1. 07 Dec, 2008 1 commit
  2. 02 Dec, 2008 1 commit
  3. 24 Sep, 2008 1 commit
    • Tiago Peixoto's avatar
      Fix edge indexing problem when modifying graph · dc184b46
      Tiago Peixoto authored
      This fixes a rather central bug, which causes duplicated indexes if
      edges are removed and then new ones are added. Edge indexes are now
      recycled as they are removed and then new ones are added. This still
      guarantees O(1) complexity when adding or removing edges.
      dc184b46
  4. 17 Jun, 2008 1 commit
    • Tiago Peixoto's avatar
      Externalize property maps by default · e984bf8e
      Tiago Peixoto authored
      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.
      e984bf8e
  5. 14 Apr, 2008 1 commit
    • Tiago Peixoto's avatar
      Fix run_action · ee25eabe
      Tiago Peixoto authored
      A couple of bugs fixed. Local frame dict is read-only in python, so the
      updated arguments are returned in a dict instead.
      ee25eabe
  6. 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
  7. 27 Mar, 2008 1 commit
    • Tiago Peixoto's avatar
      Port graph I/O to new filtering engine, enable graph pickling, and fix several issues · 99bf21c8
      Tiago Peixoto authored
      Now graphml files properly contain all the supported value types, which
      are all perfectly preserved when read (floating point data is now saved
      in hexadecimal format). Several other improvements were made, such as
      the ability to read and write to python file-like objects.
      
      It is also now possible to have arbitrary python object properties, and
      store them persistently (which is done internally with the pickling
      interface).
      
      vector<bool> was totally abolished, since its implementation is quite
      broken. See: http://www.gotw.ca/publications/N1211.pdf and
      http://www.gotw.ca/publications/N1185.pdf Now a uint8_t (aka. char) is
      used in graph properties instead of a bool.
      
      Graph types can now be fully pickled (this may not be feasible
      memory-wise if the graph is too large, since the whole XML
      representation is dumped to a string before it is saved on disc).
      99bf21c8
  8. 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
  9. 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
  10. 17 Dec, 2007 1 commit
    • Tiago Peixoto's avatar
      Fix visibility/RTTI problem with run_action() · 0c1f0df2
      Tiago Peixoto authored
      Some visibility voodoo is necessary to ensure that RTTI work properly
      across DSO boundaries, which is necessary to properly handle dynamic
      property maps and such. Additionally, the action template must have a
      different name each time the action code changes, to avoid additional
      weirdness.
      
      This also adds some other utility functions/typedefs to make writing
      "inline" c++ code easier.
      0c1f0df2
  11. 14 Dec, 2007 1 commit
    • Tiago Peixoto's avatar
      Add support for running arbitrary C++ code from python · 866bb994
      Tiago Peixoto authored
      It is now possible to run arbitrary "inline" C++ code from python, using
      scipy.weave, as such:
      
              g = graph_tool.Graph()
              g.load("foo.xml")
              value = 2.0
              g.run_action('cout << num_vertices(g) << " " << value << endl;',
                           ["value"]);
      
      The code gets compiled the first time, and is reused after that. Python
      local and global variables can be passed to C++, as shown above, by
      specifying a list of passed variables as the second argument.
      866bb994
  12. 13 Dec, 2007 1 commit
  13. 06 Dec, 2007 1 commit
  14. 30 Nov, 2007 1 commit
    • Tiago Peixoto's avatar
      Further improvements of the python interface · 1a0e9b5f
      Tiago Peixoto authored
      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)
      1a0e9b5f
  15. 26 Nov, 2007 1 commit
    • Tiago Peixoto's avatar
      Further improvement of python interface · 06358b7c
      Tiago Peixoto authored
      Vertices and edges can be accessed from the graph class, as such:
      
          import graph_tool
          g = graph_tool.Graph()
          for v in g.vertices():
              for e in v.out_edges():
                 # do something...
      
      Additionally, the --edit-{vertex|edge|graph}-property was ported to the
      new interface, and is working again, as it used to.
      
      The Vertex and Edge class no longer have the 'get_property' and
      'set_property' method. They'll be replaced by a new method of accessing
      property maps.
      06358b7c
  16. 04 Nov, 2007 1 commit
  17. 23 Oct, 2007 2 commits
  18. 12 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      Added --purge-edges and --purge-vertices option · 23e319bf
      Tiago Peixoto authored
          
      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)
      23e319bf
  19. 07 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      Remove graph rewiring · f618944c
      Tiago Peixoto authored
      Remove graph rewiring for now, since it's quite buggy. It will be
      re-commited when ready.
      f618944c
  20. 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
  21. 12 Sep, 2007 1 commit
  22. 09 Aug, 2007 1 commit
    • Tiago Peixoto's avatar
      * src/graph-tool: change layout and community graph options. · c3a6567d
      Tiago Peixoto authored
      	* 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
      c3a6567d
  23. 11 Jul, 2007 1 commit
    • Tiago Peixoto's avatar
      · 32990eb6
      Tiago Peixoto authored
              * ChangeLog: updated ChangeLog file with svn history
      
              * src/graph/graph_filtering.hh: added add_edge() and remove_edge() functions for filtered graphs
      
              * src/graph/shared_map.hh: included SharedContainer
      
              * src/graph/graph_rewiring.cc: initial support for random graph rewiring
      
      
      
      git-svn-id: https://svn.forked.de/graph-tool/trunk@114 d4600afd-f417-0410-95de-beed9576f240
      32990eb6
  24. 02 Jul, 2007 1 commit
  25. 30 Jun, 2007 2 commits
  26. 01 May, 2007 1 commit
  27. 30 Apr, 2007 1 commit
  28. 25 Jan, 2007 1 commit
  29. 12 Jan, 2007 1 commit
  30. 15 Nov, 2006 1 commit
  31. 14 Nov, 2006 1 commit
  32. 13 Nov, 2006 1 commit
  33. 12 Nov, 2006 1 commit
  34. 01 Nov, 2006 1 commit
  35. 31 Oct, 2006 1 commit
  36. 14 Oct, 2006 1 commit
  37. 09 Oct, 2006 1 commit
  38. 24 Sep, 2006 1 commit