… partition object

… partition object

… partition object

modified MutableVertexPartition to make methods virtual

…phHelper class

…nctions.

Both these vectors represent properties of the underlying graph (not the
partition) as should be instantiated as such.

… for directed vs not

Reverted changes to MutableVertexPartition.h, removed raising of Python
exceptions in C++ helper functions, and corrected some references to
nonexistent variables.

init_admin(), move_node(), diff_move(), and quality() have not been
changed and remain broken.

# Conflicts:
#	src/VertexPartition.py
#	src/python_partition_interface.cpp

inserted divide by m in modularity calculation

…o handle caching of neighbors and edge weights by layer for each vertex

fixed a few cases to make operations vector based .

fixed a few cases to make operations vector based .

The layer membership vector and per-layer edge weights are now
initialized in GraphHelper's Graph.

Before, the indices of degree_by_layers were accidentally reversed.

made _empty_communties vector protected so that it could be modified by the
inherited class.

made _empty_communties vector protected so that it could be modified by the
inherited class.

…s undirected

fixed aggregating total_community_weight to and from where all weight had been being added to the from community

# Conflicts:
#	src/RBConfigurationVertexPartitionWeightedLayers.cpp
#	tests/test_RBCVPweightedlayers.py

Before, much of the multi-layer data would not be initialized if all
nodes were assigned to the same layer (i.e. layer count of 1).

…eLayers

removed print lines
updated diff quality to account for 2* node_size.

…incorporate edge layer weights into the conglomerated graph

made layer_vec argument unnecessary for construction (default is to treat everything as sinlge layer)
modified function getting graph edges, weights, and nodes from the c++ side to create agglomerated version that returns edge weights by layers

…currently no need to do this)

fixed python facing method to get layer_weights

…r the layer valued versions

RBConfigurationVertexPartitionWeightedLayers optimization is roughly
100% faster now (i.e. it will take about half the time it used to).

Also removed an extraneous function in GraphHelper and changed the use
of IGRAPH_OUT to IGRAPH_IN in weight_from_comm.

The following files were not significantly changed and have been
reverted to their state in vtraag/louvain-igraph's master branch:
 - ModularityVertexPartition.h
 - Optimiser.h
 - MutableVertexPartition.cpp
 - python_optimiser_interface.cpp
 - RBConfigurationVertexPartition.cpp

…t PyLong_Check from failing

handle list values using PyNumber_AsSsize_t instead of PyLong_AsLong
raises python index error if unable to convert them.

…ayers

changed PyLong Check to PyNumber Check for same compatibility

Merge https://github.com/vtraag/louvain-igraph