~gabor.csardi/igraph/develop

igraph 0.6.5
============

Released February 24, 2013

The version number is not a mistake, we jump to 0.6.5 from 0.6, 
for technical reasons.

R: new features and bug fixes
-----------------------------

- Added a vertex shape API for defining new vertex shapes, and also 
  a couple of new vertex shapes.
- Added the get.data.frame() function, opposite of graph.data.frame().
- Added bipartite support to the Pajek reader and writer, closes bug
  \#1042298.
- `degree.sequence.game()` has a new method now: "simple_no_multiple".
- Added the is.degree.sequence() and is.graphical.degree.sequence()
  functions.
- rewire() has a new method: "loops", that can create loop edges.
- Walktrap community detection now handles isolates.
- layout.mds() returns a layout matrix now.
- layout.mds() uses LAPACK instead of ARPACK.
- Handle the '~' character in write.graph and read.graph. Bug
  \#1066986.
- Added k.regular.game().
- Use vertex names to plot if no labels are specified in the function
  call or as vetex attributes. Fixes issue \#1085431.
- power.law.fit() can now use a C implementation.

- Fixed a bug in barabasi.game() when out.seq was an empty vector.
- Fixed a bug that made functions with a progress bar fail if called 
  from another package.
- Fixed a bug when creating graphs from a weighted integer adjacency 
  matrix via graph.adjacency(). Bug \#1019624.
- Fixed overflow issues in centralization calculations.
- Fixed a minimal.st.separators() bug, some vertex sets were incorrectly
  reported as separators. Bug \#1033045.
- Fixed a bug that mishandled vertex colors in VF2 isomorphism
  functions. Bug \#1032819.
- Pajek exporter now always quotes strings, thanks to Elena Tea Russo.
- Fixed a bug with handling small edge weights in shortest paths 
  calculation in shortest.paths() (Dijkstra's algorithm.) Thanks to 
  Martin J Reed.
- Weighted transitivity uses V(graph) as 'vids' if it is NULL.
- Fixed a bug when 'pie' vertices were drawn together with other 
  vertex shapes.
- Speed up printing graphs.
- Speed up attribute queries and other basic operations, by avoiding 
  copying of the graph. Bug \#1043616.
- Fixed a bug in the NCV setting for ARPACK functions. It cannot be
  bigger than the matrix size.
- layout.merge()'s DLA mode has better defaults now.
- Fixed a bug in layout.mds() that resulted vertices on top of each
  other.
- Fixed a bug in layout.spring(), it was not working properly.
- Fixed layout.svd(), which was completely defunct.
- Fixed a bug in layout.graphopt() that caused warnings and on 
  some platforms crashes.
- Fixed community.to.membership(). Bug \#1022850.
- Fixed a graph.incidence() crash if it was called with a non-matrix
  argument.
- Fixed a get.shortest.paths bug, when output was set to "both".
- Motif finding functions return NA for isomorphism classes that are
  not motifs (i.e. not connected). Fixes bug \#1050859. 
- Fixed get.adjacency() when attr is given, and the attribute has some
  complex type. Bug \#1025799. 
- Fixed attribute name in graph.adjacency() for dense matrices. Bug
  \#1066952. 
- Fixed erratic behavior of alpha.centrality().
- Fixed igraph indexing, when attr is given. Bug \#1073705.
- Fixed a bug when calculating the largest cliques of a directed
  graph. Bug \#1073800.
- Fixed a bug in the maximal clique search, closes \#1074402.
- Warn for negative weights when calculating PageRank.
- Fixed dense, unweighted graph.adjacency when diag=FALSE. Closes
  issue \#1077425. 
- Fixed a bug in eccentricity() and radius(), the results were often
  simply wrong.
- Fixed a bug in get.all.shortest.paths() when some edges had zero weight.
- graph.data.frame() is more careful when vertex names are numbers, to
  avoid their scientific notation. Fixes issue \#1082221. 
- Better check for NAs in vertex names. Fixes issue \#1087215
- Fixed some potential crashes in the DrL layout generator.
- Fixed a bug in the Reingold-Tilford layout when the graph is
  directed and mode != ALL.
- Eliminate gap between vertex and edge when plotting an edge without an arrow.
  Fixes \#1118448.
- Fixed a bug in has.multiple() that resulted in false negatives for
  some undirected graphs.
- Fixed a crash in weighted betweenness calculation.
- R plotting: fixed a bug that caused misplaced arrows at rectangle
  vertex shapes.

Python news and fixes
---------------------

- Added bipartite support to the Pajek reader and writer, closes bug
  \#1042298.
- Graph.Degree_Sequence() has a new method now: "no_multiple".
- Added the is_degree_sequence() and is_graphical_degree_sequence()
  functions.
- rewire() has a new mode: "loops", that can create loop edges.
- Walktrap community detection now handles isolates.
- Added Graph.K_Regular().
- power_law_fit() now uses a C implementation.
- Added support for setting the frame (stroke) width of vertices using the
  frame_width attribute or the vertex_frame_width keyword argument in plot()
- Improved Inkscape-friendly SVG output from Graph.write_svg(), thanks to drlog
- Better handling of named vertices in Graph.delete_vertices()
- Added experimental Gephi graph streaming support; see igraph.remote.gephi and
  igraph.drawing.graph.GephiGraphStreamingDrawer
- Nicer __repr__ output for Flow and Cut instances
- Arrows are now placed correctly around diamond-shaped nodes on plots
- Added Graph.TupleList, a function that allows one to create graphs with
  edge attributes quickly from a list of tuples.
- plot() now also supports .eps as an extension, not only .ps

- Fixed overflow issues in centralization calculations.
- Fixed a bug that mishandled vertex colors in VF2 isomorphism
  functions. Bug \#1032819.
- Pajek exporter now always quotes strings, thanks to Elena Tea Russo.
- Fixed a bug with handling small edge weights in shortest paths 
  calculation in Graph.shortest_paths() (Dijkstra's algorithm.) Thanks to 
  Martin J Reed.
- Fixed a bug in the NCV setting for ARPACK functions. It cannot be
  bigger than the matrix size.
- Fixed a bug in Graph.layout_mds() that resulted vertices on top of each
  other.
- Motif finding functions return nan for isomorphism classes that are
  not motifs (i.e. not connected). Fixes bug \#1050859. 
- Fixed a bug when calculating the largest cliques of a directed
  graph. Bug \#1073800.
- Warn for negative weights when calculating PageRank.
- Fixed a bug in Graph.eccentricity() and Graph.radius(), the results were often
  simply wrong.
- Fixed a bug in Graph.get.all.shortest.paths() when some edges had zero weight.
- Fixed some potential crashes in the DrL layout generator.
- Fixed a bug in the Reingold-Tilford layout when the graph is
  directed and mode != ALL.
- Fixed a bug in Graph.layout_sugiyama() when the graph had no edges.
- Fixed a bug in Graph.community_label_propagation() when initial labels
  contained -1 entries. Issue \#1105460.
- Repaired the DescartesCoordinateSystem class (which is not used too frequently
  anyway)
- Fixed a bug that caused segfaults when an igraph Graph was used in a thread
  forked from the main Python interpreter thread
- Fixed a bug that affected file handles created from Python strings in the
  C layer
- Fixed a bug in has_multiple() that resulted in false negatives
  for some undirected graphs.
- Fixed a crash in weighted betweenness calculation.

C library news and changes
--------------------------

- Added bipartite support to the Pajek reader and writer, closes bug
  \#1042298.
- igraph_layout_mds() uses LAPACK instead of ARPACK.
- igraph_degree_sequence_game has a new method:
  IGRAPH_DEGSEQ_SIMPLE_NO_MULTIPLE.
- Added the igraph_is_degree_sequence() and
  igraph_is_graphical_degree_sequence() functions.
- igraph_rewire() has a new method: IGRAPH_REWIRING_SIMPLE_LOOPS, 
  that can create loops.
- Walktrap community detection now handles isolates.
- Added igraph_k_regular_game().
- Added igraph_power_law_fit.

- Fixed a bug in igraph_barabasi_game when outseq was an empty vector.
- Fixed overflow issues in centralization calculations.
- Fixed an invalid return value of igraph_vector_ptr_pop_back.
- Fixed a igraph_all_minimal_st_separators() bug, some vertex sets
  were incorrectly reported as separators. Bug \#1033045.
- Pajek exporter now always quotes strings, thanks to Elena Tea Russo.
- Fixed a bug with handling small edge weights in
  igraph_shortest_paths_dijkstra(), thanks to Martin J Reed.
- Fixed a bug in the NCV setting for ARPACK functions. It cannot be
  bigger than the matrix size.
- igraph_layout_merge_dla uses better default parameter values now.
- Fixed a bug in igraph_layout_mds() that resulted vertices on top of
  each other.
- Attribute handler table is not thread-local any more.
- Motif finding functions return IGRAPH_NAN for isomorphism classes
  that are not motifs (i.e. not connected). Fixes bug \#1050859.
- Fixed a bug when calculating the largest cliques of a directed
  graph. Bug \#1073800.
- Fix a bug in degree_sequence_game(), in_seq can be an empty vector as
  well instead of NULL, for an undirected graph. 
- Fixed a bug in the maximal clique search, closes \#1074402.
- Warn for negative weights when calculating PageRank.
- Fixed a bug in igraph_eccentricity() (and also igraph_radius()), 
  the results were often simply wrong.
- Fixed a bug in igraph_get_all_shortest_paths_dijkstra() when edges
  had zero weight.
- Fixed some potential crashes in the DrL layout generator.
- Fixed a bug in the Reingold-Tilford layout when the graph is
  directed and mode != ALL.
- Fixed a bug in igraph_has_multiple() that resulted in false negatives
  for some undirected graphs.
- Fixed a crash in weighted betweenness calculation.

igraph 0.6
==========

Released June 11, 2012

See also the release notes at 
http://igraph.sf.net/relnotes-0.6.html

R: Major new features
---------------------

- Vertices and edges are numbered from 1 instead of 0. 
  Note that this makes most of the old R igraph code incompatible
  with igraph 0.6. If you want to use your old code, please use 
  the igraph0 package. See more at http://igraph.sf.net/relnotes-0.6.html.
- The '\[' and '\[\[' operators can now be used on igraph graphs, 
  for '\[' the graph behaves as an adjacency matrix, for '[[' is 
  is treated as an adjacency list. It is also much simpler to
  manipulate the graph structure, i.e. add/remove edges and vertices, 
  with some new operators. See more at ?graph.structure.
- In all functions that take a vector or list of vertices or edges, 
  vertex/edge names can be given instead of the numeric ids.
- New package 'igraphdata', contains a number of data sets that can
  be used directly in igraph.
- Igraph now supports loading graphs from the Nexus online data
  repository, see nexus.get(), nexus.info(), nexus.list() and 
  nexus.search().
- All the community structure finding algorithm return a 'communities'
  object now, which has a bunch of useful operations, see 
  ?communities for details.
- Vertex and edge attributes are handled much better now. They 
  are kept whenever possible, and can be combined via a flexible API.
  See ?attribute.combination.
- R now prints igraph graphs to the screen in a more structured and 
  informative way. The output of summary() was also updated
  accordingly.

R: Other new features
---------------------

- It is possible to mark vertex groups on plots, via
  shading. Communities and cohesive blocks are plotted using this by
  default.
- Some igraph demos are now available, see a list via 
  'demo(package="igraph")'.
- igraph now tries to select the optimal layout algorithm, when
  plotting a graph.
- Added a simple console, using Tcl/Tk. It contains a text area
  for status messages and also a status bar. See igraph.console().
- Reimplemented igraph options support, see igraph.options() and 
  getIgraphOpt().
- Igraph functions can now print status messages.

R: New or updated functions
---------------------------

Community detection
-------------------
- The multi-level modularity optimization community structure detection 
  algorithm by Blondel et al. was added, see multilevel.community().
- Distance between two community structures: compare.communities().
- Community structure via exact modularity optimization,
  optimal.community().
- Hierarchical random graphs and community finding, porting the code
  from Aaron Clauset. See hrg.game(), hrg.fit(), etc.
- Added the InfoMAP community finding method, thanks to Emmanuel
  Navarro for the code. See infomap.community().

Shortest paths
--------------
- Eccentricity (eccentricity()), and radius (radius()) calculations.
- Shortest path calculations with get.shortest.paths() can now 
  return the edges along the shortest paths.
- get.all.shortest.paths() now supports edge weights.

Centrality
----------
- Centralization scores for degree, closeness, betweenness and 
  eigenvector centrality. See centralization.scores().
- Personalized Page-Rank scores, see page.rank().
- Subgraph centrality, subgraph.centrality().
- Authority (authority.score()) and hub (hub.score()) scores support 
  edge weights now.
- Support edge weights in betweenness and closeness calculations.
- bonpow(), Bonacich's power centrality and alpha.centrality(), 
  Alpha centrality calculations now use sparse matrices by default.
- Eigenvector centrality calculation, evcent() now works for 
  directed graphs.
- Betweenness calculation can now use arbitrarily large integers,
  this is required for some lattice-like graphs to avoid overflow.

Input/output and file formats
-----------------------------
- Support the DL file format in graph.read(). See 
  http://www.analytictech.com/networks/dataentry.htm.
- Support writing the LEDA file format in write.graph().

Plotting and layouts
--------------------
- Star layout: layout.star().
- Layout based on multidimensional scaling, layout.mds().
- New layouts layout.grid() and layout.grid.3d().
- Sugiyama layout algorithm for layered directed acyclic graphs, 
  layout.sugiyama().

Graph generators
----------------
- New graph generators: static.fitness.game(), static.power.law.game().
- barabasi.game() was rewritten and it supports three algorithms now,
  the default algorithm does not generate multiple or loop edges.
  The graph generation process can now start from a supplied graph.
- The Watts-Strogatz graph generator, igraph_watts_strogatz() can 
  now create graphs without loop edges.

Others
------
- Added the Spectral Coarse Graining algorithm, see scg(). 
- The cohesive.blocks() function was rewritten in C, it is much faster
  now. It has a nicer API, too. See demo("cohesive").
- Added generic breadth-first and depth-first search implementations
  with many callbacks, graph.bfs() and graph_dfs().
- Support vertex and edge coloring in the VF2 (sub)graph isomorphism 
  functions (graph.isomorphic.vf2(), graph.count.isomorphisms.vf2(), 
  graph.get.isomorphisms.vf2(), graph.subisomorphic.vf2(), 
  graph.count.subisomorphisms.vf2(), graph.get.subisomorphisms.vf2()).
- Assortativity coefficient, assortativity(), assortativity.nominal()
  and assortativity.degree().
- Vertex operators that work by vertex names: 
  graph.intersection.by.name(), graph.union.by.name(), 
  graph.difference.by.name(). Thanks to Magnus Torfason for 
  contributing his code!
- Function to calculate a non-induced subraph: subgraph.edges().
- More comprehensive maximum flow and minimum cut calculation, 
  see functions graph.maxflow(), graph.mincut(), stCuts(), stMincuts().
- Check whether a directed graph is a DAG, is.dag().
- has.multiple() to decide whether a graph has multiple edges.
- Added a function to calculate a diversity score for the vertices,
  graph.diversity().
- Graph Laplacian calculation (graph.laplacian()) supports edge 
  weights now.
- Biconnected component calculation, biconnected.components() 
  now returns the components themselves.
- bipartite.projection() calculates multiplicity of edges.
- Maximum cardinality search: maximum.cardinality.search() and 
  chordality test: is.chordal()
- Convex hull computation, convex.hull().
- Contract vertices, contract.vertices().

New in the Python interface
---------------------------

TODO

Major changes in the Python interface
-------------------------------------

TODO

New in the C layer
------------------

- Maximum cardinality search: igraph_maximum_cardinality_search() and 
  chordality test: igraph_is_chordal().
- Support the DL file format, igraph_read_graph_dl(). See 
  http://www.analytictech.com/networks/dataentry.htm.
- Added generic breadth-first and depth-first search implementations
  with many callbacks (igraph_bfs(), igraph_dfs()).
- Centralization scores for degree, closeness, betweenness and
  eigenvector centrality, see igraph_centralization().
- Added igraph_sparsemat_t, a type that implements sparse 
  matrices based on the CXSparse library by Tim Davis.
  See http://www.cise.ufl.edu/research/sparse/CXSparse/.
- Personalized Page-Rank scores, igraph_personalized_pagerank() and 
  igraph_personalized_pagerank_vs().
- Assortativity coefficient, igraph_assortativity(), 
  igraph_assortativity_nominal(), and igraph_assortativity_degree().
- The multi-level modularity optimization community structure detection 
  algorithm by Blondel et al. was added, see igraph_community_multilevel().
- Added the igraph_version() function.
- Star layout: igraph_layout_star().
- Function to calculate a non-induced subraph: igraph_subgraph_edges().
- Distance between two community structures: igraph_compare_communities().
- Community structure via exact modularity optimization,
  igraph_community_optimal_community().
- More comprehensive maximum flow and minimum cut calculation, 
  see functions igraph_maxflow(), igraph_mincut(), 
  igraph_all_st_cuts(), igraph_all_st_mincuts().
- Layout based on multidimensional scaling, igraph_layout_mds().
- It is now possible to access the random number generator(s) via an
  API. Multiple RNGs can be used, from external sources as well. 
  The default RNG is MT19937.
- Added igraph_get_all_shortest_paths_dijkstra, for calculating all
  non-negatively weighted shortest paths.
- Check whether a directed graph is a DAG, igraph_is_dag().
- Cohesive blocking, a'la Moody & White, igraph_cohesive_blocks().
- Igraph functions can now print status messages, see igraph_status()
  and related functions.
- Support writing the LEDA file format, igraph_write_graph_leda().
- Contract vertices, igraph_contract_vertices().
- The C reference manual has now a lot of example programs.
- Hierarchical random graphs and community finding, porting the code
  from Aaron Clauset. See igraph_hrg_game(), igraph_hrg_fit(), etc.
- igraph_has_multiple() to decide whether a graph has multiple edges.
- New layouts igraph_layout_grid() and igraph_layout_grid_3d().
- igraph_integer_t is really an integer now, it used to be a double.
- igraph_minimum_spanning_tree(), calls either the weighted or 
  the unweighted implementation.
- Eccentricity (igraph_eccentricity()), and radius (igraph_radius())
  calculations.
- Several game theory update rules, written by Minh Van Nguyen. See
  igraph_deterministic_optimal_imitation(),
  igraph_stochastic_imitation(), igraph_roulette_wheel_imitation(),
  igraph_moran_process(), 
- Sugiyama layout algorithm for layered directed acyclic graphs, 
  igraph_layout_sugiyama().
- New graph generators: igraph_static_fitness_game(), 
  igraph_static_power_law_game().
- Added the InfoMAP community finding method, thanks to Emmanuel
  Navarro for the code. See igraph_community_infomap().
- Added the Spectral Coarse Graining algorithm, see igraph_scg(). 
- Added a function to calculate a diversity score for the vertices,
  igraph_diversity().

Major changes in the C layer
----------------------------

- Authority (igraph_authority_score()) and hub (igraph_hub_score()) scores 
  support edge weights now.
- Graph Laplacian calculation (igraph_laplacian()) supports edge 
  weights now.
- Support edge weights in betweenness (igraph_betweenness()) and closeness
  (igraph_closeness()) calculations.
- Support vertex and edge coloring in the VF2 graph isomorphism 
  algorithm (igraph_isomorphic_vf2(), igraph_count_isomorphisms_vf2(),
  igraph_get_isomorphisms_vf2(), igraph_subisomorphic_vf2(), 
  igraph_count_subisomorphisms_vf2(), igraph_get_subisomorphisms_vf2()).
- Added print operations for the igraph_vector*_t, igraph_matrix*_t and 
  igraph_strvector_t types.
- Biconnected component calculation (igraph_biconnected_components())
  can now return the components themselves.
- Eigenvector centrality calculation, igraph_eigenvector_centrality() 
  now works for directed graphs.
- Shortest path calculations with get_shortest_paths() and 
  get_shortest_paths_dijkstra() can now return the edges along the paths.
- Betweenness calculation can now use arbitrarily large integers,
  this is required for some lattice-like graphs to avoid overflow.
- igraph_bipartite_projection() calculates multiplicity of edges.
- igraph_barabasi_game() was rewritten and it supports three 
  algorithms now, the default algorithm does not generate multiple or
  loop edges.
- The Watts-Strogatz graph generator, igraph_watts_strogatz() can 
  now create graphs without loop edges.
- igraph should be now thread-safe, on architectures that support 
  thread-local storage (Linux and Windows: yes, Mac OSX: no).

We also fixed numerous bugs, too many to include them here, sorry.
You may look at our bug tracker at https://bugs.launchpad.net/igraph
to check whether a bug was fixed or not. Thanks for all the people
reporting bugs. Special thanks to Minh Van Nguyen for a lot of bug
reports, documentation fixes and contributed code!

igraph 0.5.3
============

Released November 22, 2009

Bugs corrected in the R interface
---------------------------------
- Some small changes to make 'R CMD check' clean
- Fixed a bug in graph.incidence, the 'directed' and 'mode' arguments 
  were not handled correctly
- Betweenness and edge betweenness functions work for graphs with
  many shortest paths now (up to the limit of long long int)
- When compiling the package, the configure script fails if there is
  no C compiler available
- igraph.from.graphNEL creates the right number of loop edges now
- Fixed a bug in bipartite.projection() that caused occasional crashes 
  on some systems

New in the Python interface
---------------------------
- Added support for weighted diameter
- get_eid() considers edge directions by default from now on
- Fixed a memory leak in the attribute handler
- 'NaN' and 'inf' are treated correctly now

Bugs corrected in the C layer
-----------------------------
- Betweenness and edge betweenness functions work for graphs with
  many shortest paths now (up to the limit of long long int)
- The configure script fails if there is no C compiler available
- Fixed a bug in igraph_community_spinglass, when csize was a NULL
  pointer, but membership was not
- Fixed a bug in igraph_bipartite_projection that caused occasional
  crashes on some systems

igraph 0.5.2
============

Released April 10, 2009

See also the release notes at
http://igraph.sf.net/relnotes-0.5.2.html

New in the R interface
----------------------

- Added progress bar support to beweenness() and
  betweenness.estimate(), layout.drl()
- Speeded up betweenness estimation
- Speeded up are.connected()
- Johnson's shortest paths algorithm added
- shortest.paths() has now an 'algorithm' argument to choose from the
  various implementations manually
- Always quote symbolic vertex names when printing graphs or edges
- Average nearest neighbor degree calculation, graph.knn()
- Weighted degree (also called strength) calculation, graph.strength()
- Some new functions to support bipartite graphs: graph.bipartite(),
  is.bipartite(), get.indicence(), graph.incidence(),
  bipartite.projection(), bipartite.projection.size()
- Support for plotting curved edges with plot.igraph() and tkplot()
- Added support for weighted graphs in alpha.centrality()
- Added the label propagation community detection algorithm by
  Raghavan et al., label.propagation.community()
- cohesive.blocks() now has a 'cutsetHeuristic' argument to choose
  between two cutset algorithms
- Added a function to "unfold" a tree, unfold.tree()
- New tkplot() arguments to change the drawing area
- Added a minimal GUI, invoke it with tkigraph()
- The DrL layout generator, layout.drl() has a three dimensional mode
  now.

Bugs corrected in the R interface
---------------------------------

- Fixed a bug in VF2 graph isomorphism functions
- Fixed a bug when a sparse adjacency matrix was requested in
  get.adjacency() and the graph was named
- VL graph generator in degree.sequence.game() checks now that
  the sum of the degrees is even
- Many fixes for supporting various compilers, e.g. GCC 4.4 and Sun's
  C compiler
- Fixed memory leaks in graph.automorphisms(), Bellman-Ford
  shortest.paths(), independent.vertex.sets()
- Fix a bug when a graph was imported from LGL and exported to NCOL
  format (\#289596)
- cohesive.blocks() creates its temporary file in the session
  temporary directory
- write.graph() and read.graph() now give error messages when unknown
  arguments are given
- The GraphML reader checks the name of the attributes to avoid adding
  a duplicate 'id' attribute
- It is possible to change the 'ncv' ARPACK parameter for
  leading.eigenvector.community()
- Fixed a bug in path.length.hist(), 'unconnected' was wrong
  for unconnected and undirected graphs
- Better handling of attribute assingment via iterators, this is now
  also clarified in the manual
- Better error messages for unknown vertex shapes
- Make R package unload cleanly if unloadNamespace() is used
- Fixed a bug in plotting square shaped vertices (\#325244)
- Fixed a bug in graph.adjacency() when the matrix is a sparse matrix
  of class "dgTMatrix"

New in the Python interface
---------------------------

- Speeded up betweenness estimation
- Johnson's shortest paths algorithm added (selected automatically
  by Graph.shortest_paths() if needed)
- Weighted degree (also called strength) calculation, Graph.strength()
- Some new methods to support bipartite graphs: Graph.Bipartite(),
  Graph.is_bipartite(), Graph.get_indicence(), Graph.Incidence(),
  Graph.bipartite_projection(), Graph.bipartite_projection_size()
- Added the label propagation community detection algorithm by
  Raghavan et al., Graph.community_label_propagation()
- Added a function to "unfold" a tree, Graph.unfold_tree()
- setup.py script improvements
- Graph plotting now supports edge_arrow_size and edge_arrow_width
- Added Graph.Formula to create small graphs from a simple notation
- VertexSeq and EdgeSeq objects can now be indexed by slices

New in the C layer
------------------

- Added progress bar support to igraph_betweenness() and 
  igraph_betweenness_estimate(), igraph_layout_drl()
- Speeded up igraph_betweenness_estimate(), igraph_get_eid(), 
  igraph_are_connected(), igraph_get_eids()
- Added igraph_get_eid2()
- Johnson's shortest path algorithm added:
  igraph_shortest_paths_johnson() 
- Average nearest neighbor degree calculation,
  igraph_avg_nearest_neighbor_degree() 
- Weighted degree (also called strength) calculation,
  igraph_strength()
- Some functions to support bipartite graphs: igraph_full_bipartite(),
  igraph_bipartite_projection(), igraph_create_bipartite(),
  igraph_incidence(), igraph_get_incidence(),
  igraph_bipartite_projection_size(), igraph_is_bipartite()
- Added the label propagation community detection algorithm by
  Raghavan et al., igraph_community_label_propagation()
- Added an example that shows how to set the random number generator's
  seed from C (examples/simple/random_seed.c)
- Added a function to "unfold" a tree, igraph_unfold_tree()
- C attribute handler updates: added functions to query many
  vertices/edges at once
- Three dimensional DrL layout, igraph_layout_drl_3d()

Bugs corrected in the C layer
-----------------------------

- Fixed a bug in igraph_isomorphic_function_vf2(), affecting all VF2
  graph isomorphism functions
- VL graph generator in igraph_degree_sequence_game() checks now that
  the sum of the degrees is even
- Many small corrections to make igraph compile with Microsoft Visual
  Studio 2003, 2005 and 2008
- Many fixes for supporting various compilers, e.g. GCC 4.4 and Sun's
  C compiler
- Fix a bug when a graph was imported from LGL and exported to NCOL
  format (\#289596)
- Fixed memory leaks in igraph_automorphisms(),
  igraph_shortest_paths_bellman_ford(),
  igraph_independent_vertex_sets()
- The GraphML reader checks the name of the attributes to avoid adding
  a duplicate 'id' attribute
- It is possible to change the 'ncv' ARPACK parameter for
  igraph_community_leading_eigenvector()
- Fixed a bug in igraph_path_length_hist(), 'unconnected' was wrong
  for unconnected and undirected graphs.

igraph 0.5.1
============

Released July 14, 2008

See also the release notes at 
http://igraph.sf.net/relnotes-0.5.1.html

New in the R interface
----------------------

- A new layout generator called DrL.
- Uniform sampling of random connected undirected graphs with a 
  given degree sequence.
- Edge labels are plotted at 1/3 of the edge, this is better if 
  the graph has mutual edges.
- Initial and experimental vertex shape support in 'plot'.
- New function, 'graph.adjlist' creates igraph graphs from
  adjacency lists.
- Conversion to/from graphNEL graphs, from the 'graph' R package.
- Fastgreedy community detection can utilize edge weights now, this 
  was missing from the R interface.
- The 'arrow.width' graphical parameter was added.
- graph.data.frame has a new argument 'vertices'.
- graph.adjacency and get.adjacency support sparse matrices, 
  the 'Matrix' package is required to use this functionality.
- graph.adjacency adds column/row names as 'name' attribute.
- Weighted shortest paths using Dijkstra's or the Belmann-Ford 
  algorithm.
- Shortest path functions return 'Inf' for unreachable vertices.
- New function 'is.mutual' to find mutual edges in a directed graph.
- Added inverse log-weighted similarity measure (a.k.a. Adamic/Adar
  similarity).
- preference.game and asymmetric.preference.game were 
  rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
- Edge weight support in function 'get.shortest.paths', it uses 
  Dijkstra's algorithm.

Bugs corrected in the R interface
---------------------------------
  
- A bug was corrected in write.pajek.bgraph.
- Several bugs were corrected in graph.adjacency.
- Pajek reader bug corrected, used to segfault if '\*Vertices' 
  was missing.
- Directedness is handled correctly when writing GML files.
  (But note that 'correct' conflicts the standard here.)
- Corrected a bug when calculating weighted, directed PageRank on an 
  undirected graph. (Which does not make sense anyway.)
- Several bugs were fixed in the Reingold-Tilford layout to avoid 
  edge crossings.
- A bug was fixed in the GraphML reader, when the value of a graph
  attribute was not specified.
- Fixed a bug in the graph isomorphism routine for small (3-4 vertices)
  graphs.
- Corrected the random sampling implementation (igraph_random_sample),
  now it always generates unique numbers. This affects the 
  Gnm Erdos-Renyi generator, it always generates simple graphs now.
- The basic igraph constructor (igraph_empty_attrs, all functions 
  are expected to call this internally) now checks whether the number
  of vertices is finite.
- The LGL, NCOL and Pajek graph readers handle errors properly now.
- The non-symmetric ARPACK solver returns results in a consistent form
  now.
- The fast greedy community detection routine now checks that the graph
  is simple.
- The LGL and NCOL parsers were corrected to work with all 
  kinds of end-of-line encodings.
- Hub & authority score calculations initialize ARPACK parameters now.
- Fixed a bug in the Walktrap community detection routine, when applied 
  to unconnected graphs.
- Several small memory leaks were removed, and a big one from the Spinglass
  community structure detection function

New in the Python interface
---------------------------

- A new layout generator called DrL.
- Uniform sampling of random connected undirected graphs with a 
  given degree sequence.
- Methods parameters accepting igraph.IN, igraph.OUT and igraph.ALL
  constants now also accept these as strings ("in", "out" and "all").
  Prefix matches also allowed as long as the prefix match is unique.
- Graph.shortest_paths() now supports edge weights (Dijkstra's and
  Bellman-Ford algorithm implemented)
- Graph.get_shortest_paths() also supports edge weights
  (only Dijkstra's algorithm yet)
- Added Graph.is_mutual() to find mutual edges in a directed graph.
- Added inverse log-weighted similarity measure (a.k.a. Adamic/Adar
  similarity).
- preference.game and asymmetric.preference.game were 
  rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
- ARPACK options can now be modified from the Python interface
  (thanks to Kurt Jacobson)
- Layout.to_radial() added -- now you can create a top-down tree
  layout by the Reingold-Tilford algorithm and then turn it to a
  radial tree layout
- Added Graph.write_pajek() to save graphs in Pajek format
- Some vertex and edge related methods can now also be accessed via
  the methods of VertexSeq and EdgeSeq, restricted to the current
  vertex/edge sequence of course
- Visualisations now support triangle shaped vertices
- Added Graph.mincut()
- Added Graph.Weighted_Adjacency() to create graphs from weighted
  adjacency matrices
- Kamada-Kawai and Fruchterman-Reingold layouts now accept initial
  vertex positions
- Graph.Preference() and Graph.Asymmetric_Preference() were 
  rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).

Bugs corrected in the Python interface
--------------------------------------

- Graph.constraint() now properly returns floats instead of integers
  (thanks to Eytan Bakshy)
- Graphs given by adjacency matrices are now finally loaded and saved
  properly
- Graph.Preference() now accepts floats in type distributions
- A small bug in Graph.community_edge_betweenness() corrected
- Some bugs in numeric attribute handling resolved
- VertexSeq and EdgeSeq objects can now be subsetted by lists and
  tuples as well
- Fixed a bug when dealing with extremely small layout sizes
- Eigenvector centality now always return positive values
- Graph.authority_score() now really returns the authority scores
  instead of the hub scores (blame copypasting)
- Pajek reader bug corrected, used to segfault if '\*Vertices' 
  was missing.
- Directedness is handled correctly when writing GML files.
  (But note that 'correct' conflicts the standard here.)
- Corrected a bug when calculating weighted, directed PageRank on an 
  undirected graph. (Which does not make sense anyway.)
- Several bugs were fixed in the Reingold-Tilford layout to avoid 
  edge crossings.
- A bug was fixed in the GraphML reader, when the value of a graph
  attribute was not specified.
- Fixed a bug in the graph isomorphism routine for small (3-4 vertices)
  graphs.
- Corrected the random sampling implementation (igraph_random_sample),
  now it always generates unique numbers. This affects the 
  Gnm Erdos-Renyi generator, it always generates simple graphs now.
- The LGL, NCOL and Pajek graph readers handle errors properly now.
- The non-symmetric ARPACK solver returns results in a consistent form
  now.
- The fast greedy community detection routine now checks that the graph
  is simple.
- The LGL and NCOL parsers were corrected to work with all 
  kinds of end-of-line encodings.
- Hub & authority score calculations initialize ARPACK parameters now.
- Fixed a bug in the Walktrap community detection routine, when applied 
  to unconnected graphs.
- Several small memory leaks were removed, and a big one from the Spinglass
  community structure detection function

New in the C layer
------------------

- A new layout generator called DrL.
- Uniform sampling of random connected undirected graphs with a 
  given degree sequence.
- Some stochastic test results are ignored (for spinglass community
  detection, some Erdos-Renyi generator tests)
- Weighted shortest paths, Dijkstra's algorithm.
- The unweigthed shortest path routine returns 'Inf' for unreachable
  vertices.
- New function, igraph_adjlist can create igraph graphs from 
  adjacency lists.
- New function, igraph_weighted_adjacency can create weighted graphs 
  from weight matrices.
- New function, igraph_is_mutual to search for mutual edges.
- Added inverse log-weighted similarity measure (a.k.a. Adamic/Adar
  similarity).
- igraph_preference_game and igraph_asymmetric_preference_game were 
  rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
- The Bellman-Ford shortest path algorithm was added.
- Added weighted variant of igraph_get_shortest_paths, based on
  Dijkstra's algorithm.
- Several small memory leaks were removed, and a big one from the Spinglass
  community structure detection function

Bugs corrected in the C layer
-----------------------------

- Several bugs were corrected in the (still experimental) C attribute
  handler.
- Pajek reader bug corrected, used to segfault if '\*Vertices' 
  was missing.
- Directedness is handled correctly when writing GML files.
  (But note that 'correct' conflicts the standard here.)
- Corrected a bug when calculating weighted, directed PageRank on an 
  undirected graph. (Which does not make sense anyway.)
- Some code polish to make igraph compile with GCC 4.3
- Several bugs were fixed in the Reingold-Tilford layout to avoid 
  edge crossings.
- A bug was fixed in the GraphML reader, when the value of a graph
  attribute was not specified.
- Fixed a bug in the graph isomorphism routine for small (3-4 vertices)
  graphs.
- Corrected the random sampling implementation (igraph_random_sample),
  now it always generates unique numbers. This affects the 
  Gnm Erdos-Renyi generator, it always generates simple graphs now.
- The basic igraph constructor (igraph_empty_attrs, all functions 
  are expected to call this internally) now checks whether the number
  of vertices is finite.
- The LGL, NCOL and Pajek graph readers handle errors properly now.
- The non-symmetric ARPACK solver returns results in a consistent form
  now.
- The fast greedy community detection routine now checks that the graph
  is simple.
- The LGL and NCOL parsers were corrected to work with all 
  kinds of end-of-line encodings.
- Hub & authority score calculations initialize ARPACK parameters now.x
- Fixed a bug in the Walktrap community detection routine, when applied 
  to unconnected graphs.

igraph 0.5
=========

Released February 14, 2008

See also the release notes at http://igraph.sf.net/relnotes-0.5.html

New in the R interface
----------------------

- The 'rescale', 'asp' and 'frame' graphical parameters were added
- Create graphs from a formula notation (graph.formula)
- Handle graph attributes properly
- Calculate the actual minimum cut for undirected graphs
- Adjacency lists, get.adjlist and get.adjedgelist added
- Eigenvector centrality computation is much faster now
- Proper R warnings, instead of writing the warning to the terminal
- R checks graphical parameters now, the unknown ones are not just
  ignored, but an error message is given  
- plot.igraph has an 'add' argument now to compose plots with multiple
  graphs
- plot.igraph supports the 'main' and 'sub' arguments
- layout.norm is public now, it can normalize a layout
- It is possible to supply startup positions to layout generators
- Always free memory when CTRL+C/ESC is pressed, in all operating
  systems
- plot.igraph can plot square vertices now, see the 'shape' parameter
- graph.adjacency rewritten when creating weighted graphs
- We use match.arg whenever possible. This means that character scalar 
  options can be abbreviated and they are always case insensitive

- VF2 graph isomorphism routines can check subgraph isomorphism now,
  and they are able to return matching(s)
- The BLISS graph isomorphism algorithm is included in igraph now. See
  canonical.permutation, graph.isomorphic.bliss
- We use ARPACK for eigenvalue/eigenvector calculation. This means that the
  following functions were rewritten: page.rank,
  leading.eigenvector.community.\*, evcent. New functions based on
  ARPACK: hub.score, authority.score, arpack.
- Edge weights for Fruchterman-Reingold layout (layout.fruchterman.reingold).
- Line graph calculation (line.graph)
- Kautz and de Bruijn graph generators (graph.kautz, graph.de.bruijn)
- Support for writing graphs in DOT format
- Jaccard and Dice similarity coefficients added (similarity.jaccard,
  similarity.dice)
- Counting the multiplicity of edges (count.multiple)
- The graphopt layout algorithm was added, layout.graphopt
- Generation of "famous" graphs (graph.famous).
- Create graphs from LCF notation (graph.cf).
- Dyad census and triad cencus functions (dyad.census, triad.census)
- Cheking for simple graphs (is.simple)
- Create full citation networks (graph.full.citation)
- Create a histogram of path lengths (path.length.hist)
- Forest fire model added (forest.fire.game)
- DIMACS reader can handle different file types now
- Biconnected components and articulation points (biconnected.components,
  articulation.points)
- Kleinberg's hub and authority scores (hub.score, authority.score)
- as.undirected handles attributes now
- Geometric random graph generator (grg.game) can return the
  coordinates of the vertices
- Function added to convert leading eigenvector community structure result to
  a membership vector (community.le.to.membership)
- Weighted fast greedy community detection
- Weighted page rank calculation
- Functions for estimating closeness, betweenness, edge betweenness by 
  introducing a cutoff for path lengths (closeness.estimate,
  betweenness.estimate, edge.betweenness.estimate)
- Weighted modularity calculation
- Function for permuting vertices (permute.vertices)
- Betweenness and closeness calculations are speeded up
- read.graph can handle all possible line terminators now (\r, \n, \r\n, \n\r)
- Error handling was rewritten for walktrap community detection,
  the calculation can be interrupted now
- The maxflow/mincut functions allow to supply NULL pointer for edge
  capacities, implying unit capacities for all edges

Bugs corrected in the R interface
---------------------------------

- Fixed a bug in cohesive.blocks, cohesive blocks were sometimes not
  calculated correctly

New in the Python interface
---------------------------

- Added shell interface: igraph can now be invoked by calling the script called
  igraph from the command line. The script launches the Python interpreter and
  automatically imports igraph functions into the main namespace
- Pickling (serialization) support for Graph objects
- Plotting functionality based on the Cairo graphics library (so you need to
  install python-cairo if you want to use it). Currently the following
  objects can be plotted: graphs, adjacency matrices and dendrograms. Some
  crude support for plotting histograms is also implemented. Plots can be
  saved in PNG, SVG and PDF formats.
- Unified Graph.layout method for accessing layout algorithms
- Added interfaces to walktrap community detection and the BLISS isomorphism
  algorithm
- Added dyad and triad census functionality and motif counting
- VertexSeq and EdgeSeq objects can now be restricted to subsets of the
  whole network (e.g., you can select vertices/edges based on attributes,
  degree, centrality and so on)

New in the C library
--------------------

- Many types (stack, matrix, dqueue, etc.) are templates now
  They were also rewritten to provide a better organized interface
- VF2 graph isomorphism routines can check subgraph isomorphism now,
  and they are able to return matching(s)
- The BLISS graph isomorphism algorithm is included in igraph now. See
  igraph_canonical_permutation, igraph_isomorphic_bliss
- We use ARPACK for eigenvalue/eigenvector calculation. This means that the
  following functions were rewritten: igraph_pagerank,
  igraph_community_leading_eigenvector_\*. New functions based on
  ARPACK: igraph_eigenvector_centrality, igraph_hub_score,
  igraph_authority_score, igraph_arpack_rssolve, igraph_arpack_rnsolve  
- Experimental C attribute interface added. I.e. it is possible to use
  graph/vertex/edge attributes from C code now.

- Edge weights for Fruchterman-Reingold layout.
- Line graph calculation.
- Kautz and de Bruijn graph generators
- Support for writing graphs in DOT format
- Jaccard and Dice similarity coefficients added
- igraph_count_multiple added
- igraph_is_loop and igraph_is_multiple "return" boolean vectors
- The graphopt layout algorithm was added, igraph_layout_graphopt
- Generation of "famous" graphs, igraph_famous
- Create graphs from LCF notation, igraph_lcf, igraph_lcf_vector
- igraph_add_edge adds a single edge to the graph
- Dyad census and triad cencus functions added
- igraph_is_simple added
- progress handlers are allowed to stop calculation
- igraph_full_citation to create full citation networks
- igraph_path_length_hist, create a histogram of path lengths
- forest fire model added
- DIMACS reader can handle different file types now
- Adjacency list types made public now (igraph_adjlist_t, igraph_adjedgelist_t)
- Biconnected components and articulation points can be computed
- Eigenvector centrality computation
- Kleinberg's hub and authority scores
- igraph_to_undirected handles attributes now
- Geometric random graph generator can return the coordinates of the vertices
- Function added to convert leading eigenvector community structure result to
  a membership vector (igraph_le_community_to_membership)
- Weighted fast greedy community detection
- Weighted page rank calculation
- Functions for estimating closeness, betweenness, edge betweenness by 
  introducing a cutoff for path lengths
- Weighted modularity calculation
- igraph_permute_vertices added
- Betweenness ans closeness calculations are speeded up
- Startup positions can be supplied to the Kamada-Kawai layout
  algorithms
- igraph_read_graph_\* functions can handle all possible line
  terminators now (\r, \n, \r\n, \n\r)
- Error handling was rewritten for walktrap community detection,
  the calculation can be interrupted now
- The maxflow/mincut functions allow to supply a null pointer for edge
  capacities, implying unit capacities for all edges

Bugs corrected in the C library
-------------------------------

- Memory leak fixed in adjacency list handling
- Memory leak fixed in maximal independent vertex set calculation
- Fixed a bug when rewiring undirected graphs with igraph_rewire
- Fixed edge betweenness community structure detection for unconnected graphs
- Make igraph compile with Sun Studio
- Betweenness bug fixed, when not computing for all vertices
- memory usage of clique finding reduced
- Corrected bugs for motif counts when not all motifs were counted,
  but a 'cut' vector was used
- Bugs fixed in trait games and cited type game
- Accept underscore as letter in GML files
- GML file directedness notation reversed, more logical this way

igraph 0.4.5
=========

Released January 1, 2008

New:
- Cohesive block finding in the R interface, thanks to Peter McMahan
  for contributing his code. See James Moody and Douglas R. White,
  2003, in Structural Cohesion and Embeddedness: A Hierarchical
  Conception of Social Groups American Sociological Review 68(1):1-25 
- Biconnected components and articulation points.
- R interface: better printing of attributes.
- R interface: graph attributes can be used via '$'.

New in the C library: 
- igraph_vector_bool_t data type.

Bug fixed:
- Erdos-Renyi random graph generators rewritten.

igraph 0.4.4
=========

Released October 3, 2007

This release should work seemlessly with the new R 2.6.0 version.
Some other bugs were also fixed:
- A bug was fixed in the Erdos-Renyi graph generator, which sometimes
  added an extra vertex.
- MSVC compilation issues were fixed.
- MinGW compilation fixes.

igraph 0.4.3
=========

Released August 13, 2007

The next one in the sequence of bugfix releases. Thanks to many people
sending bug reports. Here are the changes:
- Some memory leaks removed when using attributes from R or Python.
- GraphML parser: entities and character data in multiple chunks are now handled correctly.
- A bug corrected in edge betweenness community structure detection,
  it failed if called many times from the same program/session.
- Bug corrected in 'adjacent edges' edge iterator.
- Python interface: edge and vertex attribute deletion bug corrected.
- Edge betweeness community structure: handle unconnected graphs properly.
- Fixed bug related to fast greedy community detection in unconnected graphs.
- Use a different kind of parser (Push) for reading GraphML files. This is almost
  invisible for users but fixed a nondeterministic bug when reading in GraphML
  files.
- R interface: plot now handles properly if called with a vector as the edge.width
  argument for directed graphs.
- R interface: bug (typo) corrected for walktrap.community and weighted graphs.
- Test suite should run correctly on Cygwin now.

igraph 0.4.2
=========

Released June 7, 2007

This is another bugfix release, as there was a serious bug in the 
R package of the previous version: it could not read and write graphs
to files in any format under MS Windows.

Some other bits added: 
- circular Reingold-Tilford layout generator for trees
- corrected a bug, Pajek files are written properly under MS Windows now.
- arrow.size graphical edge parameter added in the R interface.

igraph 0.4.1
=========

Released May 23, 2007

This is a minor release, it corrects a number of bugs, mostly in the 
R package.

igraph 0.4
=========

Released May 21, 2007

The major new additions in this release is a bunch of community
detection algorithms and support for the GML file format. Here 
is the complete list of changes:


New in the C library
--------------------

- internal representation changed
- neighbors always returns an ordered list
- igraph_is_loop and igraph_is_multiple added

- topological sorting
- VF2 isomorphism algorithm
- support for reading the file format of the Graph Database for isomorphism
- igraph_mincut cat calculate the actual minimum cut
- girth calculation added, thanks to Keith Briggs
- support for reading and writing GML files

- Walktrap community detection algorithm added, thanks to Matthieu Latapy 
  and Pascal Pons
- edge betweenness based community detection algorithm added
- fast greedy algorithm for community detection by Clauset et al. added
  thanks to Aaron Clauset for sharing his code
- leading eigenvector community detection algorithm by Mark Newman added
- igraph_community_to_membership supporting function added, creates 
  a membership vector from a community structure merge tree
- modularity calculation added

New in the R interface
----------------------

- as the internal representation changed, graphs stored with 'save' 
  with an older igraph version cannot be read back with the new
  version reliably.
- neighbors returns ordered lists

- topological sorting
- VF2 isomorphism algorithm
- support for reading graphs from the Graph Database for isomorphism
- girth calculation added, thanks to Keith Briggs
- support for reading and writing GML files

- Walktrap community detection algorithm added, thanks to Matthieu Latapy 
  and Pascal Pons
- edge betweenness based community detection algorithm added
- fast greedy algorithm for community detection by Clauset et al. added
  thanks to Aaron Clauset for sharing his code  
- leading eigenvector community detection algorithm by Mark Newman added
- functions for creating denrdograms from the output of the 
  community detection algorithms added
- community.membership supporting function added, creates 
  a membership vector from a community structure merge tree
- modularity calculation added

- graphics parameter handling is completely rewritten, uniform handling 
  of colors and fonts, make sure you read ?igraph.plotting
- new plotting parameter for edges: arrow.mode
- a bug corrected when playing a nonlinear barabasi.game
- better looking plotting in 3d using rglplot: edges are 3d too
- rglplot layout is allowed to be two dimensional now
- rglplot suspends updates while drawing, this makes it faster
- loop edges are correctly plotted by all three plotting functions

- better printing of attributes when printing graphs
- summary of a graph prints attribute names
- is.igraph rewritten to make it possible to inherit from the 'igraph' class
- somewhat better looking progress meter for functions which support it

Others
------

- proper support for Debian packages (re)added
- many functions benefit from the new internal representation and are 
  faster now: transitivity, reciprocity, graph operator functions like 
  intersection and union, etc.
- igraph compiles with Microsoft Visual C++ now
- there were some internal changes to make igraph a real graph algorithm
  platform in the near future, but these are undocumented now

Bugs corrected
--------------

- corrected a bug when reading Pajek files: directed graphs were read as undirected

Debian package repository available
==================================

Debian Linux users can now install and update the C interface
using the standard package manager. Just add the following two
lines to /etc/apt/sources.list and install the libigraph and
libigraph-dev packages. Packages for the Python interface are
coming soon.

deb http://cneurocvs.rmki.kfki.hu /packages/binary/

deb-src http://cneurocvs.rmki.kfki.hu /packages/source/

igraph 0.3.3
============

Released February 28, 2007

New in the C library
--------------------

* igraph_connect_neighborhood, nomen est omen
* igraph_watts_strogatz_game and igraph_rewire_edges
* K-core decomposition: igraph_coreness
* Clique and independent vertex set related functions:
  igraph_cliques, igraph_independent_vertex_sets,
  igraph_maximal_cliques, igraph_maximal_independent_vertex_sets,
  igraph_independence_number, igraph_clique_number,
  Some of these function were ported from the very_nauty library
  of Keith Briggs, thanks Keith!
* The GraphML file format now supports graph attributes
* Transitivity calculation speeded up
* Correct transitivity calculation for multigraphs (ie. non-simple graphs)

New in the R interface
----------------------

* connect.neighborhood
* watts.strogatz.game and rewire.edges
* K-core decomposition: graph.coreness
* added the 'innei' and 'outnei' shorthands for vertex sequence indexing
  see help(iterators)
* Clique and independent vertex set related functions:
  cliques, largest.cliques, maximal.cliques, clique.number,
  independent.vertex.sets, largest.independent.vertex.sets,
  maximal.independent.vertex.sets, independence.number
* The GraphML file format now supports graph attributes
* edge.lty argument added to plot.igraph and tkplot
* Transitivity calculation speeded up
* Correct transitivity calculation for multigraphs (ie. non-simple graphs)
* alpha.centrality added, calculates Bonacich alpha centrality, see docs.

Bugs corrected
--------------

* 'make install' installs the library correctly on Cygwin now
* Pajek parser corrected to read files with MacOS newline characters correctly
* overflow bug in transitivity calculation for large graphs corrected 
* an internal memcpy/memmove bug causing some segfaults removed 
* R interface: tkplot bug with graphs containing a 'name' attribute
* R interface: attribute handling bug when adding vertices
* R interface: color selection bug corrected
* R interface: plot.igraph when plotting loops

Python interface documentation
====================

Jan 8, 2007

The documentation of the Python interface is available.
See section 'documentation' in the menu on the left.

igraph 0.3.2
=========

Released Dec 19, 2006

This is a new major release, it contains many new things:

Changes in the C library
------------------------

- igraph_maxdegree added, calculates the maximum degree in the graph
- igraph_grg_game, geometric random graphs
- igraph_density, graph density calculation
- push-relabel maximum flow algorithm added, igraph_maxflow_value
- minimum cut functions added based on maximum flow:
  igraph_st_mincut_value, igraph_mincut_value, the Stoer-Wagner
  algorithm is implemented for undirected graphs
- vertex connectivity functions, usually based on maximum flow:
  igraph_st_vertex_connectivity, igraph_vertex_connectivity
- edge connectivity functions, usually based on maximum flow:
  igraph_st_edge_connectivity, igraph_edge_connectivity
- other functions based on maximum flow: igraph_edge_disjoint_paths,
  igraph_vertex_disjoint_paths, igraph_adhesion, igraph_cohesion
- dimacs file format added
- igraph_to_directed handles attributes
- igraph_constraint calculation corrected, it handles weighted graphs
- spinglass-based community structure detection, the Joerg Reichardt --
  Stefan Bornholdt algorithm added: igraph_spinglass_community,
  igraph_spinglass_my_community
- igraph_extended_chordal_rings, it creates extended chordal rings
- 'no' argument added to igraph_clusters, it is possible to calculate
  the number of clusters without calculating the clusters themselves
- minimum spanning tree functions keep attributes now and also the 
  direction of the edges is kept in directed graphs
- there are separate functions to calculate different types of
  transitivity now
- igraph_delete_vertices rewritten to allocate less memory for the new
  graph 
- neighborhood related functions added: igraph_neighborhood,
  igraph_neighborhood_size, igraph_neighborhood_graphs
- two new games added based on different node types:
  igraph_preference_game and igraph_asymmetric_preference_game
- Laplacian of a graph can be calculated by the igraph_laplacian function

Changes in the R interface
--------------------------

- bonpow function ported from SNA to calculate Bonacich power centrality
- get.adjacency supports attributes now, this means that it sets the
  colnames  and rownames attributes and can return attribute values in
  the matrix instead of 0/1
- grg.game, geometric random graphs
- graph.density, graph density calculation
- edge and vertex attributes can be added easily now when added new
  edges with add.edges or new vertices with add.vertices
- graph.data.frame creates graph from data frames, this can be used to 
  create graphs with edge attributes easily
- plot.igraph and tkplot can plot self-loop edges now
- graph.edgelist to create a graph from an edge list, can also handle 
  edge lists with symbolic names
- get.edgelist has now a 'names' argument and can return symbolic
  vertex names instead of vertex ids, by default id uses the 'name'
  vertex attribute is returned 
- printing graphs on screen also prints symbolic symbolic names
  (the 'name' attribute if present)
- maximum flow and minimum cut functions: graph.maxflow, graph.mincut
- vertex and edge connectivity: edge.connectivity, vertex.connectivity
- edge and vertex disjoint paths: edge.disjoint.paths, 
  vertex.disjoint.paths
- White's cohesion and adhesion measure: graph.adhesion, graph.cohesion
- dimacs file format added
- as.directed handles attributes now
- constraint corrected, it handles weighted graphs as well now
- weighted attribute to graph.adjacency
- spinglass-based community structure detection, the Joerg Reichardt --
  Stefan Bornholdt algorithm added: spinglass.community
- graph.extended.chordal.ring, extended chordal ring generation
- no.clusters calculates the number of clusters without calculating
  the clusters themselves
- minimum spanning tree functions updated to keep attributes
- transitivity can calculate local transitivity as well
- neighborhood related functions added: neighborhood,
  neighborhood.size, graph.neighborhood
- new graph generators based on vertex types: preference.game and
  asymmetric.preference.game

Bugs corrected
--------------

- attribute handling bug when deleting edges corrected
- GraphML escaping and NaN handling corrected
- bug corrected to make it possible compile the R package without the 
  libxml2 library
- a bug in Erdos-Renyi graph generation corrected: it had problems 
  with generating large directed graphs
- bug in constraint calculation corrected, it works well now
- fixed memory leaks in igraph_read_graph_graphml
- error handling bug corrected in igraph_read_graph_graphml
- bug corrected in R version of graph.laplacian when normalized
  Laplacian is requested
- memory leak corrected in get.all.shortest.paths in the R package

igraph 0.2.1
=========

Released Aug 23, 2006

This is a bug-fix release. Bugs fixed:
- igraph_reciprocity (reciprocity in R) corrected to avoid segfaults
- some docs updates
- various R package updated to make it conform to the CRAN rules

igraph 0.2
=========

Released Aug 18, 2006

Release time at last! There are many new things in igraph 0.2, the
most important ones:
- reading writing Pajek and GraphML formats with attributes
  (not all Pajek and GraphML files are supported, see documentation
  for details)
- iterators totally rewritten, it is much faster and cleaner now
- the RANDEDU fast motif search algorithm is implemented
- many new graph generators, both games and regular graphs
- many new structural properties: transitivity, reciprocity, etc.
- graph operators: union, intersection, difference, structural holes, etc.
- conversion between directed and undirected graphs
- new layout algorithms for trees and large graphs, 3D layouts

and many more.

New things in the R package:
- support for CTRL+C
- new functions: Graph Laplacian, Burt's constraint, etc.
- vertex/edge sequences totally rewritten, smart indexing (see manual)
- new R manual and tutorial: 'Network Analysis with igraph', still 
  under development but useful
- very basic 3D plotting using OpenGL

Although this release was somewhat tested on Linux, MS Windows, Mac
OSX, Solaris 8 and FreeBSD, no heavy testing was done, so it might
contain bugs, and we kindly ask you to send bug reports to make igraph
better.

igraph mailing lists
====================

Aug 18, 2006

I've set up two igraph mailing lists: igraph-help for
general igraph questions and discussion and
igraph-anonunce for announcements. See 
http://lists.nongnu.org/mailman/listinfo/igraph-help and
http://lists.nongnu.org/mailman/listinfo/igraph-announce
for subscription information, archives, etc.

igraph 0.1
=========

Released Jan 30, 2006

After about a year of development this is the first "official" release 
of the igraph library. This release should be considered as beta 
software, but it should be useful in general. Please send your 
questions and comments.