Ok, starting from the menu likely does not set your environment variables correctly because it runs Geany without a shell so ~/.bashrc and ~/.profile and so on are not run. Therefore Python3 is run ...

Just installed lubuntu (Ubuntu 24.10) running LXQt V2.0.0 QT V6.6.2 on an old laptop to give to a kid so he can learn Python. Then installed Geany Pryce, (built on or after 2024-03-31) Using GTK+ ...

The Contenders I’ve tried perhaps a half-dozen different Python IDEs now, spending the most time on two of them: Geany and Atom.

The team behind popular lightweight open-source IDE Geany has announced its latest release with numerous enhancements for developers.

I've used Geany quite a bit in the past, especially when I was learning Python with a very low-RAM laptop that ran Linux Mint.