The function graph_tool.spectral.adjacency returns transpose of the adjacency matrix of a directed graph that is commonly used. Is this intentional? A misinterpretation of column-major versus row-major on my part?

Compare a few standard examples:

with the output of gt.adjacency():

import graph_tool.all as gt

g = gt.Graph()
v0 = g.add_vertex()
v1 = g.add_vertex()
e01 = g.add_edge(v0,v1)
A = gt.adjacency(g)
A.todense()
[e for e in g.edges()]
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Out[2]: [<Edge object with source '0' and target '1' at 0x11fb10d60>]

A.todense()
Out[3]: 
matrix([[ 0.,  0.],
        [ 1.,  0.]])

A in this case is most commonly defined as [[0, 1], [0, 0]]