Isort fails with "ERROR: Filename override is intended only for stream (-) sorting."

Type: Bug
/bin/python -m isort - --profile black --filename /data/Dropbox/foo/bar/react_dashboard/backend/app/endpoints/banner.py
CWD Linter: /data/Dropbox/foo/bar/react_dashboard/backend
ERROR: Filename override is intended only for stream (-) sorting.
Relevant config lines:
  "isort.check": true,
  "isort.showNotifications": "onError",
  "editor.inlineSuggest.showToolbar": "always",
  "isort.importStrategy": "fromEnvironment",
  "isort.args": ["--profile black"],

Extension version: 2023.9.10931010
VS Code version: Code 1.76.2 (ee2b180d582a7f601fa6ecfdad8d9fd269ab1884, 2023-03-14T17:57:21.103Z)
OS version: Linux x64 6.2.9-zen1-1-zen
Modes:
Sandboxed: No

System Info

Item
Value

CPUs
AMD Ryzen 7 4800H with Radeon Graphics (16 x 4284)

GPU Status
2d_canvas: enabledcanvas_oop_rasterization: disabled_offdirect_rendering_display_compositor: disabled_off_okgpu_compositing: enabledmultiple_raster_threads: enabled_onopengl: enabled_onrasterization: enabledraw_draw: disabled_off_okskia_renderer: enabled_onvideo_decode: disabled_softwarevideo_encode: disabled_softwarevulkan: disabled_offwebgl: enabledwebgl2: enabledwebgpu: disabled_off

Load (avg)
2, 2, 2

Memory (System)
30.77GB (10.72GB free)

Process Argv

Screen Reader
no

VM
0%

DESKTOP_SESSION
plasma

XDG_CURRENT_DESKTOP
KDE

XDG_SESSION_DESKTOP
KDE

XDG_SESSION_TYPE
x11

@ldorigo Can you provide logs from Output > isort? Also, was the file empty when this happened?

Hi, no the file was not empty. The output contains the 3 lines I pasted above repeated everytime I save or manually run "sort imports". I can paste the startup outputs when I get home .

@ldorigo I need to see the initial part of the logs where it lists out sys.path, isort version etc.

This error seems to go away when you set
  "isort.args": ["--profile", "black"],

as separate entries.
But unless I'm misunderstanding some of these settings, it doesn't seem to be respecting the black profile when I use it as separate args.
Example:
isort settings
    "isort.args": [
        "--profile",
        "black"
    ],

Then
from some_package import (X, Y,)

# gets sorted to

from some_package import X, Y

This does not produce the filename error.
If I use a single arg for the isort args:
    "isort.args": [
        "--profile black"
    ],

Then
from some_package import (X, Y,)

# gets sorted to

from some_package import (
    X,
    Y,
)

Which is the behavior I would expect from the black profile, but now i get the filename Error ?

Hey @karthiknadig
This was the sample script:
from urllib import (parse, request, )

Which gets formatted to:
from urllib import parse, request

While (at least based on my understanding of the --profile black option) should result in:
from urllib import (
    parse,
    request
)

Here is the output of Output -> isort:
sys.path used to run Server:
   /<home-dir>/.vscode/extensions/ms-python.isort-2023.9.10931010/bundled/libs
   /<home-dir>/.vscode/extensions/ms-python.isort-2023.9.10931010/bundled/tool
   /<home-dir>/.pyenv/versions/3.10.5/envs/<project>/lib/python3.10/site-packages/_pdbpp_path_hack
   /<home-dir>/.pyenv/versions/3.10.5/lib/python310.zip
   /<home-dir>/.pyenv/versions/3.10.5/lib/python3.10
   /<home-dir>/.pyenv/versions/3.10.5/lib/python3.10/lib-dynload
   /<home-dir>/.pyenv/versions/3.10.5/envs/<project>/lib/python3.10/site-packages
Settings used to run Server:
[
    {
        "check": false,
        "cwd": "<path-to-project-workspace>",
        "workspace": "file://<path-to-project-workspace>",
        "logLevel": "error",
        "args": [
            "--profile",
            "black"
        ],
        "severity": {
            "W": "Warning",
            "E": "Hint"
        },
        "path": [],
        "interpreter": [
            "/<home-dir>/.pyenv/versions/3.10.5/envs/<project>/bin/python"
        ],
        "importStrategy": "useBundled",
        "showNotifications": "off"
    }
]

Global settings:
{
    "check": false,
    "cwd": "/",
    "workspace": "/",
    "logLevel": "error",
    "args": [
        "--profile",
        "black"
    ],
    "severity": {
        "W": "Warning",
        "E": "Hint"
    },
    "path": [],
    "interpreter": [], "importStrategy": "useBundled", "showNotifications": "off"
}

/<home-dir>/.pyenv/versions/3.10.5/envs/<project>/bin/python -m isort --version-number
CWD Linter: <path-to-project-workspace>
Version info for isort running for <path-to-project-workspace>:
5.11.5

SUPPORTED isort>=5.10.1
FOUND isort==5.11.5

/<home-dir>/.pyenv/versions/3.10.5/envs/<project>/bin/python -m isort - --profile black --filename /Users/<user>/Library/Application Support/Code/User/globalStorage/buenon.scratchpads/scratchpads/1a4f2b73c916c9af3926773a674c6453/scratch2.py
CWD Linter: /<home-dir>/Library/Application Support/Code/User/globalStorage/buenon.scratchpads/scratchpads/1a4f2b73c916c9af3926773a674c6453

@geoff-va Here is what I am seeing, running isort and black, without VS code involved:
>type isort_test.py
from urllib import (parse, request)

>type isort_test.py | isort - --profile black --filename isort_test.py
from urllib import parse, request

>type isort_test.py | isort - --profile black --filename isort_test.py | black --stdin-filename isort_test.py -
from urllib import parse, request
All done! ✨ 🍰 ✨
1 file left unchanged.

As you can see the code was formatted to:
from urllib import parse, request

This is the same result I get with VS Code:

Also, running purely via command line without stdin also gives the same result:
>type isort_test.py
from urllib import (parse, request)

>isort --profile black isort_test.py
Fixing C:\GIT\differ\isort_test.py

>type isort_test.py
from urllib import parse, request

>black isort_test.py
All done! ✨ 🍰 ✨
1 file left unchanged.

>type isort_test.py
from urllib import parse, request

So, I think the result that you are seeing is correct. If not then this is a bug in isort itself.

Thanks @karthiknadig
With the trailing comma do you still get the same result?
Based on the options I'm seeing here for the black profile with the split_on_trailing_comma option and multi_line_output=3 I would think that this:
from urllib import (parse, request, )

Would get turned into:
from urllib import (
    parse,
    request
)

? Unless I'm misunderstanding how this works?

Ah - It seems to be a mismatch between docs and implementation in isort.
When i add the --split-on-trailing-comma option it indeed sorts as I would expect based on the black profile. So looks like that option needs to be fixed on the isort side.
Thanks for checking for me, though!


doc-models.inception_v3: Add information about expected input size

While using the pretrained inception v3 model I wasnt aware that the input size has to be 299x299, as I figured out after a little bit of try and error and searching.
I hope I didn't miss something in the docs, but if not it might make sense to add a small note in the models.inception_v3 doc that the expected tensor size is different for this model.

This is currently "documented" in https://github.com/pytorch/vision/blob/master/torchvision/models/inception.py#L77, but I agree that it would be better to have it more visible in the official documentations.
Could you send a PR improving the documentation?

Sure, I take that!

@fmassa I think this can be closed :)

I'll close it 👍


engine-schema: upgrade path <IP_ADDRESS> to <IP_ADDRESS>

Description
Adds an empty <IP_ADDRESS> to  <IP_ADDRESS> upgrade path
Types of changes

[ ] Breaking change (fix or feature that would cause existing functionality to change)
[ ] New feature (non-breaking change which adds functionality)
[ ] Bug fix (non-breaking change which fixes an issue)
[ ] Enhancement (improves an existing feature and functionality)
[ ] Cleanup (Code refactoring and cleanup, that may add test cases)
[ ] build/CI

Feature/Enhancement Scale or Bug Severity
Feature/Enhancement Scale

[ ] Major
[ ] Minor

Bug Severity

[ ] BLOCKER
[ ] Critical
[ ] Major
[ ] Minor
[ ] Trivial

Screenshots (if appropriate):
How Has This Been Tested?

How did you try to break this feature and the system with this change?

@shwstppr
there are build errors
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:21:8: Unused import - java.sql.PreparedStatement. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:22:8: Unused import - java.sql.ResultSet. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:23:8: Unused import - java.sql.SQLException. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:24:8: Unused import - java.text.ParseException. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:25:8: Unused import - java.text.SimpleDateFormat. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:26:8: Unused import - java.util.Date. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:27:8: Unused import - java.util.HashMap. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:28:8: Unused import - java.util.Map. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:31:8: Unused import - org.jasypt.exceptions.EncryptionOperationNotPossibleException. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:34:8: Unused import - com.cloud.utils.DateUtil. [UnusedImports]
Error:  /home/runner/work/cloudstack/cloudstack/engine/schema/src/main/java/com/cloud/upgrade/dao/Upgrade41900to42000.java:35:8: Unused import - com.cloud.utils.crypt.DBEncryptionUtil. [UnusedImports]

@weizhouapache thanks for pointing that. Fixed


Create tooltip for REPORT BUG link

Hi,
It would be helpful to have "tooltip" , when user hover mouse over the icon or link for REPORT BUG.  There could be mentioned, that this should be used just for DOCUMENTATION RELATED issue, not for general platform or service issue.  It already happed that users try to report their issues related to their resources  via this link.

Good hint, we will try to improve the button.

Hi @lboka ,
I tried tooltips, but looks ugly. We will rename it to "Report Documentation Bug". This should be clear enough for everyone.
Are you with the solution?


Command Upgrade

With recent changes in how autopilot JSON file creation works, the command in action is Connect-MSGraph and has been updated in the doc.
Problem: https://github.com/MicrosoftDocs/windows-itpro-docs/issues/5443

Hello @greg-lindsay, this PR is ready for your review. Thank you so much.
@officedocsbot assign @greg-lindsay

(ref. #5772 )


Remove the suffix ".glitch.me" that is added to the domain

TL;DR
There is a .glitch.me suffix hardcoded in src/utils.js that breaks the generation of the instance domain and its user when bringing up a Postmarks instance without Glitch, and also produces 503 errors when federating.
Setup
I've set up an own instance without the use of Glitch, let's say into the domain example.com. I also set up the SSL in my Reverse Proxy to this domain.
I have the .env file created and the domain is set up there:
PROJECT_DOMAIN=example.com

I have the account.json file created and the user set up there:
{
  "username": "xavi",
  ...
}

Going to the About section I find the textbox with the account I should follow in the fediverse:
<EMAIL_ADDRESS>
Issue
I found:

this account (actually the domain part of it) do not conform to the SSL certificate and to the domain where the project is published. With a Webfinger lookup tool it shows that it is invalid:
https://webfinger.net/lookup/?resource=xavi%40example.com.glitch.me

Request Log
04:52:34 Looking up WebFinger data for<EMAIL_ADDRESS>04:52:34 GET https://example.com.glitch.me/.well-known/webfinger?resource=acct%3Axavi%40example.com.glitch.me
04:52:35 Error getting JRD: Get "https://example.com.glitch.me/.well-known/webfinger?resource=acct%3Axavi%40example.com.glitch.me": tls: failed to verify certificate: x509: certificate is valid for glitch.com, *.gomix.me, gomix.com, gomix.me, glitch.me, *.glitch.com, *.gomix.com, *.glitch.me, not example.com.glitch.me

JSON Resource Descriptor (JRD)
null

when trying to search for this user from my Mastodon account, it returns a "503 remote cert could not be verified".

Possible fix
I edited the code here, by removing the suffix .glitch.me:
https://github.com/ckolderup/postmarks/blob/main/src/util.js#L25
And I deleted the ./.data/activitypub.db (as I did not go beyond connectivity tests yet, so it would regenerate), and then everything worked:

the Webfinger tool returns the correct answer:

{
  "subject"<EMAIL_ADDRESS>  "links": [
    {
      "rel": "self",
      "type": "application/activity+json",
      "href": "https://example.com/u/xavi"
    }
  ]
}

The user in the fediverse instances also works, is searchable and followable.

Suggestion

Remove the hardcoded suffix
If Glitch needs to be supported, make it a parameter in the .env file

Thanks for the report, this was definitely still optimized for Glitch hosting-- I think a number of people have just replaced the entire line to hardcode const domain = 'example.com';, but it's probably time that we offer a better solution. I will put something together shortly.

@XaviArnaus if you have a moment, take a look at #113 and let me know if that works for you

Sorry, personal issues... The #113 looks good, thank you!


Fix link to audit by Inference AG.

Codecov Report
Base: 45.15% // Head: 45.02% // Decreases project coverage by -0.12% :warning:

Coverage data is based on head (2658e9e) compared to base (ce171c2).
Patch has no changes to coverable lines.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #38      +/-   ##
==========================================
- Coverage   45.15%   45.02%   -0.13%
==========================================
  Files          17       17
  Lines        2011     2012       +1
==========================================
- Hits          908      906       -2
- Misses       1103     1106       +3

Impacted Files
Coverage Δ

masp_proofs/src/circuit/convert.rs
62.85% <0.00%> (-1.43%)
:arrow_down:

masp_primitives/src/zip32.rs
76.14% <0.00%> (-0.82%)
:arrow_down:

...imitives/src/test_vectors/pedersen_hash_vectors.rs
5.40% <0.00%> (-0.16%)
:arrow_down:

masp_proofs/src/circuit/sapling.rs
71.15% <0.00%> (+0.31%)
:arrow_up:

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

:umbrella: View full report at Codecov.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.

thanks!


Migrate to ESM

Warning Breaking change: svg-chunk-webpack-plugin@5 will be ESM only

@alexander-akait Hope you are well. I would like to have your opinion on this PR please.
Is it "safe"? I did not find an example of plugin/loader available in ESM.

@yoriiis Sorry for delay, it is safe, we support ESM format out of box for webpack.config.(js|mjs)


unarchive exp docs

unarchive exp docs

🚀 Deployed on https://65cd419cb0b0eb364b4face8--cozy-fox-0defec.netlify.app


refactor: resolve should resolve

Currently, we have the resolve() utility, which is actually validating and resolving all references. I think that was a mistake.
This PR removes validation from the resolve utility.
I’ll probably add a few more changes to it, to align the output of all the utilities more.

Let’s just get this in and take it from there. :)


Verifying VS Code debugger with default configuration works on tests in our SDKs

deletes custom vs code launch.json files that mostly duplicate testing commands that already exist as npm scripts.
factors out nyc calls to its own coverage scripts in package.json files when it gets in the way of the debugger (when mocha uses ts-node).
fixes #6979 by using the default automatic debug configuration.
fixes #8088 by updating the contributing guide accordingly.

See https://code.visualstudio.com/updates/v1_45#_automatic-debug-configurations for release notes on the vs code debugger with default configuration.

@jeremymeng I guess it has something to do with source maps. I will do some digging and get back to you.
@xirzec So you do the following. Hit CTRL+SHIFT+D to open the debugger panel, click on "show" all automatic debug configurations (if you do not have other debug configs). choose Node.js (Preview) from the dropdown menu, and finally select your favorite npm testing script. Later, you can hit F5 to debug using that same npm script It remembers the automatic config you selected but sometimes it does not if it is the only config you have.
Regarding the second point, debugging samples in vscode is already not working currently on master, or does it?

@jeremymeng yup it is source maps related and is fixed by passing --produce-source-map to nyc, see https://github.com/TypeStrong/ts-node/issues/898. However, this triggers the compilation of the whole sdk including samples and I see broken samples in core-arm.

@jeremymeng yup it is source maps related and is fixed by passing --produce-source-map to nyc, see TypeStrong/ts-node#898.

We didn't use nyc in debugging before.  Is the VS Code default debug configuration picked one npm script that invokes nyc?

@jeremymeng The debugger is perfectly fine with npm scripts that call nyc as long as mocha does not register ts-node. If mocha does register ts-node, you will need to update the npm script and pass --produce-source-map to nyc. However, this flag will trigger the compilation of all ts files in the sdk directory.

@ramya-rao-a in our offline discussion, there were two follow-up items
1- investigating running samples through the debugger.
2- investigating restricting the npm scripts accessible to the debugger.
I will look at them later and I believe they are not blocking merging this PR. Does the PR look good to you?

This has been sitting idle for too long, would you guys take a look? cc @willmtemple, @jeremymeng, @richardpark-msft, @XiaoningLiu @HarshaNalluru

/azp run js - storage-queue - tests


ImageDataGenerator

Has anyone succeed in modyfing standard keras_preprocessing.image.ImageDataGenerator class for this purpose? The TextImageGenerator() is fine to start, but if you want to utilize preprocessing functions it would be beneficial to use ImageDataGenerator?

I implemented CRNN for captcha-recognition. That project's kind of like this one, I also used DataGenerator for fit_generator, so I think my repo would help
https://github.com/tuanphan09/captcha-recognition


Add message context menu and action bar

open context menu on: message ricght click or push. also show floating action bar on message hover

@fmzbl can you resolve the conflicts with main, mostly related to Makepad's new pub/use syntax? thanks.


Switch to maintained version of license-checker

You do use `https://github.com/mwittig/license-checker as a dependency.
However that is just a fork and – according to GitHub – 327 commits behind davglass:master (the upstream).
Upstream seems to be https://github.com/davglass/license-checker.
Could you please switch to the maintained upstream version? Thanks.
Because, somehow, the other fork is even giving me build errors, see https://github.com/rugk/emoji-mart-embed/issues/4.

Described origin issue at https://github.com/mwittig/npm-license-crawler/issues/40

@rugk Do you have git installed? If not, please install it on your system as it most likely will solve your installation issue as a work-around.
Switching to the maintained upstream version of license-checker is not that easy as the code-base have diverged a lot over time. I probably will replace the remaining bits used from license checker with my own implementation to get things sorted.

Of course, git is installed.


Custom field to define month and year name in categories (model)

As your documentation quotes: "We use created_at to define the month and year name in categories. So make sure your data consist of this column."
Is there a way to change that to a custom field? Thank you in advance

Hi @Tenebra233 . Sorry for the inconvenience. After I checked, there are unfinished feature about that. I will update later and make this to enhancement for now.
Thank you

Hi @Tenebra233 . Sorry for the inconvenience. After I checked, there are unfinished feature about that. I will update later and make this to enhancement for now.
Thank you

Awesome, many thanks for the prompt reply.

Hi @Tenebra233 . Sorry for the inconvenience. After I checked, there are unfinished feature about that. I will update later and make this to enhancement for now.
Thank you

any news ? i really need this feature.

I will donate you 100$ if you implement ability to use custom 'created_at' field. I'm stuck in an old project with funny naming conventions, and I love your library a lot.

Hi @msnegurski thank you for your support.
For this enhancement, please use latest version: v0.3.4 and follow this step:
https://coroo.github.io/nova-chartjs/#/?id=custom-x-axis

Awesome, thank you so much!


Manual trigger fix

Removed orDev handling because when a user updates selected NI device, it writes to the config file and will be used by default next time. Additionally, it will create new analogue and digital output channels regardless each time a new device is selected

https://github.com/CuriBio/nautilus_acquisition/assets/84344924/1bc1690c-0631-4c59-bf8c-9b66791bf726

This needs to bump the patch version

Looks good, one thing, can you add a call to QString::trimmed on the device name so the second device doesn't start with a leading space


[Regex] Infer capture types of regex literals.

When parsing a regular expression literal, accept a serialized capture structure from the regex parser, decode it and form Swift types.
Examples:
'/(.)(.)/' // ==> `Regex<(Substring, Substring)>`
'/(?<label>.)(.)/' // ==> `Regex<(label: Substring, Substring)`
'/((.))*((.)?)/' // ==> `Regex<([Substring], [Substring], Substring, Substring?)>`

Note:

This needs to land after apple/swift-experimental-string-processing#92 and after dev/4 tag has been created.
See apple/swift-experimental-string-processing#92 for regex parser changes and the capture structure encoding.
The RegexLiteralParsingFn CaptureStructureOut pointer type change from char * to void * will not break builds due to implicit pointer conversion (SE-0324) and unchanged ABI.

Resolves rdar://83253511.

apple/swift-experimental-string-processing#92
@swift-ci please test

apple/swift-experimental-string-processing#92
@swift-ci please test

Build failed
Swift Test Linux Platform
Git Sha - 1721e431578f50816f1359acb0df69dfb4d3531d

apple/swift-experimental-string-processing#92
@swift-ci please test linux

apple/swift-experimental-string-processing#92
@swift-ci please test windows

Build failed
Swift Test Linux Platform
Git Sha - 1721e431578f50816f1359acb0df69dfb4d3531d

CI didn't seem to like the nonexistent dev/4 tag (the comment mentioning the PR should ideally override that). I've created a temporary dev/4 tag off of main to get this CI rolling.

apple/swift-experimental-string-processing#92
@swift-ci please test linux

Build failed
Swift Test Linux Platform
Git Sha - 1721e431578f50816f1359acb0df69dfb4d3531d

apple/swift-experimental-string-processing#92
@swift-ci please clean test linux

Build failed
Swift Test OS X Platform
Git Sha - 1721e431578f50816f1359acb0df69dfb4d3531d

apple/swift-experimental-string-processing#92
@swift-ci please test macos

Build failed
Swift Test OS X Platform
Git Sha - 1721e431578f50816f1359acb0df69dfb4d3531d

@swift-ci please test

Build failed
Swift Test OS X Platform
Git Sha - 1b3c0b7a734f6feac5ef77b1effa1377cea5df47

Build failed
Swift Test Linux Platform
Git Sha - 1b3c0b7a734f6feac5ef77b1effa1377cea5df47

@swift-ci please test


Release v3.8.1

Includes fix for Signal test via probe-cli v3.16.4

I fixed the tests I was able to fix easily, but wasn't able to reliably reproduce the failing ones and I suspect it's going to require more fighting with the CI, so I filed an issue to fix it later: https://github.com/ooni/probe/issues/2348.


Document non string types in template literal types

I was complaining that using ${number} in template literal types was an undocumented feature so I did my best to document non string types in template literals to the best of my knowledge.
microsoft/TypeScript#46674

https://www.typescriptlang.org/dev/twoslash/ seems to error on any template literal type.

Looks good - just the CLA to go 👍🏻

Ping on the CLA ^

I'm waiting on approval from my employer
On Thu, Nov 11, 2021, 4:40 AM Orta Therox @.***> wrote:

Ping on the CLA ^
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CLA is signed, is anything blocking merge of this PR?


Support Azure OpenAI integration

Could we support the integration of Azure OpenAI in this repo? Sounds like an awesome alignment!
https://github.com/Azure/azure-openai-samples

@PamelaFox

I work on many of our Python Azure OpenAI samples (like https://github.com/Azure-Samples/azure-search-openai-demo/) and would be happy to help with this. Let me know if this is a feature you're looking for in this repo.

Thanks both - this sounds great and definitely something we'd be interested in integrating.
There's two main areas I think Azure OpenAI could be integrated within the current state of our AI packages:

Using Azure's OpenAI chat endpoints for the wagtail-ai rich text integration. This is currently built using llm, allowing us to use a plugin-based interface for adding support for different AI models. A plugin for Azure's OpenAI API for llm would make it easy for wagtail-ai users to use them.
Our other AI package; wagtail-vector-index is focused on providing developer tools and AI search using AI APIs. Adding Azure AI Search as a vector backend to this would be great.

There's loads of other nice things that Azure OpenAI can do that we'd like to consider when the packages matures/integrates more AI-oriented features.

Update: We tried wagtail-ai in a live stream. I was hoping we'd be able to use it with Azure OpenAI, as llm does actually support Azure OpenAI, but wagtail-ai would need additional options to get it to work. I'm curious why you went with llm? I love it as a CLI tool, but it doesn't seem optimal for a deployed server tool, given all its reliance on file system paths. I would think something like langchain would be more configurable in a deployed app.

Re wagtail-vector-index: very cool! I've shared that with another advocate who's been working on improving the AI search support in other OSS packages, to see if they'd have time to add Azure AI search.

Update: We tried wagtail-ai in a live stream. I was hoping we'd be able to use it with Azure OpenAI, as llm does actually support Azure OpenAI, but wagtail-ai would need additional options to get it to work. I'm curious why you went with llm? I love it as a CLI tool, but it doesn't seem optimal for a deployed server tool, given all its reliance on file system paths. I would think something like langchain would be more configurable in a deployed app.

Thanks for giving it a go @pamelafox! I'd love to hear more about what additional options we're missing to get Azure OpenAI working/what roadblocks you ran in to with llm.
On the llm choice - we wanted something simple that was easily extendable by developers (through llm plugins) and that didn't come with all the extra baggage that Langchain provides. Simon was interested in feedback on it over on issue #56 if you wanted to add any additional comments.
Saying that; we're not tied to llm. The swappable backend architecture is designed so we can switch out with a potential future LangchainBackend, or perhaps even a more specific AzureOpenAIBackend. You might have noticed we've recently added an OpenAIBackend as we experiment with multi-modal models and start running in to some of the limitations of the llm Python API.
Really appreciate your feedback - we'd still love to make sure we fully support Azure OpenAI.


Refactor Artifacts service

Move model storage code into DAO
Use names package for parsing and representing resource names
Add test suite

Fixes #92 #90 #61


Add getting started section to README

README Update
Please add a getting started section to the README so folks know how to start with this project

Added "Getting started" section in README file.


NPM showing package version v3

Hi, I can't see any updates or release notes for version 3+ which has been released on https://www.npmjs.com/package/@beam-australia/react-env was wondering if this was intentional or if the @beam-australia/react-env package maps somewhere else now?

Sorry - I have just updated the repo with breaking changes. Please see.

The docs have been updated to reflect these changes.


upgrade to latest grafana release 5.2.2

/ok-to-test
/lgtm

/assign @unguiculus

/ok-to-test
/lgtm

/assign @unguiculus

/close
in favour of https://github.com/helm/charts/pull/6820 which has updated readme and fixes formatting


Spell check range error

The algorithm that adjusts spell check results for a new string had a bug in it where it would throw an error in certain cases where the new string was shorter than the old string, such as when the user is deleting text.
Fixes https://github.com/flutter/flutter/issues/152272

Thank you for this fix! Sorry for asking, but could you please clarify if this fix will be applied to version 3.24.x?


Video not showing on Android Emu

Bug
Video component is not displaying video on Android emulator.

Video does show on iOS (both emulator and device)

The library was added via the auto-linking feature of RN 0.6.x
Platform
Android
Which player are you experiencing the problem on:

Android ExoPlayer

Environment info
info output:
System:
    OS: macOS Mojave 10.14.6
    CPU: (12) x64 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
    Memory: 902.69 MB / 16.00 GB
    Shell: 5.3 - /bin/zsh
  Binaries:
    Node: 10.14.1 - ~/.nvm/versions/node/v10.14.1/bin/node
    Yarn: 1.17.3 - ~/.nvm/versions/node/v10.14.1/bin/yarn
    npm: 6.11.3 - ~/.nvm/versions/node/v10.14.1/bin/npm
    Watchman: 4.9.0 - /usr/local/bin/watchman
  SDKs:
    iOS SDK:
      Platforms: iOS 13.1, DriverKit 19.0, macOS 10.15, tvOS 13.0, watchOS 6.0
    Android SDK:
      API Levels: 23, 26, 28, 29
      Build Tools: 28.0.3, 29.0.2
      System Images: android-29 | Intel x86 Atom, android-29 | Intel x86 Atom_64, android-29 | Google APIs Intel x86 Atom_64, android-29 | Google Play Intel x86 Atom, android-29 | Google Play Intel x86 Atom_64
  IDEs:
    Android Studio: 3.5 AI-191.8<IP_ADDRESS>00203
    Xcode: 11.1/11A1027 - /usr/bin/xcodebuild
  npmPackages:
    react: 16.9.0 => 16.9.0
    react-native: 0.61.2 => 0.61.2

Library version: 5.0.2
Steps To Reproduce

yarn add react-native-video
cd ios && pod install && cd ..
import Video from 'react-native-video'
<Video...
react-native run-android | react-native run-ios

Expected behaviour

For the video component to work the same / similar on both iOS & Android.
For the video to show.

Reproducible sample code
Not at the moment, simply added the library and used a dummy video uri | URL
Video sample
Vimeo video

Same here. Is this the expected behavior?

its happened with me at Android (RTL) only

Hi, same for me. An idea ?

+1


Invocation of form runtime

Augury: 1.14.0
Date: Tue, 22 Aug 2017 10:05:05 GMT
OS: Win32
Demo test application:
-- Git repository for demo app showing the issue (optional but very helpful for difficult issues).
-- If a code snippet will completely show the issue, please include it.
Description of issue:
-- Include (clipped) screenshot images if possible.
Angular version (required): ???
Steps to reproduce:

Additional details:

Hi @josersleal, could you provide some details with respect to the issue you are having?

I cried wolf.. apologies and thank you..


MODELIX-280 ci: only build on semantic version tags

Will ensure that only x.y.z tags are build, see https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions

The documentation doesn't mention that regular expressions are supported. It only talks about "glob patterns".

When tagging our upcoming releases with the release tag (e.g. modelix-23.1) these would then also be build and published. However, we do not need additional artifacts as we plan to provide component collections as BOM or gradle plugin. The tag is then only required for logical organization and documentation generation. Thus only building x.y.z* would be sufficient.

But I also want to publish a branch without making it an official release. See https://semver.org/#spec-item-9

If publishing pre-releases is required regularly, that should probably become part of the semantic-release configuration: https://semantic-release.gitbook.io/semantic-release/recipes/release-workflow/pre-releases

:tada: This PR is included in version 1.8.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Review the only-ordo supported is-as relationships?

In #824, there was a note about a need to review the only-ordo supported is-as relationships?
It also came up in https://github.com/EBISPOT/efo/issues/553
MONDO_0009061 'Cystic fibrosis': from @paolaroncaglia: of all its current parents in EFO, only 'autosomal recessive disease' should stay; all other parents should be deleted bcs they represent symptoms/phenotypes, CF is a multi-systemic disease.

@nicolevasilevsky
MONDO:0021001 hemochromatosis type 1 may be a similar case, see https://github.com/EBISPOT/efo/issues/568.

I think you are on top of this, do you need me to do anything here?

@paolaroncaglia has been reporting individual issues, but do you think we should look at all of the only-ordo supported is-as relationships? Is there an easy way to generate a list of all of these terms/relationships?

@zoependlington and I discussed the issue of incorrect Orphanet-derived superclasses with @nicolevasilevsky at our monthly EFO-Mondo call today. Zoe will try to query the problematic terms and their superclasses from Mondo for Nicole to look at. If necessary, we may ask Nico or Chris for help. Then we'll go from there.

Here's another example of incorrect Orphanet-derived superclasses in Mondo (that EFO inherits too):
MONDO:0009169 endocardial fibroelastosis
comment: Editor notes: ORDO classifies as both familial and non-familial
def: Endomyocardial fibroelastosis is a cause of unexplained childhood cardiac insufficiency. It results from diffuse thickening of the endocardium leading to dilated myocardiopathy in the majority of cases and restrictive myocardiopathy in rare cases. It may occur as a primary disorder or may be secondary to another cardiac malformation, notably aortic stenosis or atresia.
Subclass of:
familial restrictive cardiomyopathy
endocardium disease
non-familial restrictive cardiomyopathy
familial dilated cardiomyopathy
non-familial dilated cardiomyopathy
It follows from the def (and is supported by the editor's comment) that the only correct superclass is 'endocardium disease', and that all other superclasses should be deleted.

See also https://github.com/monarch-initiative/mondo/issues/565

(Re. reviewing Orphanet-derived incorrect parentage) While we wait for the agreed action item on EFO's part, I'll also make a note here that in some cases a disease term is correctly placed in EFO and has an EFO namespace, but gains incorrect Orphanet-derived parentage via Mondo because Mondo got the term directly from Orphanet. See e.g. 'Sneddon syndrome' that is a subclass of 'vascular disease' only in EFO, but gains 7 parents from Mondo, most of which look incorrect.

See spreadsheet

@cmungall could you do a SPARQL query to give us a list of all the Mondo classes that only have Orphanet as the source for the subClass Of assertion?
thank you!

@ShahimEssaid
could you do a SPARQL query to give us a list of all the Mondo classes that only have Orphanet as the source for the subClassOf assertion.
Zoe and I are going to review the is_a overloading and create tickets as needed. She has a spreadsheet with over 6000 terms in EFO that come from Orphanet, and have multiple parents.

@ShahimEssaid I think we talked about this SPARQL query before the holidays but I can't remember where it stands now. Would you be able to do this soon? Thanks!

@nicolevasilevsky
@ShahimEssaid
Hi, @zoependlington and I met with Open Targets today and they asked if there are any updates on this please. Many thanks!

@nicolevasilevsky to make sure I get this right, if there is a Mondo class A that has more than one parent, lets say B and C, should A be listed in the result if ALL the subclass axioms are only from Orphanet or if ANY of the subclass axioms are only from Orphanet?  In other words, if  A subclassof B only comes from Orphanet but A subclassof C comes from somewhere else with or without Orphanet, should A be listed? This is the "ANY" case.

Also, there are few subclassof axioms annotated with:
source="MONDO:Entailed"
source="MONDO:Redundant"
Would these axioms exclude the class since they aren't really Orphanet only?
About my earlier comment, this is an example of a Mondo class that has a "is_a" that is only coming from source="ORDO:*" but there is another "is_a" that is not only from ORDO.  Should this class be in the result or not?

[Term]
id: MONDO:0007060
name: spermatogenic failure 6
def: "Any azoospermia in which the cause of the disease is a mutation in the SPATA16 gene." [MONDO:patterns/disease_series_by_gene]
synonym: "acrosome malformation of spermatozoa" RELATED [OMIM:102530]
synonym: "azoospermia caused by mutation in SPATA16" EXACT [MONDO:design_pattern]
synonym: "globozoospermia" RELATED [OMIM:102530]
synonym: "round-headed spermatozoa" RELATED [OMIM:102530]
synonym: "SPATA16 azoospermia" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene]
synonym: "spermatogenic failure 6" EXACT [MONDO:Lexical, OMIM:102530]
synonym: "spermatogenic failure 6; SPGF6" RELATED [OMIM:102530]
synonym: "spermatogenic failure type 6" EXACT [MONDORULE:1, OMIM:102530]
synonym: "spermatozoa, round-headed" RELATED [OMIM:102530]
synonym: "SPGF6" RELATED [MONDO:Lexical, OMIM:102530]
xref: DOID:0070167 {source="MONDO:equivalentTo"}
xref: OMIM:102530 {source="MONDO:equivalentTo"}
xref: Orphanet:171709 {source="MONDO:subClassOf", source="OMIM:102530"}
xref: Orphanet:399808 {source="MONDO:subClassOf", source="OMIM:102530"}
xref: SCTID:236818008 {source="MONDO:equivalentTo", source="MONDO:kboom-pr-1.00/0.74/5.95"}
xref: UMLS:C0403825 {source="NCBI:mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="OMIM:102530"}

here:
is_a: MONDO:0004983 {source="DC-OMIM:102530", source="MONDO:Redundant", source="OMIM:102530"} ! azoospermia
is_a: MONDO:0015746 {source="ORDO:171709/btnt"} ! male infertility due to globozoospermia

@ShahimEssaid
@nicolevasilevsky
Thanks Shahim for your feedback! Your example above highlights that, ultimately, we're interested in all cases where there is at least one "is_a" that is only coming from source="ORDO:*". ('azoospermia' is a correct parent, while 'male infertility due to globozoospermia' is likely incorrect and should be reptresented as a phenotype instead.) So your "ANY" case above.
(@zoependlington , if you have any objection, please feel free to comment.)
As for your question on
source="MONDO:Entailed"
source="MONDO:Redundant"
I'll leave that to @nicolevasilevsky and/or @cmungall . Thanks!
Paola

Agreed with @paolaroncaglia, we'd be interested in the "ANY" case. So no objection from me. Thank you for getting back to us!

Addendum: I guess if the results are too numerous, we would then probably want to start working on the results subset corresponding to the "ALL" case above. The "ALL" case is the one we had in mind first, as a first step in fixing the issue; but ultimately, the "ANY" case will need to be examined too to carry out a thorough cleanup. Maybe we could re-assess the strategy when we have an idea of numbers from Shahim's results. Any opinion @cmungall?

@paolaroncaglia and @zoependlington
Shahim put together this list of Mondo terms for us. There are over 900 terms. I'm not sure what the best approach for this is? We could discuss further on our next call.
OrdoOrphanet6.txt

@nicolevasilevsky
Thanks! I had a quick look at the first 2-3 terms in Shahim's list and, yes, I believe they need work. The best strategy probably needs discussion as it's going to be a significant amount of work. Zoë is away until Tuesday, so I'll catch up with her next week, and we can surely discuss with you on our next call on Feb 18th if not sooner. Thanks.

sounds good!

Making a note that MONDO:0019170 'polyarteritis nodosa' also seems to have some questionable superclasses. Full list:
arteritis [ok based on def]
systemic inflammatory disease associated with an acquired peripheral neuropathy [probably not ok, unless the disease is always associated with an acquired peripheral neuropathy; otherwise that's just a symptom]
neurovascular disease [not ok; symptom]
secondary glomerular disease [not ok; symptom]
Note that the term has exactMatch not only with ORDO but also with other resources. Thanks.

@cmungall @nicolevasilevsky (cc @zoependlington )
Zoe and I agree with your suggested strategy and will try to help. For us, it'd be easier to work through a shared spreadsheet than via Mondo PRs. If you could please provide the spreadsheet, Zoe and I will then look into it and make further suggestions as appropriate. To help find the biggest offenders/grouping terms/prioritize the obsoletions, could the spreadsheet please contain:
Mondo ID
ORDO ID of the exact match
label
definition
number of children
number of parents
Mondo ID and label(s) of parent(s) (a single field separated by pipes would work)
We could then add a column with our suggestions (e.g. remove parents x and y; place under z instead, etc.) in a formatted/useful manner to be agreed upon.
Feel free to comment, and thank you!
Paola and Zoe

Parent
label
Child
label

MONDO:0015135
primary immunodeficiency due to a genetic defect in innate immunity
MONDO:0015133
quantitative and/or qualitative congenital phagocyte defect

MONDO:0015135
primary immunodeficiency due to a genetic defect in innate immunity
MONDO:0018545
primary immunodeficiency with predisposition to severe viral infection

MONDO:0015219
non-syndromic central nervous system malformation
MONDO:0017104
central nervous system cystic malformation

MONDO:0015227
non-syndromic limb malformation
MONDO:0017430
non-syndromic congenital joint dislocations

MONDO:0015227
non-syndromic limb malformation
MONDO:0017431
non-syndromic limb overgrowth

MONDO:0015227
non-syndromic limb malformation
MONDO:0019714
non-syndromic polydactyly, syndactyly and/or hyperphalangy

MONDO:0015490
predominantly small-vessel vasculitis
MONDO:0015491
immune complex mediated vasculitis

MONDO:0015502
pinnae and external auditory canal anomaly
MONDO:0044702
X-linked external auditory canal atresia-dilated internal auditory canal-facial dysmorphism syndrome

MONDO:0015594
non-paraneoplastic limbic encephalitis
MONDO:0044683
limbic encephalitis with neurexin-3 antibodies

MONDO:0015642
benign partial infantile seizures
MONDO:0015641
benign infantile focal epilepsy with midline spikes and wave during sleep

MONDO:0015652
chromosomal anomaly with epilepsy as a major feature
MONDO:0044641
9q33.3q34.11 microdeletion syndrome

MONDO:0015756
myeloid hemopathy
MONDO:0015688
myeloid neoplasms associated with eosinophilia and abnormality of PDGFRA, PDGFRB or FGFR1

MONDO:0015860
anomaly of puberty or/and menstrual cycle
MONDO:0044660
menstrual cycle-dependent periodic fever

MONDO:0015915
cerebellar malformation
MONDO:0020130
malformation of the cerebellar vermis

MONDO:0015921
ARX-related epileptic encephalopathy
MONDO:0018496
ARX-related encephalopathy-brain malformation spectrum

MONDO:0015923
acquired peripheral neuropathy
MONDO:0016137
acute and subacute inflammatory demyelinating polyneuropathy

MONDO:0015923
acquired peripheral neuropathy
MONDO:0016172
acquired sensory ganglionopathy

MONDO:0015923
acquired peripheral neuropathy
MONDO:0016178
peripheral neuropathy associated with monoclonal gammopathy

MONDO:0015923
acquired peripheral neuropathy
MONDO:0016179
acquired amyloid peripheral neuropathy

MONDO:0015932
non-syndromic urogenital tract malformation of female
MONDO:0015829
non-syndromic uterovaginal malformation

MONDO:0015933
non-syndromic urogenital tract malformation of male
MONDO:0044644
congenital agenesis of the scrotum

MONDO:0015961
genetic head and neck malformation
MONDO:0015482
otomandibular dysplasia

MONDO:0015961
genetic head and neck malformation
MONDO:0018562
genetic otorhinolaryngological malformation

MONDO:0016148
qualitative or quantitative defects of collagen 6
MONDO:0016111
non-dystrophic myopathy with collagen 6 anomaly

MONDO:0016155
qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan
MONDO:0016156
qualitative or quantitative defects of FKRP

MONDO:0016155
qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan
MONDO:0016157
qualitative or quantitative defects of fukutin

MONDO:0016155
qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan
MONDO:0016183
qualitative or quantitative defects of protein glycosyltransferase-like

MONDO:0016155
qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan
MONDO:0016184
qualitative or quantitative defects of protein O-mannosyltransferase 1

MONDO:0016155
qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan
MONDO:0016185
qualitative or quantitative defects of protein O-mannosyltransferase 2

MONDO:0016172
acquired sensory ganglionopathy
MONDO:0016173
non-paraneoplastic sensory ganglionopathy

MONDO:0016186
qualitative or quantitative defects of myofibrillar proteins
MONDO:0016187
qualitative or quantitative defects of desmin

MONDO:0016186
qualitative or quantitative defects of myofibrillar proteins
MONDO:0016188
qualitative or quantitative defects of alphaB-cristallin

MONDO:0016186
qualitative or quantitative defects of myofibrillar proteins
MONDO:0016189
qualitative or quantitative defects of filamin C

MONDO:0016186
qualitative or quantitative defects of myofibrillar proteins
MONDO:0016190
qualitative or quantitative defects of protein ZASP

MONDO:0016221
temporomandibular joint anomaly
MONDO:0018793
primary condylar hyperplasia

MONDO:0016925
partial trisomy/tetrasomy of chromosome 5
MONDO:0016942
partial trisomy/tetrasomy of the short arm of chromosome 5

MONDO:0016930
partial trisomy/tetrasomy of chromosome 9
MONDO:0016960
partial trisomy of the long arm of chromosome 9

MONDO:0016936
partial trisomy/tetrasomy of chromosome 18
MONDO:0016951
partial trisomy/tetrasomy of the short arm of chromosome 18

MONDO:0016999
X chromosome number anomaly
MONDO:0017000
X chromosome number anomaly with female phenotype

MONDO:0016999
X chromosome number anomaly
MONDO:0017001
X chromosome number anomaly with male phenotype

MONDO:0017000
X chromosome number anomaly with female phenotype
MONDO:0017002
polysomy of X chromosome

MONDO:0017083
lipoma associated with neurospinal dysraphism
MONDO:0017084
leptomyelolipoma

MONDO:0017104
central nervous system cystic malformation
MONDO:0017105
glioependymal/ependymal cyst

MONDO:0017344
Epstein-Barr virus-associated carcinoma
MONDO:0017348
lymphoepithelial-like carcinoma

MONDO:0017595
aggressive B-cell non-Hodgkin lymphoma
MONDO:0015818
aggressive primary cutaneous B-cell lymphoma

MONDO:0017595
aggressive B-cell non-Hodgkin lymphoma
MONDO:0018813
high grade B-cell lymphoma with MYC and/ or BCL2 and/or BCL6 rearrangement

MONDO:0017653
epilepsy and/or ataxia with myoclonus as major feature
MONDO:0017654
non progressive epilepsy and/or ataxia with myoclonus as a major feature

MONDO:0017653
epilepsy and/or ataxia with myoclonus as major feature
MONDO:0017655
progressive epilepsy and/or ataxia with myoclonus as a major feature

MONDO:0017710
congenital systemic veins anomaly
MONDO:0018811
congenital portosystemic shunt

MONDO:0018230
primary bone dysplasia
MONDO:0018231
primary bone dysplasia with progressive ossification of skin, skeletal muscle, fascia, tendons and ligaments

MONDO:0018230
primary bone dysplasia
MONDO:0018232
primary bone dysplasia with micromelia

MONDO:0018230
primary bone dysplasia
MONDO:0019694
spondylodysplastic dysplasia

MONDO:0018230
primary bone dysplasia
MONDO:0019699
slender bone dysplasia

MONDO:0018230
primary bone dysplasia
MONDO:0019700
primary bone dysplasia with multiple joint dislocations

MONDO:0018230
primary bone dysplasia
MONDO:0019704
primary bone dysplasia with decreased bone density

MONDO:0018230
primary bone dysplasia
MONDO:0019705
primary bone dysplasia with defective bone mineralization

MONDO:0018230
primary bone dysplasia
MONDO:0019707
primary osteolysis

MONDO:0018230
primary bone dysplasia
MONDO:0019708
primary bone dysplasia with disorganized development of skeletal components

MONDO:0018230
primary bone dysplasia
MONDO:0019709
cleidocranial dysplasia and isolated cranial ossification defect

MONDO:0018230
primary bone dysplasia
MONDO:0019718
lethal chondrodysplasia

MONDO:0018230
primary bone dysplasia
MONDO:0028741
overgrowth or tall stature syndrome with skeletal involvement

MONDO:0018454
dysostosis of genetic origin
MONDO:0019710
dysostosis with predominant craniofacial involvement

MONDO:0018454
dysostosis of genetic origin
MONDO:0019711
dysostosis with predominant vertebral and costal involvement

MONDO:0018454
dysostosis of genetic origin
MONDO:0019712
patellar dysostosis

MONDO:0018455
dysostosis of genetic origin with limb anomaly as a major feature
MONDO:0017429
joint formation defects

MONDO:0018455
dysostosis of genetic origin with limb anomaly as a major feature
MONDO:0017433
dysostosis with combined reduction defects of upper and lower limbs

MONDO:0018455
dysostosis of genetic origin with limb anomaly as a major feature
MONDO:0018236
dysostosis with limb and face anomalies as a major feature

MONDO:0018455
dysostosis of genetic origin with limb anomaly as a major feature
MONDO:0019714
non-syndromic polydactyly, syndactyly and/or hyperphalangy

MONDO:0018562
genetic otorhinolaryngological malformation
MONDO:0015502
pinnae and external auditory canal anomaly

MONDO:0018652
biological anomaly without phenotypic characterization
MONDO:0018651
lipoyl transferase 2 deficiency

MONDO:0019063
vascular anomaly
MONDO:0016235
complex vascular malformation with associated anomalies

MONDO:0019213
cerebral organic aciduria
MONDO:0017686
inborn aminoacylase deficiency

MONDO:0019704
primary bone dysplasia with decreased bone density
MONDO:0044675
LRP5-related primary osteoporosis

MONDO:0019712
patellar dysostosis
MONDO:0044641
9q33.3q34.11 microdeletion syndrome

MONDO:0020001
respiratory or thoracic malformation
MONDO:0015929
thoracic malformation

MONDO:0020001
respiratory or thoracic malformation
MONDO:0015930
respiratory malformation

MONDO:0020019
digestive tract malformation
MONDO:0019513
esophageal malformation

MONDO:0020019
digestive tract malformation
MONDO:0019998
gastroduodenal malformation

MONDO:0020019
digestive tract malformation
MONDO:0019999
intestinal malformation

MONDO:0020020
visceral malformation of the liver, biliary tract, pancreas or spleen
MONDO:0015213
non-syndromic visceral malformation

MONDO:0020052
partial autosomal trisomy/tetrasomy
MONDO:0016925
partial trisomy/tetrasomy of chromosome 5

MONDO:0020052
partial autosomal trisomy/tetrasomy
MONDO:0016930
partial trisomy/tetrasomy of chromosome 9

MONDO:0020052
partial autosomal trisomy/tetrasomy
MONDO:0016936
partial trisomy/tetrasomy of chromosome 18

MONDO:0020052
partial autosomal trisomy/tetrasomy
MONDO:0016972
partial duplication of the long arm of chromosome 22

MONDO:0020059
gonosome number anomaly
MONDO:0016999
X chromosome number anomaly

MONDO:0020059
gonosome number anomaly
MONDO:0017005
Y chromosome number anomaly

MONDO:0020133
posterior fossa malformation
MONDO:0015915
cerebellar malformation

MONDO:0020138
ataxia with dementia
MONDO:0020139
early-onset ataxia with dementia

MONDO:0020138
ataxia with dementia
MONDO:0020140
late-onset ataxia with dementia

MONDO:0020152
rare eyelid malformation
MONDO:0020155
eyelid border anomaly

MONDO:0020216
secondary dysgenetic glaucoma
MONDO:0020221
secondary glaucoma due to a proliferation and differentiation anomaly

MONDO:0020217
secondary dysgenetic glaucoma associated with neural crest cell migration anomaly
MONDO:0020219
corneogoniodysgenesis

MONDO:0020217
secondary dysgenetic glaucoma associated with neural crest cell migration anomaly
MONDO:0020220
corneoiridogoniodysgenesis

MONDO:0020223
lens and zonula anomaly
MONDO:0020235
lens size anomaly

MONDO:0020223
lens and zonula anomaly
MONDO:0020237
lens shape anomaly

MONDO:0020262
nervous system anomaly with eye involvement
MONDO:0020263
spinocerebellar ataxia with oculomotor anomaly

MONDO:0020262
nervous system anomaly with eye involvement
MONDO:0020264
spinocerebellar degenerescence and spastic paraparesis with an oculomotor anomaly

MONDO:0020266
genodermatosis with ocular features
MONDO:0016997
hereditary epidermolysis bullosa associated with ocular features

MONDO:0020266
genodermatosis with ocular features
MONDO:0020271
phakomatosis with eye involvement

MONDO:0020285
transposition of the great arteries and conotruncal cardiac anomaly
MONDO:0020286
aortic malformation

MONDO:0020285
transposition of the great arteries and conotruncal cardiac anomaly
MONDO:0020287
pulmonary artery or pulmonary branch anomaly

MONDO:0022410
retinal ciliopathy
MONDO:0022397
retinal ciliopathy due to mutation in the retinitis pigmentosa-1 gene

MONDO:0022410
retinal ciliopathy
MONDO:0022399
retinal ciliopathy due to mutation in the rpgr gene

MONDO:0022410
retinal ciliopathy
MONDO:0022400
retinal ciliopathy due to mutation in the rpgrip gene

MONDO:0022410
retinal ciliopathy
MONDO:0022404
retinal ciliopathy due to mutation in usher gene

MONDO:0022410
retinal ciliopathy
MONDO:0022405
retinal ciliopathy due to mutation in nephronophthisis gene

MONDO:0022410
retinal ciliopathy
MONDO:0022407
retinal ciliopathy due to mutation in bardet-biedl gene

MONDO:0044685
autoimmune/inflammatory optic neuropathy
MONDO:0044687
chronic relapsing inflammatory optic neuropathy

MONDO:0044685
autoimmune/inflammatory optic neuropathy
MONDO:0044688
isolated optic neuritis

MONDO:0044685
autoimmune/inflammatory optic neuropathy
MONDO:0044689
recurrent idiopathic neuroretinitis

@cmungall
Any chance you could export the table above as a Google spreadsheet, please?
Ignore me if you're still working on it. Thanks.

I can do it!

Thanks @nicolevasilevsky and @cmungall . We'll work on it over the next few days and will add comments in the spreadsheet. Will ping you when we're done and go from there.

@cmungall
I have a question on the spreadsheet already please. My understanding is that you have extracted Mondo terms that only have ORDO evidence. MONDO:0016172 acquired sensory ganglionopathy is one such term (in the spreadsheet) and has 2 children, both of which only have ORDO evidence, but only 1 of the 2 children is in the spreadsheet. Same for MONDO:0015860 anomaly of puberty or/and menstrual cycle - has several children and >1 ORDO-only, but only 1 child is in the spreadsheet. May I please make sure if I'm missing anything before I keep going? Thanks, and have a good weekend!

@cmungall @nicolevasilevsky
Sorry to disturb you again about this (do let me know if you can't address this right now). I was hoping to start work on the list/spreadsheet of ORDO terms that you prepared, but I came across an issue, see my earlier comment in this ticket. If you have a chance, could you please address my question there? Thanks! :-)

The question is for @cmungall, right?
Everything is okay in Portland (so far), I am more worried about you! Feel free to ping us anytime @paolaroncaglia.

@nicolevasilevsky and @cmungall

The question is for @cmungall, right?
Right :-)
Thank you for your concern and availability! All the best,
Paola

I'm investigating
This was a quick query intended just to give high profile candidates for obsoletion. There may be better ways of doing this

perhaps @ShahimEssaid could help with a query?

@cmungall Thank you for following up on this. May I please ask if you or @nicolevasilevsky heard back from @ShahimEssaid about possibly helping with a query? I understand if the health emergency makes it difficult to progress on this. When you can, please let me know where we are with this; because if you need more time, no problem at all, I'm happy to start looking at the list of high profile candidates for obsoletion you provided, and I'll look up their children myself via OLS or Protege. Asking just so we can avoid duplication of efforts. Thank you all, and take care.

I just pinged @ShahimEssaid again. I know he has a lot of deadlines right now, so you could proceed without him @paolaroncaglia that would be great. Hopefully Shahim will be able to comment here soon.
Thanks!

@nicolevasilevsky
Based on https://github.com/monarch-initiative/mondo/issues/1283#issuecomment-604033234, Zoe and I fear that any work on current Orphanet terms in Mondo may risk being "over-written" by an upcoming update of the Orphanet ingest. So the tasks discussed in recent comments in this thread may best be delayed. We'll discuss internally at EFO, and will then catch up with you at our next EFO-Mondo call. Of course, if there's any concern or urgency on either side, we can discuss sooner. Thanks!

Good point! It is my understanding that the new Orphanet ingest will not override any work that has currently been done though (as we've made a lot of changes already.)
I hope you don't mind putting this off. it's okay to delay on our end.

@nicolevasilevsky

Good point! It is my understanding that the new Orphanet ingest will not override any work that has currently been done though (as we've made a lot of changes already.)
That would make sense to me too! I'll aim at looking at the list of grouping terms before our next EFO-Mondo call, so we can hopefully discuss then.

It's a bit of a priority on our end, for Open Targets, so now that I'm reassured that the work wouldn't be overwritten, I'll try to spend some time on it. I'm just sticking to non-committal phrasing because you never know these days. Thanks, take care and speak soon!

Making a note here that another (Orphanet-derived) problematic term is MONDO:0016575 'primary ciliary dyskinesia'. 3 of its 5 parents represent symptoms, and it has 41 children, that inherit the incorrect ancestry. Notably, 'primary ciliary dyskinesia' is not inSubset ordo_group_of_disorders. Its parent 'ciliopathy' is, but its own parents are fine, so focusing on ORDO grouping terms alone may be of limited use - need to go deeper too.

For a quick fix while I'm looking into this, you may want to

[ ] Delete the axiom 'primary ciliary dyskinesia' Subclass of:
genetic infertility
male infertility due to sperm motility disorder
[ ] The parent 'rare pulmonary disease' is also suspicious and should be deleted. In fact the whole definition is, and may better be replaced by the Wikipedia one (https://en.wikipedia.org/wiki/Primary_ciliary_dyskinesia).

Thanks!

@nicolevasilevsky
@cmungall
Quick update on the ORDO grouping terms you highlighted in https://github.com/monarch-initiative/mondo/issues/834#issuecomment-595322698. I looked at a subset of those, and added comments in https://docs.google.com/spreadsheets/d/1KRAoGoj1O2-nm0ll5vlDMzm-9bsgMvvNza9wFIz6REA/edit#gid=656900674 (tab "Paola's summary"). The rows in red are for terms I'd suggest prioritizing for obsoletion. The comment columns for those contains some general consideration and tips I hope you'll find useful. It's still a work in progress, but I wanted to write down some notes for your consideration in case I can't come back to this before our meeting on Monday. Thanks!

The parent 'rare pulmonary disease' is also suspicious and should be deleted.

This term is obsoleted:
MONDO_0015118

[ ] Consider obsoleting: 'oculomotor apraxia or related oculomotor disease', do we need this grouping class?

closing this, duplicate with https://github.com/monarch-initiative/mondo/issues/704
@sabrinatoro and I are working on this.


modal and notification z-index bug

Version
0.7.1
Environment
linux服务器，google浏览器
Reproduction link
https://ng-zorro-antd-setup.stackblitz.io
Steps to reproduce
The development environment

when I ng build
The production environment

What is expected?
生产环境能够正常显示
What is actually happening?
生产环境modal遮住了notification
Other?

@eevin Pls provide a correct production link to reproduce this issue

when i remove node_modules and npm i  then ok
thanks


How to do multi-label classification with torchvision?

You need to change the loss that you use in your models.
This is not really related to torchvision, closing it.


any consideration of not using sqlparser

crate link: https://docs.rs/sqlparser/latest/sqlparser/

This project is aiming for zero dependency. So I will write the sql parser on my own. This is also for my learning.
But thank you for the suggestion anyway!


[FEATURE] Add SQLITE3 ODBC to all the kicad* containers

Hi everybody,
It would be nice to see SQLITE3 ODBC included in all the containers in order to use the 'new' database library available in kicad.
Following the following guide, I am currently installing it after the kicad7_auto container creation with:
apt update
apt install libodbc1 -y
apt install unixodbc -y
odbcinst -j
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/odbc:$LD_LIBRARY_PATH

apt install sqlite3 -y
apt install libsqliteodbc -y

Remark: I am not sure if the odbcinst -j is needed but the LD_LIBRARY_PATH has to be done before the libsqliteodbc install for it to register properly.
I can imagine other ODBC driver could also be usefull (MariaDB, Postgresql,...)...
Thank you for this amazing work.
Xavier

Hi @hpopols !
This looks interesting, but:

If added it will be added to kicad7_auto_full, not kicad7_auto because this is an uncommon tool. Less than 1% users will really use it.
The guide looks really strange to me.

Why it looks strange?

I don't see why a package will need to manually run odbcinst -j, this should be run in the postinst script.
Why do you need to set an LD_LIBRARY_PATH? This is needed only if some of the components isn't really compiled for the base system and you need to force something. Otherwise the code should look for plugins there.

Looking at Debian descriptions:

unixodbc: This package contains isql, a command-line tool that allows SQL commands to be entered interactively.
Is this really needed? Also note that this will pull libodbc1 as a dependency.
sqlite3: Is this really needed? libsqliteodbc pulls the libsqlite3-0 package.

And looking at libsqliteodbc I see:
odbcinst -i -d -f /usr/share/sqliteodbc/unixodbc.ini

So the tutorial you used doesn't look good to me. May be it works, but does a lot of things that doesn't seem to be needed. Try only doing this:
apt update
apt install libodbc1 libsqliteodbc -y

And let me know if provides the same functionality

Hi @set-soft !

If added it will be added to kicad7_auto_full, not kicad7_auto because this is an uncommon tool. Less than 1% users will really use it.

I agree at least for now because this functionality in kicad is pretty new and is not very polished yet (only basic functionalities are now implemented, there is performance issues and the documentation is very light). However, I have the feeling people using CI/CD and kicad_auto are likely to use database libs in the future (but perhaps not SQLite3 ones). Futhermore, database libs are widely used with most common "professional" CAD software in the electronic industry and good/bad habits are difficult to change.
My choice for SQLite was mainly driven by 2 things:

Can be versioned as binary files and included in the kicad project as a git submodule
Is able to work offline (opposed to classic databases)

Concerning the ODBC installation:

So the tutorial you used doesn't look good to me. May be it works, but does a lot of things that doesn't seem to be needed. Try only doing this:
apt update
apt install libodbc1 libsqliteodbc -y

And let me know if provides the same functionality

After digging a little into odbc and the debian packages, I realized you were right!
I did test your proposition in a kicad7_auto:1.6.3 container and it does not work but it was pretty close. Indeed, the SQLite3 driver (from libsqliteodbc) has to be installed (registrered) to ODBC with the odbcinst tool to work. However this tool is not installed by default...
So the working solution is a simple:
apt update
apt install odbcinst libodbc1 libsqliteodbc -y

From there the ODBC driver for SQLite is now known as 'SQLite3'.
For reference the "source" parameter in the library database config file *.kicad_dbl should look like:
...
    "source": {
        "type": "odbc",
        "dsn": "",
        "username": "",
        "password": "",
        "timeout_seconds": 2,
        "connection_string": "Driver={SQLite3};Database=database.sqlite"
    },
...

Hi @hpopols !
The new images with Debian 12.1, Blender 3.5.1 and KiCad 7.0.7 contains the ODBC libs.

Hi @set-soft !
Sorry for the late response, I just updated to the new image and it is working fine!
Thank you for  everything!
Xavier


Update pricing page link to go to /signup, not /signin

Pulled over from https://github.com/pulumi/pulumi-service/issues/8473

Aha, I see now that the hugo link is to https://app.pulumi.com/site/trial - so what happens is, you're not logged in (because you're a new user), so we direct you to the default login page which is signin, not signup.  I don't think it makes sense to make the default page signup, so I think what we actually want to happen here is

Execute this https://github.com/pulumi/pulumi-service/issues/11917 ticket to get query params in the url
Then once 1 is done, we can update the hugo link to https://app.pulumi.com/signup?some=newparams.  It looks like we strip query params when going from signup -> homepage, but I _think _ we can probably get around that.

I'm gonna move both issues to next milestone and take them on then.


[SP-3565] Backport of PDI-7090 - Only one user can make changes in a repository at any time. (Database Repository is locked) (6.1 Suite).

Fixed an additional problem in 6.1. When user editing or create carte server it locks database (see steps in comments [SP-3565]).
This commit uses approach from base commit https://github.com/pentaho/pentaho-kettle/pull/3857/commits/befadee3293dd4f8f3c5999dd1e345f56b4cdabd

Build Completed
:fire: This pull request has some issues. It would be preferable to fix them in order for it to be just perfect. See below for more details. Some links are also available below for further assistance in addressing those issues.
Build Commands
ant -Dtestreports.dir=bin/reports/unit-test -f engine/build.xml clean-all resolve jacoco && ant -f engine/build.xml checkstyle publish-local

Cleanup Commands
rm -r ~/.ivy2/local || echo no publish local to remove

Changed files
  engine/src/org/pentaho/di/repository/kdr/delegates/KettleDatabaseRepositoryConnectionDelegate.java

Unit test coverage change
These statistics help you identify how your changes have affected the coverage of the following files. If a file is not in this list, then its coverage was not affected by your changes. To get some help interpreting these metrics, please refer to Jacoco's documentation.
org.pentaho.di.repository.kdr.delegates.KettleDatabaseRepositoryConnectionDelegate

Instruction Change: -.00%:small_red_triangle_down:
Line Change: -.01%:small_red_triangle_down:

org.pentaho.di.repository.kdr.KettleDatabaseRepositoryCreationHelper

Branch Change: -1.64%:small_red_triangle_down:
Complexity Change: -.69%:small_red_triangle_down:
Instruction Change: -2.43%:small_red_triangle_down:
Line Change: -2.95%:small_red_triangle_down:

org.pentaho.di.trans.step.StepMeta

Instruction Change: -.19%:small_red_triangle_down:
Line Change: -.27%:small_red_triangle_down:

org.pentaho.di.trans.steps.excelwriter.ExcelWriterStepMeta

Branch Change: -1.28%:small_red_triangle_down:
Complexity Change: -.79%:small_red_triangle_down:
Instruction Change: -.08%:small_red_triangle_down:

org.pentaho.di.trans.steps.memgroupby.MemoryGroupByMeta

Branch Change:  + 3.53%
Complexity Change:  + 4.05%
Instruction Change:  + .35%
Line Change:  + 1.07%

org.pentaho.di.trans.steps.sortedmerge.SortedMergeMeta

Instruction Change: -.18%:small_red_triangle_down:

org.pentaho.di.trans.steps.uniquerows.UniqueRowsMeta

Instruction Change:  + .18%

@mbatchelor Could you please review it?

@mbatchelor Could you please review it?


container: quote registry password

When using a quote in the registry password then we have the following
error:
The error was: ValueError: No closing quotation
To fix this we need to use the quote filter.
Close: https://bugzilla.redhat.com/show_bug.cgi?id=1880252
Signed-off-by: Dimitri Savineau<EMAIL_ADDRESS>

jenkins test centos-container-all_daemons


feat: throw BoxApiError in C# fetch, add additional data to ResponseInfo (box/box-codegen#439)

Pull Request Test Coverage Report for Build<PHONE_NUMBER>
Warning: This coverage report may be inaccurate.
This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

86 of 101 (85.15%)  changed or added relevant lines in 9 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.4%) to 76.059%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

Box.Sdk.Gen/Box/CcgAuth/BoxCcgAuth.cs
4
5
80.0%

Box.Sdk.Gen/Box/DeveloperTokenAuth/BoxDeveloperTokenAuth.cs
3
4
75.0%

Box.Sdk.Gen/Box/JwtAuth/BoxJwtAuth.cs
4
6
66.67%

Box.Sdk.Gen/Box/Oauth/BoxOAuth.cs
4
6
66.67%

Box.Sdk.Gen/Networking/Fetch.cs
19
28
67.86%

Totals

Change from base Build<PHONE_NUMBER>:
0.4%

Covered Lines:
6474

Relevant Lines:
8386

💛  - Coveralls


Fix bug in not assigning material id to faces

Material ids were not assigned to faces if the first face with this material was in another thread buffer than where usemtl command was.

Super cool! Merged!


ConnectionResetError('Connection lost')

Hello,
Iam using home assistant as docker version and have installed whisper, piper and openwakeword.
Today, after I tried to use this with my analog phone, I was wondering why nothing works. In Home Assistant "Speech to text" is loading endless and in docker compose logs I can see an ConnectionResetError('Connection lost')
Here is an Log output:
whisper       | INFO:__main__:Downloading FasterWhisperModel.BASE_INT8 to /data
whisper       | INFO:__main__:Ready
piper         | INFO:__main__:Ready
whisper       | INFO:wyoming_faster_whisper.handler:
whisper       | ERROR:asyncio:Task exception was never retrieved
whisper       | future: <Task finished name='Task-11' coro=<AsyncEventHandler.run() done, defined at /usr/local/lib/python3.9/dist-packages/wyoming/server.py:28> exception=ConnectionResetError('Connection lost')>
whisper       | Traceback (most recent call last):
whisper       |   File "/usr/local/lib/python3.9/dist-packages/wyoming/server.py", line 35, in run
whisper       |     if not (await self.handle_event(event)):
whisper       |   File "/usr/local/lib/python3.9/dist-packages/wyoming_faster_whisper/handler.py", line 78, in handle_event
whisper       |     await self.write_event(Transcript(text=text).event())
whisper       |   File "/usr/local/lib/python3.9/dist-packages/wyoming/server.py", line 26, in write_event
whisper       |     await async_write_event(event, self.writer)
whisper       |   File "/usr/local/lib/python3.9/dist-packages/wyoming/event.py", line 114, in async_write_event
whisper       |     await writer.drain()
whisper       |   File "/usr/lib/python3.9/asyncio/streams.py", line 387, in drain
whisper       |     await self._protocol._drain_helper()
whisper       |   File "/usr/lib/python3.9/asyncio/streams.py", line 190, in _drain_helper
whisper       |     raise ConnectionResetError('Connection lost')
whisper       | ConnectionResetError: Connection lost
^Ccanceled

I didnt changed anything less the phone. I tested first with atom echo => works fine, but now everything is rip :´(
version: "3"
services:
  whisper:
    container_name: whisper
    image: rhasspy/wyoming-whisper
    command: --model base-int8 --language de
    volumes:
      - ./whisper-data:/data
    environment:
      - TZ=Europe/Berlin
    restart: unless-stopped
    ports:
      - 10300:10300

  piper:
    container_name: piper
    image: rhasspy/wyoming-piper
    command: --voice de_DE-thorsten_emotional-medium
    volumes:
      - ./piper-data:/data
    environment:
      - TZ=Europe/Berlin
    restart: unless-stopped
    ports:
      - 10200:10200

  openwakeword:
    container_name: openwakeword
    image: rhasspy/wyoming-openwakeword
    volumes:
      - ./openwakeword-data:/data
      - ./openwakeword-wakeword:/custom
      - /etc/timezone:/etc/timezone:ro
      - /etc/localtime:/etc/localtime:ro
    environment:
      - TZ=Europe/Berlin
    command: --preload-model 'ok_nabu' --custom-model-dir /custom
    restart: unless-stopped
    ports:
      - 10400:10400/udp
      - 10400:10400/tcp

Thank you all in advanced
A small edit cause it could be important (I think ^^) the Home Assistant, Assistant Log
stage: done
run:
  pipeline: 01hj0r5dsj486zmkxmn7p5qy2k
  language: de
events:
  - type: run-start
    data:
      pipeline: 01hj0r5dsj486zmkxmn7p5qy2k
      language: de
    timestamp: "2024-01-12T05:43:28.121428+00:00"
  - type: stt-start
    data:
      engine: stt.faster_whisper
      metadata:
        language: de
        format: wav
        codec: pcm
        bit_rate: 16
        sample_rate: 16000
        channel: 1
    timestamp: "2024-01-12T05:43:28.122022+00:00"
  - type: stt-vad-start
    data:
      timestamp: 170
    timestamp: "2024-01-12T05:43:28.140268+00:00"
  - type: stt-vad-end
    data:
      timestamp: 535
    timestamp: "2024-01-12T05:43:28.170798+00:00"
  - type: run-end
    data: null
    timestamp: "2024-01-12T05:43:58.116595+00:00"
stt:
  engine: stt.faster_whisper
  metadata:
    language: de
    format: wav
    codec: pcm
    bit_rate: 16
    sample_rate: 16000
    channel: 1
  done: false

Migrated to another hardware. Upgraded CPU and RAM, issue doesn’t persist anymore. Fixed


ReactFlow v12 - class nodrag doesn't prevent selection as it did in previous versions

What platform were you using when you found the bug?

React Flow / Svelte Flow version: 12.0.3
Browser and version: Google Chrome 126.0.6478.126
OS and version: Ubuntu 24

Live code example
https://codesandbox.io/p/sandbox/reactflow-nodrag-exmple-forked-fczk2z
Describe the Bug
The class nodrag doesn't prevent selection in the new v12 Reactflow. This class was suggested in this issue to prevent the selection on ex. input components. I couldn't find any official documentation elsewhere how to do it.
Steps to reproduce the bug or issue

Go to https://codesandbox.io/p/sandbox/reactflow-nodrag-exmple-forked-fczk2z
Click on the node containing "Not selected"
Node's state changes to selected despite having the class nodrag on it

Expected behavior
I expect the same behavior, meaning that the selection is prevented for class nodrag as in previous versions, see working example on v11.11.4 https://codesandbox.io/p/sandbox/reactflow-nodrag-exmple-forked-rq6gfv
Additional context
Eventually, it would be more straight forward to have a dedicated class (and documentation) for preventing selection.

nodrag behaves the same as it did in v11.
What did change though is the default value of nodeDragThreshold which in v11 was set to 0 (as to not introduce a breaking change) while v12 uses 1 as the default value.
If you want the same behavior as previously, set nodeDragThreshold={0} again.
For comparison a v11 sandbox with nodeDragThreshold={1} producing the same result as v12's default behavior: https://codesandbox.io/p/sandbox/dank-worker-c7f25r?file=%2FCircleNode.jsx%3A19%2C32
(use the input node on the bottom right and observe that it's gonna be selected/unselected)
And a v12 sandbox with nodeDragTheshold={0} producing the default behavior of v11: https://codesandbox.io/p/sandbox/reactflow-nodrag-exmple-forked-vtvz2d?file=%2Fsrc%2FApp.js%3A60%2C29

@bcakmakoglu Thanks for the answer. Since having nodeDragThreshold={1} has other benefits, I decided to use the workaround suggested in the related issue.
I still suggest to have a dedicated class for preventing selection.


[BUG]: Confluence crawler incorrectly does not accept subdomains

How are you running AnythingLLM?
Docker (local)
What happened?
Subdomains seem to be only supported for normal TLDs.
Something like https://confluence.myorg.at/display/SPACE/* works.
Something like https://confluence.myorg.gv.at/display/SPACE/* doesn't work.
Apparently it uses regular expression to check if an URL is valid, but it's hardcoded to only check for a single or no subdomain at all.
Are there known steps to reproduce?
Click Data Connectors, click Confluence, enter the URL, click Submit, get error

I'm assuming this is also why it doesn't work when there is a port in the URL??
Mine is http://DOMAIN.net:8090/display/PRJ and it tells me it's not in the correct format.

And you can also run confluence under a context path - which also does not work. For example:
https://my.domain.com/confluence/display/myspace/*


[Bug] Auth information should not be printed to STDOUT

I have an application using this module and output is aggregated to LogDNA.  Many more people can see the log output than the small number who should have access to the Mongo Atlas API keys.
This line:
https://github.com/mgmonteleone/python-atlasapi/blob/dea498f7230869c2502d5990ffee02ca947abdff/atlasapi/network.py#L102
is printing to STDOUT.
This could be useful, but I think it would be better to keep this by only logging it on DEBUG level so it does not show up in more public logs.

Thabks @jkirkham-ratehub , I will put take care of this in the next cycle.


Use null coalesce for $uri in prepareUrlForRequest

Saved you the hassle.

Hi @zachlm ,
Thanks a bunch!


Initial position and rotaion for solid object

Description of the problems and associated solutions

Translation and rotation for solid object in DEM were not in documentation.
Translation was previously define by 4 parameters in the .prm . Now it's by one parameter.
Rotation was only possible around one axis (0,1,2) . Now it can be define around any axis in the 3D space.

How Has This Been Tested?

Basic translation and rotation with multiple solid object were done.

Documentation
-doc/parameters/dem/floating_mesh.rst

@OGaboriault you need to rebase Lethe with current master


failed to build custom distro with mender enabled

Hi, I created a custom distro layer using the create-distro-layer script:
> ./scripts-setup/create-distro-layer -d my-mender -m

After that, I tried to build an image using this distro:
> . ./setup-env -m jetson-nano-devkit-emmc -d my-mender build-my-mender
> bitbake core-image-minimal

Bitbake gives me the following error:
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
NOTE: Your conf/bblayers.conf has been automatically updated.
ERROR: Configuration has been re-parsed over 20 times, breaking out of the loop...
ERROR: Error parsing configuration files
Traceback (most recent call last):
  File "/home/hesmar/Development/3dvisionlabs/embedded/yocto2/tegra-demo-distro/repos/poky/bitbake/lib/bb/cookerdata.py", line 281, in CookerDataBuilder.parseBaseConfiguration(worker=False):
                                      "breaking out of the loop...")
    >                    raise Exception("Too deep config re-parse loop. Check locations where "
                                         "BB_INVALIDCONF is being set (ConfigParsed event handlers)")
Exception: Too deep config re-parse loop. Check locations where BB_INVALIDCONF is being set (ConfigParsed event handlers)

If I create the distro without Mender (removing the -m argument), bitbake works fine. How can I make it work with Mender support enabled?

Hello @hesmar
Please check you BBLAYERS_CONF_VERSION

Which branch?  This sequence worked for me on dunfell.

I am on kirkstone-l4t-r32.7.x.
@ichergui This is the bblayers.conf:
# Version of layers configuration, specific to
# each defined distro in the repository.

I think the problem is at https://github.com/OE4T/tegra-demo-distro/blob/4f6b3291e07f51e94025348a8dfcc0ea924b03b6/scripts-setup/create-distro-layer#L79-L81 which is only appending to the distro.conf file but not updating REQUIRED_TD_BBLAYERS_CONF_VERSION.  I'm not sure why it's doing the append as opposed to just copying the tegrademo-mender.conf from conf/distro/tegrademo-mender.conf as the distro default.
When I did that by hand using
cp layers/meta-tegrademo/conf/distro/tegrademo-mender.conf layers/meta-my-mender/conf/distro/my-mender.conf

I got past this error, then hit:
ERROR: ParseError at /home/dan/tegra-demo-distro/layers/meta-tegrademo/conf/distro/tegrademo.conf:34: Could not include required file conf/include/gstreamer-1.14.conf

Not sure where this is coming from - I see this file at
 find . -name "gstreamer-1.14.conf"
./repos/meta-tegra/contrib/conf/include/gstreamer-1.14.conf

and I see the corresponding layer in bblayers.conf
TD_BBLAYERS_CONF_VERSION = "my-mender-7"

BBPATH = "${TOPDIR}"
BBFILES ?= ""

BBLAYERS ?= " \
  /home/dan/tegra-demo-distro/layers/meta \
  /home/dan/tegra-demo-distro/layers/meta-tegra \
  /home/dan/tegra-demo-distro/layers/meta-tegra/contrib \

I removed the require conf/include/gstreamer-1.14.conf line and started the build, then added it back to attempt to reproduce but could not.

Ok, it also helps to apply the following change in the layers/meta-my-mender/conf/distro/my-mender.conf after using the create-distro-layer script:
REQUIRED_TD_BBLAYERS_CONF_VERSION = "${DISTRO}-7"

That's was my suggestion :wink: earlier

@dwalkes Any action from our side ?  otherwise I will close this issue

Sounds like the create-distro-layer script needs a fix.

Okay
I or @dwalkes will take it

I've got some hacks in https://github.com/OE4T/tegra-demo-distro/pull/233 which I think will fix it.

I'm closing this issue since there is a fix already merged.


New ADC interface

See the conversation in #61.

This is what I see when running func_test/adc_test:
...
Channel: 10, Raw Data: 0x05e6, Raw Voltage: 1.843712
Channel: 11, Raw Data: 0x0208, Raw Voltage: 0.634921
...

This was tested against a voltage divider; the DMM measures 1.45 V.

@vogeldylan @brunofalmeida Checked V_out by hand against ground and it comes out to ~1.808V on channel 10. So it looks like everything works correctly, modulo some accuracy issues.

This references heronmkII/pcbs#14

@siddMahen done my changes

@brunofalmeida @vogeldylan Unless anyone has any more comments, I think I'll merge this.


store: Filter blocks before loading it. Sort advertise labels; Added sharding e2e test.

[X] I added CHANGELOG entry for this change.
[ ] Change is not relevant to the end user.

Fixes: https://github.com/thanos-io/thanos/issues/1664
Signed-off-by: Bartek Plotka<EMAIL_ADDRESS>

test failed ):

It's not super clear why CI failed, any ideas?

Yea, I am busy with other things, but it looks like
}); err != nil && errors.Cause(err) != context.Canceled {
			t.Fatal(err)
		}

our errors.Cause does not really find proper cause. The returned error indeed is canceled overall, but probably some wrapping masks it.


MemoryTLESource._get_tle always returns something

MemoryTLESource._get_tle(...) always return some TLE as long as the cache is not empty. This is not a bug by itself, but when WSTLESource._get_tle(...) method calls it, it will always return the TLE in the cache no matter how old it is. I don't think this is the expected behaviour, nor that is useful in any case. There should be an extra parameter to make WSTLESource._get_tle(...) for another TLE if the closes cache tle is farther away from the requested epoch than desired. If  WSTLESource._fetch_tle(...) does not return a newer TLE, the return that of the cache, with a warning message.

...I have been just hit by this. I totally agree, this is not useful. I declare it a bug.


Add method to get Flysystem driver.

A very simple addition to the new FilesystemAdapter which allows access to underlying Flysystem driver. This is especially helpful when working with libraries that implement the League\Flysystem\FilesystemInterface interface.  Give me a few minutes and I'll send an update PR. Sorry about that Taylor!


Problems that i know

Windows 10 22H2
i've forked the latest one.
Randomly crashing while a spy decloaking. No minidmps or anything. I've implemented autovaccinator so i thought that might be the problem but no. Also without backtracking enabled (and enabled also i guess) aimbot targets the old ticks and misses everything. latest fake latency update caused auto backstabbing to not work. Melee swing prediction also misses. doubletapping doesnt work after latest updates (after amalgam) That is everything i know.

My opinion: skill issue


fix: upd reqs for kg service

to fix
knowledge-grounding_1            | 2022-08-31T08:53:54.165649082Z Traceback (most recent call last):
knowledge-grounding_1            | 2022-08-31T08:53:54.167562414Z   File "/opt/conda/bin/flask", line 5, in <module>
knowledge-grounding_1            | 2022-08-31T08:53:54.167573402Z     from flask.cli import main
knowledge-grounding_1            | 2022-08-31T08:53:54.167578283Z   File "/opt/conda/lib/python3.7/site-packages/flask/__init__.py", line 14, in <module>
knowledge-grounding_1            | 2022-08-31T08:53:54.167586353Z     from jinja2 import escape
knowledge-grounding_1            | 2022-08-31T08:53:54.167591017Z   File "/opt/conda/lib/python3.7/site-packages/jinja2/__init__.py", line 12, in <module>
knowledge-grounding_1            | 2022-08-31T08:53:54.167596165Z     from .environment import Environment
knowledge-grounding_1            | 2022-08-31T08:53:54.167600908Z   File "/opt/conda/lib/python3.7/site-packages/jinja2/environment.py", line 25, in <module>
knowledge-grounding_1            | 2022-08-31T08:53:54.167605997Z     from .defaults import BLOCK_END_STRING
knowledge-grounding_1            | 2022-08-31T08:53:54.167610738Z   File "/opt/conda/lib/python3.7/site-packages/jinja2/defaults.py", line 3, in <module>
knowledge-grounding_1            | 2022-08-31T08:53:54.167615943Z     from .filters import FILTERS as DEFAULT_FILTERS  # noqa: F401
knowledge-grounding_1            | 2022-08-31T08:53:54.167621003Z   File "/opt/conda/lib/python3.7/site-packages/jinja2/filters.py", line 13, in <module>
knowledge-grounding_1            | 2022-08-31T08:53:54.167626075Z     from markupsafe import soft_unicode
knowledge-grounding_1            | 2022-08-31T08:53:54.167630727Z ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/opt/conda/lib/python3.7/site-packages/markupsafe/__init__.py)


Enables building Partition from local ranges

This PR adds a freestanding function to create a Partition from local ranges. This has to be a freestanding function, because adding it to Partition would require including MPI, which leads to our device libraries requiring MPI (or at least the headers).

needs to be rebased ?

format-rebase!

format!

format!

rebase!

rebase!

rebase!


Add a fan-in aggregate status step.

This will be used as the single status check in GH branch protection
rules.

An example of failure is here - I used a cancel to test: https://github.com/pantsbuild/pex/actions/runs/1400792877

This also needs #1496 - macos Python 3.9 IT shard keeps timing our over there :/...


Updating prometheus-kube version to fix the issue with deprecated resources

Changed the kube-prometheus clone to the latest version and changed applys to creates to avoid issues with customResourceDefintition length. Also had to change the applys to creates in order to avoid issues with custom resource definition lengths.
There might still be issues with the github runners so checking this here.

Seems were running 1.19 of kubernetes from what I found after 1.25 the relevant packages are fully deprecated (not 100% sure from what version on minikube they exceeded 1.25 but 1.30.1 minikube is running 1.26.3). Is this a case of we individually should run older minikube/kubernetes builds or is it something that needs to be bumped in the pipeline @dinogun?

Alternatively assuming we dont want to update autotune to be compatible post 1.25, we can do a check for the kubernetes version via kubectl.  Then force the user to try with the final version of minikube prior to 1.26 (1.25.2) by spawning the minikube instance with --version 1.25.2 in the common helper(I have already written this if preferred). There is currently a check done but only in the hpo_demo_setup and it extracts the version from minikube directly instead of via kubectl which means that even if you run the correct version of kubernetes via minikube with a --version command it will fail.


Invalid model after changing a Metabolite id in the reaction mask

First the compartment is Null. -> Error while saving
If a new compartment is set for metabolite then the saving works but we get an error on loading the model.

I guess the metabolite must be associated with an existing compartment. If it is in a new compartment that compartment perhaps needs to be added explicitly to the model.

Looks like this is a known issue with cobrapy. As a work around we could check for Null and unknown compartments.
For unknown compartments we could just add the compartment. But what would be the expected behavior for Null?

As long as SBML is the default model format we probably have to enforce that for every metabolite a comparmtment is defined.

For now I introduce an "undefined_compartment_please_fix" and Issue Warning if no compartment is defined.


Analyze accumulate zombie processes on Ctrl+C

If I start jobs using multiple cores, and ctrl-c the job, seems over time doing this a few times starts to accumulate zombie processes.

Its been a while since this issue was created, and shockingly, it didn't fix itself. Managed to reproduce on 6.22.0.


Added new file for custom cpmpy exceptions

Added the cpmpy_expressions.py file where we can add our own exception classes.
They would all have to inherit from the CPMpyException
Added one exception class already as an example.
Does it make sense to have this file in the expressions folder? Or is it better to have a new folder
I will be using cpmpy exceptions in other bug fixes, that's why I am posting this pull request first.

I think it should be in the root folder, e.g. where model.py is, to have an exceptions.py; it is not an expression, nor a transformation, nor a solver, nor an add-on tool; instead it is shared by all.

I realise i called the branch cpmpy_expressions in stead of exceptions that is a typo..


User should be able to configure existing (already installed) extractor / loaders from the UI

Migrated from GitLab: https://gitlab.com/meltano/meltano/-/issues/520
Originally created by @bencodezen on 2019-03-22 15:20:07

Problem to solve

Users need to configure the extractors / loaders from the UI

Target audience

Web app user

Further details

Simplifies configuration process for extractors / loaders

Proposal

API to fetch configuration variables
API to update configuration variables

What does success look like, and how can we measure that?

User can successfully configure extractors and loaders on web app without touching the files directly

Regression test

[ ] Write adequate test cases and submit test results
[ ] Test results should be reviewed by a person from the team

Links / references
Continuation of: https://gitlab.com/meltano/meltano/issues/400
Tasks

[x] work w/Micaël to determine best design for authentication in context of which settings are persisted

Will leverage db approach and will have a backend implementation issue for the work, currently I'll provide the frontend implementation for this issue

[ ] UI to support the above settings to save

[ ] extraction date range(s) This will be part of the user flow change where EL is only connector config and a downstream UI is where the entity selection occurs
[ ] extractor/loader auth
other?

[ ] backend to support persistence (likely align with #519 meltano remove ... implementation)

View 20 previous comments from the original issue on GitLab


iOS blue indicator on status bar

Hi everyone!
Is it possible to show blue indicator on status bar in iOS while this plugin is active?

Sorry, found that is shown under when in use option

BackgroundGeolocation.configure({
...
stopOnTerminate: true,
...
});
@mrnix you can show blue indicator with this stopOnTerminate true.