Wrong python binary is used

[NeroVanbiervliet]

Environment data

• VS Code version: 1.28.2 (snap)
• Extension version (available under the Extensions sidebar): 2018.9.2
• OS and version: Ubuntu 18.10
• Python version (& distribution if applicable, e.g. Anaconda): 3.6.7
• Type of virtual environment used (N/A | venv | virtualenv | conda | ...): N/A
• Relevant/affected Python packages and their versions: None

Actual behavior

Python files are execute with the wrong python3 binary. Therefore, installed packages with pip cannot be found.

Python interpreter has been set to /usr/bin/python3, but it does not seem to use that binary. The versions are different as can be seen in this screenshot:

Expected behavior

Python versions in vscode terminal and system shell should be the same.

Steps to reproduce

No idea if this can be reproduced on other machines.

Logs

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

##########Linting Output - pylint##########
************* Module update_ci
1,0,error,E0401:Unable to import 'gitlab'

------------------------------------------------------------------
Your code has been rated at 7.73/10 (previous run: 7.73/10, +0.00)

Output from Console under the Developer Tools panel (toggle Developer Tools on under Help)

bootstrap-window.js:195 [uncaught exception]: TypeError: Cannot read property 'isWrapped' of undefined
onUnexpectedError @ bootstrap-window.js:195
bootstrap-window.js:198 TypeError: Cannot read property 'isWrapped' of undefined
    at Buffer.getWrappedRangeForLine (Buffer.ts:302)
    at BufferStringIterator.next (Buffer.ts:421)
    at Linkifier._linkifyRows (Linkifier.ts:101)
    at Linkifier.ts:76
onUnexpectedError @ bootstrap-window.js:198
Buffer.ts:302 Uncaught TypeError: Cannot read property 'isWrapped' of undefined
    at Buffer.getWrappedRangeForLine (Buffer.ts:302)
    at BufferStringIterator.next (Buffer.ts:421)
    at Linkifier._linkifyRows (Linkifier.ts:101)
    at Linkifier.ts:76

[brettcannon]

What you're after is #1765 . Basically this is because we don't control your PATH when you select a global Python interpreter to prevent knock-on effects like other tools suddenly being shadowed beyond just python3 (unlike when you use a virtual or conda environment where we can activate that and get you the semantics you're after).

[NeroVanbiervliet]

I don't understand why the issue is related to PATH. In the above screenshot, I reference the python interpreters with their full path: /usr/bin/python3. They should point to the same interpreter, but don't (according to version numbers)?

[brettcannon]

That I don't know as we don't have anything to do with the terminal and its PATH resolution. But do notice your terminal is sh and not e.g. bash in VS Code.

[NeroVanbiervliet]

Good point. I verified and the same issue arises with sh:

I understand that the terminal is not of your concern, but the same issue applies for linting and executing python files. They all run with the wrong python interpreter. This is my main problem, because packages that I installed on python 3.6.7 are not detected in VS code.

[brettcannon]

Unfortunately we can't avoid it because something has to execute the commands on our behalf. Your best option is to either figure out why your system is doing this, try updating VS Code (1.29 came out the other day), or specify the full paths to things like your linters.

[brettcannon]

E.g. you should be specifying the full path to the interpreter you want in your "python.pythonPath" setting and thus be avoiding this when using the extension.

[NeroVanbiervliet]

I found the real problem: it is related to the flatpak packaging. It is explained in this issue in the flathub repo.