> With that in mind, it seems that DiGraph is fine as those points are
> differing in both hash and ==, correct?

DiGraphs consider that two points u,v with u==v are the same points.
If those (equal) points have different hash values, I have no idea of
what happens (including memory leaks, segfaults, nothing, ...). And it
happens in your code:

sage: d=DiGraph(D)
sage: [d.vertices().count(x) for x in d]
[1, 2, 2, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1]
sage: len({hash(x) for x in d})
18

Nathann

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