Pytest (and often other things) loaded with wrong PYTHONPATH

[kam193]

Type: Bug

Behaviour

Since a few weeks / months, I'm constantly falling into issues that VSCode is setting global python path instead of or before the current virtual env when invoking different extension features (tests from test explorer, Jupyter notebooks, even terminal and other Python-dependant extensions). This path was not configured anywhere, even the default interpreter has been changed. The problem existed on two independent machines, without any config sync between them. As a common thing I'd note that both VSCode instances were configured long before VSCode-Python switched to use a storage instead of config file for the Python Interpreter path.

I have managed to resolve most of the issues by removing the ~/.config/Code/Cache directory (maybe also some others), but now it came again, when calling pytest from the Python test explorer.

Basically, pytest works well when called from terminal, but fails when trying to discover any test. Please see the logs from "Output" for Python - the PYTHONPATH is set to contain the global path, and the invoked pytest does try to use pluggy from there instad of the one from venv.

My suspicion is: the global path was at some point saved somewhere by the VSCode-Python extension. As the config files are no longer used for that, how could I looked up what are settings saved by the extension and remove the bad one?

This problem is extreamly irritating, couter-productive and comes back like a bumerang :(

Steps to reproduce:

Extreamly hard to say, I suspect you should have VSCode & the extension installed before the transition, and then do anything that would expect to use the local venv instead of global interpreter.

Diagnostic data

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

2024-08-07 12:48:33.346 [info] Discover tests for workspace name: *** - uri: /home/***
2024-08-07 12:48:33.346 [info] Running discovery for pytest using the new test adapter.
2024-08-07 12:48:33.346 [info] All environment variables set for pytest discovery: {*** "PYTHONPATH":"/home/kamil/.vscode/extensions/ms-python.python-2024.12.1-linux-x64/python_files:/usr/lib/python3/dist-packages", *** , "PWD":"/home/kamil",*** ,"SHELL":"/bin/bash", *** "VSCODE_AMD_ENTRYPOINT":"vs/workbench/api/node/extensionHostProcess","VSCODE_CLI":"1","VSCODE_CODE_CACHE_PATH":"/home/kamil/.config/Code/CachedData/b1c0a14de1414fcdaa400695b4db1c0799bc3124","VSCODE_CRASH_REPORTER_PROCESS_TYPE":"extensionHost","VSCODE_CWD":"/home/kamil","VSCODE_HANDLES_UNCAUGHT_ERRORS":"true","VSCODE_IPC_HOOK":"/run/user/1000/vscode-a892cd8d-1.92-main.sock","VSCODE_NLS_CONFIG":"{\"userLocale\":\"pl\",\"osLocale\":\"pl-pl\",\"resolvedLanguage\":\"en\",\"defaultMessagesFile\":\"/usr/share/code/resources/app/out/nls.messages.json\",\"locale\":\"en\",\"availableLanguages\":{}}","VSCODE_PID":"31610", *** "ELECTRON_RUN_AS_NODE":"1","APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL":"1","PATH":"/home/kamil/.poetry/bin:/home/kamil/bin:/home/kamil/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin","TEST_RUN_PIPE":"/run/user/1000/python-test-discovery-23875f4f44d677193539.sock"}
2024-08-07 12:48:33.347 [warning] could not find a pixi interpreter for the interpreter at /home/kamil/.pyenv/versions/3.10.8/envs/***
2024-08-07 12:48:33.357 [info] > ~/.pyenv/versions/3.10.8/envs/***/bin/python -m pytest -p vscode_pytest --collect-only .
2024-08-07 12:48:33.357 [info] cwd: .
2024-08-07 12:48:33.562 [error] Traceback (most recent call last):
  File "/home/kamil/.pyenv/versions/3.10.8/lib/python3.10/runpy.py", line 187, in _run_module_as_main
    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
  File "/home/kamil/.pyenv/versions/3.10.8/lib/python3.10/runpy.py", line 146, in _get_module_details
    return _get_module_details(pkg_main_name, error)
  File "/home/kamil/.pyenv/versions/3.10.8/lib/python3.10/runpy.py", line 110, in _get_module_details
    __import__(pkg_name)
  File "/home/kamil/.pyenv/versions/3.10.8/envs/lab-analysing-pkgs/lib/python3.10/site-packages/pytest/__init__.py", line 9, in <module>
    from _pytest.assertion import register_assert_rewrite
  File "/home/kamil/.pyenv/versions/3.10.8/envs/lab-analysing-pkgs/lib/python3.10/site-packages/_pytest/assertion/__init__.py", line 11, in <module>
    from _pytest.assertion import rewrite
  File "/home/kamil/.pyenv/versions/3.10.8/envs/lab-analysing-pkgs/lib/python3.10/site-packages/_pytest/assertion/rewrite.py", line 32, in <module>
    from _pytest.assertion import util
  File "/home/kamil/.pyenv/versions/3.10.8/envs/lab-analysing-pkgs/lib/python3.10/site-packages/_pytest/assertion/util.py", line 24, in <module>
    from _pytest.config import Config
  File "/home/kamil/.pyenv/versions/3.10.8/envs/lab-analysing-pkgs/lib/python3.10/site-packages/_pytest/config/__init__.py", line 40, in <module>
    from pluggy import HookimplOpts
ImportError: cannot import name 'HookimplOpts' from 'pluggy' (/usr/lib/python3/dist-packages/pluggy/__init__.py)

2024-08-07 12:48:33.588 [error] Subprocess exited unsuccessfully with exit code 1 and signal null on workspace /home/kamil/***.
2024-08-07 12:48:33.589 [error] Subprocess exited unsuccessfully with exit code 1 and signal null on workspace /home/kamil/***. Creating and sending error discovery payload
2024-08-07 12:48:33.589 [error] pytest test discovery error for workspace:  /home/kamil/*** 
  
 The python test process was terminated before it could exit on its own, the process errored with: Code: 1, Signal: null for workspace /home/kamil/***

Extension version: 2024.12.2
VS Code version: Code 1.92.0 (b1c0a14de1414fcdaa400695b4db1c0799bc3124, 2024-07-31T23:26:45.634Z)
OS version: Linux x64 6.5.0-45-generic
Modes:

• Python version (& distribution if applicable, e.g. Anaconda): 3.10.8
• Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): Pyenv
• Value of the python.languageServer setting: Pylance

User Settings

venvFolders: "<placeholder>"

languageServer: "Pylance"

testing
• pytestArgs: "<placeholder>"
• pytestEnabled: true

Installed Extensions

Extension Name	Extension Id	Version
Bookmarks	alefragnani.Bookmarks	13.5.0
Code Spell Checker	streetsidesoftware.code-spell-checker	3.0.1
Dev Containers	ms-vscode-remote.remote-containers	0.380.0
EditorConfig for VS Code	EditorConfig.EditorConfig	0.16.4
ESLint	dbaeumer.vscode-eslint	3.0.10
Even Better TOML	tamasfe.even-better-toml	0.19.2
GitHub Actions	me-dutour-mathieu.vscode-github-actions	3.0.1
GitHub Markdown Preview	bierner.github-markdown-preview	0.3.0
GitHub Pull Requests	GitHub.vscode-pull-request-github	0.94.0
GitLens — Git supercharged	eamodio.gitlens	15.2.3
Hex Editor	ms-vscode.hexeditor	1.10.0
IntelliCode	VisualStudioExptTeam.vscodeintellicode	1.3.1
JavaScript Debugger	ms-vscode.js-debug	1.92.0
JavaScript Debugger Companion Extension	ms-vscode.js-debug-companion	1.1.3
Jupyter	ms-toolsai.jupyter	2024.7.0
Jupyter Cell Tags	ms-toolsai.vscode-jupyter-cell-tags	0.1.9
Jupyter Keymap	ms-toolsai.jupyter-keymap	1.1.2
Jupyter Notebook Renderers	ms-toolsai.jupyter-renderers	1.0.19
Jupyter Slide Show	ms-toolsai.vscode-jupyter-slideshow	0.1.6
Markdown All in One	yzhang.markdown-all-in-one	3.6.2
Markdown Checkboxes	bierner.markdown-checkbox	0.4.0
Markdown Emoji	bierner.markdown-emoji	0.3.0
Markdown Footnotes	bierner.markdown-footnotes	0.1.1
Prettier - Code formatter	esbenp.prettier-vscode	10.4.0
Pylance	ms-python.vscode-pylance	2024.7.1
Python	ms-python.python	2024.12.1
Python Debugger	ms-python.debugpy	2024.10.0
Python Test Explorer for Visual Studio Code	littlefoxteam.vscode-python-test-adapter	0.8.2
Remote - SSH	ms-vscode-remote.remote-ssh	0.112.0
Remote Explorer	ms-vscode.remote-explorer	0.4.3
Ruff	charliermarsh.ruff	2024.36.0
sidebar-markdown-notes	assisrMatheus.sidebar-markdown-notes	1.2.0
SQLite	alexcvzz.vscode-sqlite	0.14.1
ssort	mikoz.ssort	1.0.2
Supermaven	Supermaven.supermaven	1.0.8
Table Visualizer for JavaScript Profiles	ms-vscode.vscode-js-profile-table	1.0.9
Terminal.env	hzeineddine.terminal-dotenv	1.0.0
Test Adapter Converter	ms-vscode.test-adapter-converter	0.1.9
Test Explorer UI	hbenl.vscode-test-explorer	2.21.1
YAML	redhat.vscode-yaml	1.15.0

A/B Experiments

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pythonnoceb:30805159
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pythonregdiag2:30936856
pythonmypyd1:30879173
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newcmakeconfigv2:31071590
impr_priority:31102340
nativerepl2:31104044
refactort:31108082
ccpltc:31103427
pythonrstrctxtcf:31103194
wkspc-onlycs-t:31111718

[eleanorjboyd]

Hi! To clarify is only testing using the wrong environment or the extension as a whole? We are aware of an issue of incorrect environment selection for testing but if this is for the extension overall then it would be related to something else and I can loop another coworker in.

[kam193]

In my experience, it's probably everything taking the python path from the Python extension: Jupyter Notebooks, Terminal (I had to override the PYTHONPATH in terminal's env settings). When trying to debug what is wrong with the Jupyter Notebooks, I managed to narrow the issue to environmental variables delivered by the Python extension.

Side note: today I surprisingly was able to use some features that a few days ago in a different project were broken. I still don't know if something was fixed (e.g. in the newest release), or in this particular project I just didn't have anything conflicting with the system packages.

[eleanorjboyd]

Ah gotcha- so were you able to adjust the environment variables or is it still causing issues? We have make many improvements in this area (environment selection and activation) and so hopefully that was the fix that helped with the previously broken package

[kam193]

I will test it again and come back probably next week (I won't be able to do it today)

[kam193]

Hey, I've checked again, and unfortunately, it still does not work. Sometimes I have luck that what I need does not conflict with the system packages, but generally - the wrong PYTHONPATH is still here, everywhere.

[kam193]

FYI: I've just found a new workaround, let's configure Python extension to use .env file and put there manually the expected PYTHONPATH, like:

PYTHONPATH=/home/[...]/.venv/lib/python3.10/site-packages

Then in the terminal you can observe:

$ env | grep PYTHON
PYTHONPATH=/home/[...]/.venv/lib/python3.10/site-packages:/usr/lib/python3/dist-packages

And at least the Jupyter started to work. Not that in this case I used a local venv instead of the one from pyenv (I hope it's not the requirement, just a thing I needed).

This is weird.

[kam193]

I didn't intend to close the issue, it's a missclick - could you please reopen it?