Race condition in WSL: Code Runner executes before Python extension activates Conda environment

[aadarshsoni1]

Type: Bug

Behavior

When using VS Code connected to WSL, there is a race condition between the Python extension's environment activation and the Code Runner extension's execution command.

When attempting to run a Python script using Code Runner ("Run Code"), the command executes in the terminal before the Python extension has finished activating the selected Conda environment. This causes the script to run in the default base environment, leading to a ModuleNotFoundError for any packages specific to the selected environment.

The expected behavior is for the terminal to wait for the conda activate command to complete before executing the script, ensuring it runs in the correct, fully activated environment.
Steps to reproduce:

Setup the Environment:

    OS: Windows 11 with WSL 2 (Ubuntu).

    Software: Miniconda installed inside WSL. VS Code with the official Microsoft Python, WSL, and Code Runner extensions.

    Conda Environments:

        base (default, does not have pandas)

        test (created with conda create -n test python=3.9 pandas)

    Project File (test.py):

    import pandas as pd
    print("Executed correctly")

Connect to WSL: Open the project folder in VS Code using the WSL-Remote connection.

Select Interpreter: Use the Command Palette (Ctrl+Shift+P) to run Python: Select Interpreter and choose the Python interpreter from the test Conda environment. The status bar should correctly show ('test': conda).

Run with Code Runner: With test.py open, right-click and select "Run Code".

Observe the Failure: The terminal will show the script failing with ModuleNotFoundError: No module named 'pandas', followed by the delayed conda activate test command executing after the failure.

Successful Workaround & Analysis for Diagnosis

This information helps diagnose the issue:

Working Method: The bug is avoided by using the Python extension's native "Run Python File" feature (the triangular play button).

Reasoning: This method works because it calls the interpreter by its full, explicit path (/home/aadarsh/miniconda3/envs/test/bin/python), which does not depend on the shell's activation state. This confirms the issue is with the timing of shell activation for external extensions like Code Runner.

Issue with it: This method work but is not the complete solution as it do not flush the output after shell activation like it does in windows.

Diagnostic data

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

2025-07-20 19:13:36.882 [info] Experiment 'pythonTerminalEnvVarActivationcf' is active
2025-07-20 19:13:36.882 [info] Native locator: Refresh started
2025-07-20 19:13:36.882 [info] > pyenv which python
2025-07-20 19:13:36.882 [info] cwd: ~/College/Deep Learning/test
2025-07-20 19:13:38.247 [info] > conda info --json
2025-07-20 19:13:38.318 [info] Conda environment manager found at: /home/aadarsh/miniconda3/bin/conda
2025-07-20 19:13:38.318 [info] Using conda: /home/aadarsh/miniconda3/bin/conda
2025-07-20 19:13:38.821 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:13:38.901 [info] Native locator: Refresh finished in 8308 ms
2025-07-20 19:13:42.238 [info] Python interpreter path: ~/miniconda3/envs/tensor/bin/python
2025-07-20 19:13:42.588 [info] Send text to terminal: conda activate tensor
2025-07-20 19:13:44.847 [info] Starting Pylance language server.
2025-07-20 19:15:03.855 [info] Discover tests for workspace name: undefined - uri: c:/Users/aadar/AppData/Roaming/Code/User/profiles/5dd44f91/settings.json
2025-07-20 19:15:10.781 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:15:11.788 [info] Native locator: Refresh started
2025-07-20 19:15:11.818 [info] Conda environment manager found at: /home/aadarsh/miniconda3/bin/conda
2025-07-20 19:15:11.818 [info] Conda set to: /home/aadarsh/miniconda3/bin/conda
2025-07-20 19:15:17.198 [info] Native locator: Refresh finished in 5410 ms
2025-07-20 19:15:17.435 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:15:20.282 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:15:23.876 [info] Send text to terminal: conda activate tensor
2025-07-20 19:16:04.267 [info] Native locator: Refresh started
2025-07-20 19:16:04.288 [info] Conda environment manager found at: /home/aadarsh/miniconda3/bin/conda
2025-07-20 19:16:04.288 [info] Conda set to: /home/aadarsh/miniconda3/bin/conda
2025-07-20 19:16:05.558 [info] Active interpreter [/home/aadarsh/College/Deep Learning/test]: /home/aadarsh/miniconda3/envs/test/bin/python
2025-07-20 19:16:05.589 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test
2025-07-20 19:16:05.589 [info] Python interpreter path: ~/miniconda3/envs/test/bin/python
2025-07-20 19:16:06.641 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:16:07.769 [info] Send text to terminal: conda activate test
2025-07-20 19:16:10.715 [info] Native locator: Refresh finished in 6448 ms
2025-07-20 19:16:10.716 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test
2025-07-20 19:16:40.886 [info] Discover tests for workspace name: undefined - uri: c:/Users/aadar/AppData/Roaming/Code/User/profiles/5dd44f91/settings.json
2025-07-20 19:17:22.348 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:17:25.783 [info] Send text to terminal: conda activate test
2025-07-20 19:17:55.240 [info] Discover tests for workspace name: undefined - uri: c:/Users/aadar/AppData/Roaming/Code/User/profiles/5dd44f91/settings.json
2025-07-20 19:17:58.022 [info] Discover tests for workspace name: undefined - uri: c:/Users/aadar/AppData/Roaming/Code/User/profiles/5dd44f91/settings.json
2025-07-20 19:29:05.816 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:29:10.597 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:29:15.191 [info] Send text to terminal: conda activate test
2025-07-20 19:29:16.000 [info] Send text to terminal: conda activate test
2025-07-20 19:29:16.124 [info] CreateEnv Trigger - Skipping for /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:29:17.015 [info] Send text to terminal: /home/aadarsh/miniconda3/envs/test/bin/python "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 19:29:29.780 [info] Send text to terminal: conda activate test
2025-07-20 19:29:30.783 [info] Send text to terminal: /home/aadarsh/miniconda3/envs/test/bin/python "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 19:29:40.144 [info] Send text to terminal: conda activate test
2025-07-20 19:29:40.749 [info] Send text to terminal: /usr/bin/env /home/aadarsh/miniconda3/envs/test/bin/python /home/aadarsh/.vscode-server/extensions/ms-python.debugpy-2025.10.0-linux-x64/bundled/libs/debugpy/adapter/../../debugpy/launcher 46429 -- /home/aadarsh/College/Deep\ Learning/test/test.py
2025-07-20 19:36:45.910 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:36:49.832 [info] Send text to terminal: conda activate test
2025-07-20 19:36:56.225 [info] Send text to terminal: conda activate test
2025-07-20 19:44:56.569 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:45:00.470 [info] Send text to terminal: conda activate test
2025-07-20 19:45:12.209 [info] Send text to terminal: python -u "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 19:45:36.930 [info] Send text to terminal: conda activate test
2025-07-20 19:45:37.431 [info] Send text to terminal: /home/aadarsh/miniconda3/envs/test/bin/python "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 19:45:58.953 [info] Send text to terminal: conda activate test
2025-07-20 19:45:59.454 [info] Send text to terminal: /home/aadarsh/miniconda3/envs/test/bin/python "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 19:47:01.151 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:11.107 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:14.156 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:15.233 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:19.835 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:21.939 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:23.481 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:26.861 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:27.777 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:28.905 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:33.049 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:41.035 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:46.130 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:48.338 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:47:55.716 [info] Discover tests for workspace name: test - uri: /home/aadarsh/College/Deep Learning/test/test.py
2025-07-20 19:48:16.680 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 19:48:18.002 [info] Send text to terminal: /home/aadarsh/miniconda3/envs/test/bin/python "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 19:48:21.414 [info] Send text to terminal: conda activate test
2025-07-20 19:48:30.535 [info] Send text to terminal: conda activate test
2025-07-20 19:48:37.951 [info] Send text to terminal: conda activate test
2025-07-20 19:48:38.452 [info] Send text to terminal: /home/aadarsh/miniconda3/envs/test/bin/python "/home/aadarsh/College/Deep Learning/test/test.py"
2025-07-20 20:02:52.035 [info] > ~/miniconda3/bin/conda info --json
2025-07-20 20:02:55.274 [info] Send text to terminal: conda activate test

Extension version: 2025.10.0
VS Code version: Code 1.102.1 (7adae6a56e34cb64d08899664b814cf620465925, 2025-07-15T16:41:17.147Z)
OS version: Windows_NT x64 10.0.26100
Modes:
Remote OS version: Linux x64 6.6.87.2-microsoft-standard-WSL2

• Python version (& distribution if applicable, e.g. Anaconda): 3.11.13
• Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): Conda
• Value of the python.languageServer setting: Default

User Settings

languageServer: "Pylance"

Installed Extensions

Extension Name	Extension Id	Version
autodocstring	njp	0.6.1
black-formatter	ms-	2025.2.0
cmake-tools	ms-	1.21.36
code-runner	for	0.12.2
code-spell-checker	str	4.0.47
codesnap	adp	1.3.4
copilot	Git	1.344.0
copilot-chat	Git	0.29.1
cpptools	ms-	1.26.3
cpptools-extension-pack	ms-	1.3.1
datawrangler	ms-	1.22.0
debugpy	ms-	2025.10.0
hexeditor	ms-	1.11.1
indent-rainbow	ode	8.3.1
intellicode-api-usage-examples	Vis	0.2.9
js-debug	ms-	1.102.0
jupyter	ms-	2025.6.0
jupyter-hub	ms-	2024.5.1002432242
jupyter-renderers	ms-	1.3.0
LiveServer	rit	5.7.9
powershell	ms-	2025.2.0
pylint	ms-	2025.2.0
python	ms-	2025.10.0
rainbow-csv	mec	3.20.0
randomeverything	hel	0.0.3
vscode-js-profile-table	ms-	1.0.10
vscode-jupyter-cell-tags	ms-	0.1.9
vscode-jupyter-slideshow	ms-	0.1.6
vscode-pets	ton	1.32.0
vscode-pylance	ms-	2025.6.2
vscodeintellicode	Vis	1.3.2

System Info

Item	Value
CPUs	AMD Ryzen 7 8845HS w/ Radeon 780M Graphics (16 x 3793)
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)	15.31GB (1.92GB free)
Process Argv	--crash-reporter-id a0e5e44a-26c1-4205-999f-a9cc6a5a9543
Screen Reader	no
VM	0%

Item	Value
Remote	WSL: Ubuntu-24.04
OS	Linux x64 6.6.87.2-microsoft-standard-WSL2
CPUs	AMD Ryzen 7 8845HS w/ Radeon 780M Graphics (16 x 0)
Memory (System)	7.41GB (0.30GB free)
VM	0%

A/B Experiments

vsliv368:30146709
binariesv615:30325510
0bi6i642:31350688
h48ei257:31000450
nativeloc1:31344060
5fd0e150:31155592
dwcopilot:31170013
6074i472:31201624
dwoutputs:31242946
9064b325:31222308
copilot_t_ci:31333650
e5gg6876:31282496
pythoneinst12:31285622
c7cif404:31314491
pythonpulldiag:31343502
996jf627:31283433
pythonrdcb7:31342333
usemplatestapi:31297334
0aa6g176:31307128
747dc170:31275177
aj953862:31281341
generatesymbolt:31295002
convertfstringf:31295003
pylancequickfixt:31350061
9d2cg352:31346308
usemarketplace:31343026
nesew2to5:31336538
agentclaude:31350861
4f60g487:31327383
nes-diff-11:31337487
replacestringexc:31350595
nes-set-on:31350020
testaa123:31335226
6abeh943:31336334
yijiwantestdri0626-c:31336931
0927b901:31350571
f76d9909:31348711
nes-deb-00:31346719
0cj2b977:31350606
1c1c4419-mono:31350621

[eleanorjboyd]

Thank you for making this issue! I will investigatee

[eleanorjboyd]

Can you do these steps to get "shellStartup" activation set? This should fix your issue:

1. Install the Python Environments Extension (published by Microsoft): https://marketplace.visualstudio.com/items?itemName=ms-python.vscode-python-envs
2. Add "python.useEnvironmentsExtension": true, to your USER settings (there is a chance this setting will show as "unknown" but it works)
3. Add "python-envs.terminal.autoActivationType": "shellStartup" to your settings (user or workspace) which will inject the activation script into your shell script for a more automatic activation. Shell startup is only supported for zsh, fsh, pwsh, bash, and cmd. This should make it happen before Code Runner

[aadarshsoni1]

Hi @eleanorjboyd,

Thank you so much for looking into this and providing a solution!

I followed the steps you provided:

1. Installed the Python Environments Extension.

2. Set "python.useEnvironmentsExtension": true in my User settings.

3. Set "python-envs.terminal.autoActivationType": "shellStartup" in my settings.

I can confirm that this has completely solved the issue. The environment now activates correctly before Code Runner executes, and the race condition is gone.

Thanks again for your help!