chore: update C core and regenerate interfaces (#1237)

R/aaa-auto.R

@@ -927,7 +927,7 @@ widest_path_widths_floyd_warshall_impl <- function(graph, from=V(graph), to=V(gr
   res
 }
 
-spanner_impl <- function(graph, stretch, weights) {
+spanner_impl <- function(graph, stretch, weights=NULL) {
   # Argument checks
   ensure_igraph(graph)
   stretch <- as.numeric(stretch)
@@ -1880,7 +1880,6 @@ pseudo_diameter_impl <- function(graph, start.vid, directed=TRUE, unconnected=TR
   res
 }
 
-# https://github.com/igraph/igraph/commit/d455f61f4832d5207cb0a0475fb5ddc02409ae76#r138442064
 pseudo_diameter_dijkstra_impl <- function(graph, weights=NULL, start.vid, directed=TRUE, unconnected=TRUE) {
   # Argument checks
   ensure_igraph(graph)

src/rinterface.c

@@ -2725,7 +2725,7 @@ SEXP R_igraph_spanner(SEXP graph, SEXP stretch, SEXP weights) {
   c_stretch = REAL(stretch)[0];
   if (!Rf_isNull(weights)) { R_SEXP_to_vector(weights, &c_weights); }
                                         /* Call igraph */
-  IGRAPH_R_CHECK(igraph_spanner(&c_graph, &c_spanner, c_stretch, (Rf_isNull(weights) ? 0 : &c_weights)));
+  IGRAPH_R_CHECK(igraph_spanner(&c_graph, &c_spanner, c_stretch, (Rf_isNull(weights) ? 0 : (Rf_isNull(weights) ? 0 : &c_weights))));
 
                                         /* Convert output */
   PROTECT(spanner=R_igraph_vector_int_to_SEXPp1(&c_spanner));

src/vendor/cigraph/CHANGELOG.md

@@ -2,6 +2,15 @@
 
 ## [master]
 
+### Fixed
+
+ - `igraph_is_forest()` determined that a graph is not a directed forest, and the `roots` output parameter was set to `NULL`, it would incorrectly cache that the graph is also not an undirected forest.
+ - `igraph_spanner()` now correctly ignores edge directions, and no longer crashes on directed graphs.
+
+### Other
+
+ - Documentation improvements.
+
 ## [0.10.9] - 2024-02-02
 
 ### Added
@@ -26,7 +35,7 @@
  - Performance: Reduced memory usage and improved initialization performance for `igraph_strvector_t`.
  - Performance: Improved cache use by `igraph_is_bipartite()`.
  - The documentation is now also generated in Texinfo format.
- - Documentation improvements
+ - Documentation improvements.
 
 ## [0.10.8] - 2023-11-17
 

src/vendor/cigraph/interfaces/functions.yaml

@@ -17,6 +17,9 @@ igraph_add_edges:
     PARAMS: INOUT GRAPH graph, VERTEX_INDEX_PAIRS edges, ATTRIBUTES attr
     DEPS: edges ON graph
 
+igraph_empty_attrs:
+    PARAMS: OUT GRAPH graph, INTEGER n, BOOLEAN directed, ATTRIBUTES attr
+
 igraph_add_vertices:
     PARAMS: INOUT GRAPH graph, INTEGER nv, ATTRIBUTES attr
 
@@ -66,9 +69,6 @@ igraph_edges:
     PARAMS: GRAPH graph, EDGE_SELECTOR eids, OUT VECTOR_INT edges
     DEPS: eids ON graph
 
-igraph_empty_attrs:
-    PARAMS: OUT GRAPH graph, INTEGER n, BOOLEAN directed, ATTRIBUTES attr
-
 igraph_get_eid:
     PARAMS: |-
         GRAPH graph, OUT EDGE eid, VERTEX from, VERTEX to,
@@ -621,7 +621,7 @@ igraph_widest_path_widths_floyd_warshall:
 
 igraph_spanner:
     PARAMS: |-
-        GRAPH graph, OUT EDGE_INDICES spanner, REAL stretch, EDGEWEIGHTS weights
+        GRAPH graph, OUT EDGE_INDICES spanner, REAL stretch, OPTIONAL EDGEWEIGHTS weights
     DEPS: weights ON graph
 
 igraph_subcomponent:
@@ -1065,14 +1065,12 @@ igraph_radius_dijkstra:
     DEPS: weights ON graph
 
 igraph_pseudo_diameter:
-    NAME-R: pseudo_diameter
     PARAMS: |-
         GRAPH graph, OUT REAL diameter, VERTEX start_vid,
         OUT INTEGER from=NULL, OUT INTEGER to=NULL,
         BOOLEAN directed=True, BOOLEAN unconnected=True
 
 igraph_pseudo_diameter_dijkstra:
-    NAME-R: pseudo_diameter
     PARAMS: |-
         GRAPH graph, EDGEWEIGHTS weights=NULL,
         OUT REAL diameter, VERTEX start_vid,

src/vendor/cigraph/src/centrality/truss.cpp

@@ -248,7 +248,7 @@ igraph_error_t igraph_trussness(const igraph_t* graph, igraph_vector_int_t* trus
         IGRAPH_CHECK(igraph_has_mutual(graph, &is_multigraph, /* loops */ false));
     }
     if (is_multigraph) {
-        IGRAPH_ERROR("Trussness is not implemented for graph with multi-edges.", IGRAPH_UNIMPLEMENTED);
+        IGRAPH_ERROR("Trussness is not implemented for graphs with multi-edges.", IGRAPH_UNIMPLEMENTED);
     }
 
     /* Manage the stack to make it memory safe: do not change the order of

src/vendor/cigraph/src/graph/basic_query.c

@@ -29,7 +29,7 @@
 /**
  * \ingroup structural
  * \function igraph_are_connected
- * \brief Decides whether two vertices are connected.
+ * \brief Decides whether two vertices are adjacent.
  *
  * Decides whether there are any edges that have \p v1 and \p v2
  * as endpoints. This function is of course symmetric for undirected

src/vendor/cigraph/src/graph/type_indexededgelist.c

@@ -1352,20 +1352,23 @@ igraph_error_t igraph_degree(const igraph_t *graph, igraph_vector_int_t *res,
 
 /**
  * \function igraph_get_eid
- * \brief Get the edge ID from the end points of an edge.
+ * \brief Get the edge ID from the endpoints of an edge.
  *
  * For undirected graphs \c from and \c to are exchangeable.
  *
  * \param graph The graph object.
  * \param eid Pointer to an integer, the edge ID will be stored here.
+ *        If \p error is false and no edge was found, <code>-1</code>
+ *        will be returned.
  * \param from The starting point of the edge.
  * \param to The end point of the edge.
  * \param directed Logical constant, whether to search for directed
  *        edges in a directed graph. Ignored for undirected graphs.
  * \param error Logical scalar, whether to report an error if the edge
- *        was not found. If it is false, then -1 will be assigned to \p eid.
- *        Note that invalid vertex IDs in input arguments (\p from or \p to)
- *        always return an error code.
+ *        was not found. If it is false, then <code>-1</code> will be
+ *        assigned to \p eid. Note that invalid vertex IDs in input
+ *        arguments (\p from or \p to) always trigger an error,
+ *        regardless of this setting.
  * \return Error code.
  * \sa \ref igraph_edge() for the opposite operation, \ref igraph_get_all_eids_between()
  *     to retrieve all edge IDs between a pair of vertices.

src/vendor/cigraph/src/paths/all_shortest_paths.c

@@ -36,7 +36,9 @@
  * \brief All shortest paths (geodesics) from a vertex.
  *
  * When there is more than one shortest path between two vertices,
- * all of them will be returned.
+ * all of them will be returned. Every edge is considered separately,
+ * therefore in graphs with multi-edges, this function may produce
+ * a very large number of results.
  *
  * \param graph The graph object.
  * \param vertices The result, the IDs of the vertices along the paths.

src/vendor/cigraph/src/paths/sparsifier.c

@@ -119,15 +119,15 @@ static void igraph_i_clear_lightest_edges_to_clusters(
  * \function igraph_spanner
  * \brief Calculates a spanner of a graph with a given stretch factor.
  *
- * A spanner of a graph G = (V,E) with a stretch t is a subgraph
- * H = (V,Es) such that Es is a subset of E and the distance
- * between any pair of nodes in H is at most t times the distance
- * in G. The returned graph is always a spanner of the
- * given graph with the specified stretch. For weighted graphs the
- * number of edges in the spanner is O(k * n^(1 + 1 / k)), where k is
- * k = (stretch + 1) / 2,  m is the number of edges and n is the number
- * of nodes in G. For unweighted graphs the number of edges is
- * O(n^(1 + 1 / k) + kn).
+ * A spanner of a graph <code>G = (V,E)</code> with a stretch \c t is a
+ * subgraph <code>H = (V,Es)</code> such that \c Es is a subset of \c E
+ * and the distance between any pair of nodes in \c H is at most \c t
+ * times the distance in \c G. The returned graph is always a spanner of
+ * the given graph with the specified stretch. For weighted graphs the
+ * number of edges in the spanner is <code>O(k n^(1 + 1 / k))</code>, where
+ * \c k is <code>k = (t + 1) / 2</code>,  \c m is the number of edges
+ * and \c n is the number of nodes in \c G. For unweighted graphs the number
+ * of edges is <code>O(n^(1 + 1 / k) + kn)</code>.
  *
  * </para><para>
  * This function is based on the algorithm of Baswana and Sen: "A Simple and
@@ -138,10 +138,10 @@ static void igraph_i_clear_lightest_edges_to_clusters(
  *        is directed, the directions of the edges will be ignored.
  * \param spanner An initialized vector, the IDs of the edges that constitute
  *        the calculated spanner will be returned here. Use
- * \ref igraph_subgraph_from_edges() to extract the spanner as a separate
+ *        \ref igraph_subgraph_from_edges() to extract the spanner as a separate
  *        graph object.
- * \param stretch The stretch factor of the spanner.
- * \param weights The edge weights or NULL.
+ * \param stretch The stretch factor \c t of the spanner.
+ * \param weights The edge weights or \c NULL.
  *
  * \return Error code:
  * \clist
@@ -150,13 +150,14 @@ static void igraph_i_clear_lightest_edges_to_clusters(
  * \endclist
  *
  * Time complexity: The algorithm is a randomized Las Vegas algorithm. The expected
- *                  running time is O(km) where k is the value mentioned above.
+ * running time is O(km) where k is the value mentioned above and m is the number
+ * of edges.
  */
 igraph_error_t igraph_spanner(const igraph_t *graph, igraph_vector_int_t *spanner,
         igraph_real_t stretch, const igraph_vector_t *weights) {
 
-    igraph_integer_t no_of_nodes = igraph_vcount(graph);
-    igraph_integer_t no_of_edges = igraph_ecount(graph);
+    const igraph_integer_t no_of_nodes = igraph_vcount(graph);
+    const igraph_integer_t no_of_edges = igraph_ecount(graph);
     igraph_integer_t i, j, v, nlen, neighbor, cluster;
     igraph_real_t sample_prob, k = (stretch + 1) / 2, weight, lightest_sampled_weight;
     igraph_vector_int_t clustering, lightest_eid;
@@ -178,21 +179,21 @@ igraph_error_t igraph_spanner(const igraph_t *graph, igraph_vector_int_t *spanne
 
     /* Test validity of stretch factor */
     if (stretch < 1) {
-        IGRAPH_ERROR("Stretch factor must be at least 1", IGRAPH_EINVAL);
+        IGRAPH_ERROR("Stretch factor must be at least 1.", IGRAPH_EINVAL);
     }
 
     /* Test validity of weights vector */
     if (weights) {
         if (igraph_vector_size(weights) != no_of_edges) {
-            IGRAPH_ERROR("Weight vector length does not match", IGRAPH_EINVAL);
+            IGRAPH_ERROR("Weight vector length does not match.", IGRAPH_EINVAL);
         }
         if (no_of_edges > 0) {
             igraph_real_t min = igraph_vector_min(weights);
             if (min < 0) {
-                IGRAPH_ERROR("Weight vector must be non-negative", IGRAPH_EINVAL);
+                IGRAPH_ERROR("Weight vector must be non-negative.", IGRAPH_EINVAL);
             }
             else if (isnan(min)) {
-                IGRAPH_ERROR("Weight vector must not contain NaN values", IGRAPH_EINVAL);
+                IGRAPH_ERROR("Weight vector must not contain NaN values.", IGRAPH_EINVAL);
             }
         }
     }
@@ -205,7 +206,7 @@ igraph_error_t igraph_spanner(const igraph_t *graph, igraph_vector_int_t *spanne
     // explicitly; it will only exist in terms of the incidence and the adjacency
     // lists, maintained in parallel as the edges are removed from the residual
     // graph.
-    IGRAPH_CHECK(igraph_inclist_init(graph, &inclist, IGRAPH_OUT, IGRAPH_NO_LOOPS));
+    IGRAPH_CHECK(igraph_inclist_init(graph, &inclist, IGRAPH_ALL, IGRAPH_NO_LOOPS));
     IGRAPH_FINALLY(igraph_inclist_destroy, &inclist);
     IGRAPH_CHECK(igraph_adjlist_init_from_inclist(graph, &adjlist, &inclist));
     IGRAPH_FINALLY(igraph_adjlist_destroy, &adjlist);