chore: update vendor cigraph 0.10

src/vendor/cigraph/CHANGELOG.md

@@ -5,6 +5,8 @@
 ### Changes
 
  - `igraph_community_walktrap()` no longer requires `modularity` and `merges` to be non-NULL when `membership` is non-NULL.
+ - `igraph_isomorphic()` now supports multigraphs.
+ - Shortest path related functions now consistently ignore edges with positive infinite weights.
 
 ### Fixed
 
@@ -16,24 +18,27 @@
  - HRG functions now require a graph with at least 3 vertices; previous versions crashed with smaller graphs.
  - `igraph_arpack_rssolve()` and `igraph_arpack_rnsolve()`, i.e. the ARPACK interface in igraph, are now interruptible. As a result, several other functions that rely on ARPACK (eigenvector centrality, hub and authority scores, etc.) also became interruptible.
  - `igraph_get_shortest_paths_dijkstra()`, `igraph_get_all_shortest_paths_dijkstra()` and `igraph_get_shortest_paths_bellman_ford()` now validate the `from` vertex.
+ - Fixed bugs in `igraph_local_scan_1_ecount()` for weighted undirected graphs which would miscount loops and multi-edges.
 
 ### Deprecated
 
 - `igraph_automorphisms()` is now deprecated; its new name is `igraph_count_automorphisms()`. The old name is kept available until at least igraph 0.11.
 - `igraph_hub_score()` and `igraph_authority_score()` are now deprecated. Use `igraph_hub_and_authority_scores()` instead.
 - `igraph_get_incidence()` is now deprecated; its new name is `igraph_get_biadjacency()` to reflect that the returned matrix is an _adjacency_ matrix between pairs of vertices and not an _incidence_ matrix between vertices and edges. The new name is kept available until at least igraph 0.11. We plan to re-use the name in later versions to provide a proper incidence matrix where the rows are vertices and the columns are edges.
+- `igraph_hrg_dendrogram()` is deprecated because it requires an attribute handler and it goes against the convention of returning attributes in vectors where possible. Use `igraph_from_hrg_dendrogram()` instead, which constructs the dendrogram as an igraph graph _and_ returns the associated probabilities in a vector.
 
 ### Other
 
  - Improved performance for `igraph_vertex_connectivity()`.
+ - `igraph_simplify()` makes use of the cache, and avoids simplification when the graph is already known to be simple.
  - Documentation improvements.
 
 ## [0.10.4] - 2023-01-26
 
 ### Added
 
  - `igraph_get_shortest_path_astar()` finds a shortest path with the A* algorithm.
- - `igraph_vertex_coloring_greedy()` now supports the DSatur heuristics (#2284, thanks to @professorcode1).
+ - `igraph_vertex_coloring_greedy()` now supports the DSatur heuristics through `IGRAPH_COLORING_GREEDY_DSATUR` (#2284, thanks to @professorcode1).
 
 ### Changed
 

src/vendor/cigraph/CMakeLists.txt

@@ -4,6 +4,7 @@
 #  * CROSSCOMPILING_EMULATOR can be a semicolon-separated list to pass arguments (3.15)
 #  * SKIP_REGULAR_EXPRESSION to handle skipped tests properly (3.16)
 #  * CheckLinkerFlag for HAVE_NEW_DTAGS test (3.18)
+#  * cmake -E cat (3.18)
 cmake_minimum_required(VERSION 3.18...3.25)
 
 # Add etc/cmake to CMake's search path so we can put our private stuff there

src/vendor/cigraph/azure-pipelines.yml

@@ -76,21 +76,21 @@ jobs:
           extra_cmake_args: '-DBLA_VENDOR=OpenBLAS'
           build_shared: true
 
-  - job: linux_clang_15
+  - job: linux_clang_17
     pool:
       vmImage: 'ubuntu-22.04'
     steps:
       - script: |
           sudo apt-get install ninja-build ccache -y
           wget https://apt.llvm.org/llvm.sh
           chmod +x llvm.sh
-          sudo ./llvm.sh 15
+          sudo ./llvm.sh 17
         displayName: Install dependencies
 
       - template: .azure/build.yml
         parameters:
           build_type: Debug
-          extra_cmake_args: '-DUSE_SANITIZER=Address\;Undefined -DCMAKE_C_FLAGS="-Og -fno-sanitize-recover=undefined -fno-sanitize=float-divide-by-zero" -DCMAKE_CXX_FLAGS="-Og -fno-sanitize-recover=undefined -fno-sanitize=float-divide-by-zero" -DCMAKE_C_COMPILER=clang-15  -DCMAKE_CXX_COMPILER=clang++-15'
+          extra_cmake_args: '-DUSE_SANITIZER=Address\;Undefined -DCMAKE_C_FLAGS="-Og -fno-sanitize-recover=undefined -fno-sanitize=float-divide-by-zero" -DCMAKE_CXX_FLAGS="-Og -fno-sanitize-recover=undefined -fno-sanitize=float-divide-by-zero" -DCMAKE_C_COMPILER=clang-17  -DCMAKE_CXX_COMPILER=clang++-17'
 
   - job: linux_x87
     steps:

src/vendor/cigraph/include/igraph_coloring.h

@@ -38,8 +38,9 @@ __BEGIN_DECLS
  * \enumval IGRAPH_COLORING_GREEDY_DSATUR
  *    Choose the vertex with largest number of unique colors in its neighborhood, i.e. its
  *    "saturation degree". When multiple vertices have the same saturation degree, choose
- *    the one with the most not yet colored neighbors. This heuristic is known as "DSatur",
- *    and was introduced in Daniel Brélaz: New methods to color the vertices of a graph,
+ *    the one with the most not yet colored neighbors. Added in igraph 0.10.4. This heuristic
+ *    is known as "DSatur", and was proposed in
+ *    Daniel Brélaz: New methods to color the vertices of a graph,
  *    Commun. ACM 22, 4 (1979), 251–256. https://doi.org/10.1145/359094.359101
  */
 typedef enum {

src/vendor/cigraph/include/igraph_error.h

@@ -777,8 +777,8 @@ IGRAPH_EXPORT int IGRAPH_FINALLY_STACK_SIZE(void);
  *
  * \param expr An expression, usually a call to a user-defined callback function.
  * It is guaranteed to be evaluated only once.
- * \param code Pointer to an optional variable of type \c igraph_error_t; the
- * value of this variable will be set to the error code if it is not a null
+ * \param code Pointer to an optional variable of type <type>igraph_error_t</type>;
+ * the value of this variable will be set to the error code if it is not a null
  * pointer.
  */
 #define IGRAPH_CHECK_CALLBACK(expr, code) \
@@ -852,6 +852,7 @@ typedef void igraph_warning_handler_t (const char *reason, const char *file, int
  * \brief Installs a warning handler.
  *
  * Install the supplied warning handler function.
+ *
  * \param new_handler The new warning handler function to install.
  *        Supply a null pointer here to uninstall the current
  *        warning handler, without installing a new one.
@@ -976,7 +977,7 @@ IGRAPH_EXPORT void igraph_warningf(const char *reason, const char *file, int lin
  *
  * \param reason Textual description of the error.
  * \param file The source file in which the error is noticed.
- * \param line The number of the line in the source file which triggered the error
+ * \param line The number of the line in the source file which triggered the error.
  */
 
 typedef void igraph_fatal_handler_t (const char *reason, const char *file, int line);
@@ -1046,6 +1047,7 @@ IGRAPH_EXPORT IGRAPH_FUNCATTR_NORETURN void igraph_fatalf(const char *reason, co
  * \a igraph functions can use this macro when a fatal error occurs and
  * want to pass on extra information to the user about what went wrong.
  * It calls \ref igraph_fatalf() with the proper parameters.
+ *
  * \param reason Textual description of the error, a template string
  *        with the same syntax as the standard printf C library function.
  * \param ... The additional arguments to be substituted into the

src/vendor/cigraph/include/igraph_games.h

@@ -49,9 +49,6 @@ IGRAPH_EXPORT igraph_error_t igraph_barabasi_game(igraph_t *graph, igraph_intege
                                        igraph_bool_t directed,
                                        igraph_barabasi_algorithm_t algo,
                                        const igraph_t *start_from);
-IGRAPH_EXPORT igraph_error_t igraph_erdos_renyi_game(igraph_t *graph, igraph_erdos_renyi_t type,
-                                          igraph_integer_t n, igraph_real_t p_or_m,
-                                          igraph_bool_t directed, igraph_bool_t loops);
 IGRAPH_EXPORT igraph_error_t igraph_erdos_renyi_game_gnp(igraph_t *graph, igraph_integer_t n, igraph_real_t p,
                                               igraph_bool_t directed, igraph_bool_t loops);
 IGRAPH_EXPORT igraph_error_t igraph_erdos_renyi_game_gnm(igraph_t *graph, igraph_integer_t n, igraph_integer_t m,
@@ -220,6 +217,13 @@ IGRAPH_EXPORT igraph_error_t igraph_sample_sphere_volume(igraph_integer_t dim, i
 IGRAPH_EXPORT igraph_error_t igraph_sample_dirichlet(igraph_integer_t n, const igraph_vector_t *alpha,
                                           igraph_matrix_t *res);
 
+/* Deprecated functions: */
+
+IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_erdos_renyi_game(
+    igraph_t *graph, igraph_erdos_renyi_t type, igraph_integer_t n,
+    igraph_real_t p_or_m, igraph_bool_t directed, igraph_bool_t loops
+);
+
 __END_DECLS
 
 #endif

src/vendor/cigraph/include/igraph_hrg.h

@@ -98,8 +98,9 @@ IGRAPH_EXPORT igraph_error_t igraph_hrg_game(
     igraph_t *graph, const igraph_hrg_t *hrg
 );
 
-IGRAPH_EXPORT igraph_error_t igraph_hrg_dendrogram(igraph_t *graph,
-                                        const igraph_hrg_t *hrg);
+IGRAPH_EXPORT igraph_error_t igraph_from_hrg_dendrogram(
+    igraph_t *graph, const igraph_hrg_t *hrg, igraph_vector_t *prob
+);
 
 IGRAPH_EXPORT igraph_error_t igraph_hrg_consensus(const igraph_t *graph,
                                        igraph_vector_int_t *parents,
@@ -120,6 +121,12 @@ IGRAPH_EXPORT igraph_error_t igraph_hrg_create(igraph_hrg_t *hrg,
                                     const igraph_t *graph,
                                     const igraph_vector_t *prob);
 
+/* Deprecated functions: */
+
+IGRAPH_DEPRECATED IGRAPH_EXPORT igraph_error_t igraph_hrg_dendrogram(
+    igraph_t *graph, const igraph_hrg_t *hrg
+);
+
 __END_DECLS
 
 #endif  /* IGRAPH_HRG_H */

src/vendor/cigraph/interfaces/functions.yaml

@@ -224,11 +224,6 @@ igraph_barabasi_game:
         BOOLEAN directed=True, BARABASI_ALGORITHM algo=BAG,
         OPTIONAL GRAPH start_from
 
-igraph_erdos_renyi_game:
-    PARAMS: |-
-        OUT GRAPH graph, ERDOS_RENYI_TYPE type, INTEGER n, REAL p_or_m,
-        BOOLEAN directed=False, BOOLEAN loops=False
-
 igraph_erdos_renyi_game_gnp:
     PARAMS: OUT GRAPH graph, INTEGER n, REAL p, BOOLEAN directed=False, BOOLEAN loops=False
 
@@ -1711,9 +1706,6 @@ igraph_hrg_sample_many:
 igraph_hrg_game:
     PARAMS: OUT GRAPH graph, HRG hrg
 
-igraph_hrg_dendrogram:
-    PARAMS: OUT GRAPH graph, HRG hrg
-
 igraph_hrg_consensus:
     PARAMS: |-
         GRAPH graph, OUT VECTOR_INT parents, OUT VECTOR weights,
@@ -1738,6 +1730,9 @@ igraph_hrg_size:
     PARAMS: HRG hrg
     RETURN: INTEGER
 
+igraph_from_hrg_dendrogram:
+    PARAMS: OUT GRAPH graph, HRG hrg, OUT VECTOR prob
+
 #######################################
 # Conversion
 #######################################

src/vendor/cigraph/src/CMakeLists.txt

@@ -373,31 +373,31 @@ if(MATH_LIBRARY)
 endif()
 
 if(ARPACK_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${ARPACK_LIBRARIES})
+  target_link_libraries(igraph PRIVATE ${ARPACK_LIBRARIES})
 endif()
 
-if(BLAS_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${BLAS_LIBRARIES})
+if(BLAS_FOUND)
+  target_link_libraries(igraph PRIVATE ${BLAS_LIBRARIES})
 endif()
 
 if(GLPK_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${GLPK_LIBRARIES})
+  target_link_libraries(igraph PRIVATE ${GLPK_LIBRARIES})
 endif()
 
 if(GMP_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${GMP_LIBRARIES})
+  target_link_libraries(igraph PRIVATE ${GMP_LIBRARIES})
 endif()
 
 if(LAPACK_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${LAPACK_LIBRARIES})
+  target_link_libraries(igraph PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
 if(LIBXML2_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${LIBXML2_LIBRARIES})
+  target_link_libraries(igraph PRIVATE ${LIBXML2_LIBRARIES})
 endif()
 
 if(PLFIT_LIBRARIES)
-  target_link_libraries(igraph PUBLIC ${PLFIT_LIBRARIES})
+  target_link_libraries(igraph PRIVATE ${PLFIT_LIBRARIES})
 endif()
 
 # Link igraph statically to some of the libraries from the subdirectories

src/vendor/cigraph/src/community/leading_eigenvector.c

@@ -410,23 +410,18 @@ igraph_error_t igraph_community_leading_eigenvector(
         igraph_vector_list_clear(eigenvectors);
     }
 
-    IGRAPH_STATUS("Starting leading eigenvector method.\n", 0);
-
     if (!start) {
         /* Calculate the weakly connected components in the graph and use them as
          * an initial split */
         IGRAPH_CHECK(igraph_connected_components(graph, mymembership, &idx, 0, IGRAPH_WEAK));
         communities = igraph_vector_int_size(&idx);
-        IGRAPH_STATUSF(("Starting from %" IGRAPH_PRId " component(s).\n", 0, communities));
         if (history) {
             IGRAPH_CHECK(igraph_vector_push_back(history,
                                                  IGRAPH_LEVC_HIST_START_FULL));
         }
     } else {
         /* Just create the idx vector for the given membership vector */
         communities = igraph_vector_int_max(mymembership) + 1;
-        IGRAPH_STATUSF(("Starting from given membership vector with %" IGRAPH_PRId
-                        " communities.\n", 0, communities));
         if (history) {
             IGRAPH_CHECK(igraph_vector_push_back(history,
                                                  IGRAPH_LEVC_HIST_START_GIVEN));
@@ -512,7 +507,6 @@ igraph_error_t igraph_community_leading_eigenvector(
         /* depth first search */
         igraph_integer_t size = 0;
 
-        IGRAPH_STATUSF(("Trying to split community %" IGRAPH_PRId "... ", 0, comm));
         IGRAPH_ALLOW_INTERRUPTION();
 
         for (i = 0; i < no_of_nodes; i++) {
@@ -631,7 +625,6 @@ igraph_error_t igraph_community_leading_eigenvector(
         }
 
         if (storage.d[0] <= 0) {
-            IGRAPH_STATUS("no split.\n", 0);
             if (history) {
                 IGRAPH_CHECK(igraph_vector_push_back(history,
                                                      IGRAPH_LEVC_HIST_FAILED));
@@ -651,7 +644,6 @@ igraph_error_t igraph_community_leading_eigenvector(
             }
         }
         if (l == 0 || l == size) {
-            IGRAPH_STATUS("no split.\n", 0);
             if (history) {
                 IGRAPH_CHECK(igraph_vector_push_back(history,
                                                      IGRAPH_LEVC_HIST_FAILED));
@@ -667,7 +659,6 @@ igraph_error_t igraph_community_leading_eigenvector(
             mod += storage.v[size + i] * storage.v[i];
         }
         if (mod <= 1e-8) {
-            IGRAPH_STATUS("no modularity increase, no split.\n", 0);
             if (history) {
                 IGRAPH_CHECK(igraph_vector_push_back(history,
                                                      IGRAPH_LEVC_HIST_FAILED));
@@ -677,7 +668,6 @@ igraph_error_t igraph_community_leading_eigenvector(
         }
 
         communities++;
-        IGRAPH_STATUS("split.\n", 0);
 
         /* Rewrite the mymembership vector */
         for (j = 0; j < size; j++) {
@@ -720,8 +710,6 @@ igraph_error_t igraph_community_leading_eigenvector(
     igraph_vector_int_destroy(&idx2);
     IGRAPH_FINALLY_CLEAN(3);
 
-    IGRAPH_STATUS("Done.\n", 0);
-
     /* reform the mymerges vector */
     if (merges) {
         igraph_vector_int_null(&idx);

src/vendor/cigraph/src/community/louvain.c

@@ -414,7 +414,7 @@ static igraph_error_t igraph_i_community_multilevel_step(
             new_id = old_id;
 
             /* Update old community */
-            igraph_vector_int_set(communities.membership, ni, -1);
+            VECTOR(*communities.membership)[ni] = -1;
             communities.item[old_id].size--;
             if (communities.item[old_id].size == 0) {
                 communities.communities_no--;
@@ -447,7 +447,7 @@ static igraph_error_t igraph_i_community_multilevel_step(
             /* debug("Added vertex %ld to community %ld (gain %lf).\n", ni, new_id, (double) max_q_gain); */
 
             /* Add vertex to "new" community and update it */
-            igraph_vector_int_set(communities.membership, ni, new_id);
+            VECTOR(*communities.membership)[ni] = new_id;
             if (communities.item[new_id].size == 0) {
                 communities.communities_no++;
             }

src/vendor/cigraph/src/community/modularity.c

@@ -97,7 +97,7 @@
  *                   It does not have to be consecutive, i.e. empty communities
  *                   are allowed.
  * \param weights    Weight vector or \c NULL if no weights are specified.
- * \param resolution The resolutin parameter \c γ. Must not be negative.
+ * \param resolution The resolution parameter \c γ. Must not be negative.
  *                   Set it to 1 to use the classical definition of modularity.
  * \param directed   Whether to use the directed or undirected version of modularity.
  *                   Ignored for undirected graphs.

src/vendor/cigraph/src/community/walktrap/walktrap_graph.cpp

@@ -200,7 +200,7 @@ igraph_error_t Graph::convert_from_igraph(const igraph_t *graph,
          * See https://github.com/igraph/igraph/pull/2043 */
         if (G.vertices[i].total_weight == 0) {
             /* G.vertices will be destroyed by Graph::~Graph() */
-            IGRAPH_ERROR("Vertex with zero strength found: all vertices must have positive strength for walktrap",
+            IGRAPH_ERROR("Vertex with zero strength found: all vertices must have positive strength for walktrap.",
                          IGRAPH_EINVAL);
         }
         sort(G.vertices[i].edges, G.vertices[i].edges + G.vertices[i].degree);