Re: [graph-tool] graph_tool.spectral.adjacency() returns the transpose of the adjacency of a directed graph

It is true that most software and some websites use the more intuitive definition that you were expecting. However a large part of the theoretical literature uses the transposed definition, since it can be more convenient mathematically. See for instance Mark Newman's book. I know — I use Godsil and Royle, who use the “correct” untransposed version in Algebraic Graph Theory ;o) Because you cite the Wikipedia definition in your excellent documentation, I’d suggest documenting the convention you use explicitly, which is the transpose of Wiki’s (current) definition.