feat: graphlet_basis() returns a list of vertices in the "cliques" component. Replace .Call(Rx_...) with _impl functions for autogenerated entrypoints (#2472)

Co-authored-by: Kirill Müller <kirill@cynkra.com>

Author: Copilot

R/aaa-auto.R

@@ -248,7 +248,9 @@ edges_impl <- function(
     graph,
     eids - 1
   )
-
+  if (igraph_opt("return.vs.es")) {
+    res <- create_vs(graph, res)
+  }
   res
 }
 
@@ -2966,7 +2968,9 @@ topological_sorting_impl <- function(
     graph,
     mode
   )
-
+  if (igraph_opt("return.vs.es")) {
+    res <- create_vs(graph, res)
+  }
   res
 }
 
@@ -6628,6 +6632,8 @@ write_graph_edgelist_impl <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
+  check_string(outstream)
+
 
   on.exit(.Call(R_igraph_finalizer))
   # Function call
@@ -6648,6 +6654,8 @@ write_graph_leda_impl <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
+  check_string(outstream)
+
 
   on.exit(.Call(R_igraph_finalizer))
   # Function call
@@ -6669,6 +6677,8 @@ write_graph_graphml_impl <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
+  check_string(outstream)
+
   prefixattr <- as.logical(prefixattr)
 
   on.exit(.Call(R_igraph_finalizer))
@@ -6689,6 +6699,8 @@ write_graph_pajek_impl <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
+  check_string(outstream)
+
 
   on.exit(.Call(R_igraph_finalizer))
   # Function call
@@ -6710,6 +6722,8 @@ write_graph_gml_impl <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
+  check_string(outstream)
+
   options <- switch_igraph_arg(options, "default" = 0L, "encode_only_quot" = 1L)
   id <- as.numeric(id)
 
@@ -6733,6 +6747,8 @@ write_graph_dot_impl <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
+  check_string(outstream)
+
 
   on.exit(.Call(R_igraph_finalizer))
   # Function call

R/cliques.R

@@ -548,33 +548,17 @@ ivs <- function(graph, min = NULL, max = NULL) {
 #' @rdname ivs
 #' @export
 largest_ivs <- function(graph) {
-  ensure_igraph(graph)
-
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(Rx_igraph_largest_independent_vertex_sets, graph)
-  res <- lapply(res, `+`, 1)
-
-  if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
-  }
-
-  res
+  largest_independent_vertex_sets_impl(
+    graph = graph
+  )
 }
 
 #' @rdname ivs
 #' @export
 max_ivs <- function(graph) {
-  ensure_igraph(graph)
-
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(Rx_igraph_maximal_independent_vertex_sets, graph)
-  res <- lapply(res, `+`, 1)
-
-  if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
-  }
-
-  res
+  maximal_independent_vertex_sets_impl(
+    graph = graph
+  )
 }
 
 #' Maximal independent vertex sets in the graph
@@ -595,10 +579,9 @@ maximal_ivs <- function(graph) {
 #' @rdname ivs
 #' @export
 ivs_size <- function(graph) {
-  ensure_igraph(graph)
-
-  on.exit(.Call(R_igraph_finalizer))
-  .Call(Rx_igraph_independence_number, graph)
+  independence_number_impl(
+    graph = graph
+  )
 }
 
 #' @rdname ivs

R/cocitation.R

@@ -54,12 +54,12 @@
 #' bibcoupling(g)
 #'
 cocitation <- function(graph, v = V(graph)) {
-  ensure_igraph(graph)
-
-  v <- as_igraph_vs(graph, v)
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(Rx_igraph_cocitation, graph, v - 1)
+  res <- cocitation_impl(
+    graph = graph,
+    vids = v
+  )
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
+    v <- as_igraph_vs(graph, v)
     rownames(res) <- vertex_attr(graph, "name", v)
     colnames(res) <- vertex_attr(graph, "name")
   }
@@ -69,12 +69,12 @@ cocitation <- function(graph, v = V(graph)) {
 #' @rdname cocitation
 #' @export
 bibcoupling <- function(graph, v = V(graph)) {
-  ensure_igraph(graph)
-
-  v <- as_igraph_vs(graph, v)
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(Rx_igraph_bibcoupling, graph, v - 1)
+  res <- bibcoupling_impl(
+    graph = graph,
+    vids = v
+  )
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
+    v <- as_igraph_vs(graph, v)
     rownames(res) <- vertex_attr(graph, "name", v)
     colnames(res) <- vertex_attr(graph, "name")
   }

R/cohesive.blocks.R

@@ -355,9 +355,9 @@ cohesive_blocks <- function(graph, labels = TRUE) {
   # Argument checks
   ensure_igraph(graph)
 
-  on.exit(.Call(R_igraph_finalizer))
-  # Function call
-  res <- .Call(Rx_igraph_cohesive_blocks, graph)
+  res <- cohesive_blocks_impl(
+    graph = graph
+  )
   class(res) <- "cohesiveBlocks"
   if (labels && "name" %in% vertex_attr_names(graph)) {
     res$labels <- V(graph)$name

R/flow.R

@@ -411,18 +411,9 @@ min_cut <- function(
 
   if (is.null(target) && is.null(source)) {
     if (value.only) {
-      res <- .Call(Rx_igraph_mincut_value, graph, capacity)
+      res <- mincut_value_impl(graph = graph, capacity = capacity)
     } else {
-      res <- .Call(Rx_igraph_mincut, graph, capacity)
-      res$cut <- res$cut + 1
-      res$partition1 <- res$partition1 + 1
-      res$partition2 <- res$partition2 + 1
-
-      if (igraph_opt("return.vs.es")) {
-        res$cut <- create_es(graph, res$cut)
-        res$partition1 <- create_vs(graph, res$partition1)
-        res$partition2 <- create_vs(graph, res$partition2)
-      }
+      res <- mincut_impl(graph = graph, capacity = capacity)
     }
   } else {
     if (value.only) {
@@ -533,8 +524,7 @@ vertex_connectivity <- function(
   ensure_igraph(graph)
 
   if (is.null(source) && is.null(target)) {
-    on.exit(.Call(R_igraph_finalizer))
-    .Call(Rx_igraph_vertex_connectivity, graph, as.logical(checks))
+    vertex_connectivity_impl(graph = graph, checks = checks)
   } else if (!is.null(source) && !is.null(target)) {
     on.exit(.Call(R_igraph_finalizer))
     .Call(
@@ -639,8 +629,7 @@ edge_connectivity <- function(
   ensure_igraph(graph)
 
   if (is.null(source) && is.null(target)) {
-    on.exit(.Call(R_igraph_finalizer))
-    .Call(Rx_igraph_edge_connectivity, graph, as.logical(checks))
+    edge_connectivity_impl(graph = graph, checks = checks)
   } else if (!is.null(source) && !is.null(target)) {
     on.exit(.Call(R_igraph_finalizer))
     .Call(
@@ -693,20 +682,20 @@ vertex_disjoint_paths <- function(graph, source = NULL, target = NULL) {
 #' @rdname edge_connectivity
 #' @export
 adhesion <- function(graph, checks = TRUE) {
-  ensure_igraph(graph)
-
-  on.exit(.Call(R_igraph_finalizer))
-  .Call(Rx_igraph_adhesion, graph, as.logical(checks))
+  adhesion_impl(
+    graph = graph,
+    checks = checks
+  )
 }
 
 #' @rdname vertex_connectivity
 #' @method cohesion igraph
 #' @export
 cohesion.igraph <- function(x, checks = TRUE, ...) {
-  ensure_igraph(x)
-
-  on.exit(.Call(R_igraph_finalizer))
-  .Call(Rx_igraph_cohesion, x, as.logical(checks))
+  cohesion_impl(
+    graph = x,
+    checks = checks
+  )
 }
 
 #' List all (s,t)-cuts of a graph