Nvidia GPU Support

Nvidia GPU support
Some creds to @clkao for some work on the repo.
Compatibility:

Ubuntu 16.04 (Centos should not be a problem, to add, only need to add the nvidia docker repo i think)
Not all docker versions work since nvidia container runtime should match docker version, tested with 17.12 (17.09 / 17.06, 17.03 should work)

Still to do:

Add daemonset for Nvidia

# For Kubernetes v1.8
kubectl create -f https://raw.githubusercontent.com/NVIDIA/k8s-device-plugin/v1.8/nvidia-device-plugin.yml
# For Kubernetes v1.9
kubectl create -f https://raw.githubusercontent.com/NVIDIA/k8s-device-plugin/v1.9/nvidia-device-plugin.yml

What it does

install Nvidia drivers (no X, no drm) (on nodes with gpu)
install Nvidia runtime container (on nodes with gpu)
set docker container runtime to nvidia-docker on nodes with gpu

How it works:
In your inverntory you should add a group [gpu-node] which contain nodes which also have Nvidia GPU (they should also be added to the kube-node group).
In k8s-cluster.yml you should set
docker_nvidia_enabled: true
kube_feature_gates:
  - DevicePlugins=true

You can set the Nvidia Driver version
nvidia_driver_version: 384.111

After deployment, and depending of your kube version, you should apply
# For Kubernetes v1.8
kubectl create -f https://raw.githubusercontent.com/NVIDIA/k8s-device-plugin/v1.8/nvidia-device-plugin.yml
# For Kubernetes v1.9
kubectl create -f https://raw.githubusercontent.com/NVIDIA/k8s-device-plugin/v1.9/nvidia-device-plugin.yml

Thanks for making #2158 obsolete!  I wonder if the gpu-node should be a node attribute rather than group? if you have a full-gpu cluster the inventory is going to be quite verbose and redundant.

Good point, but if you make a atrribute, you should have a host_var/<hostname> for each host right?
and if you have a full gpu cluster you could also use
[gpu-node:children]
kube-node

I meant something like:
[kube-node]
node1 docker_nvidia_enabled=true
node2 docker_nvidia_enabled=true

removed the check on supported distro versions
added centos/redhat (tested on centos 7) support

Wow, nice feature , There are some conflicting files.

ah my knowledge of github pull requests is still somewhat limited. I didn't know i had to resolve the conflicts.

is the submodule properly configured? I think you need to include .gitmodules in the PR

@clkao , the nvidia module in this repo, not added as a submodule. Please let me know if you want to have it in another way. The role itself is very simple.

the file diff does say it's a submodule?

ci check this

cc @squat
Could do a short review?

Hi,
A lot has changed since k8s 1.10 (and in the end of 1.9) i see. I have to agree with @squat on most things. It is probrally going to take some time to get this working, but in the end the code on the kubespray part should be simpler. I'll be back :)

So i've almost ready with the new solution. It makes no sense to use this PR for it. I will open a new PR and close this one.

thx


Add EIP-6049 for Shanghai support

EIP-6049: Deprecate SELFDESTRUCT
This might be as simple as just adding a deprecated warning on the EVM when Shanghai is activated in an EVM instance?

Hey, we already talked about this, but it feels very strange when you are commenting like this after you said you would DM me changes


Update bb-storage and dependencies

Many of the shared config items in bb-storage have changed (like config.global), making it difficult to share that between 'latest' bb-remote-asset and bb-storage.  This is a combination of go get, bazel run //:gazelle -- update-repos -from_file=go.mod, and updating the targets in the bazel remote-execution repo that bb-storage is renaming.  But honestly I have no idea what I'm doing.

Needs buildbarn/storage#119 and another go get first.

@Qinusty Could you take a look here too

Looks like the remote-apis project is still using the go_default_library naming @jlaxson https://github.com/bazelbuild/remote-apis/blob/master/build/bazel/remote/execution/v2/BUILD#L57-L61

Yes, but it's patched by bb-storage (we were already doing this for the execution package) https://github.com/buildbarn/bb-storage/blob/master/patches/com_github_bazelbuild_remote_apis/golang.diff.  I don't really understand when/why gazelle chooses go_default_library vs execution - I fixed that patch because it insisted that the correct name was execution

hmmmm, are you able to reproduce these gazelle diffs locally? I'm not exactly sure what is causing this because the patch seems to be correct using the version of bb_storage in go_dependencies.bzl

@tomcoldrick-ct I pretty sure this is obsolete now, can you confirm, please?

This is now obsolete.


Upgrade remark-mermaidjs to latest v6.0.0 to support mermaid v11+

It appears that gatsby-remark-mermaid is locked into v10 of mermaid:
From the dependencies of gatsby-remark-mermaid's package.json:

"dependencies": {
"remark-mermaidjs": "^5.0.0",
...

From the dependencies ofremark-mermaidjs's 5.0.0 package.json:

"dependencies": {
...
"mermaid-isomorphic": "^2.0.0",
...
}

Further looking into mermaid-isomorphic's 2.0.0 package.json:

"dependencies": {
...
"mermaid": "^10.0.0",
...
}

This is preventing the use of mermaid v11+ features such as architecture and packet.
Would appreciate bumping the remark-mermaidjs package used by gatsby-remark-mermaid to the latest version 6.0.0.

I’ll get to it soon. mermaid-isomorphic 3.0.0 was just released.

Awesome, thanks @remcohaszing!


Syntax Error

If you go to packages -> react-static-tweets  folder you will find a syntax error at import time in Readme.md file.
This should be something like this -
import { fetchTweetAst } from 'static-tweets'
Take a look below-

@transitive-bullshit  Can I start working on this issue?

@transitive-bullshit Can I start working on the above issue?

@Gulshanaggarwal if you're able to fix this issue, that'd be great. I think it's just a vscode issue w/ not supporting composite tsconfigs completely, but I could be wrong.


no way to delete a patchset?

Or maybe I just don't see it

Fixed by https://codereview.chromium.org/873593007


Implements Reachable Smart Tag

Depends on: https://github.com/libp2p/go-smart-record/pull/20
This PR implements the Reachable smart tag. This smart tag detects if any of the entries of a Set or Dict is a multiaddrs, and if it is, it checks their reachability. The smart tag only keeps multiaddrs that are reachable, discarding the rest. The rest of entries in the node which aren't multiaddrs are kept "as-is".

[x] Reachable smart tag.
[x] Updates assembleContext to include host.
[x] Basic tests

Hey, @petar. I've adressed your comments and split the reachable tag into connected and dialable as suggested (I think it makes total sense to have it this way). Let me know if you have any additional feedback before merging. Thanks!


/**/ with nothing between produces an unterminated block comment

This breaks both the plugin and the runner

Also breaks if the next character after the first /* is /

fixed in the tokenizer rewrite.

jolk


'duplicated mapping key' error with unique keys

I think I've found an issue when dealing with a YAML mapping containing a large number of keys.
This can be reproduced by running this minimal example through the JS-YAML Demo
This is my minimal example (I'm not including it as a code block here due to the number of lines):
https://gist.github.com/MGough/e38b2cf7b41c151ba8216b77a08c9177
It looks almost like a hash conflict, once the final key/value pair is removed the issue goes away. You can remove a different key value pair and the issue persists. From what I can tell there aren't any duplicate keys. This was also an issue when there were more keys after the final one in this example, I've just removed them as they were redundant.

Seems like it's not specific to the number of keys, I'm guessing it's something else I've missed perhaps like a whitespace issue. Although other YAML validators online show it as valid

Minimized example
a:
<PHONE_NUMBER>8167781E58455: 2335
<PHONE_NUMBER>4352832E11281: 2452

Minimized example
10513478508167781E58455: 2335
11193430644352832E11281: 2452

both keys => big integers in scientific notation<PHONE_NUMBER>8167781 e 58455) => Infinity => duplicated infinity.
Seems work as expected. Who generated this yaml data? I would strongly recommend to quote keys. May be other langs can each huge numbers, but JS - no.

Thank you! Apologies for bringing you an issue that's ultimately not yours, my lack of JS expertise would've had me working on that for days 😆 . I hadn't spotted the E at all.
As for where it came from, it was actually generated using the python yaml library. I think what has happened is that the python yaml library quite happily serialized a python dict, which can have any object as a key, rather than serializing JSON.

https://github.com/yaml/pyyaml/issues/173 AFAIK, there may be difference between spec and real code due need of JSON compatibility. But i don't remember details.
In theory, according to spec, your dump is correct, because scientific notation must have sign before exponent: 1e+5. BUT json is ok without sign too (and YAML is declared as JSON-compatible):
node -e 'console.log(JSON.parse("1e5"))'

If anyone wish dive into spec sugges changes - i'm open to suggesion.


exposing prefixes

related to https://github.com/buda-base/public-digital-library/issues/77 : there should be a way to expose prefixes used on our platform (those of (lds-queries](https://github.com/buda-base/lds-queries/blob/master/public/prefixes.txt)) in a simple manner. I think the most simple would be to have a /prefixes.ttl endpoint, serving a ttl file with no triple but all the prefixes definitions. Note that the format of the .txt file in lds-queries is not the same as the ttl format prefix declaration.

this was addressed in  commit bd1c21e ( see http://purl.bdrc.io/prefixes)

perfect, thanks a lot!


Exception when running self host in Mono

I am having a weird exception thrown when running in Mono, I have tried to debug but I have no luck to find that mysterious type not found...
Details with the exception (including a simple example to reproduce) are here https://gist.github.com/cprieto/d70db69ecf4fcf9aaf50
Thanks a lot for your help
Running in Mono 4.0.1
Tested in MacOSX, FreeBSD and Ubuntu Linux, not luck at all :(

+1 Exact same issue here

If Swashbuckle.Core would be compiled for .net 4.5 I think it would work.
The current reference to System.Net.Http is to the NuGet package (assembly version <IP_ADDRESS>), but with .net 4.5 it would reference the framework assembly includes in .net 4.5 (assembly version <IP_ADDRESS>).
Apparently mono resolves the assemblies different from ms.net.

Same issue here with the mono docker image and the microsoft/aspnet image.

@rjvdboon +1
Mono: Failed to load assembly Swashbuckle.Core[0x10f7b10]
Mono: Could not load file or assembly 'System.Net.Http, Version=<IP_ADDRESS>, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a' or one of its dependencies.

In Mono versions prior to the latest at the time of this post (5.2.0 SR4, <IP_ADDRESS>) the assembly redirect was not working for whatever reason.  Updating Mono to the latest fixed the problem for me, and the assembly redirect is no longer necessary.
I also noted that targeting .NET Framework 4.5 will automatically update Swashbuckle.Core's internal reference to System.Net.Http to 4.x which would also likely resolve the issue on older versions of Mono.
I would recommend closing this issue.

Can confirm the above.


typing: Use user IDs instead of user ids string.

Testing Plan:

Check that correct payload is sent and the typing request is successful in devtools.

While testing this, I noticed a pretty nasty bug, which is basically that if you just keep typing, it'll randomly send stop notifications.  I fixed it in this change and pushed it back to this PR:
diff --git a/static/js/typing_status.js b/static/js/typing_status.js
index 8fa4a4fd8d..84a7a89dd1 100644
--- a/static/js/typing_status.js
+++ b/static/js/typing_status.js
@@ -91,7 +91,9 @@ exports.handle_text_input = function (worker) {
     var current_recipient = exports.state.current_recipient;

     if (current_recipient) {
-        if (new_recipient === current_recipient) {
+        // We need to use _.isEqual for comparisons; === doesn't work
+        // on arrays.
+        if (_.isEqual(new_recipient, current_recipient)) {
             // Nothing has really changed, except we may need
             // to send a ping to the server.
             maybe_ping_server(worker, new_recipient);

Because that's a pretty subtle bug that's a pain to find and track down via manual testing, it would be awesome if you can tweak the frontend node tests in frontend_tests/node_tests/typing_status.js to fail without my little fix.  It looks like they need to be updated in any case, since they have strings for current_recipient, which was wrong before and even more wrong now.

@timabbott I added test to check weather we use correct logic to compare new_recipient and old_recipient. It also fails when we use === check for arrays, thus effectively catching subtle bugs you encountered.
(As a side note, when we migrate to typescript we won't have to worry about subtle bugs of this types since typescript would complain that we can't compare arrays with ===.)

Yeah, typescript will definitely help avoid similar bugs, though I think the test improvement is still definitely valuable, since fundamentally we could have other logic bugs in this code path, and it's definitely not good that we didn't have coverage on this core part of the logic.
Merged, thanks @priyank-p!


python3Packages.catalogue: fix expression

Motivation for this change
fix a minor boo boo from 377242d5875b871faed3a942161185594b8f32fa
can't do nixpkgs-review while staging is like this :(
error: while evaluating anonymous function at /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/lib/meta.nix:46:54, called from undefined position:
while evaluating 'isDerivation' at /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/lib/attrsets.nix:305:18, called from /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/lib/meta.nix:46:62:
while evaluating 'callPackageWith' at /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/lib/customisation.nix:117:35, called from /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/pkgs/top-level/python-packages.nix:1037:15:
while evaluating 'makeOverridable' at /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/lib/customisation.nix:67:24, called from /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/lib/customisation.nix:121:8:
duplicate formal function argument 'pytestCheckHook' at /home/jon/.cache/nixpkgs-review/pr-97008-2/nixpkgs/pkgs/development/python-modules/catalogue/default.nix:5:3

Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
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 nixpkgs-review --run "nixpkgs-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[x] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Ensured that relevant documentation is up to date
[x] Fits CONTRIBUTING.md.

can't really do nixpkgs-review.... because it's broken until this gets merged, but:
[14:53:13] jon@nixos ~/projects/nixpkgs (fix-staging-catalogue)
$ nix build -f . --keep-going python3Packages.catalogue python37Packages.catalogue
[39 built, 3 copied (83.4 MiB), 16.2 MiB DL]

appears this isn't needed after  #97076


installing keras in macbook m1

I am not able to install Keras.
previously when I installed TensorFlow the ram used to crash but with python 3.4 the issue was resolved but now i am not able to install Keras. is there any fix for the issue!!
thank you!!

possible to install following https://developer.apple.com/metal/tensorflow-plugin/
but crash in runtime

You may also refer https://github.com/apple/tensorflow_macos/issues/101


MetroAE always requires VSC system interface to be UP, even when no system_ip is set

The VSC healthcheck prevents a successful upgrade in case a VSC configuration is used which has no system_ip

If possible could this be changed on new system deployment also? It's very common to not use system interface, avoiding the need to have an IGP to allow this interface connectivity. So the target is to use control interface IP as BGP source address instead of system IP.


Isolate Docker references to DockerCluster

In preparation for adding other types of clusters to presto-admin product
tests, refactor methods that mention "docker" or "containers" to not
do so, and move all uses of docker client into DockerCluster. Add some more
additional cluster arguments to BaseProductTestCase methods, so that
the cluster installation can be done by DockerCluster.
Refactor dump_and_copy_topology to use the write_content_to_host method,
since it was duplicating logic.
Testing: make clean test-all

In the next patch, I'll make a cluster that has the same methods as DockerCluster but which connects to an arbitrary cluster you specify by IP.  @rschlussel @petroav , can you review please?

looks good


Add accessibility to the glitch tag

Because these tags replace regular text, they can break self-voicing (and maybe other a11y features). This is a fix for the glitch tag, making it add alt text automatically. You can test it by hitting "V" to turn on self-voicing, then hovering over any text.
I'd love to see the other tags get alt text added, but this is the only one I'm using right now, so it's the only one I've fixed on my own.

Much appreciated. I'll try and take this and later make a more standard way of doing this so other text tags have this built in. Not sure when I'll get to it but I'll note it down.


Endorsements return non-whole numbers.

Another pesky Blizzard change for you to try to sort out.
Up until about yesterday endorsements would return whole numbers for each type of endorsement. Today, however, they return numbers below one. I believe these numbers are percentages because when they're added up, they always add up to one.

Job's done, change is live, should make it a bit easier to deal with.
Used decimal for increased precision because it seems like you might want to be precise with this.

Man, I've got to thank you for being so responsive to this project.  I'll miss that.


SGID is not truly optional

The initiation of the client will throw if the env vars are not defined. Should create a higher level wrapper.

Fixed by #111


Update create-a-shared-mailbox.md

added steps to disable Automapping

@nenonix @JohanFreelancer9 - kindly do the copy editor review for this PR. Thanks.

@cmcatee-MSFT - PR is ready for final review following your recommended changes. Please assist to merge. Thank you.


partition allocation and even distribution and resource usage across consumers in a group

Let's say I have topic with 15 partitions, which is currently consumed by a group of 3 consumers and each running on a difference instance.
Now with parallel consumers :
a) For achieving parallel partition order, is it always a good practice to start with good high max-concurrency ( even if some threads are idle). If I execute 20 max-concurrency on each instance, 5 threads will run on each consumer and rest will be idle. I am asking this because if we downscale our system ( remove an application node) from 3 to 2, will it be running 7 & 8 (total 15) threads per instance ? Does it auto-adjust the thread-pool size on every instance, based on no-of consumers in group ?
b) In same fashion (for achieving parallel partition order) , if we add more consumer ( add an instance) to the group, does load sharing among instances change automatically ? For example if I increase consumers from 3 to 4, will each instance be running 4,4,4,3 threads respectively,
c) For achieving unordered / key ordering : In case of upscale / downscale, does load distribution adjustment happens automatically among instances.

Hi @rajatgoyal247341 , do you not want any help with this anymore?
The max concurrency setting is per instance only, not global. However, this could potentially be changed to an optionally global setting. Is that something that you'd find useful?


Added Alignment docs for FractionallySizedBox

Fixes https://github.com/flutter/flutter/issues/11769
Pre-launch Checklist

[x] I read the Contributor Guide and followed the process outlined there for submitting PRs.
[x] I read the Tree Hygiene wiki page, which explains my responsibilities.
[x] I read and followed the Flutter Style Guide, including Features we expect every widget to implement.
[x] I signed the CLA.
[x] I listed at least one issue that this PR fixes in the description above.
[x] I updated/added relevant documentation (doc comments with ///).
[ ] I added new tests to check the change I am making or feature I am adding, or Hixie said the PR is test-exempt.
[ ] All existing and new tests are passing.

If you need help, consider asking for advice on the #hackers-new channel on Discord.

Should I add the example for FractionallySizedBox as well @HansMuller

test-exempt: only affects comments

Done @HansMuller


feat: redesign and wc fixes

This PR is the an attempt at giving use-contractkit a fresh look, inspired by rainbowkit slick UI.
This also attempts to refactor the tailwind css classes to make it a bit easier to maintain. (TBD: will we keep tailwind?)
This also attempts to fix the following issues:
[fix #129]
[fix #167]
[fix #166]
[fix #165]
[fix #154]
[fix #144]
[fix #143]
[fix #171]
[closes #159] from @Henrynunez112

Codecov Report

Merging #169 (fa1ec4d) into master (5ef3f4f) will decrease coverage by 0.51%.
The diff coverage is 46.84%.

@@            Coverage Diff             @@
##           master     #169      +/-   ##
==========================================
- Coverage   51.23%   50.72%   -0.52%
==========================================
  Files          44       48       +4
  Lines        1212     1378     +166
  Branches      173      202      +29
==========================================
+ Hits          621      699      +78
- Misses        447      511      +64
- Partials      144      168      +24

Impacted Files
Coverage Δ

...contractkit/src/connectors/useMetaMaskConnector.ts
17.39% <ø> (ø)

...ckages/use-contractkit/src/contract-kit-reducer.ts
42.85% <ø> (ø)

packages/use-contractkit/src/types.ts
75.00% <ø> (ø)

...es/use-contractkit/src/use-contract-kit-methods.ts
38.20% <0.00%> (-2.03%)
:arrow_down:

packages/use-contractkit/src/use-contractkit.tsx
100.00% <ø> (ø)

packages/use-contractkit/src/utils/sort.ts
57.14% <ø> (ø)

packages/walletconnect-v1/src/types.ts
86.66% <ø> (ø)

...actkit/src/connectors/useWalletConnectConnector.ts
16.21% <4.76%> (-1.65%)
:arrow_down:

packages/use-contractkit/src/components/qrcode.tsx
20.40% <20.40%> (ø)

...ges/use-contractkit/src/screens/wallet-connect.tsx
30.30% <25.80%> (-47.48%)
:arrow_down:

... and 28 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5ef3f4f...fa1ec4d. Read the comment docs.


Use SecureHeaders namespace for OPT_OUT docs

The documentation for upgrading to 4.0 suggests using OPT_OUT for
cookie values you don't wish to set however this throws a NameError
NameError: uninitialized constant OPT_OUT

To correctly resolve the OPT_OUT value, we need to use the
SecureHeaders namespace.

agggghhh, you're not going to believe that i missed the line below this that has the same error 🙄


Electrolizer blockage

Not a bug, but issue is useability
The electolizer becomes blocked if (for example) hydrogen tanks are full, but oxygen is being used.  This is an issue on space stations, for example. Either the electrolizer needs to be updated to to void excess liquids, or a block needs to be added to void the gas.
version 1.0.16 for 1.10.2
no fixes found on change log

requires similar fix as to #835

Is this still a issue? Please comment if it is and i will reopen if if you are unable? We are closing old issues to see what is still relevant and needs to be fixed.


Discord - Forum Channel

@dhh can you create a forum channel on discord? It will help to answer community questions in an organized way and also serve as documentation for future references.
Currently, I'm answering people's questions in the #general channel and that's getting disorganized.
more info on forum channels https://support.discord.com/hc/en-us/articles/6208479917079-Forum-Channels-FAQ

You can also answer and/or discuss things in a thread off of a message, that would definitely keep things organized


add test to check llama gradient with dort

Codecov Report
Attention: 30 lines in your changes are missing coverage. Please review.

Comparison is base (7ccaade) 76.16% compared to head (5badc34) 74.96%.

Files
Patch %
Lines

onnxrt_backend_dev/llama/llama_helper.py
61.53%
30 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main       #5      +/-   ##
==========================================
- Coverage   76.16%   74.96%   -1.20%
==========================================
  Files           8        9       +1
  Lines         709      787      +78
==========================================
+ Hits          540      590      +50
- Misses        169      197      +28

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


Different lifecycle for AgentInvoker vs AgentRunner when onStart hits exception

Nit picking, but:
https://github.com/real-logic/agrona/blob/master/agrona/src/main/java/org/agrona/concurrent/AgentInvoker.java#L107
The invoke will be skipped if closed, but a failure onStart does not trigger a close()
Compare with AgentRunner where we clearly skip doWork calls if onStart() fails:
https://github.com/real-logic/agrona/blob/master/agrona/src/main/java/org/agrona/concurrent/AgentRunner.java#L154
For consistency we can add a running flag, or switch to using a state enum, such that invoke does nothing if the onStart failed. This is still quite opaque to caller which will need some external visibility to the Invoker broken state.

Calling close() should be the responsibility of the caller to pair up with start().

coupled with further commit: https://github.com/real-logic/agrona/commit/8368144e804515daa635aeedf7822ad4b046be25
This is now resolved


Minimum ASCII Delete Sum for Two Strings

Problem Link
https://leetcode.com/problems/minimum-ascii-delete-sum-for-two-strings/
Coding platform
Leetcode
Programming language

[ ] C
[x] C++
[x] Java
[ ] Python

Additional context (OPTIONAL)
I want to solve it in Java

I would like to do this in c++

Hi @Nivedita967
I would like to work on it in Java . Please assign it to me.

Hi @Nivedita967
I would like to work on it in Java . Please assign it to me.

Sure @abhinav5481


[#168104305] Upgrade node version

JS target version is already es6 like other io-functions-* projects.

Affected stories

🌟 #168104305: Migrare io-functions-commons a node 10.x

  Generated by :no_entry_sign: dangerJS against 70b7b0fc3cc6ca9c43c4e8e58c9342e1321b3714

node greater than 10.8.0 supports es2018, we should start targeting that, instead of the older es6

released v1.0.0


You appear to have dropped some special characters

Describe the bug
Some special characters are not displayed inside the linked note
To Reproduce
Steps to reproduce the behavior:

Go to https://docs.microsoft.com/en-us/previous-versions/windows/it-pro/windows-server-2012-r2-and-2012/hh945104(v=ws.11)
Search for "You must type the name exactly as it appears in the Subject field"
Notice that the same note text appears 3 times. It is displayed correctly once, and incorrectly twice.

Expected behavior
* is displayed in all notes
Screenshots
Good:

Bad:

Desktop (please complete the following information):

OS: Windows 10
Browser Firefox
Version 102

Additional context
To further add to the confusion the example given nps*.example.com is not a regular expression (well, technically it is, but it matches things like npnexample.com and npsssssxexamplexcom not nps1.example.com. Proof here.). It is a glob pattern. The dialogue itself contains an example that uses real regular expressions, so it is very unclear weather I should use glob patterns or real regular expressions.

Thanks for the report. That link is an outdated one that is archived. I have updated the links in the current documentation to point to the updated documentation (https://learn.microsoft.com/en-us/windows-server/networking/technologies/extensible-authentication-protocol/network-access) that we're still working on updating.
As that your point on the confusing regex - thanks! You're correct, it should be regex, not glob patterns. I will get that updated too.


Add WalletConnect Support to Kitty Items

Working POC, demoed on Friday.
Some KI buggies to squash and hoping for an update by @MrDSGC to remove grpc


[move-stdlib] Add swap_or_fill

Adding another version of swap that supports None value prior to swap.
This can be a common use case too, and a lot easier to do within the Option library.
Added tests and updated docs.

This looks good to me and the naming is better :)
Not sure if you can land or not -- happy to land if you can't

@tzakian Indeed I cannot merge it. Thank you!
Also there seems to be a unit test failure, but I couldn't see where it actually is failing, and couldn't repro locally.

The unit test failure is a flake. Let's see whether it can
/land

:broken_heart: Test Failed - ci-test

Flake.
/land

:broken_heart: Test Failed - ci-test

So this is in fact not a flake, but something wrong with the generated artifacts. Try cargo run in move-stdlib to regenerate artifacts.,

Rebased. cargo run doesn't change anything though. Let's see if rebasing solves the issue

From the looks of it, the source hash of the move stdlib is changing, which is causing the "git up-to-date" checks for the DPN and experimental frameworks to fail -- so you need to regenerate those artifacts. You can do this by running
cargo run

and
cargo run --package experimental

in diem-move/diem-framework

Cool.
 Pushed with the changes.
However cargo run --package experimental didn't work (complains package not found)

You may need to add an additional -- in front, i.e., something like:
cargo run -- --package experimental

You should see some regenerated files under experimental as well with it. If not let me know and I can dig into it

I have pushed with the right commands. Let's try landing again? Thanks!


Document C/C++ interfaces

We essentially need to triplicate the docs: C++, C, Fortran.

Can we lift docs from C++ interface? Particularly, can we use doxygen to link to those chunks?
Can we get statistics of the number of apps using C++/C/Fortran?

Need corresponding domain model in ReadTheDocs (or Doxygen) as well for a high level overview of design and structure

For now will just document c interface as it is closer to fortran than c++ and c++ users could use or read c

Complete.


[Feature Request] Option to fill blank or new files with specified template

It's nice that new files get automatically moved to their proper location. But adding the ability to auto apply a template would significantly improve new note creation, especially when following links to non-existent files.
See this discussion: https://www.reddit.com/r/ObsidianMD/comments/wahasz/templater_file_creation_on_link_navigation/?utm_source=share&utm_medium=web2x&context=3

My immediate personal use case has been resolved. Details are in the reddit thread linked in the original post above. Since this plugin is already doing the work of identifying files by regex for relocation, this could still be a powerful and useful addition. But for my purposes, I no longer currently have a need for this, so I am closing this FR.


Standardize linting and formatting tasks

Introduction
Most projects in this workspace define in their project.json tasks to lint and/or format their codebase.
Recommend read:

What's the difference between code linters and formatters?
Prettier vs. Linters: How does it compare to ESLint/TSLint/stylelint, etc.?

This workspace uses an extensive set of tools to lint and format different types of files (e.g. JSON, YAML) and code written with different languages and framework (TypeScript, Java, Python). The tools are listed below:

ESLint
Prettier
Spotless
Hadolint
Checkstyle
Webhint
google-java-format
VS Code ESLint extension
VS Code Prettier extension
VS Code Checkstyle extension
VS Code Webhint exntesion
VS Code Run On Save extension
Nx format:check and format:write commands

Specifications

The output of linters/formatters must be the same whether they are used with the IDE and programmatically.

Developers often run the linters/formatters with the IDE via a VS Code extension.
The CI workflows and git hooks run the linters/formatters programmatically.

The most common files should be formatted automatically on save in VS Code.

The time required to format a file should be less than 1 second.

Tools
This section aims to provide some information on the linters and formatters used.
ESLint

Used as linter for TypeScript files.
Our ESLint configuration relies on Prettier: does ESLint run Prettier under the hood or just apply the Prettier rules defined in Prettier's config file?

Spotless
Spotless documentation says:

Spotless can format <antlr | c | c# | c++ | css | flow | graphql | groovy | html | java | javascript | json | jsx | kotlin | less | license headers | markdown | objective-c | protobuf | python | scala | scss | sql | typeScript | vue | yaml | anything> using <gradle | maven | anything>

Under the hood, Spotless delegate the actual formatting to third-party formatters like google-java-format. However, it seems that Spotless can only be used in Java projects, in particular the ones that use the build tool Gradle (we do use it).
Hadolint

We use the Hadolint in GitHub workflows to lint Dockerfiles.

VS Code Run On Save extension
This extension enables to associate file types (regex) to an action to perform when a given type of files is saved. This extension was identified as part of a solution to run formatters programmatically instead of relying on VS Code formatter extension, thus eliminating potential inconsistency between running a formatter programmatically VS running it via a VS Code extension.
This approach is currently applied when saving Java files (*.java) to run the task format of the projects affected since the last commit (see .vscode/settings.json).
  "emeraldwalk.runonsave": {
    "commands": [
      {
        "match": "\\.(java|sql)$",
        "cmd": "node_modules/.bin/nx affected --base=HEAD --target=format"
      }
    ]
  },

As mentioned previously, this approach eliminates any doubts regarding inconsistencies between formatters run via the IDE (auto formatting on save) and programmatically in the CI workflow and git hooks. This approach has however a few drawbacks:

Formatting a file on save takes usually longer than when using a VS Code exntesion. First, the command does not format one file but all the files that below to projects affected since the last commit. This drawback can be mitigated by committing frequently. Second, the nx command is executed to call the task format of the affected projects, which in turn executes the formatter program. VS Code formatter extensions, on the other hand, usually run as "server": when a file is saved, the file content is send to the server that is already running and the output (formatted file) is returned quickly. Running a formatter programmatically on one file takes longer because the program always need to initialize (e.g. read formatter config file).

VS Code formatter extension can provide hints to the developer in the IDE. However, this benefit is limited when formatting on save since the formatter hints are automatically applied.

Challenges
Eliminate tool output inconsistency
There have been cases where running an nx command (re)format files in multiple projects unexpectedly. For example, the items of an array in JSON files are sometimes printed one per line, and sometimes they are printed on the same line if there is enough space. If the developer does not discard the unnecessary changes, submitting them for review would contribute to make reviews slightly more complex. Either way, the inconsistent formatting introduces necessary extra work.
Other source of potential inconsistency:

The IDE version of a tool is not the same as the CLI version. For example, does the VS Code ESLint extension use the CLI command eslint or does it comes with its own ESLint binary? Depending on the answer, the output of ESLint may be different when the user follow the suggestions from the IDE from the output of the ESLint CLI run by the CI workflow.

A file type is formatted by more than one tools. For example, we have seen above that nx may change the format of JSON files. Formatting the file with VS Code default JSON formatter may lead to a different output. What should be the approach to use for JSON files?

Document how formatters and linters work
As mentioned above, it's not clear whether the VS Code ESLint extension used the ESLint CLI defined in package.json. The answer to this question should be documented and in general, how linters and formatters work and where their configuration live.
Documentation
The following document is a work in progress.

docs/linters-and-formatters.md

Help Wanted
Contributions to address the above challenges are welcome! One way to get started is to focus on a type of file you may work with (e.g. HTML files), then identify what tool this workspace could use to format these files and how they work.
Contributions

#717

Now tracked in https://sagebionetworks.jira.com/browse/ARCH-292


Control Plane Node Memory Spikes

Describe the bug

We've been noticing in our OKD 4.13 cluster (running on bare-metal) these random spikes of memory usage over a few days that eventually cause the node to be unusable but technically alive enough to not get killed by a watchdog. Unfortunately, I haven't been able to observe the machine before it goes down to gather logs / information on process usage. Luckily we've captured some of that data in datadog that you can view here: https://p.datadoghq.com/sb/44f16805b-75683e48113d2029e871c1021a559134

Version

4.11.0-0.okd-2022-08-20-022919 installed on bare-metal
How reproducible

So far I've only been able to observe this twice on a control plane node (that I can remember), but we've had some weird instability in our cluster including worker nodes in the past.
Here's a worker in our cluster:

[core@okd4-wkr05-nrh ~]$ free -h
               total        used        free      shared  buff/cache   available
Mem:           566Gi       438Gi       103Gi       122Mi        24Gi       124Gi
Swap:             0B          0B          0B
[core@okd4-wkr05-nrh ~]$

Log bundle

Logs available at: https://csh.rit.edu/~mstrodl/okd4-wkr05-nrh-kube-jul-23
Must-gather is here: https://csh.rit.edu/~mstrodl/must-gather-2023-07-23.zip

Dupe of https://github.com/okd-project/okd/issues/1310?

Upgraded to 4.12.0-0.okd-2023-04-01-051724
Will update issue if we see this happen again

We saw this happen again:

Dupe of #1310?

Seems to be the same issue, though that issue is closed. Should that one be reopened then?
Right now we have a worker that hasn't died yet that's exhibiting the symptoms (very high memory usage) and the log noise:
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.901704    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/b5deb52d-225f-4170-ae9e-bd2d15622bef/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.901863    2467 pod_container_manager_linux.go:191] "Failed to delete cgroup paths" cgroupName=[kubepods burstable pod933b5097-0cf8-47a0-adeb-8df37fb50302] err="unable to destroy cgroup paths for cgroup [kubepods burstable pod933b5097-0cf8-47a0-adeb-8df37fb50302] : Timed out while waiting for systemd to remove kubepods-burstable-pod933b5097_0cf8_47a0_adeb_8df3
7fb50302.slice"                                                                                Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.902040    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/da5daae5-fbed-4a78-b384-7581f75d0182/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.902401    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/144e2a59-5b57-4b8e-ba6c-bdf2fc11d1a6/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.902771    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/bc34b2d0-c657-493d-9ad7-ca70ff5b5687/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.903134    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/08a4fd32-a04f-4189-8d2e-651e8f99cf10/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.903475    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/4f767855-152a-45f6-af80-4de2980f78d6/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.903807    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/5f376f62-6889-4783-b5a2-a460c637f550/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.904147    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/7dfbe913-cab9-4dcc-bc5b-5a2f18c28cac/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.904346    2467 pod_container_manager_linux.go:191] "Failed to delete cgroup paths" cgroupName=[kubepods burstable pod3c380efc-8997-40ce-9b2d-c2f202
05ace2] err="unable to destroy cgroup paths for cgroup [kubepods burstable pod3c380efc-8997-40ce-9b2d-c2f20205ace2] : Timed out while waiting for systemd to remove kubepods-burstable-pod3c380efc_8997_40ce_9b2d_c2f20205ace2.slice"                                                                                Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.904507    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/adbd26e7-311d-4c6d-b874-99d17e0574e1/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.904840    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/d3e0e6fc-020e-4f32-bbde-fab3a8579f96/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.905185    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/3894888a-3eb3-4852-8d4d-4cc65fdae17f/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.905529    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/584a64e1-c256-4ae6-a17d-3e6128a5a350/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.905896    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/8739dfc2-e05f-4ccb-b40a-aab08045d2c2/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.906263    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/d8335f2e-498f-448d-b5fb-52ac930a5bfc/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.906615    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/0d16ee49-6e84-4291-87e9-07ec46061573/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.906715    2467 pod_container_manager_linux.go:191] "Failed to delete cgroup paths" cgroupName=[kubepods burstable podcf8dd628-c02e-4073-b0a9-eb2ac0
a9b4ef] err="unable to destroy cgroup paths for cgroup [kubepods burstable podcf8dd628-c02e-4073-b0a9-eb2ac0a9b4ef] : Timed out while waiting for systemd to remove kubepods-burstable-podcf8dd628_c02e_4073_b0a9_eb2ac0a9b4ef.slice"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.906956    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/9acbecca-c0f3-44b7-ab8d-cd949747da3c/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.907291    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/b158c4ff-47c1-42a1-95cb-c1e745de6897/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.907647    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/d0ba0d30-da4d-496b-8817-d290dffa3aff/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.907979    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/0f5d8ff0-3bf5-4d11-ba12-35f014f9bc87/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.908839    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/fbf14407-f65f-4538-8cf3-6b11d9b307b2/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.909184    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/a0ff938c-7919-4b57-9028-e570072b4d65/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.909346    2467 pod_container_manager_linux.go:191] "Failed to delete cgroup paths" cgroupName=[kubepods burstable podf28fe4d1-e3bf-4d58-8ec0-e6ee6f
5b8fd7] err="unable to destroy cgroup paths for cgroup [kubepods burstable podf28fe4d1-e3bf-4d58-8ec0-e6ee6f5b8fd7] : Timed out while waiting for systemd to remove kubepods-burstable-podf28fe4d1_e3bf_4d58_8ec0_e6ee6f5b8fd7.slice"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.909531    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/68e71cfd-4bfd-4e3c-9b1f-8d5d40653694/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.909889    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/22596400-bc47-4ae5-8e84-42db139b37c2/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.910234    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/4edc91c9-1569-4954-9b7b-ebaf988c2e04/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.910572    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/787a743b-20f6-4b1e-a827-81279d238f36/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.910895    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/4662f19e-4ab9-48a7-90d9-390b74a271ee/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.911239    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/0b36537b-1426-4090-98e0-5506b437a0ce/volumes"
Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.911567    2467 kubelet_getters.go:306] "Path does not exist" path="/var/lib/kubelet/pods/338b47e5-4cfb-473d-b9f2-04e3528040dd/volumes"             Aug 23 15:28:37 okd4-wkr04-nrh kubenswrapper[2467]: I0823 15:28:37.911783    2467 pod_container_manager_linux.go:191] "Failed to delete cgroup paths" cgroupName=[kubepods burstable poda79e337f-0d28-4acf-b3d3-8630a5
397f81] err="unable to destroy cgroup paths for cgroup [kubepods burstable poda79e337f-0d28-4acf-b3d3-8630a5397f81] : Timed out while waiting for systemd to remove kubepods-burstable-poda79e337f_0d28_4acf_b3d3_8630a5397f81.slice"

    PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND
   2467 root      20   0  451.7g 414.9g  66836 S 119.6  73.2  35167:53 kubelet

Note the huge CPU and memory utilisation

Should that one be reopened then?

No, its not reproducible on OKD 4.12 or 4.13. There is also workaround for 4.11 too

No, its not reproducible on OKD 4.12 or 4.13. There is also workaround for 4.11 too

We're on 4.12 and seemingly reproducing it:
Server Version: 4.12.0-0.okd-2023-04-01-051724
Kubernetes Version: v1.25.0-2786+eab9cc98fe4c00-dirty\

@vrutkovs Hi, we're still on 4.12 and still seeing this issue pretty regularly: ```
Server Version: 4.12.0-0.okd-2023-04-01-051724
Kubernetes Version: v1.25.0-2786+eab9cc98fe4c00-dirty

Are there any more specific troubleshooting steps we can try? Our nodes have a relatively large amount of memory so it's only a problem every two weeks or so, but it would be nice to not need to reboot them so frequently.

We ran into the same issue on our 4.12 2023.04.16 cluster. The problem, as I understand in #1310 that new installation uses cgroup v2, while if you are upgrading from an earlier version the machines will use cgroup v1.
Check the ticket vrutkovs mentioned, there are steps you can take to avoid the high memory and CPU utilisation, there's even a workaround cronjob.


mosaic needs to be more robust

So it works, but could be better :smile:

It seems to leave the last image off (off by one error)
Need to handle small numbers of images better
Maybe default to square mosaics?

12 images goes to: sqrt(12) = 3.46 => 4, so 4x4 arrangement?
30 => 5.47 => 6x6?

I think I made it better

I think I made it better


added calculate Neff script

Hello @tkosciol @sjanssen2 I have created this code in response to issue #26 .
I am not 100% certain the calculation is correct. Please review the code with your scientific mind. Specifically, what I noticed that could be problems are:

Missing residues (-) are treated as the 21st character, which may result in the overestimation of number of clusters.
Clustering is performed using scipy's hierarchical clustering function. Not sure if it's the desired way.

The actual code is very simple and can be compressed in five lines. The reason I created so many functions is because I guess other parts of the program may want to call some of these functions.

Coverage increased (+0.3%) to 94.573% when pulling 89f44f4847c282997d9fac5e5f7a34f69a3a044a on qiyunzhu:process into 2410216bc2f4adcf51e1efc5b17fe0d9a2805281 on biocore:master.

Coverage increased (+0.3%) to 94.595% when pulling 301b22907c576c2d6c8ec9d33a1d27c53e7020e0 on qiyunzhu:process into 2410216bc2f4adcf51e1efc5b17fe0d9a2805281 on biocore:master.

Looks good to me!
@sjanssen2 any comments? In the interest of time I want to leave it with Hamming distance for now and I'll keep an issue open, so that we know to upgrade this script later.

That's fine to me :thumbsup:

Thank you guys! @tkosciol @sjanssen2


Does the server started with the start parameter shut down at the end?

Seems from https://github.com/bahmutov/cypress-grep-example results that not:
name: ci
on: [push]
jobs:
  cypress-run:
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout 🛎
        uses: actions/checkout@v2

      - name: Install dependencies 📦
        uses: cypress-io/github-action@v2
        with:
          # just perform install
          runTests: false

      # run just the smoke tests with "@smoke" string in their names
      - name: Smoke tests 💨
        uses: cypress-io/github-action@v2
        with:
          # we have already installed all dependencies above
          install: false
          start: npm start
          # quote the url to be safe against YML parsing surprises
          wait-on: 'http://localhost:8888'
          # pass the grep string
          env: grep=@smoke
          # record the results on the Cypress Dashboard
          # https://on.cypress.io/dashboard-introduction
          record: true
          # tag the smoke tests for quick find
          tag: smoke
        # environment variables while running Cypress
        env:
          # pass the Dashboard record key as an environment variable
          CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}
          # pass GitHub token to allow accurately detecting a build vs a re-run build
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      # if smoke tests passed, run all the tests
      - name: E2E tests 💨
        uses: cypress-io/github-action@v2
        with:
          # we have already installed all dependencies above
          install: false
          start: npm start
          # quote the url to be safe against YML parsing surprises
          wait-on: 'http://localhost:8888'
          # record the results on the Cypress Dashboard
          # https://on.cypress.io/dashboard-introduction
          record: true
          tag: all
        # environment variables while running Cypress
        env:
          # pass the Dashboard record key as an environment variable
          CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}
          # pass GitHub token to allow accurately detecting a build vs a re-run build
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

The smoke tests pass just fine, but the second action launch is showing an error

Seeing similar behavior for one of our GHA workflows. Imho the action should just clean up processes rather than leaving them dangling and 🙏🏻 the GHA will clean up all leftovers.

Yeah I think the processes don't end - we're trying to start the same server right afterwards, and the port is blocked.
In the meantime, our (somewhat overkill) workaround is:
- run: killall node

This is imho a real 'documentation bug' - here
https://github.com/cypress-io/github-action#start-server
it says

the server will run in the background and will shut down after tests complete

and

Note: GitHub cleans up the running server processes automatically. This action does not stop them.

both lines seem to contradict eachother.

@commonpike
Is this just a documentation issue for you or do you have an example workflow using the current version of the action (v5) where it is causing you a problem?

Probably if there was a need to start a server a second time, then I would put it into a separate job rather than a step in the same job. I'm not sure if the original issue from 2 years ago is the optimal way to use the action. In any case the documentation could be made more precise.

I haven't looked at this too closely, but I think in the original example I would have just deleted the second start: npm start, unless there is some special reason to want to restart the server.


[Menubar] Improve keyboard controls

Description

Current dependencies on/for this PR:

main

PR #1846

PR #1847

PR #1852   👈

This comment was auto-generated by Graphite.


Add fuel consumption mode

In the contracts-pallet the wasmi fuel metering feature is used to "solve" the halting problem for Wasm smart contracts.
For this a UI usually displays the expected costs of a Wasm execution. This is done by dry-running the same Wasm smart contract and displaying the consumed fuel afterwards.
For some of the bulk instructions that wasmi supports this fuel consumption is lazy. This means that fuel is only consumed upon a successful execution. For example memory.grow 1 will only consume fuel if the memory can actually be grown to begin with.
However, it is still checked beforehand if enough fuel for a successful operation is available.
Combined with the dry-running of the Wasm smart contract this means that the estimated amount of fuel required to perform a Wasm smart contract execution can be much lower than what is actually needed if such a bulk operation fails and thus consumes a lot less fuel than needed for successful execution.
A solution to this problem could be to introduce different fuel consumption modes where Lazy is the current behavior and Eager is a new behavior that simply always consumes the amount of fuel that was consumed if the operation was successful. This way the contracts-pallet could perform the dry-run using the Eager mode and the actual run using the Lazy mode.
A problem with this approach is that Engine configurations cannot be changed after the instantiation of an Engine and therefore this approach requires to setup two different wasmi engines. Would that be a show stopper for you @athei ?

This will work for me. Thanks.


fix: removed unused indexes

fixes AM-4394

I removed also  "rt1ri1" - (refType,refId) as there are four other indexes that are more specific.


Visual Studio Community 2019 renders Agave poorly.

After i installed the new version of agave from here it works in VSCommunity but it renders the font poorly. (I guess it might be some anti-aliasing problem with VSCommunity, not sure)
Here is the example screenshot.

The font size is 10 in this picture.
Thanks.

Thanks for creating the issue. I have been looking into this after https://github.com/agarick/agave/issues/7 and have made some progress.
In the latest release (version 12), agave is now auto-hinted and auto-instructed (using FontForge).
I chose to do this not because I completely understand what I'm doing or how "hinting" really works, but because other fonts seem to render fine on VSCommunity and so should agave. So I suspected maybe adding hinting instructions would help, and followed the FontForge wiki (https://github.com/fontforge/fontforge/wiki/How-TT-Hinting-Works) to apply a sweeping generic autohint. To my pleasant surprise, the resulting font looks much better on VSCommunity.
So far, I have done very little testing with the new version, and cannot guarantee that previously good behavior will not break. (If things do break, please let me know by creating an issue.) But I did try the new version on the few Windows and Linux applications that I have, and things seem normal (I should still do a tight comparison when I have more time). I am also hopeful that agave's geometric simplicity and consistency gave FontForge's autohinter little cause for protest.
Anyway, hope the release helps.

Hey, sorry for late reply.
I downloaded and installed the version 12 and it works perfectly fine with Visual Studio Community 2019 right now. (At least for me)
Thank you so much for creating awesome content. Finally i can use Agave inside the IDE that i use most.
Since the new version solves my problem, i am going to close this issue.
Thanks.

Super happy it's working for you. Also really glad that this issue was created. -- Wish I'd known about it sooner but I had seldom used Vindows until now.
I keep postponing the italic and bold but also trying my best to levitate their priority.
Thank you as always for appreciating agave.

Reopened by https://github.com/agarick/agave/issues/14#issuecomment-658497365 but turns out, if that issues is indeed fixed, this was a false alarm.


Add signature algorithms integration test to integv2 framework.

Resolved issues:
resolves #1512
Description of changes:
Add signature algorithms integration test to integv2 framework.

s2n client and server signature algorithm tests
add new ecdsa and rsapss certs that can be verified off localhost
display an error in a new location which fixes a client auth test

Call-outs:
Added two new cert/key pairs to allow using PSS and ECDSA signatures with mutual authentication. This uncovered a bug
in the s2nd application non-blocking change where the mutual auth error was not properly displayed. That fix is also in this PR.
Testing:
Integration testing
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Codecov Report

Merging #2110 into master will not change coverage.
The diff coverage is 0.00%.

@@           Coverage Diff           @@
##           master    #2110   +/-   ##
=======================================
  Coverage   80.86%   80.86%
=======================================
  Files         247      247
  Lines       18436    18436
=======================================
  Hits        14908    14908
  Misses       3528     3528


ERROR in error TS6053: main.ts not found.

Describe the bug
I tried to migrate an Angular web project, but when I ng serve the application, I get the following error:
ERROR in error TS6053: File '-path-to-project-/what-the-song/src/src/main.ts' not found.
error TS6053: File '-path-to-project-/what-the-song/src/src/polyfills.ts' not found.
Clearly, the path is not correct! There is an unnecessary src.
The debug option -o does not print more information. Am I doing something wrong or is this a bug? I don't know where to look at to fix the path.
To Reproduce
I followed the instructions on the migration documentation.

installed nativeScript CLI
upgraded angular CLI
added schematics to the project with ng add @nativescript/schematics
ng serve to test if the web project works

Environment after schematics install
{
  "name": "what-the-song",
  "version": "0.0.0",
  "scripts": {
    "android": "tns run android",
    "ios": "tns run ios",
    "mobile": "tns run",
    "preview": "tns preview",
    "ng": "ng",
    "start": "ng serve",
    "build": "ng build",
    "test": "ng test",
    "lint": "ng lint",
    "e2e": "ng e2e"
  },
  "private": true,
  "dependencies": {
    "nativescript-angular": "~8.0.1",
    "nativescript-theme-core": "~1.0.4",
    "reflect-metadata": "~0.1.12",
    "tns-core-modules": "~6.0.0",
    "@angular/animations": "^7.2.15",
    "@angular/common": "~7.2.0",
    "@angular/compiler": "~7.2.0",
    "@angular/core": "~7.2.0",
    "@angular/fire": "^5.2.1",
    "@angular/forms": "^7.2.15",
    "@angular/platform-browser": "~7.2.0",
    "@angular/platform-browser-dynamic": "~7.2.0",
    "@angular/router": "~7.2.0",
    "@fortawesome/angular-fontawesome": "^0.3.0",
    "@fortawesome/fontawesome-svg-core": "^1.2.21",
    "@fortawesome/free-brands-svg-icons": "^5.10.1",
    "@fortawesome/free-solid-svg-icons": "^5.10.1",
    "@nativescript/schematics": "^0.7.0",
    "bootstrap-material-design": "^4.1.2",
    "core-js": "^2.5.4",
    "firebase": "^5.11.1",
    "mic-recorder-to-mp3": "^2.2.1",
    "rxjs": "~6.3.3",
    "tslib": "^1.9.0",
    "zone.js": "~0.8.26"
  },
  "devDependencies": {
    "nativescript-dev-webpack": "~1.0.0",
    "@nativescript/schematics": "~0.7.0",
    "@nativescript/tslint-rules": "~0.0.2",
    "@angular-devkit/build-angular": "~0.13.0",
    "@angular/cli": "~7.3.8",
    "@angular/compiler-cli": "~7.2.0",
    "@angular/language-service": "~7.2.0",
    "@types/node": "~8.9.4",
    "@types/jasmine": "~2.8.8",
    "@types/jasminewd2": "~2.0.3",
    "codelyzer": "~4.5.0",
    "jasmine-core": "~2.99.1",
    "jasmine-spec-reporter": "~4.2.1",
    "karma": "~4.0.0",
    "karma-chrome-launcher": "~2.2.0",
    "karma-coverage-istanbul-reporter": "~2.0.1",
    "karma-jasmine": "~1.1.2",
    "karma-jasmine-html-reporter": "^0.2.2",
    "protractor": "~5.4.0",
    "ts-node": "~7.0.0",
    "tslint": "~5.11.0",
    "typescript": "~3.2.2"
  },
  "nativescript": {
    "id": "org.nativescript.ngsample"
  }
}

I had the same problem. I solved it going into tsconfig.app.json and changing the path under the file section to:

It orginally had src/ in front of it wich did not work for some reason. Also have a look at this stackoverflow post:
https://stackoverflow.com/questions/49091956/angular5-polyfills-ts-main-ts-is-missing-from-the-typescript-compilation

Thank you @TimvdLooy, it worked for me.


BLEFF: pretrained weights and experiement setup

Thanks for providing such a nice repositoy
I was wondering of you can make your nerf-- checkpoints available

Hi @HannahHaensen,
Sorry about the delay. There are too many checkpoints for BLEFF experiments. I'll reply with a standard config we used for training in #34.


nz-table property nzShowTotal

What problem does this feature solve?
Very awesome UI,thanks very much.
Version:0.7.
One puzzle with nz-table.
What does the proposed API look like?
Can support one demo,how to use property nzShowTotal.Thanks again.

https://ng.ant.design/components/pagination/zh#components-pagination-demo-total same as pagination.


Bevy 0.14 partial update

This kind of solves https://github.com/JoJoJet/bevy-trait-query/issues/59 I'm not sure if the added test actually tests the UB but it seems to pass on my machine without panics. I'll double check it though. Update: It looks like the panic is only hit if we transmute to something which includes one of the bevy-trait-query component types (One or All). I added an additional test which highlights this. There's also an explicit panic in bevy-trait-query now which will guide users to the issue which causes the trouble and which provides minimal help.
For performance differences, see this comment: https://github.com/JoJoJet/bevy-trait-query/issues/59#issuecomment-2212516814 (TLDR: All performance improves, One performance regresses)

Any reason this is just sitting here? 👍

I've been busy with IRL stuff -- I'll see if I have time to merge this this weekend

Any updates?


error running test command in singularity mode

Hi,
I freshly installed the git and installed mamba, nextflow and singularity in a conda env.
git version: https://github.com/PacificBiosciences/pb-16S-nf/commit/763d542c5c82adb6cff769e253ebc15f61d765cb
Docker is already installed on my server
Docker version 20.10.12, build 20.10.12-0ubuntu2~20.04.1
Conda env pb-16S-nf with:

singularity version 3.8.6
mamba 0.27.0
conda 22.9.0

env details
# packages in environment at /opt/miniconda3/envs/pb-16S-nf:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
brotlipy                  0.7.0           py310h7f8727e_1002
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.18.1               h7f8727e_0
ca-certificates           2022.10.11           h06a4308_0
certifi                   2022.9.24       py310h06a4308_0
cffi                      1.15.1          py310h74dc2b5_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
cni                       1.0.1                ha975731_1    conda-forge
cni-plugins               1.0.1                ha8f183a_0    conda-forge
conda                     22.9.0          py310h06a4308_0
conda-package-handling    1.9.0           py310h5eee18b_1
coreutils                 8.25                          1    bioconda
cryptography              38.0.1          py310h9ce1e76_0
curl                      7.86.0               h2283fc2_1    conda-forge
dbus                      1.13.18              hb2f20db_0
expat                     2.4.9                h6a678d5_0
fmt                       9.1.0                h924138e_0    conda-forge
freetype                  2.12.1               h4a9f257_0
gettext                   0.21.1               h27087fc_0    conda-forge
glib                      2.74.1               h6239696_0    conda-forge
glib-tools                2.74.1               h6239696_0    conda-forge
icu                       58.2                 he6710b0_3
idna                      3.4             py310h06a4308_0
jq                        1.6               h27cfd23_1000
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.19.3               h08a2579_0    conda-forge
ld_impl_linux-64          2.38                 h1181459_1
libarchive                3.5.2                hada088e_3    conda-forge
libcurl                   7.86.0               h2283fc2_1    conda-forge
libedit                   3.1.20210910         h7f8727e_0
libev                     4.33                 h7f8727e_1
libffi                    3.4.2                h295c915_4
libgcc                    7.2.0                h69d50b8_2
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libglib                   2.74.1               h7a41b64_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libmamba                  1.0.0                h9eff5f0_2    conda-forge
libmambapy                1.0.0           py310hd5a56e8_2    conda-forge
libnghttp2                1.47.0               hff17c54_1    conda-forge
libnsl                    2.0.0                h5eee18b_0
libpng                    1.6.37               hbc83047_0
libseccomp                2.4.4                h166bdaf_3    conda-forge
libsolv                   0.7.22               he621ea3_0
libsqlite                 3.39.4               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libxcb                    1.15                 h7f8727e_0
libxml2                   2.9.14               h74e7548_0
libzlib                   1.2.13               h166bdaf_4    conda-forge
llvm-openmp               14.0.6               h9e868ea_0
lz4-c                     1.9.3                h295c915_1
lzo                       2.10                 h7b6447c_2
mamba                     1.0.0           py310h51d5547_2    conda-forge
ncurses                   6.3                  h5eee18b_3
nextflow                  22.10.0              h4a94de4_0    bioconda
oniguruma                 <IP_ADDRESS>              h27cfd23_0
openjdk                   11.0.13              h87a67e3_0
openssl                   3.0.7                h166bdaf_0    conda-forge
pcre                      8.45                 h295c915_0
pcre2                     10.37                he7ceb23_1
pip                       22.2.2          py310h06a4308_0
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h5eee18b_0
pycparser                 2.21               pyhd3eb1b0_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pysocks                   1.7.1           py310h06a4308_0
python                    3.10.6          ha86cf86_0_cpython    conda-forge
python_abi                3.10                    2_cp310    conda-forge
readline                  8.2                  h5eee18b_0
reproc                    14.2.4               h295c915_1
reproc-cpp                14.2.4               h295c915_1
requests                  2.28.1          py310h06a4308_0
ruamel_yaml               0.15.100        py310h7f8727e_0
setuptools                65.5.0          py310h06a4308_0
singularity               3.8.6                hf1ae047_0    conda-forge
sqlite                    3.39.3               h5082296_0
squashfs-tools            4.4                  hd0129a2_3    conda-forge
tk                        8.6.12               h1ccaba5_0
toolz                     0.12.0          py310h06a4308_0
tqdm                      4.64.1          py310h06a4308_0
tzdata                    2022f                h04d1e81_0
urllib3                   1.26.12         py310h06a4308_0
wheel                     0.37.1             pyhd3eb1b0_0
xz                        5.2.6                h5eee18b_0
yaml                      0.2.5                h7b6447c_0
yaml-cpp                  0.7.0                h295c915_1
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                ha4553b6_0

After and try to run the singularity command from the doc.
rem: Both tools and qiime singularity images were downloaded but the run fails as seen below
nextflow run main.nf --input test_data/test_sample.tsv     --metadata test_data/test_metadata.tsv -profile singularity     --outdir singularity_results
N E X T F L O W  ~  version 22.10.0
Launching `main.nf` [ecstatic_heyrovsky] DSL2 - revision: 6c347af324
Only 1 sample. min_asv_sample and min_asv_totalfreq set to 0.

  Parameters set for pb-16S-nf pipeline for PacBio HiFi 16S
  =========================================================
  Number of samples in samples TSV: 1
  Filter input reads above Q: 20
  Trim primers with cutadapt: Yes
  Forward primer: AGRGTTYGATYMTGGCTCAG
  Reverse primer: AAGTCGTAACAAGGTARCY
  Minimum amplicon length filtered in DADA2: 1000
  Maximum amplicon length filtered in DADA2: 1600
  maxEE parameter for DADA2 filterAndTrim: 2
  minQ parameter for DADA2 filterAndTrim: 0
  Pooling method for DADA2 denoise process: pseudo
  Minimum number of samples required to keep any ASV: 0
  Minimum number of reads required to keep any ASV: 0
  Taxonomy sequence database for VSEARCH: /opt/biotools/pb-16S-nf/databases/GTDB_ssu_all_r207.qza
  Taxonomy annotation database for VSEARCH: /opt/biotools/pb-16S-nf/databases/GTDB_ssu_all_r207.taxonomy.qza
  Skip Naive Bayes classification: false
  SILVA database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/silva_nr99_v138.1_wSpecies_train_set.fa.gz
  GTDB database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/GTDB_bac120_arc53_ssu_r207_fullTaxo.fa.gz
  RefSeq + RDP database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/RefSeq_16S_6-11-20_RDPv16_fullTaxo.fa.gz
  VSEARCH maxreject: 100
  VSEARCH maxaccept: 100
  VSEARCH perc-identity: 0.97
  QIIME 2 rarefaction curve sampling depth: null
  Number of threads specified for cutadapt: 16
  Number of threads specified for DADA2: 8
  Number of threads specified for VSEARCH: 8
  Script location for HTML report generation: /opt/biotools/pb-16S-nf/scripts/visualize_biom.Rmd
  Container enabled via docker/singularity: true
  Version of Nextflow pipeline: 0.4

[-        ] process > pb16S:write_log                  -
executor >  Local (2)
executor >  Local (9)
[74/794f1c] process > pb16S:write_log                  [100%] 1 of 1 ✔
[a4/032289] process > pb16S:QC_fastq (1)               [100%] 1 of 1 ✔
[3d/f0cab3] process > pb16S:cutadapt (1)               [100%] 1 of 1 ✔
[5d/5d385e] process > pb16S:QC_fastq_post_trim (1)     [100%] 1 of 1 ✔
[a9/67a194] process > pb16S:collect_QC                 [100%] 1 of 1 ✔
[12/90c21d] process > pb16S:prepare_qiime2_manifest    [100%] 1 of 1 ✔
[a7/8a634e] process > pb16S:import_qiime2              [100%] 1 of 1 ✔
[b0/ee1d7c] process > pb16S:demux_summarize            [  0%] 0 of 1
[df/dd6c9f] process > pb16S:dada2_denoise              [  0%] 0 of 1
[-        ] process > pb16S:filter_dada2               -
[-        ] process > pb16S:dada2_qc                   -
[-        ] process > pb16S:qiime2_phylogeny_diversity -
[-        ] process > pb16S:dada2_rarefaction          -
[-        ] process > pb16S:class_tax                  -
[-        ] process > pb16S:dada2_assignTax            -
[-        ] process > pb16S:export_biom                -
[-        ] process > pb16S:barplot_nb                 -
[-        ] process > pb16S:barplot                    -
[-        ] process > pb16S:html_rep                   -
[-        ] process > pb16S:krona_plot                 -
Error executing process > 'pb16S:dada2_denoise'

Caused by:
  Process `pb16S:dada2_denoise` terminated with an error exit status (1)

Command executed:
executor >  Local (9)
[74/794f1c] process > pb16S:write_log                  [100%] 1 of 1 ✔
[a4/032289] process > pb16S:QC_fastq (1)               [100%] 1 of 1 ✔
[3d/f0cab3] process > pb16S:cutadapt (1)               [100%] 1 of 1 ✔
[5d/5d385e] process > pb16S:QC_fastq_post_trim (1)     [100%] 1 of 1 ✔
[a9/67a194] process > pb16S:collect_QC                 [100%] 1 of 1 ✔
[12/90c21d] process > pb16S:prepare_qiime2_manifest    [100%] 1 of 1 ✔
[a7/8a634e] process > pb16S:import_qiime2              [100%] 1 of 1 ✔
[-        ] process > pb16S:demux_summarize            -
[df/dd6c9f] process > pb16S:dada2_denoise              [100%] 1 of 1, failed: 1 ✘
[-        ] process > pb16S:filter_dada2               -
[-        ] process > pb16S:dada2_qc                   -
[-        ] process > pb16S:qiime2_phylogeny_diversity -
[-        ] process > pb16S:dada2_rarefaction          -
[-        ] process > pb16S:class_tax                  -
[-        ] process > pb16S:dada2_assignTax            -
[-        ] process > pb16S:export_biom                -
[-        ] process > pb16S:barplot_nb                 -
[-        ] process > pb16S:barplot                    -
[-        ] process > pb16S:html_rep                   -
[-        ] process > pb16S:krona_plot                 -
Error executing process > 'pb16S:dada2_denoise'

Caused by:
  Process `pb16S:dada2_denoise` terminated with an error exit status (1)

Command executed:

  # Use custom script that can skip primer trimming
  mkdir -p dada2_custom_script
  cp run_dada_ccs.R dada2_custom_script/run_dada_ccs_original.R
  sed 's/minQ\ =\ 0/minQ=0/g' dada2_custom_script/run_dada_ccs_original.R >     dada2_custom_script/run_dada_ccs.R
  chmod +x dada2_custom_script/run_dada_ccs.R
  export PATH="./dada2_custom_script:$PATH"
  which run_dada_ccs.R
  qiime dada2 denoise-ccs --i-demultiplexed-seqs samples.qza     --o-table dada2-ccs_table.qza     --o-representative-sequences dada2-ccs_rep.qza     --o-denoising-stats dada2-ccs_stats.qza     --p-min-len 1000 --p-max-len 1600     --p-max-ee 2     --p-front 'none'     --p-adapter 'none'     --p-n-threads 8     --p-pooling-method 'pseudo'

Command exit status:
  1

Command output:
  ./dada2_custom_script/run_dada_ccs.R

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  ./dada2_custom_script/run_dada_ccs.R
  QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
  Plugin error from dada2:

    An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

  Debug info has been saved to /tmp/qiime2-q2cli-err-x4nhi4tu.log
  INFO:    Cleaning up image...

Work dir:
  /opt/biotools/pb-16S-nf/work/df/dd6c9f7e734807d7d69ecf5d4e856a

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

can you please help?
Thanks
dd6c9f7e734807d7d69ecf5d4e856a.tgz
NOTE: the docker version works, as you had suggested elsewhere.

Hi Stephane, I have not tested the pipeline using a Conda version of Singularity. Generally speaking containers should be installed via root, regardless of whether it's Singularity or Conda. Since the Docker version works for you I would advise just using that. Both of them are using the same Docker container, so there's no inherent issue with the container and I suspect it's likely due to installing Singularity via Conda, here.

Thanks for discovering all the issues as well. These are the exact types of things I need to know from users perspective. There are testings I run before releasing but it's hard to account for all scenarios so it's helpful for me to know what errors can happen on your end, too.
Outputs are generally in both TSV format as well as QIIME 2. The TSV formats are used to generate the reports and make it easier for you to write your own scripts for processing, but the QIIME 2 artifacts allow you to make use of the huge community tools QIIME 2 provide. This was intentional as I've heard many 16S users would like to stay within the QIIME 2 environment. But do let me know if you have any suggestions to improve your experience, too. Thanks.


Added guide pattern page

What is the context of this PR?
Added a new pattern for a guide.
How to review
Check examples and documentation.
https://trello.com/c/71iQLE9m

#1423 Has merged so we can use that in the code highlighting now


TFRS - Place compliance units in reserve when submitting a 2023 compliance report with a negative net balance

Title:
Compliance units are placed in reserve when submitting a 2023 compliance report
Description:
Compliance units should be placed "in reserve" when an organization submits a compliance report that when assessed will decrease the supplier's available compliance unit balance. The amount of compliance units that should be placed "in reserve" would be based on the amount listed in the 'Compliance unit balance change from assessment' field in the new summary section only if that value is negative.
Note: this functionality is similar to the old credit/debit scheme where TFRS places credits entered into Line 26 "in reserve" when the supplier submits a compliance report.
Wireframe of summary section for reference: https://preview.uxpin.com/59145260c7d8cc48969ac79401cc03d84843c3d9#/pages/163570088/simulate/no-panels?mode=mf
Purpose and benefit to user:
This feature will prevent suppliers from attempting to sell or other use compliance units for other purposes prior to a submitted report being assessed.
Acceptance Criteria:

[ ] Given I am a BCeID user, when I am submitting a report that has a negative value in the 'Compliance unit balance change from assessment' field in the new summary section, then the same amount of compliance units from my compliance unit balance are placed "in reserve".

Development Checklist:

[ ] Changes should aligned to new Compliance unit act
[ ] Test cases to cover all the edge cases

Notes:

Hey team! Please add your planning poker estimate with Zenhub @AlexZorkin @jig-patel @prv-proton

Tested and working on original reports but not supplemental reports. Description of task may have not been entirely clear for covering supplemental reports so a new card has been created (#2562) to handle this as part of the 8 point testing card (#2542)


Execute Sounder SIPS L1b PGE on local Kubernetes cluster

The goal is to be able to execute the Sounder SIPS Docker image for the L1b PGE on the HySDS containers running on the local cluster (specifically, via the Verdi worker).
Instructions for running the L1b Docker container can be found here:
https://github.com/unity-sds/unity-sps-workflows/blob/main/sounder_sips/sounder_sips_pges.md
There is a fair amount of static data that will be needed (around 3GB), which can be downloaded from S3 and perhaps stored on a Kubernetes PV with a hostPath.

Prototyped using a makeshift Verdi container that uses "docker run" to execute a kubectl container that submits a Calrissian pod. Worked with both docker-in-docker and docker-outside-docker patterns.


CFP-2023-10-12

This PR stores CFP-2023-10 in Git for future reference
Author of the CFP: @m-yosefpor

Is there an issue filed on https://github.com/cilium/cilium for this one? If yes, then we can adopt the issue number for that instead of the 2023-10-12 CFP number.

yes there is, that will be 25813

Could you also go through and take the title from each CFP and paste that as the title for the PR? It's a bit hard to understand the context of each PR if the title of the PR is just a number.

@m-yosefpor are you still interested in working on this CFP or should we close this PR for now?

Closing due to inactivity. If you'd like to further explore this idea, please update the latest status on the upstream issue or reopen a fresh PR on this repo.


Agent tool use case examples

Hi,
I am curious whether you have some tools_example.py to share, in order to be able to function call some sample commands or interact via new Mistral7b v0.3 (which is the first open weights model to support funccaling)?
Cheers

since mistral memo is superior to v3.0 in terms of function calling support, this issue is not uptodate anymore


[CARBONDATA-3138] Fix random count mismatch with multi-thread block pruning

problem: Random count mismatch in query in multi-thread block-pruning scenario.
cause: Existing prune method not meant for multi-threading as synchronization was missing.
only in implicit filter scenario, while preparing the block ID list, synchronization was missing. Hence pruning was giving wrong result.
solution: synchronize the implicit filter preparation, as prune now called in multi-thread
Be sure to do all of the following checklist to help us incorporate
your contribution quickly and easily:

[ ] Any interfaces changed? NA

[ ] Any backward compatibility impacted? NA

[ ] Document update required? NA

[ ] Testing done
done with huge data

[ ] For large changes, please consider breaking it into sub-tasks under an umbrella JIRA.

Build Success with Spark 2.1.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder2.1/1572/

Build Success with Spark 2.3.1, Please check CI http://<IP_ADDRESS>:8080/job/carbondataprbuilder2.3/9831/

Build Success with Spark 2.2.1, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder1/1784/

@ravipesala , @kumarvishal09 : please check this

LGTM


Fix broken handling of sampled Rectangles in CZML.

The previous code was incorrectly converting the time to radians.  Also fix Color rgba which was checking Color.length instead of the correct Color.packedLength.

Looks good @shunter, thanks!

Do you think this is worth mentioning in CHANGES?
If so, add it to master please


[diem_vm] Implement a new multi versioned hashmap.

Motivation
This is the definition of the core placeholder data structure for parallel execution. This structure is inspired by bohm protocol and serve as the multi-version scratchpad used by the parallel execution engine. The public api look like following:
impl<K: Hash + Clone + Eq, V: Clone> MVHashMap<K, V> {
    fn new_from(
        possible_writes: Vec<(K, Version)>
    ) -> (usize, MVHashMap<K, V>);

    // Write APIs
    fn write(
        &self,
        key: &K,
        version: Version,
        data: V
    ) -> Result<()>;

    fn skip_if_not_set(&self, key: &K, version: Version) -> Result<()>;

    fn skip(&self, key: &K, version: Version) -> Result<()>;

    // Read API
    fn read(
        &self,
        key: &K,
        version: Version
    ) -> Result<&V, Option<Version>>;
}

The idea is to create placeholder data structures ahead of time for each possible writes and provide apis to either:

read a key at given version
write a key at given version
skip a key if it was predicted to be written at first but didn't happen after computation.

Have you read the Contributing Guidelines on pull requests?
Yes
Test Plan
Implemented a proptest for generating random keys read and write operations and check execution in parallel.
If targeting a release branch, please fill the below out as well
Related PRs
#8829

Updated the PR to get rid of the atomic flag and use OnceCell to test if a cell is assigned or not.

Fixed comments!

/land


Inherit version from workspace for Members

This change doesnt work with Rust Version 1.58 used in Meta-rust

@satlead I was going to ask you about whether or not we would want to fix versions across the mono-repo using workspace.dependencies.
So does this not work because the build environment is using Rust 1.58? Is it possible to get it upgraded or is that not realistic?


More options documentation

A little more progress in documenting the (most important) AWS options, and the first documented cross-provider option

AWS updates seem to be good. Adding @erictune to check on introducing a cluster/-level options.md file, because I'm not sure we want to commit to maintaining another file describing config options (they're already overflowing in the .sh files and hard to maintain).

I haven't forgotten this.  Just a little backed up with other work.  Will try to loop back tomorrow.

No worries - this isn't particularly high priority or blocking in any way!
Happy to remove the cross-provider file and just keep the docs in cluster/aws.  Could also integrate it into config-default.sh, but that doesn't really feel right to me

LGTM.  Needs rebase.  Okay for next oncall to merge once mergable.

Rebased


fix: avoid using prefixIdenntifier in esm

When using VTU within vite, the version used is esm-bundler.
This version imports the esm-bundler of the compiler-core.
This version does not support prefixIdentifier.
I tried to make a conditional build of VTU.

Thanks @elevatebart, is there some way I can test this out to make sure it's going to work how we want it to? Do you have some way of testing (assuming you did with Vite etc)?

We could create a playground-like environment to run VTU in a vite/ESM environment.
I think I would like to call the environment variable with another name than __BROWSER__. Maybe ESM ? I called it this way because it is called this way in vue-next but I find it confusing.
We use __BROWSER__ in node and !__BROWSER__ in vite with in-browser testing.
The good news is there is no emergency right now as I found an "unclean" workaround.

I will release this within 24h.

thank you !!!


Update index.md

Reword for clarity, add some better talk links, add more about purpose

Merged and deployed!


staticpod-controller: introduce reason strings why nodes were chosen

2019/06/06 15:32:04 Container test in pod unit failed, exit code 2, reason OOMKilled
/retest

/lgtm


Add guidance for when user has incorrect home area set in NDelius

Context
Currently, if a user's home area does not match one of the enabled regions for the CAS3 service they will be presented with the unauthorised page.
This change updates this page with guidance for those users who may be experiencing this problem.
Screenshots of UI changes
Before

After

Release checklist
Release process documentation.
Pre-merge checklist

[ ] Are any changes required to dependent services for this change to work?
(eg. CAS API)
[ ] Have they been released to production already?

Post-merge checklist

[ ] Manually approve
release to test
[ ] Manually approve
release to preprod
[ ] Manually approve
release to prod

 Help users navigate to relevant support if they can't access the service as expected


[Issue]: roc::NullDevice::importExtSemaphore (hipImportExternalSemaphore) crash

Problem Description
When running the 20_hip_vulkan example the program crashes with the following error
hipVulkan: /usr/src/debug/hip-runtime-amd/clr-rocm-6.0.2/rocclr/device/rocm/rocdevice.hpp:241: virtual bool roc::NullDevice::importExtSemaphore(void**, const amd::Os::FileDesc&, amd::ExternalSemaphoreHandleType): Assertion `false && "ShouldNotReachHere()"' failed.

Operating System
Arch Linux
CPU
AMD Ryzen 9 3950X 16-Core Processor
GPU
AMD Radeon Pro W6800, AMD Radeon VII
ROCm Version
ROCm 6.0.0
ROCm Component
clr
Steps to Reproduce

Compile https://github.com/ROCm/hip-tests/tree/rocm-6.0.x/samples/2_Cookbook/20_hip_vulkan
Run it

(Optional for Linux users) Output of /opt/rocm/bin/rocminfo --support
ROCk module is loaded
=====================
HSA System Attributes
=====================
Runtime Version:         1.1
System Timestamp Freq.:  1000.000000MHz
Sig. Max Wait Duration:<PHONE_NUMBER>3709551615 (0xFFFFFFFFFFFFFFFF) (timestamp count)
Machine Model:           LARGE
System Endianness:       LITTLE
Mwaitx:                  DISABLED
DMAbuf Support:          YES

==========
HSA Agents
==========
*******
Agent 1
*******
  Name:                    AMD Ryzen 9 3950X 16-Core Processor
  Uuid:                    CPU-XX
  Marketing Name:          AMD Ryzen 9 3950X 16-Core Processor
  Vendor Name:             CPU
  Feature:                 None specified
  Profile:                 FULL_PROFILE
  Float Round Mode:        NEAR
  Max Queue Number:        0(0x0)
  Queue Min Size:          0(0x0)
  Queue Max Size:          0(0x0)
  Queue Type:              MULTI
  Node:                    0
  Device Type:             CPU
  Cache Info:
    L1:                      32768(0x8000) KB
  Chip ID:                 0(0x0)
  ASIC Revision:           0(0x0)
  Cacheline Size:          64(0x40)
  Max Clock Freq. (MHz):   3500
  BDFID:                   0
  Internal Node ID:        0
  Compute Unit:            32
  SIMDs per CU:            0
  Shader Engines:          0
  Shader Arrs. per Eng.:   0
  WatchPts on Addr. Ranges:1
  Features:                None
  Pool Info:
    Pool 1
      Segment:                 GLOBAL; FLAGS: FINE GRAINED
      Size:                    131805100(0x7db2fac) KB
      Allocatable:             TRUE
      Alloc Granule:           4KB
      Alloc Alignment:         4KB
      Accessible by all:       TRUE
    Pool 2
      Segment:                 GLOBAL; FLAGS: KERNARG, FINE GRAINED
      Size:                    131805100(0x7db2fac) KB
      Allocatable:             TRUE
      Alloc Granule:           4KB
      Alloc Alignment:         4KB
      Accessible by all:       TRUE
    Pool 3
      Segment:                 GLOBAL; FLAGS: COARSE GRAINED
      Size:                    131805100(0x7db2fac) KB
      Allocatable:             TRUE
      Alloc Granule:           4KB
      Alloc Alignment:         4KB
      Accessible by all:       TRUE
  ISA Info:
*******
Agent 2
*******
  Name:                    gfx1030
  Uuid:                    GPU-fa924265fc8053c4
  Marketing Name:          AMD Radeon RX 6800 XT
  Vendor Name:             AMD
  Feature:                 KERNEL_DISPATCH
  Profile:                 BASE_PROFILE
  Float Round Mode:        NEAR
  Max Queue Number:        128(0x80)
  Queue Min Size:          64(0x40)
  Queue Max Size:          131072(0x20000)
  Queue Type:              MULTI
  Node:                    1
  Device Type:             GPU
  Cache Info:
    L1:                      16(0x10) KB
    L2:                      4096(0x1000) KB
    L3:                      131072(0x20000) KB
  Chip ID:                 29631(0x73bf)
  ASIC Revision:           1(0x1)
  Cacheline Size:          64(0x40)
  Max Clock Freq. (MHz):   2575
  BDFID:                   3072
  Internal Node ID:        1
  Compute Unit:            72
  SIMDs per CU:            2
  Shader Engines:          4
  Shader Arrs. per Eng.:   2
  WatchPts on Addr. Ranges:4
  Coherent Host Access:    FALSE
  Features:                KERNEL_DISPATCH
  Fast F16 Operation:      TRUE
  Wavefront Size:          32(0x20)
  Workgroup Max Size:      1024(0x400)
  Workgroup Max Size per Dimension:
    x                        1024(0x400)
    y                        1024(0x400)
    z                        1024(0x400)
  Max Waves Per CU:        32(0x20)
  Max Work-item Per CU:    1024(0x400)
  Grid Max Size:<PHONE_NUMBER>(0xffffffff)
  Grid Max Size per Dimension:
    x<PHONE_NUMBER>(0xffffffff)
    y<PHONE_NUMBER>(0xffffffff)
    z<PHONE_NUMBER>(0xffffffff)
  Max fbarriers/Workgrp:   32
  Packet Processor uCode:: 116
  SDMA engine uCode::      83
  IOMMU Support::          None
  Pool Info:
    Pool 1
      Segment:                 GLOBAL; FLAGS: COARSE GRAINED
      Size:                    16760832(0xffc000) KB
      Allocatable:             TRUE
      Alloc Granule:           4KB
      Alloc Alignment:         4KB
      Accessible by all:       FALSE
    Pool 2
      Segment:                 GLOBAL; FLAGS: EXTENDED FINE GRAINED
      Size:                    16760832(0xffc000) KB
      Allocatable:             TRUE
      Alloc Granule:           4KB
      Alloc Alignment:         4KB
      Accessible by all:       FALSE
    Pool 3
      Segment:                 GROUP
      Size:                    64(0x40) KB
      Allocatable:             FALSE
      Alloc Granule:           0KB
      Alloc Alignment:         0KB
      Accessible by all:       FALSE
  ISA Info:
    ISA 1
      Name:                    amdgcn-amd-amdhsa--gfx1030
      Machine Models:          HSA_MACHINE_MODEL_LARGE
      Profiles:                HSA_PROFILE_BASE
      Default Rounding Mode:   NEAR
      Default Rounding Mode:   NEAR
      Fast f16:                TRUE
      Workgroup Max Size:      1024(0x400)
      Workgroup Max Size per Dimension:
        x                        1024(0x400)
        y                        1024(0x400)
        z                        1024(0x400)
      Grid Max Size:<PHONE_NUMBER>(0xffffffff)
      Grid Max Size per Dimension:
        x<PHONE_NUMBER>(0xffffffff)
        y<PHONE_NUMBER>(0xffffffff)
        z<PHONE_NUMBER>(0xffffffff)
      FBarrier Max Size:       32
*** Done ***

Additional Information
The program crashes on hipImportExternalSemaphore which albeit being documented as implemented is actually stubbed in rocclr/device/rocm/rocdevice.hpp.
The HSA backend appears to implement the same function but I couldn't find a simple way to compile the clr with that backend enabled.

Hi @opcod3, internal ticket has been created to assist with your issue. Thanks!

Hi @opcod3, HIP interoperability with Vulkan external semaphores is not supported on Linux yet. The documentation will be updated to reflect this.
Regarding using the HSA backend, could you provide a link to the documentation or source code of the function you're referring to?

Hi @sohaibnd, it's been a while but IIRC there function i was reffering to is this one:
https://github.com/ROCm/clr/blob/939c7887793f8280a3196cebc81ba1d07743f068/rocclr/device/pal/paldevice.cpp#L2831
I remember finding some flags relating to using a different backend in the cmake files but did not investigate it further.
As an aside, i'd like to say the the fragmentation of the ROCm/HIP ecosystem is VERY bad for it. As a developer I cannot expect anything to just work without testing it first. There vulkan interop examples/functions long predate HIP support on Windows so it's weird that you say they do not support linux. What OS were they originally written for?

Hi @opcod3, the function you're referring to is the implementation of the hipImportExternalSemaphore API in the PAL backend, and the PAL backend is not supported on linux.
The hip_vulkan test was meant for Windows. While the entire ROCm stack is not supported on windows, there has been support for HIP for a while.
I understand your frustration, and we're improving the documentation to address this (any suggestions are welcome!). If you have come across any other issues, please do create an issue on GitHub so we can address it.


it doesn't need any lock mechanism when you load cache?

as a sample
// Avoid caching a null value.
if (value != null)
.... update cache with long process forexample from SQL Server, and suppose it cost 3 secs.
Where it will be lock? Redis is a distrubuted cache. Many clients ask cache resource just same time. Every client try to update cache?
Thanks.

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

ID: 67f58625-4e97-1fc6-197b-8b25341f5a4f
Version Independent ID: bdabf990-9a18-ec7f-a948-3fc79dc255e0
Content: Cache-Aside pattern - Cloud Design Patterns
Content Source: docs/patterns/cache-aside.md
Service: architecture-center
Sub-service: cloud-fundamentals
GitHub Login: @dragon119
Microsoft Alias: pnp

@khaNuri Thank you for your feedback! We will review and provide an update as appropriate.

I think you would have a lock in there if before fetching from redis you would check in a in memory cache if there is any data, but, here redis is the cache, i believe all the instances should have access to it.

We've taken this item to our internal backlog for further research and will update as necessary!


Micro QR generates the same code for any text

When generating "Micro QR" barcode, the result does not depend on the input string, the same image is generated.
I tested in VCL demo.

hi Sergey, i will have a look


Smoke test: Python installation test timing out

Closing for now as this hasn't reappeared in the past couple of weeks after smoke test fixes have gone in


Is there a way to limit movement/add collisions?

For example, if I have a pendant for a character, can I somehow prevent it from going into the character?

No, it does not support collision at the moment. You can instead use the new PhysicalBone which does support collision.

Ooh, that seems to be what I'm looking for, thanks so much!