Replace .Call() expressions with _impl functions and add explanatory comments

R/attributes.R

@@ -328,7 +328,7 @@ graph_attr <- function(graph, name) {
 
   check_string(name)
 
-  .Call(Rx_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_graph)[[
+  .Call(Rx_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_graph)[[ # internal, no _impl
     name
   ]]
 }
@@ -388,7 +388,7 @@ set_graph_attr <- function(graph, name, value) {
 
   ensure_igraph(graph)
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket3_set,
     graph,
     igraph_t_idx_attr,
@@ -401,7 +401,7 @@ set_graph_attr <- function(graph, name, value) {
 #' @export
 graph.attributes <- function(graph) {
   ensure_igraph(graph)
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_copy,
     graph,
     igraph_t_idx_attr,
@@ -417,7 +417,7 @@ graph.attributes <- function(graph) {
     value <- as.list(value)
   }
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -459,7 +459,7 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 
   check_string(name)
   myattr <-
-    .Call(
+    .Call( # internal, no _impl
       Rx_igraph_mybracket2,
       graph,
       igraph_t_idx_attr,
@@ -609,7 +609,7 @@ i_set_vertex_attr <- function(
     index <- as_igraph_vs(graph, index)
   }
 
-  vattrs <- .Call(
+  vattrs <- .Call( # internal, no _impl
     Rx_igraph_mybracket2,
     graph,
     igraph_t_idx_attr,
@@ -643,7 +643,7 @@ i_set_vertex_attr <- function(
     }
   }
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -660,7 +660,7 @@ vertex.attributes <- function(graph, index = V(graph)) {
     index <- as_igraph_vs(graph, index)
   }
 
-  res <- .Call(
+  res <- .Call( # internal, no _impl
     Rx_igraph_mybracket2_copy,
     graph,
     igraph_t_idx_attr,
@@ -720,7 +720,7 @@ set_value_at <- function(value, idx, length_out) {
     )
   }
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -761,7 +761,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
     }
   } else {
     check_string(name)
-    myattr <- .Call(
+    myattr <- .Call( # internal, no _impl
       Rx_igraph_mybracket2,
       graph,
       igraph_t_idx_attr,
@@ -865,7 +865,7 @@ i_set_edge_attr <- function(
     index <- as_igraph_es(graph, index)
   }
 
-  eattrs <- .Call(
+  eattrs <- .Call( # internal, no _impl
     Rx_igraph_mybracket2,
     graph,
     igraph_t_idx_attr,
@@ -896,7 +896,7 @@ i_set_edge_attr <- function(
     }
   }
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -913,7 +913,7 @@ edge.attributes <- function(graph, index = E(graph)) {
     index <- as_igraph_es(graph, index)
   }
 
-  res <- .Call(
+  res <- .Call( # internal, no _impl
     Rx_igraph_mybracket2_copy,
     graph,
     igraph_t_idx_attr,
@@ -963,7 +963,7 @@ edge.attributes <- function(graph, index = E(graph)) {
     )
   }
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -986,7 +986,7 @@ edge.attributes <- function(graph, index = E(graph)) {
 #' graph_attr_names(g)
 graph_attr_names <- function(graph) {
   ensure_igraph(graph)
-  res <- .Call(
+  res <- .Call( # internal, no _impl
     Rx_igraph_mybracket2_names,
     graph,
     igraph_t_idx_attr,
@@ -1015,7 +1015,7 @@ graph_attr_names <- function(graph) {
 vertex_attr_names <- function(graph) {
   ensure_igraph(graph)
 
-  res <- .Call(
+  res <- .Call( # internal, no _impl
     Rx_igraph_mybracket2_names,
     graph,
     igraph_t_idx_attr,
@@ -1043,7 +1043,7 @@ vertex_attr_names <- function(graph) {
 #' plot(g)
 edge_attr_names <- function(graph) {
   ensure_igraph(graph)
-  res <- .Call(
+  res <- .Call( # internal, no _impl
     Rx_igraph_mybracket2_names,
     graph,
     igraph_t_idx_attr,
@@ -1077,15 +1077,15 @@ delete_graph_attr <- function(graph, name) {
     cli::cli_abort("No graph attribute {.arg {name}} found.")
   }
 
-  gattr <- .Call(
+  gattr <- .Call( # internal, no _impl
     Rx_igraph_mybracket2,
     graph,
     igraph_t_idx_attr,
     igraph_attr_idx_graph
   )
   gattr[[name]] <- NULL
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -1117,15 +1117,15 @@ delete_vertex_attr <- function(graph, name) {
     cli::cli_abort("No vertex attribute {.arg {name}} found.")
   }
 
-  vattr <- .Call(
+  vattr <- .Call( # internal, no _impl
     Rx_igraph_mybracket2,
     graph,
     igraph_t_idx_attr,
     igraph_attr_idx_vertex
   )
   vattr[[name]] <- NULL
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,
@@ -1157,15 +1157,15 @@ delete_edge_attr <- function(graph, name) {
     cli::cli_abort("No edge attribute {.arg {name}} found.")
   }
 
-  eattr <- .Call(
+  eattr <- .Call( # internal, no _impl
     Rx_igraph_mybracket2,
     graph,
     igraph_t_idx_attr,
     igraph_attr_idx_edge
   )
   eattr[[name]] <- NULL
 
-  .Call(
+  .Call( # internal, no _impl
     Rx_igraph_mybracket2_set,
     graph,
     igraph_t_idx_attr,

R/bipartite.R

@@ -190,7 +190,7 @@ bipartite_projection <- function(
 
   on.exit(.Call(Rx_igraph_finalizer))
   # Function call
-  res <- .Call(
+  res <- .Call( # bipartite_projection_impl lacks which/multiplicity parameters
     Rx_igraph_bipartite_projection,
     graph,
     types,

R/centrality.R

@@ -992,7 +992,7 @@ arpack <- function(
   }
 
   on.exit(.Call(Rx_igraph_finalizer))
-  res <- .Call(Rx_igraph_arpack, func, extra, options, env, sym)
+  res <- .Call(Rx_igraph_arpack, func, extra, options, env, sym) # ARPACK, no _impl
 
   if (complex) {
     rew <- arpack.unpack.complex(
@@ -1030,7 +1030,7 @@ arpack.unpack.complex <- function(vectors, values, nev) {
 
   on.exit(.Call(Rx_igraph_finalizer))
   # Function call
-  res <- .Call(Rx_igraph_arpack_unpack_complex, vectors, values, nev)
+  res <- .Call(Rx_igraph_arpack_unpack_complex, vectors, values, nev) # ARPACK, no _impl
 
   res
 }

R/cliques.R

@@ -325,7 +325,7 @@ max_cliques <- function(
       tmpfile <- FALSE
     }
     on.exit(.Call(Rx_igraph_finalizer))
-    res <- .Call(
+    res <- .Call( # maximal_cliques_file_impl doesn't support subset
       Rx_igraph_maximal_cliques_file,
       graph,
       subset,
@@ -350,7 +350,7 @@ max_cliques <- function(
     }
 
     on.exit(.Call(Rx_igraph_finalizer))
-    res <- .Call(
+    res <- .Call( # maximal_cliques_impl doesn't support subset
       Rx_igraph_maximal_cliques,
       graph,
       subset_arg,
@@ -403,7 +403,7 @@ count_max_cliques <- function(graph, min = NULL, max = NULL, subset = NULL) {
 
   on.exit(.Call(Rx_igraph_finalizer))
   # Function call
-  res <- .Call(Rx_igraph_maximal_cliques_count, graph, subset, min, max)
+  res <- .Call(Rx_igraph_maximal_cliques_count, graph, subset, min, max) # _impl lacks subset
 
   res
 }
@@ -568,30 +568,11 @@ weighted_clique_num <- function(graph, vertex.weights = NULL) {
 #'
 #' length(max_ivs(g))
 ivs <- function(graph, min = NULL, max = NULL) {
-  ensure_igraph(graph)
-
-  if (is.null(min)) {
-    min <- 0
-  }
-
-  if (is.null(max)) {
-    max <- 0
-  }
-
-  on.exit(.Call(Rx_igraph_finalizer))
-  res <- .Call(
-    Rx_igraph_independent_vertex_sets,
-    graph,
-    as.numeric(min),
-    as.numeric(max)
+  independent_vertex_sets_impl(
+    graph = graph,
+    min_size = min %||% 0,
+    max_size = max %||% 0
   )
-  res <- lapply(res, `+`, 1)
-
-  if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
-  }
-
-  res
 }
 
 #' @rdname ivs

R/community.R

@@ -1311,12 +1311,12 @@ show_trace <- function(communities) {
 #####################################################################
 
 community.to.membership2 <- function(merges, vcount, steps) {
-  mode(merges) <- "numeric"
-  mode(vcount) <- "numeric"
-  mode(steps) <- "numeric"
-  on.exit(.Call(Rx_igraph_finalizer))
-  res <- .Call(Rx_igraph_community_to_membership2, merges - 1, vcount, steps)
-  res + 1
+  res <- community_to_membership_impl(
+    merges = merges - 1,
+    nodes = vcount,
+    steps = steps
+  )
+  res$membership + 1
 }
 
 #####################################################################
@@ -1480,7 +1480,7 @@ cluster_spinglass <- function(
 
   on.exit(.Call(Rx_igraph_finalizer))
   if (is.null(vertex) || length(vertex) == 0) {
-    res <- .Call(
+    res <- .Call( # community_spinglass_impl uses different parameter names
       Rx_igraph_spinglass_community,
       graph,
       weights,
@@ -1502,7 +1502,7 @@ cluster_spinglass <- function(
     }
     class(res) <- "communities"
   } else {
-    res <- .Call(
+    res <- .Call( # community_spinglass_single_impl has different API
       Rx_igraph_spinglass_my_community,
       graph,
       weights,
@@ -1858,7 +1858,7 @@ cluster_walktrap <- function(
   }
 
   on.exit(.Call(Rx_igraph_finalizer))
-  res <- .Call(
+  res <- .Call( # community_walktrap_impl lacks output control parameters
     Rx_igraph_walktrap_community,
     graph,
     weights,
@@ -1986,7 +1986,7 @@ cluster_edge_betweenness <- function(
   }
 
   on.exit(.Call(Rx_igraph_finalizer))
-  res <- .Call(
+  res <- .Call( # community_edge_betweenness_impl lacks output control parameters
     Rx_igraph_community_edge_betweenness,
     graph,
     weights,
@@ -2078,7 +2078,7 @@ cluster_fast_greedy <- function(
   }
 
   on.exit(.Call(Rx_igraph_finalizer))
-  res <- .Call(
+  res <- .Call( # community_fastgreedy_impl lacks output control parameters
     Rx_igraph_community_fastgreedy,
     graph,
     as.logical(merges),
@@ -2100,7 +2100,7 @@ cluster_fast_greedy <- function(
 igraph.i.levc.arp <- function(externalP, externalE) {
   f <- function(v) {
     v <- as.numeric(v)
-    .Call(R_igraph_levc_arpack_multiplier, externalP, externalE, v)
+    .Call(R_igraph_levc_arpack_multiplier, externalP, externalE, v) # internal ARPACK, no _impl
   }
   f
 }