The warning comes from ctags:

https://github.com/geany/geany/blob/master/ctags/main/entry.c#L390

But it really is just a warning and I'd say it's useful to know if something is wrong. And @b4n wrote a new token-based Python parser which is already merged in uctags and and which might have fixed this already. We should backport it to Geany after #1160.

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