Kernel crashes when using a Pixi environment with Python Environments enabled

[franco-pereyra-sommer]

Description

I am experiencing a reproducible Jupyter kernel crash in VS Code when using a Python environment managed by Pixi on Windows.

The exact same Pixi environment and the exact same Matplotlib code work correctly when:

1. Running Python directly through Pixi from a terminal.
2. Running Jupyter Notebook from the Pixi environment in a web browser.
3. Using the same Pixi interpreter as a VS Code Jupyter kernel with the Python Environments extension disabled.

The crash occurs when Python Environments is enabled.

Disabling ms-python.vscode-python-envs also disables Pixi Code, since Pixi Code depends on Python Environments. After both extensions are disabled, I can manually select the Pixi python.exe as the interpreter and Jupyter kernel, and the exact same code runs correctly.

This makes me suspect an interaction between ms-python.vscode-python-envs, the Python extension, Jupyter, and Pixi environment activation.

Environment

Operating system

Windows 11, x64.

VS Code

• Version: 1.133.0 (User Setup)
• Commit: a5b500951314efd502d07465bd138dfbd714a960
• Date: 2026-08-11T22:14:08Z
• Electron: 42.8.0
• Chromium: 148.0.7778.280
• Node.js: 24.18.0
• V8: 14.8.178.38-electron.0

Pixi

• Pixi version: 0.67.0
• Platform: win-64
• Channel: conda-forge
• Environment: default

The environment is located at:

C:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default

Python

• Python: 3.12.13

Python packages

• numpy: 2.2.6
• pandas: 2.2.3
• matplotlib: 3.9.4
• ipykernel: 6.31.0

Relevant VS Code extensions

• Python: ms-python.python@2026.4.0
• Python Environments: ms-python.vscode-python-envs@1.36.0
• Jupyter: ms-toolsai.jupyter@2025.9.1
• Jupyter Notebook Renderers: ms-toolsai.jupyter-renderers@1.3.0
• Pixi Code: renan-r-santos.pixi-code@0.2.0
• Pylance: ms-python.vscode-pylance@2026.3.1
• Python Debugger: ms-python.debugpy@2026.6.0

Minimal reproduction

The following code is sufficient to reproduce the kernel crash:

import numpy as np
import matplotlib.pyplot as plt

x = np.arange(10)
y = x**2

fig, ax = plt.subplots()
ax.scatter(x, y)

plt.show()

The problem also occurs when using a Python file with VS Code's # %% interactive cells.

Steps to reproduce

1. Create/open a Pixi project on Windows.

2. Install Python, NumPy, Matplotlib and IPython kernel.

3. Open the project in VS Code.

4. Enable Python Environments.

5. Select the Pixi interpreter:

   C:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe

6. Select the same interpreter as the Jupyter kernel.

7. Run the minimal example above.

8. The kernel crashes.

Actual behavior

The following logs were captured from the same reproduction.

Jupyter output

14:29:11.771 [info] Starting interactive window for resource 'c:\BackUp\Project\11. Cruces de Emas\proyecto_11\Vamos a ver.py' with controller '.jvsc74a57bd0d61f5b99e904adbc10bd8d84ee2f59ba23b03f67c32ecc2c7ac4a21ea9a28656.c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe.c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe.-m#ipykernel_launcher (Interactive)'

14:29:11.977 [info] Starting Kernel (Python Path: c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe, Unknown, 3.12.13) for 'Interactive-1.interactive' (disableUI=false)

14:29:41.907 [warn] Failed to get activated env vars for c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe in 30026ms

14:29:41.913 [info] Process Execution: c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe -m pip list

14:29:41.995 [info] Process Execution: c:\BackUp\Project\11\ Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe -c "import pip;print('6af208d0-cb9c-427f-b937-ff563e17efdf')"

14:29:42.055 [warn] Failed to get activated env vars for c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe in 30067ms

14:29:42.060 [info] Process Execution: c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)"

14:29:42.095 [info] Process Execution: c:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe -m ipykernel_launcher --f=~\AppData\Roaming\jupyter\runtime\kernel-v38c41a242ed3053ecd7f0ad2212f3dcc6ceb92f96.json

    > cwd: c:\BackUp\Project\11. Cruces de Emas\proyecto_11

14:29:43.630 [info] Kernel successfully started

14:29:43.701 [info] Generated code for 1 = <ipython-input-1-3459f81c5a55> with 12 lines

14:29:44.441 [error] Disposing session as kernel process died ExitCode: 3228369023, Reason:

14:29:44.457 [error] Widget Error: Failed to access CDN https://unpkg.com/ after 0 attempt(s), TypeError: Failed to fetch

Python output

The Python extension attempts to obtain the activated environment variables by executing pixi shell twice:

2026-08-14 14:29:11.897 [info] > ~\AppData\Local\pixi\bin\pixi.EXE shell --manifest-path "C:\BackUp\Project\11. Cruces de Emas\proyecto_11\pixi.toml" && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python ~/.vscode/extensions/ms-python.python-2026.4.0-win32-x64/python_files/printEnvVariables.py
2026-08-14 14:29:11.897 [info] shell: commandPrompt
2026-08-14 14:29:11.993 [info] > ~\AppData\Local\pixi\bin\pixi.EXE shell --manifest-path "C:\BackUp\Project\11. Cruces de Emas\proyecto_11\pixi.toml" && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python ~/.vscode/extensions/ms-python.python-2026.4.0-win32-x64/python_files/printEnvVariables.py
2026-08-14 14:29:11.993 [info] shell: commandPrompt

2026-08-14 14:29:41.906 [error] getActivatedEnvironmentVariables [Error: Command failed: C:\Users\franc\AppData\Local\pixi\bin\pixi.EXE shell --manifest-path "C:\BackUp\Project\11. Cruces de Emas\proyecto_11\pixi.toml" && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python c:/Users/franc/.vscode/extensions/ms-python.python-2026.4.0-win32-x64/python_files/printEnvVariables.py

at genericNodeError (node:internal/errors:985:15)
at wrappedFn (node:internal/errors:539:14)
at ChildProcess.exithandler (node:child_process:418:12)
at ChildProcess.emit (node:events:521:24)
at maybeClose (node:internal/child_process:1124:16)
at ChildProcess._handle.onexit (node:internal/child_process:1124:16)] {

code: null,
killed: true,
signal: 'SIGTERM',
cmd: `C:\\Users\\franc\\AppData\\Local\\pixi\\bin\\pixi.EXE shell --manifest-path "C:\\BackUp\\Project\\11. Cruces de Emas\\proyecto_11\\pixi.toml" && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python c:/Users/franc/.vscode/extensions/ms-python.python-2026.4.0-win32-x64/python_files/printEnvVariables.py`
}

2026-08-14 14:29:42.054 [error] getActivatedEnvironmentVariables [Error: Command failed: C:\Users\franc\AppData\Local\pixi\bin\pixi.EXE shell --manifest-path "C:\BackUp\Project\11. Cruces de Emas\proyecto_11\pixi.toml" && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python c:/Users/franc/.vscode/extensions/ms-python.python-2026.4.0-win32-x64/python_files/printEnvVariables.py

at genericNodeError (node:internal/errors:985:15)
at wrappedFn (node:internal/errors:539:24)
at ChildProcess.exithandler (node:internal/child_process:418:12)
at ChildProcess.emit (node:events:521:16)
at maybeClose (node:internal/child_process:1124:16)] {

code: null,
killed: true,
signal: 'SIGTERM',
cmd: `C:\\Users\\franc\\AppData\\Local\\pixi\\bin\\pixi.EXE shell --manifest-path "C:\\BackUp\\Project\\11. Cruces de Emas\\proyecto_11\\pixi.toml" && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python c:/Users/franc/.vscode/extensions/ms-python.python-2026.4.0-win32-x64/python_files/printEnvVariables.py`
}

The pixi shell command is therefore terminated with SIGTERM after approximately 30 seconds on both attempts.

Python Environments output

2026-08-14 14:29:12.166 [info] [SYS_GET] uri=\Interactive-1.interactive, normalizedKey=/interactive-1.interactive, project=none, projectKey=none, mapKeys=[c:/backup/project/11. cruces de emas], directHit=false, projectHit=false, fallbackToGlobal=true, globalEnv=none

2026-08-14 14:30:20.036 [info] [SYS_GET] uri=c:\BackUp\Project\11. Cruces de Emas\proyecto_11\Vamos a ver.py, normalizedKey=c:/backup/project/11. cruces de emas/proyecto_11/vamos a ver.py, project=c:\BackUp\Project\11. Cruces de Emas, projectKey=c:/backup/project/11. cruces de emas, mapKeys=[c:/backup/project/11. cruces de emas], directHit=false, projectHit=true, fallbackToGlobal=false, globalEnv=none

2026-08-14 14:30:31.797 [info] [SYS_GET] uri=c:\BackUp\Project\11. Cruces de Emas\proyecto_11\Vamos a ver.py, normalizedKey=c:/backup/project/11. cruces de emas/proyecto_11/vamos a ver.py, project=c:\BackUp\Project\11. Cruces de Emas, projectKey=c:/backup/project/11. cruces de emas, mapKeys=[c:/backup/project/11. cruces de emas], directHit=false, projectHit=true, fallbackToGlobal=false, globalEnv=none

Important timing observation

The logs from the same execution show the following sequence:

1. VS Code starts the interactive window at 14:29:11.
2. The Python extension invokes pixi shell.
3. The first pixi shell attempt is terminated with SIGTERM after approximately 30 seconds.
4. Jupyter reports Failed to get activated env vars.
5. A second pixi shell attempt is made.
6. The second attempt is also terminated with SIGTERM.
7. Jupyter starts the kernel successfully at 14:29:43.
8. The cell executes at 14:29:43.
9. Approximately 0.7 seconds later, the kernel dies with ExitCode: 3228369023.
10. Jupyter then reports a failure to access https://unpkg.com/.

Control tests

I performed several tests to determine whether the problem was caused by Python, Pixi, Jupyter, Matplotlib, or the amount of data.

1. Pixi + Python + Matplotlib outside VS Code

The following command works correctly:

pixi run python -c "import matplotlib.pyplot as plt; import numpy as np; x=np.arange(10); y=x**2; fig,ax=plt.subplots(); ax.scatter(x,y); plt.show(); print('OK')"

The plot is displayed and the Python process does not crash.

2. Pixi + Jupyter Notebook outside VS Code

I installed Jupyter Notebook in the same Pixi environment and launched it with:

pixi run jupyter notebook

The same quadratic scatter plot works correctly in the browser-based Jupyter Notebook interface.

3. VS Code + Python Environments enabled

The exact same code crashes the Jupyter kernel.

4. VS Code + Python Environments disabled

I disabled:

ms-python.vscode-python-envs

This also disables:

renan-r-santos.pixi-code

because Pixi Code depends on Python Environments.

I then manually selected the exact same Pixi interpreter:

C:\BackUp\Project\11. Cruces de Emas\proyecto_11\.pixi\envs\default\python.exe

and selected it as the Jupyter kernel.

The exact same code then works correctly in VS Code.

This is currently a reliable workaround.

Version testing

I initially suspected Python 3.14 or recent package versions.

The environment was therefore changed from Python 3.14 to Python 3.12 and the packages were also changed to more conservative versions.

The issue still reproduces with:

• Python 3.12.13
• NumPy 2.2.6
• Pandas 2.2.3
• Matplotlib 3.9.4
• IPython kernel 6.31.0

Therefore, the problem does not appear to be specific to Python 3.14 or the latest NumPy/Matplotlib versions.

The issue also reproduces with only 10 points in a minimal scatter plot, so it is not related to the amount of data.

Additional observation

Jupyter reports the following immediately after the cell is executed and just after the kernel dies:

Widget Error: Failed to access CDN https://unpkg.com/ after 0 attempt(s), TypeError: Failed to fetch

I do not know whether this is related to the kernel crash, so I am including it as additional diagnostic information.

Related issues

This appears related to:

• Kernel crashes when trying to plot matplotlib figure vscode-jupyter#17142 — "Kernel crashes when trying to plot matplotlib figure"

  Kernel crashes when trying to plot matplotlib figure vscode-jupyter#17142

  This issue also reports Windows + Pixi + Jupyter and ExitCode: 3228369023, together with Failed to get activated env vars.

• Jupyter kernel startup delayed 30s when extension is installed (pixi environment) #1407 — "Jupyter kernel startup delayed 30s when extension is installed (pixi environment)"

  Jupyter kernel startup delayed 30s when extension is installed (pixi environment) #1407

  This issue reports a Pixi + Jupyter problem associated with ms-python.vscode-python-envs, including Failed to get activated env vars.

My case appears to be more severe: the environment activation attempts take approximately 30 seconds, are terminated with SIGTERM, and the Jupyter kernel subsequently dies with ExitCode: 3228369023.

Workaround

The current workaround is:

1. Disable ms-python.vscode-python-envs.
2. This also disables renan-r-santos.pixi-code.
3. Manually select the Pixi python.exe.
4. Select the same interpreter as the Jupyter kernel.

After doing this, the same Jupyter code works correctly in VS Code.

Request

Could you investigate the interaction between ms-python.vscode-python-envs, the Python extension, Jupyter, and Pixi environments on Windows?

In particular, the following sequence seems suspicious:

1. The Python extension invokes pixi shell --manifest-path ....
2. The command does not complete within approximately 30 seconds.
3. The process is terminated with SIGTERM.
4. The Python extension retries the same operation.
5. The second attempt is also terminated with SIGTERM.
6. Jupyter subsequently starts the kernel successfully.
7. The kernel dies shortly after executing the cell with ExitCode: 3228369023.

Could you also clarify whether the Widget Error: Failed to access CDN https://unpkg.com/ message could be related to the kernel termination?

---

This issue report was written entirely with the assistance of OpenAI's GPT-5.6 Luna. The technical observations, tests, logs, versions, and reproduction steps are my own.