Y24-245 - As lab users we would like to be able to make a submission from a Stock Plate for the 10x - CITEseq and Emseq pipelines so that we no longer need to do a fake cherrypick to reduce workload and remove creation of fake data

User story
As lab users we would like to be able to make a submission from a Stock Plate for the 10x - CITEseq and Emseq pipelines so that we no longer need to do a fake cherrypick to reduce workload and remove creation of fake data
Who are the primary contacts for this story
Steve / Liz
Who is the nominated tester for UAT
SSRs / ??
Acceptance criteria
To be considered successful the solution must allow:

[ ] Add stock plate to the list of acceptable puroposes for Limber PCR bespoke request type
[x] Update the appropriate relationships
[ ] Release onto UAT from branch to try and test the process end to end to ensure there are no hidden issues
[x] Add a scenario to the existing integration suite test to create a plate of purpose 'Stock Plate' with a submission for Bespoke PCR on it and check you can create the first child plate 'LBB Ligation'

Dependencies
This story is blocked by the following dependencies:

#<issue_no.>
sanger/#<issue_no.>

References
This story has a non-blocking relationship with:

#4127
sanger/#<issue_no.>

Additional context
Add any other context or screenshots about the feature request here.

For existing DB (e.g. UAT and PROD), use the following steps to manually update the Stock Plate purpose:
login to the server, e.g.
ssh sss0-uat.psd.sanger.ac.uk
Go to the current release directory:
cd /var/www/sequencescape/current/
Run the console
bundle exec rails c
#find the stock plate
p = PlatePurpose.find_by(name:"Stock Plate")
#update the type
p.type = 'PlatePurpose::Input'
#save it
p.save
Check the uat database, i.e. psdd. in Mysql Workbench, run query:
select * from sequencescape_staging.plate_purposes where name = 'Stock Plate';
check if the stock plate type is 'PlatePurpose::Input'.
If so, that should mean the update is successful.

The issue with the cucumber tests is that the pooling behaviour for an input plate is overridden for PlatePurpose::Input at app/models/plate_purpose/input.rb:54.
Attached following is the numbered trace of the execution flow:

app/models/tag_layout.rb:60
app/models/tag_layout/walk_wells_by_pools.rb:6
app/models/plate.rb:83
app/models/plate_purpose.rb:69
app/models/plate_purpose/input.rb:54

There's one more update to be done for this.
As @wendyyang has mentioned above, we need to set the stock plate as an input plate.
Also, we will have to populate request_type_plate_purposes table with a record associating the request type limber_chromium_bespoke (its ID) with plate purpose Stock Plate (its ID).
As far as I know, this is done with the record loader. However, record loader only allows purposes in config/default_records/plate_purposes and it is not possible to add Stock Plate into it as Stock Plate purpose is already populated in the purposes table.
I think we will have to add a new record to the table associating limber_chromium_bespoke (its ID) with plate purpose Stock Plate (its ID).


PDF upload corrupted

Using Rails 4 and the ActiveRecord Shrine plugin, there seems to be file corruption in PDF uploads.
At some point between being a Rack file coming into Rails and the process method being called, the copy made by Shrine into the cache is being corrupted consistently.
# Original
$ ll /tmp/*.pdf
-rw-------. 1 foo bar 2520603 Mar 17 16:28 /tmp/RackMultipart20160317-60267-1082pik.pdf

# Shrine's Cache
$ ll /project/public/uploads/cache/
... snip ...
-rw-r--r--. 1 501 foo 2520347 Mar 17 16:28 27f745231e058660d965d47bfe44fce7eb30a2c96e837227d4917567f1d1.pdf
... snip ...

Filesizes
Original: 2520603
Shrine:   2520347
I've had a bit of trouble following the stacktrace to see at what exact point the io param of process copies the original Rack file to see what could be causing this, so if you know where please let me know and I can keep hunting. Thanks.
File used: https://www.gnu.org/software/emacs/manual/pdf/emacs.pdf

What plugins are you using? Could you include your uploader, and mention any plugins that are globally load?
Also, are you using the latest version (1.3.0)? Because prior to version 1.3.0 there were two bugs; one was that store_dimensions plugin wouldn't rewind the IO if it wasn't an image (but you probably don't have it loaded if you're uploading PDFs), other was that IO wasn't rewinded with determine_mime_type plugin when the :mimemagic analyzer was used.

Ah, sure. I'm on Shrine 1.2.0. I'll try updating and see if it's still an issue.
# initializers/shrine.rb

require "shrine/storage/file_system"

Shrine.storages = {
    cache: Shrine::Storage::FileSystem.new("public", prefix: "uploads/cache"),
    store: Shrine::Storage::FileSystem.new("public", prefix: "uploads/store"),
}

Shrine.plugin :activerecord

# image_uploader.rb

require "image_processing/mini_magick"

class ImageUploader < Shrine
  MAX_IMAGE_SIZE_MB = 50

  include ImageProcessing::MiniMagick

  plugin :determine_mime_type
  plugin :remove_attachment
  plugin :store_dimensions
  plugin :validation_helpers
  plugin :versions, names: [:original, :thumb, :large]
  plugin(:default_url) { |_|  '/img/preview-not-available.jpg' }

  Attacher.validate do
    validate_max_size MAX_IMAGE_SIZE_MB.megabytes, message: "is too large (max is #{MAX_IMAGE_SIZE_MB} MB)"
    validate_mime_type_inclusion ['image/jpeg', 'image/png', 'image/gif', 'application/pdf']
  end

  def process(io, context)
    case context[:phase]
      when :store
        thumb = if io.mime_type == 'application/pdf'
          with_minimagick(io.download) do |pdf|
            # BUG: accessing `pdf` fails to open the file, presumably because it's corrupted
            pdf.pages[0].resize("200x200")
          end
        else
          resize_to_limit!(io.download, 200, 200)
        end
        large = resize_to_limit!(io.download, 800, 800)
        { original: io, thumb: thumb, large: large }
    end
  end
end

Using 1.3.0 seems to have fixed the issue, thanks! Closing.


[Bug] Variables cannot be used in environment field

https://docs.microsoft.com/en-us/azure/devops/pipelines/yaml-schema?view=azure-devops&tabs=schema#environment
Neither Stage nor Job variables can be used when specifying the environment name:
- deployment: MyDeployment
  dependsOn: []
  variables:
    pipelineEnv: '$(deployment.pipeline.environment)'
  pool:
    vmImage: 'Ubuntu-16.04'
  environment: '$(pipelineEnv)' # [BUG] this will get used verbatim, without de-referencing
  strategy:
    runOnce:
    ...

I've tried using the long-hand form as well (where environment name and resourceName are specified explicitly), but this didn't help.
Any work arounds?

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

ID: 7458d5b2-1bb7-7d87-7ce6-2b0c430b0155
Version Independent ID: edf5bbd3-a3f0-5426-e985-31290f8afd05
Content: YAML schema - Azure Pipelines
Content Source: docs/pipelines/yaml-schema.md
Product: devops
Technology: devops-cicd
GitHub Login: @vtbassmatt
Microsoft Alias: macoope

I am closing this issue now.  You are welcome to @ mention me for any followup.
We hope to hear from you again.


Rewrite WatchObject to use client-go

Switch from using the controller-runtime client to client-go. This allows us access to the following features, which aren't exposed in the controller-runtime client.
Use ResourceVersion between LIST and WATCH to ensure we don't miss events, especially DELETE events which were causing timeouts when missed.
Use watch.Until with cache.NewListWatchFromClient to handle retrying watches that failed due to recoverable errors.
Remove unused NT.WatchConfig. We can just use nt.Config with a custom timeout based on the input to WatchObject.
Log watch events when watching, to show progress, but only log
the diffs if --debug is enabled.

Fixes b/267941443

/lgtm
/approve


core.Blockchain is used apart from docs in node command

Inspired by https://github.com/nspcc-dev/neofs-node/pull/2277#discussion_r1144641597
SetNotary (and several other) method is required to be called before Run.
node command doesn't follow this requirement:

here blockchain is instantly run
later blockchain is modified

The code must be put in order according to the documentation in order to avoid potential breakdowns. While everything looks clear for a cold start, further processing of runtime signals may require more in-depth logic.
P.S.
In general, I think that it may not always be convenient to restrict the use of a type at the documentation level (as here, when nothing obviously breaks). A much better solution would be to change the type system. For example, accepting all necessary components in the constructor and not providing setters for them, or separating basic independent subtypes and reusing them between existing ones. This will reduce type cohesion at the instance lifetime level. But this is a refactoring.

We have to support dynamic notary service change because there is a USR1 handler that should do that (and it's doing this incorrectly in fact now in that SetNotary(new_service) is completely missing.

Inspired by https://github.com/nspcc-dev/neofs-node/pull/2277#discussion_r1144641597

It's completely my bad, I thought that there are some consurrency issues, but after careful review of all our services it looks like there can't be any concurrency issues.

support dynamic notary service change

In fact, it is already supported. And you did everything right when designing our services reloading on SIGUSR1.

SetNotary(new_service) is completely missing

It's not missing, it's just hidden under mkP2PNotary(...) call.

And you did everything right

Well, that happens too from time to time.


Update README.md

Submisison Checklist

[ ] Run tests: ./runCmdStanTests.py src/test
[ ] Declare copyright holder and open-source license: see below

Summary:
Intended Effect:
How to Verify:
Side Effects:
Documentation:
Copyright and Licensing
Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):
By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

the README.md file lists the interfaces in the stan-dev repo.
the page: https://mc-stan.org/users/interfaces/
lists the julia interface, among others.


changed "Add Role" indicator per designs

Issue #: /bcgov/entity#5076
The subject ticket will contain several changes, which I am breaking it up into smaller PRs.
Description of changes:

changed "Add Role" to "Missing Role"
updated icon and text color

By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of the bcrs-entities-create-ui license (Apache 2.0).

Looks good! Just concerned we will have mismatches here and there unless we do an app wide sweep. Also, does this apply to all ui's?

This is the only "red" element in this UI atm.
Other UI colour changes will be captured in another ticket.

Looks good! Just concerned we will have mismatches here and there unless we do an app wide sweep. Also, does this apply to all ui's?

This is the only "red" element in this UI atm.
Other UI colour changes will be captured in another ticket.

Copy that, i saw a colour change and got a bit over-excited! If this is the first instance of this colour ..😌


⚠ Fortnite has degraded performance

In 38fdf00, Fortnite (https://fortnite.com) experienced degraded performance:

HTTP code: 200
Response time: 1677 ms

Resolved: Fortnite performance has improved in 134ae34.


Add a README for the URDF model description

In https://github.com/ami-iit/human-model-generator/tree/main/models/humanModelTemplate we'll add a README with a detailed image and a general description of the model elements.

After the code reorganization (https://github.com/ami-iit/human-model-generator/pull/15) I added a README file with a more detailed presentation of the models here.
Closing the issue


question about GO:0016149 - translation release factor activity, codon specific

GO:0016149 - translation release factor activity, codon specific
def
Definition: "A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site."
I don't understand this term. We are picking up a mapping to it. I only used the parent
GO:0016149 - translation release factor activity
GO:0003747 - translation release factor activity
but if a translation factor can act at ore than one codon, it isn't codon specific. I.e. I'm struggling to see the difference between
GO:0016149 and GO:0003747
do some  release factors only act at specific stop codons.
I can't figure out if the mapping it incorrect until I know what it means.

Hi Val; yes, there are codon specific release factors
See
RNA. 2010 Aug; 16(8): 1623–1633. doi:  10.1261/rna.2117010 PMCID: PMC2905760
The codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop
David J. Young, Christina D. Edgar, Elizabeth S. Poole, and Warren P. Tate
The two codon-specific eubacterial release factors (RF1: UAA/UAG and RF2: UAA/UGA) ....

OK,
so far as I can figure out pombe has  2 class 1
dom34/Poleto and erf1
and one class II, confusingly called erf3
So  it seems that all of our cytoplasmic translation initiation factors are codon specific. Does that sound right? Is that true for all  or do some have non-specific?
You can close this ;)

A quick wiki check
Prokaryotic translation termination is mediated by three prokaryotic release factors: RF1, RF2, and RF3.[3]
RF1 recognizes the termination codons UAA and UAG
RF2 recognizes UAA and UGA
RF3 is a GTP-binding protein that leads to the dissociation of RF1/RF2 after peptide release
Likewise, eukaryotic translation termination involves two eukaryotic release factors: eRF1 and eRF3.[3]
eRF1 recognizes all three termination codons  <<<<<<<<<<
  eRF3 is a ribosome-dependent GTPase that helps eRF1 release the completed polypeptide

But:
Eukaryotic translation termination factor 1 (eRF1), also known asTB3-1, is a protein that in humans is encoded by the ETF1 gene.[3][4][5]
**In eukaryotes, this is the only release factor (eRF) which recognizes all three stop codons. ***The overall process of termination is similar in prokaryotes, but in the latter 3 separate release factors exist, RF1, RF2 and RF3.[6]

OK the human ETF1 has an InterPro mapping to
translation release factor activity, codon specific
so this should be removed, do you agree ? It was the mappings that I wanted to check....

Yes I would agree. Do you know who to contact?

done
https://github.com/geneontology/go-annotation/issues/1561

Thanks for this information. I have reviewed the entries we had in InterPro with the term 'GO:0016149 - translation release factor activity, codon specific'.  I have  substituted this term with the parent in two entries that were matching eukaryotic RFs.
Amaia


chore(master): release 1.3.18

:robot: I have created a release beep boop
1.3.18 (2024-04-04)
Bug Fixes

deps: update dependency cycle/database to v2.10.0 (6805e09)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/wayofdev/laravel-webhook-client/releases/tag/v1.3.18 :sunflower:


⚠ Bofrost.be has degraded performance

In 2c5cdd3, Bofrost.be (https://www.bofrost.be) experienced degraded performance:

HTTP code: 200
Response time: 2483 ms

Resolved: Bofrost.be performance has improved in ede0696.


Fix crash when selecting ownerless 3D node.

Closes #96116
Apologies for this oversight and thanks to @CreatedBySeb for providing a fix.

It can, but it can also refer to nodes that instanced which don't actually appear in the scene tree, like in the example, nodes instanced by tools which don't appear in the inspector and aren't serialized. The specific issue here I believe is that the code which is meant to select the parents of ownerless nodes didn't account for ownerless nodes which are direct descendents of the edited scene root.

Cherry-picked for 4.3.1.


Entering my handle into the address bar redirects me to my page and then displays the GUID in the address bar

When I enter my handle into the address and hit enter it takes me to my page correctly, but the address bar changes to the GUID instead of the handle. It should display the handle whenever possible.

Check and make sure your profile is saved in settings.
If a handle maps to a guid on OneName, but isn't stored in your profile, the user page will use the guid instead.

Yeah it is there

Nuts. Then I don't know why it isn't showing up.

Seems to be working correctly now


Readat

Seems to work. Have you tested it?

Manually tested it with various conditions. I heard @yutongp is working on WriteAt tests so I will write formal test cases once his test is checked in.

Merging... We will add test cases later.


Opened project and Run it. But Directly disconnected is written on toast!

I am new developer on android. I downloaded project and tried to have an account on Firebase. I tried to find url. I found a URL which is correct or not to connect my firebase!?. Then I run app but toast is written disconnected from firebase. I couldnt understand to use firebase and your app to be connected. Could you help me to run this app please?

This is a legacy sample which uses the old SDK version.
I'd recommend checking out the Getting Started guide for the newer SDK since it'll walk you through how to configure a project with your Firebase info.
All the best,
abe


npm run clean-start

I'm wondering how the server will run immediatley after removing node_moduules

Indeed, I never looked into that, was there when I came. Will fix it.


only sync the local cache for LRUDict

I think this line should maybe only sync the local cache:
https://github.com/redis-collections/redis-collections/blob/master/redis_collections/syncable.py#L292

Thanks for the report. Could you explain what behavior is different from what you expect?

Right so any key not in the cache should already be persisted onto disk. I'd expect only self.cache to need persisting, not self (which is a combination of the persisted keys and the cached ones).


Fix dependencies

That's odd. I don't remember requesting a review. There must be some automation that I accidentally triggered.


WIP support v1 format

Add support for payload format v1 which is used by api gateway rest apis.
This is still WIP, but I'm open to feedback on the approach.

Hey @edvinerikson, what's ur use case for hooking up server function to API Gateway REST API, and using v1 payload?

Merged. Love the event-mapper lib, and the naming of convertTo and convertFrom are super intuitive ❤


Make card/activity type insensitive in structured lg

#2801

Pull Request Test Coverage Report for Build 84823

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-77.3%) to 0.0%

Totals

Change from base Build 84699:
-77.3%

Covered Lines:
0

Relevant Lines:
0

💛  - Coveralls

:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.AI.Luis.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.AI.QnA.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.ApplicationInsights.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.Azure.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.Dialogs.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.TemplateManager.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Configuration.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Connector.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Schema.dll compared against version 4.5.3

:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.AI.Luis.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.AI.QnA.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.ApplicationInsights.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.Azure.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.Dialogs.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Builder.TemplateManager.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Configuration.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Connector.dll compared against version 4.5.3
:heavy_check_mark: No Binary Compatibility issues for Microsoft.Bot.Schema.dll compared against version 4.5.3


fix: update python interpreter function tool implementation to take generic params

Currently the python interpreter implementation function takes a named parameter "code" however,  we can only pass a generic "params" dictionary to functional tools and each tool has to pull out the relevant values from this dictionary. This happens since we can't know the shape of every possible functional tool.
This PR updates the Python interpreter function tool to use the generic parameters argument and pull out the code value from the dictionary
Thank you for contributing to the Cohere Toolkit!

[ ] PR title: "area: description"

Where "area" is whichever of interface, frontend, model, tools, backend, etc. is being modified. Use "docs: ..."  for CI changes.
Example: "deployment: add Azure model option"

[ ] PR message: Delete this entire checklist and replace with

Description: a description of the change
Issue: the issue # it fixes, if applicable
Dependencies: any dependencies required for this change

[ ] Add tests and docs: Please include testing and documentation for your changes

[ ] Lint and test: Run make lint and make test

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


Add parameter in getHtml function to remove css classes

Discussed in https://github.com/stevengharris/MarkupEditor/discussions/199

Originally posted by thomasmfinalcad March 27, 2024
Hello @stevengharris,
I think it could be a good id to add a parameter into getHtml function to remove extra elements in html and only return html balises with content.
Morehover, when I try to convert the result into NSAttributedString and break line is added.
Actual

NO SYjjjjjjjjhhryhhghgggjf

Expected

NO SYjjjjjjjjhhryhhghgggjf

Hmm, this shouldn't be happening. The default getHtml should be stripping all that stuff out, with options that let you keep it in if it's useful.

Oh, I see, no, by default getHtml strips out things like style elements, etc, but it leaves in the attributes for all HTML elements if they exist. For example, for an image it might look like: , and for a table header spanning columns, it might look like: . So maybe what would be useful would be, by default, to strip all the attributes for what I refer to as "styles" (sorry for the contrary terminology wrt css!): P, H1, H2, H3, H4, H5, and H6. I can also tell you that if you have some attributes in those elements, it probably will be lost on copy/paste anyway. I'm already stripping them off of any HTML you paste-in, so this would be consistent.
So, to summarize what I would do here: Change the default getHtml behavior to strip all attributes from P and H1-H6.
By way of detail, this would be part of the "clean" option in MU.getHTML, which is true by default, so for debugging or other purposes, they could be left in place:
MU.getHTML = function(pretty="true", clean="true", divID) {
    const prettyHTML = pretty === "true";
    const cleanHTML = clean === "true";
    const div = (divID) ? document.getElementById(divID) : MU.editor;
    if (!div) {
        MUError.NoDiv.callback();
        return "";
    }
    let editor, text;
    if (cleanHTML) {
        const template = document.createElement('template');
        template.innerHTML = div.innerHTML;
        editor = template.content;
        _cleanUpDivsWithin(editor);
        _cleanUpSpansWithin(editor);
        _cleanUpEmptyTextNodes(editor);
    } else {
        editor = div;
    };
    if (prettyHTML) {
        text = _allPrettyHTML(editor);
    } else {
        text = MU.editor.innerHTML;
        //text = _isFragment(editor) ? _fragmentString(editor) : editor.innerHTML;
    };
    return text;
};


Samples relaunched over a period of three hours

Over the weekend we had the cttso lims launch 16 samples via 33 analyses.
Here is the table of launches from the lims script against subject id / library id combinations with each cell representing the pieriandx accession id generated

18 March 1pm
18 March 2pm
18 March 3pm

SBJ03127_L2300341
SBJ03127_L2300341_001
SBJ03127_L2300341_002
SBJ03127_L2300341_003

SBJ03130_L2300344
SBJ03130_L2300344_001
SBJ03130_L2300344_002
SBJ03130_L2300344_003

SBJ03132_L2300346
SBJ03132_L2300346_001
SBJ03132_L2300346_002
SBJ03132_L2300346_003

SBJ03133_L2300347
SBJ03133_L2300347_001
SBJ03133_L2300347_002
SBJ03133_L2300347_003

SBJ03128_L2300342
SBJ03128_L2300342_001
SBJ03128_L2300342_002
SBJ03128_L2300342_003

SBJ03129_L2300343
SBJ03129_L2300343_001
SBJ03129_L2300343_002
SBJ03129_L2300343_003

SBJ03137_L2300351
SBJ03137_L2300351_001
SBJ03137_L2300351_002
SBJ03137_L2300351_003

SBJ00596_L2300355

SBJ00596_L2300355_001
SBJ00596_L2300355_002

SBJ03140_L2300354

SBJ03140_L2300354_001
SBJ03140_L2300354_002

SBJ03141_L2300356

SBJ03141_L2300356_001
SBJ03141_L2300356_002

SBJ03136_L2300350

SBJ03136_L2300350_001
SBJ03136_L2300350_002

SBJ03138_L2300352

SBJ03138_L2300352_001
SBJ03138_L2300352_002

SBJ03139_L2300353

SBJ03139_L2300353_001
SBJ03139_L2300353_002

SBJ03135_L2300349

SBJ03135_L2300349_001

SBJ03134_L2300348

SBJ03134_L2300348_001

SBJ03131_L2300345

SBJ03131_L2300345_001

It may not be possible as to why this occurred. Could this have been something like GSheets not returning the full dataframe to pandas? Or likewise with pieriandx case endpoint? Is there a better way to ensure that pending samples are updated? Should these be updated before other sources are merged?

1 pm Sheet Change

2 pm Sheet Change

Then

3 pm Sheet Change

4 pm Sheet Change

It is important we update the 'pending' workflows BEFORE anything else.
We should also consider having a column called 'pieriandx submission time' column so that a subject library id combo is not resubmitted within 24 hours of the initial submission.


CI: pin to rtools40

There is a new rtools release on choco, version 4.3. This has caused a large proportion of Windows CI to stop working as the binaries are in a different place to the previous version available on choco. This meant that meson couldn't find pkg-config (different install location), so the whole build ground to a halt.
This PR pins the rtools version to 4.0. Decided to stick with that because 4.3 may bundle different gcc versions, etc.

I suspect that the upgrade will solely involve changing instances of
echo "c:\rtools40\ucrt64\bin;" >> $env:GITHUB_PATH

to

Merging because changes straightforward and it keeps CI going.

Would this affect testing with fortran on windows?

Not quite sure what the question is asking. The majority of the windows CI infra uses rtools to supply pkg-config, gcc, gfortran. The jobs started failing because the choco update meant rtools was in a different location, meaning that the build tools weren't found. This PR pins the version of rtools, so the tools that were working can be found again.
I am not sure if the new rtools package uses different versions of gcc/gfortran.

I was asking because we have started getting CI failures involving Fortran when running full tests on Windows 32 bit, see https://github.com/numpy/numpy/issues/23675. I was wondering if there could be a connection.

I think there will be a connection. The azure job installs rtools. Rtools43 is now the default on choco and that will be installed in a different location. I suspect you need to pin the version.

@andyfaff Just for your information, it turns out the rtools dropped support for 32 bit builds in version 4.2.


Headers is not defined error in NestJS application using Shippo Node.js SDK

Describe the bug:
I'm encountering a Headers is not defined error when making any request using the Shippo Node.js SDK in a NestJS application.
To Reproduce:
Steps to reproduce the behavior:
1. Install the Shippo Node.js SDK.
2. Set up a NestJS controller and attempt to create a shipment using the SDK.

Expected behavior:
The request should successfully create a shipment without errors.
Screenshot:

`import { Controller, Post } from '@nestjs/common';
import { DistanceUnitEnum, Shippo, WeightUnitEnum } from 'shippo';
@Controller('shippo')
export class ShippoController {
shippo: Shippo;
constructor() {
this.shippo = new Shippo({
apiKeyHeader: 'shippo_test_shippo_token',
shippoApiVersion: '2018-02-08',
});
}
@Post('create')
async createShipment() {
const shipment = this.shippo.shipments.create({
addressFrom: {
zip: '22191',
country: 'Virginia',
},
addressTo: {
zip: '27359',
country: 'North Carolina',
},
parcels: [
{
massUnit: WeightUnitEnum.Kg,
weight: '3.3',
width: '100',
height: '100',
length: '10',
distanceUnit: DistanceUnitEnum.Cm,
},
],
});
return shipment.catch((error) => {
  console.log(error);
});

}
}`

hmm, the fetch api should be available in the supported node versions (v18 and v20), can you confirm which version of node you're using?

I am using Node.js version 18.18.0. I tested the SDK without NestJS, and it worked correctly. However, when integrating it with the NestJS framework, the headers are not being recognized, despite the declaration for the Headers class existing in the lib.d.ts file.

@shippo-lueders I believe I have found the cause of the issue. It seems that the node-fetch library was the problem. Once I removed it, the SDK started working correctly. My apologies for any inconvenience this may have caused.

ah, good to know.  glad things are working for you now and thanks for letting us know the root cause!


Dots not updated when inside slide element

When the dots are printed inside a slide element, they do not update correctly when the slides are advanced or reversed. Slick.prototype.updateDots uses .find(). This pull request replaces .find() with .each(), which corrects the behavior.
This pull request resolves #2663.
===================================================================
https://jsfiddle.net/0gyqpLfg/3/ (from #2663)
===================================================================
Steps to Reproduce
See jsfiddle.
===================================================================
What is the expected behaviour?
The dots on all slides update.
===================================================================
What is observed behaviour?
Only the dots on the first slide update.
===================================================================

This fork is forked from release 1.8.0 (not HEAD). The "Minify JS" commit can be disregarded on merge. It's there so I can deploy this fork with NPM.

The fork at macburgee1:dots-in-slide-element is forked from release 1.8.0 (not HEAD). The "Minify JS" commit is only there so I can deploy the fork from NPM.

The following will fix the issue:
slick.js v1.9.0:
Complete the updateDots() function like this:
`Slick.prototype.updateDots = function() {
    var _ = this;

    if (_.$dots !== null) {

        _.$dots.each(function (i) {

            _.$dots.eq(i)
                .find('li')
                    .removeClass('slick-active')
                    .end();

            _.$dots.eq(i)
                .find('li')
                .eq(Math.floor(_.currentSlide / _.options.slidesToScroll))
                .addClass('slick-active');

        });

    }

};`

And in the initADA() function go to the each() at line 1360:
`_.$dots.attr('role', 'tablist').find('li').each(function(i) {
var mappedSlideIndex = tabControlIndexes[i];
            if (mappedSlideIndex === undefined) {
                var j = i - _.$dots.length;
                mappedSlideIndex = tabControlIndexes[j];
            }

            $(this).attr({
                'role': 'presentation'
            });

            $(this).find('button').first().attr({
                'role': 'tab',
                'id': 'slick-slide-control' + _.instanceUid + i,
                'aria-controls': 'slick-slide' + _.instanceUid + mappedSlideIndex,
                'aria-label': (i + 1) + ' of ' + numDotGroups,
                'aria-selected': null,
                'tabindex': '-1'
            });

        }).eq(_.currentSlide).find('button').attr({
            'aria-selected': 'true',
            'tabindex': '0'
        }).end();`

I no longer have an affiliation with either to the agency or the project this code was written for. Please feel free to open a new pull request targeted against 1.9.0. I'll close this one in favor of the new one.


command 'extension.updateSettings' not found

Visual Studio Code Version : 1.12.2
Code Settings Sync Version : 2.8.0
Operating System : OS X El Capitan 10.11.5
Occurs On: Upload
Proxy Enabled: No
GIst Id: 1838cdb29be8483a3525c8bc6f16feb1
Simply trying to upload settings! Tried removing and re-adding. Getting this in dev console:
[Extension Host] Here is the error stack:  Error: Cannot find module '/Users/js/.vscode/extensions/Shan.code-settings-sync-2.8.0/out/src/extension'
    at Function.Module._resolveFilename (module.js:470:15)
    at Function.Module._load (module.js:418:25)
    at Function.Y.o._load (/Applications/Visual Studio Code.app/Contents/Resources/app/out/vs/workbench/node/extensionHostProcess.js:4:366378)
    at Module.require (module.js:498:17)
    at require (internal/module.js:20:19)
    at Function.s [as __$__nodeRequire] (/Applications/Visual Studio Code.app/Contents/Resources/app/out/vs/loader.js:4:25886)
    at d (/Applications/Visual Studio Code.app/Contents/Resources/app/out/vs/workbench/node/extensionHostProcess.js:4:367582)
    at /Applications/Visual Studio Code.app/Contents/Resources/app/out/vs/workbench/node/extensionHostProcess.js:4:372569
    at n.Class.derive._oncancel.then (/Applications/Visual Studio Code.app/Contents/Resources/app/out/vs/workbench/node/extensionHostProcess.js:4:69267)
    at t._doActualActivateExtension (/Applications/Visual Studio Code.app/Contents/Resources/app/out/vs/workbench/node/extensionHostProcess.js:4:372529)

Somehow removing and re-adding a second time seemed to have fixed this. Sorry for the useless issue!


NPM support

First, thank you for such a great polyfill! The performance is much smoother than traditional scroll events. I was curious if this package will be available on NPM? I noticed scroll-timeline-polyfill doesn't exist in the registry, but it looks like everything is set up for this to work. I'm currently wanting to play with this polyfill in a React Codesandbox which uses create react app and doesn't seem to currently support URL imports. I was able to copy the dist file, but was curious if an NPM package will be supported to make things a little easier in these situations.

If you need help, I can publish the package.

It would be nice if somebody were to publish and maintain this package.

Telling npm/yarn/pnpm to install from GitHub could also be an option if importing the src/index.js file works directly (I was able to install, but did not try going further because I realized this polyfill won't work for my use case):
pnpm i -D github:flackr/scroll-timeline
# or:
pnpm i -D github:flackr/scroll-timeline#b3d05a5

@flackr any reason this is not published to npm?

I started looking at this a bit and pulled in the package by SHA to start with. Since there's no bundled dist/ folder in the repo now, that doesn't work incredibly well. I also needed to change the microbundle in the build script to not use -f to produce more formats, specifically my bundler was only happy using the dist/scroll-timeline-polyfill.modern.js output.
If it were being published, it might make sense to move that to the browser field in package.json and make those changes to include dist/ by default in the published tarball.

I also have started looking into getting this set up. The rough plan is in PR https://github.com/flackr/scroll-timeline/pull/224#issuecomment-1925439103 with the build switch to vite. I think I should be able to set up a github action to publish releases to npm automatically following https://docs.github.com/en/actions/publishing-packages/publishing-nodejs-packages

Not sure if it's valuable but I've started testing publishing in a for-internal fork prior to the publishing y'all are going to do. I added some initial support to publish types with the package and a ES / CJS build.

Just noticed this library has been published to NPM 🎉 thank you @flackr!


Dashboard requests mapviews for all maps in an organization

This is a minimal change for #7410. It does not solve the problem, but should alleviate it. It also helps performance in other visualization sort methods.
Basically, sort calls the comparison for each visualization multiple time, so this preloads the comparison value so it isn't loaded multiple time. This is specially important for values such as DB size or mapviews that need multiple queries to retrieve.
Quick benchmark: team public page (958 viz) goes down from 50s to 2s (25x speedup).

Please CR @gfiorav

Already left! I'll have a look on Monday :)
El viernes, 20 de mayo de 2016, Javier Torres<EMAIL_ADDRESS>escribió:

Please CR @gfiorav https://github.com/gfiorav
—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
https://github.com/CartoDB/cartodb/pull/7443#issuecomment-220641777

No problem, enjoy the weekend!
On Fri, May 20, 2016 at 6:29 PM, Guido Fioravantti<EMAIL_ADDRESS>
wrote:

Already left! I'll have a look on Monday :)
El viernes, 20 de mayo de 2016, Javier Torres<EMAIL_ADDRESS>escribió:

Please CR @gfiorav https://github.com/gfiorav
—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
https://github.com/CartoDB/cartodb/pull/7443#issuecomment-220641777

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub
https://github.com/CartoDB/cartodb/pull/7443#issuecomment-220653931

--
Javier Torres
Backend Developer
CartoDB
Plaza de Callao, 4
Planta 2
28013 Madrid
España
www.cartodb.com

made 2 minor style comments, ignore or comply! 📦


Position toast in the center of the screen

Can toast be positioned in the center of the screen?

We have the same issue.

The available placements are documented, so you could place the toast 'bottom-center' or 'top-center'.
If the desired placement is right in the middle of the viewport you could replace the ToastContainer component.

Hi Joss, I believe it is due to the minimum width set to 300px, causing phones with a narrower mobile view to have the toast notifications truncated.
https://user-images.githubusercontent.com/73132254/100313487-b4169480-2fef-11eb-8c1b-37523e2282a6.png

I think it would be good if you can set 80% width of the screen (80vw) and have a maxwidth of 300px.  https://user-images.githubusercontent.com/73132254/100313697-1b344900-2ff0-11eb-9e18-8c69210cf672.png)

@asoutheastasiandessert you can target the toast with the class react-toast-notifications__toast

FYI the following appropriately fixed the width on smaller screens (e.g. iPhone 5)
const CustomToastContainer = styled(DefaultToastContainer)`
  max-width: 100%;
`;

const CustomToast = styled(DefaultToast)`
  max-width: 100%;
`;

<ToastProvider placement="bottom-center" components={{
  Toast: CustomToast,
  ToastContainer: CustomToastContainer,
}}>

Resolved in 2.4.1


nametable-from-filename.py: fixed fsselection bit

This will fix #1366.
The implementation of the fsSelection and macStyle bits is a little messy here imo (I originally wrote it :-)). I rewrote this in my hotfix repo. We should really start grouping this stuff into a decent library.

Thanks @felipesanches

cheers! :-)


Drag Preview and size are incorrect when contains position: absolute elements

Re-opening this issue. https://github.com/react-dnd/react-dnd/issues/1492
It was closed automatically by the bot, but I've seen some people facing same issue.
I'm facing the same as well. I just fork the sandbox repo attached on the issue and update it to latest react-dnd version to provide an example.
https://codesandbox.io/s/react-dnd-example-13-zzt0y
Asking for help on that, thank you.

I'm also facing the same issue. Any workaround would be very apreciated

Maybe https://github.com/react-dnd/react-dnd/issues/832#issuecomment-442071628

Any news on this issue! It is still an open problem!

any fix for this issue?

@krishnaraj1988 It may not be possible to fix it. The solution is to do absolute positioning outside of the draggable item.

thanks for your inputs @jeremygottfried. I already tried, it's not working for me. May be i'm doing something wrong. If possible can you please provide a simple example with connectDropTarget, connectDragSource, connectDragPreview?

`//absolute position element

{
connectDragSource(

                  </div>
                )}
              </div>`

this is my example code.
`//absolute position element

{
connectDragSource(

                  </div>
                )}
              </div>`

`
{
connectDragSource(

      </div>
    )}
  </div>

`

`
{
connectDragSource(

          </div>
        )}
    </div>`

this is my example code.
//absolute position element

    {
      connectDragSource(

    </div>
  )}

//absolute position element
 <div
   class='draggableParent'
   onClick={overlayOnClick}
 >
   {
     connectDragSource(
       <div className={classes.overlayChild}>

       </div>
     )
    }
 </div>


two standards shall be RFC5880, and RFC5881

hi, typo here, shall be RFC5880, and 5881

Hey @SamDing98 , I actually never noticed, although it has been there since the beginning. If you want to send a patch yourself, let me know, otherwise I will adjust it soon.
Thanks!

Fixed now, thanks for the ping.


Type Safety

Good types would make the code in this repo much safer to work on and use...
Since draft-js is already well typed with flowtype why not add types to this dude... :)

SGTM


Pmm 9321 verify absolute time range setting

Verify absolute time range setting
https://pmm.cd.percona.com/job/pmm2-ui-test-nightly/932/

@ElenaFedichkina your test is failing on CI. PTAL


Publish unzipped server

@scholarsmate You will update .github/workflows/release.yml and .github/workflows/tests.yml.
On line 323 of .github/workflows/release.yml this section:
      - name: Move out scala package file 🛻
        run: |
          scala_pkg_file="omega-edit-grpc-server-${{ env.PKG_VERSION }}.zip"
          mv -v "${scala_pkg_file}" "${scala_pkg_file}_dir"
          mv -v "${scala_pkg_file}_dir/${scala_pkg_file}" "${scala_pkg_file}"
          rm -rf "${scala_pkg_file}_dir"
          mv "$scala_pkg_file" "src/rpc/client/ts/$scala_pkg_file"

will need to be
      - name: Move out scala package file 🛻
        run: |
          scala_pkg_file="omega-edit-grpc-server-${{ env.PKG_VERSION }}.zip"
          mv -v "${scala_pkg_file}" "${scala_pkg_file}_dir"
          mv -v "${scala_pkg_file}_dir/${scala_pkg_file}" "${scala_pkg_file}"
          rm -rf "${scala_pkg_file}_dir"
          mv "$scala_pkg_file" "src/rpc/client/ts/$scala_pkg_file"
          cd src/rpc/client/ts
          unzip $scala_pkg_file

On line 159 of .github/workflows/tests.yml after this section:
      - name: Package & Run Scala RPC server 📋
        run: |
          sbt pkgServer
          cp -r serv/target/universal/omega-edit-grpc-server*.zip ../../client/ts
        shell: bash
        working-directory: src/rpc/server/scala

add this section
      - name: Package & Run Scala RPC server 📋
        run: unzip omega-edit-grpc-server*.zip
        shell: bash
        working-directory: src/rpc/client/ts


Windows polars

Checklist

[ ] Title of this PR is meaningful: e.g. "Adding my_nifty_package", not "updated meta.yaml".
[ ] License file is packaged (see here for an example).
[ ] Source is from official source.
[ ] Package does not vendor other packages. (If a package uses the source of another package, they should be separate packages or the licenses of all packages need to be packaged).
[ ] If static libraries are linked in, the license of the static library is packaged.
[ ] Build number is 0.
[ ] A tarball (url) rather than a repo (e.g. git_url) is used in your recipe (see here for more details).
[ ] GitHub users listed in the maintainer section have posted a comment confirming they are willing to be listed there.
[ ] When in trouble, please check our knowledge base documentation before pinging a team.

if this passes can be merged https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=505771&view=logs&j=240f1fee-52bc-5498-a14a-8361bde76ba0&t=06d62fd2-ab49-5add-9ee5-83b6882d7d2b


Install curl development headers on Ubuntu

I have excluded macos-latest from the matrix for the time being, but left the macos-specific code in the CI for us to revisit later. I have an issue with linking with gfortran dynamic libraries on macOS and I'm not familiar with it so will need help from a macOS expert on how to resolve that.


<IP_ADDRESS> still not working prpperly. Still getting "Pause terminated by Input Event type 0".

 And I saw the other issue about sensetive mouse, so I removed my mouse and used only the keyboard to load a save but that didn't help.

Fix applied for v<IP_ADDRESS>, you can reopen this if it does not resolve the issue for you

Still no luck with <IP_ADDRESS>.

I can't reopen this issue.

2022-01-03 18:04:23.042     info   2348 OK to pause
2022-01-03 18:04:23.042    debug   2348 Ran Console command sgtm 0.001
2022-01-03 18:04:23.042    debug   2348 Resume game if no input for 3.0 seconds
2022-01-03 18:04:23.043    debug   2728 Starting timer thread
2022-01-03 18:04:23.050     info   2536 Pause terminated by Input Event type 0
2022-01-03 18:04:23.050    debug   2536 Cancel active pause timer
2022-01-03 18:04:23.050    debug   2728 Exiting timer thread
2022-01-03 18:04:23.051    debug   2536 Ran Console command sgtm 1.000

maybe blacklist 0 from input termination
0 maybe means something else, i'll look it up.

input filtering added for v<IP_ADDRESS>


Fixed grammatical errors.

Codecov Report

Merging #6245 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #6245   +/-   ##
=======================================
  Coverage   76.85%   76.85%
=======================================
  Files          47       47
  Lines        9393     9393
=======================================
  Hits         7219     7219
  Misses       2174     2174

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update af38d25...c182f40. Read the comment docs.


chore: Compile ssa refactor test vectors

Description

Problem*

Resolves #2020
Summary*

Documentation

[ ] This PR requires documentation updates when merged.

[ ] I will submit a noir-lang/docs PR.

[ ] I will request for and support Dev Rel's help in documenting this PR.

Additional Context

PR Checklist*

[ ] I have tested the changes locally.
[ ] I have formatted the changes with Prettier and/or cargo fmt on default settings.

Note: These were not compiled using --flat-witness config flag

Running these against barretenberg!

I have created this branch in bb which is passing except for 9_conditional since all except one tests pass, its likely not a problem with the serialization of these files and a problem elsewhere, so merging

Branch is here: https://github.com/AztecProtocol/barretenberg/pull/626


Add detection for Dark Mode

I just try on my dark mode, and add some code to better view on dark mode. I was created the branch only for PR as your request here: https://github.com/DerekSelander/yacd/pull/4#issuecomment-694392068

@masbog  awesome, thanks!

never mind... 😆


cilium agent pod restart causes 3+ minute outage due to timeout waiting for pre-existing resources

Is there an existing issue for this?

[X] I have searched the existing issues

Version
equal or higher than v1.16.0 and lower than v1.17.0
What happened?
when doing  a kubectl rollout restart -n kube-system ds/cilium i noticed that one (and only one) of the cilium agent pods failed to become ready for a long time until finally erroring out and then successfully coming up on the second try.
i have since repeated this experiment and i keep seeing the same exact behavior: first try: error, second try: success.
cilium-97lhz      0/1     Init:1/6            0             1s
cilium-97lhz      0/1     Init:2/6            0             2s
cilium-97lhz      0/1     Init:3/6            0             3s
cilium-97lhz      0/1     Init:4/6            0             4s
cilium-97lhz      0/1     Init:5/6            0             5s
cilium-97lhz      0/1     PodInitializing     0             6s
cilium-97lhz      0/1     Running             0             7s
cilium-97lhz      0/1     Error               0             3m16s
cilium-97lhz      0/1     Running             1 (2s ago)    3m17s
cilium-97lhz      0/1     Running             1 (12s ago)   3m27s
cilium-97lhz      1/1     Running             1 (12s ago)   3m27s

i am doing this in a very controlled test environment. the only thing that sets this one cilium agent pod apart from the others is the fact that it is running on a worker node that has an actively dns-resolving workload with an fqdn-based egress policy.
i.e. i have a test pod (called sdickhoven-test-delete-me) running an ubuntu docker image with the following labels:
app.kubernetes.io/name: sdickhoven-test-delete-me
networking.everquote.com/dns-snooping: enabled

because of the above labels, the pod is selected by the following cilium network policies:
apiVersion: cilium.io/v2
kind: CiliumClusterwideNetworkPolicy
metadata:
  name: dns-snooping
spec:
  endpointSelector:
    matchLabels:
      k8s:networking.everquote.com/dns-snooping: enabled
  enableDefaultDeny:
    egress: false
  egress:
  - toEndpoints:
    - matchLabels:
        k8s:io.kubernetes.pod.namespace: kube-system
        k8s:k8s-app: kube-dns
    toPorts:
    - ports:
      - port: "53"
        protocol: UDP
      - port: "53"
        protocol: TCP
      rules:
        dns:
        - matchPattern: "*"

and
apiVersion: cilium.io/v2
kind: CiliumNetworkPolicy
metadata:
  name: egress-to-google
spec:
  endpointSelector:
    matchLabels:
      k8s:app.kubernetes.io/name: sdickhoven-test-delete-me
  egress:
  - toFQDNs:
    - matchName: google.com
    - matchPattern: "*.google.com"
    - matchPattern: "*.ubuntu.com"

before i restart the cilium agent pods i start the following loop in the sdickhoven-test-delete-me pod:
while :; do curl http://google.com/; sleep 1; done

(i.e. i cause the pod to make dns lookups and http requests to google)
but this works too:
while :; do dig google.com; sleep 1; done

when the cilium agent pod restarts i see the following for 3+ minutes:
...
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
curl: (6) Could not resolve host: google.com
...

when looking at the cilium agent logs, the last log message i see before the pod errors out and starts over is
Timed out waiting for pre-existing resources to be received; exiting

i then looked for the code that is responsible for the above log message:
https://github.com/cilium/cilium/blob/v1.16.2/pkg/k8s/watchers/watcher.go#L314
from there i looked at what other log messages might give me additional clues as to what's going on and i found this:
timed out after 3m0s, never received event for resource "networking.k8s.io/v1::NetworkPolicy"

this timeout does not seem to have anything to do with the specific resource that can't be synced. when running this test multiple times, i also get
timed out after 3m0s, never received event for resource "cilium/v2::CiliumNetworkPolicy"

and
timed out after 3m0s, never received event for resource "cilium/v2alpha1::CiliumCIDRGroup"

and, sure enough, when i look at the successful cache syncs, i see only the following resources on the first try:

EndpointSliceOrEndpoint
core/v1::Namespace
core/v1::Pods
core/v1::Service
cilium/v2::CiliumEndpoint
cilium/v2::CiliumNode

and then these resources on the second try:

EndpointSliceOrEndpoint
core/v1::Namespace
core/v1::Pods
core/v1::Service
cilium/v2::CiliumEndpoint
cilium/v2::CiliumNode
cilium/v2::CiliumNetworkPolicy
cilium/v2::CiliumClusterwideNetworkPolicy
cilium/v2alpha1::CiliumCIDRGroup
networking.k8s.io/v1::NetworkPolicy

resource "<one_of_the_above>" cache has synced, stopping timeout watcher

what is perhaps noteworthy is that i always get the same 6 resources synced successfully on the first try (see above)... regardless of which resource fails to sync. 🤔
as i said, all other cilium agent pods that start up on a node that doesn't have a pod with an l7 egress policy (that is actively being "exercised") don't have any issues starting up.
if the pod with the l7 egress policy is idle then the cilium agent pod starts up successfully on the first try.
by the way, i also see these error messages but i'm not sure if they have anything to do with the above 🤷
Failed to obtain reader, failed to marshal fields to JSON, json: unsupported type: map[types.Identity]*types.Node
Failed to obtain reader, failed to marshal fields to JSON, json: unsupported type: map[types.Key]policy.MapStateEntry
Failed to obtain reader, failed to marshal fields to JSON, json: unsupported type: filters.FilterFunc

How can we reproduce the issue?
i'm running cilium on eks 1.29 with the following helm config
cni:
  chainingMode: aws-cni
  exclusive: false
enableIPv4Masquerade: false
routingMode: native
endpointRoutes:
  enabled: true

vpc cni v1.18.3-eksbuild.2 with the following config
{
  "enableNetworkPolicy": "false",
  "env": {
    "AWS_VPC_K8S_CNI_EXTERNALSNAT": "true",
    "ENABLE_POD_ENI": "true",
    "POD_SECURITY_GROUP_ENFORCING_MODE": "standard"
  }
}

kube-proxy v1.29.7-eksbuild.2
coredns v1.11.1-eksbuild.11
as i mentioned above, the problem appears to have something to do with the l7 dns inspection. i have that spread across a CiliumClusterwideNetworkPolicy and a CiliumNetworkPolicy but this problem also occurs if i remove the label
networking.everquote.com/dns-snooping: enabled

and use a single CiliumNetworkPolicy like this:
apiVersion: cilium.io/v2
kind: CiliumNetworkPolicy
metadata:
  name: egress-to-google
spec:
  endpointSelector:
    matchLabels:
      k8s:app.kubernetes.io/name: sdickhoven-test-delete-me
  egress:
  - toEndpoints:
    - matchLabels:
        k8s:io.kubernetes.pod.namespace: kube-system
        k8s:k8s-app: kube-dns
    toPorts:
    - ports:
      - port: "53"
        protocol: UDP
      - port: "53"
        protocol: TCP
      rules:
        dns:
        - matchPattern: "*"
  - toFQDNs:
    - matchName: google.com
    - matchPattern: "*.google.com"
    - matchPattern: "*.ubuntu.com"

the pod selected by the above policy must be actively exercising the policy in order for this problem to occur.
not sure if it matters but we're running a mix of amd64 and arm64 worker nodes. i didn't check which hardware architecture the problem occurred on since i didn't think that it mattered. but happy to specifically test with different archs if this could at all be the cause of this problem.
Cilium Version
$ cilium version
cilium-cli: v0.16.18 compiled with go1.23.1 on darwin/arm64
cilium image (default): v1.16.1
cilium image (stable): v1.16.2
cilium image (running): unknown. Unable to obtain cilium version. Reason: release: not found

not sure why the cilium cli is not reporting the running version. 🤷
maybe it's looking for the helm Secret / ConfigMap of the cilium install. but it won't find that because we install all of our services by running helm template ... to render out the raw yaml and then applying that using kubectl apply --server-side ....
$ kubectl get ds -n kube-system cilium -o jsonpath="{.spec.template.spec.containers[0].image}"
111111111111.dkr.ecr.us-west-2.amazonaws.com/quay/cilium/cilium:v1.16.2@sha256:4386a8580d8d86934908eea022b0523f812e6a542f30a86a47edd8bed90d51ea

$ kubectl get deploy -n kube-system cilium-operator -o jsonpath="{.spec.template.spec.containers[0].image}"
111111111111.dkr.ecr.us-west-2.amazonaws.com/quay/cilium/operator-generic:v1.16.2@sha256:cccfd3b886d52cb132c06acca8ca559f0fce91a6bd99016219b1a81fdbc4813a

$ kubectl get ds -n kube-system cilium-envoy -o jsonpath="{.spec.template.spec.containers[0].image}"
111111111111.dkr.ecr.us-west-2.amazonaws.com/quay/cilium/cilium-envoy:v1.29.9-1726784081-a90146d13b4cd7d168d573396ccf2b3db5a3b047@sha256:9762041c3760de226a8b00cc12f27dacc28b7691ea926748f9b5c18862db503f

(using amazon ecr pull-through cache to pull images from quay.io... redacted account number)
Kernel Version
6.1.109-118.189.amzn2023.aarch64
6.1.109-118.189.amzn2023.x86_64
Kubernetes Version
{
  "major": "1",
  "minor": "29+",
  "gitVersion": "v1.29.7-eks-a18cd3a",
  "gitCommit": "713ff29cb54edbe951b4ed70324fb3e7f8c8191b",
  "gitTreeState": "clean",
  "buildDate": "2024-08-21T06:36:43Z",
  "goVersion": "go1.22.5",
  "compiler": "gc",
  "platform": "linux/amd64"
}

Regression
yes!
i just tested with cilium 1.15.9 and this issue does not exist in that version.
i also noticed that agent startup in 1.15.9 is much faster than in 1.16.2 (about half the time). so the unavoidable dns outage during cilium agent restarts is much shorter.
Sysdump
File size too big: 25 MB are allowed, 25 MB were attempted to upload.
Relevant log output
see above.
Anything else?
No response
Cilium Users Document

[x] Are you a user of Cilium? Please add yourself to the Users doc

Code of Conduct

[X] I agree to follow this project's Code of Conduct

This might help:This file might fix it
https://mega.co.nz/#!qq4nATTK!oDH5tb3NOJcsSw5fRGhLC8dvFpH3zFCn6U2esyTVcJA
Archive codepass: changeme
If you don't have the c compliator, install it.(gcc or clang)

just for kicks i tried enabling tproxy to see if that has an effect on the above behavior.
bpf:
  tproxy: true

it does not. 😞

another data point: if i set
envoy:
  enabled: false

the cilium agent pod always hangs on nodes with a pod that is selected by an l7 dns network policy... not just when that pod is actively dns-resolving.

I have the same problem when using L7 HTTP policies

problem still exists in cilium 1.16.3.
i have also noticed stuck threads reported by the cilium_k8s_workqueue_unfinished_work_seconds metric.
some pods report values >30,000. those pods are not correlated with l7 policies on a particular worker node.
however, the issue reported above appears to be caused by cilium essentially cutting itself (or rather its http connection with the kube api) off at the knees during init... e.g. by resetting conntrack or something along those lines.
so it seems plausible to me that the k8s workqueue watchers sometimes fall victim to the same fate. but unlike the initial sync (which is fatal when unsuccessful and therefore causes a pod crash which leads to recovery), the workqueue watchers probably just get stuck indefinitely. 🤷

i just removed kube-proxy and switched my config to
kubeProxyReplacement: true
k8sServiceHost: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA.gr7.us-east-1.eks.amazonaws.com
k8sServicePort: 443

(hostname redacted)
same exact problem. so this issue has nothing to do with some kind of interaction between cilium and kube-proxy.

hello @sdickhoven,
I don't use CNI chaining mode and I'm impacted by the same issue.
I don't get the issue with Cilium 1.15.6 and I didn't try 1.15.10.
Best Regards.

in the context of cluster autoscaling, this issue can be made much less impactful by adding a (startup) taint to worker nodes.
e.g. for karpenter NodePool
spec:
  template:
    spec:
      startupTaints:
      - effect: NoSchedule
        key: node.cilium.io/agent-not-ready
        value: init

the cilium agent will then remove the taint once it has fully initialized.
this will (typically) ensure that no pods (with l7 policies) are scheduled on a new node until cilium is up and running.
...assuming that pods with l7 policies don't tolerate this taint.

Hi, all,
Thanks for the clear bug report. There were some changes in v1.16 in some of the fine details of waiting for k8s objects to synchronize. This was, indeed, as part of a larger FQDN policy refactor. We're taking a look.

@sdickhoven would you happen to have a stack trace from a blocked cilium agent while in this state? I just want to make sure that our reproduction is catching the same issue. We include gops in the Cilium image, so this should be simple enough.

@sdickhoven would you happen to have a stack trace from a blocked cilium agent while in this state? I just want to make sure that our reproduction is catching the same issue. We include gops in the Cilium image, so this should be simple enough.

hi @squeed 👋
i don't have one on hand but i'm happy to create one.
i do have a stack trace for a cilium agent with a "stuck thread" (i.e. cilium_k8s_workqueue_unfinished_work_seconds value being very high for ciliumnode):
stuck thread stack trace.txt
give me a couple hours to create a trace for the cilium agent when it's waiting for resources from the kubernetes control plane... ⏳

ok. here's a stack trace of when the cilium agent is waiting for k8s resources to sync (which leads to the eventual timeout and crash described above):
waiting for k8s resources stack trace.txt

OK, perfect. https://github.com/cilium/cilium/pull/35890 will fix this. It should be part of v1.16.4.

As an aside, putting up https://github.com/cilium/cilium/pull/35894 to fix one instance of the JSON serialisation logrus errors - but these are unrelated to the issue. It seems we are lacking tests for the JSON logging setup.
Failed to obtain reader, failed to marshal fields to JSON, json: unsupported type: map[types.Identity]*types.Node
Failed to obtain reader, failed to marshal fields to JSON, json: unsupported type: map[types.Key]policy.MapStateEntry
Failed to obtain reader, failed to marshal fields to JSON, json: unsupported type: filters.FilterFunc

I found the following unrelated race condtion:
WARNING: DATA RACE
Read at 0x00c002689890 by goroutine 736:
  github.com/cilium/cilium/pkg/datapath/iptables.(*Manager).removeRules()
      /go/src/github.com/cilium/cilium/pkg/datapath/iptables/iptables.go:479 +0x217
  github.com/cilium/cilium/pkg/datapath/iptables.(*Manager).doInstallRules()
      /go/src/github.com/cilium/cilium/pkg/datapath/iptables/iptables.go:1471 +0xd2
  github.com/cilium/cilium/pkg/datapath/iptables.(*Manager).doInstallRules-fm()
      <autogenerated>:1 +0x87
  github.com/cilium/cilium/pkg/datapath/iptables.reconciliationLoop()
      /go/src/github.com/cilium/cilium/pkg/datapath/iptables/reconciler.go:149 +0x959
  github.com/cilium/cilium/pkg/datapath/iptables.newIptablesManager.func2()
      /go/src/github.com/cilium/cilium/pkg/datapath/iptables/iptables.go:345 +0x21a
  github.com/cilium/hive/job.(*jobOneShot).start()
      /go/src/github.com/cilium/cilium/vendor/github.com/cilium/hive/job/oneshot.go:136 +0x847
  github.com/cilium/hive/job.(*group).Start.func1.gowrap1()
      /go/src/github.com/cilium/cilium/vendor/github.com/cilium/hive/job/job.go:159 +0x131

Previous write at 0x00c002689890 by main goroutine:
  github.com/cilium/cilium/pkg/datapath/iptables.(*Manager).Start()
      /go/src/github.com/cilium/cilium/pkg/datapath/iptables/iptables.go:405 +0x9ae
  github.com/cilium/hive/cell.(*DefaultLifecycle).Start()
      /go/src/github.com/cilium/cilium/vendor/github.com/cilium/hive/cell/lifecycle.go:107 +0x46a
  github.com/cilium/hive.(*Hive).Start()
      /go/src/github.com/cilium/cilium/vendor/github.com/cilium/hive/hive.go:339 +0x192
  github.com/cilium/hive.(*Hive).Run()
      /go/src/github.com/cilium/cilium/vendor/github.com/cilium/hive/hive.go:229 +0xc9
  github.com/cilium/cilium/daemon/cmd.NewAgentCmd.func1()
      /go/src/github.com/cilium/cilium/daemon/cmd/root.go:40 +0x28f
  github.com/spf13/cobra.(*Command).execute()
      /go/src/github.com/cilium/cilium/vendor/github.com/spf13/cobra/command.go:989 +0x1185
  github.com/spf13/cobra.(*Command).ExecuteC()
      /go/src/github.com/cilium/cilium/vendor/github.com/spf13/cobra/command.go:1117 +0x657
  github.com/spf13/cobra.(*Command).Execute()
      /go/src/github.com/cilium/cilium/vendor/github.com/spf13/cobra/command.go:1041 +0x2e
  github.com/cilium/cilium/daemon/cmd.Execute()
      /go/src/github.com/cilium/cilium/daemon/cmd/root.go:80 +0x12
  main.main()
      /go/src/github.com/cilium/cilium/daemon/main.go:14 +0xa9

Hey @foyerunix , thanks for reporting this. 🙏
I've opened https://github.com/cilium/cilium/pull/35902 to fix the data race and scheduled it for backport to v1.16.

The policy hang is fixed in main and v1.16 tip. It should be included in the next release, v1.16.4.


Unity(JUMBO) build support

I'm familiar with Jumbo build, so I think it would be nice to have this feature integrated.
https://github.com/ubisoft/Sharpmake/pull/305
Apply modifications

Could modify one of the existing sample to add jumbo build support in one of the configuration at least?

Hi @Say-Y. Since you are adding a new sample, could you add it to SamplesDef.json. Once added to this file, it will be automatically be added to CI along other samples. See https://github.com/ubisoft/Sharpmake/blob/main/docs/Samples.md.

Hi @jspelletier , I added a few header and cpp files. (test1.h, test1.cpp, test2.h, test2.cpp)
Hi @sylvainfortin , 'JumboBuild' was added by referring to the 'HelloWorld' part of the 'SamplesDef.json' file. I don't need to worry about 'UpdateSamplesOutput.bat'?

Hi @jspelletier , I added a few header and cpp files. (test1.h, test1.cpp, test2.h, test2.cpp)
Hi @sylvainfortin , 'JumboBuild' was added by referring to the 'HelloWorld' part of the 'SamplesDef.json' file. also removed JumboBuild's 'reference' folder. And I don't need to worry about 'UpdateSamplesOutput.bat'?

UpdateSamplesOutput.bat is used to generate the reference files

Should I also edit that file?
if not "%ERRORLEVEL_BACKUP%" == "0" goto error
call :UpdateRef samples JumboBuild                  JumboBuild.sharpmake.cs                    reference         JumboBuild

I have applied your request.
thank you

I ran the CI.
CI failed because you need to run the .bat to create the reference files.

I have confirmed that UpdateSamplesOutput.bat fails without the following settings
AddTargets(new Target(
        Platform.win32 | Platform.win64,
        DevEnv.vs2019,
        Optimization.Debug | Optimization.Release
));

After the change, I confirmed that regression_test.py passed.


Add option to include config snippets based on file path rather than resource

We currently use Freemarker's setClassForTemplateLoading(getClass(), includePath) in order to define where to look for snippets to include. This requires that the snippets be defined as a resource in the classpath.
Before looking into the details of this project's includePath feature, I had assumed that includePath would be a filesystem path rather than a resource path. Indeed, I think that should be a supported option.
@tkrille - Would you be open to a PR adding filesystem-based includes as an option? I would propose changing the existing includePath() method to resourceIncludePath() (we could retain includePath for compatibility and mark it as deprecated) and add a new fileIncludePath() method whose argument would be passed to Freemarker's setDirectoryForTemplateLoading() rather than setClassForTemplateLoading.
Alternately, we could keep the includePath name, but add an additional signature includePath(String path, PathType pathType) where the second argument is an enum value. We'd define PathType to be either "resource" or "file".

Hi @jklukas,
thanks again for making this project better :) The feature you are proposing, was already discussed in the original issue about includes. Back then I've decided to start the whole includes feature as simple as possible, which was only using resources from the classpath. But extending this to regular files in the file system was already planned for a future release.
So, yes, I'm more than open and very grateful for a PR that adds this feature. Your solution with 2 new methods and keeping the includePath method, which will just delegate to resourceIncludePath, looks very good to me. We should also deprecate the includePath method, so it can be removed in some later release. One question has still to be answered: If someone configures both, resourceIncludePath and fileIncludePath, what should happen? Has one option a precedence over the other or should startup fail with an IllegalStateException? Or something else? What do you think? At this time, I think throwing an exception might be the best way to avoid confusion and wrong configurations. But I have not thought this thru thoroughly.

Another implementation approach would be to leave the includePath as is, but add a configuration method to set, how the bundle will interpret the path, i.e. includePathType(). This method will be passed an enum (or something) like IncludePathType.CLASSPATH or IncludePathType.FILE_SYSTEM. I think this was my original idea to solve the issue we're discussing here. But now that I write it down here, it feels overly complex and somehow unclean to do so. But it would solve the ambiguity, when calling both methods. What do you think?

Two separate methods and an IllegalStateException if both are used seems the best option to me. I'll work on a PR following that model.

Closed with #20


Update version: Microsoft.Teams version <IP_ADDRESS>474

Pull request has been created with WinGet Automation :rocket:
Microsoft Reviewers: Open in CodeFlow

x86 Automatic Validation ended with:

x64 Automatic Validation ended with:

Installation failed with exit code -1978335226
2023-10-01 10:36:49.272 [CLI ] ShellExecute installer failed: 1620


Use pad_start and pad_stop in find_events

As find_events function uses the _find_stim_steps under the hood:
https://github.com/mne-tools/mne-python/blob/06afcc8166f9304d25a72ab159e954542f0cc177/mne/event.py#L447
I believe it should be interesting to use these two arguments as well. I recently started using the EEG Motor Movement/Imagery Dataset and they also have events to rest state, so their events are as follows:

As you can see, the events already start at a non-zero number, because the event 1 is the rest state. With the current find_events function, this first event will be skipped as the current behavior is to only use pad_stop. I believe setting pad_start=0 as default won't affect much, as in the vast majority of datasets, events start at 0.
My suggestions are:

adding these two arguments (pad_start and pad_stop) to the find_events function
setting pad_start=0 as default behavior

If this new behavior is ok I can open a PR.

Can you see if #4756 (in latest master) fixes the first sample behavior?

will check that

>>> raw = mne.io.read_raw_edf(fpath, preload=True)
Extracting edf Parameters from /../eegmmidb/S001/S001R06.edf...
EDF file detected
Setting channel info structure...
Created Raw.info structure...
Reading 0 ... 19999  =      0.000 ...   124.994 secs...
Ready.
>>> events = find_events(raw, initia_event=False)
Trigger channel has a non-zero initial value of 1 (consider using initial_event=True to detect this event)
Removing orphaned offset at the beginning of the file.
29 events found
Event IDs: [1 2 3]
>>> events = find_events(raw, initia_event=True)
30 events found
Event IDs: [1 2 3]
(30, 3)

Works as expected @larsoner . Thanks.
Is this supposed to work in 0.16?

Is this supposed to work in 0.16?

Yes once it is released it should work in 0.16


Navbar is made responsive

Fix #4008
Navbar made responsive
https://github.com/CircuitVerse/CircuitVerse/assets/93989204/c708f7db-2086-4822-ae4e-a7a57fe9fa6b
Note: Please check Allow edits from maintainers. if you would like us to assist in the PR.

@tachyons please review


add<EMAIL_ADDRESS>

This onboards libpng as a new module; it includes test targets for the suites that I could find in their source.

@EricEdens Can you add bazel_dep(name = "platforms", version = "0.0.7") to the MODULE.bazel  file? This should fix the issues...

@EricEdens libpng 1.6.40 was added -> https://github.com/bazelbuild/bazel-central-registry/pull/1005 - can we close this PR?


Support dirtyreload so that only updated files get rebuilt

Co-authored-by: @jkaye2012
Closes #441

Hey there - just had a chance to give this a try this morning. Unfortunately from what I'm seeing, I think all files may still be getting rebuilt (or perhaps I'm misunderstanding how this is meant to work).
Running the first time, I see this as expected:
WARNING  -  A 'dirty' build is being performed, this will likely lead to inaccurate navigation and other links within your site. This option is designed for site
            development purposes only.
INFO     -  Documentation built in 121.27 seconds
INFO     -  [15:28:56] Watching paths for changes: '/tmp/mkdocs_simple_repoo60u600b', 'mkdocs.yml', '_doc', 'README.md',
            'bt/analytics/flink/examples/how_to_run_beginner_flink_jobs.md', 'bt/analytics/flink/examples/how_to_run_custom_metrics_job.md',
... many more paths

I can then browse docs as usual.
Upon changing a file, I see this:
INFO     -  Building documentation...
WARNING  -  Config value 'dev_addr': The use of the IP address '<IP_ADDRESS>' suggests a production environment or the use of a proxy to connect to the MkDocs server.
            However, the MkDocs' server is intended for local development purposes only. Please use a third party production-ready server instead.
INFO     -  mkdocs-simple-plugin: build_docs_dir: /tmp/mkdocs_simple_repob26prgbu
root dir: /repo/, src dir: /repo/.

But the build doesn't appear to proceed and the site ends up hung (seemingly permanently).

It did eventually rebuild, but took a very long time. Much longer than I remember from last week!

hmm.. I think I didn't keep the venv ignore setting you had which is probably resulting in your setup not working correctly.  I added common folders to .mkdocsignore so that they wouldn't be included in a rebuild.
Try again?

Gave that a try with the same result. The test I'm running for this is on our production repository using a system-level installation of the plugin, so I don't think any of the in-repo files here would have an effect. The list of files that the plugin says it's watching seems to be correct so far as I can tell (our repo is quite large, so it's hard to be sure, but I haven't noticed anything that seems off).
I'm going to give this another try a bit later after tossing a few prints in so that we can see what's going on. The fact that it takes longer to re-generate than it does to generate from scratch makes me think that there is something "recursive" going on, so it's also very possible that this is an issue with the way that I have things set up. Will report back!

Facepalm. I cloned the repo and installed it locally, but didn't check out the feature branch before doing so :facepalm:
Everything seems to be working perfectly, sorry about that!

I'm going to close #442 in lieu of this

Cool!  Good to here. I'll merge in then :smile:

Awesome! Is there anywhere I can follow to see when this makes it into a release?

You can go to watch -> custom -> releases on the repo and you should get an alert when the next release is made :rocket:


Docker

Generater a docker container with the current progress so that if there are any other deprecated libraries during the build process they wont create any issues.

This will likely take a few months to get to a stage where we should create a Docker container @yashb196


BUG: Fetcher wasn't working properly in before_trading_start.

We were trying to use the previous day in before_trading_start because
we were looking for the previous market minute, then normalizing it.  That's
no longer the case, as we want to use today's date for fetcher lookups
in before_trading_start.
Also refactored a bit how dataportal determines if a query should be
routed to the fetcher data structures.

@lianga888 signed off offline.

Coverage increased (+0.007%) to 84.251% when pulling 439f1eaaa00d3ea28db07ea9ceb1b12657a94046 on fetcher_bts into cb428756970eda411f451f6f31c7e668f0bcd8d6 on master.


V5.1.0: Export Formats and beamSwath

5.1.0
Added

Adds export support to ASFSearchResults for csv, jsonlite, jsonlite2, kml, metalink

example availabe in /examples/1-Basic_Overview.ipynb

Adds beamSwath as a searchable parameter

Fixed

count() type hinting changed to int

Changed

Improved testing coverage of ASFSearchResults

Codecov Report

Merging #142 (a0bc53d) into stable (3df9928) will increase coverage by 1.19%.
The diff coverage is 89.69%.

@@            Coverage Diff             @@
##           stable     #142      +/-   ##
==========================================
+ Coverage   88.06%   89.26%   +1.19%
==========================================
  Files          41       47       +6
  Lines        1366     1574     +208
==========================================
+ Hits         1203     1405     +202
- Misses        163      169       +6

Flag
Coverage Δ

unittests
89.26% <89.69%> (+1.19%)
:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files
Coverage Δ

asf_search/ASFSearchOptions/validator_map.py
45.45% <ø> (ø)

asf_search/search/geo_search.py
100.00% <ø> (ø)

asf_search/search/search.py
94.44% <ø> (+2.22%)
:arrow_up:

asf_search/search/search_count.py
100.00% <ø> (ø)

asf_search/export/jsonlite.py
80.19% <80.19%> (ø)

asf_search/export/jsonlite2.py
88.23% <88.23%> (ø)

asf_search/export/kml.py
95.83% <95.83%> (ø)

asf_search/export/csv.py
96.00% <96.00%> (ø)

asf_search/ASFSearchResults.py
71.42% <100.00%> (+13.09%)
:arrow_up:

asf_search/CMR/__init__.py
100.00% <100.00%> (ø)

... and 10 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.


Incorrect / out of date info on creating docker container

"The . in the docker build command tells Docker to use the current folder to find a Dockerfile." is slightly incorrect - the "." in the command line sets the build context of the image (per https://docs.docker.com/engine/reference/commandline/build/). The "-f" parameter tells Docker where to find the Dockerfile.

When first creating an image, I don't see two images in my list of "docker images", only the first that was created ("counter-image"). I don't know if this is new functionality, but docker appears to no longer create an image that the new image is templated from - only the new image.

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

ID: 4c7470d2-9a57-7654-e13a-4f912898f7aa
Version Independent ID: 58d57b81-4ca6-6536-8788-f212402b41a7
Content: Containerize an app with Docker tutorial - .NET
Content Source: docs/core/docker/build-container.md
Product: dotnet-fundamentals
Technology: dotnet-docker
GitHub Login: @IEvangelist
Microsoft Alias: dapine

Hi 👋 @cdanek
Thank you so much for posting this issue. We really appreciate it. I'm working now on addressing the concerns and points that you raised here, thanks again.


Unihertz Titan mirrors garbled screen with default encoder

[x] I have read the FAQ.
[x] I have searched in existing issues.

Environment

OS: [e.g. Debian, Windows, macOS...]
windows 10, but this is probably os independent
scrcpy version: [e.g. 1.12.1]
v2.2
installation method: [e.g. manual build, apt, snap, brew, Windows release...]
windows 10, ran out of a file
device model:
Unihertz Titan Pocket, however had the same issue with the Unihertz Titan as well
Android version: [e.g. 10]
Android 13 with lineage os
Describe the bug
the default video encoder outputs garbled video,

the default encoder on this device is --video-encoder='OMX.MTK.VIDEO.ENCODER.AVC' changing it to any other encoder fixes this

this is the list of encoders I get when punch in --list-encoders
[server] INFO: List of video encoders:
    --video-codec=h264 --video-encoder='OMX.MTK.VIDEO.ENCODER.AVC'
    --video-codec=h264 --video-encoder='c2.android.avc.encoder'
    --video-codec=h264 --video-encoder='OMX.google.h264.encoder'
[server] INFO: List of audio encoders:
    --audio-codec=opus --audio-encoder='c2.android.opus.encoder'
    --audio-codec=aac --audio-encoder='c2.android.aac.encoder'
    --audio-codec=aac --audio-encoder='OMX.google.aac.encoder'```

the default encoder on this device is --video-encoder='OMX.MTK.VIDEO.ENCODER.AVC' changing it to any other encoder fixes this

OK, so it's an encoder issue on the device (maybe only at some resolution). Does the default encoder works with scrcpy -m1024 for example?
Anyway, there's probably nothing scrcpy can do (just use another encoder).

OK, so it's an encoder issue on the device (maybe only at some resolution). Does the default encoder works with scrcpy -m1024 for example?

nope, no dice

Anyway, there's probably nothing scrcpy can do (just use another encoder).

I guessed as much, I'm posting the issue more for the sake of documentation honestly, I tried a bunch of different solutions with similar issues, only though about trying this after I saw reading through --help command.
I'm closing the issue, maybe I'll edit my main post to include the phrase "mediatek" as well, maybe it'll help someone else as well


Small bug

When a link is copied and pasted into a note, the link to the PDF (the clickable link with title+page for example) is only visible if "wiki-links" is enabled in the obsidian settings.

Thanks, this seems to be an upstream bug of Obsidian itself.
I've submitted a bug report: https://github.com/obsidianmd/obsidian-api/issues/154

I've just implemented a quick fix for this problem and released it as 0.25.0.
Feel free to re-open this issue if you find something is not working well.

Thank you for the quick fix.


Fix Request.toString leaking sensitive headers.

@okiolover have you signed the CLA? https://github.com/square/okhttp/blob/master/CONTRIBUTING.md

@yschimke Yes. Let me know if something didn't work.

Thanks! 👍🏻👍🏻


docs: ChatInputField

:tada: This issue has been resolved in version 7.26.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Automatically enable async signal handling when possible

I don't like such a behavior change. Usually you don't need async signal handling in async applications, because they're already fairly non-blocking and pcntl_signal_dispatch gets called often enough.

I just wanted to implement this to reduce the (small, but still noticeable) overhead of calling pcntl_signal_dispatch at each tick; and it doesn't really hurt to reduce overhead by delegating some stuff to PHP, when possible and not too complex.

I believe we discussed this in the past and decided it was better to not enable async signal dispatching by default because it removed the guarantee that only a single watcher callback could be invoked at any given time. With async signal dispatch, a signal watcher may be invoked at any time, making it even more difficult to reason about execution flow. Since #264 was fixed, you can invoke pcntl_async_signals in your application if you want more immediate signal handling, of course with the caveat I mentioned before. We could check if async signal dispatching is enabled before calling pcntl_signal_dispatch, but then we're adding another function call to the normal case. Feel free to test, but I'd be surprised if there was a performance benefit.

Instead of adding an additional function call, we could check if async signal handling is enabled when a new signal handler is set, or maybe add a new method to manually enable/disable signal handling (I prefer the first option).

Done

IMO this is unnecessary. You're adding complexity to avoid a single function call per tick. pcntl_dispatch_signals checks a counter for pending signals and immediately returns if there are no pending signals. There is essentially no benefit to be had here.
pcntl_async_signals can be toggled at any time, so checking it only on construction or when adding a signal watcher is insufficient.

While it is true that pcntl_async_signals can toggled at any time, it is usually toggled while setting up the signal handlers.
I don't see the point of even using pcntl_async_signals (except maybe for a more immediate call of the callback) if the AMPHP event loop already handles signals on its own: with the current unmodified event loop, pcntl_async_signals just adds more overall overhead, forcing the use of both PHP's internal signal scheduler and AMPHP's scheduler.

Closing in favor of a more predictable execution order.


Support for delete, insert, update, replace

related to https://github.com/staabm/phpstan-dba/issues/472#issuecomment-1327085284

add test-coverage / expectations for error checking and also type inference

the new statements are pretty much the same as SELECT - the logic regarding placeholders is the same. Do we need to test something more since the features are already being tested for SELECT statements?

widen the whitelist of statement types in places like

whitelisted for SELECT, INSERT, DELETE, UPDATE

make sure we did not miss a place where queries are executed against the database and don't have a transaction yet

I checked mysql/pdo-mysql/pdo-pf reflectors and transactions were used

I got a problem with the tests - in order for them to succeed, they need to succeed locally (becuase of recoridng & replay). But the output differs here and in CI
ID`, `changet' at line

vs

ID`, `chan...' at line

the 3 remaining failures seems to be caused by this. I could manually modify the recorded files but that wouldnt be easy to do after every commit.

thank you


Incompatible with postcss?

Like #1 , I'm also running into the error:
[2021-01-09 17:54:08.426] [exthost] [error] TypeError: Cannot read property 'map' of null
	at /home/cal/.vscode/extensions/divlo.vscode-styled-jsx-languageserver-1.1.1/client/out/extension.js:52:36

It seems to be caused by the presence of a postcss.config.js file in the repo.
I've put together a minimum example of the bug here:
https://github.com/CallumJHays/vscode-styled-jsx-provider-failure
cheers :beer:

Thanks for your report! @CallumJHays
I cloned your reproductible repo but I haven't got any errors, it is working fine.
Is it working without the postcss.config.js file ? Maybe you have another VSCode extension for postcss that conflicts with this one. If you have others clue so I can I reproduce, I would appreciate it.

Thanks for your report! @CallumJHays
I cloned your reproductible repo but I haven't got any errors, it is working fine.
Is it working without the postcss.config.js file ? Maybe you have another VSCode extension for postcss that conflicts with this one. If you have others clue so I can I reproduce, I would appreciate it.

Okay, so the error only pops up when the postcss file is opened in a window. I've confirmed this is happening when only the Language Server extension is enabled. Probably a harmless error.

Okay, so the error only pops up when the postcss file is opened in a window. I've confirmed this is happening when only the Language Server extension is enabled. Probably a harmless error.


Am I correct that this is now GA?

Hi
Previous issues about a GA date have been answered with a reference to the 2022 Wave 1 item for this. However, this page now shows as archived and not being updated, with no indication that GA has been achieved.
The documentation doesn't include an 'In Preview' warning and adding in Dataverse doesn't include (Preview) in the label.
Is this sufficient to confirm that the functionality is now GA?
I'm not sure how to check versions on GitHub to see when/if the preview warning has been removed.
Many thanks, Alex

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

ID: d6f7d49a-1fb0-ffba-779d-9c8b6d055d15
Version Independent ID: d6f7d49a-1fb0-ffba-779d-9c8b6d055d15
Content: Work with Dataverse formula columns - Power Apps
Content Source: powerapps-docs/maker/data-platform/formula-columns.md
Service: powerapps
Sub-service: teams
GitHub Login: @sanjeevgoyalmsft
Microsoft Alias: dikamath

Yes, Formula Columns is GA now.
From: Alex McLachlan @.>
Sent: Tuesday, January 2, 2024 9:31 PM
To: MicrosoftDocs/powerapps-docs @.>
Cc: Mention @.***>
Subject: [MicrosoftDocs/powerapps-docs] Am I correct that this is now GA? (Issue #5069)
Hi
Previous issues about a GA date have been answered with a reference to the 2022 Wave 1 item for thishttps://learn.microsoft.com/en-us/power-platform-release-plan/2022wave1/data-platform/enable-power-fx-formula-columns-inside-dataverse-tables. However, this page now shows as archived and not being updated, with no indication that GA has been achieved.
The documentation doesn't include an 'In Preview' warning and adding in Dataverse doesn't include (Preview) in the label.
Is this sufficient to confirm that the functionality is now GA?
I'm not sure how to check versions on GitHub to see when/if the preview warning has been removed.
Many thanks, Alex

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

ID: d6f7d49a-1fb0-ffba-779d-9c8b6d055d15
Version Independent ID: d6f7d49a-1fb0-ffba-779d-9c8b6d055d15
Content: Work with Dataverse formula columns - Power Appshttps://learn.microsoft.com/en-us/power-apps/maker/data-platform/formula-columns?tabs=type-or-paste
Content Source: powerapps-docs/maker/data-platform/formula-columns.mdhttps://github.com/MicrosoftDocs/powerapps-docs/blob/main/powerapps-docs/maker/data-platform/formula-columns.md
Service: powerapps
Sub-service: teams
GitHub Login: @sanjeevgoyalmsfthttps://github.com/sanjeevgoyalmsft
Microsoft Alias: dikamath

—
Reply to this email directly, view it on GitHubhttps://github.com/MicrosoftDocs/powerapps-docs/issues/5069 or unsubscribehttps://github.com/notifications/unsubscribe-auth/A5NPNS6R7XAKNHPWO7WY4RDYMQVM3BFKMF2HI4TJMJ2XIZLTSOBKK5TBNR2WLJDUOJ2WLJDOMFWWLO3UNBZGKYLEL5YGC4TUNFRWS4DBNZ2F6YLDORUXM2LUPGBKK5TBNR2WLJLJONZXKZNENZQW2ZNLORUHEZLBMRPXI6LQMWBKK5TBNR2WLJDUOJ2WLJDOMFWWLLTXMF2GG2C7MFRXI2LWNF2HTLDTOVRGUZLDORPXI6LQMWSUS43TOVS2M5DPOBUWG44SQKSHI6LQMWVHEZLQN5ZWS5DPOJ42K5TBNR2WLKJRGEYDCNRQGEYTNAVEOR4XAZNFNFZXG5LFUV3GC3DVMWVDEMBWGI3DCOBZGE2KO5DSNFTWOZLSUZRXEZLBORSQ.
You are receiving this email because you were mentioned.
Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Thanks for your comment, @alex-mcla. This issue has been assigned to the doc author for review.


after ProcessResponseBody()  can not   return  all MatchedRules info

Hi,jptosso.This is a very valuable project. Thanks for hardly working.I am currently learning about this project. I have some problems.
after ProcessResponseBody()  can not   return  all MatchedRules info .
Steps to reproduce
 ... ...
if tx.IsProcessableResponseBody() {
	tx.ResponseBodyBuffer.Write([]byte("#!/usr/bin/python"))
	tx.ProcessResponseBody()

	if it := tx.Interruption; it != nil {
		httpOutMsg := ""
		for _, res := range tx.MatchedRules {

			httpOutMsg = httpOutMsg + res.MatchedData.Key + ":" + res.MatchedData.Value + "\n"
			httpOutMsg = httpOutMsg + "Message:" + res.Message + "\n"

		}
             fmt.Println(httpOutMsg)

Expected result
deny and return all hit rules msg,should return the following rules
SecRule RESPONSE_BODY "@rx ^#!\s?/"
"id:950140,
phase:4,\
Actual result
deny ,but not return hit rules msg.
looking forward to your help!

Hey @cts2021, thank you very much for your feedback! I have reviewd your case and added a test to the seclang engine:
func TestTXIssue147(t *testing.T) {
	// https://github.com/jptosso/coraza-waf/issues/147
	waf := coraza.NewWaf()
	parser, _ := NewParser(waf)
	err := parser.FromString(`SecRule RESPONSE_BODY "@rx ^#!\s?/" "id:950140,phase:4,log,deny,status:403"`)
	if err != nil {
		t.Error(err.Error())
	}
	tx := waf.NewTransaction()
	// response body access is required
	tx.ResponseBodyAccess = true
	// we need a content-type header
	tx.AddResponseHeader("Content-Type", "text/html")
	if tx.IsProcessableResponseBody() {
		if _, err := tx.ResponseBodyBuffer.Write([]byte("#!/usr/bin/python")); err != nil {
			t.Error(err)
		}
		it, err := tx.ProcessResponseBody()
		if err != nil {
			t.Error(err)
		}
		if it != nil {
			httpOutMsg := ""
			for _, res := range tx.MatchedRules {
				httpOutMsg = httpOutMsg + res.MatchedData.Key + ":" + res.MatchedData.Value + "\n"
				httpOutMsg = httpOutMsg + "Message:" + res.Message + "\n"

			}
			if len(httpOutMsg) == 0 {
				t.Error("failed to log")
			}
		} else {
			t.Error("failed to block response body")
		}
	} else {
		t.Error("failed to process response body")
	}
}

Running tool: /usr/local/go/bin/go test -timeout 30s -run ^TestTXIssue147$ github.com/jptosso/coraza-waf/v2/seclang
ok  	github.com/jptosso/coraza-waf/v2/seclang	0.168s

Apparently you are missing the content-type header or ResponseBodyAccess.
Coraza rules for processing a requests are:

The response body must match text/html, or text/plain, you may add more to waf.ResponseBodyMimeTypes or SecResponseBodyMimeType.
waf.RequestBodyAccess must be true, you can set it using SecResponseBodyAccess On

Please review the test and tell me if that fixes your issue.
Regards,

thanks for your  response in time.
1 ,in coraza.conf file  already keep the setting:
SecRequestBodyAccess On
SecResponseBodyAccess On
SecResponseBodyMimeType text/plain text/html text/xml

I check the Response header already   include "Content-Type,text/plain".

3.httpOutMsg  print:
status:deny
hit rules count:1
ReqId:dIZNnIdQQluWIGJLLg2
host:<IP_ADDRESS>:8080
Message:Host header is a numeric IP address
4, the content of rule:
SecRule RESPONSE_BODY "@rx ^#!\s?/"
"id:950140,
phase:4,
block,
capture,
t:none,
msg:'CGI source code leakage',
logdata:'Matched Data: %{TX.0} found within %{MATCHED_VAR_NAME}: %{MATCHED_VAR}',
tag:'application-multi',
tag:'language-multi',
tag:'platform-multi',
tag:'attack-disclosure',
tag:'paranoia-level/1',
tag:'OWASP_CRS',
tag:'capec/1000/118/116',
tag:'PCI/6.5.6',
ctl:auditLogParts=+E,
ver:'OWASP_CRS/3.3.2',
severity:'ERROR',
setvar:'tx.outbound_anomaly_score_pl1=+%{tx.error_anomaly_score}',
setvar:'tx.anomaly_score_pl1=+%{tx.error_anomaly_score}'"
httpOutMsg    not include    " msg:'CGI source code leakage', "

Core Rule Set   installed  by coraza  automatically  :)

Hi,jptosso.
use：
parser.FromString(SecRule RESPONSE_BODY "@rx ^#!\s?/" "id:950140,phase:4,msg:'CGI source code leakage',log,deny,status:403")
httpOutMsg  can get  " msg:'CGI source code leakage', "
But  use  Core Rule Set  by  parser.FromFile("crs.conf") , get Message:Host header is a numeric IP address.
Regards,

It still works, I think you have an issue with the CRS operation mode:
# Default: Anomaly Scoring mode, log to error log, log to ModSecurity audit log
# - By default, offending requests are blocked with an error 403 response.
# - To change the disruptive action, see RESPONSE-999-EXCLUSION-RULES-AFTER-CRS.conf.example
#   and review section 'Changing the Disruptive Action for Anomaly Mode'.
# - In Apache, you can use ErrorDocument to show a friendly error page or
#   perform a redirect: https://httpd.apache.org/docs/2.4/custom-error.html
#
SecDefaultAction "phase:1,log,auditlog,pass"
SecDefaultAction "phase:2,log,auditlog,pass"

Check your operation mode as if you are using a default deny, it means any disruptive rules (block) that matches will stop the request and not evaluate any more rules, and if you use the anomaly scoring mode it means the only rule that will deny is the anomaly scoring rule at the end of phase 2.

Yes,Core Rule Set  should be SecDefaultAction "phase:1,log,auditlog,pass".
thanks for your kindly help :)