Renamed functions in pythonic style and expanded confusing abbreviations.
Substitue networkx for igraph in main tree construction method. Saved the igraph version igraph_tree.py. Still need to clean up the latter and test each for accuracy.
Clean up the igraph tree module. Still contains both adjacency list and matrix version; the matrix version can probably be deleted when I'm sure the new versions are working properly.
Remove duplicate setup lines from igraph tree.