chore: Update vendored sources to igraph/igraph@a166195

chore: updated changelog
chore: updated changelog
chore: run pre-commit hooks
chore: bump VERSION property in shared library
fix: fix self-loops handling during simple cycle detection, closes igraph/igraph#2692
Revert "fix: temporary fix for simple cycle search mishandling self-loops, ref igraph/igraph#2692"
fix: temporary fix for simple cycle search mishandling self-loops, ref igraph/igraph#2692
test: minimum cycle length for igraph_simple_cycles()
refactor: do not use vector_get() in simple cycle finder
refactor: cleaner parameter ordering in igraph_i_simple_cycles_circuit()
refactor: support specifying a minimum cycle length in `igraph_simple_cycles()`
interface: loops=True default for igraph_degree()
chore: updated contributors list

R/aaa-auto.R

@@ -3580,15 +3580,16 @@ find_cycle_impl <- function(graph, mode=c("out", "in", "all", "total")) {
   res
 }
 
-simple_cycles_impl <- function(graph, mode=c("out", "in", "all", "total"), max.cycle.length=-1) {
+simple_cycles_impl <- function(graph, mode=c("out", "in", "all", "total"), min.cycle.length=-1, max.cycle.length=-1) {
   # Argument checks
   ensure_igraph(graph)
   mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
+  min.cycle.length <- as.numeric(min.cycle.length)
   max.cycle.length <- as.numeric(max.cycle.length)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
-  res <- .Call(R_igraph_simple_cycles, graph, mode, max.cycle.length)
+  res <- .Call(R_igraph_simple_cycles, graph, mode, min.cycle.length, max.cycle.length)
   if (igraph_opt("return.vs.es")) {
     res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph))
   }

src/cpp11.cpp

@@ -401,7 +401,7 @@ extern SEXP R_igraph_similarity_inverse_log_weighted(SEXP, SEXP, SEXP);
 extern SEXP R_igraph_similarity_jaccard(SEXP, SEXP, SEXP, SEXP);
 extern SEXP R_igraph_similarity_jaccard_es(SEXP, SEXP, SEXP, SEXP);
 extern SEXP R_igraph_similarity_jaccard_pairs(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_simple_cycles(SEXP, SEXP, SEXP);
+extern SEXP R_igraph_simple_cycles(SEXP, SEXP, SEXP, SEXP);
 extern SEXP R_igraph_simple_interconnected_islands_game(SEXP, SEXP, SEXP, SEXP);
 extern SEXP R_igraph_simplify(SEXP, SEXP, SEXP, SEXP);
 extern SEXP R_igraph_simplify_and_colorize(SEXP);
@@ -856,7 +856,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_similarity_jaccard",                         (DL_FUNC) &R_igraph_similarity_jaccard,                          4},
     {"R_igraph_similarity_jaccard_es",                      (DL_FUNC) &R_igraph_similarity_jaccard_es,                       4},
     {"R_igraph_similarity_jaccard_pairs",                   (DL_FUNC) &R_igraph_similarity_jaccard_pairs,                    4},
-    {"R_igraph_simple_cycles",                              (DL_FUNC) &R_igraph_simple_cycles,                               3},
+    {"R_igraph_simple_cycles",                              (DL_FUNC) &R_igraph_simple_cycles,                               4},
     {"R_igraph_simple_interconnected_islands_game",         (DL_FUNC) &R_igraph_simple_interconnected_islands_game,          4},
     {"R_igraph_simplify",                                   (DL_FUNC) &R_igraph_simplify,                                    4},
     {"R_igraph_simplify_and_colorize",                      (DL_FUNC) &R_igraph_simplify_and_colorize,                       1},

src/rinterface.c

@@ -10968,12 +10968,13 @@ SEXP R_igraph_find_cycle(SEXP graph, SEXP mode) {
 /*-------------------------------------------/
 / igraph_simple_cycles                       /
 /-------------------------------------------*/
-SEXP R_igraph_simple_cycles(SEXP graph, SEXP mode, SEXP max_cycle_length) {
+SEXP R_igraph_simple_cycles(SEXP graph, SEXP mode, SEXP min_cycle_length, SEXP max_cycle_length) {
                                         /* Declarations */
   igraph_t c_graph;
   igraph_vector_int_list_t c_vertices;
   igraph_vector_int_list_t c_edges;
   igraph_neimode_t c_mode;
+  igraph_integer_t c_min_cycle_length;
   igraph_integer_t c_max_cycle_length;
   SEXP vertices;
   SEXP edges;
@@ -10986,10 +10987,12 @@ SEXP R_igraph_simple_cycles(SEXP graph, SEXP mode, SEXP max_cycle_length) {
   IGRAPH_R_CHECK(igraph_vector_int_list_init(&c_edges, 0));
   IGRAPH_FINALLY(igraph_vector_int_list_destroy, &c_edges);
   c_mode = (igraph_neimode_t) Rf_asInteger(mode);
+  IGRAPH_R_CHECK_INT(min_cycle_length);
+  c_min_cycle_length = (igraph_integer_t) REAL(min_cycle_length)[0];
   IGRAPH_R_CHECK_INT(max_cycle_length);
   c_max_cycle_length = (igraph_integer_t) REAL(max_cycle_length)[0];
                                         /* Call igraph */
-  IGRAPH_R_CHECK(igraph_simple_cycles(&c_graph, &c_vertices, &c_edges, c_mode, c_max_cycle_length));
+  IGRAPH_R_CHECK(igraph_simple_cycles(&c_graph, &c_vertices, &c_edges, c_mode, c_min_cycle_length, c_max_cycle_length));
 
                                         /* Convert output */
   PROTECT(r_result=NEW_LIST(2));

src/vendor/cigraph/.all-contributorsrc

@@ -594,6 +594,24 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "GenieTim",
+      "name": "Tim Bernhard",
+      "avatar_url": "https://avatars.githubusercontent.com/u/8596965?v=4",
+      "profile": "https://github.com/GenieTim",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "maelle",
+      "name": "Maëlle Salmon",
+      "avatar_url": "https://avatars.githubusercontent.com/u/8360597?v=4",
+      "profile": "https://masalmon.eu/",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7

src/vendor/cigraph/CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## [master]
 
+## [0.10.15]
+
 ### Added
 
  - `igraph_bitset_update()` copies the contents of one bitset into another (experimental function).
@@ -1445,7 +1447,8 @@ Some of the highlights are:
  - Provide proper support for Windows, using `__declspec(dllexport)` and `__declspec(dllimport)` for `DLL`s and static usage by using `#define IGRAPH_STATIC 1`.
  - Provided integer versions of `dqueue` and `stack` data types.
 
-[master]: https://github.com/igraph/igraph/compare/0.10.13..master
+[master]: https://github.com/igraph/igraph/compare/0.10.15..master
+[0.10.15]: https://github.com/igraph/igraph/compare/0.10.13..0.10.15
 [0.10.13]: https://github.com/igraph/igraph/compare/0.10.12..0.10.13
 [0.10.12]: https://github.com/igraph/igraph/compare/0.10.11..0.10.12
 [0.10.11]: https://github.com/igraph/igraph/compare/0.10.10..0.10.11