The mixed-dimensional branch of Fenics is good option.
The mixed-dimensional branch has a demo of doing a 1D-3D problem here, but note that the it does not feature coupling.
You can find an example of a coupled 2D-2D problem that I had and solved here. There’s another issue that I ran into when coupling the problems over different domains. It, and the solution to it, are outlined here.
I have also looked into the multiphenics library, but I can’t speak for how well it works as I haven’t tried to work with it much.