Having pygls.protocol.json_rpc ValueError after updating to 2025.6.0 from 2025.4.0

[mondwan]

Type: Bug

Behaviour

Once updated the python extension from 2025.4.0 to 2025.6.0, the vscode python extension starts behaved strange.

Before the updates, there will be a tooltip for the documentation on whatever varaible, modules I highlighted. After the updates, it stopped working after a while.

It worked fine if I rollback to 2025.4.0. Is it because I am still using python3.8 instead?

Steps to reproduce:

1. Install the latest version of Python plugin
2. Mouse hover to the variable / module
3. There should be a tooltip showing the document of that variable / module
4. After a while, it stopped showing the doc, but keep showing Loading...

Diagnostic data

Output for Python in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Python)

2025-05-13 10:22:46.286 [info] ERROR:pygls.protocol.json_rpc:Failed to handle request 80 textDocument/documentSymbol DocumentSymbolParams(text_document=TextDocumentIdentifier(uri='file:///home/vdc/....venv/lib/python3.8/site-packages/.../services.py'), work_done_token=None, partial_result_token=None)
Traceback (most recent call last):
  File "/home/vdc/.vscode-server/extensions/ms-python.python-2025.6.0-linux-x64/python_files/lib/jedilsp/jedi/cache.py", line 110, in wrapper
    return dct[key]
KeyError: ((), frozenset())

Extension version: 2025.6.0
VS Code version: Code 1.100.0 (19e0f9e681ecb8e5c09d8784acaa601316ca4571, 2025-05-07T12:48:53.763Z)
OS version: Windows_NT x64 10.0.22631
Modes:
Remote OS version: Linux x64 5.4.0-200-generic

• Python version (& distribution if applicable, e.g. Anaconda): 3.8.10
• Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): Venv
• Value of the python.languageServer setting: Jedi

User Settings

languageServer: "Jedi"

testing
• promptToConfigure: false
• pytestEnabled: true
• autoTestDiscoverOnSaveEnabled: false

Installed Extensions

Extension Name	Extension Id	Version
black-formatter	ms-	2024.6.0
debugpy	ms-	2025.8.0
docker	doc	0.6.0
gitlab-workflow	Git	6.13.1
gitlens	eam	17.0.3
hcl	has	0.6.0
intellicode-api-usage-examples	Vis	0.2.9
isort	ms-	2025.0.0
js-debug	ms-	1.100.0
live-server	ms-	0.4.15
php-cs-fixer	jun	0.3.21
php-debug	xde	1.36.1
php-docblocker	nei	2.7.0
phpcs	ika	1.0.5
phpunit	ema	4.16.1
python	ms-	2025.6.0
remote-kubernetes	Okt	0.5.2
vscode-coverage-gutters	rya	2.13.0
vscode-docker	ms-	1.29.6
vscode-eslint	dba	3.0.10
vscode-intelephense-client	bme	1.14.4
vscode-js-profile-table	ms-	1.0.10
vscode-kubernetes-tools	ms-	1.3.23
vscode-openapi	42C	4.33.2
vscode-pylance	ms-	2025.4.1
vscode-yaml	red	1.18.0
vscodeintellicode	Vis	1.3.2

System Info

Item	Value
CPUs	Intel(R) Core(TM) i7-10850H CPU @ 2.70GHz (12 x 2712)
GPU Status	2d_canvas: enabled canvas_oop_rasterization: enabled_on direct_rendering_display_compositor: disabled_off_ok gpu_compositing: enabled multiple_raster_threads: enabled_on opengl: enabled_on rasterization: enabled raw_draw: disabled_off_ok skia_graphite: disabled_off video_decode: enabled video_encode: enabled vulkan: disabled_off webgl: enabled webgl2: enabled webgpu: enabled webnn: disabled_off
Load (avg)	undefined
Memory (System)	31.78GB (18.43GB free)
Process Argv
Screen Reader	no
VM	0%

Item	Value
Remote	SSH: vm027943
OS	Linux x64 5.4.0-200-generic
CPUs	Intel(R) Xeon(R) Platinum 8462Y+ (2 x 0)
Memory (System)	7.76GB (6.03GB free)
VM	100%

[bytemain]

Encountered the same problem on remote ssh.

[karthiknadig]

@mondwan You are using Python3.8 which is deprecated. You need to pin the extension to older version for Python 3.8 support.

[mondwan]

@karthiknadig Before raising this ticket, I had considered that the issue might be version-related. However, since there was no version information included in the release log, I wasn't able to confirm this on my own. That’s why I proceeded to raise the ticket for clarification.

As a suggestion, it might be helpful to include version changes in future release logs to make it easier for others to identify such issues proactively.

Thanks again

[ZhengRui]

I am using Python 3.12, after update the extension to 2025.6.0, I also encounter the same issue. I had to change the python language server to Pylance for now. Upgrading Jedi is not working. Hovering on any variable or methods just shows "loading...".

logs:

2025-06-02 17:04:13.207 [info] WARNING:pygls.protocol.json_rpc:Cancel notification for unknown message id "2"
2025-06-02 17:04:13.243 [info] WARNING:pygls.protocol.json_rpc:Cancel notification for unknown message id "3"
2025-06-02 17:04:13.389 [info] semantic_tokens_full file:///Users/zerry/Work/Libs/ctc-forced-aligner/ctc_forced_aligner/align.py 
2025-06-02 17:04:13.397 [info] semantic_tokens_range file:///Users/zerry/Work/Libs/ctc-forced-aligner/ctc_forced_aligner/align.py 101:0-264:0
2025-06-02 17:04:13.500 [info] ERROR:pygls.protocol.json_rpc:Exception occurred for message "6": _pickle.UnpicklingError: unpickling stack underflow
NoneType: None
2025-06-02 17:04:13.500 [info] [Error - 5:04:13 PM] Request textDocument/semanticTokens/full failed.
2025-06-02 17:04:13.500 [info]   Message: _pickle.UnpicklingError: unpickling stack underflow
  Code: -32603 
[object Object]

[chenghui-lee]

I am also having the exact same issue on Python 3.12.3 with the extension version 2025.6.1. Downgrading the extension version to 2025.4.0 fixed the issue.

[Root-Core]

@karthiknadig This is still an issue on Python 3.13.7 and extension version 2025.14.0.
Both are the latest stable releases, so no deprecation.

Downgrading the extension version to 2025.4.0 fixed the issue.

This is the easiest solution at the moment.

[karthiknadig]

@Root-Core Try the pre-release the sematic token issue in Jedi should be fixed by this PR #25450