Add Best Practices for a Secure Supply Chain

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@Mikejo5000 Thank you so much for the last minute review. It's very appreciated!

My general recommendation here is to:

focus on package consumers and move package publisher recommendations to a different doc, or at least split the recommendations to two parts.
Provide additional justifications/explanation to the recommendations. Why is lock files useful? Why you should update dependencies frequently? I'm sure a lot of content can be taken from blog posts where we introduced security features.

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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: https://docs.microsoft.com/azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: https://docs.microsoft.com/azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: https://docs.microsoft.com/azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Docs Build status updates of commit 53daa60:
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Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 122, Column 23: [Warning-file-not-found] Invalid file link: '../consume-packages/package-references-in-project-files'.
Line 71, Column 138: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /visualstudio/ide/solutions-and-projects-in-visual-studio?view=vs-2019#solution-explorer. Otherwise, remove the view parameter.
Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Line 122, Column 23: [Warning-file-not-found] Invalid file link: '../consume-packages/package-references-in-project-files'.
Line 71, Column 138: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /visualstudio/ide/solutions-and-projects-in-visual-studio?view=vs-2019#solution-explorer. Otherwise, remove the view parameter.
Line 110, Column 48: [Suggestion-preserve-view-not-set] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /azure/devops/artifacts/concepts/upstream-sources?view=azure-devops. Otherwise, remove the view parameter.

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Bump to get this out. @DoRonMotter @skofman1 @anangaur @aortiz-msft please review at your convenience.


Nuxt Islands can't render

Reproduction: https://stackblitz.com/edit/nuxt-starter-cmr8kq?file=pnpm-lock.yaml
Most likely a Nuxt Islands limitation but issue here for tracking

Do you have any idea what can go wrong with the component?

I'm not sure if it is related, but I'm getting type errors again with the size property:

This actually seems to be working correctly now, closing.


sysbuild: Out Of Tree Board Fails with Sysbuild

Describe the bug
Project fails to build using Sysbuild with an out of tree board.
This issue was posted and closed in #59114 and #59130
Please also mention any information which could help others to understand
the problem you're facing:

This issue was posted and closed in #59114 and #59130, but now I am facing it again.
Issue can be bypassed if I copy the custom board to `zephyr/boards/[arm]/ direcotry.
Issue occurs only when building with sysbuild. Without --sysbuild it works just fine.

To Reproduce
Steps to reproduce the behavior:

git checkout main in zephyrproject/zephyr directory
Go to boards/st copy and paste nucleo_h743zi to samples/hello_world, and then delete it from boards/st to force custom board compilation
Go to samples/hello_world
Run west build -b nucleo_h743zi -p always --no-sysbuild ./ -- -DSB_CONFIG_BOOTLOADER_MCUBOOT=y -DBOARD_ROOT=./
See that it compiles. Yay!
Run west build -b nucleo_h743zi -p always --sysbuild ./ -- -DSB_CONFIG_BOOTLOADER_MCUBOOT=y -DBOARD_ROOT=./
See error

If there is a nucleo_h743zi in boards/st though, the step 6 will compile.

Expected behavior
It should compile!
Impact

This prevents mcuboot and application from being built using sysbuild without copying the custom board contents to the zephyr directory.
If you are developing an open-source application using zephyr and the user wants to use your software, it is really disturbing to tell them to copy the board directory to some zephyr directory. I also find it not clean to tamper with the zephyr's repository files. Also, the CI will be not clean.
A lot of time wasted trying and researching how to fix this on my own.
Feeling that the code is not clean, if not resolved, when using sysbuild.

Logs and console output
(.venv) vic@Super-ThinkPad-X1-Carbon-6th:~/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world$ west build -b nucleo_h743zi -p always --sysbuild ./ -- -DSB_CONFIG_BOOTLOADER_MCUBOOT=y -DBOARD_ROOT=./
-- west build: making build dir /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world/build pristine
-- west build: generating a build system
Loading Zephyr module(s) (Zephyr base): extensions sysbuild_extensions python west root zephyr_module boards shields hwm_v2 sysbuild_kconfig native_simulator_sb_extensions
-- Found Python3: /usr/bin/python3 (found suitable version "3.12.3", minimum required is "3.8") found components: Interpreter
-- Cache files will be written to: /home/vic/.cache/zephyr
-- Found west (found suitable version "1.2.0", minimum required is "0.14.0")
CMake Warning at /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/cmake/modules/boards.cmake:136 (message):
  BOARD_ROOT element without a 'boards' subdirectory:

  /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/share/sysbuild/./

  Hints:

    - if your board directory is '/foo/bar/boards/<ARCH>/my_board' then add '/foo/bar' to BOARD_ROOT, not the entire board directory
    - if in doubt, use absolute paths
Call Stack (most recent call first):
  /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/share/zephyr-package/cmake/ZephyrConfig.cmake:75 (include)
  /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/share/zephyr-package/cmake/ZephyrConfig.cmake:92 (include_boilerplate)
  CMakeLists.txt:26 (find_package)

No board named 'nucleo_h743zi' found.

Please choose one of the following boards:

.
.
.
segger_trb_stm32f407
esp32s2_franzininho
warp7
scobc_module1
CMake Error at /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/cmake/modules/boards.cmake:244 (message):
  Invalid BOARD; see above.
Call Stack (most recent call first):
  /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/share/zephyr-package/cmake/ZephyrConfig.cmake:75 (include)
  /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/share/zephyr-package/cmake/ZephyrConfig.cmake:92 (include_boilerplate)
  CMakeLists.txt:26 (find_package)

-- Configuring incomplete, errors occurred!
FATAL ERROR: command exited with status 1: /usr/bin/cmake -DWEST_PYTHON=/usr/bin/python3 -B/home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world/build -GNinja -DBOARD=nucleo_h743zi -DSB_CONFIG_BOOTLOADER_MCUBOOT=y -DBOARD_ROOT=./ -S/home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/share/sysbuild -DAPP_DIR:PATH=/home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world

While with --no-sysbuild
(.venv) vic@Super-ThinkPad-X1-Carbon-6th:~/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world$ west build -b nucleo_h743zi -p always --no-sysbuild ./ -- -DSB_CONFIG_BOOTLOADER_MCUBOOT=y -DBOARD_ROOT=./
-- west build: making build dir /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world/build pristine
-- west build: generating a build system
Loading Zephyr default modules (Zephyr base).
-- Application: /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world
-- CMake version: 3.28.3
-- Found Python3: /usr/bin/python3 (found suitable version "3.12.3", minimum required is "3.8") found components: Interpreter
-- Cache files will be written to: /home/vic/.cache/zephyr
-- Zephyr version: 3.6.99 (/home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr)
-- Found west (found suitable version "1.2.0", minimum required is "0.14.0")
-- Board: nucleo_h743zi, qualifiers: stm32h743xx
-- ZEPHYR_TOOLCHAIN_VARIANT not set, trying to locate Zephyr SDK
-- Found host-tools: zephyr 0.16.1 (/home/vic/zephyr-sdk-0.16.1)
-- Found toolchain: zephyr 0.16.1 (/home/vic/zephyr-sdk-0.16.1)
-- Found Dtc: /home/vic/zephyr-sdk-0.16.1/sysroots/x86_64-pokysdk-linux/usr/bin/dtc (found suitable version "1.6.0", minimum required is "1.4.6")
-- Found BOARD.dts: /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world/boards/arm/nucleo_h743zi/nucleo_h743zi.dts
.
.
.
Generating files from /home/vic/zephyr-sdk-0.16.1/zephyrproject/zephyr/samples/hello_world/build/zephyr/zephyr.elf for board: nucleo_h743zi

Environment (please complete the following information):

OS: Linux Ubuntu 24.04 LTS
Toolchain: Zephyr SDK 0.16.1
Zephyr <IP_ADDRESS>

duplicate of https://github.com/zephyrproject-rtos/zephyr/issues/73066
Please note, using absolute paths works.
Only relative paths are failing.

Fixed here: #73390


tiltfile: use sh instead of bash to make Cmd

The reason being that a lot of barebones images don't have bash, they only have `sh.


Open Time

May I ask when you will open source code and data?

Thanks for your interest. We will release the code and models shortly (hopefully within next week).


How could I append ModellingRule into the OPC UA Server Object?

Recompiling is unique way?
So where are the ModelDesign XML reference?

See:
https://github.com/OPCFoundation/UA-ModelCompiler/blob/master/ModelCompiler/UA Model Design.xsd


Teach AST verifier about thrown error contexts

The AST verifier was only correctly extracting thrown error types from
enclosing functions, without account for do...catch bodies. Switch it
over to using ASTScope's lookup to find the innermost enclosing caught
error context.
Fixes a AST verifier error reported by Paul Cantrell

@swift-ci please smoke test

@swift-ci please build toolchain

ARGH

@swift-ci please smoke test

@swift-ci please build toolchain


Add notminus1 annotation

Many API's specifically return -1 on failure (not just a negative number).

Subsumed by #55


Episode: Icebreakers

On Day 2, if there is time, add an episode on icebreakers, could be used already in beginning to "break the ice"
Or merged with collaborative notes.

Check also #95  :)

Sorry I should have coordinated this but didn't see this suggestion.

Na, it's fine, there is so much in Session 2 already!
I'll check for session 3 :)

Also no time in session 3, lets leave it out for now, but still collect all the cool icebreaker ideas in #95


added card to show who is on-call for the team

Pardon my rusty frontend skills :P

@K-Phoen can you please review?

@K-Phoen do you have any plans to review this?

Hey all!
Finally took the time to review this PR and play with it. I fixed a few little things, just waiting for the CI to be green and I'll merge this.
Thanks for the PR :)

Closes https://github.com/K-Phoen/backstage-plugin-opsgenie/issues/69

Thank you so much @K-Phoen


The entity's status don't change whit APP

hi,
When i change status via mobile app, in my HA this don't change. I must refresh the integration so status and options update.

update: the sensor values don't even update, since I turned on the air conditioner and from HA I still see 19° as the temperature in the room, while the app (and the external thermometer I have in the room) shows 23°

Hello, i have exactly the same problem here!

Yes same here with my Washingmaschine

Yeah same here, I have to reload the integration for anything to update

I have the same issue with a dishwasher

Same here, since i've had this integration, the sensors haven't been updating regularly or at all

Yes, same problem here.
The debug log in HA shows no errors and the hon integration seems to receive "updates" via mqtt. But no entity has been updated in HA.
2024-10-16 17:36:24.352 DEBUG (Dummy-57) [custom_components.hon] Manually updated hon data
2024-10-16 17:36:24.352 INFO (Dummy-57) [pyhon.connection.mqtt] haier/things/xx-xx-xx-xx-xx-xx/event/appliancestatus/update - {'parameters': [{'parName': 'currentElectricityUsed', 'parOldVal': '0.72', 'parNewVal': '0.75'}, {'parName': 'remainingTimeMM', 'parOldVal': '48', 'parNewVal': '47'}, {'parName': 'remainingMainWashTime', 'parOldVal': '15', 'parNewVal': '14'}, {'parName': 'totalElectricityUsed', 'parOldVal': '1.84', 'parNewVal': '1.87'}], 'macAddress': 'xx-xx-xx-xx-xx-xx', 'applianceTypeName': 'WM', 'eventId': '63', 'timestamp': '2024-10-16T15:36:24.1Z', 'transactionId': 'xx-xx-xx-xx-xx-xx_2024-10-16T15:36:24.1Z'}
2024-10-16 17:36:24.355 DEBUG (Dummy-57) [custom_components.hon] Manually updated hon data
2024-10-16 17:36:24.360 WARNING (Dummy-57) [homeassistant.helpers.frame] Detected that custom integration 'hon' calls async_write_ha_state from a thread other than the event loop, which may cause Home Assistant to crash or data to corrupt. For more information, see https://developers.home-assistant.io/docs/asyncio_thread_safety/#async_write_ha_state at custom_components/hon/sensor.py, line 849: self.async_write_ha_state(), please report it to the author of the 'hon' custom integration
2024-10-16 17:36:24.361 DEBUG (Dummy-5) [custom_components.hon] Manually updated hon data
2024-10-16 17:36:24.361 INFO (Dummy-5) [pyhon.connection.mqtt] haier/things/xx-xx-xx-xx-xx-xx/event/appliancestatus/update - {'parameters': [{'parName': 'currentElectricityUsed', 'parOldVal': '0.72', 'parNewVal': '0.75'}, {'parName': 'remainingTimeMM', 'parOldVal': '48', 'parNewVal': '47'}, {'parName': 'remainingMainWashTime', 'parOldVal': '15', 'parNewVal': '14'}, {'parName': 'totalElectricityUsed', 'parOldVal': '1.84', 'parNewVal': '1.87'}], 'macAddress': 'xx-xx-xx-xx-xx-xx', 'applianceTypeName': 'WM', 'eventId': '63', 'timestamp': '2024-10-16T15:36:24.1Z', 'transactionId': 'xx-xx-xx-xx-xx-xx_2024-10-16T15:36:24.1Z'}
2024-10-16 17:36:24.470 DEBUG (Dummy-7) [custom_components.hon] Manually updated hon data
2024-10-16 17:36:24.470 INFO (Dummy-7) [pyhon.connection.mqtt] haier/things/xx-xx-xx-xx-xx-xx/event/appliancestatus/update - {'parameters': [{'parName': 'currentElectricityUsed', 'parOldVal': '0.72', 'parNewVal': '0.75'}, {'parName': 'remainingTimeMM', 'parOldVal': '48', 'parNewVal': '47'}, {'parName': 'remainingMainWashTime', 'parOldVal': '15', 'parNewVal': '14'}, {'parName': 'totalElectricityUsed', 'parOldVal': '1.84', 'parNewVal': '1.87'}], 'macAddress': 'xx-xx-xx-xx-xx-xx', 'applianceTypeName': 'WM', 'eventId': '63', 'timestamp': '2024-10-16T15:36:24.1Z', 'transactionId': 'xx-xx-xx-xx-xx-xx_2024-10-16T15:36:24.1Z'}

Same here, not updating

Hello
Not wanting to undermine the great work already done with this project - however is it now dead, as this has been reported without any kind of notifcation that its even being looked into,
Again - I totally understand life ect and this is a side project - however at the moment alot of people are left without HA updating with currect and correct values from their devices.
Thanks

@c7homas I think the problem is that Andre0512 got in a legal debate with HON as this addon goes against their TNC. So I think it's unlikely that the project will be revived.

Sad news, if its true.
I've switched over to https://github.com/gvigroux/hon, which is a different but simular project. And for me and my washing machine, it is working.

On the recommendationof danielk117, I have switched to https://github.com/gvigroux/hon and all is working, unfortunatley slightly reduced functionality but more than enought to make it worth it. This can be found as an intergration is HA, it shows with alot less downloads. All entities updaing with my dishwasher.

I used that too but it kept logging me out on the official hOn app and forcing me to do first time setup stuff again and again. Although this could just be because of the horrible app itself but I haven't had it after I stopped using it

check https://github.com/Andre0512/hon/issues/269


WithDockerfile() does not build the Dockerfile hence a container cannot be created.

Describe the issue or suggestion
I would like to see the docker build logs when a WithDockerfile() method is used. Currently, I always get an error as follows and cannot solve my problem.
Unable to find image 'redis-image-db61fbc162c74c1d7fcb3344f69e92b5c3063bf2:latest' locally\nError response from daemon: pull access denied for redis-image-db61fbc162c74c1d7fcb3344f69e92b5c3063bf2, repository does not exist or may require 'docker login': denied: requested access to the resource is denied\n'"}

This is how I try to create the Redis container
IResourceBuilder<RedisResource> redis = builder
    .AddRedis("redis")
    .WithDockerfile("redis")
    .WithEndpoint("tcp", endpoint =>
    {
        endpoint.Port = 6379;
        endpoint.TargetPort = 6379;
    });

Below is the structure of my redis folder

And here is my Dockerfile content
FROM redis

COPY redis.conf /usr/local/etc/redis/redis.conf
CMD [ "redis-server", "/usr/local/etc/redis/redis.conf" ]

I had a similar problem. It turned out that while I updated all the aspire libraries in my solution to 8.1.0, I hadn't updated the workload.
dotnet workload update
dotnet workload install aspire

And restarted my IDE. That fixed it for me.

Yes, I was missing the update for the aspire workload. Thanks!


Weblab as backend for a Jupiter book.

It is possible to use a jupyter hub to launch notebooks being part of a jupyter book. At the moment I am not sure what needs to be done.

See Ryan's book and especially the ocean.pangeo.io links for inspiration.

On Weblab, it works out of the box. Use the link generator here https://jupyterhub.github.io/nbgitpuller/link.html https://jupyterhub.github.io/nbgitpuller/link.html to nbgitpull the materials. Link:
https://WEBLAB-URL/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fgeomar-tm%2Fpython-intro-201804&urlpath=lab%2Ftree%2Fpython-intro-201804%2Fsession-01_part-01_intro_to_python.ipynb

Correction (Didn't see your comment.): Doesn't work out of the box.

nbgitpuller was already installed on weblab, however the server extension needed to be enabled (jupyter is too old on weblab):
jupyter serverextension enable nbgitpuller --sys-prefix

After enabling the server extension, weblab now works as an backend for jupyter books.


OCPBUGS-12607: Bump x/net package to v0.9.0

Bump golang.org/x/net package to the latest version.

Duplicate PR to #48. Closing this.


Generate #UD exception for unsupported instructions which cause vm-exits

Generate #UD exception for unsupported instructions which cause vm-exits, instead of terminating the guest.

In what scenario do this happen?

When some application calls GETSEC, INVD, VMCALL, VMCLEAR, VMLAUNCH, VMPTRLD, VMPTRST, VMREAD, VMRESUME, VMWRITE, VMXOFF, VMXON or XSETBV instruction.
See Intel SDM 3c 25.1.2 Instructions That Cause VM Exits Unconditionally. VMREAD and VMWRITE cause vm-exits conditionally and these conditions are met in hax.

Yes technically it's absolute correct, SDM is the bible. What I'm concern is a "real" test case.
As you know the #1 client of HAXM is Android Emulator, and with the help of many enthusiastic experts like you, HAXM can support other host and guest OS. However since it's still a SW product, we'll need the actual scenario and related test cases when some new feature added, similarly a detailed reproducing step is required if it's a bug. Then when we change the code, our full cycle test could cover the change, if missing, we expand the test coverage, to try our best avoid any possible regression.
Back to this PR, do you have an existing test that may cover this?

I started a Windows 7 guest, then manually ran an application which calls some of these instructions and observed the application crash on #ud exception (before this patch the result was VM crash). The tests should do the same - wait till OS loads, then simply call these instructions. Since they result in an #ud exception, there is no need to worry about they arguments correctness. For example a test only runs a vmcall instruction and checks that it received #ud exception and the virtual machine is still working and didn't crash. I have code snippets of the tests for Visual Studio and Windows.

Interesting. Sounds like you are testing some nested virtualization stuff. We tested Windows 7 before but it's not covered in regular full test. You have tested you patch and it resolves the issue you met right? Seems VMX_EXIT_VMREAD&VMX_EXIT_VMWRITE shouldn't be there.


Make Pricegroup Combobox required if pricegroup checkbox active

Hello,
thank you for creating this pull request.
I have opened an issue on our Issue Tracker for you. See the issue link: https://issues.shopware.com/#/issues/SW-14595.
Please use this issue to track the state of your pull request.

Is already merged https://github.com/shopware/shopware/commit/6e4879f2edbbd2b10af54b715c460efb46c7e65a


System.ComponentModel.Win32Exception (2): No such file or directory

Running the cmd on Linux threw this errors.
docker run -v /var/run/docker.sock:/var/run/docker.sock
-v /ABSOLUTE/PATH/TO/MODELS:ABSOLUTE/PATH/TO/MODELS
-v /ABSOLUTE/PATH/TO/EXPORT/DIRECTORY:/results --net=host
nvcr.io/nvidia/clara/model-analyzer:ANALYZER-VERSION
--batch BATCH-SIZES
--concurrency CONCURRENCY-VALUES
--model-names MODEL-NAMES
--triton-version TRITON-VERSION
--model-folder /ABSOLUTE/PATH/TO/MODELS
--export --export-path /results/

Hello! Can you provide your exact OS (i.e. which version of Linux)? In addition, please provide the command you are trying to run and full output.
Assuming you are able to run Triton independently on your machine, this should be working. Note that the /ABSOLUTE/PATH/TO/MODELS should be the same in all three instances in the command (i.e. the absolute filepath should be the same in the host machine and container).

It's OK using .NET to build memory-analyzer.


Toc wrongly generated in HTML renderer

I'm trying to use the toc feature but it seems to not works as expected.
It does works fine in TOC renderer (ie, it correctly generated links to sections), but the HTML renderer never generate the html anchors to sections.
require 'redcarpet'
markdown = Redcarpet::Markdown.new(Redcarpet::Render::SmartyHTML.new(
                autolink: true,
                footnotes: true,
                strikethrough: true,
                superscript: true,
                tables: true),
        escape_html: false,
        filter_html: false,
        no_images: false,
        no_links: false,
        no_styles: true,
        with_toc_data: true)
puts markdown.render(
        "# First section\n" \
        "\n" \
        "| Column1 | Column2 |\n" \
        "| --------|-------- |\n" \
        "| R1 C1 | R1 C2 |\n" \
        "| R1 C1 | R1 C2 |\n" \
        "| R1 C1 | R1 C2 |\n" \
        "| R1 C1 | R1 C2 |\n" \
        "| R1 C1 | R1 C2 |\n" \
        "\n"
)

And give this output:

First section

| Column1 | Column2 |
| ——–|——– |
| R1 C1 | R1 C2 |
| R1 C1 | R1 C2 |
| R1 C1 | R1 C2 |
| R1 C1 | R1 C2 |
| R1 C1 | R1 C2 |

Is there something i missed ?
thanks

Hello,
I guess you gave up or ended up using something else but for people that might struggle with this issue, in your case, the :with_toc_data option must be passed to the SmartyHTML constructor, no the Markdown one as you do.
Thanks for reporting anyway ; I'm giving this a close.


Add compat upper bounds for Microbiome and friends

The open-ended [0] from #10262 was causing weird conflicts with the BioJulia registry. This adds upper bounds for the last version of each package that was registered in General.

I'm not sure what the source of the bug is, so I would appreciate it if someone with more expertise could review this PR (and explain the bug, if possible).

Would it be better to just revert https://github.com/JuliaRegistries/General/pull/10262?

@kescobo Just FYI since it is the weekend, this may not get reviewed before Monday.

@DilumAluthge Yeah, I suspected as much - no worries! Now that I know I can edit my local copies of the registry, I'm not in any great rush.
My impression from Kristoffer's comments on slack (in #pkg-usage) is that Pkg doesn't apply the compat entries in a registry to only versions found in that registry. So since this change capped the compat to julia 1.0, and I'm on julia 1.4, it just thinks there are no versions compatible with the julia version I was using.

Would it be better to just revert #10262?

If for some reason these changes aren't or can't be approved, then I think yes. Or if it's easy for you to revert while we wait, that's fine too - I think the problems I had with the previous state were preferable to the current totally broken state. But if it's a hassle, it's ok with me if it takes a couple of days to sort it out.


The specified network password is not correct on sign in credential from file

Hello,
I'm using Asp.Net Core with Angular in a project with IdentityServer4 for securing API and hosted the project on Plesk Service.
I created a pair of certificates with 'MakeCert' and 'pvk2fx'.
In this project SignInCredential access the certificate from 'wwwroot' folder, by creating an extension, load to '.pfx' file that gets the file's address and password from the configuration.
Here is my Extension class:
public static class SigninCredentialExtension
    {
        private const string KeyFilePath = "KeyFilePath";
        private const string KeyFilePassword = "KeyFilePassword";

        public static IIdentityServerBuilder AddSigninCredentialFromConfig(
            this IIdentityServerBuilder builder,
            IConfigurationSection options
            )
        {
            var keyFilePath = options.GetValue<string>(KeyFilePath);
            var keyFilePassword = options.GetValue<string>(KeyFilePassword);

            if (File.Exists(keyFilePath))
            {
                builder.AddSigningCredential(new X509Certificate2(
                    keyFilePath, keyFilePassword,
                    X509KeyStorageFlags.Exportable
                    ));
            }
            return builder;
        }
    }

The Startup.cs
services.AddIdentityServer()
                .AddSigninCredentialFromConfig(Configuration.GetSection("SigninKeyCredentials"))
                .AddInMemoryClients(Config.GetClients())
                .AddInMemoryIdentityResources(Config.GetIdentityResources())
                .AddInMemoryApiResources(Config.GetApiResources())
                .AddAspNetIdentity<Author>();

and The appsettings.json
{
  "SigninKeyCredentials": {
    "KeyFilePath": "wwwroot\\key\\moamma.pfx",
    "KeyFilePassword": ""
  },
  "ConnectionStrings": {
    "Author": {
      "ConnectionString": "Server=(localdb)\\MSSQLLocalDB;Database=AuthorsDb;MultipleActiveResultSets=true"
    }
  }
}

The problem is, this runs on my local machine without any problem, but when I send it to host(Plesk) it throwing an exception:
'WindowsCryptographicException: The specified network password is not correct'
Even I'm not setting any password for it!!
An error occurred while starting the application.
WindowsCryptographicException: The specified network password is not correct
Internal.Cryptography.Pal.CertificatePal.FilterPFXStore(byte[] rawData, SafePasswordHandle password, PfxCertStoreFlags pfxCertStoreFlags)

WindowsCryptographicException: The specified network password is not correct
Internal.Cryptography.Pal.CertificatePal.FilterPFXStore(byte[] rawData, SafePasswordHandle password, PfxCertStoreFlags pfxCertStoreFlags)
Internal.Cryptography.Pal.CertificatePal.FromBlobOrFile(byte[] rawData, string fileName, SafePasswordHandle password, X509KeyStorageFlags keyStorageFlags)
System.Security.Cryptography.X509Certificates.X509Certificate..ctor(string fileName, string password, X509KeyStorageFlags keyStorageFlags)
identity.Controllers.SigninCredentialExtension.AddSigninCredentialFromConfig(IIdentityServerBuilder builder, IConfigurationSection options) in SigninCredentialExtension.cs
identity.Startup.ConfigureServices(IServiceCollection services) in Startup.cs
Microsoft.AspNetCore.Hosting.ConventionBasedStartup.ConfigureServices(IServiceCollection services)
Microsoft.AspNetCore.Hosting.Internal.WebHost.EnsureApplicationServices()
Microsoft.AspNetCore.Hosting.Internal.WebHost.Initialize()
Microsoft.AspNetCore.Hosting.Internal.WebHost.BuildApplication()

So, where is the problem? Is this approach okay?
I get the whole idea from here http://amilspage.com/signing-certificates-idsv4/

This seems to be a general question - not a bug report or a feature request.
Please use one of the our free or commercial support options
See here for more details.
Thanks!


improvement: link to entities in the response

Second part of the conversation I just had with @yinaa it'd be awesome to have above or under the response json preview a list of links of the entities in the response.
When clicking on the link, it would pre-fill the url box with the proper url.
This would save me time during the demonstrations when I copy/past id's to build requests. Avoid typos as well.

assigning to betti for general backlog if we are still interested in addressing this.


[Snyk] Security upgrade node from 18.16-bullseye-slim to 18.18-bullseye-slim

This PR was automatically created by Snyk using the credentials of a real user.Keeping your Docker base image up-to-date means you’ll benefit from security fixes in the latest version of your chosen image.
Changes included in this PR

frontend/Dockerfile

We recommend upgrading to node:18.18-bullseye-slim, as this image has only 57 known vulnerabilities. To do this, merge this pull request, then verify your application still works as expected.
Some of the most important vulnerabilities in your base image include:

Severity
Priority Score / 1000
Issue
Exploit Maturity

221
CVE-2023-4039 SNYK-DEBIAN11-GCC10-5901313
No Known Exploit

221
CVE-2023-4039 SNYK-DEBIAN11-GCC10-5901313
No Known Exploit

621
Improper Access Control SNYK-UPSTREAM-NODE-5843454
Proof of Concept

514
Access Restriction Bypass SNYK-UPSTREAM-NODE-5848030
No Known Exploit

614
Arbitrary Code Injection SNYK-UPSTREAM-NODE-5848038
No Known Exploit

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs.
For more information:
🧐 View latest project report
🛠 Adjust project settings

Learn how to fix vulnerabilities with free interactive lessons:
🦉 Improper Access Control
🦉 Arbitrary Code Injection

Codecov Report

Merging #18 (df7c864) into dev (51e61b4) will increase coverage by 6.16%.
The diff coverage is n/a.

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@@            Coverage Diff             @@
##              dev      #18      +/-   ##
==========================================
+ Coverage   58.31%   64.47%   +6.16%
==========================================
  Files         897      416     -481
  Lines       24867    13372   -11495
  Branches     4508     1276    -3232
==========================================
- Hits        14500     8622    -5878
+ Misses       9943     4326    -5617
  Partials      424      424

Flag
Coverage Δ

unittests
64.47% <ø> (+6.16%)
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see 481 files with indirect coverage changes


Clean-up Importings in Backend

As requested in the previous PR:

Fix the imports for app, db, setup_required, get_user_config so that they are imported via import ufo and referenced as ufo.app, ufo.db, ufo.setup_required, ufo.get_user_config, etc, since they are each fields/functions in a module rather than a class.

Fix the import orders wherever I caught them.  Basically, the import order should be:
(1) standard library
(2) third-party modules
(3) application-specific modules

Worth mentioning again that it's sweet to have the tests in place, and makes this kind of change a breeze!

Reviewed 16 of 16 files at r1.
Review status: all files reviewed at latest revision, all discussions resolved.

Comments from the review on Reviewable.io

I'm gonna go ahead and merge this now so I can fix my branch all at once then prepare to submit it shortly.


feat: add getParameter api

It was tested manually and works. I need to write 2 more tests after I'll find how to mock the '@sap/plugin' module.
I'll really appreciate you can start a review meanwhile, because the end of the sprint is coming.
Completed including manual and unit tests.

please don't do any more force pushes as it makes it harder to do incremental review

sorry, I was sure you did not start - I only removed unused comment

Is there documentation for this getParameter? who is the consumer of this API?
How Would they know how to use it / in what scenarios it is relevant?

Yes, it should be documented. Where is a good place to document it?

Yes, it should be documented. Where is a good place to document it?
There is a types folder in the root of this repo, I am not sure what it currently contains.
We may need to handle the documentation question separately outside this PR.


Update labels and descriptions

Closes #410
Closes #409
Description
Update labels and descriptions.
Is this a breaking change (Yes/No):
No

@odendayoko @odendayoko
Please resolve the review conversation.
Otherwise, you will not be able to merge.


Consider renaming "Files"/"Models" to "Projects"

Currently, the main menu items are "Models", "Simulate", and "Visualize". "Models" has the route "/files". Strictly, speaking users have to upload COMBINE/OMEX archives rather than models. These archives include models plus descriptions of simulation experiments and visualizations. Consequently, we should consider renaming this to something like "Projects" rather than "Models".
Possible names

(Biosimulation) Project
(Biosimulation) Study
Repository (however, this would be overloaded with the entire application being a repository)

Track how models/simulations/visualizations used for publications (figures, tables, supplementary materials)

Done


[CI:DOCS] Support building either mainline or beta GCE images based on PR label

Supporting a new base-image in downstream environments is often
a time-consuming and difficult.  For Fedora, normally this work begins
when a release goes into beta.  However, beta versions of Fedora
releases are not provided in google, they must be specially imported.
Otherwise, after release the fedora-cloud project provides read-made
images that can be used in a vastly simpler manner.
Alter the base-image build workflow to use the pre-built images by
default.  However if a PR has the 'Beta' label set, cause the workflow
to import the development fedora images instead.

Ref: Successful build with 'Beta' tag.

@edsantiago and @lsm5 would you mind taking a glance at this.  Especially the README.md updates.  I don't expect y'all to grok the YAML or script changes, and they both work as intended..  This isn't an emergency or critical fix, just intended to simplify the workflow for the general (i.e. non-beta) image-update use-case.

The YAML is taking me a long time to review; looks fine on first (diff) and second (once-over) pass, and I don't think I have the ability to give it another look today.

Please don't fret too much over the YAML, it's special and specific to Packer, so I really don't expect it to be widely understandable.  That said, if you're willing to put in the effort and learn more about that tool, I'm not going to get in the way.  I will note that the docs for 1.7 have some bad links use 1.8, esp. for the plugins.

I'm going to fork off the lib.sh addition that handles reading PR labels.  I can use that feature in other PRs, whereas the support for consuming upstream GCP F36 images has hit a speed-bump: https://pagure.io/cloud-sig/issue/384

There's been no activity on my upstream issue for over a week.  I'm taking that as a sign the Fedora project doesn't take maintenance of these GCE images seriously.  And even if so, they're not updated quickly enough for our CI purposes.