configurations ignored / 2 instaces of pycodestyle running

[madonuko]

Having the following configurations:

And I am getting these warnings:

If I uncheck convert errors to warnings, I see both errors and warnings. Some of them are duplicated.

I often see this warning:

I tried uninstalling pycodestyle from atom and it's still running. Surely there is an unintended instance running.
I installed pycodestyle from both pip and apm already.

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System Information

• OS: Manjaro GNU/Linux
• Desktop Environment: KDE

Atom (--version)

- Atom    : 1.47.0
- Electron: 5.0.13
- Chrome  : 73.0.3683.121
- Node    : 12.0.0

pycodestyle from pip

• version: 2.6.0

linter-pycodestyle from atom

• version: 2.1.3