Names of positional-only arguments should be allowed to mismatch

Environment data

Language Server version: Pylance 2021.3.0
OS and version: Windows 7
Python version (& distribution if applicable, e.g. Anaconda): 3.8.5(Anaconda)

Sample code
from __future__ import annotations

from datetime import date as Date
from typing import overload

@overload
def foo(date: Date, /) -> None:
    ...

@overload
def foo(year: int, month: int, day: int, /) -> None:
    ...

"""
Overloaded function implementation is not consistent with signature of overload 1
    Type "(arg0: date | int, arg1: int | None = None, arg2: int | None = None, /) -> None" cannot be assigned
to type "(date: date, /) -> None"
        Parameter name mismatch: "date" versus "arg0" | Pylance(reportGeneralTypeIssues)
"""
def foo(arg0: Date | int, arg1: int | None = None, arg2: int | None = None, /) -> None:
    if isinstance(arg0, Date):
        assert arg1 is None and arg2 is None
        date = arg0
    else:
        assert arg1 is not None and arg2 is not None
        date = Date(arg0, arg1, arg2)

    _ = date

Actual behavior
A warning is emitted.
Expected behavior
The naming in sample code should be considered OK.
Calls to foo would be like either foo(Date(2021, 3, 5)) or foo(2021, 3, 5), and argument names would never get used outside the function implementation. So there would be no conflicts between the mismatching names.

Thanks for the bug report. This will be addressed in the next release.

I think we could have a regression here :(
Environment data

Language Server version: Pylance v2021.7.1
OS and version: RHEL 7
Python version (& distribution if applicable, e.g. Anaconda): 3.6.6 64bit

Sample code
class Foo(Bar):
    @overload
    def find_item(self, product_id: int, name: str) -> requests.Response:
        """Finds item by its name and the product id (UQ)"""

    @overload
    def find_item(self, id: int) -> requests.Response:
        """Finds item by its id"""

    def find_item(self, id_or_product_id: int, name: str = None) -> requests.Response:
        data = {
            'id': id_or_product_id if not name else None,
            'product_id': id_or_product_id if name else None,
            'name': name
        }

        return requests.get(self.url, data=data)

Actual behavior
Overloaded function implementation is not consistent with signature of overload 1
  Type "(self: Foo, id_or_product_id: int, name: str | None = None) -> Response" cannot be assigned to type "(self: Foo, product_id: int, name: str) -> Response"
    Parameter name mismatch: "product_id" versus "id_or_product_id" Pylance(reportGeneralTypeIssues)

Expected behavior
The naming should be considered ok.
Remarks
Calls to Foo.find_item would be either:
foo = Foo()

foo.find_item(60, "my_item") # Find by product ID and name
foo.find_item(183617) # Find by name

One could argue that the overloaded signatures are overlapping and it is massively easy to make a mistake there but the issue still exists in the following example:
class Foo(Bar):
    @overload
    def find_item(self, name: str, product_id: int) -> requests.Response:
        """Finds item by its name and the product id (UQ)"""

    @overload
    def find_item(self, id: int) -> requests.Response:
        """Finds item by its id"""

    def find_item(self, name_or_id: Union[int, str], product_id: int = None) -> requests.Response:
        data = {
            'id': name_or_id if isinstance(name_or_id, int) else None,
            'name': name_or_id if isinstance(name_or_id, str) else None,
            'product_id': product_id
        }

        return requests.get(self.url, data=data)

Complaining about:
Overloaded function implementation is not consistent with signature of overload 1
  Type "(self: Foo, name_or_id: int | str, product_id: int | None = None) -> Response" cannot be assigned to type "(self: Foo, name: str, product_id: int) -> Response"
    Parameter name mismatch: "name" versus "name_or_id" Pylance(reportGeneralTypeIssues)

It is to be handled by the docstring popping up in the IDE. Also note that my type checking mode is set to basic when facing this issue.

Thanks. This issue is closed. I'd appreciate it if you'd open a new one and provide a minimal, self-contained code sample - one that doesn't depend on classes and types that are not declared in the sample.

@Wayofthesin, I think I understand what you're trying to do in your example. Pylance is correct in reporting a bug here. The problem is that the find_item method implement has a parameter called name_or_id. This parameter can be specified by the caller as either positional or by keyword. If it is specified by keyword, your program will crash as it is currently defined. If you want to specify that name_or_id can be specified only positionally, you would need to make the following changes:
@overload
def find_item(self, product_id: int, /, name: str) -> requests.Response:
    ...
@overload
def find_item(self, id: int, /) -> requests.Response:
    ...
def find_item(self, id_or_product_id: int, name: str = None) -> requests.Response:
    ...

Pylance will no longer emit an error if you make this correction to your code.

Yeah I just realized it. Forget the ticket please (facepalm)


ERROR: Unable to extract uploader id; please report this issue

Checklist

[ ] I'm reporting a broken site support issue
[ x] I've verified that I'm running youtube-dl version 2021.12.17
[x ] I've checked that all provided URLs are alive and playable in a browser
[x] I've checked that all URLs and arguments with special characters are properly quoted or escaped
[x ] I've searched the bugtracker for similar bug reports including closed ones
[x] I've read bugs section in FAQ

Verbose log

PASTE VERBOSE LOG HERE
youtube-dl.exe --verbose -i -f best -o "%(title)s.%(ext)s" "https://www.youtube.com/watch?v=GWFHVBnR7G0"
[debug] System config: []
[debug] User config: []
[debug] Custom config: []
[debug] Command-line args: ['--verbose', '-i', '-f', 'best', '-o', '%(title)s.%(ext)s', 'https://www.youtube.com/watch?v=GWFHVBnR7
G0']
[debug] Encodings: locale cp1252, fs mbcs, out cp437, pref cp1252
[debug] youtube-dl version 2021.12.17
[debug] Python version 3.4.4 (CPython) - Windows-XP-5.1.2600-SP3
[debug] exe versions: none
[debug] Proxy map: {}
[youtube] GWFHVBnR7G0: Downloading webpage
ERROR: Unable to extract uploader id; please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpupik7c6w\build\youtube_dl\YoutubeDL.py", line 815, in wrapper
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpupik7c6w\build\youtube_dl\YoutubeDL.py", line 836, in__
extract_info
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpupik7c6w\build\youtube_dl\extractor\common.py", line 534
, in extract
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpupik7c6w\build\youtube_dl\extractor\youtube.py", line 17
94, in _real_extract
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpupik7c6w\build\youtube_dl\extractor\common.py", line 101
2, in _search_regex
youtube_dl.utils.RegexNotFoundError: Unable to extract uploader id; please report this issue on https://yt-dl.org/bug . Make sure
you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include i
ts complete output.
Description

Unable to extract uploader id
Also, C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org doesn't exist on my PC.

[ ] I'm reporting a broken site support issue

You are, but you shouldn't be.

[x] I've searched the bugtracker for similar bug reports including closed ones

Learn how by reading #30839 (again)?

[x] I've read bugs section in FAQ

Apply this.

...C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org doesn't exist on my PC.

The pathname is an artefact of the self-extracting single file build for Windows.


Terminal command is wrong

The documentation on github and pypi.org says Command Line Usage should be imgurdownloader [album URL] [folder to save to] but it should actually be imgur_downloader [album URL] [folder to save to]

just forgot to update readme, pushed change to remote repo and to the pypi package
closing with be85a88485ccf709b48b44f74504e2341067d770


Add Travis and scanCode.py support

In addition,  preparation for bringing the code to Apache Software Foundation (ASF) it must be brought into compliance. Meaning...

All code must be scanned properly for project conventions.

All source code has legal ASF license headers. This includes Python files and the new scanCode.py that will be dropped into openwhisk/tools/build will enable this check by default.

A preliminary scan indicated this repo had the following errors:
[./openwhisk-package-template/actions/hello_world.js]:
2: line contains tabs.
3: line contains tabs.
4: line contains tabs.
5: line contains tabs.
6: file does not end with EOL.

Closing issue as project is being archived.


Logs are automatically scrolling down when receiving new data locally but not in prod (Linux target)

This issue was fixed when added missing flags to the terminal by systemctl. Check this https://github.com/thiagoesteves/deployex/pull/60


The callback instrumentation of Kafka framework is incorrect

Please answer these questions before submitting your issue.

Why do you submit this issue?
[ ] Question or discussion
[x] Bug
[ ] Requirement
[ ] Feature or performance improvement

Background

The Kafka plugin intercepts all class that it implements callback interface and do continue the ContextSnapshot when the onComplete method invokes.
The Kafka framework creates a new callback instance when the producer sends a message without the callback parameter.
The Kafka plugin set the ConectSnapshot object into the callback parameter .

Problem
It cannot get the ContextSnapshot object from the callback instance creates by Kafka framework.
Resolve
The Kafka plugin does not intercept the instance that the Kafka framework creates

I  try do fix it.

You should be able to assign the issue to yourself now.

You should be able to assign the issue to yourself now.

OK


Usability of the 3D importing process (using gltf2.0) has further declined in Godot 4 compared to already bad import experience in Godot3

Godot version
3.4.4, 3.5.RC, 4.0 Alpha12
System information
Win Nvidea765M
Issue description
This, for me, is a regression from bad to worse.
Trying to export the Blender default cube to Godot, then make changes to the default cube in Blender in mesh and texture, export it again and have it automatically update in Godot has been unreliably in Godot3 to say it kindly. Sometimes it works, sometimes it does not. I have had better experiences in earlier versions of Godot I believe, but in Godot 3.4.4 and Godot 3.5.RC7 I can't get it to work reliably at all anymore.
Much worse is the updating of the texture, even with a simple albedo texture.
The model will reimport when Godot becomes the active window again, but the textures won't update. Unchecking the "Keep on Reimport" Material Inport option in Godot3 does not help. In Godot4 there is not even such a checkbox any more.
In Godot3, if you want to disable Filter on your textures, you would think you go to the Import Default options in the Project Settings and disable the Filter checkbox on all the Texture categories, but won't do anything at all. You have to manually disable filter on each and every texture individually after the import!
To make the changes show up in Godot 3.4, 3.5RC7 I have to create a new Inherited Scene, and then sometimes, the model will show as updated in the new inherited scene. If I then close the new inherited scene, sometimes some of the changes (mesh or texture) show up in my original scene as well. I have no idea what the criteria is for when and why. With tiny changes between multiple reexport and reimport it seems completely pointless to even try: no matter what I do the changes won't show up in Godot.
In Godot 4 this whole experience is even worse. Not only won't the model not auto-update, the hacky workaround of double clicking the glb file and opening up as "New Inherited Scene" won't work anymore, because the click behaviour changed. Double clicking the glb file will open up the "advanced" import popup, where I can click "reimport" without it making any difference. I can see the updated model in the "advanced" import popup preview, but it won't update my model in my scene.
The only solution I found was to completely delete the glb instance from every scene I have, delete the glb from res://, export from Blender again and add the new glb file back into my Godot scenes.
In Godot4, the Import Panel has been completely mutilated to a point I'm no longer sure why it exists at all. What has once (meaning in Godot3) been a good one-stop place to set up your 3D import of a file exactly as you need it (glaringly missing and enable/disable "filter" option though), has been ripped into pieces and completely crippled in it's functionality. Material options are completely gone. Everything is now spread between the Import Panel, the Project Settings Default Import Settings, the "Advanced" Popup, and the Inspector, as some things like the Filter option are now completely gone from any default import settings.
What a mess!
The "Advanced" import settings panel is almost empty and not accessible through the Project Settings Import Defaults. Why? It this not where you would typically have the split between basic and advanced settings (like it is with Godot's General project settings too?). How is this "Advanced" if there is almost nothing to do here?
It's things like this why you hear people outside of the Godot bubble say things like "Godot's 3D is bad".
A painless and seamless import-export workflow is fundamental for doing any even slightly more serious 3D development. If we want to have Godot 3D to be more than just a pretty looking gimmick, fundamentals like the import-export workflow need to be Godot's strong suit, not it's weakness.
Steps to reproduce

Export Blender default cube to Godot as gltf 2.0 directly into the Godot res:// folder

In Godot make a "New Inherited" scene, or instance the glb file to an existing 3D scene.

Back in Blender switch to the Texture painting view, set up a low res texture (like 16x16) and draw a few dots on the cube.

Export from Blender again, overwrite the glb in res://

Switch to Godot and observe it reimporting the file, without updating the model.

Try every trick in your sleeve to make the actual model show up (see description above for ideas)

Try to disable texture filter for the whole project, not just this model

Also try to do the process with some mesh edits (In Blender extrude a face of the default cube for example).

Minimal reproduction project
Minimal production project does not really make much sense here since this is about exporting the default cube experience.

Try to disable texture filter for the whole project, not just this model

There is a default texture filter project setting for 2D, but I guess this needs to be added for 3D too. It shouldn't be too difficult to do if this only affects BaseMaterial3D.

I just found in Godot4.0 Alpha12, while you can't use the trick to double click the glb file anymore to open a "New Inherited" which will update the existing model in your existing scene like in Godot3.X, you what you still can do to the same effect is to click the "Open in Editor" icon of the glb instance in the Scene Panel.
This will also open the "New Inherited" popup dialog, which you can press and then close again to have your original scene show the updated model.
In no way a solution for a stable release, but maybe a workaround for those who want to test 4.0 features right now.

Chiming in that I've had issues with it picking up texture changes, and sometimes textures AT ALL in 4.x
But yes, 4.x feels worse than 3.x in this aspect

It seems the bug  reation steps are update related:

Export from Blender again, overwrite the glb in res://
Switch to Godot and observe it reimporting the file, without updating the model.

https://github.com/godotengine/godot/pull/57606 has a attempt to bugfix.

The new importer settings is node based.

Please @golddotasksquestions try to narrow down your issue report with a clear actionable issue.
For example: "models/textures from glb files don't update when reimported"
I understand your frustration but calling Godot "a mess" and using the tone that you're using in your issue is not constructive. People have to skim through your rant to find actually actionable stuff.
In general, please keep issues clean of rants and succint in a way that contributor can easily understand the issue and work towards fixing it.

I suggest you try the .blend import route. Exporting to glb with built-in textures will not work and Blender GLTF exporter is not configured to save textures externally by default. With the .blend route, everything uses the right options so things work for you.

@reduz: Some of the gltf assets do not come from Blender/do not have .blend files attached ;(

@QbieShay
See it as "report" on the import situation, past and current.
My issue is clearly actionable. I've included the exact steps you can follow in mere minutes to test this issue.
I ran through the same tests multiple times on all current Godot branches. The issue I describe is present in all of them.
It's so bad, it makes using Godot infeasible if your project depends on an iterative workflow. Larger more serious projects tend to be iterative in nature.
I have spend a lot of time to test this issue and to break it down to it's most minimal reproduction steps anyone can try and follow. So if you have the time, please try these steps and report if you get the same or different results.
And please: Please don't start to read tone into my written text. Text does not translate tone very well. On top there are personal quirks and cultural differences which you can't possibly know of. And language barriers - all of which make it hard to actually read the tone intended by the author.
I want Godot to prosper, which is why I am participating, spending a lot of time helping newcommers and beginners, spend a lot of time to test features and write issues if they don't work. I spend more than 25h a week doing this voluntary work.
I have no ability to tell or to adjust how you read "tone" in written text which has no tone. I fully agree with the CoC to assume best intentions, which is very necessary thing to do when communication is basically only text based. I assume a nice friendly tone when I read your text, I hope you can do the same form too, regardless how much we agree or disagree on any issue.
I disagree for instance strongly with you on calling or not calling this a mess. It clearly is a mess! And it has been a mess ever since I first started using Godot in 2018. It even feels worse right now in Godot4 Alpha 12. Maybe it has something to do with my system and configuration, which is why I have broken down the issue to minimal reproduction steps. I urge you to try and share your experience.

I suggest you try the .blend import route. Exporting to glb with built-in textures will not work and Blender GLTF exporter is not configured to save textures externally by default. With the .blend route, everything uses the right options so things work for you.

Resorting to .blend is not a viable workflow solution for this issue here, since blend is specific to just one application only (and only version 3.0+ at that).
Fbx is still the current industry wide standard for 3D assent exchange in the game dev industry. But thanks to Autodesk, it is pretty hopeless to ever expect continuously stable fbx workflow support when using Godot. That's ok. Having a dependency on proprietary formats is not the best idea anyway.
Which is why having gltf work seamlessly is really crucial!
With your .blend recommendation now, Godot has gone through at least 4 different "recommended" format workflows over the past 4 years. Which I might add is also not really trust-inducing. What's next year? Yet another format and workflow which almost works well enough, but not really well enough to do productive work with Godot?
Constantly getting new only halve-working solutions replacing old unfixed halve-working solutions is what makes working with Unity so awful.

The blend file importing system makes a lot of sense within the confines of developers who are working with both of blender source files and godot directly, but it just won't work with how most game development operations work. The reasoning is mostly off-topic, so I'll put it in a collapsible section below:

For one, most large game development operations just don't use blender. They use autodesk software. So advice that assumes they can use blender as an authoring tool is automatically not even on the table for them.
Second, if I'm remembering right, fbx importing now involves converting the fbx to gltf with a third party tool. Unless you want to throw blender into the mix and automatically convert gltf files to blend files, first-class gltf support is a precondition to first-class fbx support, so blend files shouldn't even enter the conversation when we're talking about gltf support.
Third, many game development operations have a very hands-off approach to how assets are shuttled off to be integrated with the rest of the game, or managing that process is handled by a single person for whom it's their dedicated job. From the perspective of someone plopping stuff around in the game world or stuffing assets into systems, it's normal to end up with exported model file updates with no choice but to do your best with them, Source files are often extremely large and clunky and/or contain redundant data or multiple assets to be split off into distinct exported files later down the pipeline. Outsourcing also sometimes involves keeping source files private, so the game developer themselves sometimes only has access to exported model files. Naturally, professional game development operations typically have custom asset tooling, so they can construct a perfect world for themselves if they want, but that's beside the point. A single specific "recommended workflow" is not a helpful solution; there simply must be a working workflow that uses exported models, not source files.
Fourth, there are many 3d assets that simply don't come from conventional modelling programs, and blender could never, ever be a reasonable replacement for the tools that author them.

In short, the blend importing system is simply not a solution to 3d asset pipeline UX problems. It will work for some developers, but some is not enough.
In the opening post, there's a lot of different specific issues being brought up. Like, materials not updating in the scene editor and model data not updating in the scene editor are almost certainly very different issues. But the point being made is not that there are such-and-such issues that each individually need solutions. The point being made is that the experience in general, across each minor issue combined together, is extremely finicky, inconsistent, hard to understand, and hard to manage.
In godot 3, it was impossible to have all three of material reuse across different models,  models don't thrash each other's materials during import, and models reimport properly at the same time. If you managed to get two, you couldn't get the third. The importing process was simply not flexible enough. The defaults were also very bad*** (see footnote) and made it very easy for people to import several models at once and have them break each other and have no idea why it was broken.
The new importing process in godot 4 makes it possible to address these three points in much more direct and less janky ways, since it lets you extract materials and then configure mesh materials to use those external-to-scene extracted materials. It also imports materials into the scene by default (keeping external textures separate like they should be), not into separate resource files. Overall, this is a vast workflow improvement, and it is extremely welcome. But it seems like, somewhere in the process, reimporting was left to rot, so we come back to only having two of the three things that people should want out of the model reimporting process.
For example, is there a way to configure a model to automatically re-extract materials from itself when it reimports? Because something like that would be necessary to have both proper reimporting and material sharing (not just texture sharing) at the same time. You would be affecting other object's materials, perhaps, but only ones that you've already explicitly configured to load those materials from those resources, so this would not be "thrashing", unlike in godot 3 where spewing material resources across the project's file tree is the default. I can't find such a configuration.
For another example, is there a way to select a bunch of model files and tell them "look for pre-extracted materials in this folder and automatically use anything that matches"? Something like that would be necessary for it to not be extremely arduous to import (all at once) large numbers of models that you want to share materials (not just textures), which any project that's doing material reuse would have to do at least once. I can't find such a feature.
There are also a lot of problems with the editor keeping stale model state around after models or materials or textures get reimported. The workaround is to restart the editor, which is a bad workaround. This is probably a whole mess of small bugs being added together, but it still needs to be treated as the mess that it is.
(I must note, having now used it myself, that "mess" is not a strong word, and overall in this post I'm sticking closely to conventional middle-formality-level written English. I've run up and down it several times looking for poor tone of voice and haven't found any. I'm being very firm with my assertions, but that's simply because there's a tendency for UX issues to be the first things to get thrown by the wayside in open-source project management, and I don't want to act in favor of that tendency.)
UX issues like these should be sought out and addressed on their own terms, not ignored in favor of the fourth or fifth or sixth new high-level workflow change. Like godotasksquestions said, software that constantly cycles between new half-working solutions only makes working with it more awful.  In my opinion, it's less respectful to a useful/proven system in a piece of software to ignore its problems and try to replace it with something unproven than it is to recognize its flaws as flaws and attempt to fix them.
*** Why godot 3's defaults are bad in detail:

In my experience, the simplest way to avoid model importing problems in Godot 3 is to make models import materials into their scenes rather than into files (because it bypasses the keep-on-reimport system entirely + prevents materials from being thrashed by other models), which is very bad because of texture duplication etc. But I'll take that duplication if it means that my materials reimport properly and aren't thrashed by the materials of other models.
Yes, it's an issue that models can overwrite each other's textures when reimporting if things go wrong, which is why the option to make materials import into their own folder exists. But that folder option isn't the default for the reason that it prevents you from reusing materials across models without doing really complicated inherited scene and material override stuff. But it remains difficult to reuse materials across models in Godot 3 because (by default) they're kept on reimport so any updates to the material are not automatically once the model it comes from has been initially imported. But this combination of issues points to a failure to notice the conflict and find a compromise: instead of choosing defaults that prevent one model from thrashing the materials of another, or defaults that are ergonomic for material reuse, or defaults that play nicely with reimporting and the editor, godot 3 has defaults that do not prevent thrashing, are not ergonomic, and do not play nicely with reimporting. The defaults in godot 3 do not even do one of the three things that you want all three of.
For example, if you import model A, it will make a material file by default. If you then change model A to store the materials in the scene instead of as separate files, the previously-imported material will remain. If you then import model B, and it has a differently-configured material with the same name as model A's material, tell me, will it, by default, overwrite the now-stale material that model A created on import? Probably not. If you then update model B's material, it will not reimport, for the same reason that model B's material didn't overwrite model A's stale material in the first place. This involves all three of material thrashing, poor material-sharing ergonomics, and bad reimport behavior.
The defaults in should handle at least one of these three things properly, even if it's impossible to handle them all at once with godot 3's primitive importing configuration system. In my opinion, either importing materials into the scene instead of into resources, or into unique folders, should be the default, because it would allow developers to place arbitrary assets into their project and explore them in the scene viewer to see if they're rendering correctly, and examine their materials to see if they would conflict if loaded into files.
But all of this is neither here nor there, since this issue report is ultimately/mostly about godot 4.

I agree that we shouldn't rely on blender-only solutions.
In that case I think it would be useful if some of y'all that work with 3D asset workflow could open a proposal for how you envision a system working with the least friction possible for your usecases.
If the problem requires an olistic solution and not fixing bugs (like texture/meshes/materials not re-importing) it's better that a design is detailed separately in a proposal, possibly after discussions between the people involved, and ideally with mockups.
I encourage you to find a space to talk with each other and come up with a proposed workflow that you feel like would address the issue at hand, I believe that could help us push this forward.
Of note, please don't make proposals that are "do it like Unity" (or any other tool) because maintainers rarely have the time and energy to install another engine to test their import workflow in-depth to then come up with a Godot-compatible design. (This isn't targeted at something any of you said, but as a disclaimer)
Additionally, please try to formulate the proposal in terms of problems and how your design addresses them. Keeping feature scope to a minimum will also raise the chance of the design being approved and subsequentially implemented.
Lastly, I ask you to also accept the possibility that we could incur in technical limitations out of our control (what reduz mentioned above about the way Blender's gltf export works).

Note regarding the tone, in spoiler because I don't want to argue but only express my point of view:
Notes like this one:

It's things like this why you hear people outside of the Godot bubble say things like "Godot's 3D is bad".
A painless and seamless import-export workflow is fundamental for doing any even slightly more serious 3D development. If we want to have Godot 3D to be more than just a pretty looking gimmick, fundamentals like the import-export workflow need to be Godot's strong suit, not it's weakness.

Don't sit well with me.
It sounds like "well, don't you want to be a cool kid too? you just have to do what I say to be in the cool kids club". I don't find the quoted paragraph useful in any way, other than trying to push developers to prioritize specific issues over others.
While I understand the frustration, once again, I find it inappropriate to try and elect one's frustration as the reason why Godot isn't considered at the same level of other engines, when the scope of this is much much broader, and contributors have already put significant effort into reducing the friction points.

Double clicking the glb file will open up the "advanced" import popup, where I can click "reimport" without it making any difference

That's the biggest bear here, I don't think the advanced import screen is working well for GLTF :( it's great for small individual meshes like obj, but for GLTF I can't see what's there, the materials don't show up or are black even if they show up later in the actual scene, there is no quick way to reimport/refresh the frakking screen and/or open the scene itself (like "skip that screen I don't care" kinda button)
So I think the current workflow is fine, we don't need really big reworking of the workflow, just ironing out the issues

@reduz
I appreciate the explanation! What you say makes a lot of sense to me.
It sounds like a good way moving forward for existing Blender Artists and people who just started to learn 3D game dev, who use the latest versions of Godot and Blender, and know they won't change this asset creation pipeline in future for the duration of their project.
For anyone else though, it is simply out of the question.
Not for technical reasons, but because Godot does not have enough weight in the game (yet) to make any experienced 3D game Artists throw decades of experience and workflow optimization out the window and force them to start using Blender ... just so they can work productively with Godot.
No, they will pick an engine which supports common export formats, without crazy hacks, workarounds, or whatnot.
Try to tell anyone working professionally in a studio they have to add an extra step in their asset pipeline where they have to load their asset in Blender (which they don't use), just so they can export their asset to the engine of their choice. No one is going to do that, even if they have Blender experience. It's the it's like throwing a huge bolder right onto their efficiency workflow path. Maybe some are capable of automating this step, but even if that skill set exists, it would take a lot of RND since it adds an additional point of failure.
If we want experienced game devs (3D Generalists, Technical Artists, Environment Artists, VFX Artists, Animators, Modellers) to pick up and give Godot a chance, they need to be able to use their experience without having huge efficiency roadblocks thrown onto their path.
@QbieShay

(tangent, therefore spoilers)
I really have no idea how you came to this interpretation of the paragraph you quoted. This whole discussion here has imho absolutely nothing to do with "being cool", or a "cool kids club". My desire here, is to be able to have a seamless pipeline between asset creation and iteration and Godot import and reimport of the said assets. I really believe this is what we are discussing, and I really strongly believe having such a seamless pipeline is fundamental to doing any kind of productive 3D game dev work.
I'm sorry if you find (parts? of) my contribution to the discussion not useful. But like the "tone" thing, I don't think there is anything I can do about that. If I read something I find not very useful, I generally just move on. If it is something factually wrong, or misleading or misinformed, I would also speak up. So if you notice something I write is factually wrong, misleading or misinformed, please continue to speak up and correct me.

I find it inappropriate to try and elect one's frustration as the reason why Godot isn't considered at the same level of other engines

No idea why you would bring up engine comparisons. I don't believe I have compared the levels of engines here in this thread. Instead I have tried to describe my personal experience importing and reimporting 3D assets into Godot over the past 4 years. My feedback and message is: This is essential and has to work seamlessly to be able to do productive work.

Not only won't the model not auto-update, the hacky workaround of double clicking the glb file and opening up as "New Inherited Scene" won't work anymore, because the click behaviour changed.

That's still there, it just isn't the double-click functionality anymore. It's under the right-click menu.

Since we're talking usability, I have to say that the blender workflow has another major issue: performance. Importing blend files is very slow because the importer calls blender for each file, and blender takes a few seconds to start. Processing all files at once would speed it up by 10-20x (my script converting fbx->blend on ~1k files takes a couple of minutes, but importing into Godot takes about an hour).
Then there's also the lack of previews in the file explorer files that makes working with blender files a bit more difficult.

@jgillich can you file an issue for that blender workflow performance problem
This issue is merging problems which makes it hard to track. Please make a new issue for each problem. Can be a feature proposal if you have some idea how to fix and an issue if you don't.

Some points:
@golddotasksquestions

For anyone else though, it is simply out of the question.
I don't think this reasoning makes sense. The problem here is how Blender exports GLTF, this is beyond our reach but importing .blend generally works well. For non Blender users, I don't think its common to see GLTF files with bundles stuff so it should not be an issue.

Everyone else:
Reload bugs will be hopefully be fixed by the time 4.0 reaches RC status. This is a well known problem, its just not a priority to fix until we enter Beta phase.

For non Blender users, I don't think its common to see GLTF files with bundles stuff so it should not be an issue.

My understanding is that the new FBX importing pipeline uses GLTF as an intermediary format (via FBX2glTF, so it would still impact them.

@wareya I dont think so, or at least it should not because it will not bundle the assets.

@reduz
I'm not sure I understand what you mean by saying For non Blender users, I don't think its common to see GLTF files with bundles stuff so it should not be an issue.
The kind of people and situations I was predominantly talking about when I said For anyone else though, it is simply out of the question, are people from the industry art departments with years of experience under their belt, who then test how an engine fits their workflow. Maybe some decide for a side gig, have a bit of scripting experience, or their studio starts a new smallish project and they are looking for a engine that fits on their behave. It's not just the programing and legal department which has an influence on this call.
They will test their workflow and then either report to the decisions makers, or if it is their own project decide themself on how much this engine fits their workflow. In a proprietary pipeline, fbx is not a obstruction. It's not even an issue. If the pipeline Non-Blender 3D authoring software -> to -> Godot, fbx is full of issues.
Dropping years of experience in the non-Blender 3D authoring software, pick up Blender just so they can export *.blend files to Godot? Not going to happen.
Neither is using Blender as an intermediate step between the established non-Blender 3D authoring software and Godot a likely scenario, if they want to do productive work rather than just some one-time weekend tests.
This leaves all hope on wider GLTF market adoption and better usability on all sides regarding GLTF.
I'm aware you can't make do others what is best for Godot, but in case you are not already doing this anyway, maybe you can reach out to someone in the Maya, 3dsMax, Cinema4d, Houdini, 3Dcoat, Modo, ZBrush, Fusion360 teams and say to them something along the lines of you "would like the exports for their particular software to import seamlessly in Godot, but in order to for that to happen, their GLTF export needs this or that setting".
I don't just want hobbyist and newcomers to chose Godot, I would like Godot to be a viable choice for industry veterans too.
I think we need these industry veterans to really show off what Godot is capable of, and consequentially provide Godot users with a reliable job market where they can earn a living wage working with Godot full time.

Regarding reload bugs: will be hopefully be fixed by the time 4.0 reaches RC status.

This is really great to hear! I'm very much looking forward to these fixes and will definitely test them as good as I can when they are out!

@golddotasksquestions tbh, I think you are exaggerating. Have you tried exporting FBX to Unity? It does not import any texture or materials (or if it does its not useful because its not PBR or even compatible with Unity) and you have to assign everything manually.
I think workflow wise in that sense we are really good. I would definitely like to have better FBX support than using an external converter, but we do not have the resources for that, yet using GLTF2 really solves most issues.

I also agree the GLTF2 importer is far from being fast

To be clear: I have no issues with gltf import performance, it's blender files that are slow; not just because they are imported twice, but because the blender step is very slow.
@fire I made https://github.com/godotengine/godot-proposals/issues/5099

I can confirm the steps to reproduce also lead to not updated material of the mesh in 3.5. The only thing that seams to work is deleting the material and re import the scene. And even then the change is not directly visible in the editor and you have to reload the scene again.
Keep on import is off and I can see in the inspector the texture of the Albeto changed in the material. Still it's not shown in the editor. Not even restarting the Editor or cleaning cache resolved this. Only deleting material completely and re importing solves this. This looks like a bug to me.
On more complex models I did not managed to reproduce it and the material and model was re imported correctly and replaced in the mesh. But still scene needed to be reloaded for the editor to display all changes. So I can not say when this bug appears for sure but when it appears it is very frustrating.
I hope this can be fixed for the Godot 4 release. Would it be worth raising a separate issue for this?

I can confirm the steps to reproduce also lead to not updated material of the mesh in 3.5.

See https://github.com/godotengine/godot/issues/38853 and other issues. This issue is only for 4.0, not 3.x.

An option to set the default texture filter in 3D in 4.0 feels very needed to me. It already exists in 2D, why not 3D? The importing process of 3D objects is a bit annoying for me, but nowhere near as bad as 3.0's tilemap editor was so I think I can live with it.

An option to set the default texture filter in 3D in 4.0 feels very needed to me. It already exists in 2D, why not 3D? The importing process of 3D objects is a bit annoying, but nowhere near as bad as 3.0's tilemap editor was so I think I can live with it. The extra step of having to go into the material of every single object to turn it from linear to nearest is a terrible addition, however.

I opened a proposal to track this: https://github.com/godotengine/godot-proposals/issues/5228
I won't be continuing work on my WIP implementation linked there due to time constraints, so please chime in if you want to get this for 4.0 :slightly_smiling_face:

I'm glad to see some of the core issues I have mentioned here are already addressed in PRs. Thanks for linking more even more related PRs @fire
I planed to close this issue here as soon as the PRs are merged and I can test the "Steps to Reproduce" in an Alpha or Beta build.
I still think splitting up the Import settings in to various places throughout the editor is a very bad idea and makes this process worse, but I can write a specific issue regarding the UI/UX flow once the aforementioned PRs are merged and reimporting is at least fundamentally working.

Just to keep up, is it not possible to set a default texture import filter in GD4?

Just to keep up, is it not possible to set a default texture import filter in GD4?

Please continue the discussion in https://github.com/godotengine/godot-proposals/issues/5228.

Is there anything actionable to do with this bug report?
Many of the rough edges described in the OP were actual bugs and have already been fixed during beta or early 4.0 rc builds.... or else have more specific issues already open.
If we want a place to discuss how to improve the import pipeline, that belongs in a discussion, not a decaying github issue with most issues already resolved and dozens of back-and-forth comments.
I think it would be healthiest to close this issue so that specific issues can be opened for each of the bugs.
If the OP can re-test the original issue and tell us which issues they think still exist, it would be helpful.

Please open separate issues for each bug that still remains.
Thank you-all for your hard work.
Closing as stale due to above comments by lyuma and golddotasksquestions.

overview of the current status of Godot4 3D IK


Minor typo fix in tutorial.ipynb

Just found a small typo in my second read-through before we merge into datajoint/main

@kabilar, this is now ready for you to review and merge if it looks good.


Add down method to handle reverse migration

This PR add the down method to handle migration rollback

We don't use down migrations in any of our packages.


Elasticsearch carrot plugin implementation.

This is plugin implements on the fly data clustering for elastic search results.
I implemented carrot2 plugin into eleasticsearch.net project for our internal project and wanted to share it with people.
This plugin is useful if you like to have a RIPL or Foamtree chart.
https://github.com/carrot2/elasticsearch-carrot2

@akuzhan Thanks for sharing!  This is really interesting.
We've thought about ways to support community plugins (see #1144) and have made a conscience decision not to support them by default within NEST.  So unfortunately we can't pull this in.
Instead, we're leaning towards the approach of having a separate library/package for third party/community plugins- but also understand that it's not always possible to extend the client from outside without making changes to some of the internal bits.  This is something that we're actually working on improving at the moment, and this PR will help us better understand what else needs to be done, so thank you!
Stay tuned.


Readd a Camera3D icon gizmo to the 3D editor, renew Camera2D/3D icons

Marked as draft, as new Camera2D and Camera3D node icons should be created to match the new icon gizmo design.
The lack of icon gizmo made it no longer possible to select Camera3D nodes in the 3D viewport by clicking on them.
A new Camera3D icon gizmo was designed to be direction-neutral. This avoids the issue that the previous icon gizmo had, since it was always facing right.
This closes https://github.com/godotengine/godot/issues/53083.
Preview

Before
After

Before
After

Listener3D on the left, Camera3D in the middle, ReflectionProbe on the right.

Looks good to me, what is it missing?

Looks good to me, what is it missing?

As I wrote in OP:

Marked as draft, as new Camera2D and Camera3D node icons should be created to match the new icon gizmo design.

I've started working on those icons a while ago, I'll try to finish them ASAP.

I pushed new icons:

Let me know if this is OK. CameraEffects, CameraTexture, ClippedCamera3D and XRCamera3D icons still need to be changed.

It's been in draft for 2 years, maybe we can merge what's made already? Or poke MewPurPur if you need help ;)

It's been in draft for 2 years, maybe we can merge what's made already? Or poke MewPurPur if you need help ;)

I've finished all icons; it's ready for review now.

Thanks!


[Python3.11] Upgrade libs to support python3.11 with backward compatibility

What changes were proposed in this pull request?

Upgrading the libraries to support the python 3.11.
slack-sdk 3.2.0 -> 3.31.0
pandas 1.4.2 -> 2.0.3
numpy 1.23.1 ->1.24.4

How was this patch tested?

Locally
CI

@agl29 I ran into issue on my M3 Mac with older version. Have you tried on Mx macBooks?

@wing2fly which package was giving error in you mac? I am using M2 and to me looks all good.


What is YARA?

https://docs.virustotal.com/docs/browser-extensions

Hi, this project is not related to YARA. Please do not submit unrelated issues here. Thanks!


License?

First, thanks for building this!
Second, what license should is this code under? Currently, I can't find one stated anywhere--which means it's "All Rights Reserved" in most jurisdictions.
I noticed your bookmark project is under the MIT. Perhaps that was the intent here also?
It'd be helpful to clarify the license for encouraging outside contribution and further use.
Thanks!
🎩

Yes it should be MIT license. I will update in master branch. But in newer version of code https://github.com/mrgodhani/rss-reader/tree/newversion it would be MIT

Added

Thanks for the fast work on this!


Volume circuits binned by trial vs set

Suggestion from @sarah-sheldon

What is the expected behavior?

I want to take this issue. Can you elaborate a bit more on what you mean?

I don't 100% remember, but I think I mean something like fig 2(a) of https://arxiv.org/abs/2008.08571

I see. @oliverdial also mentioned that in https://github.com/Qiskit/qiskit-ignis/issues/483 I'll take a look.


Preferences dialog styles

How i can change default dialogs colors, title, description for specific preferences?

Thanks for reply. I want to customize this dialog

I do use my ComposeDialogs library for the internal dialogs - I do not expose a lot of customisation options for the dialogs to keep this library simple and independent from the the dialogs library.
You have 2 options:
Option 1
Create a custom preference based on the PreferenceInputText and adjust the underlying ComposeDialogs directly.
https://github.com/MFlisar/ComposePreferences/blob/e4ec46bfae09217e47cba787375c2957a59f4760/library/modules/screen/input/src/main/java/com/michaelflisar/composepreferences/screen/input/PreferenceInputText.kt#L72-L114
E.g. like following:
val showDialog = rememberDialogState()
if (showDialog.showing) {
   val value = rememberDialogInput(value)
   DialogInput(
       state = showDialog,
       input = value,
       title = title, // <= provide a custom title composable here...
       icon = icon
   ) {
       if (it.isPositiveButton) {
           onValueChange(value.value)
       }
   }
}
BasePreference(
   enabled = enabled,
   visible = visible,
   title = title,
   subtitle = subtitle,
   icon = icon,
   preferenceStyle = preferenceStyle,
   itemSetup = itemSetup,
   onClick = {
       showDialog.show()
   }
) {
   PreferenceContentText(value, itemSetup)
}

Option 2 - create a custom preference and provide your own dialog
BasePreference(
   enabled = enabled,
   visible = visible,
   title = title,
   subtitle = subtitle,
   icon = icon,
   preferenceStyle = preferenceStyle,
   itemSetup = itemSetup,
   onClick = {
      // show a dialog
   }
) {
   PreferenceContentText(value, itemSetup)
}

// TODO: show a fully custom dialog

Because of the simplicity of any dialog based preference I do not plan to offer more customisation for the dialogs currently.

In my opinion ComposeDialogs should had simple customization for example
Title (as @Composable function)
Description (as @Composable function)
Enable/Disable icon
Background color
Cornders shape
Buttons (as @Composable funciton)
These configuration give simple things to customize dialog and repository is still langweight

Check out the dialog code here:
https://github.com/MFlisar/ComposeDialogs/blob/53435e92b4e56d158cd5fe5354f142d9c45d739d/library/modules/input/src/main/java/com/michaelflisar/composedialogs/dialogs/input/DialogInput.kt#L64-L93
There is a lot to customise... BUT I could offer a parameter that will allow you to provide your dialog directly, something like following:
@Composable
fun PreferenceScope.PreferenceInputText(
    // Special
    value: String,
    onValueChange: (value: String) -> Unit,
    // Base Preference
    title: @Composable () -> Unit,
    enabled: Dependency = Dependency.Enabled,
    visible: Dependency = Dependency.Enabled,
    subtitle: @Composable (() -> Unit)? = null,
    icon: (@Composable () -> Unit)? = null,
    preferenceStyle: PreferenceStyle = LocalPreferenceSettings.current.itemStyle,
    itemSetup: PreferenceItemSetup = PreferenceBoolDefaults.itemSetup(),
    // Dialog
    dialog: @Composable (dialogState: DialogState) -> Unit = {
        val value = rememberDialogInput(value)
        DialogInput(
            state = showDialog,
            input = value,
            title = title,
            icon = icon
        ) {
            if (it.isPositiveButton) {
                onValueChange(value.value)
            }
        }
    }
)

This way you could use all of the customisation options of my dialog libraries directly...

Sounds good. I will be grateful if You could make these changes.

When can i expect update?


Lookup with both address and components

How can I do a geocoder lookup with both an address and components?

Currently this is unsupported behavior however since the API allows it we should modify the package to support it.


MACS2 score

How can I get the MACS2 scores?
Not sure if this is correct, but I basically downloaded the BigWig, and converted that to bedGraph. The columns are as follow, is the last column the MACS2 score?
#bedGraph section chr1:10000-36225
chr1    10000   10001   0.0524468
chr1    10001   10002   0.0786702
chr1    10002   10003   0.104894
chr1    10003   10004   0.118005
chr1    10004   10005   0.15734
chr1    10005   10006   0.196676

Hi,
This is an example of the URL for peak-call data.
http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/eachData/bed05/SRX018625.05.bed
http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/eachData/bed05/SRX018625.05.bedThe MACS2 sores are shown on the fourth column.
Best,
Shinya

2021/07/12 3:57、Rojin @.***>のメール:
How can I get the MACS2 scores?
Not sure if this is correct, but I basically downloaded the BigWig, and converted that to bedGraph. The columns are as follow, is the last column the MACS2 score?
#bedGraph section chr1:10000-36225
chr1    10000   10001   0.0524468
chr1    10001   10002   0.0786702
chr1    10002   10003   0.104894
chr1    10003   10004   0.118005
chr1    10004   10005   0.15734
chr1    10005   10006   0.196676
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub https://github.com/inutano/chip-atlas/issues/38, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADD2CTPNGZF7DOBTENXY3Q3TXHSQBANCNFSM5AFRX2GQ.

Hi,
It seems that the columns of peak-call data are changed. Can you explain the name of each column? Thank you.
Example:
[https://chip-atlas.dbcls.jp/data/hg19/eachData/bed05/SRX4394193.05.bed]

Hi,
The peak call data in ChIP-Atlas follows the output format of macs2 peak-caller and has not been changed.
https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md#output-files
Best,
Shinya

2024/01/11 23:02、Zengggg @.***>のメール:
Hi,
It seems that the columns of peak-call data are changed. Can you explain the name of each column? Thank you.
Example:
[https://chip-atlas.dbcls.jp/data/hg19/eachData/bed05/SRX4394193.05.bed]
—
Reply to this email directly, view it on GitHub https://github.com/inutano/chip-atlas/issues/38#issuecomment-1887224057, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADD2CTKKWLHJJEKI54VVMB3YN7WJDAVCNFSM5AFRX2G2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBYG4ZDENBQGU3Q.
You are receiving this because you commented.

Thank you.


Native tooltip vanishes after using the fancy tooltip

Noticed this, but it does not disturb me ATM.
In the survival guide, each cell has its native tooltip via its title attribute, which allows for a quick check of a color without losing the focused cell. When the fancy tooltip is opened for a cell, the title attribute is empty and the former title can only be found in data-original-title. When the fancy tooltip is closed, the title attribute is not restored.
In this image, the first row had its fancy tooltip opened and lost the native tooltip shown here for a cell in the second row.

This seems to be a bug in Bootstrap itself. I can probably add a fix like this to explicitly restore the title on focusout, when the fancy popover is closed.


Honkbot can't be hit by wideswing

Description

Honkbot is unable to be hit by any kind of wide-swing it seems, this makes dealing with honkbots an actual headache for any and all security players, they're worse than they already were
Reproduction

Try to wideswing a honkbot, nothing procs

Yeah and your old repo had no issues compared to the fresh one so this behavior on honkbots specifically is really weird

honkbot survival mechanism, feature


openshift: 4.10.0 -> 4.11.0

The commit needs to be pinned because the release branches are not
tagged properly.
Description of changes

Things done

Built on platform(s)

[ ] x86_64-linux
[ ] aarch64-linux
[x] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[x] Tested basic functionality of all binary files (usually in ./result/bin/)
22.11 Release Notes (or backporting 22.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 185985 run on x86_64-darwin 1

1 package built:

openshift


Warn when using non-Calico network type

Resolves #132.

Please add an identifier for the network.


ICEES returning error on Workflow C query

0fd681f9-4b08-43d4-b7a3-cf6e561d49af

Out of scope - handling gracefully now


transpile / refactor code into es5

Since version 2.0.0 this library has started shipping code which includes const and let which have dubious support in legacy browsers, but also arrow functions which cause legacy browsers such as IE11 to simply break.
Since this library isn't usually transpiled by those who depend on it due to the way it is used, this means that IE support is completely broken, since 2.x.
I believe the solution to this would be to transpile the JS before publishing, into a syntax which works on older browsers.

I think this was previously done by @rollup/plugin-typescript and was probably lost when the config switched to @rollup/plugin-sucrase

Looks like the official word from the sucrase author is that it is designed to target modern browsers and node versions, and does not have any support to ES5, so I think the best way is as ben mentioned above, to switch back to the TypeScript compiler.

instead of transpiling to es5 for all users, would it be enough to add another output and reference it from the browser field in package.json? Made a quick n dirty version here, just adds typescript, an extra output from rollup that uses it and targets es5, and adds the browser field to reference it. It is nice to be able to keep libraries from shipping es5 by default, since at this point support for es2015+ is so wide.

But this library would only get shipped for users if legacy browsers, right? So I'm not sure I understand the point of that


ci: build and push docker image on tags

Add a github workflow to build and push docker image on tag creations.

LGTM, Thanks!


Update Voyager chart for 3.0.0 release

We have released Voyager 3.0.0 with a number of changes. This pr reflects that.
https://github.com/appscode/voyager/releases/tag/3.0.0

/ok-to-test


Fix for missing empty directories when using ExtractToDirectory

Fixes: #851
This creates empty directories without skipping them when using ExtractToDirectory.

Thank you!  Please run dotnet csharpier . to run the formatter

@adamhathcock I have formatted the code using csharpier. Thank you.

thank you!


Use dataclass_transform instead of our custom one

I hope this improves support for other type-checkers, like Pyre.

/pre-release

Pre-release
:wave:
Releasing commit [8b7ba401a64b5ad94e8ee5e7042b63408c7d084c] to PyPi as pre-release! :package:

Pre-release
:wave:
Pre-release 0.134.0.dev.1664917721 [8b7ba401a64b5ad94e8ee5e7042b63408c7d084c] has been released on PyPi! :rocket:
You can try it by doing:
poetry add strawberry-graphql==0.134.0.dev.1664917721

Thanks for adding the RELEASE.md file!

Here's a preview of the changelog:

This release removes our custom __dataclass_transfor__ decorator
and replaces it with typing-extension's one.
... todo add more text

Here's the preview release card for twitter:

Here's the tweet text:
🆕 Release (next) is out! Thanks to @patrick91 for the PR 👏

Get it here 👉 https://github.com/strawberry-graphql/strawberry/releases/tag/(next)

Apollo Federation Subgraph Compatibility Results

Federation 1 SupportFederation 2 Support

_service🟢@key (single)🟢@key (multi)🟢@key (composite)🟢repeatable @key🟢@requires🟢@provides🟢federated tracing🔲@link🟢@shareable🟢@tag🟢@override🟢@inaccessible🟢@composeDirective🟢@interfaceObject🟢

Learn more:

Apollo Federation Subgraph Specification
Compatibility Tests


Add tls label (alias of tls-email)

Closes https://github.com/wemake-services/caddy-gen/issues/18

adds a tls label (that gets injected as the tls value if tls-email is not set)
update the docs

How to test:
Build container:
docker build -t caddy-gen-dev .

Create empty directory and have a docker-compose.yml file:
version: "3"
services:
  caddy-gen:
    container_name: caddy-gen
    image: "caddy-gen-dev:latest" # IMPORTANT
    restart: always
    volumes:
      - /var/run/docker.sock:/tmp/docker.sock:ro  # needs socket to read events
      - ./certs/acme:/etc/caddy/acme  # to save acme
      - ./certs/ocsp:/etc/caddy/ocsp  # to save certificates
    ports:
      - "80:80"
      - "443:443"
    depends_on:
      - whoami

  whoami:  # this is your service
    image: "katacoda/docker-http-server:v2"
    labels:
      - "virtual.host=myapp.com"  # your domain
      - "virtual.port=80"  # exposed port of this container
      -<EMAIL_ADDRESS># ssl is now on

Run:
docker-compose up

Output:
Creating test-caddy-gen-patch_whoami_1 ... done
Creating caddy-gen                     ... done
whoami_1     | Web Server started. Listening on <IP_ADDRESS>:80
caddy-gen    | 2019/03/10 19:02:33 Generated '/etc/caddy/Caddyfile' from 2 containers
caddy-gen    | forego     | starting dockergen.1 on port 5000
caddy-gen    | forego     | starting caddy.1 on port 5100
caddy-gen    | dockergen.1 | 2019/03/10 19:02:33 Contents of /etc/caddy/Caddyfile did not change. Skipping notification ''
caddy-gen    | dockergen.1 | 2019/03/10 19:02:33 Watching docker events
caddy-gen    | dockergen.1 | 2019/03/10 19:02:34 Contents of /etc/caddy/Caddyfile did not change. Skipping notification ''
caddy-gen    | caddy.1    | Activating privacy features... 2019/03/10 19:02:34 [INFO] acme: Registering account for<EMAIL_ADDRESS>
Caddy attempted to create certificates with<EMAIL_ADDRESS>which means virtual.tls gets injected as the tls directive value.
Alternatively, could attempt to use https://github.com/HugoDF/docker-compose-local-https/tree/master/caddy-gen, switch out the image at https://github.com/HugoDF/docker-compose-local-https/blob/master/caddy-gen/docker-compose.yml#L4 for caddy-gen-dev:latest and switch virtual.tls-email for virtual.tls.

Thanks!


Fix for textProperty and valueProperty when remoteSource is true

If textProperty and/or valueProperty are defined on the component and remoteSource was true, these properties were not being used. This pull request fixes this issue.

I just released v1.4.1 that includes your bugfix.
Thanks!

Thanks :)


Filename to  if linenos=table (fixes #1757)

Emit <th> for filename if linenos=table.

Added test cases for filename inclusion.

Thanks, merged! And thanks for the detailed change description as well, much appreciated!


Peer dependencies

Hi.
I have<EMAIL_ADDRESS>installed.
However the peer dependence of mapbox-gl is ^1.12.0 is there any plan to update it ?

Hi,
I have similar similar issue too.
Is there a fix coming soonest? Thank you

As the last release was 2 years ago I would guess a fix will come rather later than sooner.
For now I you could just use the mapbox-gl inside a useEffect. It works fine for me.


Srinidhi patch

Closes: #374

Title : Search-From-Here
Name: : Srinidhi Kulkarni
Idenitfy yourself: :  GSSOC'24

Describe the add-ons or changes you've made 📃
Added the Search-From-Here Website project in -> Intermediate - > Vanilla Js projects
How Has This Been Tested? ⚙

Verified on my own in local host
Screenshots 📷

Type of change ☑

What sort of change have you made:

[ x] Bug fix (non-breaking change which fixes an issue)- [ ] New feature (non-breaking change which adds functionality)

Checklist: ☑

[x ] My code follows the Contributing Guidelines & Code of Conduct of this project.
[ x] This PR does not contain plagiarized content.
[ x] I have performed a self-review of my own code.
[ x] I have commented my code, particularly wherever it was hard to understand.
[ x] My changes generate no new warnings.

Note to reviewers 📄

@Avdhesh-Varshney I have added the search-from-here project in Intermediate folder -> vanilla js projects and updated vanilla js project readme file as well and updated in vanilla.json also . I have closed previous PR, Please review it and let me know if there are any conflicts.

@srinidhifd re-fork this project and again commit your project. Still your project is not shown.  Still your project is not shown. You have to review your own pr and one more thing don't create these sequence of commits, otherwise pr can't approved.

Sure will start again, Sorry for the inconvienance


Increment version for monitor releases

Increment package version after release of azure-monitor-opentelemetry

API change check
API changes are not detected in this pull request.


Ingress controller (http-only) not working when using a deployment path

When trying to use the following ingress rule with the current ingress controller:
$ kubectl get ingress -o yaml
apiVersion: v1
items:
- apiVersion: extensions/v1beta1
  kind: Ingress
  metadata:
    annotations:
      ingress.kubernetes.io/rewrite-target: /
      kubernetes.io/ingress.class: nginx
    creationTimestamp: 2017-08-30T08:57:42Z
    generation: 1
    labels:
      function: hello-http
    name: ingress-hello-http
    namespace: default
    resourceVersion: "19462"
    selfLink: /apis/extensions/v1beta1/namespaces/default/ingresses/ingress-hello-http
    uid: 48652b35-8d61-11e7-b05a-08002706ce26
  spec:
    rules:
    - http:
        paths:
        - backend:
            serviceName: hello-http
            servicePort: 8080
          path: /hello
  status:
    loadBalancer: {}
kind: List
metadata:
  resourceVersion: ""
  selfLink: ""

every time I try to access the function I get redirected to the port 443 but the Nginx server is not listening in that port:
$ curl -vL <IP_ADDRESS>/hello
*   Trying <IP_ADDRESS>...
* Connected to <IP_ADDRESS> (<IP_ADDRESS>) port 80 (#0)
> GET /hello HTTP/1.1
> Host: <IP_ADDRESS>
> User-Agent: curl/7.46.0
> Accept: */*
>
< HTTP/1.1 301 Moved Permanently
< Server: nginx/1.13.3
< Date: Wed, 30 Aug 2017 08:58:16 GMT
< Content-Type: text/html
< Content-Length: 185
< Connection: keep-alive
< Location: https://<IP_ADDRESS>/hello
< Strict-Transport-Security: max-age=15724800; includeSubDomains;
<
* Ignoring the response-body
* Connection #0 to host <IP_ADDRESS> left intact
* Issue another request to this URL: 'https://<IP_ADDRESS>/hello'
* Found bundle for host <IP_ADDRESS>: 0x7f991df015b0
*   Trying <IP_ADDRESS>...
* connect to <IP_ADDRESS> port 443 failed: Connection refused
* Failed to connect to <IP_ADDRESS> port 443: Connection refused
* Closing connection 1
curl: (7) Failed to connect to <IP_ADDRESS> port 443: Connection refused

This is because the following piece of Nginx configuration that is generated in the ingress controller (from the Nginx controller pod):
        location ~* ^/hello\/?(?<baseuri>.*) {
            set $proxy_upstream_name "default-hello-http-8080";

            # enforce ssl on server side
            if ($pass_access_scheme = http) {
                return 301 https://$best_http_host$request_uri;
            }

A different but related issue is that with the current Nginx image used and Kubernetes 1.7 (minikube v0.21.0) the Ingress rule never shows the IP of the rule:
NAME                 HOSTS     ADDRESS   PORTS     AGE
ingress-hello-http   *                   80        3m

I tried the latest version available (gcr.io/google_containers/nginx-ingress-controller:0.9.0-beta.11) and that seems to work:
$ kubectl get ingress
NAME                 HOSTS     ADDRESS          PORTS     AGE
ingress-hello-http   *         <IP_ADDRESS>   80        2m

but the pod keeps restarting because the liveness check fails (even though the server is properly running):
  3m		33s		9	kubelet, minikube	spec.containers{nginx-ingress-lb}	Warning		Unhealthy		Liveness probe failed: Get http://<IP_ADDRESS>:10249/healthz: dial tcp <IP_ADDRESS>:10249: getsockopt: connection refused

@ngtuna Can you look at this one, please? @prydonius Any clues?

The forcing SSL can be avoided by setting a hostname on the Ingress resource, for some reason wildcard routes force https.
As for the address, I'm not sure. Perhaps the healthz endpoint has changed in that version. Have you tried this with the nginx-ingress chart which I believe uses a newer version?

it works using a nip.io hostname we need to change the usage from <IP_ADDRESS>/hello to <IP_ADDRESS>.nip.io/hello but is a valid usage. Thanks!

Oh that's interesting. I didn't know <IP_ADDRESS>/hello doesn't work. Actually I did check the ingress-controller setup yesterday but couldn't find any reason. Thanks @andresmgot for that.


fix: push automated PRs to a branch

This should fix the CLA issue.

It's a good idea to open an issue first for discussion.

[ ] Tests pass
[ ] Appropriate changes to README are included in PR

Is adding that push-to-fork attribute all that's needed, or was there out-of-band work to create the fork?

I need to fork the repo manually. I will make a note of the steps in the file.


[Bugfix] Certbot and domain problems

I recently upgraded to version 2 and it's awesome but some things do not work and I think that all of them are connected (at least some of them).
Problems
Domain
When I try to set the domain in global settings there are two possible outcomes.

If the domain is only HTTP then it is successfully saved, but when I try to login from the new domain I get this error Wrong password or email address. and the email and password are 100% correct.
If the domain is with HTTPS then the saving takes about one minute and then it fails. I think that it's because of certbot. Cerbot docker logs:

HTTPS for applications
Another problem is that anytime I set a domain of an application with HTTPS it does not generate an SSL certificate. This is probably connected to certbot too. Certbot docker logs:

I had on the same system installed version 1 and there was no problem with any of this.
My OS: Ubuntu 20.04.3 LTS x86_64

Thanks for the report!

If the domain is only HTTP then it is successfully saved, but when I try to login from the new domain I get this error Wrong password or email address. and the email and password are 100% correct.

This one is on me. It looks like the session cookie sets with Secure by default, but not on localhost, so that's why it does not come up during my tests. It will be fixed in the next version!
About the other SSL problems. I'm not sure if it's related to Coolify. Coolify only starts the helper container that verifies your DNS configurations and issues the certificate. Based on the error, it looks like Let's Encrypt tries to connect your server on port 9080 to verify that you are the owner of the domain. But it fails to connect.
 Or are you using iptables/ufw maybe that blocks connection on that port?

Yes, it will be probably the firewall, I didn't realize it. But I reinstall the whole server and I found another bug. When I fill email and password to the first login page it is loading for a few seconds and then it only refreshes the page and I can't get to the app.

Yes, I found the issue. One of the dependencies the app used introduced a giant bug. I was fixed in the latest (v2.0.13). Unfortunately, you need to reinstall Coolify to get the latest update. Sorry about that!


[Hardwaresecuritymodules] Bump up sdk and az dedicated-hsm: add parameters --mgmt-network-subnet and --mgmt-network-interfaces

This checklist is used to make sure that common guidelines for a pull request are followed.

For new extensions:

[ ] My extension description/summary conforms to the Extension Summary Guidelines.

About Extension Publish
There is a pipeline to automatically build, upload and publish extension wheels.
Once your pull request is merged into main branch, a new pull request will be created to update src/index.json automatically.
The precondition is to put your code inside this repository and upgrade the version in the pull request but do not modify src/index.json.

Hardwaresecuritymodules


give child processes access to all of process.env

right now, it doesn't seem to be possible to pass additonal environment variables to one (or all) of the autograde tests. This is a bit of a limitation when we might want to use the same test suites for students and autograding, with environment parameters modulating the precise test outcome. Looks like this should be doable in the spawn function of runner.ts, but whe nI try to make the changes myself I run into errors. Sorry I can't provide working code.

Sorry for the slow reply! You're right that passing the env is possible in spawn, unfortunately restricting the environment is done for security reasons - for example if the student has access to the GitHub Actions environment they could craft code that would automatically pass the build, change the outcome of the tests, and in some cases modify the tamper-seals, etc.
Instead of restricting specific environment variables we went with a much more strict policy to be more future-proof. We could potentially allow-list specific variables or construct a configuration for that. Can you give a more specific example of which variables you would be looking for?

Hmm, mostly I want the GitHub user id in github_actor - I want to check that there are at least n commits by the student, and maybe they the tree includes only instructor and GitHub user id commits. Is that a reasonable ask?
On May 12, 2020 11:59 a.m., Jeff Rafter<EMAIL_ADDRESS>wrote:
Sorry for the slow reply! You're right that passing the env is possible in spawn, unfortunately restricting the environment is done for security reasons - for example if the student has access to the GitHub Actions environment they could craft code that would automatically pass the build, change the outcome of the tests, and in some cases modify the tamper-seals, etc.
Instead of restricting specific environment variables we went with a much more strict policy to be more future-proof. We could potentially allow-list specific variables or construct a configuration for that. Can you give a more specific example of which variables you would be looking for?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHubhttps://github.com/education/autograding/issues/19#issuecomment-627435284, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AACY6NB7IX5QQ6ZBQSJQL7TRRFW5ZANCNFSM4MZIOM3A.

I can look into the actor's GitHub user id. I think that would be reasonable and easy to add.

I want to check that there are at least n commits by the student, and maybe they the tree includes only instructor and GitHub user id commits

Can you clarify this?

As @jeffrafter says, the security issue can not be ignored, however, some variables need to be passed to the child process since they need them. e.g. I'm currently making a course that uses golang, this language requires inheriting GOROOT and HOME variables for its development environment. I did some hard code in my fork as a workaround.
What about a allow list config so that we can specify which variables can be passed to child processes?

You're right that passing the env is possible in spawn, unfortunately restricting the environment is done for security reasons - for example if the student has access to the GitHub Actions environment they could craft code that would automatically pass the build, change the outcome of the tests, and in some cases modify the tamper-seals, etc.

Isn't this already possible? I'm not sure if GitHub Classroom has anything that verifies the author of commits made to .github.
I'm also making this comment as a +1: I currently rely on a few NIX_ environment variables, and the build tools don't work right without any of them.
Is it possible to make it configurable somewhere?


NameError: uninitialized constant PG

If PublicActivity can't connect to a MySQL Database, it will fail with the following error:
NameError: uninitialized constant PG
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record/activity.rb:38:in `rescue in <class:Activity>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record/activity.rb:30:in `<class:Activity>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record/activity.rb:6:in `<module:ActiveRecord>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record/activity.rb:3:in `<module:ORM>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record/activity.rb:2:in `<module:PublicActivity>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record/activity.rb:1:in `<top (required)>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record.rb:2:in `require_relative'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/orm/active_record.rb:2:in `<top (required)>'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity.rb:51:in `inherit_orm'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/models/trackable.rb:6:in `included'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/common.rb:25:in `include'
  /home/deploy/webapps/WEBAPP/shared/bundle/ruby/2.3.0/gems/public_activity-1.6.3/lib/public_activity/common.rb:25:in `block in <module:Common>'

We are using Rails 4.2.11 with Public Activity 1.6.3.
It links to this file https://github.com/chaps-io/public_activity/blob/2c56992a61a1a6deaca92a66f7031e83a05c4e9a/lib/public_activity/orm/active_record/activity.rb#L40

Can you share your PublicActivity config? The one you probably have in initializers

I just checked, we do not have an initializer for PublicActivity. We are running ActiveRecord.
It looks to me that the error can't propagate out of the function as the uninitialized constant error is shadowing the actual error.

It does not seem related to PublicActivity. You seem to have a PG driver in your app and ActiveRecord is using it instead of mysql2.

Mmm good catch, PG will not exist if the app is not using pg gem. This would probably need creating dummy PG constant and its exception when pg is not loaded.

You also need to do that with Mysql2::Error::ConnectionError two lines below as not all apps may use Mysql.

does it supports mongoid? I am getting uninitialized constant PG error

When would this merged in master branch..?

@zainonrails this has been released as 1.6.3. for a long time now. Do you have the problem with 1.6.3?

@ashokmiryal it doesn't. Please post the exception you are getting or submit a PR which adds a clause for Mongoid exception in a similar way to how PG/Mysql are handled: https://github.com/chaps-io/public_activity/commit/83d140696b3cd6569c9f51961b2b3528d4a90cc8

So upgrading the gem would also solve this as right now i am using 1.6.3 branch in my gemfile.

@zainonrails then upgrade to 1.6.4. It's released :) Unless I missunderstood you.


Use native WebDriver event triggering, rather than Syn ones

We have several problems due usage of Syn library for JavaScript event triggering. I propose to switch to WebDriver native event triggering capabilities instead of using Syn library.
During the change we need to carefully check, that when using native WebDriver calls all JavaScript events, that were triggered by Syn library are still triggered by WebDriver itself.
Closes:

#78
#75
#51
#20
#139

Hello from 2017! Is this still being worked on somewhere? Thanks!


CheckBox Selection doesn't effect on ADG Checkbox Column

Project Details are :
https://paste.apache.org/cpo8y
Test case is available on VDI.
Go to Inventory from Select in Menu
Go to Documents -> Verification Plans from Setups in Menu
File : com/dbz/modules/Common/dbzVerificationPlanSetup.mxml
When Include in Plan or Print Footer Checkbox is checked then ADG Checkbox related to Include in Plan or Print Footer should be checked like in Flex,but they are not checked in Royale
In Flex :

In Royale :

Try with latest changes

I have downloaded new sdk today after your this commit https://github.com/apache/royale-asjs/commit/36cbf6ae96d642ad7839b564f003c2445562a320
And this is still not working

I looked at your code and tried to re-create the same CheckBox item renderer using Flex.  In Flex the checkbox is not clickable if enabled="false" on the CheckBox as it is in your code.  I deleted the enabled="false" and then I could check the Checkbox, but it did not save that information in the data array probably because the ADG is not set to editable=true, and the column is set to editable=false and rendererisEditor is not set.
I recommend that you debug your Flex version and determine how the Checkbox could work in such a scenario or if something got changed when migrating to Royale.

In our Flex Application,ADG is set to editable=false and checkbox is set to enabled=false but on the selection of Include in Plan or Print Footer  selected="{data.inclde == '0' ? false : true}" and its setting the Checkbox selection and a function Called on the change Event of Include in Plan or Print Footer checkbox
protected function selectAll(event:Event):void
			{
				// TODO Auto-generated method stub
				for(var i:int = 0; i<edgDP.length ; i++){
					edgDP[i].inclde = chkAll.selected? "1": "0";
				}
				edgDP.refresh();
				edgEntry.validateNow();
			}

there's an exception on Royale side

inclde is id of AdvancedDataGridColumn Include in Plan
Exception is thrown on selectedField="{data.inclde}" selected="{data.inclde == '0' ? false : true}"
```
<mx:AdvancedDataGridColumn headerText="Include in Plan" width="50" editable="false" id="inclde" dataField="inclde" >
mx:itemRenderer
fx:Component
<mx:CheckBox enabled="false" textAlign="center" horizontalCenter="0" width="100%"
selectedField="{data.inclde}" selected="{data.inclde == '0' ? false : true}"/>
</fx:Component>
</mx:itemRenderer>
</mx:AdvancedDataGridColumn>

Now its working Fine Thanks


[BEAM-8019] Don't drop coders embedded in CombinePayload

Include coders embedded in CombinePayload when converting x-lang transforms to proto definition
Please add a meaningful description for your change here

Thank you for your contribution! Follow this checklist to help us incorporate your contribution quickly and easily:

[ ] Choose reviewer(s) and mention them in a comment (R: @username).
[ ] Format the pull request title like [BEAM-XXX] Fixes bug in ApproximateQuantiles, where you replace BEAM-XXX with the appropriate JIRA issue, if applicable. This will automatically link the pull request to the issue.
[ ] Update CHANGES.md with noteworthy changes.
[ ] If this contribution is large, please file an Apache Individual Contributor License Agreement.

See the Contributor Guide for more tips on how to make review process smoother.

GitHub Actions Tests Status (on master branch)

See CI.md for more information about GitHub Actions CI.

R: @robertwb

The coders currently get dropped when we do proto -> object -> proto mapping since we add stuff on a case by case basis.
When we start using the original proto (with expanded external transforms) all coders should be there.

Retest this please

Run Python PreCommit

Retest this please

Run RAT PreCommit

Run Python PreCommit

Precommit failures seems to be due to https://issues.apache.org/jira/browse/BEAM-10716

Run Python PreCommit


running it w/o using docker

Hi,
Is it possible to run CarsiDock under a python environment w/o having to use docker?  Do you have an environment definition file that I can use?
Best,
Christian

I finally figure out an environment file to create a conda env carsidock with everything.  I really had a hard time installing dockcpp; I had to modify a few files to make it work.  Still I end up with this:
(carsidock) christian@Linux00:/media/christian/VS1/VS/VS_CarsiDock$ python run_docking_inference.py --pdb_file example_data/4YKQ_hsp90_40_water.pdb --sdf_file example_data/4YKQ_hsp90_40.sdf --cuda_convert
read data...
@> 1795 atoms and 1 coordinate set(s) were parsed in 0.01s.
Traceback (most recent call last):
File "run_docking_inference.py", line 74, in
main(args)
File "run_docking_inference.py", line 31, in main
pocket, ligand = extract_carsidock_pocket(get_abs_path(args.pdb_file),
File "/media/christian/VS1/VS/VS_CarsiDock/src/utils/docking_utils.py", line 645, in extract_carsidock_pocket
protein = prody.parsePDBStream(pdb_file).select('protein or water')
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/prody/atomic/atomic.py", line 232, in select
return SELECT.select(self, selstr, **kwargs)
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/prody/atomic/select.py", line 894, in select
indices = self.getIndices(atoms, selstr, **kwargs)
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/prody/atomic/select.py", line 952, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/prody/atomic/select.py", line 1003, in getBoolArray
parser = self._getParser(selstr)
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/prody/atomic/select.py", line 1102, in _getParser
parser.enablePackrat()
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/pyparsing/util.py", line 265, in _inner
return fn(*args, **kwargs)
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/pyparsing/core.py", line 1132, in enable_packrat
ParserElement.packrat_cache = _FifoCache(cache_size_limit)  # type: ignore[assignment]
File "/home/christian/anaconda3/envs/carsidock/lib/python3.8/site-packages/pyparsing/util.py", line 105, in init
keyring = [object()] * size
TypeError: can't multiply sequence by non-int of type 'Forward'
I'm about to give up...

Hello, we do not recommend performing inference in a non-Docker environment as it may result in a decrease in performance metrics. If you really need to do so, please run the Docker image and use conda pack to package the Conda environment within the image. You can then unpack it locally for use.

Hello, we do not recommend performing inference in a non-Docker environment as it may lead to a decrease in performance metrics. If you really need to do so, there is no need to modify the code. After installing PyTorch and CUDA, you can follow the Dockerfile step-by-step to install the required dependencies.

Thank you for your feedback.  I usually like to work using environments but if it is faster under a docker, it could save me a lot of time for screening a large library.  I'll try to reinstall from scratch, maybe it will solve the problems that lead to:
"TypeError: can't multiply sequence by non-int of type 'Forward'"
Thanks again,
Christian


Update _sidebar.md

Tiny PR to remove erroneous apostrophe from Coloring Black & White Videos

Thanks for your contribution!


Bug in color scale of 3D representations in the Colab implementation

Hi!
The Colab implementation of ThermoMPNN is very nice, but I found an issue in the 3D representation (Step 6C).
The color scale for "RAW", "BEST" and "ALA" methods is set from red to blue, but should be the other way around to follow the color code in the matrix image.
if cs = "RdBu", then  "colorDomain" should be set [max_sens, min_sens], to render a scale from blue (stable) to red...
Additionally, the range of the color scale in the 3D representation differs from the matrix image. In particular defining:
min_sens, max_sens = min(sensitivity), max(sensitivity)
May create an asymmetric scale around zero, then a white color may stand for a different value in a linear gradient... A better choice may be using fixed values (e.g. min_sens=-3; max_sens=3) or setting the absolute maximum value to both variables.
Best regards

Hi Matias,
Thank you for bringing this bug to our attention! I agree that it would be good to have the matrix and 3D representation color scales match. I have updated the Colab code as follows:

color scale for 3D representation now uses min_sens, max_sens = -3, 3
switched the color scheme from RdBu to BuRd to render from blue (stable) to red (unstable)

However, it appears that a recent Colab update may have broken NGLView widgets, which generate the 3D representation. I am unable to get the 3D representation to load now, and have found some issues that report the same behavior. I have added a note explaining as much in the Colab.
Thanks,
Henry