[Snyk] Upgrade @trustwallet/wallet-core from 3.0.1 to 3.1.12

This PR was automatically created by Snyk using the credentials of a real user.Snyk has created this PR to upgrade @trustwallet/wallet-core from 3.0.1 to 3.1.12.
:information_source: Keep your dependencies up-to-date. This makes it easier to fix existing vulnerabilities and to more quickly identify and fix newly disclosed vulnerabilities when they affect your project.

The recommended version is 20 versions ahead of your current version.
The recommended version was released 21 days ago, on 2023-02-07.

Release notes

Package name: @trustwallet/wallet-core

3.1.12 - 2023-02-07What's Changed
Breaking Change
Elrond was renamed to MultiversX (change protobuf accordingly)
New features

📖 ERC4337 Transactions support by @ rsrbk

Improvements

⚡ ThorChain: change deposit function to depositWithExpiry by @ Milerius

Fix

⚡ ThorChain: fix overflow for big amount by @ Milerius
⚒ Flux: Fix empty lock script data for Flux (zelcash) by @ hewigovens

Misc

✏ Codegen: Mark java class as final to avoid kt doc confusion by @ Milerius
 Rebranding: Code-wise rebranding of Elrond to MultiversX by @ andreibancioiu
🖊 Misc: Update CODEOWNERS by @ Milerius
📱 iOS: remove catalyst for fastlane by @ Milerius
📱 iOS: Temporary disable mac build by @ Milerius
👨💻 Rust: Re-enable rust build for mac catalyst by @ Milerius
🧹 CleanUp: Some post-PR cleanups by @ rsrbk

Full Changelog: 3.1.10...3.1.12

3.1.11 - 2023-02-03Fix empty lock script data for Flux (zelcash) (#2905)

3.1.10 - 2023-01-27What's Changed
New features

📖 EIP4337: deployment address calculation by @ rsrbk
📖 Eip155-Eip712: add eip-155 + eip712 support to sign message by @ Milerius
⛓ Sui: Add SUI Implementation by @ Milerius

Improvements

⚒ Fix: fix serialization for aptos tx (pancake swap) by @ Milerius
⚒ Fix: Fix array with mismatched bound warnings in sha2.c by @ safocl

New Contributors

@ safocl made their first contribution in #2884

Full Changelog: 3.1.9...3.1.10

3.1.9 - 2023-01-19What's Changed
Breaking Change
ThorSwap EVM transactions are now using EIP-1559 tx mode by default. Use the gas parameters accordingly.
New features

⛓ TON: TON support by @ stspbu
⛓ WAX: Add WAX chain by @ miloserdow and @ Milerius
🖊 EIP1014: eip1014 support by @ Milerius

Improvements

⚡ ThorSwap: fee optimization for EVM chains by @ Milerius

Misc

✏ Misc: Rename Elrond to MultiversX (configuration change) by @ andreibancioiu
🔒 Misc: add SECURITY.MD by @ Milerius
🍎 Swift: Update Package.swift by @ Milerius

New Contributors

@ stspbu made their first contribution in #2813

Full Changelog: 3.1.8...3.1.9

3.1.8 - 2023-01-11

3.1.7 - 2022-12-16

3.1.6 - 2022-12-09

3.1.5 - 2022-11-29

3.1.4 - 2022-11-25

3.1.3 - 2022-11-22

3.1.1 - 2022-11-21

3.1.0 - 2022-11-14

3.0.9 - 2022-11-04

3.0.8 - 2022-10-19

3.0.7 - 2022-10-13

3.0.6 - 2022-10-10

3.0.5 - 2022-10-03

3.0.4 - 2022-09-20

3.0.3 - 2022-09-15

3.0.2 - 2022-09-01

3.0.1 - 2022-08-04

    from @trustwallet/wallet-core GitHub release notes

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For more information:
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We'd be happy to look into this for you
kindly file a support ticket below
https://forms.gle/CDeM1AXFjSBt7qVK8


Something wrong with the header

This is what I see in the header:
title: Azure Container Instances container groups description: Understand how multi-container groups work in Azure Container Instances services: container-instances author: dlepow manager: jeconnoc
ms.service: container-instances ms.topic: article ms.date: 03/20/2018 ms.author: danlep ms.custom: mvc

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

ID: ff247151-29f6-4a55-61b2-e5eae2d48927
Version Independent ID: 159517fe-202c-967d-f572-49c4f6988c46
Content: Container groups in Azure Container Instances
Content Source: articles/container-instances/container-instances-container-groups.md
GitHub Login: @seanmck

@Leon99  Thanks for the reporting.
Header information should not be shown in the content. There is a formatting issue for this document. We will correct it.


Enhancement suggestion: Multiple instances of the same module

Hello,
Not a bug but a feature suggestion, managing several pages (MMM-pages) on my magic mirror, I find the need to have a module behaving differently on the different pages (eg large display on the home screen, compact mode in another)
In the forums, a recurrent solution is to clone the modules to a different module directory with a different name, fiddle with the js/css file name and possibly other files depending on the module. Not really satisfactory as updating the module as it evolves becomes cumbersome.
I was thinking of something like
		{
			module: "text-clock-homescreen",
			moduleOnFile: "MMM-text-clock",
			position: "middle_center",
			config: {
				compact: false,
				size: "large",
				language: ['jp','fr','en','es'],
				languageAlternationInterval: 10
			}
		},
		{
			module: "text-clock-compact",
			moduleOnFile: "MMM-text-clock",
			position: "top_center",
			config: {
				compact: true,
				size: "medium",
				language: ['jp','fr','en','es'],
				languageAlternationInterval: 10
			}
		},

I haven't looked at the internals of MagicMirror but just wanted to run this by the active community to see if this made sense at all to others or had already been considered and discarded.
Happy to contribute to this of course.

Afaik this is already possible, but depends on the implementation of MMM-pages (not a core module). You can add the module multiple times to your config with different configs, and use the classes property to assign it to different pages.

Try this implementation:
		{
			module: "MMM-text-clock",
			classes: "text-clock-homescreen",
			position: "middle_center",
			config: {
				compact: false,
				size: "large",
				language: ['jp','fr','en','es'],
				languageAlternationInterval: 10
			}
		},
		{
			module: "MMM-text-clock",
			classes: "text-clock-compact",
			position: "top_center",
			config: {
				compact: true,
				size: "medium",
				language: ['jp','fr','en','es'],
				languageAlternationInterval: 10
			}
		},

Thanks for that swift answer @MichMich , looks like exactly what I need, I will check at enhancing MMM-pages then!

This should be possible with the current mmm-pages version. You only need to alter your config.

it really is up to the module to implement support for multiple instances. not hard, but does require some coding change

Thanks @michmich was right it work out of the box with classes in MMM-pages I've got it up and running now :)


Raspberry  pi3 not booting with meta-updater layer

Hello. I have a raspberry pi3  Model B and I have created a minimal image using the yocto project (Hardknott)
I initially created a image using the following layers:
 BBLAYERS ?= " \
    /drv2/ostree/poky/meta \
    /drv2/ostree/poky/meta-poky \
    /drv2/ostree/poky/meta-yocto-bsp \
    /drv2/ostree/poky/meta-raspberrypi \
    /drv2/ostree/poky/meta-updater \
"

bitbake core-image-minimal
This generated a *.rpi-sdimg file which I then dd'd onto a SD card and was able to successfully run.
I then updated my bblayers.conf file and added the following:
BBLAYERS ?= " \
      /drv2/ostree/poky/meta \
      /drv2/ostree/poky/meta-poky \
      /drv2/ostree/poky/meta-yocto-bsp \
      /drv2/ostree/poky/meta-raspberrypi \
     /drv2/ostree/poky/meta-updater \
     /drv2/ostree/poky/meta-openembedded/meta-filesystems \
     /drv2/ostree/poky/meta-openembedded/meta-oe \
     /drv2/ostree/poky/meta-openembedded/meta-python \
"

I also updated my local.conf by adding the following:
require conf/distro/sota.conf.inc
INHERIT += " sota"

I reran bitbake and this time flashed raspberrypi.wic file into the sd card via the dd tool.
This time however when I try to boot I see the following error:
 Warning: no boot file name; using COA884C70.img
This error basically shows up multiple times until a time out occurs.
What am I missing ?

You're missing https://github.com/advancedtelematic/meta-updater-raspberrypi. There was a long-term goal to merge the repos with dynamic layers, but we never got around to it.
Did you try following the README and the quickstart guide?
BTW, the Uptane namespace version of this repo is more actively maintained, although you still have to use the meta-updater-raspberrypi repo from this namespace.

I used the flash-image.sh script to flash the image onto the SD card. Now I am seeing the device constantly rebooting right after uboot. Is there something I need to configure after the image has been built ?

That sounds like it isn't powered enough to boot. I've seen that problem lately with more and more boards, and I know for example the RPi4 basically requires wall power to boot successfully.
Otherwise, I'm afraid I don't know. I don't have a good way to test or debug myself anymore.


Star sample doesn't handle cutout in landscape

See screenshot

err guess the cutout understandably isn't in the screenshot heh. It's on the left here, and was covering the first image


Fill in LICENSE.md

I'm just launched my doc site[1] using this Jekyll layout and love the simplicity and cleanness of it. Thanks!
But today I went back to make sure attributions were correct and realized that your license doesn't name anyone[2]. Who should I list and how?
1 - http://docs.web2project.net/
2 - https://github.com/Wiredcraft/carte/blob/gh-pages/LICENSE.md

Updating the license to MIT with names of contributors.


Foreign Objects in SVG are not converted

If I have a HTML snippet within a Foreign Object tag inside my SVG, it is not drawn in the canvas. But it does seem that it is possible to draw HTML in a Canvas as described here.
https://developer.mozilla.org/en-US/docs/Web/API/Canvas_API/Drawing_DOM_objects_into_a_canvas
Would be really nice to have this feature.

the example seems to be drawing a full svg inside a canvas, which if your browser supports, then you don't need this library right?

I though you are building on top of what is given in the example to render the canvas. With the way given in the example, other objects in my SVG are not converted.

the point of this library is for devices that don't have svg capability but do have canvas capability (HTML5).  the link you posted suggests that the browser does have svg capability, which means you can just use the browser to render svgs in canvas instead of canvg.

Hello @gabelerner ! first, thanks for building this! It is superuseful
I don't know if my issue is similar to this one, or not but I have a svg base image composed of couple texts and boxes, on which I am overlaying another svg image <image href="my.svg" now the problem is that this <image> does not render with the same dimensions (it is very small) as on the resulting svg:

moving to https://github.com/canvg/canvg/issues/671


Makefile

Please create a Makefile which purpose is to help colleagues (without talking to you) to run all steps of the project and work independently:
build
unit_test
run
docker?
lint?
etc

I have indeed created a Taskfile instead, which from a Go's perspective, is just easier and more cross-platform.
I will be updating it with the commented tasks.

Readme now has instructions and more info @arxdsilva .


Acrolinx quality improvements:bitsadmin-help.md

Closing as this seems to be duplicated with #6967


SPI environment build error on 32bit armv7

Using a NanoPi Neo (32bit Arm v7 Allwinner H3 cpu) on Linux 4.11.3-sun8i #7 (Armbian/Ubuntu) with go version go1.7.3 linux/arm and gcc (Ubuntu/Linaro 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609, for use with a IMST iC880 concentrator through SPI.
When following the build procedure on this Linux environment, every step works fine until making the final build. This throws 'Error 2' at line 36 of the makefile, which seems to have something to do with the environment variables. Normally these should be set automatically, setting them manually (after the make dev-deps step) yields the same error.
Output from the terminal:
root@nanopineo:~/work/src/github.com/TheThingsNetwork/packet_forwarder# echo $GOARM
7
root@nanopineo:~/work/src/github.com/TheThingsNetwork/packet_forwarder# make build
Generating default spi header file
Generated default spi header file
CFG_SPI=native PLATFORM=default make all -e -C lora_gateway/libloragw
make[1]: Entering directory '/root/work/src/github.com/TheThingsNetwork/packet_forwarder/lora_gateway/libloragw'
*** Checking libloragw library configuration ***
#File initialization
# Release version
Release version   : 4.0.0
SPI interface     : Linux native SPI driver
# Debug options
# end of file
*** Configuration seems ok ***
mkdir -p obj
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_hal.c -o obj/loragw_hal.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_gps.c -o obj/loragw_gps.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_reg.c -o obj/loragw_reg.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_spi.native.c -o obj/loragw_spi.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_aux.c -o obj/loragw_aux.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_radio.c -o obj/loragw_radio.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_fpga.c -o obj/loragw_fpga.o
gcc -c -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC src/loragw_lbt.c -o obj/loragw_lbt.o
ar rcs libloragw.a obj/loragw_hal.o obj/loragw_gps.o obj/loragw_reg.o obj/loragw_spi.o obj/loragw_aux.o obj/loragw_radio.o obj/loragw_fpga.o obj/loragw_lbt.o
gcc -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC -L. tst/test_loragw_spi.c -o test_loragw_spi -lloragw -lrt -lm
gcc -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC -L. tst/test_loragw_reg.c -o test_loragw_reg -lloragw -lrt -lm
gcc -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC -L. tst/test_loragw_hal.c -o test_loragw_hal -lloragw -lrt -lm
gcc -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC -L. tst/test_loragw_gps.c -o test_loragw_gps -lloragw -lrt -lm
gcc -O2 -Wall -Wextra -std=c99 -Iinc -I. -fPIC -L. tst/test_loragw_cal.c -o test_loragw_cal -lloragw -lrt -lm
make[1]: Leaving directory '/root/work/src/github.com/TheThingsNetwork/packet_forwarder/lora_gateway/libloragw'
packet_forwarder  building [CGO_ENABLED=1 CC=cc GOOS=linux GOARCH=arm GOARM= CGO_CFLAGS= CGO_LDFLAGS=-lrt CGO_ENABLED=1 go build -tags halv1 -a -ldflags -w -X main.version=v2.0.2-dev -X main.gitCommit=b64203b985c02a82ab4f3cb41d907be85fcb04e6 -X main.buildDate=2017-07-05T09:4341Z -X github.com/TheThingsNetwork/packet_forwarder/pktfwd.platform=default -X github.com/TheThingsNetwork/packet_forwarder/cmd.downlinksMargin= ./main.go ...]
runtime/internal/sys
runtime/internal/atomic
runtime
[...]
github.com/TheThingsNetwork/packet_forwarder/vendor/github.com/TheThingsNetwork/ttn/api/router
github.com/TheThingsNetwork/packet_forwarder/wrapper
.make/go/build.make:36: recipe for target 'release/packet-forwarder-linux-arm-' failed
make: *** [release/packet-forwarder-linux-arm-] Error 2

Sorry for the late reply!
If you still remember the procedure you used to compile the packet forwarder, could you:

Post specifically the logs, starting from packet_forwarder  building [...] and the end?
List the content in the release/ directory?
I'm also concerned by the fact that you set GOARM but that the building log with the environment variables indicates GOARM=[empty]. I'll check this!

Thanks for looking into this, much appreciated. For completeness, I've put the terminal output of the complete build procedure below.

Resolving deltas: 100% (505/505), done.
 Upgrading from 1.7.3 to 1.8.3 has resolved this issue. See #67 for a proposed change to the documentation.


rbd-provisioner is not being used

Hello,
I have deployed a CEPH cluster and followed the installation guide for the external-storage and everything seems to be working fine until a POD tries to use the PVC. I then get the "fail to check rbd image status with: (executable file not found in $PATH), rbd output: ()"
This error points to the fact that kube-controller-manager does not have rbd installed but I should not be using this in the fist place.
Some details:
K8S Version 1.10.4
apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
  name: fast-rbd
provisioner: ceph.com/rbd
parameters:
  monitors: <IP_ADDRESS>:6789
  adminId: admin
  adminSecretName: ceph-secret
  adminSecretNamespace: kube-system
  pool: kube
  userId: kube
  userSecretName: ceph-secret-kube
  userSecretNamespace: kube-system
  imageFormat: "2"
  imageFeatures: layering

kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: myclaim
spec:
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 8Gi
  storageClassName: fast-rbd

kubectl get pvc
NAME      STATUS    VOLUME                                     CAPACITY   ACCESS MODES   STORAGECLASS   AGE
myclaim   Bound     pvc-04f480bb-8fd7-11e8-9d8f-005056aa4c92   8Gi        RWO            fast-rbd       50m

kubectl describe pvc myclaim
Name:          myclaim
Namespace:     default
StorageClass:  fast-rbd
Status:        Bound
Volume:        pvc-04f480bb-8fd7-11e8-9d8f-005056aa4c92
Labels:        <none>
Annotations:   control-plane.alpha.kubernetes.io/leader={"holderIdentity":"28bc5912-8fbe-11e8-bad4-e20c5208f0bb","leaseDurationSeconds":15,"acquireTime":"2018-07-25T06:50:40Z","renewTime":"2018-07-25T06:50:42Z","lea...
               kubectl.kubernetes.io/last-applied-configuration={"apiVersion":"v1","kind":"PersistentVolumeClaim","metadata":{"annotations":{},"name":"myclaim","namespace":"default"},"spec":{"accessModes":["ReadWrit...
               pv.kubernetes.io/bind-completed=yes
               pv.kubernetes.io/bound-by-controller=yes
               volume.beta.kubernetes.io/storage-provisioner=ceph.com/rbd
Finalizers:    [kubernetes.io/pvc-protection]
Capacity:      8Gi
Access Modes:  RWO
Events:
  Type    Reason                 Age                From                                                                               Message
  ----    ------                 ----               ----                                                                               -------
  Normal  ExternalProvisioning   51m (x3 over 51m)  persistentvolume-controller                                                        waiting for a volume to be created, either by external provisioner "ceph.com/rbd" or manually created by system administrator
  Normal  Provisioning           51m                ceph.com/rbd rbd-provisioner-bc956f5b4-l5gwj 28bc5912-8fbe-11e8-bad4-e20c5208f0bb  External provisioner is provisioning volume for claim "default/myclaim"
  Normal  ProvisioningSucceeded  51m                ceph.com/rbd rbd-provisioner-bc956f5b4-l5gwj 28bc5912-8fbe-11e8-bad4-e20c5208f0bb  Successfully provisioned volume pvc-04f480bb-8fd7-11e8-9d8f-005056aa4c92

So all seems fine, but when I the create a pod:
kind: Pod
apiVersion: v1
metadata:
  name: task-pv-pod
spec:
  volumes:
    - name: task-pv-storage
      persistentVolumeClaim:
       claimName: myclaim
  containers:
    - name: task-pv-container
      image: nginx
      ports:
        - containerPort: 80
          name: "http-server"
      volumeMounts:
        - mountPath: "/usr/share/nginx/html"
          name: task-pv-storage

Jul 25 17:51:23 k8s-03 kubelet[1743]: E0725 17:51:23.830412    1743 nestedpendingoperations.go:267] Operation for "\"kubernetes.io/rbd/kube:kubernetes-dynamic-pvc-0b74c780-8fd7-11e8-bad4-e20c5208f0bb\"" failed. No retries permitted until 2018-07-25 17:53:25.830100282 +1000 AEST m=+1393.103569995 (durationBeforeRetry 2m2s). Error: "MountVolume.WaitForAttach failed for volume \"pvc-04f480bb-8fd7-11e8-9d8f-005056aa4c92\" (UniqueName: \"kubernetes.io/rbd/kube:kubernetes-dynamic-pvc-0b74c780-8fd7-11e8-bad4-e20c5208f0bb\") pod \"test-pod\" (UID: \"4e9393d1-8fdd-11e8-bae4-005056aa4c92\") : fail to check rbd image status with: (executable file not found in $PATH), rbd output: ()"

Seems we are trying to use kube-controller-manager to provision the storage instead of rbd-provisioner.
Maybe I am missing something but I spent quite some time checking the documentation and can't seems to find the issue.
Thanks!

the provisioner has created a volume but I think kubelets still need the rbd binary to verify that an rbd volume has been attached.
/area ceph/rbd

That was it thank you so much!
I did not see it documented anywhere that you had to install rbd on the K8S node itself but maybe I missed it.

you sent the same guide as I did


Updating changelog for 1.1.2

=### 🔧 Changes
Updating the changelog for the upcoming 1.1.2 release.
📝 Checklist

[x] All new/changed/fixed functionality is covered by tests (or N/A)
[x] I have added documentation for all new/changed functionality (or N/A)

Codecov Report
All modified lines are covered by tests :white_check_mark:

Comparison is base (2e785d6) 73.40% compared to head (0e3399c) 73.40%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #859   +/-   ##
=======================================
  Coverage   73.40%   73.40%
=======================================
  Files          92       92
  Lines       11895    11895
=======================================
  Hits         8732     8732
  Misses       2647     2647
  Partials      516      516

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


explorer: initial actions to commands transition

fixes #24900

All actions need to be transitioned into commands. Some of these commands need to get a hold of the active tree which should be done using the listService
Context keys need to be managed by the explorer when selection changes in order to show / hide the actions. e.g context key if the selected file is a folder
Need to use groups to preserve the sorting of actions

This is work in progress, currently I am simply transitioning a couple of actions into commands.
fyi @bpasero

@isidorn feedback as discussed:

[ ] autoSaveNotAfterDelayContext => config.autoSave (if possible) with the configured value
[ ] explorer should set the folder context if in single-folder mode and not having anything selected to get those commands to show up when right clicking into empty space
[ ] get rid of actions that have duplicate IDs as commands and use menu service to contribute to quick open (verify via the "Close" action when closing a tab)
[ ] "open in terminal" fails when doing on files (seems to try to open the file in the terminal and not its parent)
[ ] introduce a new context to enable "Compare with chosen" conditionally
[ ] "Add folder to workspace" command seems to fail
[ ] "Open folder settings" command seems to fail
[ ] Actions that we contribute from built in extensions should adopt our groups (e.g. "Open in Preview" for markdown)
[ ] Release Notes: our context menu groups in the explorer so that extensions can pick it up properly

Debt to think about: currently we seem to register commands not from *.contributions.ts but from other places. One alternative solution would be to only define the command handler and then do the registration all from the *.contribution.ts files. That also avoids having to pass around command IDs.

@bpasero I checked and the Open Preview in makrdown is the only built in extension which contributes. But look at my commit it shows that people were expecting navigation here even before we actually introduced it to the explroer.
So it would be nice to have the same name, however not sure how then to fix the ordering problem.

@isidorn we could maybe bring back that group and a) for the open editors make it the primary group and b) for the explorer make it the secondary one so that the group for "New" wins over it.

fyi @bpasero I am wrapping this up and will probably merge into master later today / tomorrow morning
There are still some minor issues but I will treat them as bugs and fix as we go.

I have merged in this PR, I have created https://github.com/Microsoft/vscode/issues/40909 and https://github.com/Microsoft/vscode/issues/40910 as follow up items.
Once you try it out just ping me with issues you see or just file issues (whatever suits you better)
As for release notes I propose to do that in the endgame week.


Add option to disable plugin in mkdocs.yml

Is your feature request related to a problem? Please describe.
When editing sections of my docs that are not using mkdocstrings, the live preview takes a while to update because it will run mkdocstrings on every change.
Describe the solution you'd like
A config parameter in the plugin configuration section of the mkdocs.yml to disable the plugin. Together with the !ENV functionality of mkdocs it makes it easy to disable the plugin without having to modify the mkdocs.yml. So it could look like:
plugins:
- mkdocstrings:
    disabled: !ENV [DISABLE_MKDOCSTRING, False]
    default_handler: python
    handlers:
      python:
        options:
          show_source: false

I use another plugin mkdocs-simple-hooks which uses this  pattern. Here the config option is enabled and defaults to True. I think it makes more sense to have it as disabled and default to False as you as default has it enabled and then can use this option if you want to disable it.
Describe alternatives you've considered

Comment out the mkdocstrings section of the mkdocs.yml. Works, but is annoying and I will accidentally commit the change when I run git add -u.
unwatch the sections of the docs which uses mkdocstrings. Not sure if it's possible to unwatch parts of the doc folder? In any case it would still be a problem when editing files that uses mkdocstrings but you are not focusing on that.

Additional context
I can make the PR if you think this change makes sense.

Hi, thanks for the request :slightly_smiling_face:
That's an interesting topic. I wonder if the upcoming version 1.4.0 of MkDocs would help here :thinking:
Particularly thinking about the on_startup and on_shutdown events.
In the meantime, I understand the use-case. I'm curious though: how long does mkdocstrings take to collect/render docs? Do you have a moderate/huge code base? Maybe improving performance is a path we could take?
About your proposal: it could be interesting to think of a way to offer that "degraded-mode" (disable some plugins) feature directly in MkDocs.
mkdocs serve --disable-plugins mkdocstrings

Or not: if it's only relevant to 2 plugins (mkdocstrings and mkdocs-simple-hooks, which is kind of superseded by MkDocs 1.4.0), it's probably not worth it. Happy to hear your thoughts on this @oprypin.
I'm wondering something about the implementation you suggest: is the config option really useful? Couldn't we simply check the environment variable? Do you think there would be cases where environment variables are not viable, but modifying the YAML file or config object in memory is? Seems unlikely to me :thinking:

In the meantime, I understand the use-case. I'm curious though: how long does mkdocstrings take to collect/render docs? Do you have a moderate/huge code base? Maybe improving performance is a path we could take?

~12 seconds with mkdocs, ~2 seconds without. The 10 extra seconds are very noticably in when editing with live refresh. I don't really care about it when building the docs. It's a fairly large code base. We're working on adding documentation so right now the API reference which is 100% mkdocsstring is the by far the largest component of the docs.

About your proposal: it could be interesting to think of a way to offer that "degraded-mode" (disable some plugins) feature directly in MkDocs.

I actually tried making a plugin for this, but since plugins can modify stuff in the on_config event, it's not enough for another plugin just to remove the plugin from the config object in its own on_config. Maybe those new events you mention could do it, haven't heard about them before.

Or not: if it's only relevant to 2 plugins (mkdocstrings and mkdocs-simple-hooks, which is kind of superseded by MkDocs 1.4.0), it's probably not worth it. Happy to hear your thoughts on this @oprypin.

I thought it was a fairly normal pattern - another plugin I use, with_pdf uses the same pattern.

Hi again! I'm revisiting this since 1.4.0 has landed (and because I again made a PR with the mkdocstring section commented out 🤡).
Since on_startup does not receive the config it doesn't seem to me like there is any nice way to disable another plugin using this hook. Maybe the hook could be used if you wanted to implement the disable functionally into mkdocstring but since it's only run once I'm not sure there's any reason to use on_startup over on_config for this.
I agree that we could simply check an environment variable directly, that's also less of a change.
I'm still open to making the PR if it's something you want to include.

Hello, thanks for the update! A PR would be very welcome :)


Hotfix/migrate log fix

Purpose
Fix the problem of the previous log migrate causing logs disappear on some projects. Solves https://github.com/CenterForOpenScience/osf.io/issues/2873
Changes
Instead of putting a property 'should_hide' on the log object, remove them from parent logs list and make a new attribute was_connect_to to keep a record of the reference.

@lyndsysimon Can you do a code review for this?

Got this @lyndsysimon ? -- Thanks.

Pass complete.
I've no real issue keeping us from pushing this out if it's of extreme importance. The only thing I think needs to be done is the removal of the backref from the new ForeignField. Nothing else will impact the execution of the script in production.

Consider this a "go" from me.


Document Code table update process

Notify @klefler once done.
Other info:
_I’ve recently documented a Reference Data Guide on the IIT Data Design Guidelines page (there’s a lot of info there, but this page has some high-level stuff that could be referenced… https://apps.nrs.gov.bc.ca/int/confluence/display/NRMDDDG/Reference+Data+Best+Practices and this page (still in DRAFT) starts to outline specific topics DA sees with code requests https://apps.nrs.gov.bc.ca/int/confluence/display/NRMDDDG/Common+Reference+Data+Topics). This documentation is still a work in progress, but my goal would be to use some of it to help data managers understand best practices / approaches to managing reference data. It’s a service that DA provided / provides for 50+ FLNRO applications (including IAPP), so we have lots of experience to share.
Code Management Procedures
The process for managing the code values should be documented… for example; when is a new code a new record versus just changing a code value or description? When does an existing code get expired? If a value changes does relating data also need to be changed (data conversion)? Are these code values that this program area can/should change (i.e. are they actually managed by another agency)?_

@mikeshasko Can you write up a quick summary of how we are managing code tables based on the notes above?  Then we can let Kristen know and close this one.


tests: make LAN.Scanner.prototype.stop calls safer. Fixes gh-1024, Fixes gh-1057

Thanks for this quick fix @rwaldron. Fixes https://github.com/tessel/t2-cli/issues/1024


(PUP-9323) Allow deferred functions to adhere to puppet relationships and ordering

By default, deferred functions are "preprocessed" before the catalog is applied (before prefetching, expanding the relationship graph, etc). However, in this mode puppet cannot install a prerequisite needed for the deferred function and call the function. Worse, puppet never eventually converges, because the deferred function failure prevents all resources from being managed.
This PR makes it possible to disable preprocessing so that deferred functions work in the way users expect. In other words, if a resource's parameter or property is a deferred value, then the deferred function will be called when it's resource is managed. Therefore, the function will adhere to normal puppet relationships and ordering. And if the deferred function fails, then only that resource will fail, and downstream resources that depend on it will be skipped.
In order to accomplish this, we have to delay the calls to munge, validate and unmunge. See https://github.com/puppetlabs/puppet/pull/8902/commits/983f652888ae3ab2633b8bc33f9d97dd33790b8d and https://github.com/puppetlabs/puppet/pull/8902/commits/815c9c76758ddc9be8829abc949b12e3d507a2e3 for details.

$file = '/path/to/new/file'
file { $file:
  ensure => file,
  content => "1234",
} ->
notify { 'deferred':
  message => Deferred('binary_file', [$file])
}

Using puppet#main it fails because binary_file is called before the file exists:
$ bx puppet apply deferred.pp
Notice: Compiled catalog for localhost in environment production in 0.02 seconds
Error: binary_file(): The given file '/tmp/newfile' does not exist

With this PR:
$ bx puppet apply deferred.pp
Notice: Compiled catalog for localhost in environment production in 0.02 seconds
Notice: /Stage[main]/Main/File[/tmp/newfile]/ensure: defined content as '{sha256}03ac674216f3e15c761ee1a5e255f067953623c8b388b4459e13f978d7c846f4'
Notice: MTIzNA==
Notice: /Stage[main]/Main/Notify[deferred]/message: defined 'message' as Binary("MTIzNA==")
Notice: Applied catalog in 0.02 seconds

jenkins please test this with servertests

jenkins please test this with servertests

jenkins please test this with servertests

jenkins please test this with servertests

jenkins please test this with servertests


please create an envirement for mt5

please create an envirement for mt5

what do you mean by mt5?

please create an envirement for mt5

Please explain in details… I do not follow here. Thanks!

please create an envirement for mt5

Please explain in details… I do not follow here. Thanks!

@salah2025 do you mean Metatrader 5?  (www.metatrader5.com)

There is a limited python library for MT5: https://www.mql5.com/en/docs/integration/python_metatrader5 but as you can see it is missing vital trading operations.
However, I have not gone down this path and integrate FinRL with Metatrader, but have integrated FinRL with the broker API to get data and issue trading operations (see https://github.com/AI4Finance-Foundation/FinRL/blob/master/tutorials/3-Practical/FinRL_PaperTrading_Demo.ipynb for an example integration with Alpaca broker).  You can then still use MT5 for the charting.  The other reason is that MT5 is a desktop application, not designed to be deployed on VPC, so it will be vulnerable to power or Internet access loss.
I didn't want to change the paper trading demo and introduce another version (as most of the trading logic would be the same). WIth the same approach as the layered data processors, I am creating a specific broker layer that sits beneath the papertrading demo (with small mods to point to this layer).   Hopefully then we will have a generic papertrading demo, that supports specific broker implementations for trading operations.
Hope that helps.

If people are still interested in this is relatively easy to do.
You just need to import and initialise the MT5 package and then make a copy of the data processor file and put something like the below in place of the loop to download data for whichever data processor you're using.
This example is hard coded to the hourly timeframe.
for tic in ticker_list:
temp_df = pd.DataFrame(mt5.copy_rates_range(tic, mt5.TIMEFRAME_H1, start_date, end_date))
temp_df["tic"] = tic
data_df = pd.concat([data_df, temp_df])


Blank page presented when run as a container (until container is killed)

Describe the bug
Running ollama-webui as a docker container presents a blank page.  Interestingly enough, as soon as I kill the container, the webUI will appear in the browser.  Note:  I am providing an example of running this on a remote host from where my "ollama server" container is running, but the same thing happens when I run ollama-webui on the same node.   I have to use the remote example to remove the possibility of docker networking being the culprit.
To Reproduce
Steps to reproduce the behavior:

Run ollama server as a container on Docker on my PC with NVIDIA card (<IP_ADDRESS>)
OLLAMA_ENV_FILE=${HOME}/ollama-env-file.txt echo "OLLAMA_ORIGINS=\"http://<IP_ADDRESS>:*,http://hal9000.matrix.lab:*\"" > $OLLAMA_ENV_FILE docker run -d --gpus=all -v ollama:/root/.ollama -p 11434:11434 --env-file=$OLLAMA_ENV_FILE --name ollama ollama/ollama

Run Ollama-webui on a separate host (either Ubuntu 22.04 x86 laptop, or MacOS Sonoma M2 laptop)
2.1 MacOS M2
docker run -it --platform linux/amd64 -d -p 3000:8080 -e OLLAMA_API_BASE_URL=http://<IP_ADDRESS>:11434/api --name ollama-webui --restart always ghcr.io/ollama-webui/ollama-webui:main
OR
2.2 Ubuntu x86
docker run -d -p 3000:8080  --env-file=$OLLAMA_ENV_FILE  --name ollama-webui --restart always ghcr.io/ollama-webui/ollama-webui:main

Browse to the endpoint (http://localhost:3000).  Receive a blank page (not connection refused, etc...).  Additionally, I have openen with both Chrome and Safari at the same time.

Kill the container running ollama-webu.

Instantly the webui will appear (in both browsers when I was testing with both) and is actually functional (i.e. I can update the settings to point to my ollama server endpoint and proceed.

I have reviewed the container logs of ollama-webui - and I do not see any errors.  Unfortunately without know what "good" looks like, I also don't know if something is not happening that should be.

Expected behavior
As I have yet to get this working, I am not entirely certain what to expect.  My guess, however, is that when I browse to my ollama-webui endpoint, that the webui would be presented - and that I would not need to kill the container that was running the webui for it to work.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):

OS: MacOS

Browse: Chrome/Safari

Version:  Sonoma (I am not sure what "version" we are referring to here)

OS: Ubuntu

Browse: Chrome

Version:  22:04 desktop (I am not sure what "version" we are referring to here)

Additional context
Happy to execute any testing on my side to help move this along.  Thanks all!

Hi, I cannot seem to reproduce the issue on my side using m1 mac and ubuntu server over LAN. Could you provide us with the browser console logs to better assess what the issue is? Thanks!

@tjbck - I am now unable to reproduce, as well.  I made several attempts while testing.  I apologize for taking up your time.


Wlanapi Permissions bug on Windows 10

I ran into the issue discussed here:
https://docs.microsoft.com/en-us/answers/questions/397654/34netsh-wlan-connect34-wlanapiwlanconnect-from-wit.html
I am remoting into my Windows 10 machine using the built-in openssh server and running scripts that use pywifi. I purpose that we remove the WLAN_PROFILE_USER (0x2) from the call to  WlanSetProfile  https://github.com/awkman/pywifi/blob/719baf73d8d32c623dbaf5e9de5d973face152a4/pywifi/_wifiutil_win.py#L564-L570

I also encountered the same issue . I solved the issue  with your commit. My service is Jenkins. I guess the issue is caused by the lack of permission of the windows user Jenkins logs in


Module broken

Module has broken for me as of 2016/06/02.
Traceback (most recent call last):
  File "/home/matoro/documents/scripting/aniwatch-getcookies.py", line 1, in <module>
    import cfscrape; cookie_arg, user_agent = cfscrape.get_cookie_string("https://kissanime.to"); print (cookie_arg)
  File "/usr/lib/python3.5/site-packages/cfscrape/__init__.py", line 152, in get_cookie_string
    tokens, user_agent = cls.get_tokens(url, user_agent=user_agent, js_engine=None)
  File "/usr/lib/python3.5/site-packages/cfscrape/__init__.py", line 124, in get_tokens
    resp = scraper.get(url)
  File "/usr/lib/python3.5/site-packages/requests/sessions.py", line 487, in get
    return self.request('GET', url, **kwargs)
  File "/usr/lib/python3.5/site-packages/cfscrape/__init__.py", line 30, in request
    return self.solve_cf_challenge(resp, **kwargs)
  File "/usr/lib/python3.5/site-packages/cfscrape/__init__.py", line 52, in solve_cf_challenge
    js = self.extract_js(body)
  File "/usr/lib/python3.5/site-packages/cfscrape/__init__.py", line 73, in extract_js
    "t,r,a,f.+?\r?\n[\s\S]+?a\.value =.+?)\r?\n", body).group(1)
AttributeError: 'NoneType' object has no attribute 'group'

URL of page:  https://kissanime.to/
Unblocked source of the page:  https://gist.githubusercontent.com/matoro/7b68ca646d74aa85be75c574b3ada52e/raw/88428631317b9446584e58a671f680e4383f088b/kissanime.html
A bit of further information:  I've been using this method up until this point with no problems.  It is part of a much larger bash script I'm using as a learning tool for bash.  The relevant section pastes the code import cfscrape; cookie_arg, user_agent = cfscrape.get_cookie_string("https://kissanime.to"); print (cookie_arg) into aniwatch-getcookies.py, executes it, then deletes the file.  I can post the complete bash script if it will help.
I have a debug mode built into the script, which will print the cookies to stdout.  When running it, I get the following:
[debug] Clearance cookies [!] Unable to parse Cloudflare anti-bots page. Try upgrading cloudflare-scrape, or submit a bug report if you are running the latest version. Please read https://github.com/Anorov/cloudflare-scrape#updates before submitting a bug report.

'https://kissanime.to' returned an error. Could not collect tokens. obtained.

Same for me

Hi,
replace t,r,a,f with s,t,o,p,b,r,e,a,k,i,n,g,f in line 73 seems to work.

replace t,r,a,f with s,t,o,p,b,r,e,a,k,i,n,g,f in line 73 seems to work.

I can confirm this works, thank you

PR merged. Will upload to PyPI shortly.


[WFLY-17357] [git branches] Fix problematic language usage in branches

https://issues.redhat.com/browse/WFLY-17357

There are still some "master" branches left, those still use the word "master" instead of "main" or any other variant. Few links were removed due to the fact that said link doesn't work anymore and has no alternative (helloworld-rs for example)

Thanks for looking into this @yersan , I've made the requested changes and managed to find one more problem to fix.
Can you please take a look at changes in Micrometer.adoc as I'm not sure if the code is fine now.

Thanks @petrberan


IApplicationBuilder does not contain a definition for UseSignalR

Today update Microsoft.NETCore.App and some v1.0.0-preview2-25241 version packages like Microsoft.AspNetCore.SignalR. And in Startup.cs :
before
public void ConfigureServices(IServiceCollection services) {   services.AddSignalR(); }
after
public void ConfigureServices(IServiceCollection services) {   services.AddSignalRCore(); }
and in public void Configure function at app.UseSignalr() error

IApplicationBuilder” does not contain a definition for “UseSignalR

How to setup hub now?

You need to reference the Microsoft.AspNetCore.SignalR.Http package now.

It works! Thank you!

Q: I understand why this moved, as the IApplicationBuilder UseSignalR is/was http based, however shouldn't UseSignalR be transport agnostic? in that regardless of http/tcp/UDP etc. the UseSignalR is the same? and determines the availability of transport via dependency injection and/or configuration action?

No, IApplicationBuilder is http specific.

@davidfowl Q: so if as a developer I was creating a web application that used SignalR with TCP as its transport the UseSignalR wouldn't need to be called ?

We don't have a TCP host yet (kestrel will be it though in case you were wondering post 2.0)
You wouldn't be configuring TCP things in the http pipeline (IApplicationBuilder)

@davidfowl ok, so hyperthetically if I wished to use SignalR on multiple transports I'd need to call a method on each transport pipeline, and these extension method for this would be different for each transport type? do understand this is well in the furture and SignalR hasn't be released as yet plus the team has some Big Rocks to move.

This is correct. You need to configure it in each pipeline. The first class UseSignalR is a shortcut for http scenarios because it's the most common.  The MapSocket extension method exposes an ISocketBuilder per route which is all you really need

Took me 8 hours to find out, that I need to add Microsoft.AspNetCore.SignalR.Http to my project. Is this documented anywhere?
Plus, I only could find it as Prerelease 1.0.0-alpha1-26873 ... I'm using .net core 2.1. Am I still on the right track? Did I miss something? Version 1.0.2 is on nuget.org, but not listed in my nuget package manager. Strange thing....

This is a very old issue with irrelevant info on it now.
I would suggest looking at our docs to get started: https://docs.microsoft.com/en-us/aspnet/core/tutorials/signalr?view=aspnetcore-2.1&tabs=visual-studio
If you are still having issues please open a new issue as we don't monitor closed issues as much as open ones.

@BrennanConroy thanks for your reply - I found out what mistake I did. I used Microsoft.AspNet.SignalR.* packages instead of Microsoft.AspNetCore.SignalR.* packages. However, which NuGet-packages to use is not metioned in your documentations? When searching for SignalR I always get the old packages on top (I'm using JetBrains Rider IDE).
Maybe, mentioning the package-names in the documentation would be great. Not only the client-things with npm but also the NuGets.
Didn't want to open a new issue for just telling my result now :)


Adding support for other languages

Track requests for other languages here.
We can create new issues as new language requests come in

Scala

@eliekawerk Can you clarify what you need for the Scala support? Scala code can already call into the Java code natively at the moment

@eliekawerk Can you clarify what you need for the Scala support? Scala code can already call into the Java code natively at the moment

True, can use the Java API directly. I missed that!

This is too broad scope, lets track with roadmap items around whylogs v1. We have some scala support not. closing.


Fix BZ Bug 62391

This PR fixes bug https://bz.apache.org/bugzilla/show_bug.cgi?id=62391
It is a very simple fix so might be easier to apply directly rather than accepting this patch.
If approved, I can probably apply it directly myself in SVN, which will give me some practice with that.

Closing on Github since I can now patch SVN directly if there is no objection to this change


Define a meta-controller for Camel-based Knative sources

Tracking here but work to be done in Knative.
Based on a similar idea as https://github.com/Harwayne/auto-container-source, we should define a meta-controller for Camel based sources.
The idea is that to allow people to define a CRD like MyCustomKnativeSource with k/v properties and also declare the way to translate it into a "runnable" CR through one or more annotations.
The MyCustomKnativeSource can be translated into a CamelSource or directly into a Integration skipping the first level translation step.
Long term, we'll provide tools to auto-generate the CRD from a DSL script.

Not in plans


Support for shell input redirection.

buildkite-agent doesn't seem to support reading config from an input anymore:
$ touch ~/t.yaml
$ buildkite-agent pipeline upload --replace <~/t.yaml
2018-04-18 05:11:12 INFO   Searching for pipeline config...
2018-04-18 05:11:12 FATAL  Could not find a default pipeline configuration file. See `buildkite-agent pipeline upload --help` for more information.
$ cat ~/t.yaml | buildkite-agent pipeline upload --replace
2018-04-18 05:11:26 INFO   Reading pipeline config from STDIN
2018-04-18 05:11:26 FATAL  Config file is empty

Note the two different error messages. The first one complains it couldn't find the config, the second one complains the config is empty. This used to work with the previous version, so it might have something to do with this change:
v2.6.10:
https://github.com/buildkite/agent/blob/ce612fc8406f7de031c671478c380cedf4399700/clicommand/pipeline_upload.go#L103
v3.0.1:
https://github.com/buildkite/agent/blob/3ac2abb9d4afd691c5f5acc408139aff4c26a1e4/clicommand/pipeline_upload.go#L106

🤔So looks like the first one isn't correctly detecting stdin, but the second is working correctly? I'm assuming OS is linux, in am interactive bash shell?
Tests are at https://github.com/buildkite/agent/blob/3ac2abb9d4afd691c5f5acc408139aff4c26a1e4/stdin/main_test.go. It's been very tricky to get working correctly across platforms, I'll do some, further testing.

The test I ran on 3.0.1 is on Linux, interactive bash shell. It was working before on 2.6.10 with a non-interactive shell, never tried with an interactive shell there.

+1 - we have a large number of existing pipelines using the < filename.yml syntax, so this is blocking our upgrade to v3


Cover IR 74

An INSPIRE View Service shall implement the mandatory behaviour from an [OGC 07-057r7] service, extended with the extensions required by the INSPIRE Directive and the Implementing Rules for View services.

This requirement is completely covered by tests for IR 75 (issue #2) and other INSPIRE extension specific tests.

Closed as duplicate


[BUG] - Traefik rate limited by Let's Encrypt after several pod restarts

Describe the bug
Traefik documentation warns to persist the acme.json certificate storage to avoid being rate limited by Let's Encrypt, but Nebari's deployment isn't configuring that. If the traefik pod is restarted enough times within a given week without this setup, Let's Encrypt will rate limit the certificate issue request and cause the site to default back to self-signed.
This has happened to me many, many times when I'm developing or testing changes to the platform or dealing with conda storage related node crashes, usually requiring a workaround involving installation of cert-manager and switching to zerossl or another cert issuing service until the Let's Encrypt backoff period elapses.
Expected behavior
traefik pod restarts should not result in new certificates being issued when configured for lets-encrypt.
Options:

Configure a persistent volume mount for the acme.json storage path.
Replace Traefik's native Let's Encrypt integration with cert-manager for more issuer options and improved scalability.

OS and architecture in which you are running Nebari
Linux, x64
How to Reproduce the problem?

Configure the Nebari certificate with lets-encrypt

certificate:
  type: lets-encrypt
  acme_email<EMAIL_ADDRESS>  acme_server: https://acme-v02.api.letsencrypt.org/directory

Delete the traefik pod 5 or more times in 1 week.

Command output
No response
Versions and dependencies used.
Nebari 2023.11.1
Compute environment
AWS
Integrations
No response
Anything else?
No response

I am working on this ticket, Please find the gitlab issue as below.
https://gitlab.jatic.net/jatic/team-metrostar/t-e-platform/-/issues/345

Resolved by #2352


[Mobile] Spacing needs to be 32px after image/caption Do Not’s throughout.

Description
There are missing 32px spacers after captions under “Do Not’s” though out the guidance pages.
This occurs in many of the Guidelines pages

Some of the occurrences:
https://next.carbondesignsystem.com/assets/guidelines/color/overview
https://next.carbondesignsystem.com/assets/guidelines/2x-grid/overview
https://next.carbondesignsystem.com/assets/guidelines/2x-grid/implementation
https://next.carbondesignsystem.com/assets/guidelines/pictograms/usage
https://next.carbondesignsystem.com/assets/guidelines/motion/choreography
In this case some of the “Do not” cards without captions touch each other
https://next.carbondesignsystem.com/assets/guidelines/typography/overview

Could be fixed by #811. If not, re-estimate.


1.0.0

Signed-off-by: Stephen Curran<EMAIL_ADDRESS>

Sorry — the lack of a correct favicon for the docs site was bugging me — meant to fix it before creating the PR.  Not a great solution pointing to another repo, but at least we have one.


Update libkv Godeps with migration to the new etcd client

This PR includes the latest vendor-in for docker/libkv, including support for the new coreos/etcd/client.

LGTM since CI is green

LGTM


Deleting posts and comments updates user object accordingly

Describe your changes
Deleting a post or comment now removes the ref from the user object
Issue ticket number and link
Checklist before requesting a review

[x] All code is linted and conforms to style guide
[x] All necessary context is described in the PR or Issue
[x] This branch is code and feature complete. If it is not complete, this PR is a draft.

I'm a silly goose for forgetting this lmao. Note to file an issue to make this work with over 450 comments one day, but that's exceedingly unlikely


How to fix the error "Diagonal of the variance_matrix_ has negative values or NaNs while using Gompertz function?

While running the example of Gompertz function using the waltons dataset, I encountered this error:
`.local/lib/python3.6/site-packages/lifelines/fitters/init.py:994: StatisticalWarning:
The diagonal of the variance_matrix_ has negative values or NaNs. This could be a problem with GompertzFitter's fit to the data.
It's advisable to not trust the variances reported, and to be suspicious of the fitted parameters too. Perform plots of the cumulative hazard to help understand the latter's bias.
To fix this, try specifying an initial_point kwarg in fit.`
Any idea how to fix it? Is it only me or someone else facing the same issue?

Any help on this? Thanks


Support for yarn-cluster mode

Currently, sparklyr submits a custom sparklyr.jar file through spark-submit with a given ports file. Then the jar initializes a socket and saves the socket details in the ports file. This file is used by sparklyr to rea this socket definition and connect to the running application within the jar in the driver machine. This works as expected for yarn-client; however, for yarn-cluster the file is located on a different machine that the r process running sparklyr won't be able to locate since it's not local anymore.
Marking this as feature request for discussion and planning work for next release.

UPDATE: A PR (https://github.com/rstudio/sparklyr/pull/238) has been committed which removed the use of a ports file mentioned above. However, there are still a few settings that need to be exposed in order to connect to the remove driver. If someone is interesting in helping out here, feel free to contact me at javier at rstudio.com (not much work left). Otherwise, I'll take a look at this as time permits.

+1 on this ASAP.

Works if the primary RM is online.  If ha is enabled and the primary RM is not online, it doesn't try the list of ha RMs in round robin.

@samurainate give it another shot, #997 got enough fixes to enable connection in HA mode. Issue is still open due to HIVE auth issue, but looks like that might not be related to sparklyr.


Add editorID property

This PR fixes #124354
Adds a possibly undefined editorId property so that all IEditorInputs can be checked for overrides. This is a relatively safe change and more adopters can join and dictate what they want their id to be if they want to participate.

I still believe there are cases where this would be helpful. Especially because things like search editors etc even though text based can have different editor ids and it can be hard to state that fact to the editor service in various opening scenarios. Closing for now though as I believe more discussion is needed.


Wip/mwk/pysrv

General comment - we should be pep8 compliant (or at least compliant to agreed subset).


Issue template

I made a first draft for an issue template. What do you think? Let me know!
I have kept it as easy and bare as possible, as to not 'scare away' any people opening an issue.

Yep - great work @BasThomas - this is a good start, and if people want to build off it, send more PRs 👍

Sounds good!


<EMAIL_ADDRESS>

Compared to 1.15.0.bcr.1, add a bool_flag for header_only mode.
This enables --@spdlog//:header_only=False on the bazel command line.

See also #1769 which requests a mechanism to enable USE_STD_FORMAT.  If desirable, I could try adding that option as an additional flag in this pull request.

Hello @Vertexwahn, @c8ef, modules you maintain (spdlog) have been updated in this PR. Please review the changes.

@bazel-io skip_check unstable_url

Can we test also the --@spdlog//:header_only=False variant in CI?
USE_STD_FORMAT as a flag would also be nice - but we can defer this to a later PR...

Good idea; test added.

The new presubmit matrix was failing on windows with UTF-8 complaints.  I added --cxxopt=/utf-8 to fix it, similar to the existing pattern for fmt.


why task instance is null

Describe the question
I have a workflow that is executed once every hour. Some tasks started at the time node cannot be completed normally and have been running all the time. The worker log finds errors:【[ERROR] 2020-04-26 13:10:03.627 org.apache.dolphinscheduler.server.worker.runner.FetchTaskThread:[261] - task instance is null. task id : 245 】
version1.2.0 of DolphinScheduler:
dolphinscheduler-master.log
[INFO] 2020-04-26 13:10:03.269 org.apache.dolphinscheduler.server.master.runner.MasterSchedulerThread:[114] - find one command: id: 68, type: SCHEDULER
[INFO] 2020-04-26 13:10:03.461 org.apache.dolphinscheduler.server.master.runner.MasterSchedulerThread:[119] - start master exec thread , split DAG ...
[INFO] 2020-04-26 13:10:03.465 org.apache.dolphinscheduler.server.master.runner.MasterExecThread:[296] - prepare process :158 end
[INFO] 2020-04-26 13:10:03.468 org.apache.dolphinscheduler.server.master.runner.MasterExecThread:[792] - add task to stand by list: sparkPi
[INFO] 2020-04-26 13:10:03.468 org.apache.dolphinscheduler.common.queue.TaskQueueFactory:[45] - task queue impl use zookeeper
[INFO] 2020-04-26 13:10:03.468 org.apache.dolphinscheduler.server.master.runner.MasterExecThread:[801] - remove task from stand by list: sparkPi
[INFO] 2020-04-26 13:10:03.470 org.apache.dolphinscheduler.dao.ProcessDao:[769] - start submit task : sparkPi, instance id:158, state: RUNNING_EXEUTION,
[INFO] 2020-04-26 13:10:03.474 org.apache.dolphinscheduler.common.queue.TaskQueueZkImpl:[99] - check task:2_158_2_0_-1 not exist in task queue
[INFO] 2020-04-26 13:10:03.628 org.apache.dolphinscheduler.common.queue.TaskQueueZkImpl:[99] - check task:2_158_2_245_-1 not exist in task queue
[INFO] 2020-04-26 13:10:03.628 org.apache.dolphinscheduler.dao.ProcessDao:[973] - task ready to queue: TaskInstance{id=245, name='sparkPi', taskType='SHELL', processDefinitionId=9, processInstanceId=158, processInstanceName='null', taskJson='{"depList":[],"dependence":"{}","forbidden":false,"id":"tasks-36923","maxRetryTimes":0,"name":"sparkPi","params":"{"rawScript":"sshpass -p  hadoop ssh -o StrictHostKeyChecking=no<EMAIL_ADDRESS>\"sh /data/hadoop/liucf/dsTest/sparkPi.sh\"","localParams":[],"resourceList":[]}","preTasks":"[]","retryInterval":1,"runFlag":"NORMAL","taskInstancePriority":"MEDIUM","taskTimeoutParameter":{"enable":false,"interval":0},"timeout":"{"enable":false,"strategy":""}","type":"SHELL","workerGroupId":-1}', state=SUBMITTED_SUCCESS, submitTime=Sun Apr 26 13:10:03 CST 2020, startTime=Sun Apr 26 13:10:03 CST 2020, endTime=null, host='null', executePath='null', logPath='null', retryTimes=0, alertFlag=NO, flag=YES, processInstance=null, processDefine=null, pid=0, appLink='null', flag=YES, dependency=null, duration=null, maxRetryTimes=0, retryInterval=1, taskInstancePriority=MEDIUM, processInstancePriority=MEDIUM, workGroupId=-1}
[INFO] 2020-04-26 13:10:03.628 org.apache.dolphinscheduler.common.queue.TaskQueueZkImpl:[126] - add task : /dolphinscheduler/tasks_queue/2_158_2_245_-1 to tasks queue , result success
[INFO] 2020-04-26 13:10:03.628 org.apache.dolphinscheduler.dao.ProcessDao:[975] - master insert into queue success, task : sparkPi
[INFO] 2020-04-26 13:10:03.629 org.apache.dolphinscheduler.dao.ProcessDao:[786] - submit task :sparkPi state:SUBMITTED_SUCCESS complete, instance id:158 state: RUNNING_EXEUTION
dolphinscheduler-worker.log
[INFO] 2020-04-26 13:10:03.607 org.apache.dolphinscheduler.common.queue.TaskQueueZkImpl:[211] - consume tasks: [2_158_2_245_-1],there still have 0 tasks need to be executed
[ERROR] 2020-04-26 13:10:03.627 org.apache.dolphinscheduler.server.worker.runner.FetchTaskThread:[261] - task instance is null. task id : 245
[WARN] 2020-04-26 13:10:03.627 org.apache.dolphinscheduler.server.worker.runner.FetchTaskThread:[188] - remove task queue : 2_158_2_245_-1 due to taskInstance is null
[INFO] 2020-04-26 13:10:03.627 org.apache.dolphinscheduler.common.queue.TaskQueueZkImpl:[278] - consume task /dolphinscheduler/tasks_queue/2_158_2_245_-1
Workflow instance screenshot

What is the cause of this? How to avoid it?

@lenboo ，please answer  this issue

It may be similar to this problem
#1477

After reading it, I think so

some tips for this situation：

clear the task queue in zk for path: /dolphinscheduler/task_queue
change the state of the task to failed( integer value: 6).
run the work flow by recover from failed

Thank you very much.

If you solve this problem manually, it is not ideal, because it is not applicable to solve the problem manually through timed tasks

If you solve this problem manually, it is not ideal, because it is not applicable to solve the problem manually through timed tasks

1.2.1 solved this problem，you can upgrade to latest

If you solve this problem manually, it is not ideal, because it is not applicable to solve the problem manually through timed tasks

1.2.1 solved this problem，you can upgrade to latest

OK, thank you


DescriptorSet image & buffer usage bit validation

Verify that correct usage bits are set for both image and buffer descriptor updates.
Add test that triggers all the possible usage bit errors.

cherry-picked and pushed to master


Expected release date Alamofire 5 Final version - Swift 5.1 (Xcode 11)

[*] I've read, understood, and done my best to follow the *CONTRIBUTING guidelines.
What did you do?
I wanted to upgrade my project to Swift 5.1 and go to Xcode 11. One of the dependencies in my project is Alamofire.
What did you expect?
I expected that with the release of the final version of Xcode 11, I would be able to transfer the project to Swift 5.1 and use all the cool things with the Xcode 11.
What happened instead?
Instead, 3 weeks after the release of Xcode 11, Alamofire has a release candidate version and I can’t use the new IDE and transfer the project to Swift 5.1
Alamofire Environment
Alamofire version: Alamofire 5.0.0-rc.2
Xcode version: Xcode 11.1
Swift version: Swift 5.1
Platform(s) running Alamofire: iOS 13
macOS version running Xcode: macOS 10.15

me too !

Alamofire 4 and 5 work fine under Xcode 11, all versions.

OK. Thanks.

I can run an Xcode project but I can't archive with Alamofire 4.9.0

Hey hi all.
i am running on Xcode 11 with Swift 5.1 with Alamofire" ~> 5.0.0-rc.2.
but did not find relevant methods for background downloads and completion handlers.
Is there any standard API migration guide to Alamofire5. which will be really helpfull


Docs: UI extensions

What this PR does / why we need it:
The goal is to improve the documentation of the UI extensions functionality provided in Grafana 10 and onwards.
Which issue(s) this PR fixes:

Fixes #
Special notes for your reviewer:

Nice work! At first glance, I think creating UI extension points is a subset of the "Create a plugin" category, so these should probably live under there somewhere. All the top-level categories conform to the doc team's framework. Since they're replacing content that was in the "Extend a plugin" subcategory, do you feel that this category would work at create-a-plugin/extend-a-plugin, or perhaps directly under create-a-plugin/?
Also, I would suggest htat on the first mention of an extension point there should be a definition and context given directly or by a link to other docs.
I'll give a closer review soon.

@josmperez could you clarify what the "doc team's framework" refers to?

could you clarify what the "doc team's framework" refers to?

Yes, I'm refering to the discussion of document structure in our writer's toolkit, especially this topic list. Grafana doc sets follow this specific ordering from Introduction to Reference(s). We can add an action verb like "Work with UI extensions" to this collection of documents and move it to the top level if we feel it's warranted, but it strikes me as a subset of the plugin creation process.

could you clarify what the "doc team's framework" refers to?

Yes, I'm refering to the discussion of document structure in our writer's toolkit, especially this topic list. Grafana doc sets follow this specific ordering from Introduction to Reference(s). We can add an action verb like "Work with UI extensions" to this collection of documents and move it to the top level if we feel it's warranted, but it strikes me as a subset of the plugin creation process.

Thanks for this @josmperez. I'm not sure where it most makes sense, but I do worry about overkill on nesting and burying the content. Particularly given the newness of UI extensions. Its also the only place we document it, including the conventions on how Core extension points should be configured - not "create a plugin" concern.

I'm not sure where it most makes sense, but I do worry about overkill on nesting and burying the content. Particularly given the newness of UI extensions. Its also the only place we document it, including the conventions on how Core extension points should be configured - not a "create a plugin" concern.

I think those are valid concerns. The doc team's guidelines are clear that the conceptual topic should live in the Introduction folder, ideally. However, I'm not entirely convinced that it's best in this approach. I am conferring with our Tempo writer because the Tempo does have a somewhat similar category in them. I hope to have more settled guidance on this tomorrow.

I hope to have more settled guidance on this tomorrow

After consulting on the docs team, I've decided that the structure of this PR does indeed fit within the guidance of our doc structure guidelines and doesn't require reorganization. The "UI extensions" section will function as its own subsection of the site, and if/when it expands it will need to follow our structure guidelines (e.g., with conceptual matter in an Introduction section, References at the end, etc.)

Many thanks for the review and guidance @josmperez 🙌


Is there any new template for 4.18?

Hello, I want to start developing production application with ARCore, I have tested the sample pack, but I want to know more, is there any other template that supports 4.18 and ready for production? Having the proper starter pack would help to lots of developers with their beginnings.

Hi, the current version of HelloAR sample should work with Unreal 4.18, so you can use that to get start on your development. However be aware that the ARCore support in 4.18 is still a developer preview version, it is not intended for use in production apps shipped to customers.

Hi , I want to know the different between ARCore.aar and Tango SDK.
I know ARCore is supported by Google Pixel and some Samsung.
Tango SDK is only supported by PHAB2 Pro and PHAB2,  but when UE4 integrates Tango SDK, how to mudifly?

Excuse me, when I opened this master by 4.18 UE4 editor,it showed "Missing HelloARUnreal Modules"!
The following modules are missing or built with a different engine version:
UE4Editor-HelloARUnreal.dylib
Would you like to rebuild them now?
When I rebuild this ,the log is:
HelloARUnreal could not be compiled. Try rebuilding from source manually.

Hi, you probably got this error because you build the HelloAR project with a previous version of Unreal. Can you try download a clean repo of this HelloAR project and open it with Unreal UE4 and see if it fixed the problem.
To your early question, the developer preview version of ARCore in Unreal engine is built on top of the previous Tango SDK, that is why you were seeing a TangoSDK folder in the ThirdParty folder. What are you trying to figure out exactly?

To my early question , there are two devices(PHAB2 Pro and PHAB2) that support the Tango SDK, and different from Google ARCore devices (Google Pixel and so on). But after UE4 integrated Tango SDK, it can support devices is also Google Pixel, Pixel XL, Samsung, and so on, I want to know  whether is to modify the Tango SDK or not.  But I might have asked the wrong place....

To be clear, the Tango SDK and ARCore SDKs are separate platforms. TangoSDK
requires phones with the Tango sensor suite, but ARCore works on regular
phones (currently Pixel and S8 with more coming). Our focus going forward
will be on ARCore, and that's what you'll see in our standard Unreal
integration.
On Tue, Nov 7, 2017 at 1:55 AM, Calence<EMAIL_ADDRESS>wrote:

To my early question , there are two devices(PHAB2 Pro and PHAB2) that
support the Tango SDK, and different from Google ARCore devices (Google
Pixel and so on). But after UE4 integrated Tango SDK, it can support
devices is also Google Pixel, Pixel XL, Samsung, and so on, I want to know
whether is to modify the Tango SDK or not. But I might have asked the wrong
place....
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Yeah, the Unreal Tango plugin is shipped with official Unreal 4.17 so if you are developing Tango platform, you should use that version of Unreal. The official Unreal 4.18 release remove the Tango plugin and added the GoogleARCore plugin so if you are developing ARCore platform, you can use the official Unreal 4.18 release. Google's custom Unreal branch is based on Unreal 4.18 and it only contains the ARCore plugin.

Oh ! I has downloaded  official Unreal 4.18 release, I find it has been changed to GoogleARCore, but why it loads tango_client_api.so library. I guess it may be based on TangoSDK? The pictures are Unreal4_18 ，UE4_18_ARCore_Plugin

Yeah, the dev preview version of Unreal GoogleARCore plugin is based on modified version TangoSDK right now.

Can I use the modified version TangoSDK? I also want to integrate the SDK into our project to achieve ARCore.Because ARCoreSDK is the Java version, it does't have C/C++ version.

Though ARCore is powered by Tango tech, the API is gonna be different. I think you probably should wait for ARCoreSDK the C/C++ API.

Will the Google official release API for the C/C++?Is there any official news?

If you are interested in ARCore then just use 4.18 and we'll keep updating
the integration as more of the platform comes online.
On Nov 7, 2017 8:20 PM, "Calence"<EMAIL_ADDRESS>wrote:

Will the Google official release API for the C/C++?Is there any official
news?
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You are receiving this because you commented.
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Hello,  when UE4 integrated Tango SDK in 4.18 , I don't find libtango_client_api.so,but when I integrate TangoSDK, it shows ‘I/TangoClientLibLoader: Pure Java path, not loading libtango_client_api.so at all.’. Why?
In addition, the log shows
A/tango: jni_helper.cc:19 'vm' Must be non NULL
A/libc: Fatal signal 6 (SIGABRT), code -6 in tid 20637 (GLThread 1549)
I/TangoClientLibLoader: Pure Java path, not loading libtango_client_api.so at all.

Are you trying to use the TangoSDK in UE4 and use that in your own engine? Which phone are you testing on?

Yes, I use Google Pixel XL that Android version is 8.0.0.

The problem solved ， the reason is that threads between threads are not synchronized.


Profile Views Graph: Displaying All Dates Including Zero Views

Fixes Issue
Profile Views Graph: Displaying All Dates Including Zero Views
Edit:
Closes: 8343
Closes #8569
Changes Proposed:
Modified graph rendering to display all dates within the selected time range, even if the profile views for a particular day are zero.
Utilized a headless Combobox component to implement an autocomplete input for rendering existing groups in a user-friendly manner.
Check List (Check all the applicable boxes)
My code follows the code style of this project.
My change requires changes to the documentation. I have updated the documentation accordingly.
All new and existing tests passed.
This PR does not contain plagiarized content.
The title of my pull request is a short description of the requested changes.

Will it merge?

I don't have the write access.
Only those with write access to this repository can merge pull requests.

@nilerudra please see my comment on: https://github.com/EddieHubCommunity/LinkFree/issues/8569
Can you also please update the PRs description so that it reflects what it is addressing please.

@nilerudra please see my comment on: #8569
Can you also please update the PRs description so that it reflects what it is addressing please.

Thank you for your message. I've reviewed your comment on issue #8569. I'll make the necessary updates to the PR's description to accurately reflect the issue it's addressing. I appreciate your guidance and attention to detail.

@nilerudra please see my comment on: #8569
Can you also please update the PRs description so that it reflects what it is addressing please.

@SaraJaoude I've made the necessary updates to the PR's description in accordance with the issue's details.

@nilerudra please see my comment on: #8569
Can you also please update the PRs description so that it reflects what it is addressing please.

@SaraJaoude I've made the necessary updates to the PR's description in accordance with the issue's details.

@nilerudra thank you - but you referenced the wrong issue that this PR fixes, I have now edited this.  Please also make sure that the title to the PR reflects the description rather than just saying addressed as this provides no clue to the contributors or maintainers when looking through the Issue list (I have now also edited this).

@nilerudra please see my comment on: #8569
Can you also please update the PRs description so that it reflects what it is addressing please.

@SaraJaoude I've made the necessary updates to the PR's description in accordance with the issue's details.

@nilerudra thank you - but you referenced the wrong issue that this PR fixes, I have now edited this. Please also make sure that the title to the PR reflects the description rather than just saying addressed as this provides no clue to the contributors or maintainers when looking through the Issue list (I have now also edited this).

I sincerely apologize for it.

Thank you.

What's the issue you have linked?

What's the issue you have linked?

This tag specifies that with this PR, associated issue is linked.

What's the issue you have linked?

This tag specifies that with this PR, associated issue is linked.

What's the issue you have linked?

This tag specifies that with this PR, associated issue is linked.

Thank you.

Thank you for making the changes 👍 I think it is just the date fix then we can merge

Thank you for making the changes 👍 I think it is just the date fix then we can merge

Can you please explain what's the issue?

Thank you for your contribution 👍 I will fix and resolve conflicts via a temporary branch

Thank you for your contribution 👍 I will fix and resolve conflicts via a temporary branch
You're welcome!


Version conflict with imported packages

In https://github.com/aspnet/MvcPrecompilation/pull/49 we discovered that if you try to run a task which uses a conflicting version of packages like CoreFx then the task will crash with errors like System.IO.FileNotFoundException: Could not load file or assembly 'System.Collections.Immutable, Version=<IP_ADDRESS>, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a'. The system cannot find the file specified.
@pranavkm has created a repro app here.

This also happens with Visual Studio VSIX projects that use
    Public cache As New WeakReference(Of ImmutableDictionary(Of SyntaxTree, Boolean))(ImmutableDictionary(Of SyntaxTree, Boolean).Empty)

@ryanbrandenburg did you find any workaround? It is always that exact error.

@paul1956 we did not dig in to this issue further. For precompilation, we went with an alternate route and spawned a new dotnet process (via Exec).

Fixed by #4916


Don't notify owner again if it has a delegate set

Owners were notified again if a delegate was set due to a typo

Related to #1725

Coverage remained the same at 88.133% when pulling eae2cb85f4a5c59978b4364f0e927ab8561d83dc on fix-notifying-owner-again into 5a7149aaccb2a35fa294f2fb8d20b2f6bd4f3e89 on master.


Enable status bar to show last pressed keyboard shortcut?

Just an idea.

Not going to be implemented.


Make any application launch window on the screen containing the mouse cursor

Description of the new feature / enhancement
title says it all.
works this way in gnome-shell.
lets make it work this way in windows too.
Scenario when this would be used?
every scenario you can think of. question is irrelevant.
Supporting information
No response

Thanks for sharing. I'm going to link this to an existing issue that I think more or less is asking for the same type of feature to better track.
Lmk if you disagree with my grouping.

/dup #6885


Typo

The branch on line 367 was handling a quirk of my printer, maybe others too where "//action:resume" was truncated to just "ction:resume".  This seemed to happen when printer was fully preheated prior to SD card print being started.  The branch on line 359 handles the regular "//action:resume"
https://github.com/mulcmu/esphome-marlin-uart/blob/527486af7d94756abe7f7ef56df65c60100e166f/esphome-marlin-uart.h#L358-L372


fix: last_seq lost if no changes

If there are no new changes given the request params, return lastSeq.
This replicates PouchDB changes feed behaviour.
Ref #65

just published 6.2.4, thanks for contribution


bioc submisson

To do list for the Bioconductor submission

[x] Fix build (final warning is related to not requiring R >= 4.0)
[x] Incorporate more SingleCellExperiment integration. More tests, examples, and clearer documentation. Perhaps change option seurat_out to return_object to make it clear that SingleCellExperiment objects can be passed in and out.

Warnings:

[x] Update R dependency to 4.0 (probably do last) (see warnings https://bioconductor.org/spb_reports/clustifyr_buildreport_20191127165143.html)

Notes:

[x] NOTE: Avoid sapply(); use vapply() [Rui]
[x] NOTE: Avoid 1:...; use seq_len() or seq_along() [Rui]
[x] NOTE: Consider multiples of 4 spaces for line indents, 2591 [Kent]
lines(31%) are not.
First 6 lines:
R/common_dplyr.R:29   correlation_matrix <- cor_mat
R/common_dplyr.R:30   if (threshold == "auto") {
R/common_dplyr.R:33   }
R/common_dplyr.R:34   correlation_matrix[is.na(correlation_matrix)] <- 0
R/common_dplyr.R:35   df_temp <-
R/common_dplyr.R:37   df_temp <- tidyr::gather(
See http://bioconductor.org/developers/how-to/coding-style/
See FormatR package:
https://cran.r-project.org/web/packages/formatR/index.html

Other:

[x] Add news [Rui]
[x] clean up inst directory, more manuscript to clustifyrdata [Kent]
[x] Clean up git .pack objects to smaller size [Kent]
[x] Add biorxiv to citation in inst/CITATION [Kent]
[x] Change vignette style to Bioc [Kent]
[x] Update install instructions and figure out best way to host a non-breaking version  [Kent]
[x] Fix requested notes  [Rui]
[x] Use MatrixStats instead of apply, if possible  [Rui and Kent]
[x] Change 2 spaces to 4, fix line lengths. [Kent]
[x] Deprecate seurat_out. [Rui]
[x] document how to generate inst/extdat/c2.cp.reactome.v6.2.symbols.gmt in inst/scripts

for 2, actually option obj_out is available and interchangeable with seurat_out
but I agree SCE should be mentioned on the main page and tutorial

the 4 spaces for indents Note is still present, but it is likely due to function arguments having indents longer than 4 spaces.

Fixed the warning about objects > 5Mb
git clone https://github.com/rnabioco/clustifyr.git
cd clustifyr
R

> BiocCheck::BiocCheck()
This is BiocCheck version 1.20.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking version number validity...
    Package version 0.99.3; pre-release
* Checking R Version dependency...
* Checking package size...
        Skipped... only checked on source tarball
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking vignette directory...
    This is a software package
* Checking library calls...
* Checking for library/require of clustifyr...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.........................................................
    * NOTE: Recommended function length <= 50 lines.
      There are 26 functions > 50 lines.
      The longest 5 functions are:
        plot_dims() (v9/tmp/clustifyr/R/plot.R, line 27): 187 lines
        clustify.default() (v9/tmp/clustifyr/R/main.R, line 80): 166
      lines
        clustify_lists.default() (v9/tmp/clustifyr/R/main.R, line 545):
      145 lines
        clustify_nudge.default() (v9/tmp/clustifyr/R/utils.R, line
      752): 129 lines
        compare_lists() (v9/tmp/clustifyr/R/compare_genelist.R, line
      192): 118 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      call_to_metadata.Rd, clustifyr_methods.Rd, insert_meta_object.Rd,
  seurat_meta.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      4% of man pages use one of these cases.
      Found in the following files:
        call_to_metadata.Rd
        insert_meta_object.Rd
        seurat_meta.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 299 lines (3%) are > 80 characters
      long.
    First 6 lines:
      v9/tmp/clustifyr/R/common_dplyr.R:70             dplyr::distinct_at(df_...
      v9/tmp/clustifyr/R/common_dplyr.R:174         if (!(all(unique(df_temp[...
      v9/tmp/clustifyr/R/common_dplyr.R:176                 "cluster_col from...
      v9/tmp/clustifyr/R/common_dplyr.R:256         dplyr::group_by(df_temp_f...
      v9/tmp/clustifyr/R/common_dplyr.R:267         dplyr::filter(df_temp_ful...
      v9/tmp/clustifyr/R/common_dplyr.R:279 #' @param collapse_to_cluster if ...
    * NOTE: Consider multiples of 4 spaces for line indents, 860
      lines(10%) are not.
    First 6 lines:
      v9/tmp/clustifyr/R/common_dplyr.R:144                              meta...
      v9/tmp/clustifyr/R/common_dplyr.R:145                              clus...
      v9/tmp/clustifyr/R/common_dplyr.R:146                              per_...
      v9/tmp/clustifyr/R/common_dplyr.R:147                              rena...
      v9/tmp/clustifyr/R/common_dplyr.R:295                              meta...
      v9/tmp/clustifyr/R/common_dplyr.R:296                              clus...
    See http://bioconductor.org/developers/how-to/coding-style/
    See FormatR package:
      https://cran.r-project.org/web/packages/formatR/index.html
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      bioc-devel mailing list (requires admin credentials).  Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.

Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.9/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
$error
character(0)

$warning
character(0)

$note
[1] "Recommended function length <= 50 lines."
[2] "Consider adding runnable examples to the following man pages which document exported objects:"
[3] "Usage of dontrun{} / donttest{} found in man page examples."
[4] "Consider shorter lines; 299 lines (3%) are > 80 characters long."
[5] "Consider multiples of 4 spaces for line indents, 860 lines(10%) are not."
[6] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials).  Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"

Closing and will file a new issue when revisions are requested.


fail-support in YAML-recipes

With fail one can specify which task should run on failure of a specific task, e.g.
https://github.com/deployphp/deployer/blob/ff3c33c0a47723378a5af4ee615f3466018dec93/recipe/common.php#L167-L169
When using the deploy-task there is already a fail-task defined deploy:failed, but when creating own tasks in YAML there is currently no way to execute something if a task failed. Therefore it would be good to have the fail-function also available in YAML.

Isn't it just simply
after:
    deploy:failed: deploy:unlock

Isn't it just simply
after:
    deploy:failed: deploy:unlock

untested - maybe before should be used 🤔

As said: When using the deploy-task there is already a fail-task defined deploy:failed, but when creating own tasks in YAML there is currently no way to execute something if a task failed.


Feature: Remove the Feed box from the home page

One of the suggestions I got a while back; pretty easy to implement and good to have the option, even if most won't use it.

I can take on this one


chore: initial redirects setup

👷 Deploy Preview for theonedev processing.

Name
Link

🔨 Latest commit
a82538addcdbd1c429b8954d8caf1efbd7cc1713

🔍 Latest deploy log
https://app.netlify.com/sites/theonedev/deploys/63b92d884a73ee0008e00e2f


links with two versions of clap

atomic-cli uses clap v2.33.3 and atomic-server uses clap v3.0.0-rc.3.
I guess there's at least a size benefit, but likely also a quality improvement, in modernizing both to use v3.0.0 (which allows to link against newest v3.1.6 for both).

Hmm, looks like I updated clap about one month ago.  I guess you were looking at the latest tagged release, not the main branch?
https://github.com/joepio/atomic-data-rust/commit/0800e340b56d14b3cecaa035a456a86ccca83b5c

Quoting Joep Meindertsma (2022-03-28 21:43:14)

Hmm, looks like I updated clap about one month ago.  I guess you were looking at the latest tagged release, not the main branch?
https://github.com/joepio/atomic-data-rust/commit/0800e340b56d14b3cecaa035a456a86ccca83b5c

Oh, indeed.  Sorry if I wasted your time.  Would it perhaps make sense to issue tagged releases more frequently?

no worries!
Yeah, I should make it a more common process. I've set up most of the CI specifically to make it easy to publish a new version. Let's do it right now 💯


Too slow, takes awhile to ssee the fist video

Describe the bug
I tried the extension but unfortunately, it's not as fast as I wanted to be.
Worst of all, depending of the channel's amount of videos, it can take forever just to find that channel's first video from the channel's videos section.
Also, on unrelated note, it would be nice to add support for not only the shorts section but also the live section as well.
Version
Chrome Extension

Hi, unfortunately there is nothing I can do about this. This extension does not bring back the full functionality of the original sort by oldest. All it does is invert the videos, thus it needs time to load all of them. At this time this is the best I can do since I cannot access the API oldest function.
As for the support for live section, you should be able to see it as support was added for it in 1.4.0


Abort 3dtiles

How can I make a tileset by my own collada(*.dae)?

You can use the COLLADA2GLTF converter. Once you have glTF models you can create b3dm tiles. Then you just need to create a tileset.json file that describes the positioning and hierarhcy of the models.
The 3D Tiles Spec is the best place to start for learning about the format.

Thanks,lilleyse! Let me try！

Hi,lilleyse!Could you tell me how can I create b3dm tiles by glTF models? Thanks!

The models need to be in binary glTF format. Then the code looks similar to https://github.com/AnalyticalGraphicsInc/3d-tiles-tools/blob/master/generator/lib/createB3dm.js.
Additionally there's a glbToB3dm tool in 3d-tiles-tools.


4.9.0-beta release is missing lib folder

Bug Report
<EMAIL_ADDRESS>It looks like the lib folder is missing?
After installing I see this error in VS Code:

Investigating!

Today we learned that npm 8 supports ./ as a leading path component when specifying a directory in the package.json's files array, but not npm 6.

549b5429d4837344e8c99657109bb6538fd2dbb5 fixes it, #50930 fixes it for future releases.

Why is Ryan's comment being 👎🏼'd given that the the fix in #50930 aligns with it?  Is there something I'm missing...?

We have nothing wrong with what Ryan said, we are just mad about the root cause. 😅

The 👎 is coming from inside the house (my own account)

4.9.1-beta is the new version. 😩


Force sync does not update textarea valid/invalid status

I'm submitting a...

[x] Bug report
[ ] Feature request

Reproduction steps
https://jsfiddle.net/hv352zf8/
Notice that in the example if you remove the inscrybmde the CSS changes the button color. However, if you set a markdown editor on the textarea, even with forceSync as shown in the readme, the button text does not update.
Version information
Browser type and version: Firefox 62.0a1
SimpleMDE version: 1.11.3

Will have to find time to look into this one unless you have time to do a PR

Will have to find time to look into this one unless you have time to do a PR

Normally I'd love to help, but I'm afraid that I've spent my entire career avoiding front end work (and JavaScript in particular) at all costs and have no idea how any of this works :)

I understand. I will try and find time to look into it more.

After codemirror is active the sourcecode looks like this:

and therefore your CSS selector "textarea:valid+button" won't match.


Extended YouTube video ID extraction

I added support for attribution_link forms of YouTube links and embed links to the strip_video_id_from_url() function. I also fixed a bug in the earlier version around a missing import for urllib

Need to check why this failed, I am going to merge. Sorry for the delay


Strange FS behavior after load .pck file

Godot version:
3.1.alpha.calinou.1ff772b
OS/device including version:
Win 8.1
Issue description:
Code:
extends Node2D

func _ready():
	dir_contents()
	print('-- LOADING PACKAGE --')
	# Small .pck with one scene (Node2D.tscn)
	ProjectSettings.load_resource_pack('nf.pck')
	dir_contents()

func dir_contents(path = "res://"):
	var dir = Directory.new()
	if dir.open(path) == OK:
		dir.list_dir_begin(true, true)
		var file_name = dir.get_next()
		while (file_name != ""):
			if dir.current_is_dir():
				print(dir.get_current_dir() + file_name + "/")
			else:
				print(dir.get_current_dir() + file_name)
			file_name = dir.get_next()
	else:
		print("An error occurred when trying to access the path.")

Output:
res://.import/
res://default_env.tres
res://export_presets.cfg
res://icon.png
res://icon.png.import
res://main.tscn
res://nf.pck
res://Node2D.gd
res://project.godot
-- LOADING PACKAGE --
res://.import/
res://Node2D.tscn
res://icon.png
res://icon.png.import
res://project.binary

It is normal that the structure changes after loading .pck file?
Minimal reproduction project:
dlc.zip

And if that's OK, then how can I find out about the files that have been added from the downloaded .pck file?

I was having the same issue, and also found a workaround. See #19815.
In short:

The first load replaces all the files.
Subsequent loads add files to the current list, replacing any current ones.

Was this closed for being a dupe of #19815?

@raymoo I would assume so. The two at a glance, seem to describe the same issue, though admittedly it's been nearly a year since I made #19815, so I don't remember if I thought of this as a duplicate when making my comment above.

Ahm... Yeah.


[BUG] OMBI 2022-03-14 16:54:32 : ERROR : ombi : TypeError has occurred : () got an unexpected keyword argument 'is4kRequest' while creating OmbiMovieRequest structure for movie. data attempted is

Describe the bug
2022-03-14 16:54:32 : ERROR : ombi : TypeError has occurred : () got an unexpected keyword argument 'is4kRequest' while creating OmbiMovieRequest structure for movie. data attempted is
Varken Docker Image: boerderij/varken:latest_2201.0.0
Ombi V4.14.3

see #237

I noticed this issue today as well, any update on when the above PR will be merged?

I noticed this issue today as well, any update on when the above PR will be merged?

id like to know also. feels almost like the project has given up? id happily keep it going if they wanted

#238

When do you think develop will be merged to master and this released to dockerhub?

When do you think develop will be merged to master and this released to dockerhub?

Just run the develop branch. Not had any major issues with it. Certainly not any breaking ones

When do you think develop will be merged to master and this released to dockerhub?

I will be doing one more release before moving to 2.0 (which will support influx 2.0). As @MDHMatt stated. Use develop for now until master is updated. Hopefully within the next few weeks.


How can I modify Training and loss forces of my system specially Li atoms in my LGPO system?

Dear all,
I have recently Used Nequip-Allegro Framework to retrain DFT data in the LGPO systems. I have used 30000 configurations for retraining DFT data.By using the ASE calculator  generated ML forces to compare the forces with DFT forces .Unfortunately the Loss of forces did not improve at all. I have changed rcutoff  from 5 to 7 and 14.I have Changed Max epoch from 100 to 200. I have changed  batch_size  from 1 to 4 and 6 .  I have changed different splits (80-20 and 70-30) for training and validations.I have checked Whether to shuffle the training data or not. I have checked Themathematical expression for the overall LOSS and changed the force loss  coefficient of 1.0 to 100. . I have checked different seeds to have different training and validation sets. I have checked different lmax=1 and 2.
I tried to do anything to modify ML forces (loss_f,loss_e and loss) specially for Li atoms.
The total loss still remains near 23 and loss_f is near 0.23  with the force coefficient of 100. and the total loss can be modified to 0.23 with the force coefficient of 1. and loss_f is  still unchanged and near 0.23  .However,these improvements seem not successful and still large.
Do you have any new ideas to help me improve forces and overall results?
Name	Epoch	wal (hours)	   LR	     loss_f	    loss_e	     loss	     f_mae	   f_rmse	   e_mae	    e/N_mae
Train	200	      9.969141667	0.002   0.23	   0.0368	     23.0	     0.213	    0.485	    0.867	       0.0173
Validation 200       9.969141667	 0.002   0.204	   0.000193   20.4	     0.200	    0.456	     0.699	         0.014

No suggestion for  addressing my issue???

From my personal experience, keeping batch size small like 1 or 4 is good practice in this framework and I have seen increasing batch size decreasing the performance. I would suggest keeping l_max = 2 or 3 as more angular resolution provides better accuracy.
You may then try tuning the architecture by
increasing num_layers: 2, 4;
increasing num_tensor_features: 32, 64 and also adjusting two_body_latent_mlp_latent_dimensions and latent_mlp_latent_dimensions accordingly; This will provide more channels.
adjusting learning_rate: 0.005, 0.001;
Hope this can help!

Dear David,
I will check all of them and let all  know the outcome.
Thanks a lot,
Best Regards,
Elham

From my personal experience, keeping batch size small like 1 or 4 is good practice in this framework and I have seen increasing batch size decreasing the performance. I would suggest keeping l_max = 2 or 3 as more angular resolution provides better accuracy.
You may then try tuning the architecture by increasing num_layers: 2, 4; increasing num_tensor_features: 32, 64 and also adjusting two_body_latent_mlp_latent_dimensions and latent_mlp_latent_dimensions accordingly; This will provide more channels. adjusting learning_rate: 0.005, 0.001;
Hope this can help!

Dear David,
I have a problem due to the time limitation of my system.It is 2 days and after that, the  server will stop our job.
For example I could only calculate 80 epochs of 200 after 2 days. Is there any way to start the job from where it left off??? To start from 81 epochs for example?
Thanks for your time,
Elham

Hi Elham,
Thanks for your question! Allegro will restart from the best model saved from the previous run when you keep the same run_name in your config file. In your case, the best model should be result at the 80th epoch as I assume the loss has not plateaued yet. You can also set append: true as in the example.yaml so the log will be appended.

Dear David,
Thanks for your guidance and your time.