sharjeelyunus/github-issues-dataset huggingface dataset:
Repository: pytorch
Issue: Nested tensor support for pointwise matrix multiplication of nested tensor and normal tensor
Labels: triaged,module: nestedtensor

### 🚀 The feature, motivation and pitch

I am using nested tensors (jagged layout) for my input data, and I need to apply rotary positional embeddings to qkv vectors.

At the moment I cannot see how to do this efficiently. I've landed on this slow list comprehension (see below), where I am slicing the normal tensor using and multiplying with the elements of the nested tensor.

```
def rotate_half(x):
    # x1, x2 = x[..., : x.shape[-1] // 2], x[..., x.shape[-1] // 2 :] # old implementation
    x1, x2 = x.chunk(2, dim= -1)

    return torch.cat(
        (-x2, x1), dim=-1
    )


# @torch.jit.script # TODO: I don't think this is supported for torchscript with nested tensors
# def _apply_rotary_pos_emb_torchscript(qkv, cos, sin):
def _apply_rotary_pos_emb(qkv, cos, sin): # qkv shape: (B, j1, 3, n_heads, head_dim), cos & sin shape: (1, j1.max(), 1, head_dim)

    if qkv.is_nested:

        cos = cos.squeeze(0)
        sin = sin.squeeze(0)

        # slow list comprehension
        result_list = [(t * cos[:t.shape[0]]) + (rotate_half(t) * sin[:t.shape[0]]) for t in qkv.unbind()]
         
        # Reassemble the list of tensors back into a nested tensor
        return torch.nested.as_nested_tensor(result_list)

    return (qkv * cos) + (rotate_half(qkv) * sin)
```

### Alternatives

You could convert the cos and sin tensors to nested tensors of the same shape as qkv, and multiply these, but this does also not seem like an optimal solution, and requires copying the cos and sin vectors as much as we have batch size.

There might be some way of applying rotary positional embeddings to nested tensors that I haven't thought of. If so, please let me know!

### Additional context

I am working on a project utilizing protein sequences as input data. The data varies widely in sequence length. min sequence length is probably 32 tokens, the max is whatever I set the max length to be, probably 4096 tokens. I am using layout=torch.jagged at the moment, as this seem to be the best format to 
It's the perfect project for nested tensors, but so far, FlashAttention, Rotary positional embeddings, and loss calculations are proving to be difficult to implement with efficient computations

cc @cpuhrsch @jbschlosser @bhosmer @drisspg @soulitzer @davidberard98 @YuqingJ
Repository: react-native
Issue: React native flickering issue in Screen when  Scrollview  Apply React native 0.76 version React navigation 7 version
Labels: Component: ScrollView,Needs: Author Feedback,Needs: Repro

### Description

i'm using React native **0.76.6** version and React navigation 7 version.
When i use header from react navigation and use Scrollview from react native this issue generate

### Steps to reproduce

1. Design simple screen render some Data.
2. Use React navigation stack.
3. Inside screen use Scrollview from React native.
4. And set this screen inside Stack Navigation.
5. Set inside options **hadershown** true

### React Native Version

0.76.6

### Affected Platforms

Runtime - iOS

### Output of `npx react-native info`

```text
System:
  OS: macOS 15.1.1
  CPU: (12) x64 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
  Memory: 31.86 MB / 16.00 GB
  Shell:
    version: "5.9"
    path: /bin/zsh
Binaries:
  Node:
    version: 20.11.0
    path: ~/.nvm/versions/node/v20.11.0/bin/node
  Yarn:
    version: 1.22.22
    path: ~/Desktop/SmartMonster/node_modules/.bin/yarn
  npm:
    version: 10.2.4
    path: ~/.nvm/versions/node/v20.11.0/bin/npm
  Watchman:
    version: 2024.11.11.00
    path: /usr/local/bin/watchman
Managers:
  CocoaPods:
    version: 1.16.2
    path: /usr/local/bin/pod
SDKs:
  iOS SDK:
    Platforms:
      - DriverKit 24.2
      - iOS 18.2
      - macOS 15.2
      - tvOS 18.2
      - visionOS 2.2
      - watchOS 11.2
  Android SDK: Not Found
IDEs:
  Android Studio: 2024.2 AI-242.23339.11.2421.12550806
  Xcode:
    version: 16.2/16C5032a
    path: /usr/bin/xcodebuild
Languages:
  Java:
    version: 17.0.13
    path: /usr/bin/javac
  Ruby:
    version: 2.6.10
    path: /usr/bin/ruby
npmPackages:
  "@react-native-community/cli":
    installed: 15.1.3
    wanted: ^15.1.3
  react:
    installed: 18.3.1
    wanted: 18.3.1
  react-native:
    installed: 0.76.6
    wanted: 0.76.6
  react-native-macos: Not Found
npmGlobalPackages:
  "*react-native*": Not Found
Android:
  hermesEnabled: true
  newArchEnabled: true
iOS:
  hermesEnabled: true
  newArchEnabled: true
```

### Stacktrace or Logs

```text
N/A
```

### Reproducer

 N/A

### Screenshots and Videos

https://github.com/user-attachments/assets/dbab4bb1-687e-4cc9-bd75-d1f9d833e9bb
Repository: vscode
Issue: Huge CPU usage and crashes
Labels: triage-needed,stale


Type: <b>Bug</b>

Since a few weeks, I experience huge cpu usage (a process called "node" using several cores) when running simulations from VS Code terminal. Even after stopping the simulation, the cpu usage does not get lower until VS Code entirely crashes. The whole computer is not usable in the meantime.

When I disabled GitHub Copilot, this behavior dod not show up, I did not test all other extensions.

VS Code version: Code 1.96.4 (cd4ee3b1c348a13bafd8f9ad8060705f6d4b9cba, 2025-01-16T00:16:19.038Z)
OS version: Linux x64 6.8.0-51-generic
Modes:
Remote OS version: Linux x64 6.8.0-51-generic

<details>
<summary>System Info</summary>

|Item|Value|
|---|---|
|CPUs|13th Gen Intel(R) Core(TM) i7-1355U (12 x 400)|
|GPU Status|2d_canvas: enabled<br>canvas_oop_rasterization: enabled_on<br>direct_rendering_display_compositor: disabled_off_ok<br>gpu_compositing: enabled<br>multiple_raster_threads: enabled_on<br>opengl: enabled_on<br>rasterization: enabled<br>raw_draw: disabled_off_ok<br>skia_graphite: disabled_off<br>video_decode: enabled<br>video_encode: disabled_software<br>vulkan: disabled_off<br>webgl: enabled<br>webgl2: enabled<br>webgpu: disabled_off<br>webnn: disabled_off|
|Load (avg)|4, 4, 3|
|Memory (System)|31.00GB (16.89GB free)|
|Process Argv|--crash-reporter-id c3224d8b-099b-44c6-a73d-f3c305ef4832|
|Screen Reader|no|
|VM|0%|
|DESKTOP_SESSION|ubuntu|
|XDG_CURRENT_DESKTOP|Unity|
|XDG_SESSION_DESKTOP|ubuntu|
|XDG_SESSION_TYPE|x11|

|Item|Value|
|---|---|
|Remote|Dev Container|
|OS|Linux x64 6.8.0-51-generic|
|CPUs|13th Gen Intel(R) Core(TM) i7-1355U (12 x 1900)|
|Memory (System)|31.00GB (16.87GB free)|
|VM|0%|
</details><details><summary>Extensions (5)</summary>

Extension|Author (truncated)|Version
---|---|---
remote-containers|ms-|0.394.0
copilot|Git|1.257.0
copilot-chat|Git|0.23.2
terminal-keeper|ngu|1.1.53
clang-format|xav|1.9.0

(1 theme extensions excluded)

</details><details>
<summary>A/B Experiments</summary>

```
vsliv368:30146709
vspor879:30202332
vspor708:30202333
vspor363:30204092
vscod805cf:30301675
binariesv615:30325510
vsaa593:30376534
py29gd2263:31024239
c4g48928:30535728
azure-dev_surveyone:30548225
a9j8j154:30646983
962ge761:30959799
pythonnoceb:30805159
pythonmypyd1:30879173
h48ei257:31000450
pythontbext0:30879054
cppperfnew:31000557
dsvsc020:30976470
pythonait:31006305
dsvsc021:30996838
dvdeprecation:31068756
dwnewjupyter:31046869
nativerepl2:31139839
pythonrstrctxt:31112756
nativeloc1:31192215
cf971741:31144450
iacca1:31171482
notype1:31157159
5fd0e150:31155592
dwcopilot:31170013
stablechunks:31184530
6074i472:31201624
dwoutputs:31217127

```

</details>

<!-- generated by issue reporter -->
Repository: godot
Issue: [4.4beta1] Enabling SDFGI -> Desired set (1) not used by shader
Labels: bug,topic:rendering,confirmed,crash,regression

### Tested versions

Reproducable in:

v4.4.beta1.official [d33da79d3]
v4.4.dev7.official [46c8f8c5c]
v4.4.dev6.official [1f47e4c4e]
v4.4.dev5.official [9e6098432]
v4.4.dev4.official [36e6207bb]

Not reproducable in:

v4.4.dev3.official [f4af8201b]
v4.4.dev2.official [97ef3c837]
v4.4.dev1.official [28a72fa43]


### System information

Godot v4.4.beta1 - Windows 11 (build 26100) - Multi-window, 1 monitor - Vulkan (Forward+) - dedicated NVIDIA GeForce RTX 2070 SUPER (NVIDIA; 32.0.15.6590) - AMD Ryzen 7 3800X 8-Core Processor (16 threads)

### Issue description

Enabling SDFGI throws errors (and crashes game when run outside editor):

Console output:

```
ERROR: Desired set (1) not used by shader.
   at: (servers/rendering/rendering_device.cpp:3427)
ERROR: Condition "rid.is_null()" is true. Returning: rid
   at: _allocate_from_uniforms (servers/rendering/renderer_rd/uniform_set_cache_rd.h:131)
ERROR: Parameter "uniform_set" is null.
   at: draw_list_bind_uniform_set (servers/rendering/rendering_device.cpp:4513)
```

### Steps to reproduce

1) Create new project
2) Create new scene
3) Add WorldEnvironment -> new Environment and enable SDFGI
4) Add Camera3D.
5) Run.

### Minimal reproduction project (MRP)

[sdfgi.zip](https://github.com/user-attachments/files/18476657/sdfgi.zip)
Repository: excalidraw
Issue: Feature Request: Subfolders within Collections
Labels: Excalidraw+

As users working in a team

We would like to be able to create subfolders within Collections

So that we can easily manage a growing portfolio of whiteboards.

---------------------------------------------------------------------------------------------------

The Collections feature is great and we have created a Collection for each of our microservices. 

We are now rolling out Excalidraw to the wider team who will generate more and more whiteboards. It would be great to have a ability to create subfolders within Collections (e.g. Archived / Processed / WIP) to allow a hierarchical storage structure. 

Is this something that could be considered?
Repository: react
Issue: Bug: Properties are not passed to Custom Elements that extend built-in elements
Labels: Status: Unconfirmed

<!--
  Please provide a clear and concise description of what the bug is. Include
  screenshots if needed. Please test using the latest version of the relevant
  React packages to make sure your issue has not already been fixed.
-->

React version: 19.0.0

## Steps To Reproduce

1. Define a Custom Element `x-custom-link` that extends the `a` element
2. Render the custom element using the `is` attribute: `<a is="x-custom-link"></a>`
3. Pass a property to the element

<!--
  Your bug will get fixed much faster if we can run your code and it doesn't
  have dependencies other than React. Issues without reproduction steps or
  code examples may be immediately closed as not actionable.
-->

Link to code example: https://codesandbox.io/p/sandbox/musing-shadow-ttt8hc

<!--
  Please provide a CodeSandbox (https://codesandbox.io/s/new), a link to a
  repository on GitHub, or provide a minimal code example that reproduces the
  problem. You may provide a screenshot of the application if you think it is
  relevant to your bug report. Here are some tips for providing a minimal
  example: https://stackoverflow.com/help/mcve.
-->

## The current behavior

Properties are correctly passed to autonomous custom elements but not to those that extend builtin elements.

## The expected behavior

Properties are passed to custom elements that extend builtin elements as well.
Repository: flutter
Issue: When will Flutter mark newly added classes or methods in the documentation with the Flutter version in which they became available?
Labels: waiting for customer response,in triage

<img width="1491" alt="Image" src="https://github.com/user-attachments/assets/e0cb7854-e303-467d-af25-a4f47eff098a" />

like this：

<img width="774" alt="Image" src="https://github.com/user-attachments/assets/f738bfae-3936-43b0-9006-9e6487340991" />
Repository: godot
Issue: [4.4beta1] Godot instantly crash on start with signal 11 no backtrace
Labels: bug,crash

### Tested versions

- Reproducible in : 4.4.beta1
- Not Reproducible in : 4.3.stable

### System information

Godot v4.4.beta1 - Windows 10 (build 19045) - Multi-window, 2 monitors - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1070 (NVIDIA; 32.0.15.6603) - Intel(R) Core(TM) i5-7600K CPU @ 3.80GHz (4 threads)

### Issue description

**I used to be able to launch 4.4beta1 before**, I changed nothing to my flow and today it just won't start.

Trying to launch 4.4beta does nothing, I double click and see the mouse icon changing to "loading", then nothing.
I tried removing every Godot related stuff in %AppData%, launching 4.4beta1 has been able to recreate all the folders so it at least went that far.
I tried skipping the Project Manager view by opening a .godot project directly with "Open With" but it didn't work.
Of course I restarted the computer just in case too.
I tried the console version to see if it wrote anything, most of the time it only writes this an stops immediately : 
```
PS D:\Downloads\Godot_v4.4-beta1_win64.exe> .\Godot_v4.4-beta1_win64_console.exe -d -v
WorkerThreadPool: 4 threads, 1 max low-priority.
Godot Engine v4.4.beta1.official.d33da79d3 - https://godotengine.org
TextServer: Added interface "Dummy"
TextServer: Added interface "ICU / HarfBuzz / Graphite (Built-in)"
Native OpenGL API detected: 3.3: NVIDIA - NVIDIA GeForce GTX 1070
NVAPI: Init OK!
NVAPI: Disabled OpenGL threaded optimization successfully
NVAPI: Disabled G-SYNC for windowed mode successfully
```
But once it a while, it outputs a crash report that just looks like
```
PS D:\Downloads\Godot_v4.4-beta1_win64.exe> .\Godot_v4.4-beta1_win64_console.exe -d -v
WorkerThreadPool: 4 threads, 1 max low-priority.
Godot Engine v4.4.beta1.official.d33da79d3 - https://godotengine.org
TextServer: Added interface "Dummy"
TextServer: Added interface "ICU / HarfBuzz / Graphite (Built-in)"
Native OpenGL API detected: 3.3: NVIDIA - NVIDIA GeForce GTX 1070
NVAPI: Init OK!
NVAPI: Disabled OpenGL threaded optimization successfully
NVAPI: Disabled G-SYNC for windowed mode successfully

================================================================
CrashHandlerException: Program crashed with signal 11
Engine version: Godot Engine v4.4.beta1.official (d33da79d3f8fe84be2521d25b9ba8e440cf25a88)
Dumping the backtrace. Please include this when reporting the bug to the project developer.
```
And then it stops, so there is no backtrace.

### Steps to reproduce

Download 4.4beta1
Try to launch it

### Minimal reproduction project (MRP)

N/A
Repository: kubernetes
Issue:  ListWatch vs WatchList: Memory Usage in Large-Scale Clusters
Labels: sig/scalability,help wanted,needs-triage

The APIServer's StreamWatcher continuously decodes event streams from the server in the receive() method, with each event requiring deserialization into an object using proto.Unmarshal. When a large number of watch clients are active, these deserialization operations can result in significant memory usage.

Kubernetes 1.32 introduced the Watch-List feature to reduce memory overhead caused by frequent List operations. However, it doesn't address the issue of watch requests continuously decoding event streams, which still leads to high memory consumption.

In large-scale clusters, how can kube-apiserver effectively manage memory usage when multiple watch clients are simultaneously deserializing objects using proto.Unmarshal?

releated issue: https://github.com/kubernetes/kubernetes/issues/127980
Repository: deno
Issue: Improve signature for JSON.parse
Labels: types

Version: Deno 2.1.5

Current signature for `JSON.parse`:

```ts
JSON.parse(text: string, reviver?: (this: any, key: string, value: any) => any): any
```

1. The `reviver`'s `this` parameter should be optional
2. The `reviver` should have an optional [`context`](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON/parse#context) parameter
Repository: node
Issue: Possible Null Pointer Dereference in `TLSWrap::PskClientCallback`
Labels: tls

### Version

20.18.0

### Platform

```text

```

### Subsystem

crypto

### What steps will reproduce the bug?

Problem around with part of code - https://github.com/nodejs/node/blob/da5f7aca6ac1fac2b7840dc11c0ef8e740cfc414/src/crypto/crypto_tls.cc#L1559C1-L1564C58

After creating `Utf8Value` object code checks its length, but not checks for `nullptr`. After this `nullptr` can be dereferenced in `memcpy` call

### How often does it reproduce? Is there a required condition?

Condition - `identity_buf` stores `nullptr`

### What is the expected behavior? Why is that the expected behavior?

Return 0, for consistent API, for example

```c++
if (*identity_buf == nullptr || identity_buf.length() > max_identity_len)
    return 0;
```

### What do you see instead?

-

### Additional information

Found by Linux Verification Center (linuxtesting.org) with SVACE.

Reporter: Burkov Egor ([eburkov@rvision.ru](mailto:eburkov@rvision.ru)).

Organization: R-Vision ([support@rvision.ru](mailto:support@rvision.ru)).
Repository: kubernetes
Issue: Encrypt ETCD with service account or namespace specific keys
Labels: kind/feature,needs-triage,sig/etcd

### What would you like to be added?

Right now it is possible to encrypt some resources in etcd by configuring a KVM v2 provider. However, only one "active" key is allowed for write operations as described in the section https://kubernetes.io/docs/tasks/administer-cluster/kms-provider/#developing-a-kms-plugin-gRPC-server-notes-kms-v2: `The API server considers the key_id returned from the Status procedure call to be authoritative. Thus, a change to this value signals to the API server that the remote KEK has changed, and data encrypted with the old KEK should be marked stale when a no-op write is performed (as described below). `.

This request is about adding the ability to KVM (or define a new provider type, like KVM v3 or completely new acronym)  to have more that one keys that could be used to encrypt secrets in database. As my current requirement is to have a different key for each namespace or service account, I would propose the following:
* Encryption: right now the behaviour is `The response must include the ciphertext, the key_id for the KEK used, and, optionally, any metadata that the KMS plugin needs to aid in future DecryptRequest calls (via the annotations field).`. The proposal would be to add one additional mandatory field that would represent the service account or the namespace name that the request is targeting (i.e. who tries to create the secret or where the secret will be created).
* Decryption: No change. The encryption request can use the annotations to propagate the additional field. However, if we want to be coherent we could also change the Decryption and allow this additional field.
* Status endpoint: the status endpoint can get one additional parameter (the service account or the namespace name) and return the key that corresponds to it.

My understanding is that the API server would need to be modified in order to support this functionality.

PS: As I am not familiar with the enhancement creation procedure, let me know if I should ask this question somewhere else, e.g. https://github.com/kubernetes/community/blob/master/sig-list.md.

### Why is this needed?

Use case: Different customers are using the same Kubernetes cluster and each one has their own namespace. When they create a secret in their namespace, this secret would be encrypted with a different key, so even if the ETCD data are leaked, the attacker would need one key for each namespace to decrypt them.

Right now with KMS v2 (according to the documentation: `With KMS v2, a new DEK is generated per encryption: the API server uses a key derivation function to generate single use data encryption keys from a secret seed combined with some random data. The seed is rotated whenever the KEK is rotated (see the Understanding key_id and Key Rotation section below for more details).`) each record is encrypted with a different key, but all keys are derived from a single key, so the attacker would need only to find the initial seed key and know the derivation function (which I assume is described in Kubernetes source code).
Repository: godot
Issue: Circular references in GDScript code may lead to leaks, UB and segmentation faults
Labels: bug,discussion,topic:core

### Tested versions

Current master (discovered during https://github.com/godotengine/godot/pull/100694 / https://github.com/godotengine/godot/pull/100619).

### System information

All systems are affected.

### Issue description

The GDScript parser has circular ownership (cyclic references). Through it, objects (at least `CowData`, potentially more) are accessed that are in the midst of destructing themselves. This may lead to leaks, segmentation faults, and unexpected behavior (UB). 

The cyclic reference should be sanitized, because it is partially relying on UB (accessing half destructed objects) and can lead to problems when attempting seemingly innocent refactors. I ran into it when working on https://github.com/godotengine/godot/pull/100619. I managed to avoid leaks in this particular PR by papering over the issue  - specifically improving robustness against misuse of `CowData` through https://github.com/godotengine/godot/pull/100694.


### Steps to reproduce

The objects involved in the cyclic reference are logged [here](https://github.com/godotengine/godot/actions/runs/12435300159/job/34720869143).

It is difficult for me to identify the problematic code further because I am not familiar with the GDScript parsing code.

It may be possible to identify what code accesses `CowData` while it is destructing by storing in it a boolean `is_destructing`, and if it is accessed while the boolean is true, it shall log the stack trace.


### Minimal reproduction project (MRP)

N/A
Repository: godot
Issue: [4.4] Shadows break rendering when 3D MSAA is enabled
Labels: bug,topic:rendering,topic:thirdparty,regression,topic:3d

### Tested versions

This happens since version **4.4 dev4+**, in 4.4 dev3 it does not happen

### System information

Godot v4.4.beta1 - Windows 10 (build 19045) - Multi-window, 1 monitor - Vulkan (Forward+) - dedicated Radeon RX 560 Series (Advanced Micro Devices, Inc.; 31.0.14001.45012) - Intel(R) Core(TM) i5-4570 CPU @ 3.20GHz (4 threads)

### Issue description

Recently I noticed a problem when enabling shadows, this problem is only present in **Forward+** rendering mode, in **Compatibility** mode and in **Mobile render** it does not happen:

https://github.com/user-attachments/assets/5b250255-c510-415b-873c-7a73d4ead631

In some projects the shadow works sometimes, like in this example from GDQuest:

https://github.com/user-attachments/assets/ebbc349b-3aa7-4348-9b4f-2beaf80d6ab4

I also tested this with OmniLight3D, but it only happens when the light source is moving:

https://github.com/user-attachments/assets/0dce122f-11cf-41d0-bec2-77358913000a

I have a suspicion that this only happens on **AMD** graphics cards.
Similar problem that was solved earlier - #90006


### Steps to reproduce

Enable shadow on DirectionalLight3D in PSSM 4 split mode, and enable 3D MSAA.

### Minimal reproduction project (MRP)

N/A