vendor: Update vendored sources to igraph/igraph@0878f57

krlmlr · krlmlr · commit 4ae3527388b7 · 2025-01-02T16:56:30.000+01:00
doc: more documentation improvements
diff --git a/src/vendor/cigraph/src/centrality/centralization.c b/src/vendor/cigraph/src/centrality/centralization.c
@@ -200,7 +200,7 @@ igraph_error_t igraph_centralization_degree(const igraph_t *graph, igraph_vector
  *     or total degree (\c IGRAPH_ALL). This is ignored if
  *     the \p graph argument is not a null pointer and the
  *     given graph is undirected.
- * \param loops Boolean scalar, whether to consider loop edges in the
+ * \param loops Boolean, whether to consider loop edges in the
  *     calculation.
  * \param res Pointer to a real variable, the result is stored here.
  * \return Error code.
@@ -358,7 +358,7 @@ igraph_error_t igraph_centralization_betweenness(const igraph_t *graph,
  *     above.
  * \param nodes The number of nodes. This is ignored if the
  *     \p graph argument is not a null pointer.
- * \param directed Boolean scalar, whether to use directed paths in
+ * \param directed Boolean, whether to use directed paths in
  *     the betweenness calculation. This argument is ignored if
  *     \p graph is not a null pointer and it is undirected.
  * \param res Pointer to a real variable, the result is stored here.
@@ -695,7 +695,7 @@ igraph_error_t igraph_centralization_eigenvector_centrality(
  *     above.
  * \param nodes The number of nodes. This is ignored if the
  *     \p graph argument is not a null pointer.
- * \param directed Boolean scalar, whether to consider edge
+ * \param directed Boolean, whether to consider edge
  *     directions. This argument is ignored if
  *     \p graph is not a null pointer and it is undirected.
  * \param scale This parameter is deprecated and ignored since igraph 0.10.14.
diff --git a/src/vendor/cigraph/src/cliques/glet.c b/src/vendor/cigraph/src/cliques/glet.c
@@ -785,12 +785,13 @@ igraph_error_t igraph_i_graphlets_project(
 
 /**
  * \function igraph_graphlets_project
- * Project a graph on a graphlets basis
+ * \brief Project a graph on a graphlets basis.
  *
  * Note that the graph projected does not have to be the same that
  * was used to calculate the graphlet basis, but it is assumed that
  * it has the same number of vertices, and the vertex IDs of the two
  * graphs match.
+ *
  * \param graph The input graph, it must be a simple graph, edge directions are
  *        ignored.
  * \param weights Weights of the edges in the input graph, a vector.
@@ -804,7 +805,7 @@ igraph_error_t igraph_i_graphlets_project(
  * \param startMu If true, then the supplied Mu vector is
  *        used as the starting point of the iteration. Otherwise a
  *        constant 1 vector is used.
- * \param niter Integer scalar, the number of iterations to perform.
+ * \param niter The number of iterations to perform.
  * \return Error code.
  *
  * See also: \ref igraph_graphlets() and
@@ -844,11 +845,12 @@ static int igraph_i_graphlets_order_cmp(void *data, const void *a, const void *b
 
 /**
  * \function igraph_graphlets
- * Calculate graphlets basis and project the graph on it
+ * \brief Calculate graphlets basis and project the graph on it.
  *
  * This function simply calls \ref igraph_graphlets_candidate_basis()
  * and \ref igraph_graphlets_project(), and then orders the graphlets
  * according to decreasing weights.
+ *
  * \param graph The input graph, it must be a simple graph, edge directions are
  *        ignored.
  * \param weights Weights of the edges, a vector.
@@ -857,8 +859,7 @@ static int igraph_i_graphlets_order_cmp(void *data, const void *a, const void *b
  *        vertex IDs, encoding a single basis subgraph.
  * \param Mu An initialized vector, the weights of the graphlets will
  *        be stored here.
- * \param niter Integer scalar, the number of iterations to perform
- *        for the projection step.
+ * \param niter The number of iterations to perform for the projection step.
  * \return Error code.
  *
  * See also: \ref igraph_graphlets_candidate_basis() and
diff --git a/src/vendor/cigraph/src/connectivity/components.c b/src/vendor/cigraph/src/connectivity/components.c
@@ -625,7 +625,7 @@ static igraph_error_t igraph_i_decompose_strong(const igraph_t *graph,
  *    want to limit the number of components.
  * \param minelements The minimum number of vertices a component
  *    should contain in order to place it in the \p components
- *    vector. For example, supplying 2 here ignored isolated vertices.
+ *    vector. For example, supplying 2 here ignores isolated vertices.
  * \return Error code, \c IGRAPH_ENOMEM if there is not enough memory
  *   to perform the operation.
  *
diff --git a/src/vendor/cigraph/src/core/sparsemat.c b/src/vendor/cigraph/src/core/sparsemat.c
@@ -933,9 +933,9 @@ igraph_error_t igraph_sparsemat_multiply(const igraph_sparsemat_t *A,
  *
  * \param A The first input matrix, in column-compressed format.
  * \param B The second input matrix, in column-compressed format.
- * \param alpha Real scalar, \p A is multiplied by \p alpha before the
+ * \param alpha Real value, \p A is multiplied by \p alpha before the
  *    addition.
- * \param beta Real scalar, \p B is multiplied by \p beta before the
+ * \param beta Real value, \p B is multiplied by \p beta before the
  *    addition.
  * \param res Pointer to an uninitialized sparse matrix, the result
  *    is stored here.
@@ -1291,8 +1291,7 @@ static igraph_error_t igraph_i_sparsemat_triplet(igraph_t *graph, const igraph_s
  * \param graph Pointer to an uninitialized igraph_t object, the
  *    graphs is stored here.
  * \param A The input matrix, in triplet or column-compressed format.
- * \param directed Boolean scalar, whether to create a directed
- *    graph.
+ * \param directed Whether to create a directed graph.
  * \return Error code.
  *
  * Time complexity: TODO.
@@ -2104,9 +2103,9 @@ void igraph_sparsemat_numeric_destroy(igraph_sparsemat_numeric_t *din) {
  * \param res An uninitialized sparse matrix, the result is stored
  *    here.
  * \param mat The dense input matrix.
- * \param tol Real scalar, the tolerance. Values closer than \p tol to
- *    zero are considered as zero, and will not be included in the
- *    sparse matrix.
+ * \param tol The tolerance for zero comparisons. Values closer than
+ *    \p tol to zero are considered as zero, and will not be included
+ *    in the sparse matrix.
  * \return Error code.
  *
  * \sa \ref igraph_sparsemat_as_matrix() for the reverse conversion.
@@ -2358,10 +2357,10 @@ igraph_integer_t igraph_sparsemat_count_nonzero(igraph_sparsemat_t *A) {
  * \function igraph_sparsemat_count_nonzerotol
  * \brief Counts nonzero elements of a sparse matrix, ignoring elements close to zero.
  *
- * Count the number of matrix entries that are closer to zero than \p
- * tol.
+ * Count the number of matrix entries that are closer to zero than \p tol.
+ *
  * \param The input matrix, column-compressed.
- * \param Real scalar, the tolerance.
+ * \param The tolerance for zero comparisons.
  * \return Error code.
  *
  * Time complexity: TODO.
@@ -2850,7 +2849,8 @@ igraph_error_t igraph_sparsemat_colsums(const igraph_sparsemat_t *A,
  * \function igraph_sparsemat_scale
  * \brief Scales a sparse matrix.
  *
- * Multiplies all elements of a sparse matrix, by the given scalar.
+ * Multiplies all elements of a sparse matrix, by the given factor.
+ *
  * \param A The input matrix.
  * \param by The scaling factor.
  * \return Error code.
diff --git a/src/vendor/cigraph/src/games/correlated.c b/src/vendor/cigraph/src/games/correlated.c
@@ -73,12 +73,11 @@ static void sort_edges(igraph_vector_int_t *edges, const igraph_t *graph) {
  *
  * \param old_graph The original graph, it must be simple.
  * \param new_graph The new graph will be stored here.
- * \param corr A scalar in the unit interval [0,1], the target Pearson
+ * \param corr A value in the unit interval [0,1], the target Pearson
  *        correlation between the adjacency matrices of the original and the
  *        generated graph (the adjacency matrix being used as a vector).
- * \param p A numeric scalar, the probability of an edge between two
- *        vertices, it must in the open (0,1) interval. Typically,
- *        the density of \p old_graph.
+ * \param p The probability of an edge between two vertices. It must in the
+ *        open (0,1) interval. Typically, the density of \p old_graph.
  * \param permutation A permutation to apply to the vertices of the
  *        generated graph. It can also be a null pointer, in which case
  *        the vertices will not be permuted.
diff --git a/src/vendor/cigraph/src/graph/type_indexededgelist.c b/src/vendor/cigraph/src/graph/type_indexededgelist.c
@@ -1391,9 +1391,9 @@ igraph_error_t igraph_degree(const igraph_t *graph, igraph_vector_int_t *res,
  *        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
+ * \param directed Boolean, 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
+ * \param error Boolean, whether to report an error if the edge
  *        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,
@@ -1476,9 +1476,9 @@ igraph_error_t igraph_get_eid(const igraph_t *graph, igraph_integer_t *eid,
  * \param eids Pointer to an initialized vector, the result is stored
  *        here. It will be resized as needed.
  * \param pairs Vector giving pairs of vertices to fetch the edges for.
- * \param directed Logical scalar, whether to consider edge directions
+ * \param directed Boolean, whether to consider edge directions
  *        in directed graphs. This is ignored for undirected graphs.
- * \param error Logical scalar, whether it is an error to supply
+ * \param error Boolean, whether it is an error to supply
  *        non-connected vertices. If false, then -1 is
  *        returned for non-connected pairs.
  * \return Error code.
@@ -1597,7 +1597,7 @@ igraph_error_t igraph_get_eids(const igraph_t *graph, igraph_vector_int_t *eids,
  *        here. It will be resized as needed.
  * \param source The ID of the source vertex
  * \param target The ID of the target vertex
- * \param directed Logical scalar, whether to consider edge directions
+ * \param directed Boolean, whether to consider edge directions
  *        in directed graphs. This is ignored for undirected graphs.
  * \return Error code.
  *
diff --git a/src/vendor/cigraph/src/graph/visitors.c b/src/vendor/cigraph/src/graph/visitors.c
@@ -56,7 +56,7 @@
  *        \c IGRAPH_IN means the opposite, and
  *        \c IGRAPH_ALL ignores the direction of the edges.
  *        This parameter is ignored for undirected graphs.
- * \param unreachable Logical scalar, whether the search should visit
+ * \param unreachable Boolean, whether the search should visit
  *        the vertices that are unreachable from the given root
  *        node(s). If true, then additional searches are performed
  *        until all vertices are visited.
@@ -442,7 +442,7 @@ igraph_error_t igraph_bfs_simple(
  *        \c IGRAPH_IN means the opposite, and
  *        \c IGRAPH_ALL ignores the direction of the edges.
  *        This parameter is ignored for undirected graphs.
- * \param unreachable Logical scalar, whether the search should visit
+ * \param unreachable Boolean, whether the search should visit
  *        the vertices that are unreachable from the given root
  *        node(s). If true, then additional searches are performed
  *        until all vertices are visited.
diff --git a/src/vendor/cigraph/src/io/dl.c b/src/vendor/cigraph/src/io/dl.c
@@ -55,7 +55,7 @@ void igraph_dl_yylex_destroy_wrapper (void *scanner ) {
  *
  * \param graph Pointer to an uninitialized graph object.
  * \param instream The stream to read the DL file from.
- * \param directed Logical scalar, whether to create a directed file.
+ * \param directed Boolean, whether to create a directed file.
  * \return Error code.
  *
  * Time complexity: linear in terms of the number of edges and
diff --git a/src/vendor/cigraph/src/io/graphdb.c b/src/vendor/cigraph/src/io/graphdb.c
@@ -81,7 +81,7 @@ static igraph_error_t handle_input_error(FILE *instream) {
  * \param graph Pointer to an uninitialized graph object.
  * \param instream The stream to read from. It should be opened
  *    in binary mode.
- * \param directed Logical scalar, whether to create a directed graph.
+ * \param directed Whether to create a directed graph.
  * \return Error code.
  *
  * Time complexity: O(|V|+|E|), the number of vertices plus the
diff --git a/src/vendor/cigraph/src/layout/drl/drl_layout.cpp b/src/vendor/cigraph/src/layout/drl/drl_layout.cpp
@@ -420,7 +420,7 @@ igraph_error_t igraph_layout_drl_options_init(igraph_layout_drl_options_t *optio
  * Brown, W.M., Klavans, R., Boyack, K.W., DrL: Distributed Recursive
  * (Graph) Layout. SAND Reports, 2008. 2936: p. 1-10.
  * \param graph The input graph.
- * \param use_seed Logical scalar, if true, then the coordinates
+ * \param use_seed Boolean, if true, then the coordinates
  *    supplied in the \p res argument are used as starting points.
  * \param res Pointer to a matrix, the result layout is stored
  *    here. It will be resized as needed.
diff --git a/src/vendor/cigraph/src/layout/drl/drl_layout_3d.cpp b/src/vendor/cigraph/src/layout/drl/drl_layout_3d.cpp
@@ -68,7 +68,7 @@ using namespace drl3d;
  * </para><para> This function uses a modified DrL generator that does
  * the layout in three dimensions.
  * \param graph The input graph.
- * \param use_seed Logical scalar, if true, then the coordinates
+ * \param use_seed Boolean, if true, then the coordinates
  *    supplied in the \p res argument are used as starting points.
  * \param res Pointer to a matrix, the result layout is stored
  *    here. It will be resized as needed.
diff --git a/src/vendor/cigraph/src/layout/graphopt.c b/src/vendor/cigraph/src/layout/graphopt.c
@@ -328,7 +328,7 @@ static void igraph_i_move_nodes(
  * \param max_sa_movement Real constant, it gives the maximum amount of movement
  *    allowed in a single step along a single axis. The original graphopt
  *    default is 5.
- * \param use_seed Logical scalar, whether to use the positions in \p res as
+ * \param use_seed Boolean, whether to use the positions in \p res as
  *    a starting configuration. See also \p res above.
  * \return Error code.
  *
diff --git a/src/vendor/cigraph/src/linalg/lapack.c b/src/vendor/cigraph/src/linalg/lapack.c
@@ -169,7 +169,7 @@ igraph_error_t igraph_lapack_dgetrf(igraph_matrix_t *a, igraph_vector_int_t *ipi
  *      A * X = B  or  A' * X = B
  * with a general N-by-N matrix A using the LU factorization
  * computed by \ref igraph_lapack_dgetrf.
- * \param transpose Logical scalar, whether to transpose the input
+ * \param transpose Boolean, whether to transpose the input
  *      matrix.
  * \param a A matrix containing the L and U factors from the
  *      factorization A = P*L*U. L is expected to be unitriangular,
@@ -748,8 +748,8 @@ igraph_error_t igraph_lapack_dgeev(const igraph_matrix_t *A,
  * Users' Guide. Note that the eigenvectors obtained for the balanced
  * matrix are backtransformed to those of \p A.
  *
- * \param balance Scalar that indicated, whether the input matrix
- *   should be balanced. Possible values:
+ * \param balance Indicates whether the input matrix should be balanced.
+ *   Possible values:
  *   \clist
  *     \cli IGRAPH_LAPACK_DGEEVX_BALANCE_NONE
  *          no not diagonally scale or permute.
@@ -765,21 +765,21 @@ igraph_error_t igraph_lapack_dgeev(const igraph_matrix_t *A,
  *          both diagonally scale and permute A.
  *   \endclist
  * \param A The input matrix, must be square.
- * \param valuesreal An initialized vector, or a NULL pointer. If not
- *   a NULL pointer, then the real parts of the eigenvalues are stored
+ * \param valuesreal An initialized vector, or a \c NULL pointer. If not
+ *   a \c NULL pointer, then the real parts of the eigenvalues are stored
  *   here. The vector will be resized, as needed.
- * \param valuesimag An initialized vector, or a NULL pointer. If not
- *   a NULL pointer, then the imaginary parts of the eigenvalues are stored
+ * \param valuesimag An initialized vector, or a \c NULL pointer. If not
+ *   a \c NULL pointer, then the imaginary parts of the eigenvalues are stored
  *   here. The vector will be resized, as needed.
- * \param vectorsleft An initialized matrix or a NULL pointer. If not
+ * \param vectorsleft An initialized matrix or a \c NULL pointer. If not
  *   a null pointer, then the left eigenvectors are stored here. The
  *   order corresponds to the eigenvalues and the eigenvectors are
  *   stored in a compressed form. If the j-th eigenvalue is real then
  *   column j contains the corresponding eigenvector. If the j-th and
  *   (j+1)-th eigenvalues form a complex conjugate pair, then the j-th
  *   and (j+1)-th columns contain the real and imaginary parts of the
  *   corresponding eigenvectors.
- * \param vectorsright An initialized matrix or a NULL pointer. If not
+ * \param vectorsright An initialized matrix or a \c NULL pointer. If not
  *   a null pointer, then the right eigenvectors are stored here. The
  *   format is the same, as for the \p vectorsleft argument.
  * \param ilo
diff --git a/src/vendor/cigraph/src/misc/bipartite.c b/src/vendor/cigraph/src/misc/bipartite.c
@@ -540,8 +540,7 @@ igraph_error_t igraph_full_bipartite(igraph_t *graph,
  * \param edges Vector giving the edges of the graph. The highest
  *   vertex ID in this vector must be smaller than the length of the
  *   \p types vector.
- * \param directed Boolean scalar, whether to create a directed
- *   graph.
+ * \param directed Boolean, whether to create a directed graph.
  * \return Error code.
  *
  * Time complexity: O(|V|+|E|), linear in the number of vertices and
diff --git a/src/vendor/cigraph/src/properties/degrees.c b/src/vendor/cigraph/src/properties/degrees.c
@@ -600,7 +600,7 @@ igraph_error_t igraph_i_strength_all(
  * \param mode Gives whether to count only outgoing (\c IGRAPH_OUT),
  *   incoming (\c IGRAPH_IN) edges or both (\c IGRAPH_ALL).
  *   This parameter is ignored for undirected graphs.
- * \param loops A logical scalar, whether to count loop edges as well.
+ * \param loops Boolean, whether to count loop edges as well.
  * \param weights A vector giving the edge weights. If this is a \c NULL
  *   pointer, then \ref igraph_degree() is called to perform the
  *   calculation.
diff --git a/src/vendor/igraph_version.h b/src/vendor/igraph_version.h
@@ -28,11 +28,11 @@
 
 __BEGIN_DECLS
 
-#define IGRAPH_VERSION "0.10.13-132-gbd7b3a82b"
+#define IGRAPH_VERSION "0.10.13-133-g0878f577d"
 #define IGRAPH_VERSION_MAJOR 0
 #define IGRAPH_VERSION_MINOR 10
 #define IGRAPH_VERSION_PATCH 13
-#define IGRAPH_VERSION_PRERELEASE "132-gbd7b3a82b"
+#define IGRAPH_VERSION_PRERELEASE "133-g0878f577d"
 
 IGRAPH_EXPORT void igraph_version(const char **version_string,
                                   int *major,

Original file line number	Diff line number	Diff line change
`@@ -625,7 +625,7 @@ static igraph_error_t igraph_i_decompose_strong(const igraph_t *graph,`
`625`	`625`	`* want to limit the number of components.`
`626`	`626`	`* \param minelements The minimum number of vertices a component`
`627`	`627`	`* should contain in order to place it in the \p components`
`628`		`- * vector. For example, supplying 2 here ignored isolated vertices.`
	`628`	`+ * vector. For example, supplying 2 here ignores isolated vertices.`
`629`	`629`	`* \return Error code, \c IGRAPH_ENOMEM if there is not enough memory`
`630`	`630`	`* to perform the operation.`
`631`	`631`	`*`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ void igraph_dl_yylex_destroy_wrapper (void *scanner ) {`
`55`	`55`	`*`
`56`	`56`	`* \param graph Pointer to an uninitialized graph object.`
`57`	`57`	`* \param instream The stream to read the DL file from.`
`58`		`- * \param directed Logical scalar, whether to create a directed file.`
	`58`	`+ * \param directed Boolean, whether to create a directed file.`
`59`	`59`	`* \return Error code.`
`60`	`60`	`*`
`61`	`61`	`* Time complexity: linear in terms of the number of edges and`
Original file line number	Diff line number	Diff line change
`@@ -81,7 +81,7 @@ static igraph_error_t handle_input_error(FILE *instream) {`
`81`	`81`	`* \param graph Pointer to an uninitialized graph object.`
`82`	`82`	`* \param instream The stream to read from. It should be opened`
`83`	`83`	`* in binary mode.`
`84`		`- * \param directed Logical scalar, whether to create a directed graph.`
	`84`	`+ * \param directed Whether to create a directed graph.`
`85`	`85`	`* \return Error code.`
`86`	`86`	`*`
`87`	`87`	`* Time complexity: O(\|V\|+\|E\|), the number of vertices plus the`