Support for directed, weighted graphs and code cleanup

[steenfatt]

I have [see corresponding paper] ...

• added support for directed, weighted graphs
• added support for partially embedding the graph
• cleaned up the code, in particular removed unused parts of the code
• added some missing doc strings

The changes are completely backwards compatible, i.e., any commands that you have been running previously should still work the exact same.

[joewilaj]

What adjustments are necessary to run on python3?

[MikeB2019x]

@joewilaj I got this to run in Python3. Here are the necessary changes:

• replace occurrences of 'xrange' with 'range'
• replace occurrences of 'iter.keys' with 'keys'
• where you see the use of 'G.keys()' put something to convert the output type ('dict_keys') to 'list' where required. G.keys() is usually used to populate the variable 'vertices' which is supposed to be passed to other functions as a 'list' so you have to convert or you'll end up with a "cannot save 'dict_keys' " keys error somewhere
• replace occurrences of 'cPickle' with 'pickle'
• replace occurrences of 'iteritems' with 'items'
• replace the variable names in the Word2Vec call: 'iter' -> 'epochs' and 'size' -> 'vector_size'

That should pretty much do it. As a test run Karate Kid network. BTW it doesn't look like this repo is maintained so that's a shame.