Testing: Wrong python version or environment

[SebKeb]

Type: Bug

When trying to discover the tests in my repository it throws the following error. Apparently it doesnt activate python or my environment correctly.

2025-09-04 15:48:08.376 [info] Discover tests for workspace name: modelBuilder - uri: /fast/home/s-kebrich/modelBuilder
2025-09-04 15:48:08.392 [info] arg: --rootdir already exists in args, not adding.
2025-09-04 15:48:08.393 [info] Environment variables set for pytest discovery: PYTHONPATH=/fast/home/s-kebrich/.vscode-server/extensions/ms-python.python-2025.12.0-linux-x64/python_files:/fast/home/s-kebrich/modelBuilder, TEST_RUN_PIPE=/run/user/1140/python-test-discovery-0ae26b119b3916000a75
2025-09-04 15:48:08.403 [info] > conda run -p ~/miniforge3/envs/MB2Europe --no-capture-output python ~/.vscode-server/extensions/ms-python.python-2025.12.0-linux-x64/python_files/get_output_via_markers.py ~/.vscode-server/extensions/ms-python.python-2025.12.0-linux-x64/python_files/printEnvVariables.py
2025-09-04 15:48:08.404 [info] shell: bash
2025-09-04 15:48:09.834 [info] > conda run -p ~/miniforge3/envs/MB2Europe --no-capture-output python ~/.vscode-server/extensions/ms-python.python-2025.12.0-linux-x64/python_files/get_output_via_markers.py -m pytest -p vscode_pytest --collect-only tests --rootdir=.
2025-09-04 15:48:09.834 [info] cwd: .
2025-09-04 15:48:11.052 [info] >>>PYTHON-EXEC-OUTPUT

2025-09-04 15:48:11.446 [error] ImportError while loading conftest '/fast/home/s-kebrich/modelBuilder/tests/conftest.py'.

2025-09-04 15:48:11.472 [error] tests/conftest.py:5: in
from modelBuilder.singletons import ModelLocations,ModelPaths,ModelTechnoEconomicData,InputDataInfo
modelBuilder/init.py:7: in
from .esMWorkflowManager import *
modelBuilder/esMWorkflowManager.py:1: in

2025-09-04 15:48:11.472 [error] import geopandas as gpd
E ModuleNotFoundError: No module named 'geopandas'

2025-09-04 15:48:11.472 [info] <<<PYTHON-EXEC-OUTPUT

2025-09-04 15:48:11.514 [error] ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['python', '/fast/home/s-kebrich/.vscode-server/extensions/ms-python.python-2025.12.0-linux-x64/python_files/get_output_via_markers.py', '-m', 'pytest', '-p', 'vscode_pytest', '--collect-only', 'tests', '--rootdir=/fast/home/s-kebrich/modelBuilder']' command failed. (See above for error)

2025-09-04 15:48:11.538 [error] Subprocess exited unsuccessfully with exit code 4 and signal null on workspace /fast/home/s-kebrich/modelBuilder.
2025-09-04 15:48:11.539 [error] Subprocess exited unsuccessfully with exit code 4 and signal null on workspace /fast/home/s-kebrich/modelBuilder. Creating and sending error discovery payload
2025-09-04 15:48:11.539 [error] pytest test discovery error for workspace: /fast/home/s-kebrich/modelBuilder

The python test process was terminated before it could exit on its own, the process errored with: Code: 4, Signal: null for workspace /fast/home/s-kebrich/modelBuilder

Trying to activate the environment in the terminal only works if the base environment is deactivated manually:
(base) [s-kebrich@iek3028 modelBuilder]$ conda activate /fast/home/s-kebrich/miniforge3/envs/MB2Europe
(MB2Europe) [s-kebrich@iek3028 modelBuilder]$ which python
/opt/ohpc/pub/apps/anaconda3/bin/python
(MB2Europe) [s-kebrich@iek3028 modelBuilder]$ mamba deactivate
(base) [s-kebrich@iek3028 modelBuilder]$ mamba deactivate
[s-kebrich@iek3028 modelBuilder]$ mamba activate MB2Europe
(MB2Europe) [s-kebrich@iek3028 modelBuilder]$ which python
~/miniforge3/envs/MB2Europe/bin/python
(MB2Europe) [s-kebrich@iek3028 modelBuilder]$

Discovering the tests in the terminal after manually deactivating base and activating the desired env works and the tests succesfully load.
In the free version of mobaXterm, activating the environment and sending the command "which python" also reveals the correct version.

VS Code version: Code 1.103.2 (6f17636121051a53c88d3e605c491d22af2ba755, 2025-08-20T16:45:34.255Z)
OS version: Windows_NT x64 10.0.26100
Modes:
Remote OS version: Linux x64 4.18.0-477.15.1.el8_8.x86_64

System Info

Item	Value
CPUs	12th Gen Intel(R) Core(TM) i7-1265U (12 x 2688)
GPU Status	2d_canvas: enabled 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 trees_in_viz: 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)	31.44GB (12.95GB free)
Process Argv
Screen Reader	no
VM	0%

Item	Value
Remote	SSH: iek3028.iek.kfa-juelich.de
OS	Linux x64 4.18.0-477.15.1.el8_8.x86_64
CPUs	Intel(R) Xeon(R) Gold 6154 CPU @ 3.00GHz (72 x 3698)
Memory (System)	1006.10GB (644.81GB free)
VM	0%

Extensions (29)

Extension	Author (truncated)	Version
remotehub	Git	0.64.0
jupyter-keymap	ms-	1.1.2
remote-containers	ms-	0.426.0
remote-ssh	ms-	0.121.2025081515
remote-ssh-edit	ms-	0.87.0
remote-wsl	ms-	0.99.0
vscode-remote-extensionpack	ms-	0.26.0
azure-repos	ms-	0.40.0
remote-explorer	ms-	0.5.0
remote-repositories	ms-	0.42.0
remote-server	ms-	1.5.2
docker	doc	0.16.0
gitlens	eam	17.4.1
copilot	Git	1.364.0
copilot-chat	Git	0.30.3
vscode-pull-request-github	Git	0.116.2
gitlab-workflow	Git	6.40.1
rainbow-csv	mec	3.21.0
vscode-containers	ms-	2.1.0
vscode-docker	ms-	2.0.0
debugpy	ms-	2025.11.2025072901
python	ms-	2025.12.0
vscode-pylance	ms-	2025.7.102
vscode-python-envs	ms-	1.2.0
jupyter	ms-	2025.7.0
jupyter-keymap	ms-	1.1.2
jupyter-renderers	ms-	1.3.0
vscode-jupyter-cell-tags	ms-	0.1.9
vscode-jupyter-slideshow	ms-	0.1.6

[eleanorjboyd]

does turning the setting python.useEnvironmentsExtension: false in your user settings change anything?

[SebKeb]

Hi,
First and most importantly: The issue is resolved, the terminal responds normally and the tests can be detected. We are unsure what resolved it, if there was an update or restarting the computer helped.

One of the first things we tried was downgrading the Python Environments add on to 1.2 since we expected an issue with it, but did not fully deactivate it.

Enabling python.useEnvironmentsExtension: false in the settings actually causes the issue again. Deactivating it and selecting the correct interpreter makes it work as intented.