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springer-math / Mathematics-of-Epidemics-on-Networks

Source code accompanying 'Mathematics of Epidemics on Networks' by Kiss, Miller, and Simon http://www.springer.com/us/book/9783319508047 . Documentation for the software package is at https://epidemicsonnetworks.readthedocs.io/en/latest/
MIT License
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EoN.Gillespie_Arbitrary is not implemented for python 3.6. It runs ok in python2 and python3.5. Its because nx.Digraph returns list in edges() function in python3.6. #25

Closed Kamol-Roy closed 5 years ago

joelmiller commented 5 years ago

Hi,

I see this issue was closed.

Did you mean to close it, or was that an accident? I guess I really want to know - is the algorithm working for you in 3.6 or not? I run 3.5 on my machine with networkx 2.1, so I can't easily test it.

Kamol-Roy commented 5 years ago

That was the issue in python 3.6.0

File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 866, in runfile execfile(filename, namespace)

File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)

File "C:/Users/ka464156/OneDrive - Knights - University of Central Florida/Proposal_defense/Adhoc_network/Analysis/Cooperate.py", line 54, in t, SS, SI, SR, IS, II, IR, RS, RI, RR = EoN.Gillespie_Arbitrary(G, H, J, IC, return_statuses, tmax = float('Inf'))

File "C:\ProgramData\Anaconda3\lib\site-packages\EoN\simulation.py", line 3391, in Gillespie_Arbitrary rate[transition] = spontaneous_transition_graph.edges[transition[0],transition[1]]['rate']

TypeError: 'method' object is not subscriptable

I fixed this by replacing all the relevant lines by this. rate[transition] = spontaneous_transition_graph.edge[transition[0]][transition[1]]['rate']

However, it is running fine in python3.6.7

joelmiller commented 5 years ago

Is it possible that when you switched ran with python version 3.6 you have a networkx version 1.x, but you had a more recent networkx version 2.x with the other python versions? (if you import networkx as nx, you can check the version using nx.version).

I think the error is most likely to be from a change that happened in networkx rather than a change in python version. I think the command giving the error you see won't work in networkx 1.11 or earlier, but does work in 2.0 and later. I had meant to make the code back-compatible, but it looks like I didn't.

I'll see what I can do about making it back-compatible with older networkx versions.

Kamol-Roy commented 5 years ago

Yes, you are right. It's because of networkx version. My python3.6.0 has networkx version 1.11 and python3.6.7 has version 2.2.

joelmiller commented 5 years ago

I think the code I've just uploaded on github (version 1.04rc3) is now compatible with both versions of networkx.

If you could check if it runs for the case that you had an error on , I'd appreciate it (either download the whole thing, or just copy Gillespie_Arbitrary from the github version).