italicAngle check should apply in all correct profiles

Should be triggered if "Italic" is part of the file name, or NameID2, or NameID17.
The ticked cases indicates where you can already find it.
italicAngle in post table is not 0.

Italic angle in counter-clockwise degrees from the vertical. Zero for upright text, negative for text that leans to the right (forward). https://docs.microsoft.com/en-us/typography/opentype/spec/post#header

🔥 FAIL: Checking post.italicAngle value.
* [com.google.fonts/check/italic_angle](https://font-bakery.readthedocs.io/en/latest/fontbakery/profiles/googlefonts.html#com.google.fonts/check/italic_angle)
🔥 FAIL Font is italic, so post.italicAngle should be non-zero. [code: zero-italic]

Profile

[x] in google-font profile
[ ] in universal profile
[ ] in opentype profile

Format

[ ] in VF check
[x] in static check

Let me reword this, then... You are requesting the italic angle check to be migrated from the vendor-specific googlefonts profile to the much broader opentype profile, right?
Since the semantics of the italic-angle value are defined in the OpenType spec, I think you're right!

I think I don't follow what you mean by "all correct profiles" but I think this check is valid and yes it should be included in the OpenType profile.

Although I've seen some other checks like FAIL: CFF table FontName must match name table ID 6 are also included in the Universal profile, shouldn't this one be there too?

Profiles where it should be included

[x] in google-font profile
[x] in universal profile
[x] in opentype profile

The ticked cases in the issue are the ones where the check is already included, and the one unticked are the one to do.

Let me reword this, then... You are requesting the italic angle check to be migrated from the vendor-specific googlefonts profile to the much broader opentype profile, right?

Yes, then I don't know if opentype profile is included in Universal, but that's the idea.

Inspecting again the profiles in Fontbakery I can confirm now that almost all (if not all) the Italics checks listed should be included in the OpenType set, which would be included then in the universal and therefore in the google-fonts vendor-specific.
Opentype
The checks of the opentype profile are separated in one sub-profile for each of the Open Type tables as listed below
Universal
The checks on the universal profile, documented below, evaluate adherence to the best practices shared among the type design community. Additionally, it also includes the checks from the opentype profile.
Google-Fonts
All vendor-specific profiles such as the googlefonts one also include the checks from the universal profile.


Bug processing package PackageDecs

Section 6.10.2. Package and module references allows package-name-less package reference expressions (`package`):

If there is no explicit package name, the package reference is to the package in which the package reference expression occurs.

but ceylon.ast.redhat blows up with:
Exception in thread "main" ceylon.language.AssertionError "Assertion failed
	violated nonempty components = CeylonIterable(fullPackageName.identifiers).collect(propagateUpdate(pIdentifierToCeylon, update))"
	at ceylon.ast.redhat.fullPackageNameToCeylon_.fullPackageNameToCeylon(FullPackageName.ceylon:17)
	at ceylon.ast.redhat.packageDecToCeylon_.packageDecToCeylon(PackageDec.ceylon:16)
	at ceylon.ast.redhat.decToCeylon_.decToCeylon(Dec.ceylon:32)
	at ceylon.ast.redhat.primaryToCeylon_.primaryToCeylon(Primary.ceylon:47)

This is supported by the api of PackageDec, as packageName is optional.

@lucaswerkmeister re you're Gitter question

it looks like you’ve managed to get a package literal with a non-null, but empty import path
how?

it must be that the type checker fills in this info when full type checking is performed. For the program:
Anything p = `package`;

I get:
$ ceylon compile-dart --verbose=ast,rhAst
...
-- Redhat AST simple/run.ceylon
+  [CompilationUnit] (1:0-1:22)
|  +  [ImportList]
|  +  [AttributeDeclaration] (1:0-1:22) : value p => Anything
|  |  +  [AnnotationList]
|  |  + p [Identifier] (1:9-1:9)
|  |  +  [BaseType] (1:0-1:7) : Anything : class Anything()
|  |  |  + Anything [Identifier] (1:0-1:7)
|  |  + = [SpecifierExpression] (1:11-1:21)
|  |  |  +  [Expression] (1:13-1:21) : Package
|  |  |  |  + `` [PackageLiteral] (1:13-1:21) : Package
|  |  |  |  |  +  [ImportPath]

------------------------------------------------------------
                    ** Compiler bug! **
------------------------------------------------------------
Assertion failed
	violated nonempty components = CeylonIterable(fullPackageName.identifiers).collect(propagateUpdate(pIdentifierToCeylon, update))

was encountered while compiling the file:

    source/simple/run.ceylon
------------------------------------------------------------
Exception in thread "main" ceylon.language.AssertionError "Assertion failed
	violated nonempty components = CeylonIterable(fullPackageName.identifiers).collect(propagateUpdate(pIdentifierToCeylon, update))"
	at ceylon.ast.redhat.fullPackageNameToCeylon_.fullPackageNameToCeylon(FullPackageName.ceylon:17)
	at ceylon.ast.redhat.packageDecToCeylon_.packageDecToCeylon(PackageDec.ceylon:16)
	at ceylon.ast.redhat.decToCeylon_.decToCeylon(Dec.ceylon:32)

Ah, looks like ExpressionVisitor.java is the null hater (or null burier?):
https://github.com/ceylon/ceylon/blob/3d92c0cb6faf9b5d2c93635f82b27ee1c8e26c89/typechecker/src/com/redhat/ceylon/compiler/typechecker/analyzer/ExpressionVisitor.java#L8841
Module literals may also be affected.

Indeed it does: ExpressionVisitor.java:8847. I thought it would create a proper import path with the correct components, but it looks like it doesn’t. Alright.

Github tells me I beat you by 1s :)

GitHub doesn’t even tell me second-precise timestamps :(

So yes, `Anything p = `module`;` also fails with:
Exception in thread "main" ceylon.language.AssertionError "Assertion failed
	violated nonempty components = CeylonIterable(fullPackageName.identifiers).collect(propagateUpdate(pIdentifierToCeylon, update))"
	at ceylon.ast.redhat.fullPackageNameToCeylon_.fullPackageNameToCeylon(FullPackageName.ceylon:17)
	at ceylon.ast.redhat.moduleDecToCeylon_.moduleDecToCeylon(ModuleDec.ceylon:16)
	at ceylon.ast.redhat.decToCeylon_.decToCeylon(Dec.ceylon:33)
	at ceylon.ast.redhat.primaryToCeylon_.primaryToCeylon(Primary.ceylon:47)

Should be fixed in branch fix105, can you try it out?
(`class` and `interface` should be fine afaict.)

works great, thanks!
BTW, a nice tool for testing this sort of thing is ceylon compile-dart --verbose=ast,rhAst :)

Alright, pushed to master then :)
And it seems like your compiler is a great way to debug ceylon.ast on
typechecked ASTs, so I guess I’ll install it :D
On 08.12.2015 01:17, John Vasileff wrote:

works great, thanks!
BTW, a nice tool for testing this sort of thing is |ceylon
compile-dart --verbose=ast,rhAst| :)
—
Reply to this email directly or view it on GitHub
https://github.com/ceylon/ceylon.ast/issues/105#issuecomment-162712618.


fix: Don't define backup_configuration if default DB is configured as a replica

I made a mistake in my last PR https://github.com/terraform-google-modules/terraform-google-sql-db/pull/556 which allow backups to be created if the default DB is configured as a replica (via master_instance_name), when this is not a valid configuration.
CloudSQL does not allow you to create backups of replicas, so this block should be blanked if the intance is configured as a replica.

/gcbrun

@OscarVanL integration test failed with following error:
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185: Error: Reference to undeclared input variable
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185:
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185:   on ../../../modules/mysql/main.tf line 71, in resource "google_sql_database_instance" "default":
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185:   71:       for_each = var.master_instance_name != null ? [] : [var.backup_configuration]
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185:
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185: An input variable with the name "master_instance_name" has not been declared.
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185: This variable can be declared with a variable "master_instance_name" {}
TestMySqlHaModule 2023-12-19T14:08:05Z command.go:185: block.
TestMySqlHaModule 2023-12-19T14:08:05Z retry.go:99: Returning due to fatal error: FatalError{Underlying: error while running command: exit status 1;
Error: Reference to undeclared input variable

  on ../../../modules/mysql/main.tf line 71, in resource "google_sql_database_instance" "default":
  71:       for_each = var.master_instance_name != null ? [] : [var.backup_configuration]

An input variable with the name "master_instance_name" has not been declared.
This variable can be declared with a variable "master_instance_name" {}
block.}
    validate.go:11:
        	Error Trace:	/builder/home/go/pkg/mod/github.com/gruntwork-io/terratest@v0.46.7/modules/terraform/validate.go:11
        	            				/builder/home/go/pkg/mod/github.com/!google!cloud!platform/cloud-foundation-toolkit/infra/blueprint-test@v0.10.2/pkg/tft/terraform.go:411
        	            				/builder/home/go/pkg/mod/github.com/!google!cloud!platform/cloud-foundation-toolkit/infra/blueprint-test@v0.10.2/pkg/tft/terraform.go:442
        	            				/builder/home/go/pkg/mod/github.com/!google!cloud!platform/cloud-foundation-toolkit/infra/blueprint-test@v0.10.2/pkg/tft/terraform.go:469
        	            				/builder/home/go/pkg/mod/github.com/!google!cloud!platform/cloud-foundation-toolkit/infra/blueprint-test@v0.10.2/pkg/utils/stages.go:31
        	            				/builder/home/go/pkg/mod/github.com/!google!cloud!platform/cloud-foundation-toolkit/infra/blueprint-test@v0.10.2/pkg/tft/terraform.go:469
        	Error:      	Received unexpected error:
        	            	FatalError{Underlying: error while running command: exit status 1;
        	            	Error: Reference to undeclared input variable

        	            	  on ../../../modules/mysql/main.tf line 71, in resource "google_sql_database_instance" "default":
        	            	  71:       for_each = var.master_instance_name != null ? [] : [var.backup_configuration]

        	            	An input variable with the name "master_instance_name" has not been declared.
        	            	This variable can be declared with a variable "master_instance_name" {}
        	            	block.}
        	Test:       	TestMySqlHaModule
--- FAIL: TestMySqlHaModule (9.55s)
FAIL

@imrannayer What version of the module is that testing against? That variable was only added in my last commit: https://github.com/terraform-google-modules/terraform-google-sql-db/commit/6cda644a136a1cac3ada9358007619f02f90a169, so if it is pinned on the latest release (v18.1.0) that wouldn't include the variable. That variable will exist if it runs against HEAD of this repo.

/gcbrun


Improving the Accordion documentation based on user feedback

I added a link to the Bootstrap Accordion documentation so readers can see what is meant by an accordion.

Thanks!


[Improvement][Helm] Refactor configmap control in master

Search before asking

[X] I had searched in the issues and found no similar feature requirement.

Description
No response
Are you willing to submit a PR?

[X] Yes I am willing to submit a PR!

Code of Conduct

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

This issue has been automatically marked as stale because it has not had recent activity for 30 days. It will be closed in next 7 days if no further activity occurs.

remove stale


Aliased unicode box drawing characters

Windows Terminal version
1.13.11432.0
Windows build number
10.0.22000.318
Other Software
No response
Steps to reproduce
Test out some of the unicode box drawing characters like U+256D (╭), U+256E (╮), U+256F (╯) in Windows Terminal and you will see that they are aliased. I am using the same font in both Console Host and Windows Terminal. As you zoom in, it seemingly randomly gets anti-aliased and looks normal, but most of the time it doesn't:
https://user-images.githubusercontent.com/65787561/173909326-fdeffd3a-1f02-4c04-a401-3ab62d53dae0.mp4

| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | A | B | C | D | E | F
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | --
U+250x | ─ | ━ | │ | ┃ | ┄ | ┅ | ┆ | ┇ | ┈ | ┉ | ┊ | ┋ | ┌ | ┍ | ┎ | ┏
U+251x | ┐ | ┑ | ┒ | ┓ | └ | ┕ | ┖ | ┗ | ┘ | ┙ | ┚ | ┛ | ├ | ┝ | ┞ | ┟
U+252x | ┠ | ┡ | ┢ | ┣ | ┤ | ┥ | ┦ | ┧ | ┨ | ┩ | ┪ | ┫ | ┬ | ┭ | ┮ | ┯
U+253x | ┰ | ┱ | ┲ | ┳ | ┴ | ┵ | ┶ | ┷ | ┸ | ┹ | ┺ | ┻ | ┼ | ┽ | ┾ | ┿
U+254x | ╀ | ╁ | ╂ | ╃ | ╄ | ╅ | ╆ | ╇ | ╈ | ╉ | ╊ | ╋ | ╌ | ╍ | ╎ | ╏
U+255x | ═ | ║ | ╒ | ╓ | ╔ | ╕ | ╖ | ╗ | ╘ | ╙ | ╚ | ╛ | ╜ | ╝ | ╞ | ╟
U+256x | ╠ | ╡ | ╢ | ╣ | ╤ | ╥ | ╦ | ╧ | ╨ | ╩ | ╪ | ╫ | ╬ | ╭ | ╮ | ╯
U+257x | ╰ | ╱ | ╲ | ╳ | ╴ | ╵ | ╶ | ╷ | ╸ | ╹ | ╺ | ╻ | ╼ | ╽ | ╾ | ╿

Expected Behavior
I expected it to look like regular CMD/Console Host that looks pretty much perfect no matter the zoom.
https://user-images.githubusercontent.com/65787561/173909556-b31458ba-310c-47b1-99a4-8707561713b4.mp4
Actual Behavior
It looks aliased at most zoom levels, including the default.

Note: Sometimes in Console Host the box characters have slight gaps in them when zooming, but it is a minor issue and that is why I said that it is almost perfect in Console Host.
https://user-images.githubusercontent.com/65787561/173910284-e6bc33ab-f8cd-4e27-9906-04e17d4e0e3e.mp4

Duplicate of https://github.com/microsoft/terminal/issues/6161 and https://github.com/microsoft/terminal/issues/5897, I apologise.


Respect Gitlinks per Attached Repository

Hello dear community, in e.g. mkdocs-material there is nice feature: https://squidfunk.github.io/mkdocs-material/setup/adding-a-git-repository/#adding-a-git-repository
By simple config in yaml file:
repo_name: Trolololo
repo_url: https://somehost.com/Trololo
edit_uri: "edit/master/docs/"

will enable this:

By clicking you are jumping into the Repositroy to exact file.
When I use monorepo no links will be provided.
Please respect config per attached repository.

Hi! This is a great feature, but is a bit broken with this plugin at the moment. There are issues open for this problem, see #2 and #45.

Seems partly works now. I can see Edit Button, but Links are broken - there is a site_name: Value taken from the merged mkdocs.yml.
I need to apply workaround to html directly what is not really good way of doing this (as per your README example):
find v1/ -name '*.html' -exec sed -i 's/\/versions\/v1//' {} \;
find v2/ -name '*.html' -exec sed -i 's/\/versions\/v2//' {} \;


[Subtask] HiveSQLEngine with execute statement support

@yaooqinn, could you please assign this ticket to me?

#2013 is ready for review


feat(build): #0 update commitlint

Hi @sebas031811,
First of all, thank you so much for your contribution!

You need to update the lockfile by using the makeNodeJsLock builtin for lintGitCommitMsg to actually use a newer commitlint version.
Please specify in the commit and PR bodies: Updagraded from X to Y

Hi @sebas031811,
First of all, thank you so much for your contribution!

You need to update the lockfile by using the makeNodeJsLock builtin for lintGitCommitMsg to actually use a newer commitlint version.
Please specify in the commit and PR bodies: Upgraded from X to Y

Oh NVM I just saw the lockfile was updated too!

You're referencing issue #0, please specify a valid issue.

Hi @sebas031811,
First of all, thank you so much for your contribution!

You need to update the lockfile by using the makeNodeJsLock builtin for lintGitCommitMsg to actually use a newer commitlint version.
Please specify in the commit and PR bodies: Upgraded from X to Y

Oh NVM I just saw the lockfile was updated too!

Did you update the lockfile using the makeNodeJsLock builtin? If not please do so.

/lintGitMailMap not passing. Please read https://makes.fluidattacks.com/contributing/

Hello @dsalaza4, thanks for your feedback!
/lintGitMailMap runs OK in local, did you mean /lintGitCommitMsg ?

It looks like you need to add another entry: https://github.com/fluidattacks/makes/actions/runs/5337582823/jobs/9674088936?pr=1112

LGTM!


python3Packages.ldap: 3.4.0 -> 3.4.2

https://github.com/python-ldap/python-ldap/releases/tag/python-ldap-3.4.2
Description of changes

Things done

Built on platform(s)

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

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[x] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
22.11 Release Notes (or backporting 22.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

Failures are on the target branch.


Improve insertion into pollfd table

Fixes #64

@robertsipka Thank you for patch. It seems improvement and may fixed the error refusing the connection. However, as mentioned in #64, we also need to prevent pollfd table's growing. I think we need two more changes as suggested #64.

check loop->npollfds is always less than the fixed size of the array (TUV_POLL_EVENTS_SIZE, which defaults to 32)
copy uv_rem_pollfd code into uv__platform_invalidate, hopefully it willl alleviate the growing of table

What do you think? If these further change would not help, let me know.

Thanks @glistening , I've added a checker if loop->npollfds is always less than the fixed size of the array.
I think copy the uv_rem_pollfd code into uv__platform_invalidate is not needed, because this fix already prevents the unnecessary growing by insterting new pollfds into invalidated places.

@vprunet I am going to land this first. further enhancements are always welcome.

LGTM


fix-up 404 urls

fix some 404 urls
ref:#17649
@Rajakavitha1

/cc @Rajakavitha1

/assign @mrbobbytables

/cc @mrbobbytables

@mrbobbytables I have modified these links, please let me know if there is any problem

Thanks!
/lgtm

@mrbobbytables Can you give me a label named approved ?

@Aresforchina I can, but it'll only apply for the blog links. Need another approver to take care of the others.
/approve

/assign @rajakavitha1

/cc @sftim

@Aresforchina would you be willing to rebase against master?
(https://kubernetes.io/docs/contribute/intermediate/#work-on-the-local-repository explains a typical workflow including a rebase if needed)

@sftim I have rebased those redundant commits. please give me a label lgtm,thanks!

@sftim
how about  this  pr now ?

/approve

/lgtm


WRKLDS-1421: Incorporate changes in cli-manager

This PR incorporates the changes in https://github.com/openshift/cli-manager/pull/91 into the cli manager operator.

unrelated:
/retest

/test e2e-aws-operator

/retest

/retest

/test e2e-aws-operator

/retest


Colab getting stuck at "from demo import load_checkpoints, make_animation"

I have the same issue and it bothers me that no one is around to help :/

If it is failing at the line "import ffmpeg", you need to run "!pip install ffmpeg-python" first to install the module.


Add imagemin task to compress lossy images

Related PR: https://github.com/patw0929/react-intl-tel-input/pull/25
Added task to compress images by pngquant.
We will get much smaller image file size, but actually it is a lossy, not lossless.
Maybe it will get worst quality in some flag or for someone.
Any advice?

Has been implemented at v2.0.9.


Fragmented messages using JsonSerializer sometimes don't send properly

There seems to be some kind of heisenbug when sending long messages using JsonSerializer - the receiving end gets a fragment with no header information somehow. I've uploaded a project to my fork demonstrating the issue.
If I put a conditional breakpoint on SocketBase.Listen (as below), everything seems to run just fine:

But if I disable it, I almost immediately get an exception because it doesn't recognise the message type:

On the iteration of the loop which threw the exception, count contains a value which would have triggered the breakpoint:

On a bit of further investigation, it seems that the fragments all get sent ok, but sometimes the client will only read part of one, then the next read picks up where the previous one finished. I think this comes down to the SocketBase treating received data as packets, where TCP is stream based. I believe I have seen a related issue where two messages are sent in quick succession (or in parallel), and the client's receive buffer is filled with the end of one message and the start of the next.

I am working on different message framing. the current FragmentFormatter introduced the problem you mentioned plus it degrades the TCP performance because it tries to meet UDP requirements (fragments re-order). I hope I can commit in 2 days.

Hi, sorry for being late on this. I have fixed message framing for streaming transport. please check the new version and let me know if things are still wrong.


[Feature, Request], about, API, parameters, for, upload

Existing Component
是
Component Name
upload
Description
detailed definition and example of server API parameters

OK，It's just send a options request before post


Adding support to nuke selected region

Adds --region flag to select specific regions.
Updated README.md

This also improves on the UX by:

Calling out the regions in the first log message.
Not mixing Skipping region log message with Checking region as the user is interested only in the target region.
Adding current_n / total_n so that the user is aware of the retrieval progress.

Instead of
go run main.go aws  --exclude-region eu-north-1 --exclude-region ap-south-1 --exclude-region eu-west-1 --exclude-region ap-northeast-2

INFO[2019-09-21T17:10:38+00:00] Retrieving all active AWS resources
INFO[2019-09-21T17:10:38+00:00] Skipping region: eu-north-1
INFO[2019-09-21T17:10:38+00:00] Skipping region: ap-south-1
INFO[2019-09-21T17:10:38+00:00] Checking region: eu-west-3
INFO[2019-09-21T17:10:47+00:00] Checking region: eu-west-2
INFO[2019-09-21T17:11:00+00:00] Skipping region: eu-west-1
INFO[2019-09-21T17:11:00+00:00] Skipping region: ap-northeast-2
INFO[2019-09-21T17:11:00+00:00] Checking region: ap-northeast-1
.
.

We now have
go run main.go aws  --exclude-region eu-north-1 --exclude-region ap-south-1 --exclude-region eu-west-1 --exclude-region ap-northeast-2

INFO[2019-09-21T17:11:23+08:00] Retrieving active AWS resources in [eu-west-3, eu-west-2, ap-northeast-1, sa-east-1, ca-central-1, ap-southeast-1, ap-southeast-2, eu-central-1, us-east-1, us-east-2, us-west-1, us-west-2]
INFO[2019-09-21T17:11:23+00:00] Checking region [1/12]: eu-west-3
INFO[2019-09-21T17:11:32+00:00] Checking region [2/12]: eu-west-2
INFO[2019-09-21T17:11:42+00:00] Checking region [3/12]: ap-northeast-1
INFO[2019-09-21T17:11:46+00:00] Checking region [4/12]: sa-east-1
INFO[2019-09-21T17:11:58+00:00] Checking region [5/12]: ca-central-1
.
.
.

Makes --region and --exclude-region mutually exclusive.

$ go run main.go aws --region us-east-1 --exclude-region us-west-1

ERRO[2019-09-21T17:59:25+00:00] --region and --exclude-region are mutually exclusive  error="--region and --exclude-region are mutually exclusive"
exit status 1

Improves function signature of  GetAllResources  from

func GetAllResources(regions []string, excludedRegions []string, excludeAfter time.Time, resourceTypes []string) (*AwsAccountResources, error)

to
func GetAllResources(targetRegions []string, excludeAfter time.Time, resourceTypes []string) (*AwsAccountResources, error)

@Etiene Could you review?

@Etiene  with the updated code as per the feedback, when I tested aws_test.go's test function TestGetTargetRegions I got the error:
~/go/packages/src/github.com/gruntwork-io/cloud-nuke/aws/mocks/EC2API.go:389:72: undefined: ec2.ApplySecurityGroupsToClientVpnTargetNetworkInput
~go/packages/src/github.com/gruntwork-io/cloud-nuke/aws/mocks/EC2API.go:389:128: undefined: ec2.ApplySecurityGroupsToClientVpnTargetNetworkOutput
.
.

which points to an older version of https://github.com/gruntwork-io/cloud-nuke/blob/master/aws/mocks/EC2API.go
I regenerated the same file by following - https://github.com/gruntwork-io/cloud-nuke/blob/master/aws/ec2_unit_test.go#L7 as
mockgen -source vendor/github.com/aws/aws-sdk-go/service/ec2/ec2iface/interface.go -destination aws/mocks/EC2API.go

and the tests worked. The new EC2API.go has significant changes from the older ones. I have pasted a diff here - https://gist.github.com/saurabh-hirani/fe8419c08d60fe734952b5a36972194f
Should this be tracked in a separate issue? I didn't want to pollute the existing PR with the same and wanted your advice on it.

@brikis98 @Etiene - can you please check and let me know if this is good to merge?

Sorry for the delay, @saurabh-hirani . I can take a look at this.

Thanks @autero1

I re-ran the tests with your latest commits and the tests passed. Unfortunately I didn't get to make a final pass on this PR, but will try and finalize this first thing Monday morning.

Thanks for the review and merge @autero1!

Still waiting for the tests to pass before I release.

https://github.com/gruntwork-io/cloud-nuke/releases/tag/v0.1.11


Segfault on repeated fits of large datasets

Hi !
While trying to adapt Boruta to work with LGBM on a fairly large dataset (18000 features, each of them being 0, 1 or 2, and 26500 examples) I ran into the following crash (simplified for clarity) :
Steps to reproduce
for i in range(100):     Generate large dataset X, y     clf = LGBMClasssifier()     clf.fit(X, y)
When executing this, the first iterations always work, but most of the times the program crashes after ~10 iterations. Some additional details :

it sometimes runs for much longer than others (it once managed to go to 100 iterations, but the size of the dataset was reduced each time). Restarting the computer seemed to grant an extra 5 iterations at least.

adding garbage collection / removing all useless copies of the data in the rest of the code has been done, it did improve slightly but did not make it disappear.

same for switching to the native Dataset / lgbm.train API

the problem should be memory related : although not 100% of the memory is used by python, the crash seems to happen when all memory is either used or cached by python

the crash always happens just before the first iteration of boosting, likely when the data is being copied for the fit.

Environment info
Operating System: Ubuntu 16.04 LTS
CPU: AMD Ryzen 7 1700 Eight-Core Processor × 16
C++/Python/R version: Python 3.6
Error Message:
Segmentation Fault (core dumped)

hi @AFanthomme , can you provide the type of X and y, e.g. 2d matrix or CSR matrix ? what is the data type? float32 or float64 ?

You're right, this is relevant info
X is a 2D dense matrix of int8 (to avoid extra memory), and once loaded in a dataset it is encoded in 3 bins as expected

@AFanthomme refer to the code here: https://github.com/Microsoft/LightGBM/blob/master/python-package/lightgbm/basic.py#L757-L761
even when your data type is int8, it will be converted to float32. As a result, there may have some memory problem in the above code.

@guolinke Thanks a lot, this is probably where the problem lies (the data barely fits into memory when on float32, since I also keep some intermediate results this could explain why the error happens only after some time). Is there a workaround to keep memory usage lower at this step?
Also it seemed the error happened during the fit and not the Dataset construction when I separated the two, but I will have to check

@AFanthomme The data construction is by lazy fashion unless you call dataset.construct() explicitly.
you can save your data to csv flie, then construct dataset it from csv file with parameter two_round=True.

how do you pass two_round=True? can you provide a code?

The relevant portion of the code is here :
X, X_val, y, y_val = train_test_split(X, y, test_size=0.25, random_state=np.random.randint(2**12))
        # Dump dataset as csv to reload it as dataset without float32 conversion
        y = y.astype(np.int8)
        y_val = y_val.astype(np.int8)
        X = np.hstack((np.reshape(y, (-1,1)), X))
        print(X.shape, X.dtype)
        df = pd.DataFrame(X)
        del X
        print('Start dumping temporary csv train')
        toc = time.time()
        df.to_csv("./files/X_train_ordinal_boruta_tmp.csv", header=False, index=False)
        print('Done dumping temporary csv train in {}s'.format(time.time()-toc))
        del df

        X_val = np.hstack((np.reshape(y_val, (-1,1)), X_val))
        df = pd.DataFrame(X_val)
        del X_val
        print('Start dumping temporary csv val')
        toc = time.time()
        df.to_csv("./files/X_val_ordinal_boruta_tmp.csv", header=False, index=False)
        del df
        print('Done dumping temporary csv val in {}s'.format(time.time()-toc))

        data_train = lgb.Dataset("./files/X_train_ordinal_boruta_tmp.csv")
        data_val = lgb.Dataset("./files/X_val_ordinal_boruta_tmp.csv", reference=data_train)

        print('Start fitting estimator')
        params = {'learning_rate':0.02, 'num_boost_round':2000, 'objective':'binary', 'metric': 'auc', 'two_round':True}
        bst = lgb.train(params, data_train, valid_sets=[data_val])`

can you try:
        params = {'learning_rate':0.02, 'num_boost_round':2000, 'objective':'binary', 'metric': 'auc', 'two_round':True}
        data_train = lgb.Dataset("./files/X_train_ordinal_boruta_tmp.csv", params=params)
        data_val = lgb.Dataset("./files/X_val_ordinal_boruta_tmp.csv", reference=data_train)
        data_train.construct()
        data_val.construct()
        print('Start fitting estimator')
        bst = lgb.train(params, data_train, valid_sets=[data_val])

@guolinke No change unfortunately...

@AFanthomme what is your memory capacity ?

16Gb
It seems like it could store this dataset, especially since the first fits work

how about add force gc in the loop ?

@AFanthomme I may have had a similar issue before where my first call to lgb.train ran fine and then I ran out of memory on the 2nd fit.  Adding 2 explicit calls to gc before each lgb.train solved the problem for me.  When I monitored the memory usage at each step, it looked like some memory would not get freed until the 2nd call to gc.  You could give that a try.

I tried with two gc, still does not solve the problem
I also switched back to constructing from numpy arrays, csv is long to write and did not help
It seems that the available memory (monitored by "free -m") is 6,5Gb after constructing datasets and gc, it then drops to 3.1 during beginning of training and that is at that point that it segfaults (did not catch the precise value at time of segfault, but the memory consumption seems perfectly cyclic and never got below 3 on the 5 first fits before it broke)

@AFanthomme can you try histogram_pool_size=1024 or is_sparse=false or both of them ?

That did make a change : using
        params = {'learning_rate':0.02, 'objective':'binary', 'metric': 'auc', 'two_round':True,
                    'histogram_pool_size':1024, 'is_sparse':False}
        data_train = lgb.Dataset(X, label=y, params=params)
        data_val = lgb.Dataset(X_val, label=y_val, reference=data_train)
        print('Begin constructing datasets')
        data_train.construct()
        data_val.construct()
        del X, X_val, y, y_val
        print('Start fitting estimator')
        gc.collect()
        print('First gc done')
        gc.collect()
        print('Second gc done')
        bst = lgb.train(params, data_train, valid_sets=[data_val], num_boost_round=4)

The segfault happens during the construct calls (the memory usage is still cyclic, now it drops at 2.7 (but immediately backs up to 5 at beginning of fit)

how about set is_sparse=true ?

Also dies at construct...

Do you think that could help even if the dataset is really not sparse at all?

from your log, it seems your dataset is sparse, as a reslut, using the dense format is memory costly.

With csr matrix, if i use int8 matrices lightgbm yields :
TypeError: Expected np.float32 or np.float64, met type(int8)
If I switch back to float32 (during csr_matrix construction) the memory consumption is increased and segfault at dataset construction as before

@AFanthomme can you send your data(int8 type) to pickle, and send it to me ?
I think it is more efficient for me to debug on it directly.

after some offline syncs, it seems this problem is casued by AMD Ryzen CPU. close for now.


No module named bfio | backsub error

Dear @kbestak  and @FloWuenne ,
I am trying to run an mcmicro fork of mine https://github.com/josenimo/mcmicro.
It crashed starting background subtraction, it seems we are missing the bfio module from aicsimageio.readers.bfio_reader.OmeTiledTiffReader. Have you seen this before?
mcmicro was running the following from defaults.yml
background:
name: backsub
container: ghcr.io/schapirolabor/background_subtraction
version: v0.3.3
Here is the full exit message:
Workflow execution completed unsuccessfully
The exit status of the task that caused the workflow execution to fail was: 137

Error executing process > 'background:backsub (1)'

Caused by:
  Process `background:backsub (1)` terminated with an error exit status (137)

Command executed:

  python3 /background_subtraction/background_sub.py -o Whole_HNC_Sonja_backsub.ome.tif -mo ./markers_bs.csv -r Whole_HNC_Sonja.ome.tif -m markers.csv

Command exit status:
  137

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Attempted file (Whole_HNC_Sonja.ome.tif) load with reader: aicsimageio.readers.bfio_reader.OmeTiledTiffReader failed with error: No module named 'bfio'
  /opt/conda/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0.  To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).
    d = to_dict(os.fspath(xml), parser=parser, validate=validate)
  .command.sh: line 2:    37 Killed                  python3 /background_subtraction/background_sub.py -o Whole_HNC_Sonja_backsub.ome.tif -mo ./markers_bs.csv -r Whole_HNC_Sonja.ome.tif -m markers.csv

Work dir:
  /fast/AG_Coscia/Jose/Nextflow/Work/7f/53b1c68ed01ed67ae9bb409d28f252

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Best,
Jose

Dear @josenimo
As written in the comment I'm linking, the 'bfio' module missing error doesn't affect background subtraction, as it just indicates that one reader did not work so another one was used.
Regarding why the process was terminated, it was likely due to not providing enough RAM. Currently, Backsub requires 2-3x memory as the input image size and I'm working on increasing the efficiency.
Best,
Krešo

Hi @kbestak,
I also encountered this issue when working with large (>100GB) datasets. It would be impractical for us to purchase 100-200GB additional ram due to cost (our computer already has 128GB), so I plan to downsample these images, which is not preferable. Are there still plans on reducing the memory utilization? I am using this package via MCMICRO and this memory utilization is a bottleneck for analysis. Thank you for supporting this valuable tool!
Thank you,
Matt

Hi @josenimo and @mdposkus,
I've developed a new, RAM-efficient version of Backsub with v0.4.1 --> https://github.com/SchapiroLabor/Background_subtraction/pull/14.
I was able to process an 88GB large image with only 13GB of RAM so I hope it will suffice for your usecases!
Best,
Kreso

Hi @kbestak,
Thank you for the update! I look forward testing it in the coming weeks and analyzing some full-resolution images. If the RAM usage scaling is similar for my image sets then this will perfectly suit our needs.
Best,
Matt

Hey @kbestak , wonderful news, you should update the MCMICRO config.nf :)
will report back on its use

Almost there ;) https://github.com/labsyspharm/mcmicro/pull/528


InfoSheets & Webinars - Issue Year

Typically we only post the year that an infosheet is released, not the day. Is there a way just to post the year. Should that be put in the title?

With webinars, when they are archived they are also included just under the year

You should switch to using proper dates.  For those of which you're unsure,
perhaps just pick a generic date like January 1?
On Tue, Jun 13, 2017 at 16:56 peterfiala<EMAIL_ADDRESS>wrote:

With webinars, when they are archived they are also included just under
the year
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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the thread
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.

Yeah I suppose so, thanks
Peter
Peter Fiala
Technology & Events Coordinator
Wisconsin Coalition Against Sexual Assault (WCASA)
[link to wcasa's Facebook page]http://www.facebook.com/wcasa [link to wcasa's Twitter feed] http://twitter.com/wcasa_vpcc  [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS8fWOIOHiKkDuBEon9eoc4_Rkp-EW-KLKXvst0VMmewXeOO9ZF] http://www.youtube.com/user/wcasavpcc
From: Micah Henning<EMAIL_ADDRESS>Sent: Tuesday, June 13, 2017 9:56 PM
To: enove/Thriver<EMAIL_ADDRESS>Cc: Peter Fiala<EMAIL_ADDRESS>Author<EMAIL_ADDRESS>Subject: Re: [enove/Thriver] InfoSheets & Webinars - Issue Year (#273)
You should switch to using proper dates. For those of which you're unsure,
perhaps just pick a generic date like January 1?
On Tue, Jun 13, 2017 at 16:56 peterfiala <notifications<EMAIL_ADDRESS>wrote:

With webinars, when they are archived they are also included just under
the year
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Fix errant keys in Redis scripts

The metric labels and command types were inappropriately specified as
KEYS in the Redis scripts. This meant there was no way to avoid a
CROSSSLOT Keys in request don't hash to the same slot error when using
a Redis cluster that hashes keys to select a specific node.

Resolves: #110


Status on Cohort Definition JSON Schema?

Hi @pmadril ,
I was wondering, what is the status of the JSON Schema for Cohort Definitions within OHDSI? Is this draft you show here accurate or is there more work being done elsewhere? Wondering if the JSON Schema has been standardized yet.
Thanks!
jz

Hi, Jacob
Thank you for your interest in the JSON Schema for Cohort Definitions
https://github.com/OHDSIBr/ATLAS-JSON-Schema.
This is an initiative developed by myself and my wife Tereza, with the hope
to be useful for anyone that wants to create tools, other than Atlas, for
Cohort definitions.
It was complete at the time it was developed and I didn't see changes in
the Atlas cohort definition interface, but maybe I'm wrong.
It is described using JSON Schema draft-04, a lower common denominator in
JSON Schema Standards, because it also has the most tools supporting it
(validators, webui generators, etc).
I also made contributions to https://github.com/json-editor/json-editor,
which I use to test the Schema.
Actually, you can copy an Atlas cohort definition and paste in the JSON
Editor, to get a form where you can change values, and then go back to
Atlas.
Anyway, that's not my intended use, Atlas already does a good job as UI,
but I needed a way to test the schema.
My intended use is to be able to have validators which can check a cohort
definition received in an API against the Schema before processing it.
This will enable tools that process cohort definitions.
I'm not aware of initiatives in OHDSI to standardize a cohort definition.
If there is interest in doing it, I hope this schema helps to start the
process.
Thanks a lot for your interest!
Pablo Madril
On Sat, Mar 4, 2023 at 9:45 PM Jacob S. Zelko @.***>
wrote:

Hi @pmadril https://github.com/pmadril ,
I was wondering, what is the status of the JSON Schema for Cohort
Definitions within OHDSI? Is this draft you show here accurate or is there
more work being done elsewhere? Wondering if the JSON Schema has been
standardized yet.
Thanks!
jz
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You are receiving this because you were mentioned.Message ID:
@.***>

Hey @pmadril ,

This is an initiative developed by myself and my wife Tereza, with the hope to be useful for anyone that wants to create tools, other than Atlas, for Cohort definitions. It was complete at the time it was developed and I didn't see changes in the Atlas cohort definition interface, but maybe I'm wrong.

This is a fantastic resource! I fully agree and was looking around for a specification just for that person -- to develop other tools beyond just OHDSI. Was hoping to create a parser that could understand the Cohort Definition JSON Schema for another project I am developing. I'll definitely use your reference here as a guide in my efforts.

I'm not aware of initiatives in OHDSI to standardize a cohort definition. If there is interest in doing it, I hope this schema helps to start the process.

Ah that is unfortunate! I think this is a very good idea and hope it could be adopted within the OHDSI community.
Either way, thanks for sharing on this work and idea! Feel free to close this issue as I was wondering what was the status of this Schema in general (if it had been standardized, where it was being worked on, etc.).
~ tcp :deciduous_tree:

Very glad to know it's been useful to you.
Use any JSON Schema parser with this schema and you will get  a full in memory representation to work on.
JSON Schema already has available a parser for most modern languages, refer to Implementations and I'm sure you will find your favourite language there.
The single file version is for you, pure JSON Schema without editor enhancements  in a single file (no need of ajax).
I will close this issue after your reply, but feel free to contact me for help.
I'm very interested in your use of the schema, indeed, you are the first real user of it.
Let me know about your progress, problems and deficiencies that you find.
Best regards, Pablo

Hi, Jacob
Obviously, as soon as I wrote and post my reply, I discovered that there are no JSON Schema implementations for Julia, which seems to be your favourite language.
My shame, I apologise  for that. I knew Julia just by reference but never went deeper about it. Now, thanks to you, I knew a bit more about Julia and I got interest to learn more about it.
Julia stands to have native call to C functions and may be the WJElement is useful to make some tests. It has some support for draft 4. For C++ there are a lot of options.
As far as I know, any draft-7 support library is already backward compatible with draft-4 but I didn't test it.
I'm thinking about to make a draft-7 version of the schema, which seems to be the new lowest common denominator.
Let me know if I can help you, Pablo.

Hi,
I found this:
A Julia Schema validator with support for draft-4:
JSONSchema
Please, I don't know Julia language, so this validator need to be tested with the cohort schema.
Pablo


[Snyk] Security upgrade follow-redirects from 1.15.2 to 1.15.4

This PR was automatically created by Snyk using the credentials of a real user.Snyk has created this PR to fix one or more vulnerable packages in the `yarn` dependencies of this project.
Changes included in this PR

Changes to the following files to upgrade the vulnerable dependencies to a fixed version:

package.json
yarn.lock

Note for zero-installs users
If you are using the Yarn feature zero-installs that was introduced in Yarn V2, note that this PR does not update the .yarn/cache/ directory meaning this code cannot be pulled and immediately developed on as one would expect for a zero-install project - you will need to run yarn to update the contents of the ./yarn/cache directory.
If you are not using zero-install you can ignore this as your flow should likely be unchanged.
Vulnerabilities that will be fixed
With an upgrade:

Severity
Priority Score (*)
Issue
Breaking Change
Exploit Maturity

686/1000  Why? Proof of Concept exploit, Has a fix available, CVSS 7.3
Improper Input Validation SNYK-JS-FOLLOWREDIRECTS-6141137
No
Proof of Concept

(*) Note that the real score may have changed since the PR was raised.
Check the changes in this PR to ensure they won't cause issues with your project.

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs.
For more information:
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Learn how to fix vulnerabilities with free interactive lessons:
🦉 Improper Input Validation

👷 Deploy Preview for effortless-cendol-07821c processing.

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Link

🔨 Latest commit
b747d20ccd619cb2052136aae43fb6dd5d5e00f8

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Query with SQL command always assumes querying for JSON

This block of code works:
var result = session.QueryAsync<long>(
    "SELECT SUM(data->'SomeCount')) FROM mt_doc_item WHERE id = ? GROUP BY id",
    CancellationToken.None,
    "key-value").GetAwaiter().GetResult();

Where this one does not:
var result = session.Query<long>(
    "SELECT SUM(data->'SomeCount')) FROM mt_doc_item WHERE id = ? GROUP BY id",
    "key-value");

It throws and InvalidCastException with the following stack trace:
GetTextReader() not supported for type int8
at Npgsql.NpgsqlDataReader.GetTextReader(Int32 ordinal)
at Marten.Linq.DeserializeSelector`1.Resolve(DbDataReader reader, IIdentityMap map, QueryStatistics stats)
at Marten.Linq.SelectorExtensions.Read[T](ISelector`1 selector, DbDataReader reader, IIdentityMap map, QueryStatistics stats)
at Marten.Linq.QueryHandlers.UserSuppliedQueryHandler`1.Handle(DbDataReader reader, IIdentityMap map, QueryStatistics stats)   at Marten.Services.CommandRunnerExtensions.<>c__DisplayClass2_0`1.<Fetch>b__0(NpgsqlCommand c)
at Marten.Services.ManagedConnection.Execute[T](NpgsqlCommand cmd, Func`2 func)
at Marten.Services.CommandRunnerExtensions.Fetch[T](IManagedConnection runner, IQueryHandler`1 handler, IIdentityMap map, QueryStatistics stats, ITenant tenant)
at Marten.QuerySession.Query[T](String sql, Object[] parameters)
at <snip>

It looks like the difference in the implementation of Resolve and ResolveAsync in DeserializeSelector.cs causes the error. I think duplicating the check for typeof(T).IsSimple() between the two methods will fix this.

@jeffesp yes, your observation is right,  using the logic as in the async method will solve this issue. Essentially we have to add a failing test and then apply a fix for the same.

Do you prefer that to be in a specific bug test, or in with the other tests for DeserializeSelector?

I vote for a separate, bug specific test for now. Those things usually end up being kind of involved and it's often cleaner to see it in isolation

Thanks. I will see if I can get to this in the next couple days.

Fixed by https://github.com/JasperFx/marten/pull/913. Thanks @jeffesp !


Nested route generation

Generating a route using:
   ng g route admin/group

results in a doubling of file path names:
    src/client/app/admin/group/admin/group.service.ts

instead of:
   src/client/app/admin/group/group.service.ts

happens on:
angular-cli: 0.0.30
node: 4.1.2
os: darwin x64

@amindunited we are in the process of refactoring the route generations and that work can be tracked under issue #316.
Closing this issue in favor of the mentioned issue.


Typing error

Issue " " character between the word "tuned" and "!" character
File path /www_mapod4d_it/index.html
Row 144

Issue has been resolved in local closed i #25


multi-package go unit tests failing because previous test server not shutdown

I am attempting to use the in-memory database for go unit testing a sdk that contains multiple packages (each package connects to a different database & or api). I'm running into an issue where the first package runs great, but all packages after have issues with the previous test's go-mysql-server still running. (using go test ./... from module root)
A new server is being created for each package because my understanding is that TestMain exits and cannot init resources for sub or other packages
Each package has a TestMain to setup the server and the db connection it will be using. I cannot find a way to know that the server has actually successfully shut down so the Next package unit test can successfully create a new server on the same port & free up memory before the next test. (2nd test errors; panic: Port localhost:3306 already in use)
...
var wg sync.WaitGroup()
func TestMain(m *testing.M) {
	config := server.Config{
		Protocol: "tcp",
		Address:  fmt.Sprintf("%s:%d", address, port),
	}
	s, err := server.NewDefaultServer(config, engine)
	wg.Add(1)
	go StartServer(s)`

	tdb, err := sql.Open("mysql".......
	// then ping here until server is up and running
	code := m.Run()
	tdb.Close()
	s.Close()
	wg.Wait()
	os.Exit(code)
}

func StartServer(s *server.Server) {
	if err := s.Start(); err != nil {
		panic(err)
	}
	wg.Done()
}

If there were to a way to ask or wait to know that the server has fully shutdown before exiting the test, this would be a lot easier to accomplish..
Is this the wrong approach? Do anyone have any suggestions? (making a single TestMain and not using sub packages isn't an option, there are dozens of packages out of my control & only some of them use go-msyql-server).


Change dependencies to devDependencies

Change dependencies to devDependencies

This is intentional. There are many similar closed issues and PRs. Please see those to understand why.


⚠ ClamAV has degraded performance

In cded7d4, ClamAV (https://spamassassin.apache.org/) experienced degraded performance:

HTTP code: 200
Response time: 95 ms

Resolved: ClamAV performance has improved in 7c8e09d after 5 minutes.


[2.0.x] ResultSet#getInt returns 0 on a long

I'm not sure, but I think this violates the spec: http://download.oracle.com/otn-pub/jcp/jdbc-4_1-mrel-spec/jdbc4.1-fr-spec.pdf?AuthParam=1450886516_9f782c0a6b934f329a1d48bed1d51d87.
I think ResultSet#getInt on long should return a value at least when there is no overflow and maybe fail otherwise. WDYT?

Yes, you're right, it should use ((Number)value).intValue() I think.
wanna senda  PR ?

Yep, will do tomorrow :)


[BUG] DP02_13a_Image_Cutout_SciDemo.ipynb does not work on USDF RSP

Describe the bug
Attempting to run the DP02_13a_Image_Cutout_SciDemo.ipynb on USDF RSP at usdf-rsp.slac.stanford.edu results in an unhelpful crash resulting from a 404 of the backend service.
This does not happen on the data.lsst.cloud instance, which leads me to believe it is somehow a USDF issue.
To Reproduce
Steps to reproduce the behavior:

Start a Jupyter notebook on the USDF RSP.
Upload the linked notebook

Run the cells individually to see the error in section marked "Error occurs here"
Run subsequent cells to see that this is a USDF RSP issue where there is not a repository for the butler URL of sample data.
Note that the error does not occur when this sequence of steps is repeated on the cloud RSP at (data.lsst.cloud)
Note that similar behavior can be achieved on both RSPs with the DP02_13a_Image_Cutout_SciDemo.ipynb  notebook during execution of section 2.2.

Expected behavior
I would expect requests for DP0.2 data in tutorial notebooks to be available on the USDF RSP.
I would separately want the libraries involved to accurately report error conditions. See pvo issue 625 for the issue of accurate reporting of errors.
Desktop (please complete the following information):

OS: OSX
Browser Firefox
Version 132.0

Additional context
Add any other context about the problem here.

Hi @mtauraso, thanks for this and apologies for the delayed response. DP0.2 is not supported at the USDF, but is available via the RSP at data.lsst.cloud. The tutorial notebooks will run just fine there.
For the process to get an account at data.lsst.cloud:
https://rsp.lsst.io/guides/getting-started/get-an-account.html

I think that solves the issue so I'm going to close it but please don't hesitate to reach out again.

Got it, thanks


Add semantic highlighting for XPath expressions

Closes #123
This is a draft PR because the other suggestion of including the DeltaXML as an extension dependency and importing its code as needed has not been fully investigated yet. This seems like it should be doable.
The Rat checks are going to fail because there was some discussion on how these files should be licensed, but, as far as I can remember, no final solution had been decided on. Ideally, if we use the dependency solution, this becomes moot because we won't need to provide a license for these files.
I removed what I could from the original set of files so that we're only including code related to XPath (and not XSLT). This is mostly meant as a first pass over the code to remove what is obviously not being used by XPath.

I think this is the comment that referenced including DeltaXML as a dependency rather than including the code.
https://github.com/apache/daffodil-vscode/pull/117#discussion_r886867014
I thought there was a more concrete suggestion than that, but I can't find it.

I don't think that using the DeltaXML extension is going to be possible. From what I understand, for that to happen, our extension would need to be able to reference the API returned from the DeltaXML extension's activate function. However, it has no return value, so there will be no API.
I will make another pass through the code in this PR to see if anything else can be removed, but a lot of it will come down to the differences between XPath and XSLT, which I am not too familiar with.

@stevedlawrence @mbeckerle
We've got some questions on the licensing that we hope you can help clear up. The DeltaXML extension, which is where most of the code comes from, uses MIT licensing, which requires us to use the MIT license in all copied files. However, we have a couple of scenarios:

We've copied the file from DeltaXML, but we have removed portions of the code as the extension will never use it. Is the MIT license appropriate here?

We've made a small modification to the copied DeltaXML file. I think out of the two modifications, one was reverting where I took too much code out, and the other was adding in new code. Do we need to combine the MIT and Apache licenses somehow?

We have a file that has both significant portions of copied sections of a DeltaXML file and sections written by us. Is a combined license appropriate here?

If we do need a combined license, what would that look like?
@NolanMatt Is this an accurate characterization of the changes you've made, and/or am I missing anything?

@stevedlawrence @mbeckerle
We've got some questions on the licensing that we hope you can help clear up. The DeltaXML extension, which is where most of the code comes from, uses MIT licensing, which requires us to use the MIT license in all copied files. However, we have a couple of scenarios:

We've copied the file from DeltaXML, but we have removed portions of the code as the extension will never use it. Is the MIT license appropriate here?
We've made a small modification to the copied DeltaXML file. I think out of the two modifications, one was reverting where I took too much code out, and the other was adding in new code. Do we need to combine the MIT and Apache licenses somehow?
We have a file that has both significant portions of copied sections of a DeltaXML file and sections written by us. Is a combined license appropriate here?

If we do need a combined license, what would that look like?
@NolanMatt Is this an accurate characterization of the changes you've made, and/or am I missing anything?

This is spot on, not missing anything.

The MIT license does allow modifications to be licensed under different terms, you really just need to include the copyright header and MIT license. So you could in theory license your changes using ALv2. However, it adds a extra complexity, since you need to make it clear which parts are MIT and which are ALv2. And it doesn't really gain much having some parts be ALv2. It's recommended, and fine with the ASF, to license minor modifications under the original license.
In fact, this page has some information about this exact thing in "Treatment of Third-Party Works": https://www.apache.org/legal/src-headers.html, and says exactly that in bullet 4:

Minor modifications/additions to third-party source files should typically be licensed under the same terms as the rest of the third-party source for convenience.

If the changes are "major" then we probably need to have a discussion to determine if mixing licenses is appropriate, and "major" vs "minor" is pretty subjective, but based on your description it sounds like they are pretty clearly minor changes.
So I'd just keep everything under the same MIT license terms.

Thanks, that sounds like it covers us for almost everything. We do have one file that has what I would consider to be major changes - I'd estimate it on the order of 50/50 with code that we pulled from the extension versus code we wrote ourselves, and, if it changes anything, there's probably more code in the original file that we didn't use than code we did use.
Their file: https://github.com/DeltaXML/vscode-xslt-tokenizer/blob/master/src/extension.ts
Our file: https://github.com/michael-hoke/daffodil-vscode-fork/blob/daffodil-vscode-semantic-highlighting/src/language/semantics/dfdlExt.ts
That is also assuming that removing significant portions of code isn't going to be considered a major change.

@michael-hoke, can we close this in place of #705?

Yes - closing in favor of #705


Add changelog overwrite capability

When you work a lot with branch, sometime merge don't merge well changelog file, so it's preferable to rewrite it than use it to start .
Created an option to delete changelog before create new one.

@BobCashStory are you using GitFlow? When are you bumping the version, only on main and syncing back to develop or on both branches? (just out of curiosity since I'm working on a release workflow and want to avoid this issue)

Is this still needed? I'm closing it for now, I think users can add a step to remove the CHANGELOG.md before running this action


Define BaseTemporalAlignmentInterface

fix #439 by making it a pure feature; a new interface with the new methods that existing interfaces now use exclusively, but maintains back-compatibility of previously created custom data interfaces

Dang, GitHub actions having trouble all day long now. First time I've seen that...

Something that I don't see is the warning that @bendichter mentioned on the issue.

Changelog is already somewhat large for a minimal change, I was thinking of adding and testing the warning in a follow-up

@h-mayorquin OK this seems ready now


Output 'NA' as subtype when no subtype found

Hi @peterk87, could you let me know if the changes I made are acceptable to fix the problem highlighted by @dankein in  issue#112?

The development branch version of biohansel already outputs #N/A for null subtype results (added in PR #81)
See:
https://github.com/phac-nml/biohansel/blob/development/bio_hansel/main.py#L248

Yes you're right @peterk87 , I had not checked it before making the modifications.  Will cancel this pull request.


Lookahead decoding

They claim lookahead decoding provides a 1.5~2x decoding speedup without a speculative model.
Blog post: https://lmsys.org/blog/2023-11-21-lookahead-decoding/
Twitter thread: https://twitter.com/lmsysorg/status/1727056892671950887
Reference implementation: https://github.com/hao-ai-lab/LookaheadDecoding/tree/main
Not sure if this would be possible to integrate into vllm?

Hi @WoosukKwon @zhuohan123 2x decoding speedup. Is this possible to integrate into vllm?
Tested it with llama 7B:
autoregressive:
Generated Tokens: 256 Generation Speed:  22.751232013756066  tokens/s
lookahead decoding:
Generated Tokens: 256 Generation Speed:  58.286426484772186  tokens/s

Does lookahead decoding only support greedy decoding?

Seems like it.

It could probably also work for beam search decoding, but not sampling.

What is this compared to speculative decoding?

Will lookahead decoding generate the same results compared with autoregressive decoding?

How is this compared to speculative decoding?

This doesn't require a smaller approximation model, also known as a "draft model" in the blog. This work aims to address the limitations of using one, namely that 1. the maximum speedup is limited by the token acceptance rate and 2. creating a good draft model is non-trivial.

Will lookahead decoding generate the same results compared with autoregressive decoding?

Yes, it produces the exact same results that would be created by greedy decoding. This work can be easily extended to work with beam search decoding, but not with sampling (at least not in a trivial way).

It could probably also work for beam search decoding, but not sampling.

We're working on a feature to support top-p or top-k sampling. It is doable.

How is this compared to speculative decoding?

thank @shermansiu for your nice answer, my additional points:

lookahead decoding has no theoretical upper bound on achievable speedup. As long as you're willing to pay flops, you can get unlimited speedup.
No draft model or data store is needed. Draft models or any auxiliary components can be hard to obtain and difficult to deploy.

The article does mention the limitation on throughput.

Given this property, lookahead decoding should be used in scenarios where latency is vital, e.g., surplus FLOPs exist that can be traded for latency, or it is even worthwhile to pay extra FLOPs for latency.

Does this mean there will be slowdowns when there are more than one concurrent requests in the batch, especially in non A100 machine used for serving? @zhisbug curious to hear if there's any evaluation done in high throughput front and learn more about the FLOPs and memory penalties of this approach. 🙏

The article does mention the limitation on throughput.

Given this property, lookahead decoding should be used in scenarios where latency is vital, e.g., surplus FLOPs exist that can be traded for latency, or it is even worthwhile to pay extra FLOPs for latency.

Does this mean there will be slowdowns when there are more than one concurrent requests in the batch, especially in non A100 machine used for serving? @zhisbug curious to hear if there's any evaluation done in high throughput front and learn more about the FLOPs and memory penalties of this approach. 🙏

eventually it is a scheduling problem about how you plan to allocate your flops -- for throughput or latency

Will lookahead decoding generate the same results compared with autoregressive decoding?

Yes, it produces the exact same results that would be created by greedy decoding. This work can be easily extended to work with beam search decoding, but not with sampling (at least not in a trivial way).

But when lookahead decoding selects some n-gram from the pool, will the tokens in the chosen n-gram be different from what greedy decoding will not generate? (because I think the n-gram may not start from the current position when it is generated)

But when lookahead decoding selects some n-gram from the pool, will the tokens in the chosen n-gram be different from what greedy decoding will generate? (because I think the n-gram may not start from the current position when it is generated)

The verification step checks whether they are they same and only adds it to the output if they are.

Also, it seems like for smaller GPUs, you don't get as big of a performance decrease and if the parameters aren't ideal, you actually get a performance decrease.
See the attached GitHub comment for details: https://github.com/huggingface/transformers/issues/27649#issuecomment-1824621466

We're working on a feature to support top-p or top-k sampling. It is doable.

Also, for sampling decoding... I suppose you can approximate the conditional next token distribution, but then you'd be sampling from a "close enough"[^1] distribution guesstimated ahead of time, as opposed to from the true conditional distribution.
[^1]: The KL-divergence between the two distributions is below a certain configurable threshold

Also, note that discussions for using lookahead decoding with sampling are here: https://github.com/hao-ai-lab/LookaheadDecoding/pull/6
Also, there is indeed a way to validate that the generation from a "close enough" distribution could have been a valid generation from the true distribution.

In their blog also says

The 7B, 13B, and 33B models require 120x, 80x, and 56x extra FLOPs per step

And I aslo test this decoding method,  in auto regression model input_ids' shape is (1, 1)  , and LookAheadDecoding input_ids ' shape (1, 103) in llama 13b model.
so It's low lantency but the cost aslo is significant.

lookahead decoding supports flash attention and sampling both now.
https://github.com/hao-ai-lab/LookaheadDecoding

m


HOW - Dynamically add values to String Match Map

How to dynamically add new entries to stringmatchmap during runtime?
PS: Re-initializing the controller with new map throws controller has already been initialized error.

Currently there's no implementation for such thing, but will add this to my to-dos, adding a dynamic controller can be a nice enhancement. Thank you!

Closed and updated in version 2.0.0
Sorry, I haven't been active lately.
Thank you for your support!


Move all existing translation data from Crowdin v1 to v2

Our Crowdin v1 project: https://crowdin.com/project/casbin
v2 project: https://crowdin.com/project/casbin-website

done.


[Python API] RuntimeError: Unknown parameter type <class 'uuid.UUID'> (Prepared statements)

Thanks a lot for implementing native UUID types! It seems, Python API client does not support UUID in prepared statements yet?
CREATE NODE TABLE V (id UUID, PRIMARY KEY(id));

import uuid
conn.execute("CREATE (:V {id: $1});", {'1': uuid.uuid4()})

Traceback (most recent call last):
File "proj/kuzu_api.py", line 38, in execute
results = conn.execute(query, parameters)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "proj/venv/lib64/python3.11/site-packages/kuzu/connection.py", line 82, in execute
_query_result = self._connection.execute(
^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: Unknown parameter type <class 'uuid.UUID'>

Hi @sapalli2989,
thanks for reporting. I'll take a look at this issue.
Meanwhile there is a workaround to pass uuid as a string. So something along the line of
conn.execute("CREATE (:V {id: cast($1, "UUID")});", {'1': str(uuid.uuid4())})

@sapalli2989 FYI, this should be fixed with PR #2926

@andyfengHKU Confirmed it works. Thanks!


Is it possible to have a separate webpack config for tests?

We have a separate alias that is only used for tests and it would be nice to have this supported in eslint-plugin-import.

You can re-specify import/resolver in an .eslintrc for your test folder.
I do this for one of my projects, where I use the webpack resolver for ./src and the stock node resolver for ./test.
I think this covers what you're asking?

It seems like it should but I'm still having some issues. Might be related
to how the base weback configuration interacts with the test config.
Definitely possible that it's user error.
On Tue, Mar 22, 2016, 11:02 AM Ben Mosher<EMAIL_ADDRESS>wrote:

You can re-specify import/resolver in an .eslintrc for your test folder.
I do this for one of my projects, where I use the webpack resolver for
./src and the stock node resolver for ./test.
I think this covers what you're asking?
—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub
https://github.com/benmosher/eslint-plugin-import/issues/223#issuecomment-200024295

Can you provide more details about the folder structure and the contents of the config files?

closing for now, let me know if you want to discuss further


NMS.GEN.SECU.004 - Don't log personal information

The NMS system shall not log any personal information that can identify a user.
There may not be an automated way to detect or prevent this.  Instead disk encryption for the log files may be used and the log files will be purged on a regular pre-defined schedule (e.g. using logrotated).

Putting in sprint 3 for us to review and ensure we haven't logged any personal info.

Does this only apply to log files, or should it also include "error log" tables that we might create for requirements like #117  and #107?

I think just files.  The database will have PII in it already so adding
more in a logging table isn't an issue.
On Wed, May 20, 2015 at 1:57 PM, Lauren Lavoie<EMAIL_ADDRESS>wrote:

Does this only apply to log files, or should it also include "error log"
tables that we might create for requirements like #117
https://github.com/motech-implementations/mim/issues/117 and #107
https://github.com/motech-implementations/mim/issues/107?
—
Reply to this email directly or view it on GitHub
https://github.com/motech-implementations/mim/issues/129#issuecomment-104035330
.


Declarative Migrations with Just a Schema File (no migrations table and directory)

One question; Do I really need that "migration" table and "migrations" directory? Is there a way to turn that off? As my CI simply has a sql-file with the latest schema and the CI always compares the "production" database with the schema and changes it, what exactly would I need the migration table for? I take a backup of the database before, so I don't really need any revert functionality. I am not checking in any versions or rollback features in git. I simply want it to compare the .sql-file with the database-file and create a "migration-file" in RAM and then execute it without leaving any traces.
Originally posted by @buzzy in https://github.com/SanderGi/sqlite-auto-migrator/issues/1#issuecomment-2372377631

TL;DR: the migration files remove ambiguity. We can add a feature that allows leaving no trace by limiting the schema changes to creates+deletes (no renames). We just have to decide how to expose it in the API
Excellent question. The migration files in the directory and table are not just for reverting or automatically migrating the database when checking out a new branch/commit in git (in fact, this could be achieved without migration files by just diffing the schema and database as you suggest). They are mainly there to clarify ambiguity between equivalent schemas that represent different data migration changes. For instance, deleting a column and creating a new column would result in the exact same schema as instead renaming the old column to the new name. However the latter would move over all the data whereas the former would fill in new NULL/default data and lose the old data. Storing migration files allows sqlite-auto-migrator to prompt the user for which data change they intend with the schema change (e.g., a rename or a delete+create) and then save that decision for applying to the remote production database or another developers local database, etc. If the decision was not stored, it would be possible for the different instances of the database under the same schema to handle the schema changes differently which could lead to unintended side effects in production that do not appear locally. After all, production is likely to receive many schema changes at once bundled into one big schema change that thus contains more ambiguity than the incremental changes made locally). The reason there is both a table and directory is to track ambiguity in which migration files have been applied. After all, it is possible to have the same schema come about through different data changes so two migration states could have equivalent schemas but represent different manipulations to the data.
That said, it is also possible to resolve the ambiguities declaratively without storing migration state by limiting the operations that can be performed during a migration. If, for instance, you are okay only allowing creates/deletes and manually handling renames (e.g. by ssh-ing into your production database to execute sql commands or by re-enabling migration state), I could add that feature to the library. I propose to do this by adding a boolean trackUnambiguousMigrationState flag to the migrator class config that defaults to true but you can set to false. Then the library would not create any migration table/directory/files unless you prompt it that your change was a rename. It would instead handle any deletes/creates by diffing the schema and database declaratively in RAM. The downside is that it would have to assume any changes not documented in migration files are deletes/creates that have deliberately not been tracked so it would not be able to warn about changes you have made directly to the database and not captured in the schema (it would instead just undo these changes to match the schema). Happy to hear what your thoughts are on exposing it this way in the API and if you have better ideas

That actually sounds exactly what I want! I totally understand (and agree) to the logic behind the migration history for larger teams and projects. But in small teams as mine, I try to never make destructive changes as old backend endpoints still needs to function. There are many different versions of the client running at customers that all uses different versions of the backend endpoints. So in my case, I will only let the migration do non-destructive things like adding fields, indexes etc. I have set all destructive things to MANUAL_MIGRATION so that the CI stops and forces me to do those upgrades manually (which happens rarely). Thus, having a flag that you mention would be perfect for me.
Until now, I have done all database changes manually anyways, so I was thinking of creating this "diff and update" thing myself, but then I found your library :)

I have pushed a version of declarative diffing to main (still have to write tests+documentation and get your input before publishing to npm).
You can try it out with bun install github:SanderGi/sqlite-auto-migrator and changing your code to something like the following:
import { Migrator } from "sqlite-auto-migrator";
import { config } from "../config/config";

// @ts-ignore
import sessions from "../databases/sessions.sql";
// @ts-ignore
import main from "../databases/main.sql";

export async function updateDatabase() {
  // Exit early if --update-database flag is not present
  if (Bun.argv.indexOf("--update-database") === -1) return;

  try {
    // Session database
    const migrator = new Migrator({
       dbPath: config.auth.database,
       schemaPath: sessions,
       createDBIfMissing: true,
       onlyTrackAmbiguousState: true,
    });
    await migrator.migrate('latest', {
      onRename: Migrator.REQUIRE_MANUAL_MIGRATION,
      onDestructiveChange: Migrator.REQUIRE_MANUAL_MIGRATION,
      onChangedView: Migrator.REQUIRE_MANUAL_MIGRATION,
      onChangedIndex: Migrator.PROCEED,
      onChangedTrigger: Migrator.PROCEED,
    });

    // Main database
    const migrator2 = new Migrator({
       dbPath: config.database,
       schemaPath: main,
       createDBIfMissing: true,
       onlyTrackAmbiguousState: true,
    });
    await migrator2.migrate('latest', {
      onRename: Migrator.REQUIRE_MANUAL_MIGRATION,
      onDestructiveChange: Migrator.REQUIRE_MANUAL_MIGRATION,
      onChangedView: Migrator.REQUIRE_MANUAL_MIGRATION,
      onChangedIndex: Migrator.PROCEED,
      onChangedTrigger: Migrator.PROCEED,
    });
  } catch (e) {
    console.error(e);
    process.exit(1);
  }

  console.log("Databases updated successfully!");

  process.exit(0);
}

I renamed the flag to onlyTrackAmbiguousState to avoid negation in the variable name and have the default be false. I also added the option to specify how migrate should handle the untracked changes (onDestructiveChange, onChangedView, etc.). For your use case, you will no longer need the make call since you will manually handle renames. You can add it at any point in the future if you need to make a rename and want to start tracking the associated ambiguous state. Let me know what your thoughts are and if you run into any bugs with this early version of declarative diffing

I'm afraid I still get deadlocks:

Happy to hear the flag is working for your use case. I'll ping you when I've published this functionality to npm. For me, it seems the deadlocks go away when replacing node-sqlite3 with bun:sqlite (#2)

Version 1.2.0 has been published to NPM and includes the declarative migrations


Create a pip installable package out of Pelops

All code is moved into ./pelops/ and a setup.py is added to make it installable.

Hold off on merging, I just wanted to get the PR in so CircleCI can have a look and it's easier to get feedback.

Current coverage is 75.89% (diff: 100%)

Merging #20 into master will decrease coverage by 0.21%

@@             master        #20   diff @@
==========================================
  Files             2          2
  Lines           113        112     -1
  Methods           0          0
  Messages          0          0
  Branches          9          9
==========================================
- Hits             86         85     -1
  Misses           27         27
  Partials          0          0

Powered by Codecov. Last update 295e5b1...575f9b1

Should be good-to-go. Please give it a look over!


add the yarn error log to gitignore

Does what it says on the tin...

Personally I have it on my global ignore list


Laravel 5.4 support

In the current version, you still have a reference to app->share in your service provider.
I see that the development version is using the app->singleton method. Could you release an update to get compatibility with L5.4?

@vpratfr update your composer dependency to dev-master and you should be fine.
https://github.com/letrunghieu/active/blob/master/src/ActiveServiceProvider.php#L43-L54
its been updated to use $app->singleton

I updated the version number to 3.4.0


Describe character

Players can now use describe [description] to change their character's description. Using desc by itself will show the current description.

Still working on this since it seems the description does not save if the server is reset.

I fixed the issue by having the description be part of the player's attributes.

I'm not sure how this description works because I haven't tried it yet, but does it include wearables? For example, if I'm wearing a "black leather cloak", then that should be appended to the description. Does it do this?

@Xarcell It does not. This is the written description. I think the look command would have to be improved further to show the character's name, description, and their wearables, rather than appending it to this description, which is essentially flavor text.

@shawncplus This one will cause a merge conflict with one of the previous PRs in player.js
Just keep the line 	self.getDescription  = function () { return self.attributes.description; };
and it should work like gravy.


IDE requires optional resource property (warning is shown)

Prerequisites

[x] Ensure you have latest version of plugin installed
[x] Search for possible issue duplicates

Installation details

[x] IDE version PhpStorm 2020.1 Build #PS-201.6668.153, built on April 13, 2020
[x] intellij-hcl plugin version 0.7.10
[x] Terraform version: 1.0.6.

Terraform Configuration Files
resource "aws_iam_role" "lambda_iam" {
  name               = "lambda_iam"
  assume_role_policy = file("./policies/lambda_iam.json")
}

resource "aws_lambda_function" "this" {
  function_name = "<name>"
  package_type  = "Image"
  image_uri     = "<id>.dkr.ecr.eu-central-1.amazonaws.com/<repo-name>:latest"
  role          = aws_iam_role.lambda_iam.arn
}

Exception
/
Expected Behavior

handler and runtime aren't mandatory if the package_type is "Image".
The warning shouldn't be shown.

Actual Behavior

Plugin detected missing properties (handler, runtime) even with present package_type="Image"
https://registry.terraform.io/providers/hashicorp/aws/latest/docs/resources/lambda_function#package_type

Steps to Reproduce

Please update the plugin to 0.7.13

New plugin versions support:
0.7.11 — IDE 2020.3 and newer;
0.7.12+ — IDE 2021.1 and newer;
0.7.10 is outdated.

Yet you can try newest metadata, see readme at https://github.com/vladrassokhin/terraform-metadata


Inlining css styles from fornac.css and rnaplot.css into javascript (issue #5)

Peter,
So, I've inlined fornac.css completely and am looking to inline rnaplot.css.
I have 2 questions so far.
First, was it right for me to apply css in FornaContainer.update()? It seems to work, but not sure, if it's a perfect solution: https://github.com/BurkovBA/fornac/blob/master/app/scripts/fornac.js#L1692
Second, I can't get the build system work to deliver changes to dist/ - it chokes on uglification. When I say gulp build, it fails with the following error:
[17:10:01] gulp-debug: app/index.html

events.js:160
      throw er; // Unhandled 'error' event
      ^
Error
    at new JS_Parse_Error (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:1534:18)
    at js_error (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:1542:11)
    at croak (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2089:9)
    at token_error (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2097:9)
    at unexpected (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2103:9)
    at expr_atom (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2630:9)
    at maybe_unary (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2792:19)
    at expr_ops (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2827:24)
    at maybe_conditional (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2832:20)
    at maybe_assign (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2856:20)
    at expression (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2875:20)
    at simple_statement (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2314:55)
    at eval (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2178:20)
    at eval (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2136:24)
    at eval (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2904:23)
    at Object.parse (eval at <anonymous> (/Users/burkov/Documents/Projects/ebi/fornac/node_modules/uglify-js/tools/node.js:28:1), <anonymous>:2915:7)

I have gulp-cli and bower installed globally and said npm install and bower install.
Thanks!

One potential issue with applying styles in javascript is that if the RNA structure changes (e.g. somebody adds a link), the styles won't be applied to the newly created elements.  If you make the container editable, you should be able to add links by "shift" clicking nodes and dragging to other nodes. Can you make sure that the styles are applied to the new links?
As for the uglify error, it appears to be an old error that there may or may not be a solution to:
https://github.com/mishoo/UglifyJS2/issues/348
Unfortunately, I don't think I can offer any help beyond what is in that thread.

Peter,
as for Uglify error - it was choking on javascript in html files. I'm not sure, what was wrong with it, so I just removed html goal from gulp build task. Instead, I made it process all the javascript files in .tmp folder and output them to dist. Downside is that index.html is not bundled into dist.
Could you explain, how to make a container editable? I can't see such a configuration object in FornaContainer. Thanks!

@pkerpedjiev
Came up with a better solution than this. Instead of dynamically adding styles to element, I'd better dynamically add <link rel="stylesheet"> with your css, preceded by element selector. This shouldn't be breaking anything.

@pkerpedjiev
Ok, instead of applying styles to elements directly, I started to dynamically create <link> element on <head> that applies those styles.
Don't think that change could break anything (well, maybe formatting only). So ready for merge and release.


vhdl code snippets of case statements have inconsistent syntax highlighting

Hello!
We love your bot in the MiSTer FPGA discord. I have noticed a possible issue recently. Case statements in vhdl do not apparently get syntax highlighting
https://github.com/MiSTer-devel/GBA_MiSTer/blob/master/rtl/gba_sound.vhd#L422-L425
https://github.com/MiSTer-devel/GBA_MiSTer/blob/master/rtl/gba_sound_ch1.vhd#L265-L271
It looks like the vhdl markdown tag doesn't get applied for some reason. I made sure to test that it wasn't the linter/parser (which I assumed might be shared between this project and discord).

Thank you!

Lovely to know you like the bot!
As for the issue, what's happening is that what is passed to discord as the language for formatting is just the file extension (so vhd instead of vhdl in your case), which so far had always worked for all languages I'd tested (e.g. py for Python or cpp for C++) - but apparently not all!
I figured this issue could pop up when I first made the bot a few years ago, but it never did, so I never bothered to do the syntax highlighting properly. Unfortunately nowadays I am completely out of time, so I have no idea when I'll be able to get to this (naturally help is welcome if you can!).
As a starting point for the fix, discord appears to use highlight.js, with a list of available languages and corresponding aliases available here. As for mapping file extensions to the language, the list used for github syntax highlighting could be useful.


First figure (9.42a) of IPCC AR5 ch.9 recipe (Flato 2013)

Closes #352.

I fixed a couple of minor errors in the recipe.
It runs fine, but figure ch09_fig09-42a.ps is empty (only the plot axes are shown, no data is plotted).

Hmm, this is weird. My plot (created 20 minutes ago) looks fine, but I selected pdf as output format. I will test the recipe with ps.

I have the same problem, pdf looks fine while ps has axis and legend but no data. I think this is an issue of matplotlib, I'll try to figure out a solution. Did you test it with pdf?

With pdf looks fine.

For some reason, the keyword argument markerfacecolor='none' in the axes.plot function caused the problem. I fixed it by removing it for plotting ps files, but that is not really a good solution.
I think the problem is the matplotlib backend Agg which is chosen in diag_scripts/shared/plot/__init__.py  (which is not really suited for ps, see here), but once this is set it can't be modified later. Do you have any ideas how to handle this @bouweandela?
Can you test it again @mattiarighi?

The Agg backend should work fine for the PS file format too according to this article: https://matplotlib.org/faq/howto_faq.html#matplotlib-in-a-web-application-server


Placeholder var/sight and var/see_in_dark

See title.
Closes https://github.com/wixoaGit/OpenDream/issues/77 and closes https://github.com/wixoaGit/OpenDream/issues/72

i would hardly say it closes those issues

Fine


Idea: transformRequest return Promise

transformRequest mutation would be more useful if asynchronous work could be done before sending the request. For example, aws4fetch could be used as a request interceptor and make form a nice pluggable s3 interface. Note signing requests use subtle.crypto and introduces async execution: https://github.com/mhart/aws4fetch#promiserequest-awssigninput-init, I can expect quite a few auth header attachments might want to be able to use subtle.crypto and thus an async capable transformRequest function seems a generally useful ask.

As simple as awaiting the function - going out in the next release!

Live in v0.9.x 🚀


Type 'unknown' on 'data' Attributes leads to Problems

Since upgrading this library from 0.15 the type of several data attributes has been changed to unknown, e.g.
https://github.com/onsip/SIP.js/blob/53d3307f3b6f449e94a699fa92e74e74753524e3/src/api/session.ts#L70
To properly use that attribute, type any was correct to prevent errors like
TS2339: Property 'active' does not exist on type 'unknown'.
Now, one would have to 'cast' every access with (session.data as any).active.
What is the rationale behind this change?

We are working toward removing any from the entire project. There's a handful more to go, but we're getting there.
Using the any type defeats the purpose of using TypeScript. When any is used, all compiler type checks around that value are ignored.
unknown is the type-safe counterpart of any. Anything is assignable to unknown, but unknown isn’t assignable to anything but itself and any (without control flow based narrowing or a type assertion). Likewise, no operations are permitted on an unknown without first narrowing to a more specific type or asserting.
The safe and recommended way to narrow the unknown type to a more specific type is to use the typeof operator, the instanceof operator, or custom type guard function. If you want to force the compiler to trust you that a value of type unknown is of a given type, you can use a type assertion ("cast").


[add-resource] New Plugin

I would like to add my new plugin to the Grav Repository.
Here are the project details: cppl/grav-gosquared
Cheers
Craig

should show up in an hour or so...


'HumanRendering' object has no attribute 'window' (#1078)

Description
Place initialization before asserts to avoid exit/close code to access uninitialized instance variables.
Fixes # (1078)
Type of change
Please delete options that are not relevant.

[x] Bug fix (non-breaking change which fixes an issue)

Checklist:

[x] I have run the pre-commit checks with pre-commit run --all-files (see CONTRIBUTING.md instructions to set it up)
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have added tests that prove my fix is effective or that my feature works

Can you add tests showing the bug, that would fail on current main branch, and pass with this fix?

The bug is automatically ignored. But if you look in the logs you get very confused...
Take this as an example - Cliffwalker (both 3.8 and 3.12 shown)
https://github.com/Farama-Foundation/Gymnasium/actions/runs/9441854500/job/26015351276
tests/wrappers/vector/test_human_rendering.py::test_render_modes
/usr/local/lib/python3.8/site-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function VectorEnv.del at 0x7f15c0b5e820>
  Traceback (most recent call last):
    File "/usr/local/gymnasium/gymnasium/vector/vector_env.py", line 324, in __del__
      self.close()
    File "/usr/local/gymnasium/gymnasium/wrappers/vector/rendering.py", line 178, in close
      if self.window is not None:
  AttributeError: 'HumanRendering' object has no attribute 'window'

    warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))

https://github.com/Farama-Foundation/Gymnasium/actions/runs/9441854500/job/26015353030
tests/wrappers/vector/test_human_rendering.py::test_render_modes
  /usr/local/lib/python3.12/site-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function VectorEnv.__del__ at 0x7f87153c49a0>

  Traceback (most recent call last):
    File "/usr/local/gymnasium/gymnasium/vector/vector_env.py", line 324, in __del__
      self.close()
    File "/usr/local/gymnasium/gymnasium/wrappers/vector/rendering.py", line 178, in close
      if self.window is not None:
         ^^^^^^^^^^^
  AttributeError: 'HumanRendering' object has no attribute 'window'

    warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))


Make SentryNative configurable

I would like to be able to use the frames integration on macOS. Currently that's not possible because it depends on native code, which is also not able to provide frame information.
However I could gather frame informations in pure Flutter code, based on https://github.com/getsentry/sentry-dart/pull/699 . That would also enable that feature on Linux and Windows and it's compatible from Flutter 2.0 onwards.
Therefore, I would like to have a way to somehow achieve this.

@ueman we're experimenting with a new public API for adding custom measurements, See https://github.com/getsentry/sentry-python/pull/1359
Not sure if we will make SentryNative flexible enough, but rather give you a proper way to report any measurement based on your own way.

Yeah, but then I would also have to write my own NavigationObserver and so on. The support for custom metrics is pretty exciting.

We will make an abstraction in the API that when you use the custom instrumentation, slow and frozen frames are attached automatically.


[WIP] Hide TestCafe UI completely during screenshot creating (fixes #2076)

I've changed some things here. Please review again
/cc @helen-dikareva @miherlosev


feat: ensure pair aex9 compliance

Closes #15

Can we align this with #32? There seem to be a lot of things here that are already overwritten there....


Add a HTML App section to the OVE server

Connect the Flask app endpoints to an OVE HTML App Using the OVE Python API.
Steps:

[x] Manually set up one HTML App using the front end GUI. Requires Adding a Section to a Space and setting it up as an HTML App using http://localhost:8050/plot1 as the source.
[x] Replicate that manual step with the Python API
[ ] Determine how to move/reassign views into different spaces. Does it require moving the section to a different space or just changing the source url for a given section?

It appears that the Python Client Library is just an incomplete wrapper around the OVE Core API. So the best option is to probably persist with interacting directly with the Core API.
I suggest we approach this using the Uplink library, which allows for an Object Oriented approach to interacting with APIs

Determine how to move/reassign views into different spaces. Does it require moving the section to a different space or just changing the source url for a given section?

When changes from api_test branch are merged in, this final point should be clarified.


Starting docker-compose test containers as non-root user

Similar to: https://github.com/testcontainers/testcontainers-java/issues/2590
I'm trying to start our docker-compose based testcontainers tests, and pass in the local username from the running system, in order that the container can write files to mounted volumes with the correct permissions.
I tried a compose with:
version: "3.7"
services:
  myservice:
    image: xxx
    user: ${CURRENT_USER}
    ...
    volumes:
      ./target/:/target

And passed in CURRENT_USER environment variable to testcontainers using:
  env = new DockerComposeContainer(new File("src/main/docker/docker-compose.yml"));
  env.withLocalCompose(true);
  env.withEnv("CURRENT_USER", System.getProperty("user.name"));

However, this fails with:
Cannot start service my server: unable to find user bmiddleton: no matching entries in passwd file

I presume it's looking for that user in the ryuk container, and not the OS - where the user does exist.
How can I get a testcontainers test running from a docker compose file to write its files using the current user of the operating system?

Any further thoughts on this?