Python 3.1x from Conda environment sometimes detected as 3.1

[maresb]

Type: Bug

Behaviour

When the Python extension loads, it often detects Python 3.11 as Python 3.1.

As originally reported by @niemiaszek in #22968 (comment),

One strange thing for me is the fact that VS Code detects python 3.1.x in Select Interpreter context. Is that some bug related to current version of VS Code or Pixi? Could it have some implications on integration with other VS Code extensions like Ruff?

My suspicion is that this has to do with the symlink python3.1 -> python3.1X present in Conda environments.

Here's what I see:

And here's my Jupyter log output, which doesn't seem particularly informative:

Visual Studio Code (1.90.1, dev-container, desktop)
Jupyter Extension Version: 2024.5.0.
Python Extension not installed.
Pylance Extension not installed.
Platform: linux (x64).
Workspace folder /workspaces/projectname, Home = /home/mambauser
09:45:12.525 [info] Starting Kernel (Python Path: /opt/conda/bin/python, Conda, 3.11.undefined) for '/workspaces/projectname/Untitled-3.ipynb' (disableUI=true)
09:45:15.783 [info] Process Execution: /opt/conda/bin/python -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)"
09:45:15.800 [info] Process Execution: /opt/conda/bin/python -m ipykernel_launcher --f=/home/~/.local/share/jupyter/runtime/kernel-v2-416foZ3dcdQ2w4v.json
    > cwd: //workspaces/projectname
09:45:15.837 [info] Process Execution: /opt/conda/bin/python -m pip list
09:45:17.364 [info] Kernel successfully started

What really tipped me off was the output from the Ruff extension since their logs are very targeted:

2024-06-20 07:48:37.054 [info] Name: Ruff
2024-06-20 07:48:37.054 [info] Module: ruff
2024-06-20 07:48:37.054 [error] Python version 3.1 is not supported.
2024-06-20 07:48:37.054 [error] Selected python path: /opt/conda/bin/python
2024-06-20 07:48:37.054 [error] Supported versions are 3.7 and above.
2024-06-20 07:48:37.054 [error] Python version 3.1 is not supported.
2024-06-20 07:48:37.054 [error] Selected python path: /opt/conda/bin/python
2024-06-20 07:48:37.054 [error] Supported versions are 3.7 and above.
2024-06-20 07:48:37.054 [error] Python interpreter missing:
[Option 1] Select Python interpreter using the ms-python.python.
[Option 2] Set an interpreter using "ruff.interpreter" setting.
Please use Python 3.7 or greater.

EXPAND FOR PYTHON LOG EXCERPTS

I have to be really careful here about leaking sensitive info since these logs include full environment variable dumps.

...

2024-06-20 07:45:12.407 [debug] Probing conda binary: conda
2024-06-20 07:45:12.446 [info] > conda info --json
2024-06-20 07:45:12.524 [debug] No cached env found for /opt/conda/bin/python
2024-06-20 07:45:12.558 [debug] No cached env found for /opt/conda/bin/python
2024-06-20 07:45:12.593 [debug] Extension ms-toolsai.jupyter accessed resolveEnvironment with args: "/opt/conda/bin/python"
2024-06-20 07:45:12.602 [debug] No cached env found for /opt/conda/bin/python
2024-06-20 07:45:12.602 [debug] No cached env found for /opt/conda/bin/python
2024-06-20 07:45:12.706 [debug] Extension ms-toolsai.jupyter accessed resolveEnvironment with args: {"internal":{"path":"/opt/conda/bin/python","id":"/opt/conda/bin/python","executable":{"uri":{"$mid":1,"fsPath":"/opt/conda/bin/python","external":"file:///opt/conda/bin/python","path":"/opt/conda/bin/python","scheme":"file"},"bitness":"Unknown","sysPrefix":"/opt/conda"},"environment":{"type":"Conda","name":"base","folderUri":{"$mid":1,"path":"/opt/conda","scheme":"file"}},"version":{"major":3,"minor":11},"tools":["Conda"]},"id":"/opt/conda/bin/python"}
2024-06-20 07:45:12.707 [debug] Extension ms-toolsai.jupyter accessed resolveEnvironment with args: {"internal":{"path":"/opt/conda/bin/python","id":"/opt/conda/bin/python","executable":{"uri":{"$mid":1,"fsPath":"/opt/conda/bin/python","external":"file:///opt/conda/bin/python","path":"/opt/conda/bin/python","scheme":"file"},"bitness":"Unknown","sysPrefix":"/opt/conda"},"environment":{"type":"Conda","name":"base","folderUri":{"$mid":1,"path":"/opt/conda","scheme":"file"}},"version":{"major":3,"minor":11},"tools":["Conda"]},"id":"/opt/conda/bin/python"}
2024-06-20 07:45:12.710 [debug] Extension ms-toolsai.jupyter accessed onDidEnvironmentVariablesChange with args: undefined
2024-06-20 07:45:12.711 [debug] Extension ms-toolsai.jupyter accessed getEnvironmentVariables with args: undefined
2024-06-20 07:45:12.712 [debug] Extension ms-toolsai.jupyter accessed resolveEnvironment with args: {"internal":{"path":"/opt/conda/bin/python","id":"/opt/conda/bin/python","executable":{"uri":{"$mid":1,"fsPath":"/opt/conda/bin/python","external":"file:///opt/conda/bin/python","path":"/opt/conda/bin/python","scheme":"file"},"bitness":"Unknown","sysPrefix":"/opt/conda"},"environment":{"type":"Conda","name":"base","folderUri":{"$mid":1,"path":"/opt/conda","scheme":"file"}},"version":{"major":3,"minor":11},"tools":["Conda"]},"id":"/opt/conda/bin/python"}
2024-06-20 07:45:12.713 [debug] Extension ms-toolsai.jupyter accessed resolveEnvironment with args: {"internal":{"path":"/opt/conda/bin/python","id":"/opt/conda/bin/python","executable":{"uri":{"$mid":1,"fsPath":"/opt/conda/bin/python","external":"file:///opt/conda/bin/python","path":"/opt/conda/bin/python","scheme":"file"},"bitness":"Unknown","sysPrefix":"/opt/conda"},"environment":{"type":"Conda","name":"base","folderUri":{"$mid":1,"path":"/opt/conda","scheme":"file"}},"version":{"major":3,"minor":11},"tools":["Conda"]},"id":"/opt/conda/bin/python"}

...

2024-06-20 07:45:13.689 [debug] Received shell integration sequence for bash
2024-06-20 07:45:13.723 [debug] Found hatch binary hatch
2024-06-20 07:45:13.724 [debug] Finished searching for Hatch envs
2024-06-20 07:45:14.236 [debug] conda info --json: {
  "GID": 1000,
  "UID": 1000,
  "active_prefix": "/opt/conda",
  "active_prefix_name": "base",
  "av_data_dir": "/opt/conda/etc/conda",
  "av_metadata_url_base": null,
  "channels": [
    "https://conda.anaconda.org/conda-forge/linux-64",
    "https://conda.anaconda.org/conda-forge/noarch"
  ],
  "conda_build_version": "not installed",
  "conda_env_version": "24.5.0",
  "conda_location": "/opt/conda/lib/python3.11/site-packages/conda",
  "conda_prefix": "/opt/conda",
  "conda_shlvl": 1,
  "conda_version": "24.5.0",
  "config_files": [
    "/home/mambauser/.condarc"
  ],
  "default_prefix": "/opt/conda",
  "env_vars": {
    "CIO_TEST": "<not set>",
    "CONDA_DEFAULT_ENV": "base",
    "CONDA_EXE": "/opt/conda/bin/conda",
    "CONDA_PREFIX": "/opt/conda",
    "CONDA_PROMPT_MODIFIER": "(base) ",
    "CONDA_PYTHON_EXE": "/opt/conda/bin/python",
    "CONDA_ROOT": "/opt/conda",
    "CONDA_SHLVL": "1",
    "CURL_CA_BUNDLE": "<not set>",
    "GDAL_DRIVER_PATH": "/opt/conda/lib/gdalplugins",
    "LD_PRELOAD": "<not set>",
    "PATH": "/vscode/vscode-server/bin/linux-x64/611f9bfce64f25108829dd295f54a6894e87339d/bin/remote-cli:/home/mambauser/.local/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/mambauser/.local/bin",
    "PYTHONIOENCODING": "utf-8",
    "PYTHONUNBUFFERED": "1",
    "REQUESTS_CA_BUNDLE": "<not set>",
    "SSL_CERT_FILE": "<not set>"
  },
  "envs": [
    "/opt/conda"
  ],
  "envs_dirs": [
    "/opt/conda/envs",
    "/home/mambauser/.conda/envs"
  ],
  "netrc_file": null,
  "offline": false,
  "pkgs_dirs": [
    "/opt/conda/pkgs",
    "/home/mambauser/.conda/pkgs"
  ],
  "platform": "linux-64",
  "python_version": "3.11.9.final.0",
  "rc_path": "/home/mambauser/.condarc",
  "requests_version": "2.32.3",
  "root_prefix": "/opt/conda",
  "root_writable": true,
  "site_dirs": [],
  "solver": {
    "default": true,
    "name": "libmamba",
    "user_agent": "solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8"
  },
  "sys.executable": "/opt/conda/bin/python",
  "sys.prefix": "/opt/conda",
  "sys.version": "3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]",
  "sys_rc_path": "/opt/conda/.condarc",
  "user_agent": "conda/24.5.0 requests/2.32.3 CPython/3.11.9 Linux/5.15.0-107-generic ubuntu/22.04.4 glibc/2.35 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8",
  "user_rc_path": "/home/mambauser/.condarc",
  "virtual_pkgs": [
    [
      "__archspec",
      "1",
      "skylake"
    ],
    [
      "__conda",
      "24.5.0",
      "0"
    ],
    [
      "__glibc",
      "2.35",
      "0"
    ],
    [
      "__linux",
      "5.15.0",
      "0"
    ],
    [
      "__unix",
      "0",
      "0"
    ]
  ]
}


2024-06-20 07:45:14.236 [debug] Found conda via filesystem probing: conda
2024-06-20 07:45:14.255 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.259 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.263 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.265 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.268 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.270 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.277 [debug] Best effort version B for /opt/conda/bin/python {"major":3,"minor":1,"micro":-1}
2024-06-20 07:45:14.278 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.278 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.279 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.279 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.279 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.279 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.279 [debug] Best effort version C for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.283 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.285 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.285 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.286 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.287 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.288 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.289 [debug] Best effort version D for /opt/conda/bin/python {"major":-1,"minor":-1,"micro":-1,"release":{"level":"final","serial":-1}}
2024-06-20 07:45:14.292 [info] Environments refresh finished (event): 3074 milliseconds
2024-06-20 07:45:14.292 [debug] Finished with environment resolver
2024-06-20 07:45:14.292 [debug] Finished with environment reducer
2024-06-20 07:45:14.292 [info] Environments refresh paths discovered: 3074 milliseconds
2024-06-20 07:45:14.293 [debug] Environment resolver resolved /opt/conda/bin/python for {"name":"base","location":"/opt/conda","kind":"virt-conda","executable":{"filename":"/opt/conda/bin/python","sysPrefix":"","ctime":1718314262335,"mtime":1718314262335},"display":"Python 3.1.x ('base')","version":{"major":3,"minor":1,"micro":-1},"arch":1,"distro":{"org":"Anaconda, Inc."},"source":[],"type":"Conda","id":"/opt/conda/bin/python","detailedDisplayName":"Python 3.1.x ('base': conda)"} to {"arch":1,"executable":{"filename":"/opt/conda/bin/python","ctime":-1,"mtime":-1,"sysPrefix":"/opt/conda"},"version":{"major":3,"minor":1,"micro":-1}}
2024-06-20 07:45:14.295 [debug] Resolved /opt/conda/bin/python using downstream locator
2024-06-20 07:45:14.295 [debug] Python API env change detected /opt/conda/bin/python update
2024-06-20 07:45:14.295 [debug] Flushing env to cache /opt/conda/bin/python
2024-06-20 07:45:14.296 [info] Python interpreter path: /opt/conda/bin/python
2024-06-20 07:45:14.297 [debug] Found cached env for /opt/conda/bin/python
2024-06-20 07:45:14.297 [debug] Environment resolver resolved /opt/conda/bin/python for {"name":"base","location":"/opt/conda","kind":"virt-conda","executable":{"filename":"/opt/conda/bin/python","sysPrefix":"","ctime":1718314262335,"mtime":1718314262335},"display":"Python 3.1.x ('base')","version":{"major":3,"minor":1,"micro":-1},"arch":1,"distro":{"org":"Anaconda, Inc."},"source":[],"type":"Conda","id":"/opt/conda/bin/python","detailedDisplayName":"Python 3.1.x ('base': conda)"} to {"arch":1,"executable":{"filename":"/opt/conda/bin/python","ctime":-1,"mtime":-1,"sysPrefix":"/opt/conda"},"version":{"major":3,"minor":1,"micro":-1}}
2024-06-20 07:45:14.297 [debug] Resolved /opt/conda/bin/python using downstream locator
2024-06-20 07:45:14.297 [debug] Flushing env to cache /opt/conda/bin/python
2024-06-20 07:45:14.298 [error] Invalid version for /opt/conda/bin/python: {"name":"base","location":"/opt/conda","kind":"virt-conda","executable":{"filename":"/opt/conda/bin/python","sysPrefix":"/opt/conda","ctime":1718314262335,"mtime":1718314262335},"display":"Python 3.1.x ('base')","version":{"major":3,"minor":1,"micro":-1},"arch":1,"distro":{"org":"Anaconda, Inc."},"source":[],"type":"Conda","id":"/opt/conda/bin/python","detailedDisplayName":"Python 3.1.x ('base': conda)"}
2024-06-20 07:45:14.298 [debug] Environment resolver resolved /opt/conda/bin/python for {"name":"base","location":"/opt/conda","kind":"virt-conda","executable":{"filename":"/opt/conda/bin/python","sysPrefix":"","ctime":1718314262335,"mtime":1718314262335},"display":"Python 3.1.x ('base')","version":{"major":3,"minor":1,"micro":-1},"arch":1,"distro":{"org":"Anaconda, Inc."},"source":[],"type":"Conda","id":"/opt/conda/bin/python","detailedDisplayName":"Python 3.1.x ('base': conda)"} to {"arch":1,"executable":{"filename":"/opt/conda/bin/python","ctime":-1,"mtime":-1,"sysPrefix":"/opt/conda"},"version":{"major":3,"minor":1,"micro":-1}}
2024-06-20 07:45:14.298 [debug] Resolved /opt/conda/bin/python using downstream locator
2024-06-20 07:45:14.298 [debug] Flushing env to cache /opt/conda/bin/python
2024-06-20 07:45:14.298 [error] Invalid version for /opt/conda/bin/python: {"name":"base","location":"/opt/conda","kind":"virt-conda","executable":{"filename":"/opt/conda/bin/python","sysPrefix":"/opt/conda","ctime":1718314262335,"mtime":1718314262335},"display":"Python 3.1.x ('base')","version":{"major":3,"minor":1,"micro":-1},"arch":1,"distro":{"org":"Anaconda, Inc."},"source":[],"type":"Conda","id":"/opt/conda/bin/python","detailedDisplayName":"Python 3.1.x ('base': conda)"}
2024-06-20 07:45:14.304 [debug] Found cached env for /opt/conda/bin/python
2024-06-20 07:45:14.322 [debug] Activating Environment to capture Environment variables, conda run -n base --no-capture-output python /home/mambauser/.vscode-server/extensions/ms-python.python-2024.8.1/python_files/get_output_via_markers.py /home/mambauser/.vscode-server/extensions/ms-python.python-2024.8.1/python_files/printEnvVariables.py
2024-06-20 07:45:14.322 [info] > conda run -n base --no-capture-output python ~/.vscode-server/extensions/ms-python.python-2024.8.1/python_files/get_output_via_markers.py ~/.vscode-server/extensions/ms-python.python-2024.8.1/python_files/printEnvVariables.py
2024-06-20 07:45:14.322 [info] shell: bash

...

---

---

Steps to reproduce:

1. Start VS Code and initialize the Python extension. (Unfortunately this is not 100% reproducible for me, and I haven't been able to isolate precisely which conditions cause it.)

Diagnostic data

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

XXX

Extension version: 2024.8.1
VS Code version: Code 1.90.1 (611f9bfce64f25108829dd295f54a6894e87339d, 2024-06-11T21:02:43.666Z)
OS version: Linux x64 5.15.0-107-generic
Modes:
Remote OS version: Linux x64 5.15.0-107-generic

• Python version (& distribution if applicable, e.g. Anaconda): 3.11.9
• Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): Conda
• Value of the python.languageServer setting: Pylance

User Settings

condaPath: "<placeholder>"

languageServer: "Pylance"

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

terminal
• activateEnvironment: false

experiments
• enabled: false

Installed Extensions

Extension Name	Extension Id	Version
Docker	ms-azuretools.vscode-docker	1.29.1
Git History	donjayamanne.githistory	0.6.20
GitHub Copilot	GitHub.copilot	1.204.0
GitHub Copilot Chat	GitHub.copilot-chat	0.16.1
GitLens — Git supercharged	eamodio.gitlens	15.1.0
hadolint	exiasr.hadolint	1.1.2
JavaScript Debugger	ms-vscode.js-debug	1.90.0
Jupyter	ms-toolsai.jupyter	2024.5.0
Jupyter Cell Tags	ms-toolsai.vscode-jupyter-cell-tags	0.1.9
Jupyter Notebook Renderers	ms-toolsai.jupyter-renderers	1.0.18
Jupyter Slide Show	ms-toolsai.vscode-jupyter-slideshow	0.1.6
Live Share	ms-vsliveshare.vsliveshare	1.0.5932
markdownlint	DavidAnson.vscode-markdownlint	0.55.0
Pylance	ms-python.vscode-pylance	2024.6.1
Python	ms-python.python	2024.8.1
Python Debugger	ms-python.debugpy	2024.6.0
Resource Monitor	mutantdino.resourcemonitor	1.0.7
Ruff	charliermarsh.ruff	2024.28.0
Table Visualizer for JavaScript Profiles	ms-vscode.vscode-js-profile-table	1.0.9
Xonsh IDE	jnoortheen.xonsh	0.3.3

System Info

Item	Value
CPUs	Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz (8 x 3708)
GPU Status	2d_canvas: enabled canvas_oop_rasterization: disabled_off 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: disabled_software vulkan: disabled_off webgl: enabled webgl2: enabled webgpu: disabled_off
Load (avg)	7, 6, 7
Memory (System)	62.75GB (15.50GB free)
Process Argv	--log ms-python.python=debug
Screen Reader	no
VM	0%
DESKTOP_SESSION	ubuntu
XDG_CURRENT_DESKTOP	Unity
XDG_SESSION_DESKTOP	ubuntu
XDG_SESSION_TYPE	x11

Item	Value
Remote	Dev Container: projectname
OS	Linux x64 5.15.0-107-generic
CPUs	Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz (8 x 3708)
Memory (System)	62.75GB (15.50GB free)
VM	0%

[kilianjn]

Exactly the same problem. I have as well problems with the debugger which requires at least version 3.7 .
Have problems calling figures from matplotlib from the debugger.

I switched to the pre release version of Python Debugger and the Python version seems to be the correct again. Problems with the debugger persist though

[thiagojramos]

Same issue here. The conda base environment shows as Python 3.1. Both conda and VS 2022 are up to date. Conda.exe and the scripts folder are set in the options. The Python version in the conda base is 3.12.

Details

[Himanshunitrr]

Having the same issue, any updates on this?

[karthiknadig]

Please try the pre-release version of the python extension. It has a potential fix for this.

[Himanshunitrr]

Thanks, it works

[CHLEE-Leo]

Please try the pre-release version of the python extension. It has a potential fix for this.

I had the same issue and fixed it following your advice. What was the cause of error? @karthiknadig

[lalvarezpoli]

Please try the pre-release version of the python extension. It has a potential fix for this.

Sorry for the dumb question, but what does this mean exactly? Is it within the VsCode settings, or update the virtual env?

[maresb]

@lalvarezpoli:

See the "Switch to pre-release version" button

[rubensa]

I think this is caused because conda creates a symlink called python3.1 pointing to python3.10, python3.11 or python3.12 (whichever version you installed) for Python >=3.10. See: conda/conda#11423 (comment)