Launching via GitHub Desktop causes tests to fail

[pstjohn]

Related to #18431

I was able to track down steps to reproduce my issue. On a Mac, using GitHub Desktop Version 3.0.0 with vscode as my default editor. Using a basic repo here, which just uses a conda environment to run a some pytest tests: https://github.com/pstjohn/vscode-pytest-demo

If I open the repo using the github desktop "open in external editor" command, pytests fail with the following error, indicating that the editor is picking up the system's python 2.7; not my local conda environment.

If I manually open the repository (in this case using code . from the repository's directory in iTerm2), the tests are able to be discovered and run fine.

conda run -n pytest_issue --no-capture-output python ~/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/get_output_via_markers.py ~/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir . -s --cache-clear tests
cwd: .
[ERROR 2022-4-9 14:53:28.667]: Error discovering pytest tests:
 [n [Error]: Traceback (most recent call last):
  File "/Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/get_output_via_markers.py", line 26, in <module>
    runpy.run_path(module, run_name="__main__")
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 252, in run_path
    return _run_module_code(code, init_globals, run_name, path_name)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 82, in _run_module_code
    mod_name, mod_fname, mod_loader, pkg_name)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ImportError: No module named pytest
ERROR conda.cli.main_run:execute(41): `conda run python /Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/get_output_via_markers.py /Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir /Users/pstjohn/Packages/vscode_pytest -s --cache-clear tests` failed. (See above for error)

	at ChildProcess.<anonymous> (/Users/pstjohn/.vscode/extensions/ms-python.python-2022.6.0/out/client/extension.js:2:227541)
	at Object.onceWrapper (node:events:510:26)
	at ChildProcess.emit (node:events:390:28)
	at maybeClose (node:internal/child_process:1064:16)
	at Process.ChildProcess._handle.onexit (node:internal/child_process:301:5)]

Diagnostic data

• Python version (& distribution if applicable, e.g. Anaconda): 3.9.10
• Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): Conda
• Value of the python.languageServer setting: Pylance

User Settings

defaultLS: {"defaultLSType":"Pylance"}

envFile: "<placeholder>"

venvPath: "<placeholder>"

venvFolders: "<placeholder>"

condaPath: "<placeholder>"

pipenvPath: "<placeholder>"

poetryPath: "<placeholder>"

languageServer: "Pylance"

linting
• enabled: true
• cwd: "<placeholder>"
• Flake8Args: "<placeholder>"
• flake8Enabled: true
• flake8Path: "<placeholder>"
• lintOnSave: true
• banditArgs: "<placeholder>"
• banditEnabled: false
• banditPath: "<placeholder>"
• mypyArgs: "<placeholder>"
• mypyEnabled: false
• mypyPath: "<placeholder>"
• pycodestyleArgs: "<placeholder>"
• pycodestyleEnabled: false
• pycodestylePath: "<placeholder>"
• prospectorArgs: "<placeholder>"
• prospectorEnabled: false
• prospectorPath: "<placeholder>"
• pydocstyleArgs: "<placeholder>"
• pydocstyleEnabled: false
• pydocstylePath: "<placeholder>"
• pylamaArgs: "<placeholder>"
• pylamaEnabled: false
• pylamaPath: "<placeholder>"
• pylintArgs: "<placeholder>"
• pylintPath: "<placeholder>"

sortImports
• args: "<placeholder>"
• path: "<placeholder>"

formatting
• autopep8Args: "<placeholder>"
• autopep8Path: "<placeholder>"
• provider: "black"
• blackArgs: "<placeholder>"
• blackPath: "<placeholder>"
• yapfArgs: "<placeholder>"
• yapfPath: "<placeholder>"

testing
• cwd: "<placeholder>"
• debugPort: 3000
• nosetestArgs: "<placeholder>"
• nosetestsEnabled: undefined
• nosetestPath: "<placeholder>"
• promptToConfigure: true
• pytestArgs: "<placeholder>"
• pytestEnabled: true
• pytestPath: "<placeholder>"
• unittestArgs: "<placeholder>"
• unittestEnabled: false
• autoTestDiscoverOnSaveEnabled: false

terminal
• activateEnvironment: true
• executeInFileDir: "<placeholder>"
• launchArgs: "<placeholder>"

experiments
• enabled: true
• optInto: []
• optOutFrom: []

tensorBoard
• logDirectory: "<placeholder>"

[karrtikr]

Can you try to change the setting terminal.integrated.inheritEnv to false as outlined in https://code.visualstudio.com/updates/v1_36#_launch-terminals-with-clean-environments and see if it helps?

[pstjohn]

Looks like that's already unchecked -- here's my settings.json:

{
    "terminal.integrated.fontFamily": "Menlo for Powerline",
    "python.linting.flake8Enabled": true,
    "python.formatting.provider": "black",
    "python.linting.flake8Path": "/Users/pstjohn/mambaforge/bin/flake8",
    "python.formatting.yapfPath": "/Users/pstjohn/mambaforge/bin/yapf",
    "git.autofetch": true,
    "git.ignoreLegacyWarning": true,
    "workbench.colorTheme": "Solarized Dark",
    "editor.fontSize": 13,
    "python.formatting.blackPath": "/Users/pstjohn/mambaforge/bin/black",
    "python.sortImports.args": [
        "--profile=black"
    ],
    "python.sortImports.path": "/Users/pstjohn/mambaforge/bin/isort",
    "[python]": {
        "editor.formatOnSaveMode": "file",
        "editor.codeActionsOnSave": {
            "source.organizeImports": true
        }
    },
    "editor.formatOnSave": true,
    "editor.rulers": [
        88
    ],
    "python.languageServer": "Pylance",
    "python.testing.autoTestDiscoverOnSaveEnabled": false,
    "editor.formatOnSaveMode": "modificationsIfAvailable",
    "python.linting.flake8Args": [
        "--max-line-length=88",
        "--extend-ignore=E203"
    ],
    "terminal.integrated.customGlyphs": false,
    "terminal.integrated.inheritEnv": false,
    "terminal.integrated.env.osx": {
        "PATH": ""
    },
    "python.terminal.activateEnvInCurrentTerminal": true
}

[karrtikr]

I suspect VSCode is launched via an activated conda environment when using Github Desktop, in that case this is a dup of #19070 and is caused due to conda conda/conda#11305, conda/conda#11174.

What happens if you run the following command in VSCode terminal?

python -c"import sys;print(sys.executable)"

conda run -n graphenv --no-capture-output python ~/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/get_output_via_markers.py ~/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/linter.py -p flake8 ~/mambaforge/bin/flake8 --max-line-length=88 --extend-ignore=E203 ./tests/test_tsp.py

Is VIRTUAL_ENV set in the terminal?

[pstjohn]

whoops, I pasted the pytest failure for my larger repo -- I changed it above to reflect the small demo repo I created as a minimal example, and translated your commands here to that repo as well.

Launching via github desktop with the tests failing --

The conda environment seems to be activated correctly:

$ python -c"import sys;print(sys.executable)"
$HOME/mambaforge/envs/pytest_issue/bin/python

The conda run command seems to work as well -- it really seems limited to just pytest.

$ conda run -n pytest_issue --no-capture-output python ~/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/get_output_via_markers.py ~/.vscode/extensions/ms-python.python-2022.6.0/pythonFiles/linter.py -p flake8 ~/mambaforge/bin/flake8 --max-line-length=88 --extend-ignore=E203 ./tests/test_my_module.py 
>>>PYTHON-EXEC-OUTPUT
<<<PYTHON-EXEC-OUTPUT

VIRTUAL_ENV doesn't appear to be set:

$ echo $VIRTUAL_ENV