_pglasso.get_pathway_graph() error

[mspivakov]

Hello! I've installed pglasso with python 2.7 and networkx 2.2, and I'm getting the following error when trying to execute your example script:

T = pglasso.pglasso(AML1_S, pathways, 0.15)

TypeError Traceback (most recent call last)
in ()
----> 1 T = pglasso.pglasso(AML1_S, pathways, 0.15)

_pglasso.pyx in _pglasso.cpglasso_DC()

_pglasso.pyx in _pglasso.get_pathway_graph()

TypeError: add_edge() takes exactly 3 arguments (4 given)

Would really appreciate your help as pglasso seems like a really useful approach for our work. Many thanks!

[mspivakov]

The problem is in the syntax of add_edge, which I suppose has changed:

It should be:

pathway_graph.add_edge(name1, name2, weight=-t)

Rather than:

pathway_graph.add_edge(name1, name2, {"weight": -t})

[mspivakov]

I've patched the package source code accordingly and it works now. Perhaps you may want to update it?