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You can test if $G_1\cong G_2$ using the following function f.
sage: f = lambda g,h: g.is_isomorphic(h)
sage: G = graphs.CubeGraph(3)
sage: H = graphs.HexahedralGraph()
sage: f(G,H)
True
If you really want to use the canonical label then, given a Graph g, you can obtain it by using g.canonical_label() and then just compare the adjacency matrices.
