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A Complete Guide to Resolving the ‘Ghost’ Virtual Environment Issue in VS Code with WSL

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A Complete Guide to Resolving the “Ghost” Virtual Environment Issue in VS Code with WSL

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The Symptom 😵‍💫

When you connect to WSL with VS Code and create a new folder, you might encounter a strange phenomenon: the (.venv) prefix appears in your terminal prompt, even though you haven’t created a virtual environment.

Of course, the .venv directory doesn’t actually exist. Running the deactivate command only results in an error message, and you can’t exit the “virtual environment” as you normally would.

When Does This Occur? 🤔

This phenomenon only happens under specific conditions:

When it Happens ❌

  • When you open the problematic directory directly in VS Code.
  • If you previously created a directory with the same name in the same location and used a virtual environment there.
  • If that setting remains in VS Code’s internal storage.

When it Doesn’t Happen ✅

  • If you create a directory with a different name.
  • If you open a different directory in VS Code first and then navigate to the problematic directory using the cd command.
  • If you have already run the Python: Clear Workspace Interpreter Setting command.

In short, this is a very specific issue caused by VS Code’s workspace functionality.

Why Does This Happen? 👻

The cause of this mysterious phenomenon lies in VS Code’s interpreter setting persistence mechanism.

The New Settings Management System (Since 2021)

The VS Code Python extension significantly changed its settings management method around 2021:

  1. Old Method (Deprecated): Saved the python.pythonPath setting in .vscode/settings.json.
  2. New Method (Current): Saves settings to VS Code’s internal storage (an SQLite database).

Where Settings Are Stored

Workspace settings are now saved in VS Code’s internal storage, not in settings.json or .code-workspace files. Specifically:

  • Windows: %APPDATA%\Code\User\globalStorage\state.vscdb
  • macOS: ~/Library/Application Support/Code/User/globalStorage/state.vscdb
  • Linux: ~/.config/Code/User/globalStorage/state.vscdb

Within this SQLite database, the path to the Python interpreter is stored using the workspace path as the key.

The Mechanism of the Problem

  1. Initially, you create and use a .venv virtual environment in /home/user/project.
  2. VS Code records this in its internal storage: WORKSPACE_FOLDER_INTERPRETER_PATH_/home/user/project → /home/user/project/.venv/bin/python.
  3. You delete the folder.
  4. You recreate a folder with the same name at the same path.
  5. VS Code detects the old setting and tries to activate the non-existent .venv.
  6. Result: Only (.venv) appears in the prompt.

Solutions 🛠️

Method 1: Temporary Fix (If you want to remove the display immediately)

Run the following command in the terminal:

exec $SHELL

This command restarts the current shell. The settings applied by VS Code will be reset, and the (.venv) display will disappear.

Note: This is a temporary workaround. The (.venv) will reappear if you restart VS Code or open a new terminal.

You can clear the stored value using the Python: Clear Workspace Interpreter Setting command.

  1. Open the Command Palette Press Ctrl + Shift + P (or Cmd + Shift + P on Mac).
  2. Clear the Setting Type Python: Clear Workspace Interpreter Setting and execute it.
  3. Select a New Interpreter Run the Python: Select Interpreter command and choose the appropriate Python interpreter.

Method 3: Refresh the Cache

If the interpreter list is showing outdated information:

  1. Open the Command Palette with Ctrl + Shift + P.
  2. Run Python: Clear Cache and Reload Window.
  3. VS Code will restart, and the cache will be cleared.

Method 4: Manual Database Editing (For Advanced Users)

If the problem persists, you can edit the SQLite database directly:

  1. Completely close VS Code.
  2. Install an SQLite browser tool (like DB Browser for SQLite).
  3. Open the state.vscdb file.
  4. Find the ms-python.python key in the ItemTable table.
  5. Delete or modify the entry for the corresponding workspace path.

The New Setting Method (python.defaultInterpreterPath)

For team collaboration or version-controlling your settings, you can use the python.defaultInterpreterPath setting:

{
  "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python"
}

Important Notes:

  • This setting is only read when you open the project for the first time.
  • After you select an interpreter once, changes to this setting will not be reflected.
  • VS Code will not automatically modify this setting.

WSL-Specific Considerations

Additional points when working in a WSL environment:

Check the Remote-WSL Extension

  1. Ensure the Remote-WSL extension is installed in VS Code.
  2. Check that you are connected to WSL via the green button in the bottom-left corner.
  3. Verify that your terminal is WSL’s bash/zsh.

Be Aware of Path Differences

  • Windows path: C:\Users\username\project
  • WSL path: /home/username/project
  • Mounted Windows path: /mnt/c/Users/username/project

Different paths are treated as separate workspaces, so their settings are stored separately.

Prevention Methods 🛡️

To avoid this issue in the future:

  1. Use different names for each project.
  2. Run Python: Clear Workspace Interpreter Setting before deleting a virtual environment.
  3. Add .vscode/ to your .gitignore to avoid conflicts with local settings.
  4. Use python.defaultInterpreterPath for standardization in team development.

Troubleshooting 🔍

Checklist if the Problem Isn’t Solved

  1. Is VS Code completely closed?
    • Close all windows.
    • Check Task Manager for any remaining Code.exe processes.
  2. Are you working in the correct workspace?
    • In a multi-root workspace, each folder can have individual settings.
  3. Is the Python extension up to date?
    • Check for updates to the extension.
    • Reinstall it if necessary.
  4. Is the WSL integration working correctly?
    • Check the WSL status with wsl --status.
    • Reinstall the Remote-WSL extension.

Summary

VS Code’s convenient workspace feature can sometimes cause confusion. This issue stems from the new settings management system adopted by VS Code since 2021, where interpreter settings are persisted in internal storage.

The main solutions are:

  • Immediate fix: Reset the shell with exec $SHELL.
  • Fundamental solution: Clear the setting with Python: Clear Workspace Interpreter Setting.
  • Preventive measure: Use different project names or clear the setting beforehand.

If you see a strange display in your terminal, thinking, “Maybe there’s an old setting left in VS Code’s internal storage?” might lead you to a solution.

Last updated: September 2, 2025 Compatible with VS Code version: 1.90 and later Compatible with Python extension: 2023.14.0 and later

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