Fix docstring for compute_module_merge

Was missing all information about return values.
Change empty_module to being EmptyModuleError, a real exception.
BF: remove [] from call to cost2thresh in format_matrix, as it is not an input to the function
BF: change GraphPartition to use set(range(number_of_nodes)) as _node_set, not nodes defined in graph to avoid index error when using this to index adjacency_matrix
NF: add test that GraphPartition handles graph with nodes that are not contiguous integers 0->nnodes, cleanup
NF: GraphPartiton new method index_as_node_names to retrieve index(partition) as node names and not as ints
RF: node/index checking now uses set functions, cleanup error string
Merge pull request #8 from cindeem/graphpart_fixnodes

RF: Fix GraphPartition Class

Change GraphPartition from using node_names to using integers representing nodes since it is used in indexing into adjacency_matrix