Pyrefly VS Code extension ignores the interpreter selected in “Python: Select Interpreter”

[c0rychu]

Describe the Bug

Even if I selected the Python interpreter in VS Code via > Python: Select Interpreter, the Pyrefly extension does not respect that. For instance, in an open .py file, it complains about Could not find import ... like

Could not find import of `rich.console`
  Looked in these locations (from config in `/Users/username/XXXXX/pyproject.toml`):
  Search path (from config file): ["/Users/username/XXXXX/src"]
  Import root (inferred from project layout): "/Users/username/XXXXX/src"
  Site package path queried from interpreter: ["/Users/username/.pyenv/versions/3.12.12/lib/python3.12", "/Users/username/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload", "/Users/username/.pyenv/versions/3.12.12/lib/python3.12/site-packages"]
Pyrefly(missing-import)

Only if I set

[tool.pyrefly]
python-interpreter-path = ".venv/bin/python"

in my pyproject.toml, the Pyrefly extension can then find the correct interpreter.

Sandbox Link

No response

(Only applicable for extension issues) IDE Information

VS Code:

Version: 1.106.2 (Universal)
Commit: 1e3c50d64110be466c0b4a45222e81d2c9352888
Date: 2025-11-19T16:56:50.023Z
Electron: 37.7.0
ElectronBuildId: 12781156
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Darwin arm64 25.1.0

Pyrefly Extension:

Identifier
meta.pyrefly
Version
0.42.2

[kinto0]

Sorry about the issue!

us finding the /Users/username/.pyenv/versions/3.12.12/lib/python3.12 interpreter is surprising. can you confirm a few things?

• are you using the new Microsoft python-environments extension or the normal Python (ms-python.python) extension? (we don't yet support the new one as it's in early adopters)
• how many workspace folders do you have?
• where is the workspace folder root compared to your pyrefly.toml/project root? (we prioritize scope of the workspace folder over the pyrefly.toml)
• which workspace folder setting did you set the interpreter to?
• do you have a "workspace level" interpreter set in addition to the workspace-folder level interpreter setting?

if you could turn on pyrefly > trace: server verbose and send the output from pyrefly language server (after changing the interpreter again) that would help a lot in debugging this!

thanks for the report!

[c0rychu]

I'm using

ms-python.python
ms-python.debugpy
ms-python.vscode-python-envs
charliermarsh.ruff
meta.pyrefly

I'm a little bit confused about what a workspace is. But I just have a single directory as my "workspace/project", where the pyproject.toml

I do not have a pyrefly.toml, instead, I have the following section in my pyproject.toml:

[tool.pyrefly]
python-interpreter-path = ".venv/bin/python"
project-includes = [ "src", "tests" ]
search-path = [ "src" ]

If I comment out this line:

# python-interpreter-path = ".venv/bin/python"

The Pyrefly will give the "Could not find import" mentioned above.

I have the following lines in my ~/.bash_profile

  export PYENV_ROOT="$HOME/.pyenv"
  command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"
  eval "$(pyenv init -)"

Maybe that's the reason why pyright found /Users/username/.pyenv/versions/3.12.12/lib/python3.12?

Minium example:

Anyway, I created a minimum example project with ms-python.vscode-python-envs disabled to demonstrate the issue:

pyrefly-trace.txt

pyrefly-demo.mp4

[kinto0]

I'm using

ms-python.python
ms-python.debugpy
ms-python.vscode-python-envs
charliermarsh.ruff
meta.pyrefly

I'm a little bit confused about what a workspace is. But I just have a single directory as my "workspace/project", where the pyproject.toml

I do not have a pyrefly.toml, instead, I have the following section in my pyproject.toml:

[tool.pyrefly]
python-interpreter-path = ".venv/bin/python"
project-includes = [ "src", "tests" ]
search-path = [ "src" ]

If I comment out this line:

# python-interpreter-path = ".venv/bin/python"

The Pyrefly will give the "Could not find import" mentioned above.

I have the following lines in my ~/.bash_profile

  export PYENV_ROOT="$HOME/.pyenv"
  command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"
  eval "$(pyenv init -)"

Maybe that's the reason why pyright found /Users/username/.pyenv/versions/3.12.12/lib/python3.12?

Minium example:

Anyway, I created a minimum example project with ms-python.vscode-python-envs disabled to demonstrate the issue:

pyrefly-trace.txt

pyrefly-demo.mp4

thank you for the video and logs! those are very useful.

I think #1654 will fix it. I'm adding tests and verifying it today, hopefully we can have it in the release for monday.

edit: this does not fix it
edit2 12/1: this should fix it