Merge branch 'cran-2.0.0'

igraph · Jan 23, 2024 · 016ccf1 · 016ccf1
2 parents 7be41f4 + 2572c9a
commit 016ccf1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: igraph
-Version: 1.99.99.9003
+Version: 2.0.0
 Title: Network Analysis and Visualization
 Authors@R: c(
     person("Gábor", "Csárdi", , "[email protected]", role = "aut",
@@ -16,6 +16,7 @@ Authors@R: c(
     person("Kirill", "Müller", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1416-3412")),
     person("Maëlle", "Salmon", role = "ctb"),
+    person("Michael", "Antonov", role = "ctb"),
     person("Chan Zuckerberg Initiative", role = "fnd")
   )
 Description: Routines for simple graphs and network analysis. It can

diff --git a/NEWS.md b/NEWS.md
@@ -1,63 +1,6 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
-# igraph 1.99.99.9003
-
-## Chore
-
-- Use proper version in cff file.
-
-- Declare system libraries as mandatory.
-
-- Final NEWS.
-
-## Documentation
-
-- Add description for `normalized` argument to `assortativity()` (#1153).
-
-- Improve Edge connectivity docs (#1119).
-
-## Testing
-
-- Add `as_biadjacency_matrix()` tests for named vectors (#1155).
-
-- Split as_biadjacency_matrix() tests (#1154).
-
-
-# igraph 1.99.99.9002
-
-## Testing
-
-  - Use specific skip() function (#1149).
-
-
-# igraph 1.99.99.9001
-
-## Chore
-
-  - Update vendored igraph/C to igraph/igraph@9de3ecdf0097ba01f6cc5f8ef5a6a58e6cf984a4 (#1130).
-
-  - Update vendored igraph/C to igraph/igraph@fb82a46e36cf9bf4851b6d17a58e4653b8769ad5 (#1129).
-
-  - Groom NEWS intro.
-
-  - Groom "Bug fixes" section in NEWS.
-
-  - Fix NEWS heading.
-
-## Documentation
-
-  - Add some missing diacritics.
-
-## Testing
-
-  - Prevent `decompose()` test from being reported as skipped (#1128).
-
-## tests
-
-  - Unskip all `is_tree()` tests (#1127).
-
-
-# igraph 1.99.99.9000
+# igraph 2.0.0
 
 This major release brings development in line with the C core at <https://github.com/igraph/igraph>.
 See <https://github.com/igraph/rigraph/blob/1bd2bf79/src/vendor/cigraph/CHANGELOG.md> for a complete changelog, in particular the section "Breaking changes".
@@ -86,6 +29,9 @@ The change log below is a summary of the additional changes in the R interface.
 
 - Use `lifecycle::deprecate_soft()` for most deprecated functions (#1024, #1025, #1104).
 
+- The system libraries GLPK, GMP, and libxml2 are now mandatory for compiling from source.
+
+
 ## Bug fixes
 
 - Add scalar conversion checks in a few critical places (#1069).
@@ -124,6 +70,10 @@ The change log below is a summary of the additional changes in the R interface.
 
 - Clarify that Infomap considers edge directions.
 
+- Improve edge connectivity docs (#1119).
+
+- Add some missing diacritics.
+
 ## Internal
 
 - Use `[]` assignment for converting matrices (#1035).
@@ -160,7 +110,7 @@ The change log below is a summary of the additional changes in the R interface.
 
 ## Testing
 
-- Remove top-level code in `test-indexing.R` (#1085).
+- Add `as_biadjacency_matrix()` tests for named vectors (#1154, #1155).
 
 - Test transferring colors in isomorphism functions (#1050).
 

diff --git a/R/community.R b/R/community.R
@@ -372,11 +372,7 @@ code.length <- function(communities) { # nocov start
 #' [igraph.plotting] on how to change the plot.
 #'
 #' @rdname communities
-#' @family community
-#' print.communities plot.communities
-#' length.communities
-#' as.dendrogram.communities as.hclust.communities
-#' showtrace code.length
+#' @family Community detection
 #' @param communities,x,object A `communities` object, the result of an
 #'   igraph community detection function.
 #' @param graph An igraph graph object, corresponding to `communities`.

diff --git a/R/make.R b/R/make.R
@@ -1753,7 +1753,7 @@ graph_from_lcf <- lcf_vector_impl
 #' S. L. Hakimi,
 #' On Realizability of a Set of Integers as Degrees of the Vertices of a Linear Graph,
 #' Journal of the SIAM 10, 3 (1962).
-#' \doi{https://doi.org/10.1137/0111010}
+#' \doi{10.1137/0111010}
 #'
 #' D. J. Kleitman and D. L. Wang,
 #' Algorithms for Constructing Graphs and Digraphs with Given Valences and Factors,

diff --git a/R/structural.properties.R b/R/structural.properties.R
@@ -1076,7 +1076,7 @@ all_shortest_paths <- function(graph, from,
 #' An algorithm for finding shortest routes from all source nodes to a given
 #' destination in general networks.
 #' Quarterly of Applied Mathematics. 27 (4): 526–530. (1970)
-#' <https://doi.org/10.1090/qam/253822>
+#' \doi{10.1090/qam/253822}
 #' @export
 #' @family structural.properties
 #' @seealso [shortest_paths()], [all_shortest_paths()]

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,4 @@
-Resubmission.
-
-igraph 1.6.0
+igraph 2.0.0
 
 ## R CMD check results
 
@@ -10,10 +8,5 @@ igraph 1.6.0
 
 ## Current CRAN check results
 
-- [x] Checked on 2023-12-06, problems found: https://cran.r-project.org/web/checks/check_results_igraph.html
-- [x] LTO issues to be fixed in igraph 2.0.0.
-- [x] WARN: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang
-     Found the following significant warnings:
-     rinterface_extra.c:255:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]: Fixed
-- [x] NOTE: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
-     checkRd: Lost braces: Fixed
+- [x] Checked on 2024-01-23, problems found: https://cran.r-project.org/web/checks/check_results_igraph.html
+- [x] LTO issues: fixed by updating the C core to igraph/C 0.10.
diff --git a/man/aaa-igraph-package.Rd b/man/aaa-igraph-package.Rd
diff --git a/man/communities.Rd b/man/communities.Rd
diff --git a/man/k_shortest_paths.Rd b/man/k_shortest_paths.Rd
diff --git a/man/realize_degseq.Rd b/man/realize_degseq.Rd
diff --git a/src/rinterface.c b/src/rinterface.c
@@ -11376,7 +11376,8 @@ SEXP R_igraph_stochastic_imitation(SEXP graph, SEXP vid, SEXP algo, SEXP quantit
 /*-------------------------------------------/
 / igraph_has_attribute_table                 /
 /-------------------------------------------*/
-SEXP R_igraph_has_attribute_table() {
+// FIXME: Change Stimulus to generate (void) instead of ()
+SEXP R_igraph_has_attribute_table(void) {
                                         /* Declarations */
   igraph_bool_t c_result;
   SEXP r_result;
@@ -11479,7 +11480,8 @@ SEXP R_igraph_vertex_path_from_edge_path(SEXP graph, SEXP start, SEXP edge_path,
 /*-------------------------------------------/
 / igraph_version                             /
 /-------------------------------------------*/
-SEXP R_igraph_version() {
+// FIXME: Change Stimulus to generate (void) instead of ()
+SEXP R_igraph_version(void) {
                                         /* Declarations */
   const char* c_version_string;
   int c_major;