igraph 2.0.2

See https://github.com/igraph/rigraph/blob/f3fa58b/src/vendor/cigraph/CHANGELOG.md for a complete changelog of the bundled C core, and https://github.com/igraph/rigraph/compare/1bd2bf79..f3fa58b#diff-aeb78e0159780a9b26daabaf6f95f450b0cfec7161fc735f27ad69145a57dc84 for the changes since the igraph 2.0.1.
(A permanent link to the most recent changelog of the C core used in the R package is
https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md.)

Bug fixes

• g + vertices(1, 2, foo = 3) works again, regression introduced in igraph 2.0.0 (#1247).
• sample_pa() respects the out.seq and out.dist arguments again, regression introduced in igraph 2.0.0 (#1226).
• isomorphisms() and subgraph_isomorphisims(method = "vf2") work again, regression introduced in 2.0.0 (#1219).
• biconnected_components() now returns edge and vertex sequences again, regression introduced in 2.0.0 (#1213).
• Remove zeros from the order and order.out components returned by dfs(), regression introduced in 2.0.0 (#1179).
• Memory leaks when converting data to C (#1196).

Features

• realize_bipartite_degseq() creates a bipartite graph from two degree sequences (#1212).
• is_biconnected() checks if a graph is biconnected (#1204).
• distances() now supports the Floyd-Warshall algorithm (#1186).

Documentation

• Use more culturally diverse names in intro vignettes (#1246).
• Formatting tweaks in introductory vignettes (#1243).
• Recommend {pak} instead of {remotes} (#1228).
• Fix typo in mean_distance() docs.
• Update troubleshooting document, emphasize issues with Anaconda environments (#1209).
• Improved docs for shortest path functions (#1201).
• Document "dsatur" heuristic for greedy_vertex_coloring() (#1206).
• Remove scg related docs (#1167).
• Fix typo in ?articulation_points (#1191).
• Improve installation and troubleshooting instructions (#1184).
• Improve docs of assortativity (#1151).

Testing

• Add tests for isomorphisms() and subgraph_isomorphisms() (#1225).

Packaging

• Always use bundled mini-gmp (#1233).
• config.h defines HAVE___UINT128_T (#1216).
• Do not rely on which program during configuration (#1232).
• configure manage libxml multiple include paths (#1197).
• Remove empty string in configure (#1235).
• Link Fortran runtime on Windows as needed by arpack. (#1215).
• Workaround for deprecated enum values not being supported with old GCC (#1205).
• HAVE_GFORTRAN flag for win and ucrt (#1171).
• make_empty_graph() is now fully auto-generated (#1068).
• Eliminate manual edits from autogenerated files (#1207).
• Add read-only comments for RStudio IDE (#1152).

Internal

• Remove unused patch files (#1234).
• Update stimulus to 0.21.4 (#1210).
• Avoid duplicate objects (#1223).
• Eliminate a compiler warning from simpleraytracer (#1185).

igraph 2.0.1.1

Bug fixes

• Avoid is.R() which is deprecated in R 4.4.0.

igraph 2.0.1

Bug fixes

• Use cpp11 for simpleraytracer glue to avoid -Wlto warnings (#1163).

igraph 1.6.0

## Breaking changes

- New `arpack_defaults()` replaces `igraph.arpack.default` and `arpack_defaults` lists (#800), with consistent usage checks (#966).

- Define methods for `ape::as.phylo()` instead of own `as_phylo()` generic, remove deprecated `asPhylo()` (#763).

- `bfs()` with unreachable nodes returns zero instead of `NaN` as `rank` (#956), and negative instead of `NaN` for `dist` (#926).

- `random_walk()` adds one more step, the resulting list of vertices is of length `steps + 1` (#934).

- `girth()` returns `Inf` for acyclic graphs (#931).

- Remove some behaviour / parameters that were deprecated in 1.3 (#842).

- Remove `scg_eps()`, `scg_group()` and `scg_semi_proj()`, broken and no longer maintained (#946).

## Bug fixes

- Fix `printf()` warning (#975).

- Fix calls to `isSymmetric()` for matrix objects with a class (#965).

- Reduce frequency of interruption checks (#957).

## Features

- Change "incidence matrix" naming to "biadjacency matrix" (#962).

- Add aliases using the neighborhood terminology for all ego functions: (#950).

- Rename arguments to `assortativity(values, values.in)` from `types1` and `types2` (#952).

- Add ellipsis to `cluster_label_prop()` (#954).

- Placeholders for `is_acyclic()` and `is_forest()`, to be implemented in igraph 2.0.0 (#945).

- `is_tree(details = TRUE)` designates the first vertex as root for non-trees (#935).

- `all_shortest_paths()` returns the vertex list in both `res` and `vpaths` components (#930).

- Improve symmetry check for adjacency matrices on input (#911).

- Warn if non-symmetric undirected adjacency matrix (#904).

## Documentation

- Remove duplicate `\seealso{}` (#948).

- Update `knnk()` and `sir()` docs.

- Fix formula in `reciprocity()` docs.

- `strength()` does not give a warning when no weights are given.

- Update `sample_smallworld()` manual page (#895).

- Correct documentation for weighted cliques.

- Update Erdos-Renyi model docs.

## Testing

- Clean up tests (#967).

- Stabilize tests for `cluster_label_prop()` (#932), `sample_pa()` (#927), `cluster_louvain()` (#933), SIR (#936), `sample_forestfire()` (#929).

- Hard-code graph used in test (#928).

- Update GML test file (#925).

- Improve test for sampling from Dirichlet distribution (#923).

- Omit test that no longer holds with igraph 0.10 (#922).

- Stabilize test in preparation for upgrade (#920).

- Stabilize plot test (#919).

- Fix checks.

igraph 1.5.1

Breaking changes

• Breaking change: start deprecation of estimate_betweenness(), estimate_edge_betweenness(), estimate_closeness() (#852).

Bug fixes

• identical_graphs() now correctly detects identical graphs without node or edge attributes (#757).

Internal

• Change ownership rules of attribute objects (#870).

• R_SEXP_to_igraph() and R_SEXP_to_igraph_copy() get igraph_t object from external pointer (#865).

• Remove ETIME() call from Fortran code, already in CRAN version 1.5.0.1 (#858).

• Ensure that _GNU_SOURCE is always defined (#877).

• Fix make clean (#860).

• Fix generation of code for functions with VERTEX_COLOR out-arguments (#850).

• Use -lquadmath in Makevars.win, for compatibility with alternative R distributions such as Microsoft R Open (#855).

• getRversion() uses strings.

Documentation

• Add cffr file and a GHA workflow that updates it automatically (#873).

• Undeprecate neighborhood() (#851).

• Remove redundant reference to AUTHORS from DESCRIPTION.

Refactoring

• Breaking change: start deprecation of estimate_betweenness(), estimate_edge_betweenness(), estimate_closeness() (#852).

igraph 1.5.0.1

• Remove ETIME() call from Fortran code.

igraph 1.5.0

Breaking changes

The internal format of graph objects has changed in a mostly backward-compatible way, to prepare for upgrading the C core to 0.10. Details are described at https://github.com/igraph/rigraph/wiki/The-igraph-object-format. Accessing graph objects that have been created with an older igraph version give a clean error message with instructions (#832). The new format cannot be read by igraph 1.4.3 or older, the following error is raised when trying to do so:

This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
Error in is_directed(object) : 
  REAL() can only be applied to a 'numeric', not a 'NULL'

The only supported remedy is to upgrade the igraph package to version 1.5.0 or later.

graph_version() now returns an integer scalar (#832, #847), 4 as of igraph 1.5.0 (#835).

Features

• Vertex and edge sequences are converted to numeric vectors when used in attributes (#808).

• New largest_component() returns the largest connected component (#786, @ngmaclaren).

Bug fixes

• Fix error message in make_graph() when simplify = ... is used with a non-formula (#834).

Testing

• Add more tests for graph_from_literal() (#826).

• Reenable serialization test and tests for dyad_census(), stabilize tests (#809, #822, #823).

Documentation

• The documentation for the R package is now hosted at https://r.igraph.org/ (#780).

• Update vignette("installation-troubleshooting").

• Fix use of deprecated functions in examples, e.g., replace gsize() by ecount() (#827).

• Fix typos in ?eigen_centrality docs (@JJ).

• Update CONTRIBUTING.md and ORCID information (#791, #774).

• Add DOI to CITATION (#773).

Internal

• Add data for old igraph versions as constructed objects, and tests (#838).

• Ensure we're always using named indexes to access the internal data structure (#784).

• Prepare migration to igraph/C 0.10 (#781).

• Update generated interface (#765).

igraph 1.4.3

Internal

• Fix tests for dev waldo (#779, @hadley).

• Fix linking on Windows: gfortran needs quadmath. (#778).

Documentation

• Mention limitation of Pajek reader (#776).

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.