GitLab

This implements a general "blockmodel" generation / rewiring algorithm,
using Gibbs acceptence / rejection sampling (a.k.a Metropolis-Hastings).

This also implements some optimizations in the rewiring code, which
makes it more efficient on filtered graphs.

This introduces several simplifications and corrections to the graph
rewire algorithm, to guarantee unbiased sampling.

Now a move is outright rejected if it produces a
self-loop/parallel-edge, instead of retried. This also adds a
"non-sweep" mode, where edges are rewired randomly, possibly with
repetition.

The edge moves are now simplified to the target of the edges only,
since swaping sources is redundant.

The number of iterations can now be explicitly modified, so it is not
necessary to call the function more than once, and it is emphasized in
the documentation that only after sufficiently many iterations can the
graph be guaranteed to be fully mixed.

This enables support for older versions of GCC (>=4.2), by falling back
to the boost tr1 implementation when the GCC version is less than 4.4.

Vectors are used now instead of unordered_sets, which dramatically
improves performace.

Now the degree sequence is verified with Erdös-Gallai inequalities, and
the edges are connected in a deterministic fashion. The edges then are
rewired with the random_rewire() function.

Target degrees were not being sampled correctly from their probability.

random_graph() now uses a modified algorithm for generation of
correlated graphs, which is more efficient. Instead of giving a function
which returns a sample of the correlated target degree, the user must
give a function which will just compute its probability. This
probability will then be used to choose the edges.

The generators from boost::random seem to have a bug which causes them
to be biased. The generators from tr1::random seem to be in better
shape.

See: http://thread.gmane.org/gmane.comp.lib.boost.user/48006

Thins changes the graph filtering code slightly to wrap graph types with
GraphWrap, which automatically updates the edge index list when edges
are removed and added to the graph.

This also changes how graphs are passed to algorithms, which is now by
reference instead of pointer. (hence this touches lots of code, but
changes are trivial)

Fix possible deadlock condition in random graph generation with
no_parallel and/or no_self_loops.

It is now much simpler, and works better.