fix python linting using venv

[mira-miracoli]

Should fix this:

Run pip install --upgrade pip
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
    python3-xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a non-Debian-packaged Python package,
    create a virtual environment using python3 -m venv path/to/venv.
    Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
    sure you have python3-full installed.
    
    If you wish to install a non-Debian packaged Python application,
    it may be easiest to use pipx install xyz, which will manage a
    virtual environment for you. Make sure you have pipx installed.
    
    See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
Error: Process completed with exit code 1.

[bgruening]

Is this the correct way of doing it, or should we use something like this action for it?

https://github.com/galaxyproject/iwc/blob/main/.github/workflows/setup.yml#L63C1-L65C53

@arash77 you know these things correct?

[arash77]

Both ways will work to set up a virtual environment, but you're right that using actions/setup-python is better. It handles the setup automatically and makes sure everything is ready without needing to manually activate the virtual environment.

[mira-miracoli]

Suggested change

	- name: Setup Python
	uses: actions/setup-python@v5
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	cache: 'pip'
	cache-dependency-path: '.github/requirements-python-lint.txt'

[arash77]

For chacing pip, it would be better to use requirements.txt instead of direct pip install.

[mira-miracoli]

Is that stored in the repo's root or under .github? (sorry I tried to google this but did not find anything)

[arash77]

It could be anywhere but the address is based on the repo's root. For example, it may be saved in the .github folder, and used like this:
pip install -r .github/requirements.txt

[mira-miracoli]

I think this should do it now. Thanks for showing me :)

[mira-miracoli]

In general, we could also use the super-linter which I did for WALLE, but I did not want to change too much in the beginning and just fix the action.