Environment data

• Language Server version: 2022.9.41 (pyright 59bdc42e)
• OS and version: macOS 12.5.1
• Python version (& distribution if applicable, e.g. Anaconda): 3.9.12 (miniconda)

Repro Steps

Analysis enabled at workspace level:

    "python.analysis.diagnosticMode": "workspace",

Several errors in the bundled spipy stubs are showing up, of the form "PyCapsule" is not defined.

These files are in "~/.vscode-insiders/extensions/ms-python.vscode-pylance-2022.9.41/dist/bundled/stubs/scipy-stubs/spatial/ckdtree.pyi". When analyzing an open directory I wouldn't expect errors in stubs defined in VS Code's own folders to be included.

I've tried excluding these using python.analysis.ignore and python.analysis.exclude, with full absolute paths, relative paths, wildcards... but regardless of what is tried these errors still show up. An example of what I've tried:

    "python.analysis.ignore": [
        "**/dist/bundled/stubs/**"
    ],

Deleting the bundled stubs resolves the problem until PyLance is next updated, but this has to be repeated every time. Ideally I'd like a way to globally exclude these bundled stubs from a workspace analysis.

Logs if those are useful:

[Info  - 10:55:25 AM] (99752) Pylance language server 2022.9.41 (pyright 59bdc42e) starting
[Info  - 10:55:25 AM] (99752) Server root directory: /Users/<user>/.vscode-insiders/extensions/ms-python.vscode-pylance-2022.9.41/dist
[Info  - 10:55:25 AM] (99752) Starting service instance "<project>"
[Info  - 10:55:25 AM] (99752) Notebook support: LSP
[Info  - 10:55:25 AM] (99752) Interactive window support: LSP
[Info  - 10:55:26 AM] (99752) No configuration file found.
[Info  - 10:55:26 AM] (99752) pyproject.toml file found at /Users/<user>/Projects/<project>.
[Info  - 10:55:26 AM] (99752) Setting pythonPath for service "<project>": "/Users/<user>/opt/miniconda3/bin/python"
[Info  - 10:55:26 AM] (99752) Loading pyproject.toml file at /Users/<user>/Projects/<project>/pyproject.toml
[Info  - 10:55:26 AM] (99752) Assuming Python version 3.9
[Info  - 10:55:26 AM] (99752) Assuming Python platform Darwin
[Info  - 10:55:26 AM] (99752) No include entries specified; assuming /Users/<user>/Projects/<project>
[Info  - 10:55:26 AM] (99752) Auto-excluding **/node_modules
[Info  - 10:55:26 AM] (99752) Auto-excluding **/__pycache__
[Info  - 10:55:26 AM] (99752) Auto-excluding **/.*
[Info  - 10:55:26 AM] (99752) Searching for source files
[Info  - 10:55:27 AM] (99752) Found 79 source files
[Info  - 10:55:27 AM] (99752) Background analysis(1) root directory: /Users/<user>/.vscode-insiders/extensions/ms-python.vscode-pylance-2022.9.41/dist
[Info  - 10:55:27 AM] (99752) Background analysis(1) started
[Info  - 10:55:29 AM] (99752) [BG(1)] Long operation: analyzing: /Users/<user>/Projects/<project>/src/pipeline.py (2407ms)
[Info  - 11:33:20 AM] (99752) No configuration file found.
[Info  - 11:33:20 AM] (99752) pyproject.toml file found at /Users/<user>/Projects/<project>.
[Info  - 11:33:20 AM] (99752) Setting pythonPath for service "<project>": "/Users/<user>/opt/miniconda3/bin/python"
[Info  - 11:33:20 AM] (99752) Loading pyproject.toml file at /Users/<user>/Projects/<project>/pyproject.toml
[Info  - 11:33:20 AM] (99752) Assuming Python version 3.9
[Info  - 11:33:20 AM] (99752) Assuming Python platform Darwin
[Info  - 11:33:20 AM] (99752) No include entries specified; assuming /Users/<user>/Projects/<project>
[Info  - 11:33:20 AM] (99752) Auto-excluding **/node_modules
[Info  - 11:33:20 AM] (99752) Auto-excluding **/__pycache__
[Info  - 11:33:20 AM] (99752) Auto-excluding **/.*
[Info  - 11:33:20 AM] (99752) Searching for source files
[Info  - 11:33:20 AM] (99752) Found 79 source files
[Info  - 11:34:58 AM] (99752) No configuration file found.
[Info  - 11:34:58 AM] (99752) pyproject.toml file found at /Users/<user>/Projects/<project>.
[Info  - 11:34:58 AM] (99752) Setting pythonPath for service "<project>": "/Users/<user>/opt/miniconda3/bin/python"
[Info  - 11:34:58 AM] (99752) Loading pyproject.toml file at /Users/<user>/Projects/<project>/pyproject.toml
[Info  - 11:34:58 AM] (99752) Assuming Python version 3.9
[Info  - 11:34:58 AM] (99752) Assuming Python platform Darwin
[Info  - 11:34:58 AM] (99752) No include entries specified; assuming /Users/<user>/Projects/<project>
[Info  - 11:34:58 AM] (99752) Auto-excluding **/node_modules
[Info  - 11:34:58 AM] (99752) Auto-excluding **/__pycache__
[Info  - 11:34:58 AM] (99752) Auto-excluding **/.*
[Info  - 11:34:58 AM] (99752) Searching for source files
[Info  - 11:34:58 AM] (99752) Found 79 source files
[Info  - 11:37:15 AM] (99752) No configuration file found.
[Info  - 11:37:15 AM] (99752) pyproject.toml file found at /Users/<user>/Projects/<project>.
[Info  - 11:37:15 AM] (99752) Setting pythonPath for service "<project>": "/Users/<user>/opt/miniconda3/bin/python"
[Info  - 11:37:15 AM] (99752) Loading pyproject.toml file at /Users/<user>/Projects/<project>/pyproject.toml
[Info  - 11:37:15 AM] (99752) Assuming Python version 3.9
[Info  - 11:37:15 AM] (99752) Assuming Python platform Darwin
[Info  - 11:37:15 AM] (99752) No include entries specified; assuming /Users/<user>/Projects/<project>
[Info  - 11:37:15 AM] (99752) Auto-excluding **/node_modules
[Info  - 11:37:15 AM] (99752) Auto-excluding **/__pycache__
[Info  - 11:37:15 AM] (99752) Auto-excluding **/.*
[Info  - 11:37:16 AM] (99752) Searching for source files
[Info  - 11:37:16 AM] (99752) Found 79 source files

Have you opened the files that are showing the error? If the file is opened, then you will see these errors. Is they are not opened, then you should not see the errors.

Please reopen this issue if you are still seeing the error when the file is not opened.

Yes, this is regardless of whether the files are opened or not. I understand that any errors in opened files will always be shown.

Do I have permission to reopen this issue? I'm not seeing the option...

the log you shared, did you set the python.analysis.logLevel to Trace ? It doesn't show what files are actually analyzed or not.

I didn't, but I've added that setting now, so here are the full logs:

@jackwhelpton I can't repro and I don't see any scipy in bundled stub being analyzed from your log. I do see you have your own scipy stubs in your typing folder and those files are being analyzed. I also see your stub in typing folder picks up our scipy stub in the bundled folder, is that intentional? actual issue might be due to your stubs got mixed up with our stubs.

can you share your scipy stubs so we can try repro the issue locally?

thank you.

Is there a good way to share multiple files? My own stub dragging in yours is not intentional, and I think you're right that that could be the root of the problem, but I need to understand how/why that's happening. I'm only providing a stub for cdist; I also have a stub for numpy's NDArray which allows me to specify the shape of arrays.

from typing import TypeVar, Union

import numpy as np
from numpy.typing import NDArray
from typing_extensions import TypeVarTuple, Unpack

_ShapeType = TypeVarTuple("_ShapeType")
_ScalarType = TypeVar("_ScalarType", bound=Union[int, float])

def cdist(
    XA: NDArray[int, Unpack[_ShapeType], _ScalarType],
    XB: NDArray[int, Unpack[_ShapeType], _ScalarType],
) -> NDArray[int, int, float]: ...

Looking at this afresh as I post it I realize that import numpy as np is redundant, but removing that line doesn't change the results of the analysis. The directory structure, if that's useful, is:

- typings
  - scipy
    - spatial
      * __init__.py
      * distance.py
    * __init__.py

so, what is happening is the scipy stub we have in the bundled is a partial stub (https://peps.python.org/pep-0561/#partial-stub-packages). what it means is it pretends it exists where scipy package actually exists. so in your case, it pretends it exists under typings/scipy and since files under typings are considered as user files, those bundled files are also considered as user files and that's why it shows the errors.

a workaround you can do is putting this in your settings.

"python.analysis.exclude": ["**/node_modules", "**/__pycache__", "**/.*", "typings"]

this will tell pylance to consider files under typings as non user files and we will no longer show the errors.

another workaround is putting empty py.typed file at the root of your scipy folder in typings so we don't overlay our bundled partial stubs on yours since you claim yours are fully typed. but since yours are not actually fully completed, probably not a good workaround.

another workaround will be changing your stub to a partial stub. change the folder name to scipy-stubs and put py.typed with partial\n in it, so we pick it up as partial stub and overlay it over real scipy package.