chore: Update vendored sources to igraph/igraph@857a125

Author: krlmlr

R/aaa-auto.R

@@ -2835,6 +2835,18 @@ list_triangles_impl <- function(graph) {
   res
 }
 
+join_impl <- function(left, right) {
+  # Argument checks
+  ensure_igraph(left)
+  ensure_igraph(right)
+
+  on.exit( .Call(R_igraph_finalizer) )
+  # Function call
+  res <- .Call(R_igraph_join, left, right)
+
+  res
+}
+
 induced_subgraph_map_impl <- function(graph, vids, impl) {
   # Argument checks
   ensure_igraph(graph)
@@ -3744,6 +3756,17 @@ tree_from_parent_vector_impl <- function(parents, type=c("out", "in", "undirecte
   res
 }
 
+is_complete_impl <- function(graph) {
+  # Argument checks
+  ensure_igraph(graph)
+
+  on.exit( .Call(R_igraph_finalizer) )
+  # Function call
+  res <- .Call(R_igraph_is_complete, graph)
+
+  res
+}
+
 random_spanning_tree_impl <- function(graph, vid=0) {
   # Argument checks
   ensure_igraph(graph)

src/cpp11.cpp

@@ -8797,6 +8797,34 @@ SEXP R_igraph_list_triangles(SEXP graph) {
   return(r_result);
 }
 
+/*-------------------------------------------/
+/ igraph_join                                /
+/-------------------------------------------*/
+SEXP R_igraph_join(SEXP left, SEXP right) {
+                                        /* Declarations */
+  igraph_t c_res;
+  igraph_t c_left;
+  igraph_t c_right;
+  SEXP res;
+
+  SEXP r_result;
+                                        /* Convert input */
+  R_SEXP_to_igraph(left, &c_left);
+  R_SEXP_to_igraph(right, &c_right);
+                                        /* Call igraph */
+  IGRAPH_R_CHECK(igraph_join(&c_res, &c_left, &c_right));
+
+                                        /* Convert output */
+  IGRAPH_FINALLY(igraph_destroy, &c_res);
+  PROTECT(res=R_igraph_to_SEXP(&c_res));
+  IGRAPH_I_DESTROY(&c_res);
+  IGRAPH_FINALLY_CLEAN(1);
+  r_result = res;
+
+  UNPROTECT(1);
+  return(r_result);
+}
+
 /*-------------------------------------------/
 / igraph_induced_subgraph_map                /
 /-------------------------------------------*/
@@ -11119,6 +11147,30 @@ SEXP R_igraph_tree_from_parent_vector(SEXP parents, SEXP type) {
   return(r_result);
 }
 
+/*-------------------------------------------/
+/ igraph_is_complete                         /
+/-------------------------------------------*/
+SEXP R_igraph_is_complete(SEXP graph) {
+                                        /* Declarations */
+  igraph_t c_graph;
+  igraph_bool_t c_res;
+  SEXP res;
+
+  SEXP r_result;
+                                        /* Convert input */
+  R_SEXP_to_igraph(graph, &c_graph);
+                                        /* Call igraph */
+  IGRAPH_R_CHECK(igraph_is_complete(&c_graph, &c_res));
+
+                                        /* Convert output */
+  PROTECT(res=NEW_LOGICAL(1));
+  LOGICAL(res)[0]=c_res;
+  r_result = res;
+
+  UNPROTECT(1);
+  return(r_result);
+}
+
 /*-------------------------------------------/
 / igraph_random_spanning_tree                /
 /-------------------------------------------*/

src/rinterface.c

@@ -540,6 +540,24 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "aagon",
+      "name": "aagon",
+      "avatar_url": "https://avatars.githubusercontent.com/u/10883752?v=4",
+      "profile": "https://github.com/aagon",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "GanzuraTheConsumer",
+      "name": "Quinn Buratynski",
+      "avatar_url": "https://avatars.githubusercontent.com/u/19657136?v=4",
+      "profile": "https://github.com/GanzuraTheConsumer",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7

src/sources.mk

@@ -2,15 +2,28 @@
 
 ## [master]
 
+### Added
+
+ - `igraph_is_complete()` checks there is a connection between all pairs of vertices (experimental function, contributed by Aymeric Agon-Rambosson @aagon in #2510).
+
 ### Fixed
 
  - Fixed a corruption of the "finally" stack in `igraph_write_graph_gml()` for certain invalid GML files.
  - Fixed a memory leak in `igraph_write_graph_lgl()` when vertex names were present but edge weights were not.
  - Fixed the handling of duplicate edge IDs in `igraph_subgraph_from_edges()`.
  - Fixed conversion of sparse matrices to dense with `igraph_sparsemat_as_matrix()` when sparse matrix object did not make use of its full allocated capacity.
+ - `igraph_write_graph_ncol()` and `igraph_write_graph_lgl()` now refuse to write vertex names which would result in an invalid file that cannot be read back in.
+ - `igraph_write_graph_gml()` now ignores graph attributes called `edge` or `node` with a warning. Writing these would create an invalid GML file that igraph couldn't read back.
+ - `igraph_disjoint_union()` and `igraph_disjoint_union_many()` now check for overflow.
+ - `igraph_read_graph_graphml()` now correctly compares attribute values with certain expected values, meaning that prefixes of valid values of `attr.type` are not accepted any more.
+ - Empty IDs are not allowed any more in `<key>` tags of GraphML files as this is a violation of the GraphML specification.
+ - `igraph_is_separator()` and `igraph_is_minimal_separator()` now work correctly with disconnected graphs.
+ - `igraph_linegraph()` now considers self-loops to be self-adjacent in undirected graphs, bringing consistency with how directed graphs were already handled in previous versions.
 
 ### Other
 
+ - Performance: `igraph_degree()` now makes use of the cache when checking for self-loops.
+ - The performance of `igraph_is_minimal_separator()` was improved.
  - Documentation improvements.
 
 ## [0.10.10] - 2024-02-13

src/vendor/cigraph/.all-contributorsrc

@@ -96,6 +96,9 @@ to convince the project's developers of the merits of this feature.
 <a name="pull-requests"></a>
 ## Pull requests
 
+_**Note:** The wiki has a lot of useful information for newcomers, as well as a
+[quick start guide](https://github.com/igraph/igraph/wiki/Quickstart-for-new-contributors)!_
+
 Good pull requests - patches, improvements, new features - are a fantastic help.
 They should remain focused in scope and avoid containing unrelated commits.
 Please also take a look at our [tips on writing igraph code](#tips) before

src/vendor/cigraph/CHANGELOG.md

@@ -82,6 +82,8 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="https://github.com/larah19"><img src="https://avatars.githubusercontent.com/u/54937363?v=4?s=100" width="100px;" alt=""/><br /><sub><b>larah19</b></sub></a><br /><a href="https://github.com/igraph/igraph/commits?author=larah19" title="Code">💻</a></td>
     <td align="center"><a href="https://github.com/Biswa96"><img src="https://avatars.githubusercontent.com/u/31443074?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Biswapriyo Nath</b></sub></a><br /><a href="https://github.com/igraph/igraph/commits?author=Biswa96" title="Code">💻</a></td>
     <td align="center"><a href="http://cecinestpasunefromage.wordpress.com/"><img src="https://avatars.githubusercontent.com/u/2363820?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Gwyn Ciesla</b></sub></a><br /><a href="https://github.com/igraph/igraph/commits?author=limburgher" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/aagon"><img src="https://avatars.githubusercontent.com/u/10883752?v=4?s=100" width="100px;" alt=""/><br /><sub><b>aagon</b></sub></a><br /><a href="https://github.com/igraph/igraph/commits?author=aagon" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/GanzuraTheConsumer"><img src="https://avatars.githubusercontent.com/u/19657136?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Quinn Buratynski</b></sub></a><br /><a href="https://github.com/igraph/igraph/commits?author=GanzuraTheConsumer" title="Code">💻</a></td>
   </tr>
 </table>
 

src/vendor/cigraph/CONTRIBUTING.md

@@ -59,6 +59,8 @@ professorcode1 (@professorcode1)
 larah19 (@larah19)
 Biswapriyo Nath (@Biswa96)
 Gwyn Ciesla (@limburgher)
+aagon (@aagon)
+Quinn Buratynski (@GanzuraTheConsumer)
 
 This project follows the [all-contributors][1] specification. Contributions of any kind welcome!
 

src/vendor/cigraph/CONTRIBUTORS.md

@@ -794,7 +794,9 @@ IGRAPH_EXPORT int IGRAPH_FINALLY_STACK_SIZE(void);
 #define IGRAPH_CHECK_CALLBACK(expr, code) \
     do { \
         igraph_error_t igraph_i_ret = (expr); \
-        *(code) = igraph_i_ret; \
+        if (code) { \
+            *(code) = igraph_i_ret; \
+        } \
         if (IGRAPH_UNLIKELY(igraph_i_ret != IGRAPH_SUCCESS && igraph_i_ret != IGRAPH_STOP)) { \
             IGRAPH_ERROR("", igraph_i_ret); \
         } \

src/vendor/cigraph/CONTRIBUTORS.txt

@@ -78,6 +78,7 @@ IGRAPH_EXPORT igraph_error_t igraph_is_same_graph(const igraph_t *graph1, const
 IGRAPH_EXPORT IGRAPH_FUNCATTR_PURE igraph_bool_t igraph_i_property_cache_get_bool(const igraph_t *graph, igraph_cached_property_t prop);
 IGRAPH_EXPORT IGRAPH_FUNCATTR_PURE igraph_bool_t igraph_i_property_cache_has(const igraph_t *graph, igraph_cached_property_t prop);
 IGRAPH_EXPORT void igraph_i_property_cache_set_bool(const igraph_t *graph, igraph_cached_property_t prop, igraph_bool_t value);
+IGRAPH_EXPORT void igraph_i_property_cache_set_bool_checked(const igraph_t *graph, igraph_cached_property_t prop, igraph_bool_t value);
 IGRAPH_EXPORT void igraph_i_property_cache_invalidate(const igraph_t *graph, igraph_cached_property_t prop);
 IGRAPH_EXPORT void igraph_i_property_cache_invalidate_all(const igraph_t *graph);
 

src/vendor/cigraph/include/igraph_error.h

@@ -49,6 +49,8 @@ IGRAPH_EXPORT igraph_error_t igraph_union(igraph_t *res, const igraph_t *left, c
                                igraph_vector_int_t *edge_map1, igraph_vector_int_t *edge_map2);
 IGRAPH_EXPORT igraph_error_t igraph_union_many(igraph_t *res, const igraph_vector_ptr_t *graphs,
                                     igraph_vector_int_list_t *edgemaps);
+IGRAPH_EXPORT igraph_error_t igraph_join(igraph_t *res, const igraph_t *left,
+                                         const igraph_t *right);
 IGRAPH_EXPORT igraph_error_t igraph_intersection(igraph_t *res,
                                       const igraph_t *left, const igraph_t *right,
                                       igraph_vector_int_t *edge_map1,

src/vendor/cigraph/include/igraph_interface.h

@@ -85,6 +85,7 @@ IGRAPH_EXPORT igraph_error_t igraph_is_perfect(const igraph_t *graph, igraph_boo
 /* Structural properties                              */
 /* -------------------------------------------------- */
 
+IGRAPH_EXPORT igraph_error_t igraph_is_complete(const igraph_t *graph, igraph_bool_t *res);
 IGRAPH_EXPORT igraph_error_t igraph_minimum_spanning_tree(const igraph_t *graph, igraph_vector_int_t *res,
                                                const igraph_vector_t *weights);
 IGRAPH_EXPORT igraph_error_t igraph_minimum_spanning_tree_unweighted(const igraph_t *graph,

src/vendor/cigraph/include/igraph_operators.h

@@ -2002,6 +2002,9 @@ igraph_disjoint_union:
 igraph_disjoint_union_many:
     PARAMS: OUT GRAPH res, GRAPH_PTR_LIST graphs
 
+igraph_join:
+    PARAMS: OUT GRAPH res, GRAPH left, GRAPH right
+
 igraph_union:
     PARAMS: |-
         OUT GRAPH res, GRAPH left, GRAPH right,
@@ -2512,6 +2515,9 @@ igraph_to_prufer:
 igraph_tree_from_parent_vector:
     PARAMS: OUT GRAPH graph, INDEX_VECTOR parents, TREE_MODE type=OUT
 
+igraph_is_complete:
+    PARAMS: GRAPH graph, OUT BOOLEAN res
+
 igraph_minimum_spanning_tree:
     PARAMS: GRAPH graph, OUT EDGE_INDICES res, EDGEWEIGHTS weights=NULL
     DEPS: res ON graph, weights ON graph

src/vendor/cigraph/include/igraph_structural.h

@@ -231,6 +231,7 @@ add_library(
   operators/difference.c
   operators/disjoint_union.c
   operators/intersection.c
+  operators/join.c
   operators/misc_internal.c
   operators/permute.c
   operators/reverse.c
@@ -258,6 +259,7 @@ add_library(
   paths/widest_paths.c
 
   properties/basic_properties.c
+  properties/complete.c
   properties/constraint.c
   properties/convergence_degree.c
   properties/dag.c

src/vendor/cigraph/interfaces/functions.yaml

@@ -460,8 +460,8 @@ static igraph_error_t igraph_i_eigenvector_centrality_directed(const igraph_t *g
  * </para><para>
  * In the weighted case, the eigenvector centrality of a vertex is proportional
  * to the weighted sum of centralities of its neighbours, i.e.
- * <code>c_i = sum_j w_ij c_j</code>, where <code>w_ij</code> is the weight
- * of the edge connecting vertices \c i and \c j. The weights of parallel edges
+ * <code>c_j = sum_i w_ij c_i</code>, where <code>w_ij</code> is the weight
+ * of the edge connecting vertex \c i to \c j. The weights of parallel edges
  * are added up.
  *
  * </para><para>

src/vendor/cigraph/src/CMakeLists.txt

@@ -168,8 +168,8 @@ static igraph_error_t igraph_i_find_k_indsets(
  * Patric R. J. Östergård, http://users.aalto.fi/~pat/cliquer.html
  *
  * \param graph The input graph.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \param min_size Integer specifying the minimum size of the cliques to be
  *   returned. If negative or zero, no lower bound will be used.
  * \param max_size Integer specifying the maximum size of the cliques to be
@@ -280,8 +280,8 @@ igraph_error_t igraph_cliques_callback(const igraph_t *graph,
  * \param vertex_weights A vector of vertex weights. The current implementation
  *   will truncate all weights to their integer parts. You may pass \c NULL
  *   here to make each vertex have a weight of 1.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \param min_weight Integer specifying the minimum weight of the cliques to be
  *   returned. If negative or zero, no lower bound will be used.
  * \param max_weight Integer specifying the maximum weight of the cliques to be
@@ -326,8 +326,8 @@ igraph_error_t igraph_weighted_cliques(const igraph_t *graph,
  * \param vertex_weights A vector of vertex weights. The current implementation
  *   will truncate all weights to their integer parts. You may pass \c NULL
  *   here to make each vertex have a weight of 1.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \return Error code.
  *
  * \sa \ref igraph_weighted_cliques(), \ref igraph_weighted_clique_number(), \ref igraph_largest_cliques()
@@ -413,8 +413,8 @@ static igraph_error_t igraph_i_maximal_or_largest_cliques_or_indsets(
  * 6:505--517, 1977.
  *
  * \param graph The input graph.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \param min_size Integer specifying the minimum size of the sets to be
  *   returned. If negative or zero, no lower bound will be used.
  * \param max_size Integer specifying the maximum size of the sets to be
@@ -537,8 +537,8 @@ igraph_error_t igraph_independent_vertex_sets(const igraph_t *graph,
  * 6:505--517, 1977.
  *
  * \param graph The input graph.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \return Error code.
  *
  * \sa \ref igraph_independent_vertex_sets(), \ref
@@ -758,8 +758,8 @@ static void free_set_array(igraph_set_t *array, igraph_integer_t n) {
  * use \ref igraph_independence_number() instead.
  *
  * \param graph The input graph.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \return Error code.
  *
  * \sa \ref igraph_maximal_cliques(), \ref
@@ -948,8 +948,8 @@ static igraph_error_t igraph_i_largest_cliques_store(const igraph_vector_int_t*
  * these two versions.
  *
  * \param graph The input graph.
- * \param res Pointer to a list of integer vectors, the result will be stored
- *   here. The pointer vector will be resized if needed.
+ * \param res Pointer to an initialized list of integer vectors. The cliques
+ *   will be stored here as vectors of vertex IDs.
  * \return Error code.
  *
  * \sa \ref igraph_cliques(), \ref igraph_maximal_cliques()

src/vendor/cigraph/src/centrality/eigenvector.c

@@ -339,11 +339,8 @@ static igraph_error_t igraph_i_maximal_cliques_up(
  * almost surely be different between these three versions.
  *
  * \param graph The input graph.
- * \param res Pointer to a pointer vector, the result will be stored
- *   here, i.e. \p res will contain pointers to \ref igraph_vector_int_t
- *   objects which contain the indices of vertices involved in a clique.
- *   The pointer vector will be resized if needed but note that the
- *   objects in the pointer vector will not be freed. Note that vertices
+ * \param res Pointer to list of integer vectors. The maximal cliques
+ *   will be returned here as vectors of vertex IDs. Note that vertices
  *   of a clique may be returned in arbitrary order.
  * \param min_size Integer giving the minimum size of the cliques to be
  *   returned. If negative or zero, no lower bound will be used.

src/vendor/cigraph/src/cliques/cliques.c

@@ -341,6 +341,8 @@ static igraph_error_t igraph_i_split_join_distance(const igraph_vector_int_t *v1
  * <code>VI(C_1, C_2) = [H(C_1) - MI(C_1, C_2)] + [H(C_2) - MI(C_1, C_2)]</code>.
  * Lower values of the variation of information indicate a smaller difference between
  * the two clusterings, with <code>VI = 0</code> achieved precisely when they coincide.
+ * igraph uses natural units for the variation of information, i.e. it uses the
+ * natural logarithm when computing entropies.
  *
  * </para><para>
  * The Rand index is defined as the probability that the two clusterings agree

src/vendor/cigraph/src/cliques/maximal_cliques.c

@@ -696,7 +696,7 @@ igraph_error_t igraph_community_fastgreedy(const igraph_t *graph,
     } else {
         debug("Calculating degrees\n");
         IGRAPH_VECTOR_INT_INIT_FINALLY(&degrees, no_of_nodes);
-        IGRAPH_CHECK(igraph_degree(graph, &degrees, igraph_vss_all(), IGRAPH_ALL, 1));
+        IGRAPH_CHECK(igraph_degree(graph, &degrees, igraph_vss_all(), IGRAPH_ALL, true));
         for (i = 0; i < no_of_nodes; i++) {
             VECTOR(a)[i] = VECTOR(degrees)[i];
         }