/functions_worker/bindings/meta.py", line 176, in _parse_datetime
    dt = datetime.datetime.strptime(datetime_str, fmt)
  File "/root/.pyenv/versions/3.6.6/lib/python3.6/_strptime.py", line 565, in _strptime_datetime
    tt, fraction = _strptime(data_string, format)
  File "/root/.pyenv/versions/3.6.6/lib/python3.6/_strptime.py", line 362, in _strptime
    (data_string, format))

Steps to reproduce issue
#### STEP 1: CREATE AZURE FUNCTION

groupName="<resource_group_name>"
location="westeurope"
functionStorageName="<function_storage_account_name>"
appinsightsKey="<application_insights_instrumentation_key>"
appName="<function_app_name>"

#### CREATE RESOURCE GROUP

az group create --name $groupName --location $location

#### REGISTER EVENT GRID PROVIDER NAMESPACE

az provider register --namespace Microsoft.EventGrid

#### CREATE STORAGE ACCOUNT FOR FUNCTION APP
az storage account create --name $functionStorageName --location $location --resource-group $groupName --sku Standard_LRS --kind StorageV2

#### CREATE FUNCTION APP
az functionapp create --resource-group $groupName --os-type Linux --consumption-plan-location $location --runtime python --name $appName --storage-account $functionStorageName

#### CONFIGURE APP INSIGHTS FOR FUNCTION
az functionapp config appsettings set --name $appName --resource-group $groupName --settings "APPINSIGHTS_INSTRUMENTATIONKEY=$appinsightsKey"

#### STEP 2: WRITE FUNCTION CODE AND PUBLISH
func init testfunction --worker-runtime python
cd testfunction
func new --language python --template "Azure Event Grid trigger" --name EventGridTrigger
func azure functionapp publish $appName

#### STEP 3: CREATE A STORAGE ACCOUNT WHOSE EVENTS NEED TO BE RECORDED
generalStorageName="<storage_account_name>"
az storage account create --name $generalStorageName --location $location --resource-group $groupName --sku Standard_LRS --kind StorageV2
storageId=$(az storage account show --name $generalStorageName --resource-group $groupName --query id --output tsv)
accountKey=$(az storage account keys list --account-name $generalStorageName | grep "value" | awk -F ": " '{print $NF}' | sed 's/"//g' | head -1)

#### STEP 4: GET FUNCTION MASTER KEY FROM AZURE PORTAL (browse to 'Manage' section under the EventGridTrigger function)
functionMasterKey="<function_master_key>"
endpoint="https://$appName.azurewebsites.net/runtime/webhooks/eventgrid?functionName=EventGridTrigger&code=$functionMasterKey"

#### STEP 5: REGISTER EVENT GRID SUBSCRIPTION
az eventgrid event-subscription create --resource-id $storageId --name "myevtgridtrig" --endpoint $endpoint

#### STEP 6: UPLOAD A FILE TO STORAGE BLOB TO TEST EVENT
az storage container create --name test1 --account-name $generalStorageName --account-key $accountKey
echo "hello" > hello.txt
az storage blob upload --container-name test1 --account-name $generalStorageName --account-key $accountKey --file hello.txt --name "hello.txt"

STEP 7: REVIEW MONITOR OR APP INSIGHTS FOR LOGS/ERRORS
Resources

https://docs.microsoft.com/en-us/azure/azure-functions/functions-bindings-event-grid#python-example
https://docs.microsoft.com/en-us/azure/storage/blobs/storage-blob-event-quickstart?toc=%2Fazure%2Fevent-grid%2Ftoc.json

@kavithamadhavaraj In this particular case, unfortunately, there are no workarounds.

@elprans Any workarounds for this issue until the pull request is closed? Thanks in advance.

After we publish linux function app to Azure, we will be able to find a ZIP file in project folder, which is uploaded to storage and our function app will run from it.
https://github.com/Azure/Azure-Functions/wiki/Azure-Functions-V2-hosting-options
So we can unzip the ZIP file and chance the code as https://github.com/Azure/azure-functions-python-worker/pull/306/commits/ecab0cf2ac64720b76c9e61cbf045f1162cf03e0
Then upload it to a storage account as a blob, get Shared Access Signature for the uploaded ZIP file (make sure you set expired date properly)
Copy the SAS URL and replace WEBSITE_RUN_FROM_ZIP value in your function app Application Settings, then restart your function app.
Now your function app will run from the modified ZIP file you upload.

@nicklooo Tried the option you had shared but after restarting, my function is not listed anymore. (Both in portal & vscode, I could not see my function). This is how I generated the SAS.

@kavithamadhavaraj  You need both Read and List Permissions

@nicklooo @elprans  I made changes to the meta.py file present in /worker_venv/lib/python3.6/site-packages/azure/functions_worker/bindings/ of the zip file. Uploaded to blob storage and updated the SAS url, restarted the app, still facing the same error. The app is picking up the zip provided. However it doesn't seem to use the ./site packages folder from the zip. Am I missing something? Will be really helpful if you could provide some pointers here. Have been struggling with this for hours. Thanks.

@kavithamadhavaraj
Should be this folder: {zip folder}.python_packages\lib\python3.6\site-packages\azure\functions_worker
Works well for me:

@nicklooo Hi, my zip folder has /worker_venv/lib/python3.6/site-packages/azure/functions_worker/bindings/ this path only. I'm using --build-with-native-deps flag. This makes the folder structure to the above mentioned one. If not, I can see {zip folder}\.python_packages\lib\python3.6\site-packages\azure\functions_worker in my zip file. Nevertheless, when i made changes to the packages & my function app code, the new changes from the later was reflecting the portal but the fix in the package file didn't work.


SDK-3355

Added support for BodyListener in sample apps for video as well as webcam.
Annotated output video supported with body points, csv file contains all the body points info with X and Y coordinates
Adding everyone as reviewer, feel free to review it

@adennie @umangmehta12 @ahmedalmoraly anyone of you can review this!


🔧 Update template

This pull request merges the current state of the template used here into this project so that it is up to date.

:tada: This PR is included in version 2.0.9-develop.1 :tada:
The release is available on:

v2.0.9-develop.1
GitHub release
Docker container (sebbo2002/ble2mqtt:2.0.9-develop.1)
v2.0.9-develop.1

Your semantic-release bot :package::rocket:

:tada: This PR is included in version 3.0.0 :tada:
The release is available on:

v3.0.0
GitHub release
Docker container (sebbo2002/ble2mqtt:3.0.0)
v3.0.0

Your semantic-release bot :package::rocket:


UI freezes (logs don't scroll) when repo taking too long to build.

I was trying to open the binder for Bloomberg's bqplot and it seems there's an issue with the repo, b/c the binder is taking too long to build.
But the binder-relevant problem is that the UI is basically frozen. The page looks like this:

The red lines, which are part of a spinner, are almost frozen (they will move slowly, only if the mouse hovers over them) and the console can't be scrolled.
Platform: macOS, tested on both Chrome and Safari.

yeah the logs not scrolling is pretty annoying - it's using xterm so perhaps a bug in the way that we're writing data to the xterm process. I think we should try to nail the "how do I see my logs more effectively" problem before v0.1

Several people have also independently told me that the "is taking a long time to load" feels like an error message so they close the tab, even though it is not an error message. The GIF also stops spinning, which reinforces the error message setup...
I think there are several bugs here:

Why does the circle stop spinning?
Should we reword it so it does not sound like an error message?
Bug with xterm?

I've also seen this screen on every repo I've tried to launch, so the timeout is definitely too short.

Maybe we can also change the wording from "is taking a long time to load, please check logs" to "Is taking a long time to load, please hang tight." or some such that makes it sound more like "we are sorry this is taking so long, please be patient"

Yeah, another person just said in gitter:
"Just fyi, all binders i've tried are currently fail to start with "taking
a long time to load""
except it hadn't actually failed :(
On Wed, Feb 7, 2018 at 2:02 AM, Tim Head<EMAIL_ADDRESS>wrote:

Maybe we can also change the wording from "is taking a long time to load,
please check logs" to "Is taking a long time to load, please hang tight."
or some such that makes it sound more like "we are sorry this is taking so
long, please be patient"
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Ah - there's another problem in there, which is that we only want the "taking a long time to load" text to appear when it's still loading but taking a while, but we want it to explicitly say fail somewhere if it actually does fail

Closing as outdated and likeley resolved


Issue#18

resolves #18 and #19

Can one of the admins verify this patch?

ok to test

@cxoltero
This PR should really be broken up, to as least set apart the bug from the improvement work.  In addition, per the CONTRIBUTING.md, please make sure you are following the expected feature branch naming convention.
Thansk!


When I run setup and then plug my pi into my windows pc, windows says that the recently conected usb device is malfunctioning.

I know this is an old project, but i'd appreciate any insight into what's going wrong because I would really like to use this.

Ok I got the keyboard to output some characters by releasing the keypress (code below)
echo -ne "\x06" > /dev/hidg0
echo -ne "\x00\x00\x00\x00\x00\x00\x00" > /dev/hidg0
however I am unable to output the character g...I have done some reading and it is saying because the hid keycode 0x0a is also used as a new line character and raspberry pi may be getting confused..
any insight?

raspberry pi zero w

I had that same issue. I ended up opening the serial port using C instead of just echoing to /dev/ttyAMA0

Hi,
Interesting, on Windows too ?

/bin/echo will work...its because 0x0A is linux bash for nl as well
On Tue, Mar 13, 2018 at 5:47 PM, Brosseau Valentin<EMAIL_ADDRESS>
wrote:

Hi,
Interesting, on Windows too ?
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I've got an odd issue, windows 98 computer is not recognizing the hid device?
Any thoughts?

Windows 98 oO. No clue! Windows 98 usb HID management is special... I'm not really sure if it's will be working.
Certainly need a driver


Add grains to detect default gateway

For what it's worth, you can obtain the default gateway if the "route" command is installed, even with "ip" not being available:
/usr/sbin/route -n | head -n 3 | tail -n 1 | awk '{print $2}'

Let's see, I swear there was a reason I used ip instead of route. I'll have to think about that more.
I'd have to do more work than just your command, because honestly the thing we care about most is whether there is a default gateway, not what it is, at least for our use case. We want to differentiate between data center hosts with no outbound and hosts that can hit the internet.
Additionally, route output is much less standardized because of all the potential for multiple routing tables and the like. The first line will not always be the default gateway.
We could still probably get most of the way there, and it's not a bad idea to have a fallback even if it's a naïve one.

As far as Linux goes the ip command is pretty standard now. And if all else fails, there is /proc/net/route.
Another way get to the goal is to query the host routing table for the address you're interested in. For example, if you want to make sure you have a route for github.com resolve the domain (<IP_ADDRESS> in this case) and issue command ip route get <IP_ADDRESS>. A host with a route for that domain will respond with output similar to:
<IP_ADDRESS> via <IP_ADDRESS> dev ens3  src <IP_ADDRESS>
    cache

and exit code 0
while the host with no route will respond with output
RTNETLINK answers: Network is unreachable

and exit code 2.
This can cover even cases where the host does not have a default route, but still has a specific route to a needed domain (hosts running bgp routing with full internet routing tables).

That's not a bad idea. Doesn't fit very cleanly into the "grain" paradigm, but would be useful if we found that some hosts could reach github or azure but didn't have a default gateway.

Successful run of the command will tell you the gateway that the host will use for that domain/ip (3rd value). But it's not necessarily the "default".

Yeah, route will be everywhere even if iproute2 is missing for some reason. I'd probably grep for actual default routes (route -n | grep ^<IP_ADDRESS> | head -n 1) rather than just the 1st or 3rd line.
But note that even without a default route, you might have a route to the splunk (or whatever) endpoints that doesn't go through the default gateway. You could have a static route to some private network. It's totally conceivable.
Along those lines, I'd try to ask ip route get $splunk_IP_here and see if I get a route out of it.

Good points, but again, those types of changes belong in https://github.com/hubblestack/hubble/pull/286 rather than in general-use grains.
I think I'm going to stick with ip here for now, to match the unreleased grains in upstream salt.
@fossam @jettero could one of you approve this if you agree so we can merge it?

right, I didn't understand the context apparently.


Add support for JSDOM HTML-parsing library

Some users requested we also support jsdom, the same way we support cheerio. For example, we can add new JsdomCrawler class similar to CheerioCrawler.

I don't think this will ever happen.


memory optimization for Linux build

Summary
There is a significant difference in the memory map between the linker output of GCC and CCS for the same code base for GBCV1. Issue #204
Test Plan
The memory occupied by .data, .bss symbols was verified as well the output of Makefile. Attached the build and test log of CCS and Linux image. After the optimization changes the code behavior was verified to be same as master branch. Attached logs.
logs_204.zip
Issues
resolves #204

ok to test

Rerun tests


[#85067926] Fix and test for pip install bug

Improve acceptance test for graphite-web service
Test that Graphite can successfully serve a request for the dashboard rather
than just testing that it has bound to the port.
This exposes a problem introduced by the python::pip changes first in
ed5642d when used with the default root_dir of /opt/graphite. It
prevents graphite-web from being able to load whisper and causes it to
respond with a backtrace ending in:
ImportError: No module named whisper

This was first noticed when bringing up our graphite-1.management machine
and recorded in Pivotal [#85067926]. I'm not sure what the fix for this is
yet, so that will follow in a subsequent commit.
PS: I could have use the curl_on helper instead of shell but it's not
clear to me whether I need to wrap it in an expect{} or what value it
provides.
Extend acceptance tests to cover custom root_dir
This will prevent us from breaking the functionality in ed5642d again.
Fix graphite-web service with default root_dir
Add lib/ to PYTHONPATH so that graphite-web is able to load the
whisper module when it's installed to the default root_dir of
/opt/graphite.
This was fixed for custom root_dir values in ed5642d but broke the default
use case. I don't really understand the specifics of why, but this seems
like a reasonable fix.
Add script to end-to-end test Carbon and Graphite
This sends a metric to Carbon and then reads it back out of Graphite to
ensure that everything is working correctly. It should give us greater
confidence when reviewing pull requests to this repo in future.
Add vagrant-wrapper to Gemfile
This appears to be an implicit dependency of later Beaker versions.
Otherwise I get this error:
➜  puppet-graphite git:(85067926-pip_install_bug) b rake acceptance:ubuntu1204
Running acceptance tests for Ubuntu
/opt/rubies/1.9.3-p545/bin/ruby -S rspec spec/acceptance
Beaker::Hypervisor, found some vagrant boxes to create
/Users/dcarley/vendor/bundle/gems/beaker-2.3.0/lib/beaker/hypervisor/vagrant.rb:172:in `block (2 levels) in vagrant_cmd': Failed to exec 'vagrant destroy --force'. Error was /opt/rubies/1.9.3-p545/lib/ruby/gems/1.9.1/gems/bundler-1.5.3/lib/bundler/rubygems_integration.rb:240:in `block in replace_gem': vagrant-wrapper is not part of the bundle. Add it to Gemfile. (Gem::LoadError) (RuntimeError)

Whoops, fixed build.


Chunk.hasEntryModule has been deprecated

[DEP_WEBPACK_CHUNK_HAS_ENTRY_MODULE] DeprecationWarning: Chunk.hasEntryModule: Use new ChunkGraph API

I don't know of a way to check whether a chunk has entry modules without calling hasEntryModule(), and also don't have a strong desire to research it further since it's just a deprecation warning. If someone knows how to do so, please share.

I could be totally wrong on this, since webpack plugin docs are severely lacking, but it appears that you can do
- if (chunk.hasEntryModule()) {
+ if (compilation.chunkGraph.getNumberOfEntryModules(chunk) > 0) {

Based on what I'm seeing from this PR https://github.com/fqborges/webpack-fix-style-only-entries/pull/41/files
However, I think that's a webpack 5 only thing, so you would then need to do some sort of webpack version checking (or drop support for 4?) in order to use that. I think. Again, webpack docs are horrible.


Simple JuliaBox API containers installation

I can imagine that for production deployments, the API container backend of JuliaBox can be quite interesting, as it simplifies deployment and also provides auto-scaling.
It would be nice if there was a quick way to install just this part, without all the other portions that we need to make all of JuliaBox work.

I would be very interested in being able to use the harness that JuliaBox provides, but to launch things like Escher applications.

Currently, JuliaBox has basic ability to serve APIs that are implemented in Julia. It is buried in the settings as of now, but we hope to make it more first class as we figure out how to scale JuliaBox.
Escher is doing WebSockets and the plan is to also support Escher containers on JuliaBox. Our plan over the next few months is to have large parts of JuliaBox UI move to Escher, and even make it possible for users to write Escher applications hosted on JuliaBox.
Cc @shashi

Just getting a local juliabox up now with 0.4 and some local packages.
Is there anything preventing one from having it run any arbitrary api endpoint, including escher apps today?
The whole design seems rather simple and spare, without an overwhelming amount of layers.

....that is, it seems pretty elegant and well done.

API endpoints should run right away. Needs some more work, but that is along the lines of making it production quality. We have a list of things we need to do, but on your local box you should be good to start trying it out.
For Escher's websocket connections, I recollect @shashi saying that we need to do some work to make it all work seamlessly on JuliaBox.

Oh the issue I was facing was with URLs needing to have a common prefix
such as /jboxplugin/escher/...
This can be addressed by making this configurable in Escher.
On Fri, Oct 23, 2015, 12:07 PM Viral B. Shah<EMAIL_ADDRESS>wrote:

API endpoints should run right away. Needs some more work, but that is
along the lines of making it production quality. We have a list of things
we need to do, but on your local box you should be good to start trying it
out.
For Escher's websocket connections, I recollect @shashi
https://github.com/shashi saying that we need to do some work to make
it all work seamlessly on JuliaBox.
—
Reply to this email directly or view it on GitHub
https://github.com/JuliaLang/JuliaBox/issues/289#issuecomment-150489261.

Could I ask where in the escher code base is that happening?   Happy to take a look.


Use of angle brackets around file names for include statements

Would you like to replace any double quotes by angle brackets around file names for include statements?

Why? It looks correct as it is to me...

I suggest to reconsider the consequences of the following wording from the section "16.2 Source file inclusion" in the standard specification for the programming language "C++".
…
The named source file is searched for in an implementation-defined manner. If this search is not supported, or if the search fails, the directive is reprocessed as if it read

#include <h-char-sequence> new-line
…

How do you think about to avoid "a duplicated file search" here?
Would you like to restrict the searched directories for header files of your software?

16.2.7
7 [ Note: Although an implementation may provide a mechanism for making arbitrary source files available to
the < > search, in general programmers should use the < > form for headers provided with the implementation,
and the " " form for sources outside the control of the implementation. For instance:
#include <stdio.h>
#include <unistd.h>
#include "usefullib.h"
#include "myprog.h"
— end note ]

There are different opinions about the handling of the involved implementation-defined behaviour.

Will header files be also searched outside the specified include directories if double quotes are used for the discussed preprocessor statement?
Is there a speed difference measurable if a file is not found there and the search will be retried with "the angle brackets inclusion method"?


haproxy: 2.5.3 -> 2.5.4

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/haproxy/versions.
meta.description for haproxy is: "Reliable, high performance TCP/HTTP load balancer"
meta.homepage for haproxy is: "https://haproxy.org"
meta.changelog for haproxy is: ""
Updates performed

Version update

To inspect upstream changes
Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
Warning: no invocation of /nix/store/ygj9bn5qyz64cv5f8qz0v5975wszv8px-haproxy-2.5.4/bin/haproxy had a zero exit code or showed the expected version
0 of 1 passed binary check by having a zero exit code.
0 of 1 passed binary check by having the new version present in output.
found 2.5.4 with grep in /nix/store/ygj9bn5qyz64cv5f8qz0v5975wszv8px-haproxy-2.5.4
found 2.5.4 in filename of file in /nix/store/ygj9bn5qyz64cv5f8qz0v5975wszv8px-haproxy-2.5.4

Rebuild report (if merged into master) (click to expand)

2 total rebuild path(s)

1 package rebuild(s)

1 x86_64-linux rebuild(s)
1 x86_64-darwin rebuild(s)

First fifty rebuilds by attrpath
haproxy

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/ygj9bn5qyz64cv5f8qz0v5975wszv8px-haproxy-2.5.4 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A haproxy https://github.com/r-ryantm/nixpkgs/archive/bfa2e783815ca422914c35c1735783f529ebb37f.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/ygj9bn5qyz64cv5f8qz0v5975wszv8px-haproxy-2.5.4
ls -la /nix/store/ygj9bn5qyz64cv5f8qz0v5975wszv8px-haproxy-2.5.4/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

haproxy

Maintainer pings

nixpkgs-review happy, nixos x86_64. haproxy.tests passes.


Revert schema updates

Revert the schema updates
First one is because of itemId non-uniqueness
Second one needs mysql 8 (We have this locally but not in cloud)

:white_check_mark: Apply Succeeded (shareable-lists-api-cdk)
CI link
Apply complete! Resources: 1 added, 0 changed, 0 destroyed.
Details (Click me)
Acquiring state lock.  Resource actions are indicated with the following symbols:
  + create

Terraform will perform the following actions:

  # local_file.application_ecs_service_appspec_94386B9C will be created
  + resource "local_file" "application_ecs_service_appspec_94386B9C" {
      + content              = jsonencode(
            {
              + Resources = [
                  + {
                      + TargetService = {
                          + Properties = {
                              + LoadBalancerInfo = {
                                  + ContainerName = "app"
                                  + ContainerPort = 4029
                                }
                              + TaskDefinition   = "arn:aws:ecs:us-east-1:996905175585:task-definition/ShareableListsApi-Prod:294"
                            }
                          + Type       = "AWS::ECS::Service"
                        }
                    },
                ]
              + version   = 1
            }
        )
      + content_base64sha256 = (known after apply)
      + content_base64sha512 = (known after apply)
      + content_md5          = (known after apply)
      + content_sha1         = (known after apply)
      + content_sha256       = (known after apply)
      + content_sha512       = (known after apply)
      + directory_permission = "0777"
      + file_permission      = "0777"
      + filename             = "appspec.json"
      + id                   = (known after apply)
    }

Plan: 1 to add, 0 to change, 0 to destroy.
local_file.application_ecs_service_appspec_94386B9C: Creating...
local_file.application_ecs_service_appspec_94386B9C: Creation complete after 0s [id=a62fbaaa55446f7238055c0b34030da62f796291]

Apply complete! Resources: 1 added, 0 changed, 0 destroyed.


Spring Boot sample

This adds gradle configuration to create an empty Spring Boot project. Is this what you had in mind?

This pull request is meant for #1

Thanks for the feedback @jzheaux. I've tried to squash the changes, but I can't find how to do that in Intellij. The Squash Into option in the Git Log window remains disabled. I tried some things, and hope that I haven't messed it up too badly ;-)

Thanks for the contribution, @tomvandenberge!
I'm sorry that you had some issues with rebase, git can be a challenge sometimes. No worries, though, I was able to clean it up. I've merged everything to master via 82be38c00b993d55d3f17a4b85a876510080a258.


DCOS-37420: adjust Framework struct to improve performance

Change the Framework speck to create only one instance of the spec instead of creating a new instance every time a user calls getSpec(). This should lower the load and improve the performance.
Backport of https://github.com/dcos/dcos-ui/pull/2672/commits/2372ea59526b9df101ed7cc05ecb5c8774fcdb33
Closes DCOS-37420
Checklist

[x] Did you add a JIRA issue in a commit message or as part of the branch name?
[ ] Did you add new unit tests?
[ ] Did you add new integration tests?
[ ] If this is a regression, did you write a test to catch this in the future?

This repo has @mesosphere-mergebot integration. You can interact with the following commands.
@mesosphere-mergebot integrate
@mesosphere-mergebot ship-it
@mesosphere-mergebot test

@orlandohohmeier okay, but then adding it as text seems a bit unnecessary as you can find the same info by git blaming, right?

@DanielMSchmidt I'm not following... It is a part of a commit body, isn't it?


don't warn on db creation

do not warn on db creation if the user runs a
"single-node-cluster". given the suggestions i got on IRC
currently the best way is not to modify N and just let it default
to three, also for a cluster-of-one.
This closes COUCHDB-2594
This superseeds https://github.com/apache/couchdb-setup/pull/4

I worry about the following: that warning existed with some meaning, for some reason. In fact, it could notice that cluster is in "incomplete" state what may explain various errors and failures. If so, may be add special clause for NodeCount=1, but keep the warning for else? If my worries are false - go ahead (:

that's a really cool idea, i can do that on monday if no one else objects

ping @rnewson @chewbranca @banjiewen

The error exists because N is ~silently reduced to NodeCount.
To quote @rnewson's comment in the related ticket, which I still believe is definitive here:

A strong mechanism would be to remove the silent reduction of N when creating a database, to instead return a 400 or 500 error message (we'll have to bikeshed a little on whether the user is in error for asking for more replicas than the cluster can create or the server is in error for not having enough nodes to satisfy the user).
When choosing "single node" in setup, the default N value should be set to 1, so that database creations do not return the error.

IMO removing the error is all fine and good - it's not really the crux of the interest here. If there's a "Single Node Mode", that should set N to 1, and N should never be silently reduced.

The problem with changing N is forgetting to change up back up when adding nodes. Silently making N=1 dbs when you have one node is infinitely preferable to making N=1 dbs when you have three nodes or more.
The reason we log is so that the observant admin can notice that they didn't join their multi-node cluster up properly, but I don't think it's a very good mechanism.
Of all the options, the best one is to leave things as they are. Someone with a single node 'cluster' will see warnings for this and learn to ignore them (since they don't apply to them). For everyone else, it helps them avoid a data loss scenario.
The second best option is to remove the warning, which is what I advocate for given the number of voices that dislike the warning.
All other options involve more work and just change one compromise into another one.

How about this for a compromise?

make this a warning and not an error
add a clause about “if you run a single-node instance, ignore this” (wording TBD)

+1

See https://github.com/apache/couchdb-mem3/pull/20 for new PR


Implement Connection Manager for bridge clients

Bridge clients need to be Clone. See the comment here https://github.com/movementlabsxyz/movement/pull/153#discussion_r1684345723
We need a nicely designed connection manager because of this https://github.com/movementlabsxyz/movement/pull/153#issuecomment-2247596412

Closing as this was solved and the fix implemented a few days ago.


[AutoPR sql/resource-manager] Update databaseVulnerabilityAssessments.json

Created to sync https://github.com/Azure/azure-rest-api-specs/pull/7560

(message created by the CI based on PR content)

This PR has been merged into https://github.com/Azure/azure-sdk-for-python/pull/8425


Fix CVE-2024-36623 for moby-cli

Merge Checklist

All boxes should be checked before merging the PR (just tick any boxes which don't apply to this PR)

[x] The toolchain has been rebuilt successfully (or no changes were made to it)
[x] The toolchain/worker package manifests are up-to-date
[x] Any updated packages successfully build (or no packages were changed)
[x] Packages depending on static components modified in this PR (Golang, *-static subpackages, etc.) have had their Release tag incremented.
[x] Package tests (%check section) have been verified with RUN_CHECK=y for existing SPEC files, or added to new SPEC files
[x] All package sources are available
[x] cgmanifest files are up-to-date and sorted (./cgmanifest.json, ./toolkit/scripts/toolchain/cgmanifest.json, .github/workflows/cgmanifest.json)
[x] LICENSE-MAP files are up-to-date (./LICENSES-AND-NOTICES/SPECS/data/licenses.json, ./LICENSES-AND-NOTICES/SPECS/LICENSES-MAP.md, ./LICENSES-AND-NOTICES/SPECS/LICENSE-EXCEPTIONS.PHOTON)
[x] All source files have up-to-date hashes in the *.signatures.json files
[x] sudo make go-tidy-all and sudo make go-test-coverage pass
[x] Documentation has been updated to match any changes to the build system
[x] Ready to merge

Summary

What does the PR accomplish, why was it needed?
Fix CVE-2024-36623 for moby-cli
Change Log

Fix CVE-2024-36623

Does this affect the toolchain?

NO
Associated issues

#xxxx

Links to CVEs

https://nvd.nist.gov/vuln/detail/CVE-2024-36623

Test Methodology

Pipeline build: https://dev.azure.com/mariner-org/mariner/_build/results?buildId=691771&view=results

Auto cherry-pick results:

main :white_check_mark: -> https://github.com/microsoft/azurelinux/pull/11418

Auto cherry-pick pipeline run -> https://dev.azure.com/mariner-org/mariner/_build/results?buildId=692804&view=results


ML supervised learning generating tiff distort

When using(fully filled with data value) tiff
toMultibandRaster throws null pointer exception,which I still yet cannot understand why there are some null tile in the RasterFrameLayer.
Input geojson
Output classified result
My rough code
So I think out changing the rf by
    val rr: RDD[(SpatialKey, MultibandTile)] = rf.select(rf.spatialKeyColumn, array($"bd_6")).as[(SpatialKey, Array[Tile])]
      .rdd
      .filter {
        case (_: SpatialKey, b) if b(0) == null ⇒ false  // remove any null Tiles
        case _ ⇒ true
      }
      .map { case (sk, tiles) ⇒
        (sk, MultibandTile(tiles))
      }

And the classified result is distorted, the whole raster is squeezed in upper left direction compared with original one.

It seems the tlm meta doesn't behave correctly and I really cannot explain what causes this weird behavor.

And I even create a new tlm to generate the tiff,it's better than the one above with only tiles in the right-most and bottom cannot output normally. Code is here

For now,I still cannot figuire out what the point is.

And I even create a new tlm to generate the tiff,it's better than the one above with only tiles in the right-most and bottom cannot output normally. Code is here

For now,I still cannot figuire out what the point is.

This can easily reproduce by using demo data L8_LB2-Elkton-VA with tile size 16.
The result is:

This can easily reproduce by using demo data L8_LB2-Elkton-VA with tile size 16.
The result is:


Update raylib to work with Zig >=0.10

The updated raylib isn't an official raylib release. (it says 4.5-dev)

raylib version has been updated in 1e06706bff87c39738b339eec90e8d20db2ba122. The orelse is valid in Zig 0.10.1

I removed orelse because it should not fail.


[NextMajor] Processing dependency leads to an error

We are using your DevOps-Pipeline.ps1 script for quite a while.
Starting from last monday (26.02.2024) with the NextMajor build 16561 our pipelines show an error.
(latest BC23 build and NextMinor are fine...)
After compiling the main app, the dependent app cannot find the main app and attempts to download it:
Dependency App exists [before] -> Downloading symbols [now]
in both cases the BcContainerHelper is version 6.0.6
Compiling C:\a\1\s\IndustryDE
Using Symbols Folder: C:\a\1\s\.packages
Processing dependency Microsoft_Application_<IP_ADDRESS> ()
Dependency App exists
Processing dependency Microsoft_System_<IP_ADDRESS> ()
Dependency App exists
Processing dependency BE-terna_BE-terna Automotive_<IP_ADDRESS> (bc455598-e208-4c92-bdff-5bbe6b9ed3c3)
Downloading symbols: BE-terna_BE-terna Automotive_<IP_ADDRESS>.app
Url : http://<IP_ADDRESS>:7049/BC/dev/packages?appId=bc455598-e208-4c92-bdff-5bbe6b9ed3c3&versionText=<IP_ADDRESS>&tenant=default
Downloading using WebClient
ERROR Exception calling "DownloadFile" with "2" argument(s): "The remote server returned an error: (404) Not Found."

before 26.02.2024:
Compiling C:\a\1\s\IndustryDE
Using Symbols Folder: C:\a\1\s\.packages
Processing dependency Microsoft_Application_<IP_ADDRESS> ()
Dependency App exists
Processing dependency Microsoft_System_<IP_ADDRESS> ()
Dependency App exists
Processing dependency BE-terna_BE-terna Automotive_<IP_ADDRESS> (bc455598-e208-4c92-bdff-5bbe6b9ed3c3)
Dependency App exists
Compiling...

No idea...

Right now, Next Major requires the latest prerelease of BcContainerHelper.
The log included above is very limited and shows the problem, but doesn't help resolving the problem.
If latest prerelease of BcContainerHelper doesn't solve the problem, then please include a full log of the script running


Selectlist: Auto sizing not working again #980

Selectlist: Auto sizing not working again #980

@mbeard Reason I did that is because I have to create the elements and have them display the same way they normally would to figure out the sizes.


Defer data directory creation.

UI version
1.1.6
Your idea
The Joulescope UI automatically creates the default data directory:
https://github.com/jetperch/pyjoulescope_ui/blob/59b6b44ffbb3e28e092265547040c8a89c6e93d5/joulescope_ui/pubsub.py#L446
However, the user can change the data directory.  Some users may not want a "Documents" directory, which the UI currently creates at start.
While this does not at all affect the Joulescope UI performance, it will create the Documents directory at start.  Most users should not care, since the Documents directory is pretty standard across all platforms as of 2024.  I don't think Windows and macOS will function right without a Documents directory, so this is likely only an issue with Linux user's who highly customize their system.  You sound like you have deleted the Documents directory, so this behavior is annoying.
The UI should defer data directory creation.  In the case that the data directory is default and not found, it should be created.  In the case that the data directory is not the default and not found, it needs to do something meaningful.  For save, perhaps it reverts to the default and creates that directory?  For read, perhaps default to the Documents directory or the user directory?
See the forum.

Fixed in 1.1.7.


add missing 3D module mplot3d

required when calling projection='3d' in add_subplot

Coverage increased (+0.2%) to 88.211% when pulling 667d16cec2ed11edff89bd85e4df1b47c2c67e58 on bricaud:patch-1 into 8ce5bde39206129287375af24fdbcd7edddca8c5 on epfl-lts2:master.

When was this necessary? It should be imported in plotting.py.

I don't know. It does not work when I try to run the wavelet tutorial even
if in the tutorial I import plotting.
Let see if someone else get the same problem...
Le jeu. 30 mai 2019 à 15:09, Michaël Defferrard<EMAIL_ADDRESS>a écrit :

When was this necessary? It should be imported in plotting.py
https://github.com/epfl-lts2/pygsp/blob/8ce5bde39206129287375af24fdbcd7edddca8c5/pygsp/plotting.py#L46
.
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OpenML connector for MLModels

OpenML connector for fetching OpenML flows to AIoD ml models.
Note:

All sklearn pipelines are ignored while fetching flows from OpenML. ToDo: discuss how to handle pipelines. Bonus: only fetch pipelines which have >= 1 run on OpenML.
improve mlmodel.name.
extract pipelines which have at least 1 run.
Discuss how to save flow parameters in Aiod.
Discuss where to save language (human language) of flow (maybe ai_resource.metadata_language).

ToDo (after PR https://github.com/aiondemand/AIOD-rest-api/pull/204 approval):

define "creator" as a dynamic class using resource_create.

I do not see KeyError: 'last_id' error anymore, though I did not do anything specific to resolve it.


Recursive processing with sub-folders (for sub-domains)

Is it possible to run brunch recursively, with each sub-folder having its own configuration file (and its own output folder)?
We have this scenario:
   Root - index.html
       |- services
       |- products
       |- blogs

Now, each of those are actually mapped as sub-domains and have their own site structure (styling, content so on) and the root itself has its own landing page and what not.
The problems we are facing:

Currently, we have brunch-config.js in each of those sub-folders, but we have to manually go and build each one separately. Is there a way to trigger build on the root and all sub-folder automatically gets built?
We do not see much of support for debug vs release specification in the configuration file. Would like to specify different paths for debug mode and release mode in the configuration files - how to do that easily? Maintaining two different configuration files is not easy (even if possible)

We do not see much of support for debug vs release specification in the configuration file. Would like to specify different paths for debug mode and release mode in the configuration files - how to do that easily? Maintaining two different configuration files is not easy (even if possible)

Brunch has the environments concept — you can totally use it. In release just specify different joinTo paths.
Take a glance here, section "overrides" http://brunch.io/docs/config#overrides

Currently, we have brunch-config.js in each of those sub-folders, but we have to manually go and build each one separately. Is there a way to trigger build on the root and all sub-folder automatically gets built?

There is no way of doing that right now, maybe something worth considering.


Unexpected throw

@XVincentX At $DAYJOB, we've started to use Prism as a shadow experiment in order to perform validation of requests/responses. We log and compare inputs/outputs of the current validation implementation we're using against a Prism powered one.
This PR puts under the light a corner case usage of Prism that makes the lib crash.
I understand the use case looks weird and I apologize about it. Indeed, this doesn't provide a lot of context to work with. But this is all what we've got to work with as well on our side.
This is the simplest repro case I've been able to produce.

@nulltoken I think there's a file missing in this PR. Can you check it out?

@nulltoken I think there's a file missing in this PR. Can you check it out?

Sorry. I pushed a little to early while I was uncrufting the repro case. Should be fixed now.

@XVincentX The CI failure is consistent with what I'm seeing at $DAYJOB:
    Error name:    "TypeError"
    Error message: "target.split is not a function"

          42 |
          43 | export function splitUriParams(target: string) {
        > 44 |   return target.split('&').reduce((result: Dictionary<string>, pair: string) => {
             |                 ^
          45 |     const [key, ...rest] = pair.split('=');
          46 |     result[key] = rest.join('=');
          47 |     return result;

          at splitUriParams (packages/http/src/validator/validators/body.ts:44:17)
          at deserializeAndValidate (packages/http/src/validator/validators/body.ts:69:28)
          at packages/http/src/validator/validators/body.ts:116:26
          at node_modules/fp-ts/lib/Option.js:87:60
          at Object.pipe (node_modules/fp-ts/lib/pipeable.js:13:23)
          at packages/http/src/validator/validators/body.ts:106:11
          at node_modules/fp-ts/lib/Option.js:87:60
          at Object.pipe (node_modules/fp-ts/lib/pipeable.js:9:20)
          at HttpBodyValidator.validate (packages/http/src/validator/validators/body.ts:101:12)
          at packages/http/src/validator/index.ts:51:43

@nulltoken How did you end up with such input? This is something that shall never happen in Prism. Do you have a reproducible curl command I can use to get in such situation?
Basically what's happened here is that you claim that the content is formdata, but the body property has been parsed, which means it's JSON Compatible. As far as I remember, there is no way you can get in such situation in Prism.

Please reopen when you have more informations.


Remove dependency to "linked-list-typescript" use regular javascript arrays for roList

Addressed by #173


Discussion : Performance improvements, but some strange bugs

Hello.
I've been tinkering with an additive rotations...  https://github.com/d3x0r/stfrphysics#live-demos
Using Log-Quaternions, or just angular velocities.  Since a physics engine internally thinks in angular velocity anyway, there is less math to just update the angle-angle-angle representation of a quatrernion.
https://d3x0r.github.io/cannon.js/examples/worker.html  This demo with cubes, once the cubes are on the plane, they seem to have a ghost rotation force, that seems to want to turn them upright (somewhat).
And https://d3x0r.github.io/cannon.js/examples/hinge.html (raycast vehicle demo) has a strange behavior - (need to improve rendering constraints in debug info)... if you could take a moment and give me an insight where angularVelocity is actually updated?
I was also attempting to apply velocity/position as a (final+initial)/2; which gives closer results across varying framerates; that in itself doesn't cause the issue.
https://github.com/d3x0r/cannon.js/blob/improve_accuracy/src/math/lnQuaternion.js#L390  (multiple angular rotation to a point, is a couple less multiplications than the equivalent quaternion https://github.com/d3x0r/cannon.js/blob/improve_accuracy/src/math/Quaternion.js#L251  Although the quaternion mult() to rotate a rotation is slightly more work... on the other side though, integrate becomes a direct scaled addition; and conversion from internal angle-angle-angle to axis-angle is just getting the length of the vector, and normalizing it, and then building cos(length/2), sin(length/2)*(x,y,z) for the quaternion.
The lnQuaternion/Quaternion is switchable with a new 'config.js' setting, so I can swap between one or the other just by changing which is require()ed.  It passed all tests, but still failed the container test; added a container test, and now the stacks of balls in containers works well.  Previously they spilled all over the plane, and appeared to rotate correctly... and thie spheres on a mesh appear to rotate correctly so I'm not sure where the constraint resolutions are failing; or really where the real work to update the angular velocity is done.  It's not built as a change at the end... when the body is updated it's angularVelocity already has a value, and there's no torque to apply.

I did fix several of these tests by fixing the integrate.  The only thing that malfunctions is the point pick on a cube.  The rotational velocity increases without bound.

@d3x0r  looks great but i think you should add your findings to https://github.com/pmndrs/cannon-es


Is the there any way to authenticate and authorize users connecting to channels and how to prevent users from pushing to channel

Hey. Sorry i am a little bit new to these stuff. I wanted to implement a chat system for exercise. What i have in mind is
the path of Telegram.
As you know such this project requires push from server to client. My problem is that:
1- How may i authenticate and authorize users that are connecting to every channel.
Lets assume that there is a channel for every group that the messages are being pushed inside it.
The problem is that if someone leaves the channel, he still can listen the channel for the messages
that are being sent.
2- I just want to push the messages just from the servers and users don't be authorized for sending
any data from server or otherwise the users will be sending messages that are not being recorded in database.
Is there anything that supports something like this? And I'm using golang for my project.

@zytell3301 thanks for looking into Sarama for your application. However, this is more of a general kafka question that anything specific to Sarama. I’d suggest researching “kafka acls and SASL” as your search terms. There are numerous good articles and presentations on the topic from a selection of cloud vendors and their developer experience people that should be able to help with this

really really thanks for you help


Some updates to the cloud formation template

Parameterize the AMI so the template can be used in different regions (#44)
Don't hardcode the region, use the one where the template is running (#44)
Change the Airflow setup process so that it works on new AMIs (#46)
Add the /efs filesystem to /etc/fstab so the system can be rebooted (#45)
Change the name "SpotInstanceType" to "WorkerInstanceType" since we're not
using spot yet and we don't want to confuse users.

Also, please note that this updates the Airflow version to 1.10.1b1. We need this beta for what we're doing because otherwise the combo of SQS and instance roles breaks Airflow.
The release should be finalized within the next few days and I'll update the PR to point at Airflow 1.10.1 at that point.

Looks great! Good stuff. I'll do some testing now and get back soon.

Hey @tomfaulhaber, here's the results of my experimenting:
✔ I was able to issue airflow backfill -s 2018-11-09 tutorial and the tasks were correctly executed by a Celery worker after send/receive from SQS.
❌ I was not able to make DAGs run by manually running them in the UI, task instances are entering a null state and are not being seen by the scheduler
Here's my config:
[core]
executor = CeleryExecutor
parallelism = 100
dag_concurrency = 100
max_active_runs_per_dag = 10

fernet_key = SOMEVERYLARGEVALUEHEREFORSAFETYPUPORSESpKFf87WFwLbfzqDDho=

load_examples = False

[cli]
api_client = airflow.api.client.local_client

[operators]
default_owner = Airflow
default_cpus = 1
default_ram = 512
default_disk = 512
default_gpus = 0

[webserver]
base_url = http://localhost:8080
web_server_host = <IP_ADDRESS>
web_server_port = 8080

workers = 4
worker_class = sync
web_server_worker_timeout = 120
worker_refresh_batch_size = 1
worker_refresh_interval = 30

secret_key = temporary_key
expose_config = True
authenticate = False
filter_by_owner = False

log_fetch_timeout_sec = 5

[celery]
celery_app_name = airflow.executors.celery_executor
celeryd_concurrency = 1
worker_log_server_port = 8793

[scheduler]
# Task instances listen for external kill signal (when you clear tasks
# from the CLI or the UI), this defines the frequency at which they should
# listen (in seconds).
job_heartbeat_sec = 5

# The scheduler constantly tries to trigger new tasks (look at the
# scheduler section in the docs for more information). This defines
# how often the scheduler should run (in seconds).
scheduler_heartbeat_sec = 5

# after how much time should the scheduler terminate in seconds
# -1 indicates to run continuously (see also num_runs)
run_duration = -1

# after how much time a new DAGs should be picked up from the filesystem
min_file_process_interval = 0

dag_dir_list_interval = 300

# How often should stats be printed to the logs
print_stats_interval = 30

# child_process_log_directory => let the default: $AIRFLOW_HOME/logs

# Local task jobs periodically heartbeat to the DB. If the job has
# not heartbeat in this many seconds, the scheduler will mark the
# associated task instance as failed and will re-schedule the task.
scheduler_zombie_task_threshold = 300

# Turn off scheduler catchup by setting this to False.
# Default behavior is unchanged and
# Command Line Backfills still work, but the scheduler
# will not do scheduler catchup if this is False,
# however it can be set on a per DAG basis in the
# DAG definition (catchup)
catchup_by_default = True

# Statsd (https://github.com/etsy/statsd) integration settings
statsd_on = False
statsd_host = localhost
statsd_port = 8125
statsd_prefix = airflow

# The scheduler can run multiple threads in parallel to schedule dags.
# This defines how many threads will run. However airflow will never
# use more threads than the amount of cpu cores available.
max_threads = 2

authenticate = False

A few of those have been deprecated already, I'll keep digging a bit to find out more.
In the meantime, I'll merge the PR because it accomplishes what it's meant for.

Hmm, interesting. I was having the same problem starting tasks from the UI. I had to run a backfill from the cli to get the job to start. I figured I was doing something wrong, but I guess something is misconfigured.
Let's both dig in and see if we can sort it.


Add localAgentPort in the options

 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.


Streaming support

Have you thought about / planned a way to support streaming audio instead of sending the entire audio clip? If its not currently supported, how would you solve it? I would appreciate some guidance to send a proper PR to support streaming, if possible.

At the moment (w/ WASM backend), the latency for the encoder is just too much to do real-time streaming. Fortunately, the onnxruntime-web team have been busy improving their WebGPU backend, and it's at a stage where we can do testing with it now.
So, we hope to add support for it soon! If you're up for the challenge, you can fork transformers.js, build onnxruntime-web from source w/ webgpu support, and replace the import with the custom onnxruntime-web build.

Well yes, you can just send 30-second chunks of audio to whisper, but as stated above, you won't get a response for at least 1-2 seconds due to the encoder latency. Then on top of that, depending how much you are decoding, you'd have to wait for the full chunk to be decoded before merging with the current predicted text.
That said, I do think this will be feasible with webgpu, at which point I'll probably take a look at this (unless you'd be interested in starting, working with the wasm backend for now).


Update DEVELOP.md to reflect new codegen (#119)

Description of Changes
#123 reverted the non-code-changes in #119. This cherrypicks them back.
See the discussion at https://github.com/clockworklabs/com.clockworklabs.spacetimedbsdk/commit/732dd2872b501ef3d41060ac9da06cb8d7f07226#r146042766 for more context.

As suggested in the other issue, please rename tools to tools~, so that it's ignored by Unity, otherwise it will consider those scripts assets, will generate meta files and so on.
(this will also need relevant change in DEVELOP.md)

As suggested in the other issue, please rename tools to tools~, so that it's ignored by Unity, otherwise it will consider those scripts assets, will generate meta files and so on.
(this will also need relevant change in DEVELOP.md)

Dammit. Thank you. Done. The minute I switched to my terminal window to cherrypick, I lost all my mental state.


[Relay, TOPI] Add numpy style cumsum op

This adds a numpy style cumsum op to Relay/TOPI. The spec is identical with numpy one except there is no promotion of int32 -> int64 output dtype, for the case when the input is a int32 tensor and output dtype is not provided.
https://numpy.org/doc/stable/reference/generated/numpy.cumsum.html
Both CPU and GPU are supported, and it is especially efficient if thrust is available. I updated TIR scan IR to support cumsum on any rank. But scan is still done only on the innermost axis, so transposing is required when the scan axis is not the innermost one.
please review @jwfromm @mbrookhart @zhiics @kevinthesun @junrushao1994 @antinucleon

@tkonolige @mbrookhart Comments were addressed. CPU cumsum is now done in parallel for non-scan axes, and binop argument is now a function. Thanks for reviews.

@tkonolige @mbrookhart Comments were addressed. CPU cumsum is now done in parallel for non-scan axes, and binop argument is now a function. Thanks for reviews.

Thanks @tkonolige @mbrookhart

Thanks @tkonolige @mbrookhart

Hi @masahi ,
Thanks for your contribution for the "cumsum". I want to use this op in onnx model.
I meet the problem when I want to compile an onnx model with "CumSum" op to relay.
When I use "relay.frontend.from_onnx" and add "CumSum": AttrCvt("cumsum",{"axis": axis, "dtype": dtye})," in python/tvm/relay/frontend/onnx.py
But it still does not work.
Thanks for your attention!

Hi @masahi ,
Thanks for your contribution for the "cumsum". I want to use this op in onnx model.
I meet the problem when I want to compile an onnx model with "CumSum" op to relay.
When I use "relay.frontend.from_onnx" and add "CumSum": AttrCvt("cumsum",{"axis": axis, "dtype": dtye})," in python/tvm/relay/frontend/onnx.py
But it still does not work.
Thanks for your attention!

typo -> "CumSum": AttrCvt("cumsum",{"axis": "axis", "dtype": "dtye"}),"

typo -> "CumSum": AttrCvt("cumsum",{"axis": "axis", "dtype": "dtye"}),"

@ybai62868 please post this to the discuss forum or open an issue, clarifying what exactly you mean by "it still does not work"

@ybai62868 please post this to the discuss forum or open an issue, clarifying what exactly you mean by "it still does not work"

@masahi Hi， what I mean "it still does not work" is that it will report this message " tvm.error.OpNotImplemented: The following operators are not supported for frontend ONNX: CumSum " although I add and change the AttrCvt("cumsum",{"axis": axis, "dtype": dtye}) and rename the CumSum to cumsum.

@ybai62868 This PR adds cumsum support at the topi level. The work to add support to onnx has not been done yet.


Error With Jupyter Notebook

Environment data

VS Code version: XXX
Jupyter Extension version (available under the Extensions sidebar): XXX
Python Extension version (available under the Extensions sidebar): XXX
OS (Windows | Mac | Linux distro) and version: XXX
Python and/or Anaconda version: XXX
Type of virtual environment used (N/A | venv | virtualenv | conda | ...): XXX
Jupyter server running: Local | Remote | N/A

Expected behaviour
XXX
Actual behaviour
XXX
Steps to reproduce:
[NOTE: Self-contained, minimal reproducing code samples are extremely helpful and will expedite addressing your issue]

XXX

Logs

Output for Jupyter in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Jupyter)

XXX

Can you provide the error message, steps that led to it, and the logs from the Jupyter output (command: Jupyter: Show Output?


Annotations for nucleasome and clustering issues

tensorsignatures version: latest as of 12/18/2020
Python version: N/A
Operating System: Linux (HPC)

Description
Trying to annotate melanoma dataset from the PCAWG MAF files.
What I Did
Tried to annotate for the different categories using the R scripts and reference sets provided in Mutations.R and Constants.Rdata respectively. However, looking at the nucleosome annotation function I noticed that it only annotates 0 or 1, not the 4 states specified in the preprint. Similarly, looking at the mutation clustering annotation, it seems that the transition probabilities are different from those specified in the paper.

getNucleosomeData <- function(){
    nucleosomes <- read.table(nucleosomePath)
    NucRanges = GRanges(seqnames=nucleosomes$V1,
        ranges=IRanges(start=nucleosomes$V2, end=nucleosomes$V3),
        strand="+")
    NucRanges <- reduce(NucRanges)
    NucRanges <- NucRanges[!width(NucRanges)>2] # get rid of strange points
    NucleosomeCovered <- NucRanges+73
    NucleosomeCovered <- reduce(NucleosomeCovered) # genomic regions within nucleosomes
    NucleosomeCovered <- toNCBI(NucleosomeCovered)
    GRCh37 <- getStandardChromosomes()
    NotNucleosomeCovered <- setdiff(GRCh37, NucleosomeCovered, ignore.strand=T)
    NucleosomePartition <- sort(c(NotNucleosomeCovered, NucleosomeCovered), ignore.strand=T)
    mcols(NucleosomePartition)$state <- 0
    mcols(NucleosomePartition[strand(NucleosomePartition) == "+"])$state <- 1

    return(NucleosomePartition)
}

kataegis <- function(vcf, p=1e-3, q=0.1, r=100) {
d <-  diff(start(vcf))
w <- d > 1 & diff(as.numeric(seqnames(vcf))) == 0
#p <- 1e-3 # P N>Kat
#q <- 0.05 # P Kat>N
P <- matrix(c(1-p,p,q, 1-q), ncol=2, byrow=TRUE) # Transition matrix
p0 <- c(1,0)
s <- c(mean(d[w]), r)
dw <- d[w]
l <- length(dw)
T1 <- T2 <- matrix(0,ncol=l, nrow=2)
T1[,1] <- log(c(q/(q+p), p/(q+p)))
lP <- log(P)
dg <- rbind(dgeom(dw, prob=1/s[1], log=TRUE), dgeom(dw, prob=1/s[2], log=TRUE))
for(i in 2:l){
x <- ((T1[,i-1] + lP) + dg[,i])
T2[1,i] <- (x[1,1] < x[2,1])+1
T2[2,i] <- (x[1,2] < x[2,2])+1
T1[1,i] <- x[T2[1,i],1]
T1[2,i] <- x[T2[2,i],2]
}
z <- numeric(l)
z[l] <- 1
for(i in l:2){
z[i-1] <- T2[z[i],i]
}
k <- numeric(nrow(vcf))
k[-1][w][-1] <- z[-l]-1
k[-nrow(vcf)][w][-1] <- (z[-l]-1) | k[-nrow(vcf)][w][-1]
#k[-1][w] <- z-1
#k[-nrow(vcf)][w] <- (k[-nrow(vcf)][w]) | (z-1)
kf <- factor(k, levels=0:1)
return(kf)
}

Hi emauryg,
thanks for your interest in tensorsignatures. You can find the nucleosome state annotations in the NUC object of the constants.Rdata object:
> load("project/constants.rdata")
> NUC
GRanges object with 86116192 ranges and 1 metadata column:
             seqnames              ranges strand |     state
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]        1                1-58      * |         0
         [2]        1           59-834155      * |         0
         [3]        1<PHONE_NUMBER>13      * |         3
         [4]        1<PHONE_NUMBER>18      * |         2
         [5]        1<PHONE_NUMBER>23      * |         1
         ...      ...                 ...    ... .       ...
  [86116188]        X 154929674-155270502      * |         0
  [86116189]        X 155270503-155270560      * |         0
  [86116190]        Y                1-58      * |         0
  [86116191]        Y         59-59373508      * |         0
  [86116192]        Y   59373509-59373566      * |         0
  -------
  seqinfo: 24 sequences from an unspecified genome

The state column of the NUC object represents nucleosome states (0 baseline: i.e. not on a nucleosome, 1 minor out, 2 minor in, 3 linker region). You can use these annotations to classify the variants of your MAF files (this should be somewhat similar to getNucleosomeState of mutations.R).
Thanks for pointing out incoherence of reported transition probabilities in the kataegis function, I'll double check if there is a typo.
Best wishes,
Harald.

I see. Do you have a particular tissue from PCAWG for which you found mutations with a nucleosomal genomic context that is not 0? When I tried to annotate all the PCAWG from their MAFs it seems the intervals provided by NUC are all annotated by state 0.
Has there been any update regarding the kataegis function?
Thank you for the comments!

Certainly most of the tissues should have SNVs on various nucleosome states. Perhaps double check your annotation function ? It should somewhat follow the lines of
getNucleosomeState <- function(vcf, consensusState) {
    h <- findOverlaps(vcf, consensusState, ignore.strand=T) # ignore.strand is important
    stopifnot(length(h) == length(granges(vcf))) # sanityCheck
    factor(mcols(consensusState[subjectHits(h)])$state, levels=c(0,1,2,3))
}

Running the kataegis function with default settings should give you the same results as we report in our preprint.
Hope this helps, best wishes.

Certainly most of the tissues should have SNVs on various nucleosome states. Perhaps double check your annotation function ? It should somewhat follow the lines of
getNucleosomeState <- function(vcf, consensusState) {
    h <- findOverlaps(vcf, consensusState, ignore.strand=T) # ignore.strand is important
    stopifnot(length(h) == length(granges(vcf))) # sanityCheck
    factor(mcols(consensusState[subjectHits(h)])$state, levels=c(0,1,2,3))
}

Running the kataegis function with default settings should give you the same results as we report in our preprint.
Hope this helps, best wishes.

I used the same function from getNucleosomeState() to try to annotate the SNVs, and still got all 0 annotation. The same does not happen when I annotate the epigenomic states etc, so there shouldn't be anything wrong with the GRanges object.

I used the same function from getNucleosomeState() to try to annotate the SNVs, and still got all 0 annotation. The same does not happen when I annotate the epigenomic states etc, so there shouldn't be anything wrong with the GRanges object.

Hm interesting, if you do not mind to share an example MAF file and the script you used to annotate it I could have a look it (harald at ebi.ac.uk).

Hm interesting, if you do not mind to share an example MAF file and the script you used to annotate it I could have a look it (harald at ebi.ac.uk).


Replace mailchimp-api-v3 with mailchimp-marketing package

mailchimp-marketing is a library package provided by Mailchimp's team for interacting with the marketing APIs.
This is maintained better than the existing package for this purpose, mailchimp-api-v3.

Hear, hear. I'm completely bemused by all this. Firebase functions provide a Node.js server environment and yet const mailchimp = require("@mailchimp/mailchimp_marketing") is rejected by Firebase deployment with a 'couldn't find module' error. Why? The mailchimp-api-v3 approach described here is extremely unattractive

I think this is the correct package: @mailchimp/mailchimp_marketing

Resolved by #66


Parallax Carousel text & image overlapping in mobile

Describe the bug
A clear and concise description of what the bug is.
To Reproduce
see in web

adjust z-index won't help.


Investigate Changing PMC Deposit from Zip to Zipped Tar Archive

According to PMC specs, PASS should deposit as a gzipped tar archive
For reference: https://github.com/eclipse-pass/main/issues/616#issuecomment-1771553450

pmc assembler config set to:
"assembler": {
      "specification": "nihms-native-2017-07",
      "beanName": "nihmsAssembler",
      "options": {
        "archive": "TAR",
        "compression": "GZIP",
        "algorithms": [
          "sha512",
          "md5"
        ]
      }
    },


Add to conda-forge

Would be great if this package was available via conda-forge: https://github.com/conda-forge/staged-recipes/issues/26891

https://github.com/conda-forge/staged-recipes/pull/26904

Now available in conda-forge: https://github.com/conda-forge/orjsonl-feedstock
https://anaconda.org/conda-forge/orjsonl

@corneliusroemer Thanks for this! I was going get on this today but glad to hear you got it done. I don't use conda, however, I may look into making my other libraries available on it if others will find it useful :)

@umarbutler this was never meant to be a todo for you - just an expression of interest in case someone else gets to it before me.
We're using conda a lot in my sphere of bioinformatics because it's probably the best cross-platform package manager there is, going well beyond Python: many bioinfo tools (and also general utilities) have been packaged so one can spin up an environment on all sorts of architectures and oses, across the whole product of {linux, macos} x {x86_64, arm/aarch}
It's very easy to add pure Python packages with grayskull, compiled things can be a bit more tricky but it's not too bad.
While it's possible to install pip-only (i.e. not conda-packaged) packages in conda environments, the conda solver won't know about them so it's best to only do this temporarily - hence my packaging up orjsonl

@corneliusroemer Thanks for the crash course! I didn't know conda could be used for more than just Python, that's bring a lot of things into perspective, I wondered why not just use venv and/or pyenv.
Having a look at the instructions now, they seem a bit involved 😅 (at least relative to pip which is just py -m build; py -m twine upload --repository pypi dist/*). Do you know an easier way than this?


Make a post request to invoke intent without user communication

Hi,
Is there anyone who knows about invoke an intent by making a post request on dialogflow?
I have integrated my chatbot with facebook but to invoke an intent I need to make a post request with some text so that it got invoked automatically(without user interaction).Is there any way to do this? I know it is possible for the customizable bot (using angular etc.) as defined in this link
[(https://dialogflow.com/docs/reference/agent/query)] but having hard time to do with third party like facebook.Please if anyone knows help me out here!
Thanks

Well, you can do that using API.

There's some docs here on using curl.
The client library may be your best bet though, hope that helps.


Unify Attribute Representation

In nix-gui we repeat ourselves in handling conversions from different representations of the attribute path and potentially create bugs with inconsistent representation of Attributes. They could be either a list of attribute keys (["environment", "etc", "resolv.conf", "text"]) or string (environment.etc."resolv.conf".text). It was unclear what type attributes were and they'd have to be converted back and forth multiple times.
This change introduces the Attribute class. An immutable class which defines both a str representation, a bool representation, and allows iteration over the list of attribute keys.
Now we needn't apply any conversions between the representation of an Attribute except in cases where a string is expected such as title setting within Qt.

LGTM.