Update CODEOWNERS

Add missing Goat code owners

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

/ok-to-test

/test all


Athena Assembly olc error

Hello,
I have a metagenomic dataset that I would like to assembly using athena. However I am running into this issue, which I have attached. Can you please help me identify a solution?
Thanks in Advance,
Kevin Nguyen
athena_olc_error.txt

@abishara I am getting the same error as @knguyenjcvi .  Was there every any help regarding this error?

Can you upload your log file?  I can take a look.
alex

Can you upload your log file? I can take a look.
alex

The relevant portion of the error on assemble_olc
1537799375.1094469.txt

Hmm, this looks like something may be a bit funky with your bwa/samtools binary/install.  Can you successfully run bwa independently of athena with it finishing successfully?
The command that is failing is:
% bwa mem -t 4 /home/slomka/CDiff/spadesoutCdiff/contigs.fasta /home/slomka/CDiff/results/olc/pre-flye-input-contigs.fa | samtools view -bS - | samtools sort -o /home/slomka/CDiff/results/olc/align-inputs.bam -
How about trying it on the first 8 lines of pre-flye-input-contigs.fa, which is just the first two reads to see if we can narrow it down if it isn't your bwa/samtools install?  If this fails, can you upload those two reads as well as the reference /home/slomka/CDiff/spadesoutCdiff/contigs.fasta
Thanks!

so it looks like the pre-flye-input-contigs.fa is actually empty on my system. 0kb empty file

Were you able to successfully run the small example dataset on the github:
https://storage.googleapis.com/gbsc-gcp-lab-bhatt-public/readclouds-l-gasseri-example.tar.gz
with your install?  Also can you copy the result of the following, which should be executed relative to your run directory:
% ls -lhS ./results/bin.*/*fa | head
Let's see if any of the subassemblies actually went through.

The result is
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:47 ./results/bin.0/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.100/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.101/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.102/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.103/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.104/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.105/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.106/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.107/local-asm-merged.fa
-rw-r--r-- 1 slomka slomka 0 Sep 24 11:50 ./results/bin.108/local-asm-merged.fa
I also tried running the example dataset and it failed as well.  I never mentioned that I was running on lsf setup.  When running on a regular server (i tried with the example dataset after it gets passed the part where on the lsf it fails.

Can you try to get the example dataset to go through successfully first using multiprocessing mode (and local mode if that fails) so we can determine that the environment is setup so that it can run properly?  There is also a docker image referenced in the github that can be used to help get the dependencies properly set up.
Once this goes through, then perhaps we can try the example dataset with the lsf setup.  Although I will mention that I am planning to phase out support soon for running through queueing submission systems in favor of running it on 32+ core machines, which works well and is straightforward.
Thanks!

Can you try to get the example dataset to go through successfully first using multiprocessing mode (and local mode if that fails) so we can determine that the environment is setup so that it can run properly? There is also a docker image referenced in the github that can be used to help get the dependencies properly set up.
Once this goes through, then perhaps we can try the example dataset with the lsf setup. Although I will mention that I am planning to phase out support soon for running through queueing submission systems in favor of running it on 32+ core machines, which works well and is straightforward.
Thanks!

I got the example running multiprocessing mode.  I actually did not change anything in the config file (i already had cluster setting multiprocessing but was then sending the job to a lsf.  I wasn't quite sure how to set up the json file for an actual lsf cluster

I also think I've narrowed it down to the step before olc generation for my data.  Like i said before somehow the pre-flye-input-contigs is empty and I don't know why.  Looking at the logs i get
seed NODE_138_length_1412_cov_4351.597004 contig does not have high enough coverage
for all assemble bins

Great, glad you were able to get it running. That file is likely empty because none of the subassemblies actually went through.  It's possible that the barcodes are not attached as expected to either the input *fastq or *bam and that it still went through this far in process.  I am working on providing better error checking for inputs to catch that earlier in the process.
For now, if you are willing to send me an email with a link to the inputs, I can have a look.  This would be the easiest way for me to figure this out.

I actually figured out my issue,  it was with my .fq file, it did not have a tab before the BC tag so there were actually no barcodes being read by flye.  After that it fixed my issue.

Hi,
Thanks for the update and I had a feeling this might be the case.  I'm hoping to make a release that will check for these and provide an error/warning if the inputs are not tagged with the barcodes as expected.
If you haven't figured out already, I advise you rerun everything from the beginning (remove your scratch/working directory) so that the barcodes are seen thru the entire process.
alex

I was getting the same error with athena_meta v1.1 due to the "pre-flye-input-contigs.fa" file being empty. My fastq read headers looked like the following:
@NS500418:354:H27G3BGXY:3:12612:25572:11380 RG:Z:readgroup1 BC:Z:GCCAATTCAAGTTT-1

...which is shown in the athena_meta readme. I removed the "RG:Z:readgroup1" section from the read headers and that fixed the problem.

It turns out that the additional tags actually have to be tab-delimited to work with 'bwa mem -C' otherwise the barcodes are not properly detected in the *bam.  Commit 02f26e74d1fc64fc specifies this additional restriction.  Better error checking for the input *fastq and *bam have also been included in commit 11dbe60f0d1383.


Multi-threading debugging and test

Summary

[ ] use rng directly in torch.randn instead of relying on the global rng state
[ ] add option in server to switch between 1-by-1 and multi-thread
[ ] test 2 options under 1/5/10 perturb, 1/3/5 local updates, 1/3/5 clients. They should give same result

Some suggestions about option to switch between serial and parallel and test, you should split that server-client local update out of the main step

Which step? Any code reference?

I mean this def train_one_step(self, iteration: int) -> tuple[float, float]: function. It becomes longer and longer (consider we may add some attack/defend aggregation in the future). It is a good time to split them more. For this PR specifically, this with ThreadPoolExecutor() as executor: part can be extracted out as another sub-function. It will also result in a more reasonable architecture for the switching the parallel and serial I think

result running test

main train speed:

this branch parallel=True

this branch parallel=False


IntelliCode whole line completion API

Are there any plans to implement IntelliCode whole line completion public API?
There is a need in:

an ability to determine that whole line completion is active/shown for the extension not to process Tab and Right Arrow keys and not to break the completion;
an ability to pass a custom completion text to implement an integration of custom completion with IntelliCode whole line completion.

I have filed a corresponding issue on a developer community website as requested https://developercommunity.visualstudio.com/t/IntelliCode-full-line-completion-API/1547442

Thanks Sergey. So your basic request is to have a hook that allows you to pass the changed IntelliSense selection from your own implementation of an IntelliSense UI, to line completions so that we update our prediction.  I appreciate the clarification and we'll consider what we can do there.

We've provided hooks that address the need for coordination in the first bullet, in the Visual Studio 2022  Preview 7.0 build. @Denis-Korneev has confirmed that these hooks are working as expected and deliver the needed coordination - they should be available to ReSharper customers in an upcoming EAP build. This will mean ReSharper users should be able to see and use IntelliCode’s line completions for all cases where the ReSharper custom completions list is not showing, and this will provide a satisfactory experience.
We're not currently planning to expose the ability for extenders to drive IntelliCode line completions from their own custom completions lists. Of course, we’ll monitor customer feedback for future updates.
I believe this issue is now complete.


Add the posibility to use koji's fast upload API.

This commit adds the possibility to set a flag in the configmap
to use or not Koji's fast upload API.
This solves https://pagure.io/fedora-infrastructure/issue/7846
Signed-off-by: Clement Verna<EMAIL_ADDRESS>osbs-docs PR : https://github.com/containerbuildsystem/osbs-docs/pull/78
Maintainers will complete the following section:

[x] Commit messages are descriptive enough
[x] "Signed-off-by:" line is present in each commit
[x] Code coverage from testing does not decrease and new code is covered
[x] JSON/YAML configuration changes are updated in the relevant schema
[x] Changes to metadata also update the documentation for the metadata
[x] Pull request includes link to an osbs-docs PR for user documentation updates

I think we could safely default to using fast upload, especially as the koji client uses it by default.
What do other approvers think?

@twaugh works for me

Works for me too :+1:

@cverna it seems that there are no objections against having fast upload enabled by default. Could you please change the default?

@cverna it seems that there are no objections against having fast upload enabled by default. Could you please change the default?

Sure, I just updated the PR

Release notes added:

Use Koji fast upload by default
Add a use_fast_upload option to allow disabling koji fast uploads


External Secret From another Namespace

Would be cool to have an external secret be created from another namespace or even another cluster. Would be simple too. One use case would be some service makes a secret in one namespace and another service wants to use it in another. Would also be nice to transform the keys too, sometimes generated key names in secrets are not so useful.

@kferrone not sure what you refer to as generated key names? ExternalSecret resource allows you to specify any key name you want by setting the name property (which is required). Unless you are using dataFrom in which case I'd recommend using data if you want more control.
Would it not make more sense to have the other service create the external secret in the right place over having an externalsecret target another namespace? Seems like it could add abit of complexity and also potential naming conflicts, like what happens if two externalsecrets try to create a secret in the same place?

What I meant to say is for ExternalSecret to have another backend called something like kubernetes. Then the GoDaddy ExternalSecret would copy a core Kubernetes secret from another namespace into the one it's in. When I say generated names I mean another service like the many Helm charts from Bitnami and the Stable repo will often times include a secret which is controlled and named by the Helm chart.
I imagine something like this:
apiVersion: kubernetes-client.io/v1
kind: ExternalSecret
metadata:
  name: mysql
  namespace: my-cool-app # this is the namespace I want it to be in
spec:
  backendType: kubernetes # a backend which is simply this cluster, or maybe even another
  data:
    - key: /databases/mysql # databases is the namespace and mysql is a secret
      name: MYSQL_PASSWORD # here is what I want the name to be
      property: mysql-root-password # this is the name from the helm chart

I see! Having a kubernetes backend type sounds like an interesting idea.

@kferrone  You could pair this module with something like https://github.com/appscode/kubed to automatically copy your secrets over to other namespaces using annotations.

any thoughts about actually implementing it? I would love to have default secrets added to all namespaces and maybe connect second backend with scope namespace annotation for "common" secrets


[Update chatgpt-quick-actions] Custom model for each command & move custom pref

Description

Allows custom model for each command
Improved preferences

Checklist

[x] I read the extension guidelines
[x] I read the documentation about publishing
[x] I ran npm run build and tested this distribution build in Raycast
[x] I checked that files in the assets folder are used by the extension itself
[x] I checked that assets used by the README are placed outside of the metadata folder

Hi @alanzchen 👋
Thanks for your update 🔥
Could you add a changelog entry?

@pernielsentikaer Hi, just added it!


libgcrypt: 1.8.3 -> 1.8.4, drop included patch \o/

Another project with a (tiny) @dtzWill contribution :D
Muahahaah

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Fits CONTRIBUTING.md.

Success on x86_64-darwin (full log)
Attempted: libgcrypt
Partial log (click to expand)
stripping (with command strip and flags -S) in /nix/store/vp6kwm9rar1gyi8z9zqcsxksjzrj6g3z-libgcrypt-1.8.4/lib
patching script interpreter paths in /nix/store/vp6kwm9rar1gyi8z9zqcsxksjzrj6g3z-libgcrypt-1.8.4
gzipping man pages under /nix/store/0lnnqcb27gnav2shl728i80dbw0v5cy0-libgcrypt-1.8.4-dev/share/man/
strip is /nix/store/g5r4apl0za012ffs6ladinwa5w0m1l3k-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/0lnnqcb27gnav2shl728i80dbw0v5cy0-libgcrypt-1.8.4-dev/bin
patching script interpreter paths in /nix/store/0lnnqcb27gnav2shl728i80dbw0v5cy0-libgcrypt-1.8.4-dev
/nix/store/0lnnqcb27gnav2shl728i80dbw0v5cy0-libgcrypt-1.8.4-dev/bin/libgcrypt-config: interpreter directive changed from "/bin/sh" to "/nix/store/n9hba031gjky8hpjgx9fnlaxhidyzxbz-bash-4.4-p23/bin/sh"
strip is /nix/store/g5r4apl0za012ffs6ladinwa5w0m1l3k-cctools-binutils-darwin/bin/strip
patching script interpreter paths in /nix/store/fnj2mwd7sl7v9vmp7jpvyilavc3dxp37-libgcrypt-1.8.4-info
/nix/store/vp6kwm9rar1gyi8z9zqcsxksjzrj6g3z-libgcrypt-1.8.4

Success on aarch64-linux (full log)
Attempted: libgcrypt
Partial log (click to expand)
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev/bin
patching script interpreter paths in /nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev
/nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev/bin/libgcrypt-config: interpreter directive changed from "/bin/sh" to "/nix/store/dsyc1z7ck08ga7l0b1jcxx35wj69qcii-bash-4.4-p23/bin/sh"
checking for references to /build in /nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev...
shrinking RPATHs of ELF executables and libraries in /nix/store/7fps6qsz0338m5rgy9axwr6s11j0n399-libgcrypt-1.8.4-info
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/7fps6qsz0338m5rgy9axwr6s11j0n399-libgcrypt-1.8.4-info
checking for references to /build in /nix/store/7fps6qsz0338m5rgy9axwr6s11j0n399-libgcrypt-1.8.4-info...
/nix/store/w3kaircmfq2afwd7qwvp8qn5dqr74isk-libgcrypt-1.8.4

Success on x86_64-linux (full log)
Attempted: libgcrypt
Partial log (click to expand)
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev/bin
patching script interpreter paths in /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev
/nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev/bin/libgcrypt-config: interpreter directive changed from "/bin/sh" to "/nix/store/r47p5pzx52m3n34vdgqpk5rvqgm0m24m-bash-4.4-p23/bin/sh"
checking for references to /build in /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev...
shrinking RPATHs of ELF executables and libraries in /nix/store/yamaps3b10k1rzggdh7czasn9vm66nvr-libgcrypt-1.8.4-info
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/yamaps3b10k1rzggdh7czasn9vm66nvr-libgcrypt-1.8.4-info
checking for references to /build in /nix/store/yamaps3b10k1rzggdh7czasn9vm66nvr-libgcrypt-1.8.4-info...
/nix/store/47jqqbc0cnf34z0cw88fs6y0qcaill5v-libgcrypt-1.8.4

Failure on x86_64-darwin (full log)
Attempted: libgcrypt
Partial log (click to expand)
cannot build derivation '/nix/store/wbp29k76zk6cj7vq0yyg3s5rnvnylnp3-cctools-binutils-darwin-wrapper.drv': 6 dependencies couldn't be built
cannot build derivation '/nix/store/6qsq5f2pnxs9jhqpcwzviwi1sz2d41lc-clang-wrapper-5.0.2.drv': 10 dependencies couldn't be built
cannot build derivation '/nix/store/c4x9sql8bm8znr08vl3ssjw240gp5dmx-libkrb5-1.15.2.drv': 6 dependencies couldn't be built
cannot build derivation '/nix/store/15cmf158q2d2m8kchm4c7hsr9d04ly4d-curl-7.61.1.drv': 9 dependencies couldn't be built
cannot build derivation '/nix/store/n3l61aqhxyhjr3xkisx5vvi545vzcqp8-swift-corefoundation.drv': 6 dependencies couldn't be built
cannot build derivation '/nix/store/i582qicviz5vdixpf542jgvi9gvc5d91-stdenv-darwin.drv': 41 dependencies couldn't be built
cannot build derivation '/nix/store/gfc41iwvfzfa4j0xa88h5j1dg8nwrzs2-gettext-<IP_ADDRESS>.drv': 4 dependencies couldn't be built
cannot build derivation '/nix/store/h3k17fjpr3j0zisbqwh9d47r311l3ldg-libgpg-error-1.32.drv': 4 dependencies couldn't be built
cannot build derivation '/nix/store/ilicrzqxlwrgbz84139l1bvn1z6aw5db-libgcrypt-1.8.4.drv': 5 dependencies couldn't be built
error: build of '/nix/store/ilicrzqxlwrgbz84139l1bvn1z6aw5db-libgcrypt-1.8.4.drv' failed

Success on x86_64-linux (full log)
Attempted: libgcrypt
Partial log (click to expand)
gzipping man pages under /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev/share/man/
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev/bin
patching script interpreter paths in /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev
/nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev/bin/libgcrypt-config: interpreter directive changed from "/bin/sh" to "/nix/store/r47p5pzx52m3n34vdgqpk5rvqgm0m24m-bash-4.4-p23/bin/sh"
checking for references to /build in /nix/store/0y1r5z9ycz11a9v4w39l69mf08k2a9w9-libgcrypt-1.8.4-dev...
shrinking RPATHs of ELF executables and libraries in /nix/store/yamaps3b10k1rzggdh7czasn9vm66nvr-libgcrypt-1.8.4-info
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/yamaps3b10k1rzggdh7czasn9vm66nvr-libgcrypt-1.8.4-info
checking for references to /build in /nix/store/yamaps3b10k1rzggdh7czasn9vm66nvr-libgcrypt-1.8.4-info...

Success on aarch64-linux (full log)
Attempted: libgcrypt
Partial log (click to expand)
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev/bin
patching script interpreter paths in /nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev
/nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev/bin/libgcrypt-config: interpreter directive changed from "/bin/sh" to "/nix/store/dsyc1z7ck08ga7l0b1jcxx35wj69qcii-bash-4.4-p23/bin/sh"
checking for references to /build in /nix/store/rbp2sd02pxg5qa36724zyjg5n6vfg3gw-libgcrypt-1.8.4-dev...
shrinking RPATHs of ELF executables and libraries in /nix/store/7fps6qsz0338m5rgy9axwr6s11j0n399-libgcrypt-1.8.4-info
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/7fps6qsz0338m5rgy9axwr6s11j0n399-libgcrypt-1.8.4-info
checking for references to /build in /nix/store/7fps6qsz0338m5rgy9axwr6s11j0n399-libgcrypt-1.8.4-info...
/nix/store/w3kaircmfq2afwd7qwvp8qn5dqr74isk-libgcrypt-1.8.4


TF 8726 and 8727

I came across these in an answer from Paul White on TopAnswer.xyz and just realized they are not in your list (which I reference frequently, so thanks for compiling it!).
I've included the info, and repros for both flags.  Both repros use the StackOverflow2010 database, and require these indexes to be present:
CREATE INDEX IX_UserID ON dbo.Comments (UserID, PostID);
CREATE INDEX IX_PostID ON dbo.Comments (PostID, UserID);

Trace Flag: 8726
Undocumented trace flag
Function: Disables the heuristic that discourages the optimizer from producing an index union plan
Link: Why are (seemingly) suitable indexes not used on a LEFT JOIN with OR
Repro
Execution Plan: https://www.brentozar.com/pastetheplan/?id=B1mSzXGv8
-- No index union (seek on Users, multiple scans on Comments)
SELECT *
FROM Users u
	LEFT JOIN Comments c
		ON u.Id = c.UserId
		OR u.Id = c.PostId
WHERE u.DisplayName = 'alex';

-- Gets the index union plan
SELECT *
FROM Users u
	LEFT JOIN Comments c
		ON u.Id = c.UserId
		OR u.Id = c.PostId
WHERE u.DisplayName = 'alex'
OPTION (QUERYTRACEON 8726);

Trace Flag: 8727
Undocumented trace flag
Function: Can be used to prevent unwanted index union plans
Link: Why are (seemingly) suitable indexes not used on a LEFT JOIN with OR
Repro
Execution Plan: https://www.brentozar.com/pastetheplan/?id=HkwhlQGwL
-- Gets an index union plan normally
SELECT *
FROM dbo.Users u
OUTER APPLY
(
	SELECT *
	FROM dbo.Comments c
	WHERE
		u.Id = c.UserId
		OR u.Id = c.PostId
) c
WHERE u.DisplayName = 'alex';

-- No index union (seek on Users, multiple scans on Comments)
SELECT *
FROM dbo.Users u
OUTER APPLY
(
	SELECT *
	FROM dbo.Comments c
	WHERE
		u.Id = c.UserId
		OR u.Id = c.PostId
) c
WHERE u.DisplayName = 'alex'
OPTION (QUERYTRACEON 8727);

Awesome, great thanks! I will add this info tomorrow.

@jadarnel27 Do you have twitter account? I added you in thanks to section with awesome blog link  (https://joshthecoder.com/) and can added twitter link too.
Also on Sunday I will add this trace flags to main document.

Oh cool, thanks!  My twitter is @josh_the_coder (https://twitter.com/josh_the_coder).

@jadarnel27 Added via and ca3a42ce2dd445664ad9ebc0e2478b5fadf848bd and 5bd38c7b6657d339faf2c89a74c83b3257589626. Great thanks for your contribution.


AttributeError: 'TimeLimit' object has no attribute 'get_language_instruction'

https://colab.research.google.com/github/simpler-env/SimplerEnv/blob/main/example.ipynb no longer works.
The error is:
AttributeError: 'TimeLimit' object has no attribute 'get_language_instruction'

@branyang02 This is due to Gymnasium 1.0; use env.unwrapped.get_language_instruction() instead, or downgrade Gymnasium.

Forced gymnasium < 1.0 in latest commit


Proper release to PyPI

[ ] Get someone else to review documentation
[ ] Make sure there's a wheel
[ ] Push to PyPI
[ ] Announce!

[ ] Blog
[ ] Twitter
[ ] IRC

Invalid after Haskell rewrite.


Will add a Mario Game made using Javascript and Kaboom.js

Project title
Mario Game in JavaScript with Kaboom.js!.
Project Description
A game of Mario using JavaScript and Kaboom.js.
Stack:
And in order to tick the check box just but x inside them for example - [x] like this. Please delete options that are not relevant.

[x] Html
[x] JavaScript
[x] KaboomJS

Screenshots
https://user-images.githubusercontent.com/90490253/156549075-5bb0560b-8c20-401e-9842-303e06e5fe26.mov

If applicable, add screenshots to help explain your problem.

I am a GSSOC'22 Participant.

@aroramrinaal Make a new issue when u r ready with your code and live link!


Migrate to Github Actions

@mbudiu-vmw Are Github actions enabled for this repository?

Had no idea you have to enable them

They should be on by default, but they are not triggered. I will check if there is something off with the script.

This being a vmware repository I am not sure what rules apply.

Yes, it looks like Actions are disabled here. So there is not much I can do for now.

Is there something I could do?

Are you able/allowed to enable actions for this repository? It can be done in the settings.

I can't see a "settings" button for this repository.

Looks like we do not have permission to enable actions for the repository then.

For what it's worth, you can see the passing tests here on my fork:
https://github.com/fruffy/p4c-xdp/runs/5515901442?check_suite_focus=true
All tests pass now, so we can remove the xfails.
Another thing to note is how fast P4C builds because ccache is properly setup. It only takes a minute. I would like to do this for the main compiler repo but have not gotten it to work because of docker complications.

I have checked and github actions are enabled


Add has_many links

I'd like to add a has_many association to a Link model which consists of a URL and a title. I think it would be a good idea to link to a Wikipedia page for a specific word or to a "Sendung mit der Maus" episode. The internet is a medium which grows with links.
@cabotine What is your opinion about this?

@cabotine told me that he is afraid for evil links. I don't want to cancel the feature yet but I put it into deep freeze for now. We have bigger fish to fry.


Variable editing panel does not expand on keyboard focus

A team member will update this issue with more details soon.

This is your friendly Microsoft Issue Bot. I created this issue automatically as requested by a team member.


Streaming MP3

Using lame npm assume the rough sudo code...
var lame = require('lame');
var decoder = new lame.Decoder();
decoder.pipe(connection.inputStream());

I hear the mp3 audio but it's very distorted. I checked the "lame" npm with "speaker" npm and can hear it just fine there so I am wondering if there is something special needed to fix the stream? Perhaps a connection option that I missing?

This could be due to wrong samplerate, maybe lame is outputting 44100KHz but you need 48000Khz.
You need to sample up or down your stream, there currently is no real stable library to do this, but you can use my wrapper for libsamplerate.

Is it fair to say that if the sample rate was wrong then it should be distorted on my speakers? This is my first real step in steaming so my ignorance might be the issue as well.  :-)

Yes, for example:

If you have a stereo stream and output it as mono it sounds like half the speed with lowered pitch
If you play back a lower samplerate as a higher one (22000 as 48000) it will be faster and sound like played back with a higher pitch
The other way around it will sound like the pitch was lowered and be slower

Check how much channels you have and which samplerate your audio is

Yes I see. That makes sense. Per your suggestions, I tried changing a few settings on the decoder and think I have made progress.
Would adding to the project (manifest/json) the lame npm (or some other alternative) be out of the question? Working with mp3 files would certainly add to the overall value.
I'm having a ball working with this code.

I do not think this is needed, I would keep this in a seperate project.

I'm against adding lame as a dependency to node-mumble as well but we should certainly make sure it is easy to inter-operate the two libraries.

Perhaps adding to the examples folder a sample of playing a mp3 file to the current channel then?
As far as the issue is concerned; it looks closed. You have clearly shown me where the problem is and I do appreciate the schooling. :-)

@johnrnelson That sounds good :)

Improved the MumbleInputStreams to do resampling etc.
See: https://github.com/Rantanen/node-mumble/blob/master/examples/mp3.js
The resampling especially is very dirty sample duplication. Not the best quality but fast and it works.

@Prior99 If node-samplerate is stable, feel free to replace the resampling in lib/util.js#resample with your implementation.

@Rantanen Thanks for the new addition. Is the stdin on line 38
stream = process.stdin.pipe( decoder );
where you would read the file path for the mp3 file as in
input = fs.createReadStream(FilePath);
input.pipe(decoder)
Again, thanks for the code! :-)

Yeah. You can do that. Or just pipe it into the process with: node mp3 < file.mp3

I still get that same distortion. Seems to be at 1/4th the speed it should be. I'll try to pipe it but I'm afraid that will be just a band-aid as the overall solution will have multiple files that will, no doubtfully, come from fs.

Any chance you could share the mp3 file? I'm curious what it contains.

Sure. What is the best method? I've tried both music and audio books.
I've already forked the project but does not sound like the best method to share files. :-)

If the files you've used for testing are publicly available somewhere you could just link to them. If they aren't, you can always mail it with jubjub a jubjubnest net

@Rantanen I mainly want it to be a stream but I do not know about streams in node and currently do not have the time available working on it.

Ah, okay. Streaming on that level would be difficult as well as currently the processing is taking part on the frame-packet level where we only have 10ms buffer segments instead of streams.
Let's leave the quick solution in for now then. We can always implement proper resampling in JavaScript later. Also given we got lossy celt codec there, I'm not sure if the resampling artifacts are that noticeable.

okay

Perhaps open an issue for streaming if not now then for a later time?
I've put some files in my fork but network issues and smartgit are preventing me from pushing. Should be good by Monday though.
BTW: http://mumble-protocol.readthedocs.org/en/latest/voice_data.html#codecs was a good read for me.


Support ssl for Postgis connection

Running tegola against a postgres db which requires ssl yields the following error:
tegola@tegola-osm:~/repos/tegola-osm$ tegola serve --config=tegola.toml
2018-05-30 18:10:59 [INFO] config.go:191: loading local config (tegola.toml)
# This Tegola configuration file reads environment variables for sensitive and installation-specific set2018/05/30 18:10:59 root.go:74: Failed while creating connection pool: FATAL: SSL connection is required. Please specify SSL options and retry. (SQLSTATE 28000)

I was able to get it running by modifying provider/postgis/postgis.go as follows:
p := Provider{
	srid: uint64(srid),
	config: pgx.ConnPoolConfig{
		ConnConfig: pgx.ConnConfig{
			Host:     host,
			Port:     uint16(port),
			Database: db,
			User:     user,
			Password: password,
			TLSConfig: &tls.Config{
				InsecureSkipVerify: true,
			},
		},
		MaxConnections: int(maxcon),
	},
}

Also of interest, is this error message ecountered during the process of b-lining to a working version.
tls: either ServerName or InsecureSkipVerify must be specified in the tls.Config

@ear7h - just to be clear about the expectations here, what options from the config type should be configurable? Seems like we at least need ServerName and  InsecureSkipVerify - is that good enough?

@nickelbob I think the options should match that of postgres (disable, prefer, require, etc.). You can use pgx's (unexported) implementation as a guide here.


new parameter for insecure request if needed

introduced parameter to request external ip with http and no ssl verification.
Using --insecure-requests now uses the http version of api.ipify and does not check on ssl. The cloudflare API however, is still handled as before, because on http it does not work.
regarding #33
Tested with
Python2.7.17
Python3.6.9
Python3.7.5
Ubuntu 18.04.4 LTS

This change itself looks fine to me but why is preferring HTTP the solution? I don't think there's any good reason we should not be using HTTPS. As you mentioned, Cloudflare API for example does not even support HTTP.

Obviously using http should never be the first way to go if something does not work correctly. However, it is an option for experienced users. As described  in the mentioned issue there are already cases where users needed such an option.
I understand the risk of this change and I understand if you do not want to offer this option.

My question was more "why does HTTP instead of HTTPS solve this problem?"

Guess it is an user error most of the time. If someone has a weird network setup or something else is misconfigured, using http can help.
As I said, it shouldn't be the default way of automatically handling things, but why not providing the parameter for experienced users?

Maybe I should rewrite the output message a bit to make the impact clear

Looks like this is solved now in a more robust way by having multiple redundant data sources. Thanks for thr contribution.

No worries @LINKIWI. I also like the new approach more.
Thanks for giving me the chance to get into open source ^.^


Fix SQL Stored Procedures Race Conditions / Locks

Description

Fix issue with AddInstanceV6 where the sproc intentionally allows concurrent inserts but does not properly handle the error as the transaction can no longer be committed
Fix issue with ISleepIfBusy to no longer fetch settings from (currently missing) settings table

Always run the sproc regardless of SQL edition

CHECKPOINT in DeleteExtendedQueryTagV16 to avoid building up large logs

Related issues
AB#90184
AB#88316
AB#90068
Testing
Describe how this change was tested.

Unsure why the checks aren't detecting this, but the build is here: https://microsofthealthoss.visualstudio.com/DicomServer/_build/results?buildId=18966&view=results


um...@include not working..

hi~!
You've created a really cool library!

but, @include is not working... (my case)
[ just my code (for phpstorm syntax) ]
application/libraries/Slice.php -- 24
ㄴ public $slice_ext       = '.blade.php';

application/config/slice.php -- 19
ㄴ $config['slice_ext'] = '.blade.php';

[ view folder ]
ㄴ main.blade.php
ㄴ main_modal.blade.php
[ main.blade.php ]
@include('main_modal')
[error msg]

You should pass path from root of views folder in app separated by dot (.) instead forward slash (/) - than it should work for you ;)

@Jarzebowsky Sorry, I'm late...
anyway, It's WORK !!!
Many Thank's !!


fix(prettier): incorrect order of print in AssignmentTargetPropertyProperty

Current dependencies on/for this PR:

main

PR #1545   👈

This stack of pull requests is managed by Graphite.


[SPARK-46995][DOCS][FOLLOWUP] Update sql-migration-guide.md documentation

What changes were proposed in this pull request?
Fixing the documentation.
Why are the changes needed?
Migration guide for 3.5.0 said a default was enabled, but upcoming changes for 4.0.0 will disable it but there are no documentation updates indicating this.
Does this PR introduce any user-facing change?
Yes, this fixes the documentation to align with actual Spark behavior introduced in https://github.com/apache/spark/commit/becc04a9b6e27ffdaf56b35530db1e923254861a.
How was this patch tested?
Documentation only change.
Was this patch authored or co-authored using generative AI tooling?
NO

Thanks for the high quality bar Dongjoon, you're right, all of the commits on branch-3.5 have it set to true and inspecting all of the zip sources from the tags shows that's the case too.
After further investigation, the issue I was experiencing seems to be due to JARs published by AWS on EMR differing from that in the Spark source.
Running on EMR 7.2.0, AWS states that they vend Spark 3.5.1. So I pulled down /usr/lib/spark/jars/spark-streaming_2.12-3.5.1-amzn-0.jar and this is what the Scala decompiled down into.
        this.CAN_CHANGE_CACHED_PLAN_OUTPUT_PARTITIONING = this.buildConf("spark.sql.optimizer.canChangeCachedPlanOutputPartitioning").internal().doc((new StringBuilder(326)).append("Whether to forcibly enable some optimization rules that can change the output partitioning of a cached query when executing it for caching. If it is set to true, queries may need an extra shuffle to read the cached data. This configuration is enabled by default. The optimization rules enabled by this configuration ").append("are ").append(this.ADAPTIVE_EXECUTION_ENABLED().key()).append(" and ").append(this.AUTO_BUCKETED_SCAN_ENABLED().key()).append(".").toString()).version("3.2.0").booleanConf().createWithDefault(BoxesRunTime.boxToBoolean(false));

I'm not sure why they changed it, but it's my bad for not checking to make sure the AWS vended JAR was the same first; I got mislead by the value on the master branch being false. Thankfully this does explain the behavior I was seeing.
I will change in PR to instead to include a note in the 3.5 to 4.0.0 documentation that this flag has been redisabled since I don't see that present yet.

Commit has been updated to include 4.0.0 documentation.

spark.sql.optimizer.canChangeCachedPlanOutputPartitioning is an internal config. We rarely add migration guides for private things.
Also, documenting whether it is true or false does not capture the underlying changes made by #45054. Those changes are unlikely to be noticed by users.

Oh, right. I missed that this is an internal conf. In that case, ya, we can ignore this.


[Excel] (Custom Functions) Updated filenames to match yo office template updates

Yo Office Templates renames a bunch of the CF files. Will need to be held until 12/10, when fork rolls out.

:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

docs/excel/custom-functions-overview.md
:white_check_mark:Succeeded

docs/excel/custom-functions-runtime.md
:white_check_mark:Succeeded

For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.

OPS Build status updates of commit 9118446:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

docs/excel/custom-functions-overview.md
:white_check_mark:Succeeded

docs/excel/custom-functions-runtime.md
:white_check_mark:Succeeded

docs/includes/file-tutorial-excel-custom-functions.md
:white_check_mark:Succeeded

For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


Keep the module backward compatible with v12

This is more of a recommendation than an issue. It concerns the inability to update to the latest version due to the requirement for Foundry v13. Many users may not feel comfortable transitioning to an unstable version immediately, or even several months after its release, so it will be great if you keep it also compatible with v12 or provide v12 version for those who are not moving to v13 in case the new version has backward incompatible code.

The V13 version of Manage Player Targets doesn't have any more features than the V12 version. It's just an update for compatibility with V13. With changes in V13 it would be too much of a burden to also continue support for V12 and earlier versions. So that's why I dropped support for V12 and earlier. You may ignore this warning. The warning does not mean that something is wrong with your current installation of the module. It just means that there's a newer version available that needs V13.

@dev7355608  so the recommendation is to lock the module, so it does not check for updates until V13 is out? What prevents to put compatibility for 12 and 13, I think this was possible in the manifest?

You can lock it if you feel like the warning is too annoying, you just need to remember to unlock it when you update to V13, because the version of Manage Player Targets you have installed now in V12 is not V13 compatible and will break in V13. But you don't need to lock it: you can just ignore the warning. It won't install the new version that is not V12 compatible.
Maintaining V12 and earlier compatibility would have required me to maintain basically twice as much code and css styling rules going forward. I also didn't want risk accidently breaking anything about the module in V12 with a V13 compatibility update.

Got it. Thanks and agree with the approach in this situation :)


fiix stm32wl rng example to use MSI instead of LSI

Small change to avoid confusion for people trying the random example for stm32wl.

I just did it in #2082 :sweat_smile:

oh :D


E2e: Mark the graceful shutdown spec as pending

The e2e graceful shutdown spec from #3287 always fails.
Marked as pending.

And of course now it doesn't fail.

Doesn't fail anymore.


Add support for Multitouch.inputMode = GESTURE

In addition to TOUCH_POINT support, we should look at the work to support TransformGestureEvent, PressAndTapGestureEvent and GestureEvent
More information here
http://help.adobe.com/en_US/FlashPlatform/reference/actionscript/3/flash/ui/MultitouchInputMode.html

SDL appears to have gesture support
https://hg.libsdl.org/SDL/file/default/docs/README-gesture.md
We should either implement gesture support in Haxe (based on touch event input) or we should leverage SDL and HTML5 gesture events separately

Is there any progress for Multitouch events ?
I tried to use  touch pinch and zoom , but two libs which I found are for NME ( https://github.com/postite/Gestouchx and https://github.com/rockswang/roxlib )


Maybe add more features to the condition parameter in QueryATNF?

You have already added support for querying the catalogue using logical conditions, but some things are still not supported, such as the RANGE function, or specifying a range of RA/DEC using the HMS/DMS functions or h/d keywords. It would be nice if this feature was expanded to include these functions, along with the SURVEY, DISCOVERY functions. All the functions I just mentioned are (as you probably know) described here, in section 2.3.

Thanks for the suggestion. It should be pretty easy to implement the SURVEY and DISCOVERY functions, so I will try and add them in soon. It will take a bit more effort to add range properly and I don't really have the time at the moment. I am more than happy to take pull requests for any code changes though!

I've added the survey and discovery functions. I'll make a new release that's available via pip and conda when I've merged another issue about the references.

I would like to learn how to use the astroquery vizier to download two catalogs, a pulsar catalog and a Fast Radio Bursts catalog. Would you help me?

Hi @renato10nr, I'm afraid I have no experience downloading VizieR catalogs via astroquery, so can't be of much help. From the looks of things VizieR's pulsar catalogs are those extracted from individual papers, whereas this software (psrqpy) gets the catalog of all pulsars as held in the ATNF Pulsar Catalog.


Update Intent Optional Field is not Optional

In the updateIntent method, the language_code is listed as optional, but if you try to call the library without passing in that argument you get it error that it is required.
https://github.com/googleapis/dialogflow-python-client-v2/blob/master/dialogflow_v2/gapic/intents_client.py#L518-L547

language_code is described as an optional field in the RPC API Reference as well
https://cloud.google.com/dialogflow/docs/reference/rpc/google.cloud.dialogflow.v2beta1#updateintentrequest

Hey folks, any update here?

It looks like Dialogflow has not been migrated to use the new proto annotations, so required/optional is determined by the GAPIC config. https://github.com/googleapis/googleapis/blob/2e23b8fbc45f5d9e200572ca662fe1271bcd6760/google/cloud/dialogflow/v2beta1/dialogflow_gapic.yaml#L838 line makes language_code required.
Opening a CL now to fix it.

Hey Bu Sun, checking back in. Did that other CL you mentioned go through?

Closed by #175


Wants List Items not implemented?

First of all thanks for the effort you have put into this awesome Python module.
I've looked closely at api_map.py and am unable to figure out how to use the wantslist items api endpoint. This endpoint returns the items in a specified wants list. I am able to get a list of want lists, but not the cards on the lists.
This is the documentation for the endpoint I am referring to: https://www.mkmapi.eu/ws/documentation/API_2.0:Wantslist_Item

Hi @koenbud, that endpoint has been added recently in API 2.0 of Magic Kard Market. As you can see from their documentations 2.0 works only on their sandbox servers.

With the introduction of the 2.0 version all versions of the API will run parallel on our servers (2.0 beta currently only on the sandbox server).
Once 2.0 hits the live servers, we'll discontinue support for 1.0, while support for 1.1 will last until the next major API version. Nevertheless you can still access all 1.0 requests as normal.

As of now MKM-SDK supports only API 1.1, the endpoint you're referring to doesn't exist in this version.
In the coming weeks I should be able to start work on supporting API 2.0 at least on their sandbox.

Thanks for the quick reply. I was not aware of that.

Just want to leave a quick update about API 2.0 and why work hasn't started on MKM-SDK.
Magic Kard Market's official sandbox is down or having issues by a month or so, until they fix it I can't test anything or see what's new in API 2.0. As of now I can only wait for them to release a fix before starting to work on it.

Alright, thanks for the update!

Fixed in #40


Logging of triggered Routes

Hi and thanks for this awesome library.
We are using several Coordinators in our App. Now we would like to log which route has been triggered.
We could implement this in each Coordinator implementation in prepareTransition(for route:). But this could easily be forgotten.
Is there a way to hook into the Coordinator or some other place to generically print each triggered Route to the console?
Thanks for any help.
Jonas

Hey @cornr - thank you for your interest in this library.
Unfortunately, there is no such functionality at the moment. You might however be possible to create your own subclasses to NavigationCoordinator, TabBarCoordinator, etc with that logging functionality to at least reduce code duplication.


Change the photo on the "Credits" page

Let's add some variety and not use the same photo everywhere :)

Done.


Docs don't indicate structure of expected markup

I had a great deal of frustration trying to use this plugin, until I realized that I could make my .locality group stop disappearing if I wrapped label-input pairs in a container (e.g. div.form-group). The usage docs could use some explicit detail about the requirements for marking up the form.

Thanks for the report @thedaniel.  I also just received an independent report about this issue through Twitter.
I'll be working on better docs for this project soon; naturally, I'd also accept a PR.


cross-platform: Embed ICU statically

Download ICU 57 [ if user accepts the license ] and build
Link to ChakraCore statically

@dapont @digitalinfinity Thanks for the review. I did update the text accordingly.


[Bug] [Connector-V2][ES] timestamp type conversion fails and sink stage there will be redundant "

Search before asking

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

What happened
timestamp for es

SeaTunnel Version
2.3.0
SeaTunnel Config
env {
  execution.parallelism = 8
  job.mode = "BATCH"
  job.name = "opensearch to console"
}

source {
  Elasticsearch {
    hosts = ["https://xxx:9200"]
    index = "arkime_sessions3*"
    source = ["firstPacket","event.id","event.kind","source.ip","client.nat.ip","source.port","client.nat.port","source.mac","source.hostname","destination.ip","server.nat.ip","destination.port","destination.nat.port","destination.mac","destination.hostname","client.user.name","client.user.domain","client.user.id","host.ip","suricata.alert.severity","rule.name","event.action","event.result","http.response.bytes","event.sequence","network.protocol","network.application","suricata.http.status","suricata.http.http_method","suricata.http.url","suricata.http.hostname","suricata.http.http_user_agent","http.request.referrer","user_agent.device.name","http.authTypeCnt","zeek.smb_cmd.command","file.path","threat.technique.name","related.oui","file.pe.product","suricata.flow.start","event.duration","event.type","host.geo.country_name","host.geo.region_name","host.geo.city_name","source.geo.country_name","source.geo.region_name","source.geo.city_name","source.geo.longitude","source.geo.latitude","destination.geo.country_name","destination.geo.region_name","destination.geo.city_name","destination.geo.longitude","destination.geo.latitude","event.original","network.direction","tags","event.hash"]
    username = "xxx"
    password = "xxx"
    tls_keystore_path = "opensearch.keystroe"
    tls_verify_hostname = false
  }
}

transform {

}

sink {
    Console {}

}

Running Command
bin/seatunnel.sh --config ../seatunneljob/job-es-no-transform-to-console.conf -m local

Error Exception
Caused by: java.time.format.DateTimeParseException: Text '1065823369239' could not be parsed at index 0
	at java.time.format.DateTimeFormatter.parseResolved0(DateTimeFormatter.java:1949)
	at java.time.format.DateTimeFormatter.parse(DateTimeFormatter.java:1851)
	at java.time.LocalDateTime.parse(LocalDateTime.java:492)
	at org.apache.seatunnel.connectors.seatunnel.elasticsearch.serialize.source.DefaultSeaTunnelRowDeserializer.parseDate(DefaultSeaTunnelRowDeserializer.java:209)
	at org.apache.seatunnel.connectors.seatunnel.elasticsearch.serialize.source.DefaultSeaTunnelRowDeserializer.convertValue(DefaultSeaTunnelRowDeserializer.java:161)
	at org.apache.seatunnel.connectors.seatunnel.elasticsearch.serialize.source.DefaultSeaTunnelRowDeserializer.convert(DefaultSeaTunnelRowDeserializer.java:121)
	... 13 more

	at org.apache.seatunnel.engine.client.job.ClientJobProxy.waitForJobComplete(ClientJobProxy.java:118)
	at org.apache.seatunnel.core.starter.seatunnel.command.ClientExecuteCommand.execute(ClientExecuteCommand.java:151)
	... 2 more

Flink or Spark Version
No response
Java or Scala Version
No response
Screenshots
No response
Are you willing to submit PR?

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

Code of Conduct

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

I have submitted a PR #4233


Added nullptr initialization for frame context.

Description of changes: If a WebSocketConnection was deleted without calling connect it resulted in a crash in dlfree. Added a initialisation of p_wslay_frame_Context_ as nullptr within the WebSocketConnection constructor to fix this crash.
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Hi @Fischiii,
Thank you for your pull request.  We will merge it into master after testing the changes internally.
Varun


User defined network requires a subnet when using --ip flag on docker run

I'm using a (libnetwork) network driver to handle networking and IPAM.  I've noticed that if you specify an IP address on the docker run command, it errors if you do not specify a subnet when creating the network.
$ docker run -tid --net net1 --name test --ip <IP_ADDRESS> busybox sh
27011decc0af611e9c060bfa2f3dbe0e1664af824c0c99764f1b25d86fecf635
docker: Error response from daemon: User specified IP address is supported only when connecting to networks with user configured subnets.

It seems overly restrictive to have to specify a subnet on the docker network create since my driver is taking care of all the networking and IPAM and the container is not connected to the docker bridge (the other end of the veth is dangling in the host ns).  I did see a comment related to this in issue #19418, but it didn't seem to cover the case of user defined networks.
I can include the JSON requests and responses from the network and IPAM driver if that would be useful.  Just let me know.
I've got a few questions:

Since I am using my own network plugin that handles IPAM and networking (and the container is not connected to the docker bridge), why is it necessary to specify a subnet when creating the network?
Can I work around this by specifying a subnet of <IP_ADDRESS>/0 for my user-defined networks, or will that have disastrous consequences elsewhere (such as other containers that are using --net=bridge)?
Is it possible to just remove this restriction in docker for user defined networks?
Are there any plans to put in options on the docker run command that are passed to the network and ipam driver?

$ docker version
Client:
 Version:      1.10.1
 API version:  1.22
 Go version:   go1.5.3
 Git commit:   9e83765
 Built:        Thu Feb 11 20:39:58 2016
 OS/Arch:      linux/amd64

Server:
 Version:      1.10.1
 API version:  1.22
 Go version:   go1.5.3
 Git commit:   9e83765
 Built:        Thu Feb 11 20:39:58 2016
 OS/Arch:      linux/amd64

$ docker info
Containers: 4
 Running: 1
 Paused: 0
 Stopped: 3
Images: 14
Server Version: 1.10.1
Storage Driver: aufs
 Root Dir: /var/lib/docker/aufs
 Backing Filesystem: extfs
 Dirs: 103
 Dirperm1 Supported: true
Execution Driver: native-0.2
Logging Driver: json-file
Plugins:
 Volume: local
 Network: bridge null host calico
Kernel Version: 3.19.0-15-generic
Operating System: Ubuntu 15.10
OSType: linux
Architecture: x86_64
CPUs: 1
Total Memory: 3.86 GiB
Name: calicodev
ID: H2E7:VK52:6P4T:A2X5:ZZPQ:CAPE:63GT:F2JB:QSG6:UDTQ:6GWN:BF4T
Debug mode (server): true
 File Descriptors: 21
 Goroutines: 40
 System Time: 2016-02-20T11:34:22.387875756-08:00
 EventsListeners: 0
 Init SHA1:
 Init Path: /usr/bin/docker
 Docker Root Dir: /var/lib/docker
WARNING: No swap limit support
Cluster store: etcd://<IP_ADDRESS>:2379

$ uname -a
Linux calicodev 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

@robbrockbank

Since I am using my own network plugin that handles IPAM and networking (and the container is not connected to the docker bridge), why is it necessary to specify a subnet when creating the network?

There are 2 important reasons for this design.

If a container is assigned a static ip using --ip, it is expected that the container should be able to run even after a daemon restart. Daemon cannot assume or guarantee how an IPAM plugin is going to behave on a restart. If the IPAM driver that backs a network decides to use a different subnet, then the container will fail after the daemon restart. That impacts the UX badly.

Though your IPAM might be able to guarantee a stable subnet across reboots, docker also provides a modular way for operators to change the network and ipam plugins without the need to change the application. For example, developer can run a compose file (or) container just by specifying the network name and --ip. While the operator will decide which network or IPAM plugin to use based on the infrastructure that runs that particular application / container. This provides a mechanism to not bind the container to the infrastructure. Hence, the only way to guarantee a static --ip is by making sure the docker network create is done with the appropriate --subnet.

HI @mavenugo
Thanks for the details.
I'm not sure I follow what you mean though by tying the container to the underlying infrastructure.  Surely by specifying the --net option on the docker run command you're tying it to the infrastructure in that you are tying network and ipam management to the appropriate network and ipam driver.
Even considering points (1) and (2), it still seems that the necessity have the subnet specified on the network is more a property of the particular network and ipam drivers because your network driver can assign a different subnet on different runs.  For my particular use case, and with our drivers - we don't want to necessarily assign a subnet to network.
Given that this limitation does exist, and given that I'm using a separate ipam and network driver - will docker/libnetwork actually do anything with the subnet configuration, other than police the ip parameter and pass the information to the driver?  i.e. Is my particular workaround of specifying a full 0/0 subnet going to have any odd side-effects?

@robbrockbank
Regarding

Can I work around this by specifying a subnet of <IP_ADDRESS>/0 for my user-defined networks, or will that have disastrous consequences elsewhere (such as other containers that are using --net=bridge)?

AFAIK there should not be any side-effect, libnetwork is not doing any other check other than ip belongs to the pool.

@robbrockbank

I'm not sure I follow what you mean though by tying the container to the underlying infrastructure. Surely by specifying the --net option on the docker run command you're tying it to the infrastructure in that you are tying network and ipam management to the appropriate network and ipam driver.

Please consider this compose application -
$ cat docker-compose.yml
version: "2"

services:
  voting-app:
    image: docker/example-voting-app-voting-app
    ports:
      - "80"
    networks:
      - votenet
  result-app:
    image: docker/example-voting-app-result-app
    ports:
      - "80"
    networks:
      - votenet
  worker:
    image: docker/example-voting-app-worker
    networks:
      - votenet
  redis:
    image: redis
    networks:
      - votenet
  db:
    image: postgres:9.4
    volumes:
      - "db-data:/var/lib/postgresql/data"
    networks:
      - votenet
volumes:
  db-data:

networks:
  votenet:

for a dev votenet is a network created automatically by docker-compose and the dev doesnt care which driver it is using or which IPAM configs are being used. Infact, the above compose file will work as is and the default network driver bridge will be used and a subnet is automatically assigned.
Now, when an operator schedules the application say in staging... the op might add another override compose file, which extends the above application (or) create the above network independently before running the application.
$ cat docker-compose.override.yml
version : "2"

networks:
  votenet:
    driver: overlay
    ipam:
      config:
        - subnet: <IP_ADDRESS>/16
          gateway: <IP_ADDRESS>

In this example, the same application creates (or uses an existing network) with a different driver and different subnet configuration.
Hope that answers the reason how the network specified in the application/container is not tied to the infrastructure where it is executed.
Infact that is one of the reasons why we have docker network command isolated from docker run and not tie in the operator view of the infrastructure impact the container execution. Portability is one of the key requirement.

i.e. Is my particular workaround of specifying a full 0/0 subnet going to have any odd side-effects?

It is a clever workaround and is kinda equivalent to specifying multiple subnets in the network create which covers all the subnets. But libnetwork will fail with this error : Error response from daemon: Pool overlaps with other one on this address space because it is an overlapping address with existing default bridge docker0 network. Hence you can infact create a network outside of the docker0 subnet and that will take care of it.

Hi @mavenugo
I guess that specifies what you mean about infrastructure, but I'm not sure that it answers why the IP/subnet validation check is not the property of the network driver.  Sure it might be that most network drivers need to perform that validation and therefore building it into docker makes sense, but it is not the case that all network drivers have that requirement and so having that additional enforcement seems overly prescriptive given that there is no way to "opt out" of this checking.

@mavenugo
Regarding your point about the 0/0 subnet.  I have been able to create multiple networks using our driver that all have a 0/0 subnet which you inferred may not be possible.   Why is that?  It's good from my perspective because it allows me to do what I actually need to do given the subnet/IP restriction - but I'm nervous if you think that it shouldn't actually work.

@robbrockbank My comment was on default IPAM driver which will NOT allow overlapping subnet ranges across networks. By default, docker0 bridge is allocated a range from the global range (typically it is <IP_ADDRESS>/16). When that happens, if any other network tries to allocate 0/0, it will fail because of the overlapping range.
If you are using your own IPAM driver & if you ignore this case, then yes, you may not hit this issue. But, if the containers using this IPAM plugin happens to overlap with that of the docker0 network range, it will result in forwarding issues and  you must be aware of it.

This issue can be closed.


Simplify Rakefile

During recent work on streamlining the process to build Puppet as a gem, I noticed several parts of the Rakefile that were added for historical reasons, but are no longer needed. This PR comprises changes to simplify the Rakefile.

LGTM could you check that one of the benchmarks can be run before merging (if you didn't already)?

LGTM could you check that one of the benchmarks can be run before merging (if you didn't already)?

Just ran the benchmark:catalog_memory benchmark and it seemed to behave the same between main and my branch. I also compared the number of Rake tasks between the two branches and they remain the same, even after the change.


Animation is snatchy and shaky in Mozilla Firefox

When using animation, all browsers except mozilla(latest) are working fine. In Mozilla is hard to watch(even examples in documentation are doing that). Does not matter which animation I choose, it always shakes and snatches. Maybe it has to do with calculating movement, rounding. My goal was to achieve of slow motion approaching effect and whatever value I put into **animationDuration ** parameter it is always quite fast (tried 80000). It is pitty if this nice plugin could not be used with animation because of mozilla.

Hello,
I don't see any problem on my Firefox 43 (Mac).
You're the first one to report this issue.
Can you test another Firefox on another computer ?

Hello,
I tested on another 2 computers (both win7), one of them has the same problem, the second one was drawing correctly. Weird.

So it's on specific Firefox versions.
Animation just use CSS animation. This is not a Vegas bug but a poor Firefox implementation I guess.
Can't do much on this sorry.

I figured it out in vegas.css based on article on the web I changed this CSS rule
@keyframes kenburns
{
    0%
    {
        -moz-transform: scale(1.5) rotate(0.1deg);
        -ms-transform: scale(1.5) rotate(0.1deg);
        -o-transform: scale(1.5) rotate(0.1deg);
        -webkit-transform: scale(1.5) rotate(0.1deg);
        transform: scale(1.5) rotate(0.1deg);
    }

    100%
    {
        -moz-transform: scale(1);
        -ms-transform: scale(1);
        -o-transform: scale(1);
        -webkit-transform: scale(1);
        transform: scale(1);
    }
}

where rotate(0.1deg); somehow fixes the problem for firefox and explorer and makes it smoother.

Thanks for the tip! I will try it.


Improvement request: only sync tiddlers with a 'lastmodified' date  that is more recent than the last sync

I have a very large wiki that contains all my notes from several years of university. Currently, syncing to Anki takes around 3-5 minutes, and sends my laptop fan spinning like crazy.
Would it be possible to add a setting that allows only syncing tiddlers that have been modified since the last sync, as well as new tiddlers? This should dramatically reduce the amount of tiddlers that need to be rendered (and thus improve performance)
Keep up the great work, this plugin has tremendously improved my learning experience !

Just curious, how many tiddlers do you have in your wiki?

Just curious, how many tiddlers do you have in your wiki?

Maybe you can reduce the time it takes to sync by changing the filter used by the Anki plugin. By default it is [type[text/vnd.tiddlywiki]] [type[]] +[!is[system]] but you can be more restrictive. Maybe you can use some tags or a cutoff date.
However, be extremely careful because if you exclude tiddlers with questions, those will be wiped out of anki. I recommend you to backup you collection before trying changes.

Maybe you can reduce the time it takes to sync by changing the filter used by the Anki plugin. By default it is [type[text/vnd.tiddlywiki]] [type[]] +[!is[system]] but you can be more restrictive. Maybe you can use some tags or a cutoff date.
However, be extremely careful because if you exclude tiddlers with questions, those will be wiped out of anki. I recommend you to backup you collection before trying changes.

I don't think a date cutoff could be made to work reliably without completely rearchitecting TiddlyRemember (and making it less flexible), because there is not a one-to-one correspondence between the tiddler on which a TiddlyRemember note is placed and the data within that note. A tiddler can, for instance, transclude data from another tiddler into the remember* macros, and TiddlyRemember's syncer has no way of figuring out where that data came from and thus where it would need to look for a modified date (it would basically have to reimplement the wikitext parser, with some additional features to track the provenance of every bit of wikitext, to pull that off).
I'm also interested in what your wiki is like. I have a wiki with thousands of tiddlers and it syncs in an entirely reasonable amount of time (probably less than 15 seconds). I have experienced problems where it takes forever when binary files, images, etc. end up in the hopper, though, so I'm wondering if that's really what's going on here. I haven't looked too closely into the cause of that because it was really easy to exclude them with the filter in my test.

I have approx 5.000 tiddlers, of which approx. 2500 are binary files (or associated meta files). This includes around 500 pdf files which can be quite large. But the default filter seems to exclude those, so I'm not sure why they would slow things down?
(note that I'm currently working on a 10 year old laptop, so 15 seconds on a fast new computer could reasonably translate to 2-3 minutes.)

So, I timed it, and it seems like most of the time is actually spent before the progress bar starts counting.
It took 50 seconds before numbers appeared on the progress bar, and 30 seconds after that (I closed everything else for this test, which explains that it was faster - it takes at least double the time with a normal cpu load).

But the default filter seems to exclude those, so I'm not sure why they would slow things down?

Correct, it shouldn't, but we all know should and does are different things in IT :). Are you transcluding those PDFs/images/etc into some of the tiddlers that you're rendering with TiddlyRemember? Though I wouldn't really expect that to make a difference.
Also, are your tiddlers possibly making really heavy use of macros or transclusions or anything like that? Just trying to figure out what might cause the rendering component of the sync to take longer than usual.

So, I timed it, and it seems like most of the time is actually spent before the progress bar starts counting.

That's expected. The first stage is that TW running on Node.js renders the tiddlers, and it doesn't provide any progress as it does. Then TiddlyRemember picks up with extracting the contents of those rendered tiddlers, and it's able to provide a count on this. The first step is usually quite a bit slower in my experience.
One other thing -- I'm guessing you're using a folder wiki directly on your computer, with the "Folder" option chosen in the syncing settings? If the files are large, a download from a URL or extract from a file wiki could take significant additional time. But since you were talking about meta tiddlers and you do have so many files, I'm assuming you're already using a folder wiki.

(note that I'm currently working on a 10 year old laptop, so 15 seconds on a fast new computer could reasonably translate to 2-3 minutes.)

This seems possible. I can try on my old Windows laptop this evening and see what the speed factor is to my main development machine.
If the cause is just that your computer is old, and none of the earlier notes apply to your situation, I'm afraid I don't have any ideas for you to speed it up, aside from sortega's suggestion of trying to limit the set of tiddlers you need to search for TR notes (even something as simple as searching for the word remember on tiddlers might work OK here, as long as you don't have custom macros that would result in the word remember not showing up in your wikitext).  As noted in my earlier comment, I don't think a sync-only-changed-tiddlers approach is workable.

Also, are your tiddlers possibly making really heavy use of macros or transclusions or anything like that?

Virtually all of my tiddlers contain a "table of contents" that lists tiddler below them in the content hierarchy, it's done by transcluding the following template tiddler:
<div class="tc-table-of-contents">
<<toc-selective-expandable $(currentTiddler)$ sort[created]>>
</div>

and I use it by adding {{||tocsel}} wherever I want it to appear. Could this be the problem?

This seems possible. I can try on my old Windows laptop this evening and see what the speed factor is to my main development machine.

I am back home now and have access to my much newer and faster desktop, so I can also time it - before I do so, can you confirm that syncing the same wiki folder (I have it on dropbox and synced on both computers) to the same anki collection (shared via anki's built-in cloud sharing) on two different computers won't incur any loss of data?

Could this be the problem?

Maybe? I'm not sure how intensive the TOC macros are. You could try blanking the template tiddler temporarily to see what impact it has.

can you confirm that syncing the same wiki folder (I have it on dropbox and synced on both computers) to the same anki collection (shared via anki's built-in cloud sharing) on two different computers won't incur any loss of data?

I haven't tried it, but I can't think of any reason why it would. If you're concerned, just restart Anki or sync to AnkiWeb before trying, then watch the balloon that appears briefly in the lower-left and indicates what changes have been made. If it does something wrong, you can restore an automatic backup of your Anki collection (this is why you restart/sync first, to take a backup).

Results of my test: 11 seconds to sync on my development machine, 29 seconds to sync on my 8-year-old laptop, with 2300  tiddlers matching the filter. Didn't close out of anything on either machine, on both a few things open but not actively doing much. And data was on a FreeNAS fileserver (presumably in the RAM cache as I am constantly hitting the wiki files) over gigabit Ethernet for both machines.
My 8-year-old laptop was fairly nice when it was new, but even so I'm somewhat doubtful yours is almost 3 times slower under zero load without some other factor involved.

@ldorigo: Any updates on this? I don't think the improvement requested in the title is possible, but if there are other things I can do to improve performance for you I'd be happy to think about them.


Long pause, wondering if anything is happening or crashed, from flutter run + ios

flutter run --checked --debug-port=16230 --start-paused --device-id 2175d44c48c2ba9a5bbad10262cf8e7f04aab8e7 • flutter logs
mute_field_6440/ • checked mode • debug
Starting lib/main.dart on iPod touch...
Fetching the Xcode project archive from the cloud...
Downloading https://storage.googleapis.com/flutter_infra/flutter/d1515e676438d79046508ca009044df246564ced/ios/FlutterXcode.zip...
Unzipping Xcode project to local directory...
Xcode project created at /Users/sethladd/Code/mute_field_6440/ios/.generated/.
User editable settings are in /Users/sethladd/Code/mute_field_6440/ios/.

At this point, a long pause (10 secs ish?) before the next thing prints to my screen. I don't know: did it crash? Is anything happening? What should I expect? These long pauses make users wonder if they should Control-C and start over.
Could we print a spinner here? Or a progress bar? Thanks!

There's also a long pause at:
~/Code/mute_field_6440 $ flutter -d 2175d44c48c2ba9a5bbad10262cf8e7f04aab8e7 run
Starting lib/main.dart on iPod touch...

Printing a spinner/progress bar here would be really helpful, too. Thanks!

I'm not sure what to do here.  Xcode can take a while.  We could have a tools spinner I guess?

A spinner would be helpful. Something to signal "we're working on it".

I suspect it's a console output issue. @sethladd: did you run from the command line or from an IDE?
There's a spinner currently but I did notice instances of it not showing when running inside VSCode.


Add more C# language features and syntax sugar to highlightning

Describe the enhancement
Currently not all syntax features of C# are highlighted.
My suggestion includes the following (if you would find something missing, feel free to add):
Missing features
For the sake of completeness, I have tried to explicitly assign a feature to a language version here. I could not find the associated standard/proposal for each feature but they do exist.
Standard (Draft v6)
C# language standard - ECMA-TC49-TG2
Unsafe blocks (ECMA Draftv6 22.2)
public void Method() {
    unsafe {
        // Unsafe operations
    }
}

Pointers & pointer fixture (ECMA Draftv6 22.7)
public unsafe void Method() {
    fixed(int* ptr = &refVar) {
        // Some cool pointer operations
    }
}

C# 9
Native Integer Primitives (CSharp 9.0 Proposal)
public void Method() {
    nint myNativeInteger = -123;
    nuint myNativeUnsignedInteger = 123;
}
public void Method(nint param1, nuint param2) {}

Function pointers (CSharp 9.0 Proposal)
public void Method() {
    delegate* managed<int, int>;
    delegate* unmanaged<int, int>;
    delegate* unmanaged[Cdecl] <int, int>;
    delegate* unmanaged[Stdcall, SuppressGCTransition] <int, int>;
}

Static anonymous functions (CSharp 9.0 Proposal)
public void X() {
    Y(static (i) => i + 1);
    Y(static i => i + 1);
}

public void Y(Func<int, int> x) {}

With expressions (CSharp 9.0 Proposal)
public record MyRecord(string Name);

public MyRecord ModifyName(MyRecord rec) {
    return rec with { Name = "My new name" };
}

C# 10
Global Using Directives (CSharp 10.0 Proposal)
global using System;
global using System.Linq;
global using System.Runtime.CompilerServices;

Records (CSharp 10.0 Proposal)
public partial record struct Record {}
public partial sealed record Record {}
public record struct Record {}
public sealed record Record {}

Enhanced Pattern Matching (CSharp 9.0 Proposal + CSharp 10.0 Proposal)
void M(object o1, object o2)
{
    var t = (o1, o2);
    if (t is (int, string)) {}
    switch (o1) {
        case int: break;
        case string: break;
    }
}

bool IsLetter(char c) => c is (>= 'a' and <= 'z') or (>= 'A' and <= 'Z');

Null checks
public void Method(object? nullable) {
    if(nullable is null) {}
    if(nullable is not null) {}
}

Defaults
public void X() {
    int x = default;
}

implicit new
public void Method() {
    MyKnownType value = new();
}

Wrong implemented features
Extension method resolving
namespace N1
{
    public static class D
    {
        public static void F(this int i) => Console.WriteLine($"D.F({i})");
    }
}

namespace N2
{
    using N1;

    class Test
    {
        static void Main(string[] args)
        {
            1.F();
            // ^^ Why is this red?
        }
    }
}

Closing as this is not a problem with Linguist


Minor fix for masking regex from logs. We were filtering the regex based on the variables. Removing that check

Minor fix for masking regex from logs. We were filtering the regex based on the variables. Removing that check

Looks good

looks good to me too.


support for HmIP-WRCR

Is your feature request related to a problem? Please describe.
Detection for push and rotation for HmIP-WRCR

Please publish the data you get from this script as a gist.

I have done it but I am not sure If or what to do next? :) just leaving the link to the gist here? If yes: https://gist.github.com/dustnppunkt/ab7aa205470d80bec0f73a73432a7ddb


Way to use gt-filter to only apply to samples with variant?

Is there a logical way to make it so that gt-filter only apply to samples with a variant in question?
Our main use case is filtering for all variants in a given gene where the variant call is of good quality (gt_qual>=20 and gt_depth >=6). If you do (gt_quals).(*).(>=20) then you'll only get variants where all samples in the database have GQ>=20, when what you really want is all variants where any sample who has a non-ref genotype has GQ>=20.

I just pushed a what to do this. It would be great if you could give it a try and let me know if you have any issues.

From reading your commit notes, it seems like if you had samples A, B, and C; A and B are het for a particular variant, but A's GQ==42 but B's GQ==12, then you wouldn't not retrieve this variant?

if you use .(all), then yes, your interpretation is correct.

So I'm trying to retrieve all variants where at least one affected individual is not homref and any individual who is not homref has a good quality call. Here's what I think should do that?
    gemini query --header --show-samples -q "SELECT chrom,start,end,ref,alt,gene,impact" \
    --gt-filter "(gt_types).(phenotype==2).(!=HOM_REF).(any) and (gt_quals).(!=HOM_REF).(>=20).(all) and (gt_depths).(!=HOM_REF).(>=6).(all)" myDB.db

I get an error though sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) near "!=": syntax error [SQL: u'SELECT samples.sample_id, samples.name \nFROM samples \nWHERE !=HOM_REF']

It currently has to be of the form:
(=HET) not !=HOM_REF
I can probably expand to make the latter possible.

Ah the latter would be useful. But I still get the same error when I use (=HET)

The condition has to be in the 2nd block. So
(gt_types).(phenotype==2).(=HET).(any) is not allowed.
but:
(gt_quals).(=HET)(>20).(all) is allowed

Ok to make testing simpler I just simplified it down to --gt-filter "(gt_quals).(=HET).(>=20).(all)"
but I'm still getting sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) near "=": syntax error [SQL: u'SELECT samples.sample_id, samples.name \nFROM samples \nWHERE =HET']

Ok, just did some testing and I realized this doesn't go all the way to what we would need although it is useful.
The goal is to be able to replicate the built-in tools analyses, where so long as all the individuals in a given family have good quality calls, the variant will show up in the results, even if other samples not in that family have missing calls. So I think the analogous situation I'm aiming for with gt-filter, since it isn't family-aware, is to output all good quality calls that meet the genotype criteria in at least one sample.
In this example, when I am looking for GQ>=20 and DP>=6, I would want to keep this variant in the output because sample4 and sample6 are both het and meet my GQ and DP cutoffs. Right now it gets excluded because sample1 is het and fails the cutoff.

sample1
sample2
sample3
sample4
sample5
sample6
sample7

A/.
A/A
A/A
A/AAAAAT
A/A
A/AAAAAT
A/A

DP
13
23
32
12
8
13
22

GQ
3
60
63
84
21
99
60


Review Web Annotations specs

@slightlyoff: We'd be happy to dig in and understand these specs. Perhaps we could chat in an upcoming TAG call to get better acquainted?

The Web Annotation WG is scheduled to meet at TPAC on Monday and Tuesday, 26-27 October. I see that the TAG is scheduled for one day, Monday 26 October.
It might be useful to schedule some time for a joint session on Monday to discuss two Web Annotation WG deliverables to socialize them and get early feedback on the architectural approach.
(1) Web Annotation Protocol
One of the deliverables of the Web Annotation WG is a Web Annotation protocol. Some questions were raised earlier about the RESTful nature of the specification.
(2) FindText
We'd appreciate general feedback (by TPAC this should be a FPWD, but we can make changes to subsequent WDs)
Would it be possible to schedule a session with the TAG on Monday to review/discuss the protocol spec? If so, when might be possible times?
Thanks
regards, Frederick

taken up 11-11

Some initial notes:

This specification is effectively profiling HTTP by using language like "The server must support the following HTTP methods on the Annotation Container's URI." It should just describe the representations and interaction expectations upon resources that use them.
Likewise, it's very MUST/SHOULD heavy; when specs overuse the RFC2119 terms, it doesn't help readability or interoperability.
"When a paging preference is received, instead of returning the representation of the container, the server must return a response with the status code of 303 and a Location header with the URI for the first page." What if the user isn't authorised? What if other parts of the request are malformed? What if the resource doesn't exist? MUSTs like this are seldom helpful.

Error Conditions creates application-specific semantics for standard HTTP status codes. This is an anti-pattern; the point of HTTP status codes is that any application (including intermediaries) can understand them; application-specific semantics belong in the payload.

Picked up in teleconf 25-November-2015: https://github.com/w3ctag/meetings/blob/gh-pages/2015/telcons/11-25-agenda.md

Discussed in Melbourne F2F; reminded ourselves that we need to arrange a discussion with one or more folks from the Annotations community about this spec.

See https://github.com/w3c/web-annotation/issues/313#issuecomment-229681515 for a more complete, and up-to-date response of the WA Working Group

Discussed on 6 July Call

Seems we need to feed back on https://github.com/w3c/web-annotation/issues/313#issuecomment-229681515. Pending feedback from @mnot....


Email of the paying user

Hi,
how can I retrieve the email of the account paypal that paid through this implementation?
regards
James

Hey that's something that Mobile SDK is not providing, take a look to this stackoverflow answer http://stackoverflow.com/questions/23201544/how-to-get-buyers-info-in-paypal-mobile-sdk this is something that you'll need to do in server side.
PayPal Ref:
https://developer.paypal.com/docs/api/payments/#payment_get

Please can you tell me how can I retrieve the email of the buyer on Paypal server side?
I searched in server side PayPal sdk documentation but I have not found any code to retrieve the email of the buyer.
Please if you find a solutions please write some links.
Thanks.
James.

@acolangelo86 please check the above links, basically is to call this endpoint /v1/payments/payment/payment_id you can see the sample curl call with that you will be able to do that call in the language that you want


internalModuleBaseUrls always points to https://localhost:4321/

Category

[ ] Question
[ ] Typo
[ X] Bug
[ ] Additional article idea

Expected or Desired Behavior
After:
gulp clean
gulp bundle --ship
gulp deploy-azure-storage --ship
gulp package-solution --ship
I expect in manifest.json the internalModuleBaseUrls set to CDN url which is not the case. internalModuleBaseUrls always points to https://localhost:4321/.
Steps to Reproduce
Create an ApplicationCustomizer and select tenant wide activation.
In write-manifests.json set CDN URL:
"cdnBasePath": "https://somestorage.blob.core.windows.net/spfx/"
In package-solution.json set:
"includeClientSideAssets": false,
"skipFeatureDeployment": true,
Configure deploy-azure-storage.json:
"account": "somestorage",
"container": "spfx",
"accessKey": "********************************************=="
Run above gulp sequence and check dist/manifest.json
internalModuleBaseUrls stillpoints to https://localhost:4321/

An update:
The json file 875f8463-ede2-4fc7-b6ff-1feeaf02ecda.json in azure storage has the right CDN url in internalModuleBaseUrls.
And everything is working now well. Don't know what the problem was :-(


Update README.md

Layer5 logo added

@raghavaggarwal99 will you take a moment to sign-off on your commit? - https://github.com/layer5io/service-mesh-benchmark-spec/pull/9/checks?check_run_id=349211147


merge pause and unpause functions, also event

Fixed in https://github.com/soroswap/aggregator/pull/28


Schema prep

This request includes code refactor to move initialization of lookup data from during amber session creation to amberdb instantiation so that this initialization will only be called once.

@scoen @terenceingram @brycollins @ato @AaronCMuller could you please have a look?

Summarising the discussion we had in person:

Moving the schema migration into AmberDb is good.
Using a single global Lookups DAO is unnecessary as creating them is relatively cheap and sharing DAOs means sharing database connections which can cause threading issues (particularly when transactions, multi-step temporary-table queries, or high contention are involved)
The use of statics should be avoided (the correct way to pass objects between the two classes would be do it via the AmberSession constructor, but in this case we don't actually need to do that)

So I think the right approach to this is:

Create one local Lookups DAO for the schema migration and close it immeidately after schema migration is complete.
Create one Lookups DAO for each AmberSession in AmberSession.init() and store it as an instance field.

This still means that the session is holding onto two database connections. It would be best to share the same DBI between AmberGraph and Lookups, that might require some more refactoring.

Actually just realised the Lookups DAO is onDemand, so it won't be holding a database connection. That's not too bad then.

Looks good to me! :+1:

@scoen can you give this a quick look too? I'm not super familiar with the AmberDb code and while this looks good to me I might be missing something.

@scoen, @ato, @AaronCMuller,I've updated code to include suggested changes, please have another look.


SignalRClient.start() may get stuck on keepalive timeout and closed TCP connection

Discussed in https://github.com/theOehrly/Fast-F1/discussions/627

Originally posted by supremeremixx August 19, 2024
Hello!
I'm trying to run endless loop with SignalRClient.
import time
import logging
from fastf1.livetiming.client import SignalRClient

log = logging.getLogger()
log.setLevel(logging.DEBUG)

def signalr():
  client = SignalRClient(filename="output.txt", timeout=1800, debug=True)
  client.start()

while True:
  signalr()
  time.sleep(60)

After random amount of time (3, 5 , 11 hours...) I get keepalive timeout error. In logs I see that TCP connection is closed, but function client.start() still blocked, it never ends. Loop is never finished and that's why program not creating a new client instance after error.
python3[282709]: 2024-08-09 21:36:44,532 - DEBUG: ! timed out waiting for keepalive pong
python3[282709]: 2024-08-09 21:36:44,533 - DEBUG: ! failing connection with code 1011
python3[282709]: 2024-08-09 21:36:44,535 - DEBUG: = connection is CLOSING
python3[282709]: 2024-08-09 21:36:44,535 - DEBUG: > CLOSE 1011 (internal error) keepalive ping timeout [24 bytes]
python3[282709]: 2024-08-09 21:36:54,536 - DEBUG: ! timed out waiting for TCP close
python3[282709]: 2024-08-09 21:36:54,536 - DEBUG: x closing TCP connection
python3[282709]: 2024-08-09 21:37:04,539 - DEBUG: ! timed out waiting for TCP close
python3[282709]: 2024-08-09 21:37:04,539 - DEBUG: x aborting TCP connection
python3[282709]: 2024-08-09 21:37:04,540 - DEBUG: = connection is CLOSED
python3[282709]: 2024-08-09 21:59:44,619 - WARNING: Timeout - received no data for more than 1800 seconds!

I've tried running it with and without timeout (in SignalRClient), but the function remains locked.
Is it possible to somehow terminate it after receiving an error?

Hello @theOehrly !
I made a little research so maybe this information will help you to fix this bug.
When I tried to run SignalRClient with timeout, after receiving an error and the timeout time has expired, the function client.start() was stucked in loop while self._connection.started in _supervise (livetiming->client.py).
    async def _supervise(self):
        self._t_last_message = time.time()
        while True:
            if (self.timeout != 0
                    and time.time() - self._t_last_message > self.timeout):
                self.logger.warning(f"Timeout - received no data for more "
                                    f"than {self.timeout} seconds!")

                self._connection.close()
                while self._connection.started:
                    await asyncio.sleep(0.1)
                return

            await asyncio.sleep(1)

Apparently, since the connection has already been closed due to the error that occurred, the self._connection.close() function does not set the self._connection.started flag to False. For testing I manually added self._connection.started = False after close() function and SignalRClient was shutted down!
For another example, you can add these lines to the received message handler. If only the self._connection.close() function is there, I can see in the logs how the connection is closed, but the function remains in a blocking state (in fact it is a simulation of an error occurrence), but if you add self._connection.started = False after that, the function is terminated.
In normal conditions after self._connection.close() is called it trying to call self.__transport.close() (signalr_aio->transports->_transport.py) which is sents CloseEvent() to ws_loop.
def close(self):
    asyncio.Task(self.invoke_queue.put(CloseEvent()), loop=self.ws_loop)

And when _producer_handler receive this event it trying to close websocket connection and set self._connection.started = False (essentially the same behavior as in _supervise)
  async def _producer_handler(self, ws):
      while True:
          try:
              event = await self.invoke_queue.get()
              if event is not None:
                  if event.type == 'INVOKE':
                      await ws.send(dumps(event.message))
                  elif event.type == 'CLOSE':
                      await ws.close()
                      while ws.open is True:
                          await asyncio.sleep(0.1)
                      else:
                          self._connection.started = False
                          break
              else:
                  break
              self.invoke_queue.task_done()
          except Exception as e:
              raise e

So as I understand this bug can be fixed by adding self._connection.started = False to some error handler of websocket connection. I tried to find it myself, but couldn't. That is why I decided to detail my observations for you.
Hope it helps!

@supremeremixx thank you for investigating this more. This is helpful information, for sure. Maybe I'll be able to fix it soon.
Also, it would probably be best to raise an exception here instead of simply returning from the function. After all, this is not an intended or expected way to close the connection, but rather it is some sort of connection error.


Allow non .aprc File.readable? calls

stub_dotfile! was blocking all calls to File.readable? instead
of just calls to load the .aprc file. This meant that trying to
use other libraries, such as pry, which relied on File.readable?
would fail in instances where stub_dotfile! had been called.
This change fixes that, while keeping the original intended
behaviour.

The reason for the build failures is that ActiveRecord 5 was just realeased: https://github.com/travis-ci/travis-ci/issues/6243

Those failed checks should now be fixed by https://github.com/awesome-print/awesome_print/pull/252


README: add @chenrui333

[x] Have you followed the guidelines in our Contributing document?
[x] Have you checked to ensure there aren't other open Pull Requests for the same change?
[x] Have you added an explanation of what your changes do and why you'd like us to include them?
[x] Have you written new tests for your changes? Here's an example.

[x] Have you successfully run brew tests with your changes locally?

Have contributed many changes in homebrew-core, want to join the homebrew team :)

Sure
On Aug 23, 2019 4:06 PM, "chenrui"<EMAIL_ADDRESS>wrote:
Have contributed many changes in homebrew-core, want to join the homebrew
team :)
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/Homebrew/brew/pull/6399?email_source=notifications&email_token=AMWGPGOSQK3OB6HD5O7G6GDQGA7OBA5CNFSM4IPC47HKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5BGMGQ#issuecomment-524445210,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AMWGPGOYTBGV2FA5WHXVUMLQGA7OBANCNFSM4IPC47HA
.

@chenrui333 Welcome to the team! Please rebase this on origin/master, run brew man, commit the changes and let me know when it's ✅.

@MikeMcQuaid Just did:

 git rebase master
brew man
forced update

@chenrui333 You need to also git commit those changes from brew man.

I just copied the brew man changes into the repo. Not sure if that works.

You need to also pull the latest changes from Homebrew/brew. Try:
cd `brew --repo`
git checkout -- docs/Manpage.md manpages/brew.1 manpages/brew-cask.1
git pull --rebase origin master
brew man

and commit/push those changes.

That seems much more clear, thanks @EricFromCanada !

I should also point out that the file you need to add your name to is /README.md. The brew man command reads this file to generate the Markdown and manpage files.

I see, 🤣 I am adding the README.md change now.


left for lunch and came back, system was out of sync after I logged back in to my cpu

Product and Version [VS/VSCode]:
OS Version [macOS/Windows/Linux]:
Live Share Extension Version:
Target Platform or Language [e.g. Node.js]:
What were you doing when you encountered the desync?
How often have you encountered desyncs?

I'm going to close this as a dupe of #2086. If you encounter this problem again, please upload your logs to #2086 and join the conversation there.


Add support to include kid claim to backend JWT header

Purpose

Resolves https://github.com/wso2/api-manager/issues/1839

Closing since the changes were added via https://github.com/wso2/product-apim/pull/13268


request: publish the artifact on public maven repository

Thank you for your interest in this library!
It is unfortunately not production-grade, as I designed it at a time when I was playing around with functional program design in Scala. For that matter, a public release as a Maven artifact is not planned, but you may choose to use the library as you please.


Add travis.ci support

beginning with https://github.com/ontodev/robot to parse the ontology
The robot utility was recommended by Mathew Horridge, a core committer on the OWL-API.
connected to #24

If using robot is accepted, as proposed here in this PR, additional validations are possible, e.g.
robot validate-profile --profile DL -i ./target-ontologies/bibliotek-o.owl > /tmp/owl-dl_validation.txt
cat /tmp/owl-dl_validation.txt
# grep the file "/tmp/owl-dl_validation.txt" for any specific errors


fix csv links in the Submission List sidebar

@willemarcel did you test that issue we discussed on Slack? Where the CSV was only downloading some of the submissions and not all of them?


easel checks the existence of tables every time even after the installation

I was working on the cache for the easel, and realised that the framework checks the existence of table every time.
I think an install.lock file would be more appropriate.
I commented all unnecessary code in SetupHelper personally

@ChristianYeah What do you mean it checks for the existence of a table every time? The requiredTablesExists() method is meant to check for existing tables on a fresh installation, and then it's unused throughout the rest of the application. What code did you comment out in SetupHelper.php?

@austintoddj problem is, it still work after the installation. Can you double check it again? or only I have this problem

@ChristianYeah this should resolve your issue: https://github.com/cnvs/easel/commit/f9ff298b4feed4eadd45435712d5596777df8430


Replace pydocstyle with Ruff

Fixes #86
Pydocstyle was deprecated in favor of Ruff. Ruff has the exact same lints via the D ruleset.
As before, we only run the doc checks on source code and not tests.

Thanks @Eric-Arellano !

@Mergifyio backport stable/0.7


NotNull vs NotEmpty

 public virtual Task<IReadOnlyList<string>> ReverseEngineerAsync(
        [NotNull] string runtimeProviderAssemblyName,
        [NotNull] string connectionString,
        [NotNull] string rootNamespace,
        [NotNull] string projectDir,
        CancellationToken cancellationToken = default(CancellationToken))
    {
        *Check.NotNull(runtimeProviderAssemblyName, nameof(runtimeProviderAssemblyName));*
        Check.NotEmpty(connectionString, nameof(connectionString));
        Check.NotEmpty(rootNamespace, nameof(rootNamespace));
        Check.NotEmpty(projectDir, nameof(projectDir));

Why check.NotNull here, and not Check.NotEmpty?

Correct. Should be NotEmpty. Maybe a leftover from when we passed around the actual assembly rather than it's name.

@lajones I am happy to do a PR - ??

@ErikEJ Don't worry. I'm working in that area right now. I'll just include it on my next check-in.

Fixed by #2598