Oh shoot that's a really silly implementation of intersection. One
should of course just do

def intersect_submodules(M,S1,S2):
    F1=span([b.lift() for b in S1.gens()])
    F2=span([b.lift() for b in S2.gens()])
    M.submodule([M(b) for b in F1.intersection(F2).gens()])

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