improve from_networkx performance

[szhorvat]

This attempts to address #401. It only fixes from_networkx, not from_graph_tool. I need some feedback before proceeding. I don't really know much Python, and this was merely an exercise for me. Take a very careful look before merging.

[szhorvat]

Benchmark:

import random
random.seed(123)
g = nx.gnm_random_graph(1000,10000)

then in ipython,

%timeit ig.Graph.from_networkx(g)

The speedup is from ~2.0 seconds to ~12 milliseconds.

[szhorvat]

I notice that the name Graph.from_networx seems inconsistent with other graph constructors, all of which are capitalized. Shouldn't this be corrected?

[szhorvat]

Why is the test for this functionality in src/igraph/test while everything else is in tests? Is this test run when doing python -m unittest as in the instructions?

Originally I messed up and forgot to convert vertex names to IDs, yet tests did not seem to fail. Assuming I ran the tests correctly, the tests should be improved to catch this mistake.

[ntamas]

I notice that the name Graph.from_networx seems inconsistent with other graph constructors, all of which are capitalized. Shouldn't this be corrected?

The capitalization is a leftover from the early days of the development of the Python interface where I thought this would be a good idea to distinguish class methods from "normal" methods. Nowadays I don't use this convention in new code and prefer normal underscore_case instead. When we re-design the python-igraph API in the future such that we won't have a monolithic Graph class any more, this inconsistency will probably not be relevant any more. Until then, we can alias from_networkx with From_Networkx if we want to. Opinions?

Why is the test for this functionality in src/igraph/test while everything else is in tests?

Because I probably forgot to move them when I switched from the tests-within-the-package layout to the tests-outside-the-package layout as advocated here :) It should be in tests by all means.

[ntamas]

Thanks a lot!

[szhorvat]

Until then, we can alias from_networkx with From_Networkx if we want to. Opinions?

No preference from me, just want to note that if this is done, it should be From_NetworkX and not From_Networkx.

[iosonofabio]

Thank you. Let's not rename and break API and also go against Python conventions.