I noticed that when trying to enable ruff formatting in Jupyter notebooks with import sorting enabled as well, the Ruff native server doesn't correctly format the cells, leading to garbled imports and sometimes completely missing lines of code.

When I change "ruff.nativeServer": true to "ruff.nativeServer": false to disable the native server, format on save works correctly without any problem.

ruff.toml:

line-length = 120

[lint]
extend-safe-fixes = ["E712", "E711"]

.vscode/settings.json

{
    "editor.formatOnSave": true,
    "[python]": {
        "editor.defaultFormatter": "charliermarsh.ruff",
        "editor.codeActionsOnSave": {
            "source.organizeImports": "explicit"
        }
    },
    "ruff.nativeServer": true,
    "notebook.formatOnSave.enabled": true,
    "notebook.codeActionsOnSave": {
        "source.organizeImports": "explicit"
    },
    "notebook.defaultFormatter": "charliermarsh.ruff",
    "ruff.trace.server": "verbose"
}

Environment details:
Extension version: v2024.54.0
Extension uses Ruff version: 0.7.1
VS Code version: 1.95.1
OS: MacOS Sequoia 15.1
Python Version: 3.12.7

Code sample:

A new blank notebook with this example code in 2 cells:

from typing import Optional
from typing import Literal
from typing import TypedDict

# Comment
Test = Literal["test"]

Note: the code doesn't have to be the same in both cells, and it doesn't have to just be 2 cells in the notebook, but this is a minimal example I've found where the issue happens. The issue doesn't seem to happen when there is just 1 cell in the notebook.

Extension logs: https://pastebin.com/pvXc9HZY

Video (with native server enabled):

Video (with native server disabled):

If you need any more information or need to clarify anything else with me please let me know, thanks.