That didnt answer the main question - did you use sudo with one of those python package managers at some point?
Well that, and, the general question around this:
Your virtual environments are where you should do your development things…
We are technically not interested in how gnome-tweaks functions there … we care more about regular use - ‘outside of’ those environments.
(However you abuse your virtual environment is up to you. If you break it make a new one.)
Did I modify my Python with pip outside a virtual environment? Maybe.
Trying now to modify, I get the neat error message:
alba@mac2011-manjaro% pip install gi
× This environment is externally managed
╰─> To install Python packages system-wide, try 'pacman -S
python-xyz', where xyz is the package you are trying to
So I doubt I modified, unless the security net was installed very recently.
I try this
alba@mac2011-manjaro% sudo pacman -S python-gobject
warning: python-gobject-3.46.0-1 is up to date -- reinstalling
I don’t see how I could break the Python used by Gnome.
miniconda3 disturbs Python path, in Terminal and Activities.
This can be avoided in Terminal with conda deactivate and in Activities by uninstalling miniconda3 or less radically by copying /usr/share/applications/org.gnome.tweaks.desktop to ~/.local/share/applications/mytweaks.desktop and replacing in the new file Exec=gnome-tweaks by Exec=/usr/bin/python /usr/bin/gnome-tweaks.
In Activities, search Tweaks and click the second icon.