igraph 2.2.1

Chore

• Fix ASAN checks.

• Add protection to fix rchk error.

Testing

• Improve centralitystress test (#2214).

• Fix flaky test.

igraph 2.2.0

Update C core to version 0.10.17. See https://github.com/igraph/rigraph/blob/20552ef94aed6ae4b23465ae8c7e4d3b0e558c71/src/vendor/cigraph/CHANGELOG.md for a complete changelog, in particular the section "Breaking changes".

Features

• Generate almost all R implementations (#2047).

• Expose align_layout() and add to layout_nicely() to align layout with axis automatically (#1907, #1957, #1958).

• Expose simple_cycles() which lists all simple cycles (#1573, #1580).

• Expose is_complete(), is_clique() and is_ivs() (#1316, #1388, #1581).

• Expose find_cycle() (#1471, #1571).

• Expose feedback_vertex_set() to find a minimum feedback vertex set in a graph (#1446, #1447, #1560).

• Add weights parameter to local_scan() (#1082, #1448, #1982).

• Add more layouts to tkplot() (#160, #1967).

• Add plot(mark.lwd = ) to change line width of mark.groups (#306, #1898).

• Add plot(vertex.label.angle = , vertex.label.adj = ) arguments to rotate vertex labels (#106, #1899).

• Add relative size scaling to vertices in plot() (@gvegayon, #172).

• Split sample_bipartite() into two functions for the G(n, m) and G(n, p) case (#630, #1692).

• Implement multi attribute assignment (#55, #1916) and adding attributes via data frames (#1373, #1669, #1716). Support factors in graph_from_data_frame() (#34, #1829).

• All _hrg() functions check their argument (#1074, #1699).

• HRG printing with type = "auto" uses "plain" for large trees (#1879).

• get_edge_ids() accepts data frames and matrices (#1663).

• igraph_version() returns version of C core in an attribute (#1208, #1781).

Breaking changes

• Breaking change: change arguments default and order for graph_from_lcf() (#1858, #1872).

• Breaking change: Subset assignment of a graph avoids addition of double edges and ignores loops unless the new loops argument is set to TRUE (#1662, #1661).

• Breaking change: remove deprecated neimode parameter from bfs() and dfs() (#1105, #1526).

• Breaking change: stricter deprecation of non-functional parameters of layout_with_kk() and layout_with_fr() (#1108, #1628).

Bug fixes

• NA attribute values are replaced with default values in plot() (#293, #1707).

• NA checking only in from/to columns of edge data frame (#1906).

• Keep vertex attribute type for disjoint_union() (#1640, #1909).

• Error in bipartite projection if type is not a vertex attribute (#898, #1889).

• Do not try to destroy non-initialized SIR objects upon error (#1888).

• Added proper NA handling for matrix inputs (#917, #918, #1828).

• Remove string matrix support from functions operating on biadjacency matrices (#1540, #1542, #1803).

• Integer vectors are validated before transferring them to the C library (#1434, #1582).

• Changed base location for graph_from_graphdb() and added tests (#1712, #1732).

• Recycling of logical vectors when indexing into edge/vertex selectors now throws an error (#848, #1731).

• Use function() instead of (x) in arrow.mode (#1722).

• Temporarily disable generating an interface for igraph_simple_cycles_callback() as the framework for handling callback functions is not yet present.

Plotting bug fixes

• Adjust loop position to vertex size in plot() (#1980).

• Don't rescale plot coordinates to [-1,1] x [-1,1] by default (#1492, #1956, #1962).

• Fail if "layout" attribute doesn't match the number of vertices (#1880).

• Automatically arrange loops in plot() (#407, #556, #1881).

• Vectorized drawing of arrows in plot() (#257, #1904).

• Allow more than one edge label font family in plot() (#37, #1896).

• Pie shapes now work as intended (#1882, #1883).

• Loops not plotted on canvas (#1799, #1800).

• Replace NA values in label attributes in plot() with default values (#1796, #1797).

• Removed duplicated plotting of arrow heads (#640, #1709).

• Correct mapping of edge label properties in plots when loops are present (#157, #1706).

Documentation

• Welcome Maëlle Salmon and David Schoch as authors (#1733), add author links (#1821).

• Remove demos (#2008).

• Add 2023 preprint (#1240, #1984).

• Update allcontributors info (#1975).

• Link to replacements of deprecated functions (#1823).

• Add documentation of all file formats to read_graph() and write_graph() (#777, #1969). Recommend saveRDS() and readRDS() for saving and loading graphs (#1242, #1700).

• Document return value of make_clusters() (#1794).

• Clarify that girth() returns Inf for acyclic graphs (@eqmooring, #1831).

• Clarify the use of weights in layout_with_kk().

• Refer to current latest version of R in troubleshooting page.

• Fix typos in laplacian_matrix() documentation.

• Document ellipsis in cohesion() (#971, #1985).

• Correct the description of the weights parameter of hits_scores().

• Better describe output of all_shortest_paths() (#1029, #1778).

• make_graph() now supports "Groetzsch" as an alias of "Grotzsch". This change was implemented in the C core.

• Update description of order parameter of ego() and related functions (#1746).

• Added lifecycle table (#1525).

• Add more about igraph.r2cdocs in the contributing guide (#1686, #1697).

Performance

• Accelerate check if an index sequence corresponds to the entire list of vertices (#1427, #1818).

• Faster single bracket querying of a graph (#1465, #1658).

igraph 2.1.4

Testing

• Tweak tests that use the graph package.

igraph 2.1.3

Features

• Use _pv destroy functions to satisfy ASAN checks (#1630).

• Use safe accessor to vector elements (#1633).

Chore

• Replace graph.isomorphic() with isomorphic() (#1583, #1623).

Documentation

• Convert plot.common.Rd to roxygen2 (#1424, #1636).

• Remove broken example from graph_from_graphdb() manual page (#1622, #1637).

• Document argument for NCOL format in read_graph() (#1621).

• Make documentation of disjoint_union() consistent with behavior (#1587, #1641).

• Add central note about experimental functions (#1624).

igraph 2.1.2

Bug fixes

• adjacent_vertices() and incident_edges() are now correct if the "return.vs.es" option is FALSE (@stibu81, #1605, #1606).

• Fix protection errors reported by rchk (#1592).

• Fix the incorrect handling of the sample parameter in sample_motifs() and ensure that the default sample.size is integer (#1568).

Documentation

• Clarify what type of graph each community detection function supports.

• Improve ?read_graph and ?write_graph documentation.

• Improve all_simple_paths() documentation.

• cluster_optimal() does support directed graphs.

Testing

• Test handling of "return.vs.es" in several functions (@stibu81, #1610).

igraph 2.1.1

See https://github.com/igraph/rigraph/blob/9828d7b11be330f994f07ae93a071b356eced903/src/vendor/cigraph/CHANGELOG.md for a complete changelog, in particular the section "Breaking changes".

Lifecycle

Breaking changes

• Breaking change: remove tkigraph from {igraph} proper (#1474).
• Breaking change: Hard-deprecate get.edge() and layout.grid.3d() which have been deprecated for 10 years (#1398).
• Breaking change: use rlang::arg_match() in igraph.match.arg() (#1165).

In-progress deprecations

We are working towards a more consistent interface, especially as regards function naming: ultimately we want the igraph functions to use snake case.
Please update your scripts and codebases as soon as you can.

• Deprecate eigen_centrality(scale = ) (#1543).
• Put deprecation message at the beginning not the end of the similarity functions (#1549).
• Add independence_number() as an alias of ivs_size() (#1522).
• Add get_edge_ids() as an alias of get.edge.ids() (#1510).
• Increase the deprecation signal to a warning for hub.score() and authority.score() both replaced by hits_scores() (#1352).
• Soft-deprecate erdos.renyi.game() and random.graph.game() (#1509).

Features

C library

• Update vendored C/igraph sources to igraph/igraph@d2e0f4e.

New functionality

• Add p.value and p.precision arguments to fit_power_law() to control the computation of the p-value (#1546, #1386).
• Add max_degree() (#1403).
• Add experimental sample_chung_lu() (#1416).
• Rename methods available for sample_degseq() and add the "edge.switching.simple" method (#1376).
• Weight support for eccentricity() and radius() (#1211).
• Add some argument checking to add_shape() (#1478).

More informative errors

• Export .from() etc. with behavior similar to dplyr::across() (#1436): functions like .from() are meant to be used inside [ but now if an user misuses them, the error is more informative.

Bug fixes

• Fix including diagonal elements in dense adjacency matrices (#1437).
• Align the body of graph.lattice() with its replacement make_lattice() (#1439).
• Use deprecated() as default value for circular argument to make_lattice() (#1431).
• subgraph_centrality() now ignores edge directions (#1414).
• Remove unintended type conversions when using disjoint_union() (#1375).
• Add missing PROTECT() (#1382).
• Fix reading of LGL and NCOL files (broken in 2.0.0) (#1347).
• Fixed potential memory leak in R_igraph_community_to_membership2() (#1367).

Documentation

• Update allcontributors table (#1552).
• Use mathjax for now (#1538).
• Improve the manual page of sample_() (#1477).
• Improve cross-links from make_() manual page (#1476).
• Update is_separator() documentation based on C docs (#1467).
• Add DOI to citation (#1450).
• Improve documentation of normalization methods for laplacian_matrix() (#1420).
• Fix typos in ?plot.common (@gvegayon) (#1413).
• Fix sample_degseq() example (#1297).
• Fix graph_from_adjacency_matrix() examples to avoid warnings (#1302).
• Replace \dontrun{} with @examplesIf (#1307).
• Improve sample_gnp() examples.
• Improve centralization docs.
• Further clarifications for betweenness() (#1489).
• Clarify how betweenness with cutoff is normalized.
• Fix centr_eigen_tmax() docs.
• Make edge_density() examples relevant.
• Improve eigen_centrality() documentation.
• Improved cluster_edge_betweenness() documentation.
• sample_forestfire() tests and example (#1318).

Developer-facing docs

• Add slightly tweaked boilerplate CONTRIBUTING.md (#1423).
• Update troubleshooting document.
• Use {devtag} for internal function docs (#1507).
• Make .igraph.progress() and .igraph.status() more internal (#1516).

Internal

• Prepare for libxml2 depending on bcrypt, use pkg-config (#1556, @kalibera).

igraph 2.0.3

See https://github.com/igraph/rigraph/blob/3299d31/src/vendor/cigraph/CHANGELOG.md for a complete changelog of the bundled C core, and https://github.com/igraph/rigraph/compare/f3fa58b..3299d31#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.)

Features

• GMP is no longer a dependency (#1256), libxml2 (#1282) and glpk are optional.
• Update vendored sources to igraph/igraph@857a125.
• New voronoi_cells() to compute the Voronoi partitioning of a graph (#1173).

Bug fixes

• Fix rglplot(edge_label = ) (#1267).

Continuous integration

• Run examples with sanitizer (#1288).
• Add scheduled builds.

Documentation

• Make x11() usage in example happen only in interactive sessions (#1301).
• Remove misleading comment about warning given as no warning is given (#1294).
• Improve min_st_separators() documentation (#1264).
• Add link to discussion forum (#1279) and logo (#1280).
• Add code finding duplicate @seealso, and use it (#1270).
• Remove duplicate @seealso from ?sample_pa (#1268).
• Remove incorrect claim about handling of complete graphs by is_separator() and is_min_separator() (#1263).
• Fix error messages mentioning to mention upgrade_graph() instead of the nonexisting upgrade_version() (#1252).
• Split is_bipartite() manual page from other manual page (#1230).
• Improve bug report template.
• CITATION.cff contains only the first three version components.
• Install lock workflow to lock stale discussions after one year (#1304).

Internal

• Replace use of deprecated barabasi.game() with sample_pa() (#1291).
• Auto-generate are_adjacent(), avoid deprecated igraph_are_connected() C function (#1254).

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).