Edit the content of the NeuroAI session

This pr initiate the content of the NeuroAI session with a new logo design which is completely prone to change as needed.

Thank you, @complexbrains !!
It looks like the temporary deployments are no longer active (AFAICT ?), so I can't preview them. But from the files themselves, the site looks great ! The only issue I could see is that you have an extra .DS_Store in there 😸
Do you want to remove that and merge it ? We can then iterate from there, if you'd like !

Thank you Elizabeth! Appreciate it a lot! That file somehow missed from my eyes 🙈 I cannot preview it even I changed the deployment of the website to my branch. The deployment passes successfully but the website does not preview. Maybe @pbellec might have an idea.

Ah, I think because it's building from main rather than from this branch. This likely makes sense (since the actual site should be built from the main branch rather than from PRs), but if you wanted to modify we'd need to add a file like the one shown here on to the main branch.
Previews aren't yet out of alpha for GHA, so we'd either need to either (1) manage PRs from a set dev branch, for example, or (2) use another service like netlify to handle PR previewing.
At this point, I'd suggest we just merge this in and edit from there -- since the site isn't officially advertised yet, I don't think we need to be particularly worried if information is temporarily poorly formatted / misspelled, etc !

Thank you Elizabeth! Ok, I guess merging it and iterating over the main branch seems like the simplest solution as you suggested. Let me do it with the hope that it will work 😊

Pierre made a pass on the errors, now I am completing those that I can to try this evening again.

Just to follow-up : The issue is that this was directed to build with Jekyll on GH-pages but it's a Jupyter-Book site, so it needs to be built with the action I added ! I just need to figure out how to disable the zombie Jekyll action.

We need to elevate this to write-access :

@complexbrains if you have permissions, could you update that setting ?

Oh I see. That makes sense indeed! Thank you so much for looking into it!
Also it didn't let me in the repo but apparently can be done in the organization level.  So I made the setting so hope it will work now.

Thank you so much Elizabeth for deploying all those! They work like a charm! 💐


Hand-write the parser

Hand-written parser could eliminate the translation phace, the surface syntax would be the program tree for parsing, and the error messages could be now more informative too.

Pratt parsing might be kinda hard to write in hand, let me see some.

Considering using winnow.

Or https://crates.io/crates/chumsky since you are already on its stack

https://crates.io/crates/chumsky

That's definitely a go, wow.

For now it’s kinda challenging to change the front end, and it’s quite hard for me to clarify the this decision again. I guess I need to improve the error messages upon parsing first, and then possibly re-open related discussions with respect to changing the front end.


tracker-miners: drop libgrss

Motivation for this change
libgrss hasn't seen activity in years (last commit 2 years ago, last release 6 years ago), and (afaik) the only application that uses it, gnome-news, is similarly unmaintained and not part of nixpkgs anyway.
As a reported security bug was present since 2016 (only getting a CVE assigned to it this year), it doesn't seem to be a great idea to keep depending on it, as tracker-miners is a core part of GNOME.
This drops the dependency completely. I don't think this should be backported to 21.05.
This PR is a follow-on from #131478.
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/)
21.11 Release Notes (or backporting 21.05 Relase notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

It would be good to also actually drop that package or mark it insecure, I think.

Yup, and patched/backported in the other PR too now.
I don't quite understand what the ofborg failure is, could someone help me/point me in the right direction?

@ofborg eval


Note: There is an idea to implement the ability to animate the opening not to the height of the nested content, but to the height of the parent.

There is an idea to implement the ability to animate opening not to the height of the embedded content, but to the height of the parent. Necessary for cards with hidden content that appears when hovering or clicking on the button.

It will be implemented in version 3.2.0


Error in robyn_allocator

When executing the robyn_allocator function, this message appears, but I am not sure what it means since I have checked the data table and the format of the variables is correct.
Here's my code:
AllocatorCollect1 <- robyn_allocator(
InputCollect = InputCollect,
OutputCollect = OutputCollect,
select_model = select_model,
scenario = "max_historical_response", #simulates the scenario "what's the optimal media spend allocation given the same average spend level in history?"
date_min = date_min,
date_max = date_max,
optim_algo="SLSQP_AUGLAG", # "SLSQP_AUGLAG" , "MMA_AUGLAG"
channel_constr_low = c(0.7),
channel_constr_up = c(1.25, 1.25, 1.25, 1.25, 1.25, 1.25, 1.25, 1.25, 1.25, 1.25),
export = FALSE
)

Environment & Robyn version
Make sure you're using the latest Robyn version before you post an issue.

Check and share Robyn version: 3.9.0
R version: 4.2.1

Haven't seen this one before. Can you extend the min max dates and see if it works?

I receive the same error when extend the min max dates. I've modified 2 weeks for 5 weeks and it doesn't seem to work.

For what it's worth, I've tried to do the same execution with a model with version 3.10.3 and it works.

Please use the later version. 3.9 is very old


Update README.md

Mocked up my idea so it's clear
#78
This creates 3 categories:
Production, testnet, and development

Will update furter

you can use the draft feature of github to represent draft mode. What the reasoning for separating this category into three sub groups?

Because they're very different things.
Production chains are live, and have economies that can be studied and learned from.
Testnets are much more mature than chains in development, and are interesting to devs, validators, and investors in a different way from production chains.
Chains in development may be nothing more than a person, an idea and a GitHub repo (maybe not even the repo)
so you'd want to present production first, then testnet, and then in-development, so that a reader can know which is which at a glance.

Hey, thanks for your PR!
We've since moved the ecosystem section to https://cosmos.network/ecosystem/apps.


Properly pass vias to Element clients

Should fix joining rooms by roomid via matrix.to.
fixes #270
Signed-off-by: Nicolas Werner<EMAIL_ADDRESS>THIS IS ENTIRELY UNTESTED SINCE I DON'T HAVE AN ELEMENT TO TEST WITH

It seems like it should support it: https://github.com/matrix-org/matrix-react-sdk/blob/d87cfae0c97f53097f37533be8f66606aa55912b/src/utils/permalinks/ElementPermalinkConstructor.ts#L65

rooms appear to work, but permalinks result in the lovely "Failed to load timeline position" dialog. That's probably just a timing bug though.


signalbackup-tools: 20230510 -> 20230518

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/bepaald/signalbackup-tools/releases.
meta.description for signalbackup-tools is: Tool to work with Signal Backup files
meta.homepage for signalbackup-tools is: https://github.com/bepaald/signalbackup-tools
Updates performed

Version update

To inspect upstream changes

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 20230515-1 in filename of file in /nix/store/ynbacpb72ax388379nzixscmmsl506rj-signalbackup-tools-20230515-1

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

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
signalbackup-tools

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/ynbacpb72ax388379nzixscmmsl506rj-signalbackup-tools-20230515-1 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A signalbackup-tools https://github.com/r-ryantm/nixpkgs/archive/640d61e6e4d58df23adee31bb2e751fbe379df5d.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/ynbacpb72ax388379nzixscmmsl506rj-signalbackup-tools-20230515-1
ls -la /nix/store/ynbacpb72ax388379nzixscmmsl506rj-signalbackup-tools-20230515-1/bin

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

1 package built:

signalbackup-tools

Maintainer pings
cc @malob for testing.

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/bepaald/signalbackup-tools/releases.
meta.description for signalbackup-tools is: Tool to work with Signal Backup files
meta.homepage for signalbackup-tools is: https://github.com/bepaald/signalbackup-tools
Updates performed

Version update

To inspect upstream changes

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 20230518 with grep in /nix/store/h2b5h88prabs1gkmrvcwwiaxrjx3x13j-signalbackup-tools-20230518
found 20230518 in filename of file in /nix/store/h2b5h88prabs1gkmrvcwwiaxrjx3x13j-signalbackup-tools-20230518

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

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
signalbackup-tools

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/h2b5h88prabs1gkmrvcwwiaxrjx3x13j-signalbackup-tools-20230518 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A signalbackup-tools https://github.com/r-ryantm/nixpkgs/archive/a08884b3c5f0d699affbd186c5013c674f1d929f.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/h2b5h88prabs1gkmrvcwwiaxrjx3x13j-signalbackup-tools-20230518
ls -la /nix/store/h2b5h88prabs1gkmrvcwwiaxrjx3x13j-signalbackup-tools-20230518/bin

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

1 package built:

signalbackup-tools

Maintainer pings
cc @malob for testing.


1.16.5 This mod removes transparency from the hotbar

dungeons_gear-1.16.5-3.2.3.jar
The bg behind the items in your hotbar is transparent until I add this mod

We don't touch the hotbar at all. However, I made some changes to our artifact bar, so it no longer uses the vanilla hotbar icons. Can you tell me which modpack you are using here?
It might be fixed with that. Please check if it still happens in Dungeons Libraries 1.0.4 (released soon)

Not fixed yet. I discovered the issue, will be releasing 1.0.5 later today :)

Fixed in Dungeons Libraries 1.0.5
https://www.curseforge.com/minecraft/mc-mods/dungeons-libraries/files/4287841


error: 'Algorithm' is only available on tvOS 10.0 or newer

It seems like there are errors with tvOS as well.
error: 'Algorithm' is only available on tvOS 10.0 or newer
public func encrypted(with key: PublicKey, algorithm: Data.Algorithm) throws -> EncryptedData? {

Here the error log
carthage-xcodebuild.SVs1Np.log

Closing since this should be fixed in the 3.5.1 release


Fix a tiny typo

I just happened upon this tiny typo in post #2 so I thought I'd make a PR for it!
No biggie, thanks for the great tutorials!

Thanks!


Results Problem?

Hello,
Really amazing work.
While doing inference, i faced the results are not as good as shown.
I tested using the pre trained models:

faster_rcnn_RoITrans_r50_fpn_1x_dota

faster_rcnn_RoITrans_r50_fpn_1x_dota1_5

Can You help Explain why?

What is the image source that you use? Have you conducted the multi-scale inference?

@dingjiansw101 i am using demo_large_image.py for inference.
I have downloded these images from https://unsplash.com/s/photos/military-base-aerial-view

First, model trained with DOTA-v1.5 should be more accurate than the DOTA-v1.0. Second, I think there is a domain shift between your images and DOTA images, which may decrease the performance.


Add 0.19upgrade command

Upgrading to Terragrunt 0.19.x (so you can use Terraform 0.12.x) can be a lot of work, including converting many terraform.tfvars files to terragrunt.hcl. Terraform comes with a 0.12upgrade command that updates .tf files to Terraform 0.12 syntax. It's not perfect, but saves a ton of work.
We should add an analogous 0.19upgrade command that updates terraform.tfvars to terragrunt.hcl. It doesn't need to be perfect, but if it can update all files recursively within a subfolder, and get them 95% of the way there, it would still be worth it.
If anyone is up for a PR to add this, we'd be more than grateful!

Should the command be called terragrunt 0.19upgrade? Since it is really about upgrading to tg19 syntax as opposed to tf12.

Oh, yea, good point! Will update the description.

This would be great when we have a fairly large footprint of tfvars files!

I think the ship has sailed on this one. Closing!


add missing fields to BatchRecordChange

Description of the Change

Add missing fields in BatchRecordChange as per #55
Adhered to existing convention of representing timestamps as strings

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

@haardikk21 Thank you very much!


From where is DefaultJsonSerialization coming?

What is DefaultJsonSerialization and why isn't "new JsonSerializerOptions(JsonSerializerDefaults.Web (or General))" used?

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

ID: 1a42e9c6-2624-e047-ed1c-03ec047b538a
Version Independent ID: 3b1dd30f-82a8-2526-bd51-fb6401c52e81
Content: HttpClient guidelines for .NET - .NET
Content Source: docs/fundamentals/networking/http/httpclient-guidelines.md
Product: dotnet-fundamentals
GitHub Login: @gewarren
Microsoft Alias: gewarren

@dasCodeaffe Can you clarify where in the article this is used?

@DasCodeaffe Can you clarify where in the article this is used?

It's used multiple times on this page:
https://learn.microsoft.com/en-us/dotnet/core/extensions/httpclient-factory


Support for SAM variants

This branch is intended to provide support for several SAM variants, in particular ESAM, SS-SAM, LookSAM and ASAM. These variants can be run together or separately as part of a larger SAM algorithm (see 'SAM Algorithm' below).
Brief Algorithms Overview
ASAM (Adaptive Sharpness-aware Minimization)
Proposes a scale-invariant calculation of sharpness that is used when finding the local maximum.
LookSAM
Proposes to only periodically compute the SAM gradient, and for all other iterations use the project of the SAM gradient instead of recalculating it.
Note that the paper also includes a layer-wise LookSAM variant for larger batches that was not included here.
SS-SAM (Stochastic Scheduled Sharpness-aware Minimization)
Proposes different stochastic functions to randomly determine if a SAM update should be done at each step.
ESAM (Efficient Sharpness-aware Minimization)
Adds Stochastic Weight Perturbation (SWP), where "the sharpness measure is approximated by perturbing a stochastically chosen set of weights" and Sharpness-Sensitive Data Selection (SDS), where the "SAM loss is optimized using only a judiciously selected subset of data that is sensitive to the sharpness."
Note that this implementation only adds support for SWP. SDS requires that the loss not be reduced (or to recompute the loss again) which could be a larger change for integration.
SAM Algorithm PseudoCode
// T = total number of iterations, theta = model parameters
for t in 1...T:
  Sample batch B
  // ESAM SWP
  for p in theta:
    if random() > ESAM_SWP_beta:
      p.requires_grad = False  // don't use for SAM calculation
  // Check if should do SAM-update or not. This supports SS-SAM as well as the
  // current interval system in the codebase.
  if should_do_sam_this_iteration(t):
    g_orig = loss(theta, B)
    if ASAM:
      t_w = abs(theta)
      grad_norm = norm(g_orig * t_w)
    else:
      grad_norm = norm(g_orig)
    scale = rho / grad_norm
    if ESAM_SWP:
      scale /= (1 - ESAM_SWP_beta)
    eps_w = g_orig * scale
    if ASAM:
      eps_w *= t_w ** 2
    g_new = loss(theta + eps_w, B)
    if LookSAM:
      cos_proj = (g_orig * g_new) / (norm(g_orig) * norm(g_new))
      g_v = g_new - abs(g_new) * cos_proj * g_orig / norm(g_orig)
  else:
    g_new = loss(theta, B)
    if LookSAM:
      g_new += alpha * norm(g_new) / norm(g_v) * g_v
  theta -= lr * g_new // SGD Update

Running
Specifying the SAM variants to choose is passed as arguments to the SAM class.
trainer = Trainer(
    ...
    algorithms=[SAM(
         interval=SAM_FixedInterval, // type of interval scheduler to use (for backwards compatibility,
            // can also just accept an int which will then default to a SAM_FixedInterval which is the current behavior
         interval_num = 3, // if specifying a SAM_FixedInterval, what interval to use (in future may make sense to remove
           // and just specify interval as an int when wanting to use SAM_FixedInterval
         use_LookSAM=True, // whether to use LookSAM
         use_ESAM_SWP=True, // whether to use ESAM SWP
         use_ASAM=False) // whether to use ASAM
])

Different SAM variants can be combined as desired.
As of now each SAM variant is specified with its own boolean variable if it should be run, and any arguments specific to that variant. This can become unwieldy, and in the future may require some redesign (ex: have subclasses of SAM for each variant, and a master parent class that can still run each at each part so the variants can be combined if desired).
The current SAM implementation in the codebase (and this modified one) can also support WASAM (which combines SAM and SWA) as referenced in #817 by appending a SWA step after the SAM updates. (Usually SWA is done at the epoch level, so this would be after N SAM updates, where N is the number of steps per epoch). Something like this may work:
swa_algorithm = SWA(swa_start="6ep", swa_end="8ep")
sam_algorithm = SAM()
trainer = Trainer(
    ...
    algorithms=[sam_algorithm swa_algorithm[
)

Note: this requires more testing to replicate some of the experiments in the original papers. I'm currently running some of those experiments and will add results here when I have them.

Thanks @rahulvigneswaran and @Pikus16  for the contribution! We've created another repository where third-party contributions (https://github.com/mosaicml/experimental) can go first for validation, testing, and eventual upstreaming into Composer. Could you perhaps make a PR into that repository?


SOFRIA export fails with verse straddling partial paragraph preceded by note.

Some USX, when rendered as SOFRIA, throws the following error:
TypeError: Cannot read property 'push' of undefined
    at e.exports.action (/home/mark/repos/proskomma-js/dist/index.js:121:56362)
    at e.exports.renderEvent (/home/mark/repos/proskomma-js/dist/index.js:8:115328)
    at e.exports.renderItem (/home/mark/repos/proskomma-js/dist/index.js:121:46054)
    at e.exports.renderContent (/home/mark/repos/proskomma-js/dist/index.js:121:44829)
    at e.exports.renderSequence (/home/mark/repos/proskomma-js/dist/index.js:121:44628)
    at e.exports.renderDocument1 (/home/mark/repos/proskomma-js/dist/index.js:121:42927)
    at e.exports.renderDocument (/home/mark/repos/proskomma-js/dist/index.js:8:114742)
    at Xa.sofria (/home/mark/repos/proskomma-js/dist/index.js:121:308821)
    at Object.sofria (/home/mark/repos/proskomma-js/dist/index.js:121:354468)
    at Xu (/home/mark/repos/proskomma-js/dist/index.js:121:258849)

I managed to replicate the error with some short USX fragments. The error seems to happen when a verse started in one paragraph ends halfway through another paragraph, and when the first paragraph also contains a note. (Both these conditions must be true to see the error.)
sofria_works_usx.txt
sofria_also_works_usx.txt
sofria_no_works_usx.txt
sofria_this_no_works_neither_usx.txt

I made ProskommaRender errors more informative:
Error: Exception from action 'identity' for event startWrapper: Error: outputContentStack is empty before pushing to its first element

So it looks like a stack management thing.

My previously failing tests now pass. The issue was that I was clearing the chapter and verse state at the end of every sequence, when in fact this should only happen at the end of the main sequence.

Made a PR to proskomma-json-tools. Once that has been merged we'll refresh that module in Proskomma, which ought to fix the issue.


specs: add predeploys

Description
PR to add specs for the predeploys. These need to be upgraded in a backwards compatible way for bedrock, its worth specifying their interfaces since they will always be in the state.

Codecov Report

Merging #379 (4b5c5d9) into main (3068429) will not change coverage.
The diff coverage is n/a.

:exclamation: Current head 4b5c5d9 differs from pull request most recent head 83a2432. Consider uploading reports for the commit 83a2432 to get more accurate results

@@           Coverage Diff           @@
##             main     #379   +/-   ##
=======================================
  Coverage   40.77%   40.77%
=======================================
  Files          46       46
  Lines        5791     5791
=======================================
  Hits         2361     2361
  Misses       3146     3146
  Partials      284      284

Continue to review full report at Codecov.

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The following script was used to find the existing predeploys:
import { providers, utils } from 'ethers'
import * as fs from 'fs'

const outfile = 'predeploys.json'

;(async function () {
  const provider = new providers.StaticJsonRpcProvider('https://mainnet.optimism.io')

  const prefixes = [
    '0x420000000000000000000000000000000000',
    '0xDeadDeAddeAddEAddeadDEaDDEAdDeaDDeAD'
  ]

  // we don't need to search the entire space
  // const MAX_U16 = 0xffff
  const predeploys = []

  for (const prefix of prefixes) {
    for (let i = 0; i <= 100; i++) {
      const buf = Buffer.alloc(2);
      buf.writeUInt16BE(i, 0);
      const addr = utils.hexConcat([prefix, utils.hexZeroPad(buf, 2)])
      predeploys.push(addr)
    }
  }

  const detected = []

  for (const predeploy of predeploys) {
    const code = await provider.getCode(predeploy)
    if (code !== '0x') {
      console.log(`Predeploy detected at ${predeploy}`)
      detected.push({
        address: predeploy,
        code: code,
      })
    }
  }

  fs.writeFileSync(outfile, JSON.stringify(detected, null, 2))
})()

Results:
$ cat predeploys.json | jq -r '.[].address'
0x4200000000000000000000000000000000000000
0x4200000000000000000000000000000000000002
0x4200000000000000000000000000000000000006
0x4200000000000000000000000000000000000007
0x420000000000000000000000000000000000000f
0x4200000000000000000000000000000000000010
0x4200000000000000000000000000000000000011
0x4200000000000000000000000000000000000012
0x4200000000000000000000000000000000000013
0xdeaddeaddeaddeaddeaddeaddeaddeaddead0000

Thank you for the review! Addressed your nits

For some reason there is a CircleCI build error
# No configuration was found in your project. Please refer to https://circleci.com/docs/2.0/ to get started with your configuration.

For some reason there is a CircleCI build error
# No configuration was found in your project. Please refer to https://circleci.com/docs/2.0/ to get started with your configuration.

@mslipper Somethings acting up.
@tynes don't worry about circle CI blocking this PR

@norswap great feedback, thank you! Will address

This PR will need to be rebased and updated based on https://github.com/ethereum-optimism/optimistic-specs/pull/421

I've pushed a fix to this PR to address comments. I've removed the majority of the interfaces so that we don't need to maintain the interfaces here as well as in the repo. We can link directly to the contracts once they are all in the same repo

Closing in favor of https://github.com/ethereum-optimism/optimism/pull/2568


[vm/ffi] Provide memcopy function

After adressing https://github.com/dart-lang/sdk/issues/43967 we might also expose a memcopy function in the dart:ffi API to provide faster mem copying in and out of TypedData that is still GC-safe.

The internal API:
https://github.com/dart-lang/sdk/blob/706f6b2ca4b82c3f7103a13984587b3f5ce1181a/sdk/lib/_internal/vm/lib/ffi_patch.dart#L241-L247
A public API should probably have some more guardrails.

FWIW I would prefer that we simply provide fast path in List.setRange (and possibly a TFA based specialization of TypedData.setRange(TypedData).

I took a stab at this and modelled the API after the asTypedList extension methods on Pointers.
https://dart-review.googlesource.com/c/sdk/+/307040
extension Int64Pointer on Pointer<Int64> {
  /// ...
  external Int64List asTypedList(
    int length, {
    @Since('3.1') Pointer<NativeFinalizerFunction>? finalizer,
    @Since('3.1') Pointer<Void>? token,
  });

  /// Copies memory from `this` to [target].
  ///
  /// Copies `8 * length` bytes of memory.
  ///
  /// The memory backing `this` and [target] must not overlap.
  ///
  /// The [length] must not be larger than [target.length].
  @Since('3.1')
  external memCopyToTypedList(Int64List target, int length);

  /// Copies memory from [source] to `this`.
  ///
  /// Copies `8 * length` bytes of memory.
  ///
  /// The memory backing `this` and [source] must not overlap.
  ///
  /// The [length] must not be larger than [source.length].
  @Since('3.1')
  external memCopyFromTypedList(Int64List source, int length);

  /// Copies memory from `this` to [target].
  ///
  /// Copies `8 * length` bytes of memory.
  ///
  /// The memory backing `this` and [target] must not overlap.
  @Since('3.1')
  external memCopy(Pointer<Int64> target, int length);
}

Any feedback on the API is welcome. @mkustermann @lrhn
Some design decisions:

I have aligned the TypedData types and Pointer type arguments so that we can talk about length in element (similar to asTypedList).
I did not expose any offsets, rather typed data views and Pointer.elementAt should be used to do this. This makes giving nice error messages when the length/offset is out of range easier.

FWIW I would prefer that we simply provide fast path in List.setRange (and possibly a TFA based specialization of TypedData.setRange(TypedData). This way we can also improve memory copying for non-FFI scenarios.

That is an interesting idea, using asTypedList on the pointer and making memcopy between TypedDatas faster.

FWIW I would prefer that we simply provide fast path in List.setRange (and possibly a TFA based specialization of TypedData.setRange(TypedData). This way we can also improve memory copying for non-FFI scenarios.

The only downside of this is that it's not visible from the Dart code whether it's going to be a fast copy or not. E.g. if the call sites are polymorphic, or have mismatched element sizes. How much do we care about predictable performance? @mraleph @mkustermann?
If we want predictable performance, and support TypedData copies, we could consider introducing a memoryCopy method on Int64List and friends. And then in addition rewrite it in the TFA to use that copy method. (Of course that would lead to the question what kind of predictable performance we could get in the JS/WASM backends as well, since it's a shared API. cc @askeksa-google @rakudrama.)

This would greatly accelerate protobuf parsing using https://github.com/protocolbuffers/upb. Profiles currently show ~40% of the overall parsing cost is just copying the data into an FFI buffer.
Ideally we could just parse directly out of the Uint8List buffer as proposed in https://github.com/dart-lang/sdk/issues/44589, but in cases where that is not possible for whatever reason a memcopy() function would help a lot.

FWIW I would prefer that we simply provide fast path in List.setRange (and possibly a TFA based specialization of TypedData.setRange(TypedData). This way we can also improve memory copying for non-FFI scenarios.

I agree with @mraleph we should make List.setRange() and TypedData.setRange() faster - which is already tracked at https://github.com/dart-lang/sdk/issues/42072.

The only downside of this is that it's not visible from the Dart code whether it's going to be a fast copy or not. E.g. if the call sites are polymorphic, or have mismatched element sizes. How much do we care about predictable performance? @mraleph @mkustermann?

Specifically for memory copies of pointers / typed data, I don't see any such concern. We guarantee any TypedData.setRange(TypedData) will be fast.

@sstrickl is going to work on optimizing memory copies (we may not want a separate API though - as this issue suggests - as one can always make views on ffi memory and use existing TypedData.setRange() calls)

@dcharkes @mraleph if we agree we don't need a new API, maybe we can close this issue in favor of https://github.com/dart-lang/sdk/issues/42072 ?

@dcharkes @mraleph if we agree we don't need a new API, maybe we can close this issue in favor of #42072 ?

sgtm, I can abandon https://dart-review.googlesource.com/c/sdk/+/307040.
@sstrickl you might want to copy the test from that CL (and massage it to use setRange). We should check that the cases covered in the test are all working.
Probably irrelevant but also worth checking: How much overhead does the typed-data object creation add if we're just talking about copying between two pointers? (Or a typed data and a pointer.)
final p1 = malloc<Int8>(1024);
final p2 = malloc<Int8>(1024);
p2.asTypedList(1024).setRange(0, 1024, p1.asTypedList(1024));

How much overhead does the typed-data object creation add if we're just talking about copying between two pointers? (Or a typed data and a pointer.)

We should try to come to a solution where the TypedData object creation will be optimized away (will get there soon).

After all the work @sstrickl has done here, the code
dest.asTypedList(n).setRange(0, n, src.asTypedList(n))

now compiles to a MemoryCopyInstr without typed data view allocation etc. - see IL test

After all the work @sstrickl has done here

Thanks @sstrickl !


vela svc not found

https://kubevela.io/#/en/developers/port-forward

but

thanks for reporting, will fix it. You can use vela ls instead of vela svc ls.

ok, thanks


Windows Firewall PORQUDAPROBLEMAS PC

[Escriba sus comentarios aquí]

Detalles del documento
⚠ No edite esta sección. Se requiere para docs.microsoft.com ➟ Vinculación de problema de GitHub.

ID: 8c552a93-32b2-294c-6b95-8e78bcf3055d
Version Independent ID: 02adbfec-c878-1227-bfe2-8cb8d331276f
Content: Lista de comprobación Para implementar un diseño de directiva de aislamiento de dominio (Windows) - Windows security
Content Source: windows/security/threat-protection/windows-firewall/checklist-implementing-a-domain-isolation-policy-design.md
Product: m365-security
Technology: windows-sec
GitHub Login: @Dansimp
Microsoft Alias: dansimp

Thanks @arixdjw for taking the time to share this with the Windows documentation team. I’m sorry that you’re having problems, and I want to make sure it gets to the right people that can help. There are a couple of options available to provide the best level of support for this issue:

Post to Windows on Q&A. These are moderated by community members who are very experienced, knowledgeable, and helpful.
Use Microsoft Support to search for the issue, or open a case with professional support.
Contact your Microsoft Unified Support team, such as a Customer Engineer or Customer Success Account Manager.

I'm closing this issue as there's nothing actionable for docs at this time.


Add support for GetObjectAttributesRequest(ObjectAttributes.OBJECT_PARTS)

Hi,
So, my use case is to use pre-signed URLs for multipart downloads. And there are two ways to perform those downloads:

If the object has been uploaded as multipart, I generate the URL with the query parameter partNumber=N;
If not, I use the header Range: bytes=X-Y.

To determine which one shall be used I check for GetObjectAttributesRequest(ObjectAttributes.OBJECT_PARTS) and if the parts are null then I use ObjectAttributes.OBJECT_SIZE to determine the byte range.
I am currently using version 2.16.0 which supports ObjectAttributes.OBJECT_SIZE already, thanks for that, but I also need a way to know whether it is a multipart upload.
Cheers!

related to #536

@campidelli
Do you have a working test case against the real S3 API?
When I was implementing #536, I couldn't figure out how the parts are supposed to work. Citing myself:

The implementation for the "HeadObject" attributes is straightforward, but I struggle to understand how the "ListParts" attributes are supposed to work.
I can't get a test case against the S3 API to work.
There is no way to pass in an "uploadId", so a call to an object where the multipart upload is still running returns a 404 key not found.
After the multipart upload is completed, the "parts" in the response are empty because there are no more parts.

This is a use case https://github.com/campidelli/file-storage-service/blob/main/src/test/java/campidelli/file/storage/AsyncMultipartDownloadIIntegrationTest.java#L66
BTW, I have found more things in this new version:

Now I need to provide basic credentials to my S3Client, the DefaultCredentialsProvider doesn't work anymore.
When I use .withVolumeAsRoot(TEMP_DIR.getAbsolutePath()) it times out looking for /favicon.ico and the test doesn't run.

@campidelli just to reiterate:
this application and the tests are working as-is against the real S3 backend?
After looking at the code, I'm pretty sure they will not.
There are multiple problems with the test setup, none have anything to do with S3Mock:

The application can't reach the S3Mock testcontainer.
The WebTestClient request timeout is so low (5 seconds) that if the application can reach S3(Mock) and makes multiple requests, we run into timeouts.
The file uploaded is so small that the S3Client uses a "putObject" instead of a MultipartUpload.
The part size calculation is wrong, object size is always returned in bytes, so parts are expected to be 8 bytes long in your implementation.
Since MultipartUpload is not used, getObjectAttributes returns all needed properties in the response.
...

Please make sure that your code works before asking me to debug problems in S3Mock. I'm doing this in my free time... ;)
Also: run S3Mock as an external process / Docker container to see the logs. Make sure to use the "debug" setting. You can see which requests come in, which controller methods they are being routed to etc. Using "trace" gives even more output, though that may be hard to read - Spring logs a lot on "trace".
You'd have seen that there are no errors in the logs, getObjectAttributes is never called and the problem is within your test and application.
https://github.com/campidelli/file-storage-service/pull/3

Also:
DefaultCredentialsProvider is provided by the AWS SDK. In your test application, I can see in the debugger that DefaultCredentialsProvider is used and works, and withVolumeAsRoot does not throw an error when used.
Not sure how you can reproduce these problems.

This is a use case https://github.com/campidelli/file-storage-service/blob/main/src/main/java/campidelli/file/storage/controller/AsyncMultipartDownloadController.java
BTW, I have found more things in this new version:
1. Now I need to provide basic credentials to my S3Client, the `DefaultCredentialsProvider` doesn't work anymore.

2. When I use `.withVolumeAsRoot(TEMP_DIR.getAbsolutePath())` it times out looking for `/favicon.ico` and the test doesn't run.

@campidelli I'll close this ticket.
If you have any more questions / challenges then re-open or open a new issue with a reproducer I can easily execute :)


problem using tf.compat.v1.get_variable in tf2

System information

Have I written custom code (as opposed to using a stock example script provided in TensorFlow): No
OS Platform and Distribution (e.g., Linux Ubuntu 16.04): macos mojave 10.14.6
Mobile device (e.g. iPhone 8, Pixel 2, Samsung Galaxy) if the issue happens on mobile device: No
TensorFlow installed from (source or binary): binary
TensorFlow version (use command below): 2.0.0
Python version: 3.6
Bazel version (if compiling from source):no
GCC/Compiler version (if compiling from source):no
CUDA/cuDNN version:
GPU model and memory:

Describe the current behavior
reference：https://www.tensorflow.org/api_docs/python/tf/compat/v1/get_variable?hl=en
I referenced the above links and got the following results
v1:<tf.Variable 'foo/v:0' shape=(1,) dtype=float32, numpy=array([1.3727096], dtype=float32)>
v2:<tf.Variable 'foo/v:0' shape=(1,) dtype=float32, numpy=array([-1.0603657], dtype=float32)>
Describe the expected behavior
v1 should be equal to v2
When I use tf1, I get the following results：
v1:[0.91463006]
v2:[0.91463006]
Contributing - Do you
want to contribute a PR? (yes/no): no
(if contributing):
Standalone code to reproduce the issue
reference：https://www.tensorflow.org/api_docs/python/tf/compat/v1/get_variable?hl=en
tf2 version:
def foo():
    with tf.compat.v1.variable_scope("foo", reuse=tf.compat.v1.AUTO_REUSE):
        v = tf.compat.v1.get_variable("v", [1], initializer=tf.compat.v1.glorot_uniform_initializer())
        return v
v1 = foo()
v2 = foo()
print(v1)
print(v2)

tf1 version:
def foo():
    with tf.compat.v1.variable_scope("foo", reuse=tf.compat.v1.AUTO_REUSE):
        v = tf.compat.v1.get_variable("v", [1], initializer=tf.compat.v1.glorot_uniform_initializer())
        return v
v1 = foo()
v2 = foo()
with tf.Session() as sess:
    sess.run(tf.global_variables_initializer())
    print(f'v1:{sess.run(v1)}')
    print(f'v2:{sess.run(v2)}')

In TF2 you are in graph mode right?
So in TF2
import tensorflow as tf
@tf.function
def foo():
  with tf.compat.v1.variable_scope("foo", reuse=tf.compat.v1.AUTO_REUSE):
    v = tf.compat.v1.get_variable("v", [1])
  return v

v1 = foo()  # Creates v.
v2 = foo()  # Gets the same, existing v.
assert v1 == v2

In TF1 you are in graph mode right?
So in TF2
import tensorflow as tf
@tf.function
def foo():
  with tf.compat.v1.variable_scope("foo", reuse=tf.compat.v1.AUTO_REUSE):
    v = tf.compat.v1.get_variable("v", [1])
  return v

v1 = foo()  # Creates v.
v2 = foo()  # Gets the same, existing v.
assert v1 == v2

Why do I get different values when I use  Eager Execution  and Graph Execution

It Is documented.
Check;
https://github.com/tensorflow/tensorflow/issues/45876
https://github.com/tensorflow/tensorflow/issues/46133

Hi, I am facing this error with tf.compat.v1.get_variable.
TypeError: Dimension value must be integer or None or have an index method, got value '27876.0' with type '<class 'float'>'


Actions that may take a while to complete/show progress should be explicit about starting

Pulled from #558. Examples:
|merge should print out "starting merge..." to let the user know we're merging in the background.
On %init merge, mention that the new desk is not mounted tell the user how to mount it.
|mount of nonexistent desk should either give a readable error or succeed and tell the user it doesn't exist yet.

I'm going to close this as I think it's too broad to ever really resolve as-is.  There are a probably lot of such commands, and I think more focused/specific issues (e.g. "|merge should print.." or |mount should print..") would prove to be more useful.


Consolidate pages?

Is there anything more that needs to go on the project overview page? If not, could the issues be listed on that page, rather than having to click through again to them? This might make the interface a bit slicker as you'd have all the project details on one page.

@zenduo felt the same about this, but I have left this page "intentionally blank" as I'd like to move towards more project management oriented features once we hit release, for example, communication between clients (a la Basecamp). For now, it can serve as  the base for some quick information about this particular project - such as LMS deployment information, and who the lead employees are.


EthosConnectProvider enteres infinite re-render cycle without ethosConfiguration

When instantiating the provider in a vanilla create-react-app, when the EthosConnectProvider is passed without a ethosConfiguration, the component enters an infinite re-render loop.

Thank you. We'll take a look.

This should be fixed with the latest build.


[Bug] When writing a partitioned table for Paimon using Flink SQL and storing the table on HDFS, the partition directory name on HDFS is displayed abnormally. For example, it shows as SCAN_DATE=19415 instead of the correct format of SCAN_DATE=2023-03-01, where SCAN_DATE is of type date.

Search before asking

[X] I searched in the issues and found nothing similar.

Paimon version
paimon-flink-1.15-0.4-20230330.002117-12.jar
Compute Engine
flink1.15.3
Minimal reproduce step
When writing a partitioned table for Paimon using Flink SQL and storing the table on HDFS, the partition directory name on HDFS is displayed abnormally. For example, it shows as SCAN_DATE=19415 instead of the correct format of SCAN_DATE=2023-03-01, where SCAN_DATE is of type date.
What doesn't meet your expectations?
When writing a partitioned table for Paimon using Flink SQL and storing the table on HDFS, the partition directory name on HDFS is displayed abnormally. For example, it shows as SCAN_DATE=19415 instead of the correct format of SCAN_DATE=2023-03-01, where SCAN_DATE is of type date.
Anything else?
No response
Are you willing to submit a PR?

[X] I'm willing to submit a PR!

Direct fixes may have compatibility issues, we should be careful.

Direct fixes may have compatibility issues, we should be careful.

I’m trying to fix this bug, can you assign it to me?
My idea is to format the DATE type in the org.apache.paimon.utils.RowDataPartitionComputer#generatePartValues method. For example, converting the int value 19996 of the DATE type into the correct date string 2024-09-30.

I think this issue need to fix. For example, we develop a paimon connector of seatunnel which use java api of paimon also has the same problem.The types in date,time,timestamp all have the same problem.

@JingsongLi Hi, how about this problem?


Fixes dependency not being cleaned by keeping the uavcan artifacts in th...

...e BUILD_DIR

Sorry for the late PR.


v4.0.0

Codecov Report

Merging #97 (8552500) into main (ef56698) will increase coverage by 6.76%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##             main       #97      +/-   ##
===========================================
+ Coverage   93.23%   100.00%   +6.76%
===========================================
  Files           8         4       -4
  Lines         133        59      -74
  Branches       41        27      -14
===========================================
- Hits          124        59      -65
+ Misses          9         0       -9

Impacted Files
Coverage Δ

src/make-runtime-config.ts
100.00% <100.00%> (ø)

src/middleware.ts
100.00% <100.00%> (ø)

src/with-split.ts
100.00% <100.00%> (ø)

Continue to review full report at Codecov.

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Update documentation to reflect latest recommendations

Hello, first of all thanks for open sourcing this project!
As I was searching through some older issues I came across this recommendation:

Our recommendation moving forward is to use Spectral's Node API and import our ruleset as a dependency to get consistent behavior with the CLI tool. That's what the CLI tool is doing behind the scenes.

To be honest this is the first time I have heard about Spectral and therefore it was not immediately clear to me how to hook this API validation ruleset up with the Spectral NPM package. I was wondering if you could provide a simple update to the current README to reflect your latest recommendation.
Many thanks :)

Hello @dustinmoris - I'm glad the project looks beneficial to you!
That's a good suggestion. We'll look at adding that in the docs. In the meantime, we do have a quick guide in our README for the ruleset package itself. The way to hook it up is to install our ruleset (which is a standalone package), install Spectral separately, and write a Node program to utilize them together as in the linked example.

:tada: This issue has been resolved in version 1.19.0 :tada:
The release is available on npm package (@latest dist-tag)
Your semantic-release bot :package::rocket:

:tada: This issue has been resolved in version 1.20.0 :tada:
The release is available on npm package (@latest dist-tag)
Your semantic-release bot :package::rocket:

:tada: This issue has been resolved in version 1.4.0 :tada:
The release is available on npm package (@latest dist-tag)
Your semantic-release bot :package::rocket:


0.9.4-rc.2: Only create 1 managed NatGateway per AZ

The new flexibility of how you can create and manage subnets with/without managed NATGateways is really great.  IMHO there is only one downside however.  If you let kube-aws manage the NATGateways for private subnets, it creates 1 NATGateway per subnet.
This causes slight problems if you define a lot of private subnets in your cluster.yaml.  In my use case I have 6 private subnets (3 in each of 2 AZ's).  This produces 6 NATGateways when I really only need 2 ( 1 for each AZ for high availability).  This produces slightly higher costs but more importantly puts you more easily in reach of Amazon's resource limits on NATGateways.

@drock Sorry for the silence and thanks for the suggestion.
I guess we can also complicate (😋) cluster.yaml to support something like:
natGateways:
- name: managedNAT1a
  availabilityZone: us-west-1a

subnets:
- name: managedPrivateSubnetForFoo1a
  # *snip*
  natGateway:
    name: managedNAT1a
- name: managedPrivateSubnetForBar1a
  # *snip*
  natGateway:
    name: managedNAT1a

to define NAT gateways and reference ones from subnet definitions.
Do you have any preference and this and #303 and even another ideas?

I am also getting hit by a related issue. We use managed NAT gateways with EIPs allocated outside kube-aws, and we have many (managed) private networks all of whom want to use a NAT gateway with the specified EIPs.
My use case would also be solved by allowing subnets to specify and share NAT gateways by name, as specified by @mumoshu. Thanks!

@mumoshu I think your suggestion would work great.  I don't think it should replace what is requested in #303 though.  I think there is still the use case for that.  Basically, when specifying a subnet you have 5 options regarding the natGateway

Leave it empty and a nat gateway will automatically be created for that subnet for it.
Specify an aws id of an existing gateway
Specify an output from another cloudformation stack
Specify the name of the gateway from the managed list in cluster.yaml (your suggestion)
Specify a cloud formation reference to a gateway manually defined in stack-template.json (#303)

Its a lot of modes of operation but I think it would cover all of the bases.

Has there been any movement on this? If not, I could try and get someone from my team to tackle it. Thanks!

@soellman Unfortunately no 😢 Could you assign someone from your team to this? Thanks!

I will see what I can do :)

@mumoshu @drock im working on this also, i've found that for now a simple workaround is to resort to instruct kube-aws to use an existing vpc, this should be fixed in cluster.yaml definition as @mumoshu proposed anyway.

@Fsero Yes.  That is ultimately what we ended up doing anyway to better facilitate upgrading versions of kube-aws.


Input from file only works with parameter -f

https://github.com/windytan/redsea/blob/67c76f5d23454a26c1063495f123b98475305809/src/redsea.cc#L33
This hint seems not to work, I get no RDS data.
The only way is the parameter -f [FILE].
andreas@E535:~$ more Downloads/radiostetin.wav.s16 | redsea -r 192k
{"pi":"0x0000"}
andreas@E535:~$ redsea -r 192k < Downloads/radiostetin.wav.s16 | head -5
{"pi":"0x0000"}
andreas@E535:~$ redsea -r 192k -f Downloads/radiostetin.wav.s16 | head -5
{"pi":"0x34EB"}
{"pi":"0x34EB","group":"0A","di":{"dynamic_pty":false},"is_music":true,"prog_type":"No PTY","ta":false,"tp":true}
{"pi":"0x34EB","group":"0A","di":{"compressed":false},"is_music":true,"prog_type":"No PTY","ta":false,"tp":true}
{"pi":"0x34EB","group":"0A","di":{"artificial_head":false},"is_music":true,"prog_type":"No PTY","ta":false,"tp":true}
{"pi":"0x34EB","group":"0A","di":{"stereo":true},"is_music":true,"prog_type":"No PTY","ta":false,"tp":true}

radiostetin.wav.zip
(just a sample file, taken from a friend)

Seems that although it has the extension, this file is not in the s16 format (raw 16-bit signed integer PCM), instead it is a 24-bit WAV file.
$ file radiostetin.wav.s16
radiostetin.wav.s16: RIFF (little-endian) data, WAVE audio, Microsoft PCM, 24 bit, mono 192000 Hz

Some WAV files can works as raw PCM as the 16-bit aligned RIFF headers gets interpreted as a burst of noise, and they even can be piped to redsea as such, but the 24-bit sample width becomes a problem here.
Raw PCM normally looks like this (unless by coníncidence the noise starts looking like a file header):
$ file gen-yksi-171k.s16
gen-yksi-171k.s16: data

I have renamed it as I thought it might work then. The original extension of the file was .wav

You can convert any audio file (well, almost) into the S16LE format with sox: sox radiostetin.wav radiostetin.s16 (this format has no headers for metadata, so make sure of the correct number of channels and sample rate).
For now, I'm not planning to add WAV input via stdin, but if such a need arises this can very well be reopened.

-f seemes to convert 24bit into 16bit as well. So it's worth mentioning it in the wiki as well.

Good idea! For the wiki change, note that it’s converted direct to float32 (this also happens to the raw 16-bit input)

https://github.com/windytan/redsea/blob/c6e6b47ac2c7a9aac9409483b00ca61cd6eb47bd/src/input.cc#L92

Sent from mobile


Release ?

It seems like the main website is now just a redirect to github. The recipe we have at HaikuPort now points to a 404 :-(
Would it be possible to make a release tarball on github so at least we can fix the recipe?

Hey there, is this issue still open for you? And if yes, what would be the best type of tarball reference? Fixed ones by version, or just a "most recent" one?

gophernicus.org is up again and under my control, so I can add some fixed location with the most recent stable release tarball. Would a redirection work, or should it be a tarball directly on gophernicus.org?

Any zip or tgz anywhere should be fine, yeah :-)

I've set up http://gophernicus.org/download/master.zip with the most recent production code.
It should remain a stable and constant URL. Is that ok for you?
Zip is the easiest for the time being, as I can pull it directly from github; but of course I could also locally generate a tarball, if that's better.

Ah, hmm no, I meant it'd be better to have a release, because we check the SHA256 with the one in the recipe, so if the content changes it will break.
See https://github.com/haikuports/haikuports/blob/c2a214e6473117adfdbf84d0f792341b30e1bbd7/net-misc/gophernicus/gophernicus-1.5.recipe

Ok, I'll have a look into this. Sorry, new to the party! ^-^
I'll get back to this ASAP.

On Tue, Mar 05, 2019 at 07:27:34PM -0800, François Revol wrote:

Ah, hmm no, I meant it'd be better to have a release, because we check the SHA256 with the one in the recipe, so if the content changes it will break.
See https://github.com/haikuports/haikuports/blob/c2a214e6473117adfdbf84d0f792341b30e1bbd7/net-misc/gophernicus/gophernicus-1.5.recipe
My only concern with this is that gophernicus isn't release-ready yet.
Making it a release might make it seem so.

Currently that would mean for every commit we would have to make a
release, and you would have to continuously update.
Since you seem to be following in the steps of Gentoo, why not make a
Gentoo-style 9999 recipe with a git clone and build from that?

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Reply to this email directly or view it on GitHub:
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Ok then I suppose I'll just use the commit archives on github and rename the recipe to show version as 1.5~git and increase the revision count when updating it.

Oh… your method of generating a Changelog breaks build with HaikuPorter… because it actually copies the sources elsewhere and does a git init & git commit on it, so we can use git am to apply patches.

Ok, I updated the recipe, I'll have to fix the Makefile someday.

Looks like there are some things to fix anyway, we don't use /boot/common anymore.

Is that in your side or gophernicus?
If there's no further issues, can this be closed?


Exam mode: Grade bonus is not applied properly

Describe the bug
The 0.3 bonus is not applied to the grade (should be 3.7 instead)
To Reproduce

1 instructor
1 student who participated in the course which is used for applying a bonus (the course needs to have a grading key with type bonus)
graded exam with participation and released exam results (student review date in the past)

Expected behavior
The bonus should be applied properly (grade 3.7)
Screenshots

Which version of Artemis are you seeing the problem on?
6.6.4
What browsers are you seeing the problem on?
Chrome

@Jan-Thurner Do you have more insights on the exact bonus configuration that lead to this behaviour?
You can also directly link the test course and user that was used as we want to fix it in the upcoming week

It was this exam . The User was test user 1.

It does not seem to be an issue for me.

5,3 points are still the grade 4.0 - however, I am wondering if it is intended that the points are not displayed that are associated. I will investigate this but close this issue for now as it seems to work fine for me.


Synonyms added/corrected for neurons in Wolff et al 2015

fixes #260

Looks fine (although I can't imagine anyone searching on such horrible names...)


Sidebar rows and switch stretch with size of icon

I'm not entirely sure what this is supposed to look like or how to use it, but this looks pretty broken as-is.

That is (almost) exactly what it's supposed to look like after creating a 128x128 icon. (The "almost" is because those buttons with the red stripes should have shades of gray in them, to match the fill and stroke colors of the default path.) The bar on the side is similar to the Layers panel on GIMP, including a view of the path. I could scale down that view of the paths on the side so it doesn't stretch out everything else. All of the buttons have tooltips, but that doesn't help with the editing viewport. You need to double-click on the path to select it, and editing can be done from there. I agree that the interface is unintuitive to begin; what could I do to make interaction more obvious?

Was this fixed by #15? If so, could you submit a new release to AppCenter for review?

I'm still working on a few more updates. In particular, a basic tutorial so new users can get started. I'll should submit a new version soon.


test-branch/execute-job/wrong-commit-sha-on-pr/a6b93c8b-280a-4404-8479-da4a305b69ac

PR for testing 7194d37c4849da068003a603ddf1bfeca1d84b13

/canonical/self-hosted-runners/run-workflows 931ad21dd9ace68aaa0a7d341e94de96ad93fa6b


Add navigation bar, show and hide sections with javascript

Implemented changes acording to the Awesome books: a complete website with navigation activity:

Add a navigation bar.
Add onclick events to ul li tags on the navigation bar to show and hide diferent sections calling JavaScript functions.
Add list, add-new, contact sections and a footer.

Please be aware the webhint mark linter check is a global bug affecting other stundents as well.


prepare mlperf submission

merging this to start, will fill in system details later.
the idea is to run setup.sh first (30 minutes untimed limit) and then run_and_time.sh, i picked some parameters so that it fits in compile time limit now. with this green has 94 TFLOPS (3h53m) and red has 56 TFLOPS

@chaosagent @flammit fyi


feat: updating datasource endpoints contract

Description
With introduction of new collection called datasourceStorage the api contracts need to change.
This Pr addresses the same.
Fixes: #https://github.com/appsmithorg/appsmith-ee/issues/1348
The following flows are likely to be affected, where we would require testing:

comprehensive testing for CRUD is required for all Datasource. i.e. (DB, SAAS, API, OAuth, AuthenticatedAPI, RESTApiDatasource)
Import export, git flow,  (import from older version of appsmith, export to older version from this version)
templates and forks without config & with config, mark forkable, e.t.c
Reconnect datasources after import.
Query's, JSObject and there data bindings, onpageload actions.
DB schema
Database name update.
Generate page flows.
Welcome tour
Preview mode and data bindings.

Test Plan:
Testsmith Link

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/build-deploy-preview skip-tests=true

/build-deploy-preview skip-tests=true

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/ok-to-test

/ok-to-test

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/build-deploy-preview skip-tests=true

//build-deploy-preview skip-tests=true

/build-deploy-preview skip-tests=true

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/build-deploy-preview skip-tests=true recreate=true

/build-deploy-preview skip-tests=true recreate=true

/build-deploy-preview skip-tests=true recreate=true

/ok-to-test

/build-deploy-preview skip-tests=true recreate=true

/ok-to-test

/build-deploy-preview skip-tests=true recreate=true

/build-deploy-preview skip-tests=true recreate=true

As part of this second round, based on Ayush's suggestions in this thread, these are the test cases covered by QA:

Creation and updation of ds one of all types - Done [Also covered Firestore, Snowflake, Redis, Mongo, SMTP, Oracle, Redshift]
DB- Postgres/mongo - Done [Also covered Firestore, Snowflake, Redis, Mongo, SMTP, Oracle, Redshift]
Gsheets - Done- identified issues - resolved.
OAuth2.0 - Done - identified issues - resolved.
Saas- airtable - Done [Also covered - hubspot, Twillio]
Rest/graphql - Done [Also covered - cURL API, Auth rest API, Auth GraphQL] - identified issues - resolved.
Creation, updation and execution of a query made from these datasources - Done
Creation, updation and execution of an API without a datasource ( please try to navigating away and coming back to the query. Also check with  refresh after updating the query) - Done
Git operations / git import - export - Done
Import - Done - identified issues. - resolved.
Fork from inside app [Make application forkable] - is working. Done

Also to reiterate - Fork issues still exist on release, fix has not been merged. So we have not tested fork on this DP. This PR looks good to go.

/build-deploy-preview skip-tests=true

/ok-to-test

/ok-to-test

/ok-to-test

/build-deploy-preview skip-tests=true

/ok-to-test

/ok-to-test


New version: AdGuard.dnsproxy version 0.73.3

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

Automatic Validation ended with:

Executable C:\Users\validator\AppData\Local\Microsoft\WinGet\Links\dnsproxy.exe returned exit code: 1
Executable C:\Users\Validator\AppData\Local\Microsoft\WinGet\Links\dnsproxy.exe returned exit code: 1

(Automated response - build 897.)


docs(projects): add e-learning

It's a basic website. I changed in two files one is projects.json and another one is WEBSITE_BASIC.md.

Hey I have done what you have said. And I committed again. Can you check it?


How how to pass a jasmine.json in a custom dir?

For example, if my  jasmine.json is on /test/jasmine.json how can I set him?

You can pass only directory with tests. Reference: http://jasmine.github.io/edge/node.html#section-9

tks


Added .mcap format to recording

Added class Mcap to depthai_record and  added option to record files into .mcap format

TODO: when recording depth and using mcap, use pointCloudSave()

I will be adding depth->pcl conversion and add these commits to the record refactor PR: https://github.com/luxonis/depthai-experiments/pull/369


DRY out this code (PE Report 0.1.1)

💡 Summary
This Issue has been split for both PE Report 0.1.1 "main" and for PE Report 1.0.0 "develop" -  Issue #18,  as both repos need updated, but constitute separate efforts.
There is a repeat pattern of code used in pages.py. Noted in comments bug-unusable-package, here and here  The code should be re-written as a single function/class, unambiguous and non-repeatable.
Please provide details for implementation, such as:

An evaluation of updated Matplotlib code to pptx file code is needed.
Remove repetitive code - standardize graphing output.

Acceptance criteria
How do we know when this work is done?

[ ] Repetition of code is reduced.

This reference to 'dry out code' was relevant prior to PR#31 and has been addressed per PR#31.


[Refactoring] large class ActionButtonsPanel

Consider breaking these down into smaller, more focused classes to improve maintainability and readability.

Refactored ActionButtonsPanel and Introduced an ActionPanelController


Add Codes Command

Summary

Added Add codes command.
Fixed bug claiming password with spaces.
Replaced the 🤔 for the claimed code when user DM the password twice or more.

gh pr checkout 4

551f2dc747c9f37d0c7096fb42289ad6ebdb9726

149002da7b51cfb8b1563b2547dbe80c93ffc86d


Picard error: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException

Description of the bug
Hello again!
After solving previous problems https://github.com/DIncalciLab/samurai/issues/19 I rerun the pipeline but after a while I'm getting a new error related with picard metrics and the process gets stuck. I hope you have a better idea of what's going on. Thanks in advance!
  Elapsed time: 00:14:20s.  Time for last 10,000,000:    9s.  Last read position: 16:29,718,966
  INFOim2024-10-18 09:47:4394624CollectWgsMetrics       Processed   990,000,000 loci.  Elapsed time: 00:14:29s.  Time for last 10,000,000:    9s.  Last read position: 16:39,718,966
  INFOet2024-10-18 09:47:51roadiCollectWgsMetricso/picarProcessed 1,000,000,000 loci.  Elapsed time: 00:14:38s.  Time for last 10,000,000:    8s.  Last read position: 16:49,819,466
  INFOpt2024-10-18 09:48:02" javCollectWgsMetricsOutOfBoProcessed 1,010,000,000 loci.  Elapsed time: 00:14:48s.  Time for last 10,000,000:   10s.  Last read position: 16:59,819,466
  INFO  2024-10-18 09:48:11AbstrCollectWgsMetricsector.iProcessed 1,020,000,000 loci.  Elapsed time: 00:14:57s.  Time for last 10,000,000:    9s.  Last read position: 16:69,819,466
  INFO  2024-10-18 09:48:21WgsMeCollectWgsMetricsl.proceProcessed 1,030,000,000 loci.  Elapsed time: 00:15:08s.  Time for last 10,000,000:   10s.  Last read position: 16:79,819,466
  INFO  2024-10-18 09:48:32ColleCollectWgsMetricsrk(CollProcessed 1,040,000,000 loci.  Elapsed time: 00:15:18s.  Time for last 10,000,000:   10s.  Last read position: 16:89,869,466
  INFO  2024-10-18 09:48:43ommanCollectWgsMetricsanceMaiProcessed 1,050,000,000 loci.  Elapsed time: 00:15:30s.  Time for last 10,000,000:   11s.  Last read position: 17:9,541,121
  INFO  2024-10-18 09:48:54icardCollectWgsMetricsnceMainProcessed 1,060,000,000 loci.  Elapsed time: 00:15:41s.  Time for last 10,000,000:   11s.  Last read position: 17:19,541,121
  INFO  2024-10-18 09:49:06icardCollectWgsMetricsPicardCProcessed 1,070,000,000 loci.  Elapsed time: 00:15:52s.  Time for last 10,000,000:   11s.  Last read position: 17:29,541,121
  INFO  2024-10-18 09:49:17     CollectWgsMetrics       Processed 1,080,000,000 loci.  Elapsed time: 00:16:04s.  Time for last 10,000,000:   11s.  Last read position: 17:39,541,121
  INFOir2024-10-18 09:49:43     CollectWgsMetrics       Processed 1,090,000,000 loci.  Elapsed time: 00:16:30s.  Time for last 10,000,000:   26s.  Last read position: 17:65,522,841
  INFOe/2024-10-18 09:49:55c9d14CollectWgsMetricsf464   Processed 1,100,000,000 loci.  Elapsed time: 00:16:41s.  Time for last 10,000,000:   11s.  Last read position: 17:76,072,841
  INFO  2024-10-18 09:50:07     CollectWgsMetrics       Processed 1,110,000,000 loci.  Elapsed time: 00:16:54s.  Time for last 10,000,000:   12s.  Last read position: 18:2,825,400
  INFOou2024-10-18 09:50:18issueCollectWgsMetricshe procProcessed 1,120,000,000 loci.  Elapsed time: 00:17:04s.  Time for last 10,000,000:   10s.  Last read position: 18:12,825,400
  INFO  2024-10-18 09:50:28     CollectWgsMetrics       Processed 1,130,000,000 loci.  Elapsed time: 00:17:14s.  Time for last 10,000,000:    9s.  Last read position: 18:22,825,400
  INFOec2024-10-18 09:50:38ile fCollectWgsMetrics       Processed 1,140,000,000 loci.  Elapsed time: 00:17:25s.  Time for last 10,000,000:   10s.  Last read position: 18:32,825,400
  INFO  2024-10-18 09:50:49     CollectWgsMetrics       Processed 1,150,000,000 loci.  Elapsed time: 00:17:36s.  Time for last 10,000,000:   10s.  Last read position: 18:43,199,414
  INFO  2024-10-18 09:51:00     CollectWgsMetrics       Processed 1,160,000,000 loci.  Elapsed time: 00:17:47s.  Time for last 10,000,000:   11s.  Last read position: 18:53,289,416
  INFO  2024-10-18 09:51:10     CollectWgsMetrics       Processed 1,170,000,000 loci.  Elapsed time: 00:17:57s.  Time for last 10,000,000:   10s.  Last read position: 18:63,289,421
  INFO  2024-10-18 09:51:21     CollectWgsMetrics       Processed 1,180,000,000 loci.  Elapsed time: 00:18:07s.  Time for last 10,000,000:   10s.  Last read position: 18:73,289,421
  INFO  2024-10-18 09:51:32     CollectWgsMetrics       Processed 1,190,000,000 loci.  Elapsed time: 00:18:19s.  Time for last 10,000,000:   11s.  Last read position: 19:2,976,136
  INFO  2024-10-18 09:51:44     CollectWgsMetrics       Processed 1,200,000,000 loci.  Elapsed time: 00:18:30s.  Time for last 10,000,000:   11s.  Last read position: 19:12,976,136
  INFO  2024-10-18 09:51:55     CollectWgsMetrics       Processed 1,210,000,000 loci.  Elapsed time: 00:18:42s.  Time for last 10,000,000:   11s.  Last read position: 19:22,976,136
  INFO  2024-10-18 09:52:08     CollectWgsMetrics       Processed 1,220,000,000 loci.  Elapsed time: 00:18:54s.  Time for last 10,000,000:   12s.  Last read position: 19:32,976,136
  INFO  2024-10-18 09:52:20     CollectWgsMetrics       Processed 1,230,000,000 loci.  Elapsed time: 00:19:07s.  Time for last 10,000,000:   12s.  Last read position: 19:42,976,136
  INFO  2024-10-18 09:52:32     CollectWgsMetrics       Processed 1,240,000,000 loci.  Elapsed time: 00:19:18s.  Time for last 10,000,000:   11s.  Last read position: 19:53,233,836
  INFO  2024-10-18 09:52:44     CollectWgsMetrics       Processed 1,250,000,000 loci.  Elapsed time: 00:19:31s.  Time for last 10,000,000:   12s.  Last read position: 2:4,726,520
  INFO  2024-10-18 09:52:56     CollectWgsMetrics       Processed 1,260,000,000 loci.  Elapsed time: 00:19:42s.  Time for last 10,000,000:   11s.  Last read position: 2:14,727,522
  INFO  2024-10-18 09:53:08     CollectWgsMetrics       Processed 1,270,000,000 loci.  Elapsed time: 00:19:55s.  Time for last 10,000,000:   12s.  Last read position: 2:24,727,522
  INFO  2024-10-18 09:53:21     CollectWgsMetrics       Processed 1,280,000,000 loci.  Elapsed time: 00:20:08s.  Time for last 10,000,000:   13s.  Last read position: 2:34,777,522
  INFO  2024-10-18 09:53:34     CollectWgsMetrics       Processed 1,290,000,000 loci.  Elapsed time: 00:20:20s.  Time for last 10,000,000:   12s.  Last read position: 2:44,842,710
  INFO  2024-10-18 09:53:46     CollectWgsMetrics       Processed 1,300,000,000 loci.  Elapsed time: 00:20:33s.  Time for last 10,000,000:   12s.  Last read position: 2:54,842,710
  INFO  2024-10-18 09:53:59     CollectWgsMetrics       Processed 1,310,000,000 loci.  Elapsed time: 00:20:46s.  Time for last 10,000,000:   13s.  Last read position: 2:64,842,710
  INFO  2024-10-18 09:54:13     CollectWgsMetrics       Processed 1,320,000,000 loci.  Elapsed time: 00:21:00s.  Time for last 10,000,000:   13s.  Last read position: 2:74,842,710
  INFO  2024-10-18 09:54:26     CollectWgsMetrics       Processed 1,330,000,000 loci.  Elapsed time: 00:21:12s.  Time for last 10,000,000:   12s.  Last read position: 2:84,842,710
  INFO  2024-10-18 09:54:39     CollectWgsMetrics       Processed 1,340,000,000 loci.  Elapsed time: 00:21:26s.  Time for last 10,000,000:   13s.  Last read position: 2:94,842,710
  INFO  2024-10-18 09:54:53     CollectWgsMetrics       Processed 1,350,000,000 loci.  Elapsed time: 00:21:40s.  Time for last 10,000,000:   13s.  Last read position: 2:104,842,710
  INFO  2024-10-18 09:55:09     CollectWgsMetrics       Processed 1,360,000,000 loci.  Elapsed time: 00:21:55s.  Time for last 10,000,000:   15s.  Last read position: 2:114,842,710
  INFO  2024-10-18 09:55:23     CollectWgsMetrics       Processed 1,370,000,000 loci.  Elapsed time: 00:22:09s.  Time for last 10,000,000:   14s.  Last read position: 2:124,843,010
  [Fri Oct 18 09:55:35 GMT 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 22.37 minutes.
  Runtime.totalMemory()=775946240
  To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
  Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 133275309 out of bounds for length 133275309
        at picard.analysis.AbstractWgsMetricsCollector.isReferenceBaseN(AbstractWgsMetricsCollector.java:218)
        at picard.analysis.WgsMetricsProcessorImpl.processFile(WgsMetricsProcessorImpl.java:92)
        at picard.analysis.CollectWgsMetrics.doWork(CollectWgsMetrics.java:242)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:280)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:115)

Work dir:
  /home/pperez/work/be/b7f4c9d1465da71a4b2ab38270f464

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

-- Check '.nextflow.log' file for details

Relevant files
nextflow.log
System information
Nextflow version <IP_ADDRESS>91
Hardware: Desktop
Executor: Local
Container engine: Docker
OS: Linux
Version of dincalcilab/samurai: Latest master commit

Wow, that's new! Never seen anything like this before...
How many samples are you processing? Would it be feasible to you to start with one sample, and check with each one of them (just use a single line in the samplesheet)?
Also what type of samples are you using? Can you also tell me the file sizes of the BAM indices that are created? The error is kind of cryptic and can have multiple causes.

I just realized that the span in the sample.wig is not what I expected. I'm having a single bin per chromosome like
fixedStep chrom=1 start=1 step=248956422 span=248956422
while the gc.wig has the correct binning like
fixedStep chrom=1 start=1 step=1000000 span=1000000
I've tested ichorCNA before with these samples generating 1M bp binning and although the chrom didin't exactly match between both wig (sample and gc/map) it worked properly just by limiting the analysis to 1:22.
Here in the pipeline I set --binsize 1000000 (default was 500). I just made a couple of tests and I see that the input binsize its specified in kb? It works if I set --binsize 1000
Now I get another error, although the outputs I was looking for are generated correctly, but just to let you know:
executor >  local (7)
[e9/ee209c] process > DINCALCILAB_SAMURAI:SAMURAI:SAMTOOLS_INDEX (004_0256_0155)                                     [100%] 1 of 1 ✔
[32/e11c2f] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS (004_0256_0155)        [  0%] 0 of 1
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTHSMETRICS                              -
[23/45790e] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155)             [  0%] 0 of 1
[9e/c05c76] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:HMMCOPY_READCOUNTER_ICHORCNA (004_0256_0155)         [100%] 1 of 1 ✔
executor >  local (7)
[e9/ee209c] process > DINCALCILAB_SAMURAI:SAMURAI:SAMTOOLS_INDEX (004_0256_0155)                                     [100%] 1 of 1 ✔
[32/e11c2f] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS (004_0256_0155)        [  0%] 0 of 1
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTHSMETRICS                              -
[23/45790e] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155)             [  0%] 0 of 1
[9e/c05c76] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:HMMCOPY_READCOUNTER_ICHORCNA (004_0256_0155)         [100%] 1 of 1 ✔
[fc/04ce25] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:RUN_ICHORCNA (004_0256_0155)                         [100%] 1 of 1 ✔
executor >  local (7)
[e9/ee209c] process > DINCALCILAB_SAMURAI:SAMURAI:SAMTOOLS_INDEX (004_0256_0155)                                     [100%] 1 of 1 ✔
[32/e11c2f] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS (004_0256_0155)        [  0%] 0 of 1
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTHSMETRICS                              -
[23/45790e] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155)             [  0%] 0 of 1
[9e/c05c76] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:HMMCOPY_READCOUNTER_ICHORCNA (004_0256_0155)         [100%] 1 of 1 ✔
[fc/04ce25] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:RUN_ICHORCNA (004_0256_0155)                         [100%] 1 of 1 ✔
executor >  local (7)
[e9/ee209c] process > DINCALCILAB_SAMURAI:SAMURAI:SAMTOOLS_INDEX (004_0256_0155)                                     [100%] 1 of 1 ✔
[32/e11c2f] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS (004_0256_0155)        [  0%] 0 of 1
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTHSMETRICS                              -
[23/45790e] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155)             [100%] 1 of 1, failed: 1 ✘
[9e/c05c76] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:HMMCOPY_READCOUNTER_ICHORCNA (004_0256_0155)         [100%] 1 of 1 ✔
[fc/04ce25] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:RUN_ICHORCNA (004_0256_0155)                         [100%] 1 of 1 ✔
[b0/42894e] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:AGGREGATE_ICHORCNA_TABLE (Assemble IchorCNA outputs) [100%] 1 of 1 ✔
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CORRECT_LOGR_ICHORCNA                                -
[7b/90d0a6] process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF)              [100%] 1 of 1, failed: 1 ✘
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:MULTIQC                                                            -
ERROR ~ Error executing process > 'DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF)'
Caused by:
Process DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF) terminated with an error exit status (2)
Command executed:
qpdf --empty --pages 004_0256_0155_genomeWide.pdf -- genome_plot.pdf
cat <<-END_VERSIONS > versions.yml
"DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS":
qpdf: $(qpdf --version | sed -n '1p' | cut -d' ' -f3)
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
Unable to find image 't0shy/qpdf-docker:11.3.0' locally
11.3.0: Pulling from t0shy/qpdf-docker
677076032cca: Pulling fs layer
45c48f78416f: Pulling fs layer
3a9d29db235a: Pulling fs layer
3a9d29db235a: Verifying Checksum
3a9d29db235a: Download complete
45c48f78416f: Verifying Checksum
45c48f78416f: Download complete
677076032cca: Verifying Checksum
677076032cca: Download complete
677076032cca: Pull complete
45c48f78416f: Pull complete
3a9d29db235a: Pull complete
Digest: sha256:744f00189f4b0f3f1273073212102b32e0505fea528c9516e4252b9345e482d3
Status: Downloaded newer image for t0shy/qpdf-docker:11.3.0
qpdf: unrecognized argument -c
For help:
qpdf --help=usage       usage information
qpdf --help=topic       help on a topic
qpdf --help=--option    help on an option
qpdf --help             general help and a topic list
Work dir:
/home/pperez/work/7b/90d0a6e2445834bbb3062e0d95f01b
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
-- Check '.nextflow.log' file for details
.nextflow.log
: 0; error: -; workDir: /home/pperez/work/fc/04ce25f75aa2bfade26253cc7e8c26]
Oct-18 16:04:11.582 [Actor Thread 178] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.001 s; total time: 0.001 s
Oct-18 16:04:11.588 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-18 16:04:11.589 [Task submitter] INFO  nextflow.Session - [b0/42894e] Submitted process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:AGGREGATE_ICHORCNA_TABLE (Assemble IchorCNA outputs)
Oct-18 16:04:11.593 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-18 16:04:11.593 [Task submitter] INFO  nextflow.Session - [7b/90d0a6] Submitted process > DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF)
Oct-18 16:04:11.614 [Actor Thread 178] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/pperez/work/collect-file/9b921b7c5e304fac035ad83b07159c3e
Oct-18 16:04:11.616 [Actor Thread 178] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-326867740876979458
Oct-18 16:04:16.869 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF); status: COMPLETED; exit: 2; error: -; workDir: /home/pperez/work/7b/90d0a6e2445834bbb3062e0d95f01b]
Oct-18 16:04:16.873 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF); work-dir=/home/pperez/work/7b/90d0a6e2445834bbb3062e0d95f01b
error [nextflow.exception.ProcessFailedException]: Process DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF) terminated with an error exit status (2)
Oct-18 16:04:16.886 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF)'
Caused by:
Process DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS (Concatenate_PDF) terminated with an error exit status (2)
Command executed:
qpdf --empty --pages 004_0256_0155_genomeWide.pdf -- genome_plot.pdf
cat <<-END_VERSIONS > versions.yml
"DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:CONCATENATE_BIN_PLOTS":
qpdf: $(qpdf --version | sed -n '1p' | cut -d' ' -f3)
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
Unable to find image 't0shy/qpdf-docker:11.3.0' locally
11.3.0: Pulling from t0shy/qpdf-docker
677076032cca: Pulling fs layer
45c48f78416f: Pulling fs layer
3a9d29db235a: Pulling fs layer
3a9d29db235a: Verifying Checksum
3a9d29db235a: Download complete
45c48f78416f: Verifying Checksum
45c48f78416f: Download complete
677076032cca: Verifying Checksum
677076032cca: Download complete
677076032cca: Pull complete
45c48f78416f: Pull complete
3a9d29db235a: Pull complete
Digest: sha256:744f00189f4b0f3f1273073212102b32e0505fea528c9516e4252b9345e482d3
Status: Downloaded newer image for t0shy/qpdf-docker:11.3.0
qpdf: unrecognized argument -c
For help:
qpdf --help=usage       usage information
qpdf --help=topic       help on a topic
qpdf --help=--option    help on an option
qpdf --help             general help and a topic list
Work dir:
/home/pperez/work/7b/90d0a6e2445834bbb3062e0d95f01b
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
Oct-18 16:04:16.889 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Oct-18 16:04:16.895 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-18 16:04:16.904 [Actor Thread 237] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 3; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s
Oct-18 16:04:16.911 [Actor Thread 237] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/pperez/work/collect-file/e98a83b7004194b0d89e6b7ffb3d7b93
Oct-18 16:04:16.912 [Actor Thread 237] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6789232397934683170
Oct-18 16:04:31.839 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:AGGREGATE_ICHORCNA_TABLE (Assemble IchorCNA outputs); status: COMPLETED; exit: 0; error: -; workDir: /home/pperez/work/b0/42894e66f8c7633273b955866aeabf]
Oct-18 16:05:29.799 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155); status: COMPLETED; exit: 1; error: -; workDir: /home/pperez/work/23/45790ea4eb00910c2bbd70628cf65b]
Oct-18 16:05:29.799 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155); work-dir=/home/pperez/work/23/45790ea4eb00910c2bbd70628cf65b
error [nextflow.exception.ProcessFailedException]: Process DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS (004_0256_0155) terminated with an error exit status (1)
Oct-18 16:07:37.844 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS (004_0256_0155); status: RUNNING; exit: -; error: -; workDir: /home/pperez/work/32/e11c2fae076d0205791a11abcbf616]
Oct-18 16:07:54.305 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS (004_0256_0155); status: COMPLETED; exit: 0; error: -; workDir: /home/pperez/work/32/e11c2fae076d0205791a11abcbf616]
Oct-18 16:07:54.325 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Oct-18 16:07:54.325 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-18 16:07:54.402 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Oct-18 16:07:54.404 [main] INFO  nextflow.Nextflow - -[dincalcilab/samurai] Pipeline completed with errors-
Oct-18 16:07:54.409 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=5; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=28m 25s; failedDuration=6m 34s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=6; peakMemory=26 GB; ]
Oct-18 16:07:54.409 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Oct-18 16:07:54.411 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Oct-18 16:07:55.244 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Oct-18 16:07:55.453 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-18 16:07:55.453 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin<EMAIL_ADDRESS>Oct-18 16:07:55.453 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon
Oct-18 16:07:55.453 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin<EMAIL_ADDRESS>Oct-18 16:07:55.453 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Oct-18 16:07:55.484 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Oct-18 16:07:55.487 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'S3TransferManager' shutdown completed (hard=false)
Oct-18 16:07:55.487 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

It looks like there was a change in qpdf options. I'll give it a look on Monday.

And I wanted to ask another question. Does any other caller give Tumor Fraction information apart from ichorCNA?

You can use WisecondorX (--caller wisecondorx) as a proxy of TF (it's not the same thing, though) with its Copy Number Profile Abnormality (or CPA): a few papers that compared the two showed a good (0.9) degree of correlation. Raman et al., 2021 has the details for how CPA works (NSCLC, using ctDNA).
However WisecondorX requires a signficantly large panel of normals (because under the hood it relies on Z-scores to do its magic) to work well. In our tests at least > 40, and the WisecondorX people recommend close to 100.

@SaraPotente If you have time, can you test with a fresh (without any local Docker / singularity images) checkout and see if the error reported by @pblpez occurs?

I was trying to test --caller wisecondorx with a minimal call:
nextflow run samurai --input /media/nas252/OMICS/CNA/samurai/004_0256_CRC_AA_bam_paths.csv --outdir /media/nas252/OMICS/CNA/samurai/output     --genome GRCh38 --binsize 1000 --analysis_type liquid_biopsy --caller wisecondorx --wisecondorx_yfrac 0 -profile docker
But I got this error:

   ] process > DINCALCILAB_SAMURAI:SAMURAI:SAMTOOLS_INDEX                              -

[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS -
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTHSMETRICS       -
[-        ] process > DINCALCILAB_SAMURAI:SAMURAI:BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS      -
ERROR ~ Argument of file function cannot be null

I see that there are not many parameters to tune for WisecondorX, and I don't know what does it mean by "file function". I repeated it but this time adding the parameters used previously for the ichorCNA call (look at the .nextflow.log). I got an error related to the PoN provided. Does this caller use the parameters from ichorCNA even if ichorCNA is set as the caller? I want to reproduce the ichorCNA analysis but using WisecondorX, focusing only on autosomic chromosomes. Below the error I got this time:

ERROR ~ Error executing process > 'DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:WISECONDORX_PREDICT (004_0256_0155)'
Caused by:
Process DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:WISECONDORX_PREDICT (004_0256_0155) terminated with an error exit status (1)
Command executed:
WisecondorX predict
004_0256_0155.npz
PoN_004_0256_sWGS_no_dedup_1000000_median.rds
004_0256_0155
--zscore 5

--plot
--bed
--add-plot-title
cp 004_0256_0155.plots/genome_wide.png 004_0256_0155_genome_plot.png
cat <<-END_VERSIONS > versions.yml
"DINCALCILAB_SAMURAI:SAMURAI:LIQUID_BIOPSY:WISECONDORX_PREDICT":
wisecondorX: 1.2.4
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
[INFO - 2024-10-21 09:29:17]: Starting CNA prediction
[INFO - 2024-10-21 09:29:17]: Importing data ...
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/numpy/lib/npyio.py", line 421, in load
return pickle.load(fid, **pickle_kwargs)
_pickle.UnpicklingError: invalid load key, '\x1f'.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/WisecondorX", line 10, in
sys.exit(main())
File "/usr/local/lib/python3.10/site-packages/wisecondorX/main.py", line 410, in main
args.func(args)
File "/usr/local/lib/python3.10/site-packages/wisecondorX/main.py", line 146, in tool_test
ref_file = np.load(args.reference, encoding='latin1', allow_pickle=True)
File "/usr/local/lib/python3.10/site-packages/numpy/lib/npyio.py", line 423, in load
raise pickle.UnpicklingError(
_pickle.UnpicklingError: Failed to interpret file 'PoN_004_0256_sWGS_no_dedup_1000000_median.rds' as a pickle
Work dir:
/home/pperez/work/63/2e761b61166ead8ac7661d0ce190b5
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
-- Check '.nextflow.log' file for details

nextflow.log
Thank you!

No, WisecondorX requires its own PoN, the options are not compatible (you need to use the ones that start with wisecondor), the whole format is fundamentally different.
Argument cannot be null means that the code expects a file, but nothing is provided, so it errors out. It's a bug (it should explicitly tell you what's wrong), but in this case it's because you don't have a PoN set.
Would you be able to file a separate issue mentioning that WisecondorX should require a PoN? I might be able to do something next week as I should have some time for hacking.


Update node.js (v.0.12.0 -> v.0.12.6)

AFAICT, I'm the only person still updating node.js at this time...
I tested this locally, it works. Please place some trust in me and merge it.
My previous PR for node.js sat until two more node.js releases went by (both security critical). You accept my io.js updates, and that's practically the same as my node.js updates...

Err wait, there's already an equivalent PR....


WIP Build Docker container

Docker container should be built from requirements.txt
This PR should remove informaticslab/forest Docker Hub dependency

@rhattersley should this also migrate to the new repo?

I've started looking at this, in conjunction with the provision of quick-turnaround AWS infrastructure for testing.

@rhattersley this is no longer needed given our latest infrastructure changes


typo fix

I hit one of these error descriptions when I forgot to rerun build_runner--this PR changes 'WhatchItMixin' to 'WatchItMixin'.
This is such a cool package, thanks!

thanks a lot


Add github action to check WIP in PR title.

Going to merge this in order to troubleshoot. Possible actions need a stub already on the repo


feat: Balance, Currency and Country commands

To Do

[x] Currency and Country controller functions
[x] Addition of Currency and Country controller functions to the server create file
[ ] Creation of  BalanceCommand,SetCountryCommand and SetCurrencyCommand
[ ] Write new tests for WalletDAO WalletController WalletClient and related  commands
[ ] Integrate SetCountryCommand and SetCurrencyCommand in the wallet creation flow

@Ktoxcon
let's write these in a separate PR

[ ] Creation of  BalanceCommand,SetCountryCommand and SetCurrencyCommand
[ ] Write new tests for WalletDAO WalletController WalletClient and related  commands
[ ] Integrate SetCountryCommand and SetCurrencyCommand in the wallet creation flow


update api for getting USD balance

The bittrex version 1 API has been deprecated https://bittrex.com/api/v1.1/public/getticker?market=USDT-DCR, and fetching USD balance no longer works.
We should resolve to the v3 API https://api.bittrex.com/v3/markets/DCR-USDT/ticker

Add binance and kucoin while at it.

@dreacot What do thing about including this functionality in: https://github.com/planetdecred/dcrlibwallet/pull/255

Sounds good, let's add it


Unable to create an Owning Group with no include and no excludinig components.

Problem
Not able to create an Owning Group with no includes and no exludes.
pub const Position = struct { x: f32, y: f32 };

pub fn main() !void {
    var reg = ecs.Registry.init(std.heap.c_allocator);
    defer reg.deinit();

    var e = reg.create();
    reg.add(e, Position { .x = 1, .y = 1 });

    var group = reg.group(.{Position }, .{}, .{});   // <-----
}

Result
fails assert in registry.zig: 471
std.debug.assert(owned.len + includes.len + excludes.len > 1);
Am I using the library incorrectly?

Am I using the library incorrectly?
Yes. There is no point at all in creating an owning group of one component. It has no meaning. There is nothing to own. Just use a View or access the component storage directly for a single component.


Reduce perceived startup time

Atm takes quite a while to load on 3G-like pings and bandwidths. The least we can do is show some sort of process-indicator, that is hidden once the app finishes it's startup.

this is more a goal or claim than an issue or user story... enhancing performance and reducing (load) times should always be a factor -> closing this issue


EXP bar for current job

If possible, an exp bar that looks like the the ender dragon's health bar can be used to display progress in the player's current job.

Sounds interesting, I'd suggest three modes:

Hidden
Fade out (just display a few seconds after exp gain)
Always shown

Agreed. We could adjust the /job toggle command to take in a third argument in order to specify what is being toggled (notifications or exp bar). This way we can avoid creating a completely separate command.

Yup and remember to use GenericArguments.choices so Sponge handles autocompletion for us.

I think this should wait till this PR is merged: https://github.com/SpongePowered/SpongeAPI/pull/1534. Currently, as far a I can tell, the only way to see what boss bar a player is attached to would be to store them all in a list. I feel like this could become an issue if we had to loop through that list every single time we needed to update the boss bar.

Agreed


Wrong balance displaying on many accounts

I'm seeing the wrong balance display on several accounts for the Nifty Wallet. I've provided pictures below showing a web3.eth.getBalance call along with the associated wallet.

@acravenho Is this inconsistency found only for POA network?

@vbaranov This might be a far edge case. I just solved the issue by deactivating the extension and reactivating it. It seems to be updating just fine now.
What I believe caused the issue was interacting with my desktop computer and then coming back to my laptop. Since Chrome shares data between the same logged in account including extensions I might have been receiving stale data.
I believe this issue can be closed. Sorry for the inconvenience. I'll let you know if I see this issue occur more frequently.


Schema Graph doesn't handle wildcard as expected

Please select the area your bug applies to. (Multiple selections are Possible)

[ ] Onboard. Initial vault setup and import/export pods
[ ] Create. Note creation, lookup, snippets and templates
[x] Retrieve. Backlinks, references, graph view
[ ] Structure. Refactoring, multi-vault and schemas
[ ] Publish. Sharing your repo with the world
[ ] Misc (Choose this if your not sure)

Describe the bug
Using wildcards in a pattern is shown as random strings of alphanumeric values in the Schema Graph.
To Reproduce
Steps to reproduce the behavior:

Add the following to a schema:

  - id: misc
    title: Unsorted notes
    desc: "Notes without category"
    namespace: true
    template:
      id: templates.pkm
      type: note
    children:
      - pattern: "**/*"

CTRL+SHIFT+P
Dendron: Show Schema Graph
Look at the node corresponding to the wildcard (* also gives the same result as **/*)

Expected behavior
Want to set my own title or just show the actually entered data (* or **/*)
Screenshots

Desktop (please complete the following information)

OS: Windows 10
VSCode: 1.62.3
Dendron: 0.69.1

Thank you for the report. We plan to work on improving the graph view once we sort out some stability issues. We'll keep this tracked so we can get a fix in once we get to that milestone. 🙏🏼