rigraph - igraph 2.1.4

Testing

• Tweak tests that use the graph package.

- R
Published by github-actions[bot] about 1 year ago

rigraph - 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).

- R
Published by github-actions[bot] about 1 year ago

rigraph - 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).

- R
Published by github-actions[bot] about 1 year ago

rigraph - 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@d2e0f4eb567dfc505227c346a015bef574c4ccd1.

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).

- R
Published by krlmlr over 1 year ago

rigraph - 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@857a125069c226f266562b3781b82833fe1d59d9.
• 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).

- R
Published by krlmlr over 1 year ago

rigraph - 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).

- R
Published by github-actions[bot] about 2 years ago

rigraph - igraph 2.0.1.1

Bug fixes

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

- R
Published by github-actions[bot] about 2 years ago

rigraph - igraph 2.0.1

Bug fixes

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

- R
Published by github-actions[bot] about 2 years ago

rigraph - igraph 1.6.0

- R
Published by github-actions[bot] about 2 years ago

rigraph - 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).

- R
Published by github-actions[bot] over 2 years ago

rigraph - igraph 1.5.0.1

• Remove ETIME() call from Fortran code.

- R
Published by krlmlr over 2 years ago

rigraph - 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).

- R
Published by krlmlr over 2 years ago

rigraph - 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).

- R
Published by krlmlr over 2 years ago

rigraph - 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).

- R
Published by github-actions[bot] almost 3 years ago

rigraph - 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.

- R
Published by krlmlr almost 3 years ago

rigraph - 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.

- R
Published by ntamas about 3 years ago

rigraph - 1.2.10

Fixed:

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

- R
Published by ntamas about 4 years ago

rigraph - 1.2.9

No user visible changes.

- R
Published by ntamas about 4 years ago

rigraph - 1.2.8

No user visible changes.

- R
Published by ntamas over 4 years ago

rigraph - 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.

- R
Published by ntamas over 4 years ago

rigraph -

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

- R
Published by vtraag over 5 years ago

rigraph - 1.1.0

See the NEWS.md file for a change log.

- R
Published by gaborcsardi almost 9 years ago