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This implements a GraphView class which allows for convenient,
independent filtering graphs.

This is a large commit which replaces lambda::bind with boost::bind in
most parts of the code. This improves compilation time, and slightly
decreases compilation memory usage in some cases.

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)

This includes a new vector property map type (fast_vector_property_map)
which has optional disabling of bounds checking, through its associate
map type (unchecked_fast_vector_property_map). This should improve
performance on algorithms which depend on tight loops which access
property maps.

Bounds checking is only disabled locally just before the algorithms run,
and proper care is taken for bounds checking _beforehand_. The property
maps exposed to python still have internal bounds checking.

This commit removes the internal property maps from the GraphInterface
class, and makes all property maps external by default. The internal
property maps were moved to the python layer.

The whole histogram code has been redone, and the code has been
simplified. The three-point vertex-edge-vertex correlation has been
scrapped, since it's not frequently used, and would make compilation
even more expensive.

This also adds some missing files to the generation routine.

This commit splits libraph_tool into different libraries:
 
   - libgraph_tool_core
   - libgraph_tool_clustering (*)
   - libgraph_tool_community (*)
   - libgraph_tool_correlations (*)
   - libgraph_tool_distance (*)
   - libgraph_tool_generation (*)
   - libgraph_tool_layout (*)
   - libgraph_tool_misc (*)
   - libgraph_tool_stats (*)

It also adds the python sub-module 'test', which provides extensive unit
testing of the core functionality. The core library is fully functional
and all test pass successfully.

(*) -> module needs to be ported to new refactoring, and does not yet build

This is a huge commit which completely refactors the metaprogramming
engine which generates and selects (at run time) the graph view type and
the desired algorithm implementation (template instantiation) that runs
on it.

Things are laid out now as following. There exists a main underlying
graph type (GraphInterface::multigraph_t) and several other template
classes that mask it some way or another, in a hierarchic fashion:

     multigraph_t -> filtered_graph (edges only, vertices only, both)
         |                               |           |           |
         |                               |           |           |
         |-------(reversed_graph)--------|-----------|-----------|
         |                               |           |           |
         \------(UndirectedAdaptor)------------------------------/

The filtered_graph filters out edges and/or vertices from the graph
based on some scalar boolean property. The reversed_graph reversed the
direction of the edges and, finally, the UndirectedAdaptor treats the
original directed graphs as undirected, transversing the in- and
out-edges of each vertex indifferently. Thus, the total number of graph
view types is 12. (The option --disable-graph-filtering can be passed to
the configure script, which will disable graph filtering altogether and
bring the total number down to 3, to reduce compile time and memory
usage)

In general, some specific algorithm, implemented as a template function
object, needs to be instantiated for each of those types. Furthermore,
the algorithm may also depend on other types, such as specific
property_maps. Thus, the following scheme is used:

    struct my_algorithm // algorithm to be implemented
    {
        template <class Graph, class PropertyMap>
        void operator()(Graph *g, PropertyMap p, double& result) const
        {
            // ...
        }
    };

    // in order for the above code to be instantiated at compile time
    // and selected at run time, the run_action template function object
    // is used from a member function of the GraphInterface class:

    double GraphInterface::MyAlgorithm(string prop_name)
    {
        double result;
        boost::any vprop = prop(property, _vertex_index, _properties);
        run_action<>()(*this, bind<void>(my_algorithm(), _1, _2,
                                         var(result)),
                       vertex_scalar_properties())(vprop);
        return result;
    }

The whole code was changed to reflect this scheme, but now things are
more centralized and less ad-hoc code needed to be
written. Unfortunately, due to GCC's high memory usage during template
instantiations, some of the code (namely all the degree correlation
things) had to be split in multiple compilation units... Maybe this will
change in the future if GCC gets optimized.

This commit also touches other parts of code. More specifically, the way
filtering gets done is very different. Now we only filter on boolean
properties, and with the above scheme, the desired implementation runs
with the correct chosen type, and no implicit type conversions should
ever happen, which would have a bad impact on performance.

Property maps can now be obtained as such:

         weight = g.edge_properties['weight']
         print weight[v] # v is a Vertex object
         weight[v] = 2.0
         # and so on...

The list of properties is obtained from g.vertex_properties,
g.edge_properties and g.graph_properties, which can be read as
dictionaries. The last can be set also, as such:

         g.graph_properties = {foo:"bar", baz:42}

Functions to add and remove vertices or adges were also added
(add_{vertex|edge}, remove_{vertex|edgge}).

Vertex and Edge types can also now be printed for convenience, as such:

       for v in g.vertices():
           print v
       for e in g.edges():
           print e

which results, for example, in:
0
1
2
3
4
5
6
(0,1)
(1,2)
(2,6)
(3,4)
(4,5)
(4,2)
(5,6)
(6,1)

(this also adds the forgotten graph_tool.py file, which was previously
on .gitignore)

Line breaks at column 80 were added, and all trailing whitespace was deleted. Code
comments were modified and some more were added.

It should be 'size_t' instead of 'long'.

This fixes the same problem as commit 6663be71, but which arises
when a filter range boundary is -inf (such as "<=100").

    
When only one of vertex or edge filtering was disabled, the allowed
range of the disabled filter was set to
]numeric_limits<double>::min(), numeric_limits<double>::max()[, and
the selected filtering property was the respective index. But
according to the STL documentation from GCC,
numeric_limits<>::min() returns:
    
   "The minimum finite value, or for floating types with
    denormalization, the minimum positive normalized value."
    
which is always positive for double (!), thus introducing a weird
regression, where the first vertex (index 0) is always filtered out if
only the edge filter is active, and vice-versa.

    
Filtered vertices and edges can be permanently removed from the graph
with --purge-vertices and --purge-edges, respectively. The edge or
vertex filter is automatically removed, afterwards. This is useful if
maximum speed is necessary, and saving and reloading the graph without
filtering is not desired.
    
(this commit also removes some trailing whitespaces)

Complete overhaul of command line parsing, and support for loading graph-tool as whole as a python module
    
The command line parsing was completely rewritten. It now supports
better parsing of sub-options, with type checking and grouping
support. Error reporting was also significantly improved, and it now
warns of invalid options and option values, before the option is
executed. Some syntax has changed, such as range filtering:
--[vertex|edge]-range-filter was replaced by
--exclude-[vertex|edge]-range and --keep-[vertex|edge]-range, which
should have a clearer meaning. Ranges can also be specified now by
comparison operators (>,<,>=,<=,=), such as ">=10", to indicate a
range of (10, inf). In addition, ranges can now be easily open or
closed at either end, by suffixing the specific end with '*', to
indicate it is closed, ex: "10 700*" means (10,700].
    
The graph-tool script can now be loaded as a python module (it must be
renamed first to 'something.py'). All the command line options (except
'for' and 'history' which become irrelevant) are available as
functions, with full description and optional parameter support. In
addition, pure function objects can be given as parameters where
expressions are asked, instead of strings and files, which enables
convenient extension of graph-tool.

Simplify range filtering, and definitely remove python filtering
    
Simplify range filtering of vertices and edges, by always filtering
both at once, even if all vertices or edges are being considered. This
severely reduces compilation time and memory, at a small potential
cost in run-time speed, which will probably be overshadowed by other
things, such as dynamic_map look-ups ("premature optimization is the
root of all evil"). Also, remove python-filtering, since, in the end,
it is just code bloat, since it is quite slow for most uses and can be
replaced, generally, by python property editing + range filtering.

	* src/boost-workaround/boost/graph/kamada_kawai_spring_layout.hpp: annotated code with openmp constructs.

	* src/graph/graph_adaptor.hh: graph_type should be a typedef to the original graph.

	* src/graph/graph_properties.hh, src/graph/graph_properties.cc: added pos_t type.

	* src/boost-workaround/boost/graph/fruchterman_reingold.hpp: annotated code with openmp constructs.

	* src/graph/graph_layout.cc: new file with graph layout routines.

	* src/graph/graph.cc: removed graph layout routines.

	* src/graph/graph_community_network.cc (struct get_community_network): fixed inversion of directedness test.

	* src/graph/graph.cc (GraphInterface::LabelComponents): use vector_property_map instead of HashedDescriptor. Don't use a static map!

	* src/graph/graph_adaptor.hh: fixed edge descriptor equality comparison, which must rely on underlying edge, regardless of whether it's inverted or not.


git-svn-id: https://svn.forked.de/graph-tool/trunk@121 d4600afd-f417-0410-95de-beed9576f240

* src/graph/graph.cc (GraphInterface::LabelParallelEdges): use long instead of size_t for parallel edges property.

* src/graph/graph_properties.cc: call size_t by "size_t" not "long", since those are not the same type. This removes a bug where it is impossible to create/edit properties with type long.

* src/graph/graph.cc (GraphInterface::LabelParallelEdges): use vector_property_map instead of HashedDescriptorMap.


git-svn-id: https://svn.forked.de/graph-tool/trunk@120 d4600afd-f417-0410-95de-beed9576f240

        * src/graph/graph.cc (GraphInterface::LabelParallelEdges): use vector_property_map instead of HashedDescriptorMap.


git-svn-id: https://svn.forked.de/graph-tool/trunk@119 d4600afd-f417-0410-95de-beed9576f240

* removed exeption throwing in scalarS to improve performance


git-svn-id: https://svn.forked.de/graph-tool/trunk@113 d4600afd-f417-0410-95de-beed9576f240

git-svn-id: https://svn.forked.de/graph-tool/trunk@101 d4600afd-f417-0410-95de-beed9576f240

* further code parellelization with openmp (vertex and edge histograms, correlations, and reciprocity)



git-svn-id: https://svn.forked.de/graph-tool/trunk@99 d4600afd-f417-0410-95de-beed9576f240

* src/graph-tool allow for parameter setting before loading property editing script


git-svn-id: https://svn.forked.de/graph-tool/trunk@74 d4600afd-f417-0410-95de-beed9576f240

* accept external files for property editing routines
* include in_PROP() andd out_PROP() functions to be used in python filtering/property editing routines.


git-svn-id: https://svn.forked.de/graph-tool/trunk@71 d4600afd-f417-0410-95de-beed9576f240

included option to disable python and range filtering during compilation, thus reducing compile-time memory requirements


git-svn-id: https://svn.forked.de/graph-tool/trunk@64 d4600afd-f417-0410-95de-beed9576f240

git-svn-id: https://svn.forked.de/graph-tool/trunk@59 d4600afd-f417-0410-95de-beed9576f240

git-svn-id: https://svn.forked.de/graph-tool/trunk@58 d4600afd-f417-0410-95de-beed9576f240

git-svn-id: https://svn.forked.de/graph-tool/trunk@57 d4600afd-f417-0410-95de-beed9576f240

* fixed saving of undirected filtered graphs in graph_io.cc
* fixed correlated community detection in graph_community.cc


git-svn-id: https://svn.forked.de/graph-tool/trunk@53 d4600afd-f417-0410-95de-beed9576f240

* fix command line help


git-svn-id: https://svn.forked.de/graph-tool/trunk@49 d4600afd-f417-0410-95de-beed9576f240

* Range filters now support all kinds of scalar properties without falling back to python code


git-svn-id: https://svn.forked.de/graph-tool/trunk@46 d4600afd-f417-0410-95de-beed9576f240