Import third-party packages causes the kernel to crash

[chenyulue]

Environment data

• VS Code version: 1.106.3
• Jupyter Extension version (available under the Extensions sidebar): 2025.9.1
• Python Extension version (available under the Extensions sidebar): 2025.18.0
• OS (Windows | Mac | Linux distro) and version: Windows
• Python and/or Anaconda version: python 3.13.9
• Type of virtual environment used: pixi
• Jupyter server running: Local

Expected behaviour

When importing a third-party packages, everything should work properly.

Actual behaviour

When importing the built-in package, the kernel works properly. Once I import a third-party package, the kernel crashes.

Steps to reproduce:

I have a pixi global environment base, and the following is my global environment.

Global environments as specified in 'C:\Users\cheny\.pixi\manifests\pixi-global.toml'
└── base
    ├─ dependencies: python 3.13.9, matplotlib 3.10.8, altair-all 6.0.0, jupyterlab 4.5.0, plotly 6.5.0, pandas 2.3.3, polars 1.35.2, marimo 0.18.0, openpyxl 3.1.5, streamlit 1.8.0, jupyter 1.1.1, python-kaleido 1.2.0, pip 25.3
    └─ exposes: idle, pydoc, python, pythonw, jupyter-lab, jupyter-labextension, jupyter-labhub, jlpm, marimo, streamlit, jupyter, pip, pip3, ipython

If I start the jupyter lab from terminal and edit it in browser, I can import the installed third-party packages. However, in vscode, when importing a third-party package, the kernel will crash.

Logs

14:24:50.432 [info] Restart requested ~\codes\py\python_notes\pandas\notes.ipynb
14:24:50.434 [warn] Cancel all remaining cells due to dead kernel
14:24:50.494 [error] Failed to get activated conda env vars for ~\.pixi\envs\base\python.exe
                 in 37ms
14:24:50.496 [error] Unable to determine site packages path for python ~\.pixi\envs\base\python.exe (Conda)
14:24:50.499 [info] Process Execution: ~\.pixi\envs\base\python.exe -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)"
14:24:50.504 [info] Process Execution: ~\.pixi\envs\base\python.exe -Xfrozen_modules=off -m ipykernel_launcher --f=~\AppData\Roaming\jupyter\runtime\kernel-v334a645a02345535c3ce0b397a6d0be3c3dd27041.json
    > cwd: ~\codes\py\python_notes\pandas
14:24:51.383 [info] Restarted 2af35a85-863a-4dfe-99c6-1cba345e1460
14:28:10.730 [error] Disposing session as kernel process died ExitCode: 3228369023, Reason: 
14:28:38.735 [error] Error in notebook cell execution Error: 内核 "base(Pixi) (Python 3.13.9)" 已终止。有关详细信息，请单击[此处](https://aka.ms/vscodeJupyterKernelCrash)。有关更多详细信息，请查看 Jupyter [log](command:jupyter.viewOutput)。
    > Kernel Id = .undefined.-xfrozen_modules=off.~\.pixi\bin\python.exe.~\.pixi\envs\base\python.exe.-xfrozen_modules=off#-m#ipykernel_launcher
    > Interpreter Id = ~\.pixi\envs\base\python.exe
    > at n.verifyKernelState (~\.vscode\extensions\ms-toolsai.jupyter-2025.9.1-win32-x64\dist\extension.node.js:309:81661)
    > originalException = undefined
14:28:38.736 [error] Error in execution (get message for cell) Error: 内核 "base(Pixi) (Python 3.13.9)" 已终止。有关详细信息，请单击[此处](https://aka.ms/vscodeJupyterKernelCrash)。有关更多详细信息，请查看 Jupyter [log](command:jupyter.viewOutput)。
    > Kernel Id = .undefined.-xfrozen_modules=off.~\.pixi\bin\python.exe.~\.pixi\envs\base\python.exe.-xfrozen_modules=off#-m#ipykernel_launcher
    > Interpreter Id = ~\.pixi\envs\base\python.exe
    > at n.verifyKernelState (~\.vscode\extensions\ms-toolsai.jupyter-2025.9.1-win32-x64\dist\extension.node.js:309:81661)
    > originalException = undefined

I'm not sure whether this is related to the error `Unable to determine site packages path for python `

[DonJayamanne]

Thank you for share the logs, please can you you enable logging as follows (and please share all of the logs):

• Open settings & go into Jupyter->Logging
• Change the value to trace
• Reload VS Code,
• Attempt to repro the issue & then copy the output from the Jupyter output panel (use the command Jupyter: Show Output to get to the logs).

I need all of the logs to get more context on Python env, versions, what happens and when, etc
If you want to remove any sensitve information (like paths) please feel free to do so, but let me know what was removed and what it was replaced with.

[chenyulue]

The full log are as follows @DonJayamanne

Visual Studio Code (1.106.3, undefined, desktop)
Jupyter Extension Version: 2025.9.1.
Python Extension Version: 2025.18.0.
Python Environment Extension not installed.
Pylance Extension Version: 2025.10.3.
Platform: win32 (x64).
Home = c:\Users\cheny
Temp Storage folder ~\AppData\Roaming\Code\User\globalStorage\ms-toolsai.jupyter\version-2025.9.1
Workspace folder ~\codes\py\python_notes
19:26:01.083 [debug] getDataDirsImpl, Class name = zr (started execution), Arg 1: undefined, Arg 2: undefined
19:26:01.084 [debug] Start refreshing Kernel Picker (1764674761084)
19:26:01.157 [debug] Start refreshing Interpreter Kernel Picker
19:26:02.868 [trace] Search for KernelSpecs in Interpreter ~\.pixi\envs\base\python.exe
19:26:02.868 [trace] Search for KernelSpecs in Interpreter c:\ghcup\msys64\ucrt64\bin\python.exe
19:26:02.868 [trace] Search for KernelSpecs in Interpreter c:\ghcup\msys64\ucrt64\bin\python3.12.exe
19:26:02.868 [trace] Search for KernelSpecs in Interpreter c:\ghcup\msys64\ucrt64\bin\python3.exe
19:26:02.869 [trace] Search for KernelSpecs in Interpreter usr\bin\python.exe
19:26:02.869 [trace] Search for KernelSpecs in Interpreter usr\bin\python3.12.exe
19:26:02.869 [trace] Search for KernelSpecs in Interpreter usr\bin\python3.exe
19:26:02.872 [debug] Get Custom Env Variables, Class name = Gm, completed in 1788ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunPythonCode"
19:26:02.872 [debug] Jupyter Paths : 
19:26:02.874 [debug] getDataDirsImpl, Class name = zr, completed in 1791ms, has a truthy return value, Arg 1: undefined, Arg 2: undefined, Return Value: <Uri:/C:/Users/<username>/AppData/Roaming/jupyter>, <Uri:/C:/ProgramData/jupyter>
19:26:02.874 [warn] No interpreter with path ~\.pixi\bin\python.exe found in Python API, will convert Uri path to string as Id ~\.pixi\bin\python.exe
19:26:02.876 [debug] Kernel Spec Root Paths, ~\AppData\Roaming\jupyter\kernels, c:\ProgramData\jupyter\kernels
19:26:04.583 [trace] Hiding default KernelSpec ~\.pixi\env\base\python.exe for interpreter ~\.pixi\envs\base\python.exe (KernelSpec file ~\.pixi\envs\base\share\jupyter\kernels\python3\kernel.json)
19:26:04.741 [trace] Python API env change detected, update => '~\.pixi\envs\base\python.exe'
19:26:04.741 [trace] Search for KernelSpecs in Interpreter ~\.pixi\envs\base\python.exe
19:26:04.746 [trace] Hiding default KernelSpec ~\.pixi\env\base\python.exe for interpreter ~\.pixi\envs\base\python.exe (KernelSpec file ~\.pixi\envs\base\share\jupyter\kernels\python3\kernel.json)
19:26:04.752 [trace] Python API env change detected, update => '~\.pixi\envs\base\python.exe'
19:26:04.752 [trace] Search for KernelSpecs in Interpreter ~\.pixi\envs\base\python.exe
19:26:04.754 [trace] Hiding default KernelSpec ~\.pixi\env\base\python.exe for interpreter ~\.pixi\envs\base\python.exe (KernelSpec file ~\.pixi\envs\base\share\jupyter\kernels\python3\kernel.json)
19:26:04.791 [debug] KernelProvider switched kernel to id = .undefined.-xfrozen_modules=off.~\.pixi\bin\python.exe.~\.pixi\envs\base\python.exe.-xfrozen_modules=off#-m#ipykernel_launcher
19:26:04.791 [debug] start the kernel, options.disableUI=true for ~\codes\py\python_notes\pandas\notes.ipynb
19:26:04.825 [trace] Registering commtarget jupyter.widget
19:26:04.826 [debug] Controller selection change completed
19:26:04.835 [info] Starting Kernel (Python Path: ~\.pixi\envs\base\python.exe, Conda, 3.13.9) for '~\codes\py\python_notes\pandas\notes.ipynb' (disableUI=true)
19:26:04.835 [trace] Creating raw notebook for resource '~\codes\py\python_notes\pandas\notes.ipynb'
19:26:04.952 [debug] Refreshed Environments
19:26:04.953 [debug] Launching kernel .undefined.-xfrozen_modules=off.~\.pixi\bin\python.exe.~\.pixi\envs\base\python.exe.-xfrozen_modules=off#-m#ipykernel_launcher for ~\codes\py\python_notes\pandas\notes.ipynb in ~\codes\py\python_notes\pandas with ports 9001, 9000, 9004, 9002, 9003
19:26:04.965 [trace] Python API env change detected, update => '~\.pixi\envs\base\python.exe'
19:26:04.965 [trace] Search for KernelSpecs in Interpreter ~\.pixi\envs\base\python.exe
19:26:04.968 [trace] Hiding default KernelSpec ~\.pixi\env\base\python.exe for interpreter ~\.pixi\envs\base\python.exe (KernelSpec file ~\.pixi\envs\base\share\jupyter\kernels\python3\kernel.json)
19:26:04.968 [debug] Get Custom Env Variables, Class name = Gm, completed in 1ms, has a truthy return value, Arg 1: "/C:/Users/<username>/codes/py/python_notes", Arg 2: "RunPythonCode"
19:26:04.968 [debug] Get Custom Env Variables, Class name = Gm, completed in 1ms, has a truthy return value, Arg 1: "/c:/Users/<username>/codes/py/python_notes/pandas/notes.ipynb", Arg 2: "RunPythonCode"
19:26:05.046 [trace] Conda file is conda
19:26:05.102 [error] Failed to get activated conda env vars for ~\.pixi\envs\base\python.exe
                 in 135ms
19:26:05.103 [error] Unable to determine site packages path for python ~\.pixi\envs\base\python.exe (Conda)
19:26:05.103 [trace] Prepend PATH with python bin for ~\.pixi\envs\base\python.exe
19:26:05.104 [debug] Getting activated env variables, Class name = Wd, completed in 137ms, has a truthy return value, Arg 1: "/C:/Users/<username>/codes/py/python_notes", Arg 2: "~\\.pixi\\envs\\base\\python.exe", Arg 3: undefined
19:26:05.111 [info] Process Execution: ~\.pixi\envs\base\python.exe -m pip list
19:26:05.115 [error] Failed to get activated conda env vars for ~\.pixi\envs\base\python.exe
                 in 148ms
19:26:05.116 [error] Unable to determine site packages path for python ~\.pixi\envs\base\python.exe (Conda)
19:26:05.116 [trace] Prepend PATH with python bin for ~\.pixi\envs\base\python.exe
19:26:05.117 [debug] Getting activated env variables, Class name = Wd, completed in 149ms, has a truthy return value, Arg 1: "/c:/Users/<username>/codes/py/python_notes/pandas/notes.ipynb", Arg 2: "~\\.pixi\\envs\\base\\python.exe", Arg 3: undefined
19:26:05.123 [info] Process Execution: ~\.pixi\envs\base\python.exe -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)"
19:26:05.131 [info] Process Execution: ~\.pixi\envs\base\python.exe ~\.vscode\extensions\ms-toolsai.jupyter-2025.9.1-win32-x64\pythonFiles\vscode_datascience_helpers\kernel_interrupt_daemon.py --ppid 16244
    > cwd: ~\.vscode\extensions\ms-toolsai.jupyter-2025.9.1-win32-x64\pythonFiles\vscode_datascience_helpers
19:26:06.214 [trace] ipykernel version & path 7.1.0, ~\.pixi\envs\base\Lib\site-packages\ipykernel\__init__.py for ~\.pixi\envs\base\python.exe
19:26:06.217 [debug] End refreshing Kernel Picker (1764674761084)
19:26:06.488 [trace] Got a response of 2644 for INITIALIZE_INTERRUPT:0
19:26:06.497 [info] Process Execution: ~\.pixi\envs\base\python.exe -Xfrozen_modules=off -m ipykernel_launcher --f=~\AppData\Roaming\jupyter\runtime\kernel-v391d87d3b33e9bb13cd5b72fa5402441d551bb25f.json
    > cwd: ~\codes\py\python_notes\pandas
19:26:06.497 [debug] Kernel process 19744.
19:26:07.780 [debug] Kernel output 19744: To connect another client to this kernel, use:
--existing ~\AppData\Roaming\jupyter\runtime\kernel-v391d87d3b33e9bb13cd5b72fa5402441d551bb25f.json
19:26:07.981 [debug] Waiting for Raw Session to be ready in postStartRawSession
19:26:07.981 [debug] Waiting for Raw session to be ready, status: connected
19:26:07.981 [trace] Raw session connected
19:26:07.982 [debug] Waited for Raw session to be ready & got status: connected
19:26:07.982 [debug] Successfully waited for Raw Session to be ready in postStartRawSession
19:26:07.982 [debug] Kernel status is 'unknown' before requesting kernel info and after ready
19:26:07.982 [debug] Sending request for kernelInfo
19:26:08.010 [trace] Got response for requestKernelInfo
19:26:08.010 [debug] Successfully completed postStartRawSession after 1 attempt(s) in 28ms
19:26:08.012 [trace] Executing silently Code (idle) = import sys as _VSCODE_sys\nprint(_VSCODE_sys.executable); del _VSCODE_sys
19:26:08.028 [trace] Executing silently Code (completed) = import sys as _VSCODE_sys\nprint(_VSCODE_sys.executable); del _VSCODE_sys with 1 output(s)
19:26:08.028 [trace] Started running kernel initialization for ~\codes\py\python_notes\pandas\notes.ipynb
19:26:08.029 [trace] Executing silently Code (idle) = try:\nimport ipywidgets as _VSCODE_ipywidgets\nprint("e976ee50-99ed-4aba-9b6b-9dcd5634d07d:IPy
19:26:08.099 [trace] Executing silently Code (completed) = try:\nimport ipywidgets as _VSCODE_ipywidgets\nprint("e976ee50-99ed-4aba-9b6b-9dcd5634d07d:IPy with 1 output(s)
19:26:08.099 [trace] Determined IPyWidgets Version as 7
19:26:08.099 [trace] Version of IPyWidgets 7 determined after 3.274s
19:26:08.100 [trace] Executing silently Code (idle) = def __VSCODE_inject_module():\ndef __VSCODE_call_function(function, callback, data=None):
19:26:08.111 [trace] Executing silently Code (completed) = def __VSCODE_inject_module():\ndef __VSCODE_call_function(function, callback, data=None): with 0 output(s)
19:26:08.111 [debug] Requesting Kernel info
19:26:08.112 [trace] Got Kernel info
19:26:08.112 [trace] End running kernel initialization, now waiting for idle
19:26:08.112 [trace] Waiting for idle on (kernel): 0df810f7-f3a8-4b9d-aed4-c5b7cb659d01 -> idle
19:26:08.112 [trace] Finished waiting for idle on (kernel): 0df810f7-f3a8-4b9d-aed4-c5b7cb659d01 -> idle
19:26:08.112 [trace] End running kernel initialization, session is idle
19:26:08.113 [trace] Registering Kernel Completion Provider from kernel base(Pixi) (Python 3.13.9) for language python
19:26:08.113 [trace] IPyWidgetScriptSource.initialize
19:26:08.114 [info] Kernel successfully started
19:26:08.116 [debug] getDataDirsImpl, Class name = zr (started execution), Arg 1: "/c:/Users/<username>/codes/py/python_notes/pandas/notes.ipynb", Arg 2: "~\\.pixi\\envs\\base\\python.exe"
19:26:08.124 [info] Process Execution: ~\.pixi\envs\base\python.exe ~\.vscode\extensions\ms-toolsai.jupyter-2025.9.1-win32-x64\pythonFiles\printJupyterDataDir.py
19:26:08.172 [debug] getDataDirsImpl, Class name = zr, completed in 56ms, has a truthy return value, Arg 1: "/c:/Users/<username>/codes/py/python_notes/pandas/notes.ipynb", Arg 2: "~\\.pixi\\envs\\base\\python.exe", Return Value: <Uri:/C:/Users/<username>/AppData/Roaming/jupyter>, <Uri:/C:/Users/<username>/.pixi/envs/base/share/jupyter>, <Uri:/C:/ProgramData/jupyter>
19:26:08.631 [trace] Web view is ready to receive widget messages
19:26:08.637 [trace] Widget Message: Received IPyWidgets_kernelOptions in ScriptManager
19:26:08.638 [trace] Widget Message: Received IPyWidgetMessages.IPyWidgets_kernelOptions
19:26:08.650 [trace] Widget Message: data-base-url set to https://file%2B.vscode-resource.vscode-cdn.net/c%3A/Users/<username>/.vscode/extensions/ms-toolsai.jupyter-2025.9.1-win32-x64/temp/scripts/b7f97af617b03e99b6d5b66ba7c87ed97b07090bffc285d66e8fca9253abb3f5/jupyter
19:26:08.651 [trace] Widget Message: Received IPyWidgets_kernelOptions in ScriptManager
19:26:08.651 [trace] Widget Message: Received IPyWidgetMessages.IPyWidgets_kernelOptions
19:26:08.651 [trace] Widget Message: data-base-url set to https://file%2B.vscode-resource.vscode-cdn.net/c%3A/Users/<username>/.vscode/extensions/ms-toolsai.jupyter-2025.9.1-win32-x64/temp/scripts/b7f97af617b03e99b6d5b66ba7c87ed97b07090bffc285d66e8fca9253abb3f5/jupyter
19:26:08.652 [trace] Widget Message: Received IPyWidget scripts [{"moduleName":"anywidget","scriptUri":"https://file%2B.vscode-resource.vscode-cdn.net/c%3A/Users/<username>/.vscode/extensions/ms-toolsai.jupyter-2025.9.1-win32-x64/temp/scripts/b7f97af617b03e99b6d5b66ba7c87ed97b07090bffc285d66e8fca9253abb3f5/jupyter/nbextensions/anywidget/index","source":"local"}]
19:26:08.652 [trace] Widget Message: Source for IPyWidget anywidget found in local @ https://file%2B.vscode-resource.vscode-cdn.net/c%3A/Users/<username>/.vscode/extensions/ms-toolsai.jupyter-2025.9.1-win32-x64/temp/scripts/b7f97af617b03e99b6d5b66ba7c87ed97b07090bffc285d66e8fca9253abb3f5/jupyter/nbextensions/anywidget/index.
19:26:08.652 [trace] Widget Message: Registering IPyWidget anywidget found in https://file%2B.vscode-resource.vscode-cdn.net/c%3A/Users/<username>/.vscode/extensions/ms-toolsai.jupyter-2025.9.1-win32-x64/temp/scripts/b7f97af617b03e99b6d5b66ba7c87ed97b07090bffc285d66e8fca9253abb3f5/jupyter/nbextensions/anywidget/index.
19:26:09.006 [error] Widget Error: Failed to access CDN https://unpkg.com/ after 0 attempt(s), TypeError: Failed to fetch
19:26:50.982 [debug] Handle Execution of Cells 3 for ~\codes\py\python_notes\pandas\notes.ipynb
19:26:50.983 [trace] Execute Notebook ~\codes\py\python_notes\pandas\notes.ipynb. Step 1
19:26:50.983 [trace] Connect to Kernel ~\codes\py\python_notes\pandas\notes.ipynb. Step 2
19:26:50.984 [trace] Connected to Kernel ~\codes\py\python_notes\pandas\notes.ipynb. Step 3
19:26:50.984 [trace] executeCell 3. Step 4
19:26:50.985 [trace] Cell Index:3 sent to kernel
19:26:50.991 [trace] Start cell 3 execution @ 1764674810990 (clear output)
19:26:50.991 [debug] Kernel acknowledged execution of cell 3 @ 1764674810990
19:26:51.008 [trace] Cell 3 completed in 0.018s (start: 1764674810990, end: 1764674811008)
19:26:51.009 [trace] Cell 3 executed successfully     【Notes: Successfully because only a built-in package is imported】
19:27:00.726 [debug] Handle Execution of Cells 4 for ~\codes\py\python_notes\pandas\notes.ipynb
19:27:00.727 [trace] Execute Notebook ~\codes\py\python_notes\pandas\notes.ipynb. Step 1
19:27:00.727 [trace] Connect to Kernel ~\codes\py\python_notes\pandas\notes.ipynb. Step 2
19:27:00.727 [trace] Connected to Kernel ~\codes\py\python_notes\pandas\notes.ipynb. Step 3
19:27:00.728 [trace] executeCell 4. Step 4
19:27:00.728 [trace] Cell Index:4 sent to kernel
19:27:00.734 [trace] Start cell 4 execution @ 1764674820733 (clear output)
19:27:00.734 [debug] Kernel acknowledged execution of cell 4 @ 1764674820733
19:27:03.213 [debug] KernelProcess Exited 19744, Exit Code - 3228369023 【Notes: Kernel exits because only a third-party package is imported】
19:27:03.214 [error] Disposing session as kernel process died ExitCode: 3228369023, Reason: 
19:27:03.214 [debug] Dispose Kernel process 19744.
19:27:03.220 [debug] Disposed Kernel process 19744.
19:27:03.247 [trace] Cell 4 completed in -1764674820.733s (start: 1764674820733, end: undefined)