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  1. 02 Aug, 2009 1 commit
  3. 01 Mar, 2009 1 commit
  5. 21 Feb, 2009 1 commit
  7. 14 Feb, 2009 1 commit
    • Tiago Peixoto's avatar
      Add centrality module · 96b9c5e7
      Tiago Peixoto authored 
      This adds the centrality module, which supports betweenness, eigentrust,
pagerank and absolute trust.
      96b9c5e7
  9. 06 Feb, 2009 2 commits
  11. 07 Dec, 2008 1 commit
  13. 01 Dec, 2008 1 commit
  15. 26 Oct, 2008 1 commit
  17. 23 Oct, 2008 1 commit
  19. 13 Oct, 2008 2 commits
  21. 15 Jul, 2008 2 commits
  23. 15 Apr, 2008 1 commit
  25. 14 Apr, 2008 1 commit
  27. 10 Apr, 2008 1 commit
    • Tiago Peixoto's avatar
      Correlations algorithms refactoring · 360a3395
      Tiago Peixoto authored 
      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.
      360a3395
  29. 17 Feb, 2008 1 commit
    • Tiago Peixoto's avatar
      Split libgraph_tool into sub-modules and add test cases · 3cfff0cb
      Tiago Peixoto authored 
      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
      3cfff0cb
  31. 10 Feb, 2008 1 commit
    • Tiago Peixoto's avatar
      Refactor metaprogramming engine · 0b66e272
      Tiago Peixoto authored 
      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.
      0b66e272
  33. 24 Jan, 2008 1 commit
    • Tiago Peixoto's avatar
      Fix problem with linkers that don't support the '-E' flag · 20574c73
      Tiago Peixoto authored 
      The '-E' flag is necessary with GNU ld so that all dynamic symbols are
properly exported, and things like typeid() work across DSO
boundaries. However there are other linkers out there which don't accept
this option. This commit checks for this and drops the option in that
case. Let us hope those linkers do the right thing, or wait until
someone complains...
      20574c73
  35. 21 Dec, 2007 1 commit
    • Tiago Peixoto's avatar
      Directory restructuring of graph_tool Python module (now a package) · 4a7da8a9
      Tiago Peixoto authored 
      Everything was moved into the graph_tool directory, which should have,
after installation, the following structure:

graph_tool/                          Top-level package
      __init__.py                    Initialize the graph_tool package
      libgraph_tool.so               libgraph_tool submodule
      libgraph_tool.la               libtool file for libgraph_tool
      include/                       C++ include files for dynamically
                                     compiled code
      4a7da8a9
  37. 07 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      Complete overhaul of command line parsing, and support for loading graph-tool... · cb61cc74
      Tiago Peixoto authored 
      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.
      cb61cc74
  39. 04 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      · 8e962092
      Tiago Peixoto authored 
      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.
      8e962092
  41. 12 Sep, 2007 1 commit
  43. 31 Jul, 2007 1 commit
  45. 05 Jul, 2007 2 commits
  47. 02 Jul, 2007 2 commits
  49. 15 Jun, 2007 1 commit
  51. 18 May, 2007 1 commit
  53. 17 May, 2007 1 commit
  55. 16 May, 2007 2 commits
  57. 06 May, 2007 1 commit
  59. 05 May, 2007 3 commits
  61. 29 Jan, 2007 1 commit
  63. 27 Jan, 2007 1 commit