igraph 1.4.2

Breaking changes

• Remove igraph.eigen.default() and eigen_defaults, introduce internal eigen_defaults() as a function (#741).

• Remove broken nexus*() functions (#705), and srand() (#701).

C core

• Update C core.

• ARPACK-based calculations are now interruptible.

• shortest_paths() and all_shortest_paths() no longer crash when an invalid from vertex is passed and weights are being used.

See diff for details.

Printing

• Use true vertex names for printing vertex sets. If a vertex set captures a relationship between vertices (e.g., the father component of bfs()), the vertex set is printed as a named vector (#754).

• Suggest restarting R session after fatal error (#745).

Bug fixes

• as_long_data_frame() now correctly processes vertex attributes and works with graphs without vertex attributes (#748).

• as.hclust(hrg.fit(g)) works again (#721).

Documentation

• The documentation is now available at https://igraph.org/ (#743).

• Reorganize function reference (#662).

• Replace graph() with make_graph() in examples (#738).

• Add docs for as.hclust.igraphHRG() (#733).

• Merged man page of hub_score() and authority_score() (#698).

• Refactor contributors listing (#647).

• Improve "family" titles (#679).

• Improve docs of ego/neighborhood functions.

• Improve transitivity() docs.

Internal

• Introduce cpp11 package to improve error handling in the long run (#720).

• Avoid longjmp for error handling and interrupts (#751).

• as.hclust.igraphHRG uses .Call() interface (#727).

igraph 1.4.1

Bug fixes

• console() now works again and provides a Tcl/Tk based UI where igraph can post status messages and progress info (#664).

• Fix errors when printing long vertex names (#677, @ahmohamed).

• Fix regression that broke builds on some systems (e.g., GCC version 5 or earlier), introduced in igraph 1.4.0 (#670, #671).

• fit_hrg() does not crash any more when called with a graph that has less than three vertices.

Documentation

• Various improvements (#663, @maelle; #667).

Internal

• Fix warning about yyget_leng() returning wrong type when using LTO (#676).

• Don't mention C++11 or C++17 for best compatibility with both newest R and older compilers, while still requesting a C++ compiler for linking.

• Don't ignore build/ when building the package because the vignette index is built there.

• Skip plot test entirely on R-devel.

• Avoid submodules for building igraph (#674).

• Makevars cleanup (#671).

• Add Zenodo configuration file.

igraph 1.4.0

Breaking changes

• Breaking change: Allow change of attribute type when setting attribute for all vertices or edges; only attributes of length 1 or the length of the target set allowed (#633).

Added

• tkplot() gained a palette argument and it is now using the same palette as plot() by default, for sake of consistency.
• plot.igraph() gained a loop.size argument that can be used to scale the common radius of the loop edges.

Fixed

• The default maximum number of iterations for ARPACK has been increased to 3000 to match that of the igraph C core.
• Rare convergence problems have been corrected in cluster_leading_eigen().
• All ARPACK-based functions now respect random seeds set in R when generating a random starting vector.
• igraph_version() returned an invalid value in 1.3.4, this is now corrected.
• The value of par(xpd=...) is now restored after plotting a graph.
• Fixed a bug in as.dendrogram.communities() for large dendrograms, thanks
  to @pkharchenko (see PR #292).
• Fixed two bugs in graph_from_incidence_matrix() that prevented the creation of directed graphs with mode="all" from dense or sparse matrices.
• dfs() accidentally returned zero-based root vertex indices in the result object; this is now fixed and the indices are now 1-based.
• as_graphnel() does not duplicate loop edges any more.
• convex_hull() now returns the vertices of the convex hull with 1-based indexing.
• Some rgl.*() function calls in the codebase were replaced with equivalent *3d() function calls in preparation for upcoming deprecations in rgl (see PR #619)
• plot.igraph() does not use the frame=... partial argument any more when calling plot.default(). The default NULL value of frame.plot is now also handled correctly.
• hub_score() and authority_score() considered self-loops only once on the diagonal of the adjacency matrix of undirected graphs, thus the result was not identical to that obtained by eigen_centrality() on loopy undirected graphs. This is now corrected.
• distances() no longer ignores the mode parameter when algorithm='johnson'.

Deprecated

• automorphisms() was renamed to count_automorphisms(); the old name is still available, but it is deprecated.

Other

• Documentation improvements.
• The Github repository was now moved to a single-branch setup where the package can be built from the main branch directly.
• Added igraph extended tutorial as an R vignette (#587).
• igraph now has a homepage based on pkgdown thanks to @maelle (see #645). This will eventually become the official homepage.

1.2.10

Fixed:

• The macOS versions of igraph were accidentally built without GraphML support on CRAN; this should now be fixed.

1.2.9

No user visible changes.

1.2.8

No user visible changes.

1.2.7

Added

• cluster_leiden() added as an interface to the Leiden community detection algorithm in the C core of igraph (#399.
• cluster_fluid_communities() added as an interface to the fluid communities algorithm of the C core of igraph (#454.

Fixed

• make_lattice() correctly rounds length to the nearest integer while printing a warning (#115.
• make_empty_graph(NULL) now prints an error instead of producing an invalid graph (#404).
• make_graph(c()) now produces an empty graph instead of printing a misleading error message (#431).
• Printing a graph where some edges have NA as the names of both endpoints does not produce a misleading error message any more (#410).
• The types argument of functions related to bipartite graphs now prints a warning when the types are coerced to booleans (#476).
• Betweenness normalisation no longer overflows (#442).
• layout_with_sugiyama() returns a layout of type matrix even if there is only one vertex in the graph (#408).
• Plotting a null graph (i.e. a graph with no vertices) does not throw an error any more (#387).

Deprecated

• The membership argument of modularity.matrix() is now deprecated as the function never needed it anyway.
• modularity() now prints a warning when it is applied on a directed graph because the implementation in igraph's C core does not support directed graphs as of version 0.8.5. The warning will be turned into an error in the next minor (1.3.0) version of the R interface; the error will be removed later when the C core is updated to a version that supports modularity for directed networks.
• transitivity() now prints a warning when its local variant (type="local") is called on a directed graph or a graph with multiple edges beecause the implementation in the C core of igraph does not work reliably in these cases as of version 0.8.5. The warning will be turned into an error in the next minor (1.3.0) version of the R interface; the error will be removed later when the C core is updated to a version that supports transitivity for networks with multiple edges.

Misc

• Documentation improvements.

1.2.6

No user visible changes. See NEWS.md for details.

1.1.0

See the NEWS.md file for a change log.