refactor: Switch from .Call() to autogenerated _impl functions (#2443)

Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: krlmlr <[email protected]>
Co-authored-by: Kirill Müller <[email protected]>

Author: Copilot

AGENTS.md

@@ -120,7 +120,7 @@ See `tools/README.md` for guidelines on code generation using the Stimulus frame
 Do not commit: `*.d`, `*.o`, `*.so` files in `src/`, and `tests/testthat/testthat-problems.rds`.
 These are build artifacts that are regenerated automatically (see `src/README.md` for details on dependency tracking).
 
-Revert all changes to `*.dd` but keep these files version-controlled.
+Careful with changes to `*.dd`, keep system headers out, only expect changes if new source files are added or their local dependencies change.
 
 ## Testing
 

R/centralization.R

@@ -478,9 +478,12 @@ centr_betw <- function(graph, directed = TRUE, normalized = TRUE) {
   directed <- as.logical(directed)
   normalized <- as.logical(normalized)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_centralization_betweenness, graph, directed, normalized)
+  res <- centralization_betweenness_impl(
+    graph = graph,
+    directed = directed,
+    normalized = normalized
+  )
 
   res
 }

R/community.R

@@ -984,9 +984,13 @@ modularity_matrix <- function(
   resolution <- as.numeric(resolution)
   directed <- as.logical(directed)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_modularity_matrix, graph, weights, resolution, directed)
+  res <- modularity_matrix_impl(
+    graph = graph,
+    weights = weights,
+    resolution = resolution,
+    directed = directed
+  )
 
   res
 }
@@ -2516,9 +2520,12 @@ cluster_louvain <- function(graph, weights = NULL, resolution = 1) {
   }
   resolution <- as.numeric(resolution)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_community_multilevel, graph, weights, resolution)
+  res <- community_multilevel_impl(
+    graph = graph,
+    weights = weights,
+    resolution = resolution
+  )
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
     res$names <- V(graph)$name
   }
@@ -3047,16 +3054,8 @@ i_compare <- function(
   } else {
     as.numeric(as.factor(comm2))
   }
-  method <- switch(
-    igraph.match.arg(method),
-    vi = 0L,
-    nmi = 1L,
-    split.join = 2L,
-    rand = 3L,
-    adjusted.rand = 4L
-  )
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_compare_communities, comm1, comm2, method)
+  method <- igraph.match.arg(method)
+  res <- compare_communities_impl(comm1 = comm1, comm2 = comm2, method = method)
   res
 }
 
@@ -3104,8 +3103,7 @@ split_join_distance <- function(comm1, comm2) {
   } else {
     as.numeric(comm2)
   }
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_split_join_distance, comm1, comm2)
+  res <- split_join_distance_impl(comm1 = comm1, comm2 = comm2)
   unlist(res)
 }
 

R/conversion.R

@@ -624,17 +624,14 @@ as_undirected <- function(
 ) {
   # Argument checks
   ensure_igraph(graph)
-  mode <- switch(
-    igraph.match.arg(mode),
-    "collapse" = 1L,
-    "each" = 0L,
-    "mutual" = 2L
-  )
-  edge.attr.comb <- igraph.i.attribute.combination(edge.attr.comb)
+  mode <- igraph.match.arg(mode)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_to_undirected, graph, mode, edge.attr.comb)
+  res <- to_undirected_impl(
+    graph = graph,
+    mode = mode,
+    edge.attr.comb = edge.attr.comb
+  )
 
   res
 }

R/flow.R

@@ -906,17 +906,10 @@ dominator_tree <- function(graph, root, mode = c("out", "in", "all", "total")) {
   }
   root <- as_igraph_vs(graph, root)
 
-  mode <- switch(
-    igraph.match.arg(mode),
-    "out" = 1,
-    "in" = 2,
-    "all" = 3,
-    "total" = 3
-  )
+  mode <- igraph.match.arg(mode)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_dominator_tree, graph, root - 1, mode)
+  res <- dominator_tree_impl(graph = graph, root = root, mode = mode)
   if (igraph_opt("return.vs.es")) {
     res$leftout <- create_vs(graph, res$leftout)
   }

R/hrg.R

@@ -251,9 +251,8 @@ fit_hrg <- function(graph, hrg = NULL, start = FALSE, steps = 0) {
   start <- as.logical(start)
   steps <- as.numeric(steps)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_hrg_fit, graph, hrg, start, steps)
+  res <- hrg_fit_impl(graph = graph, hrg = hrg, start = start, steps = steps)
 
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
     res$names <- V(graph)$name

R/incidence.R

@@ -80,11 +80,12 @@ graph_incidence_build <- function(
 
   # Handle dense unweighted matrices first
   if (!inherits(incidence, "Matrix") && is.null(weighted)) {
-    mode(incidence) <- "double"
-    on.exit(.Call(R_igraph_finalizer))
-
-    mode_num <- switch(mode, "out" = 1, "in" = 2, "all" = 3, "total" = 3)
-    res <- .Call(R_igraph_biadjacency, incidence, directed, mode_num, multiple)
+    res <- biadjacency_impl(
+      incidence = incidence,
+      directed = directed,
+      mode = mode,
+      multiple = multiple
+    )
     return(set_vertex_attr(res$graph, "type", value = res$types))
   }
 

R/make.R

@@ -267,8 +267,7 @@ line.graph <- function(graph) {
   lifecycle::deprecate_soft("2.1.0", "line.graph()", "make_line_graph()")
   ensure_igraph(graph)
 
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_linegraph, graph)
+  res <- linegraph_impl(graph = graph)
   if (igraph_opt("add.params")) {
     res$name <- "Line graph"
   }
@@ -473,8 +472,7 @@ graph.lattice <- function(
 graph.kautz <- function(m, n) {
   # nocov start
   lifecycle::deprecate_soft("2.1.0", "graph.kautz()", "make_kautz_graph()")
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_kautz, as.numeric(m), as.numeric(n))
+  res <- kautz_impl(m = m, n = n)
   if (igraph_opt("add.params")) {
     res$name <- sprintf("Kautz graph %i-%i", m, n)
     res$m <- m
@@ -500,13 +498,8 @@ graph.full.citation <- function(n, directed = TRUE) {
     "graph.full.citation()",
     "make_full_citation_graph()"
   )
-  # Argument checks
-  n <- as.numeric(n)
-  directed <- as.logical(directed)
-
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_full_citation, n, directed)
+  res <- full_citation_impl(n = n, directed = directed)
 
   res <- set_graph_attr(res, "name", "Full citation graph")
   res
@@ -545,8 +538,7 @@ graph.full.bipartite <- function(
     "total" = 3
   )
 
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_full_bipartite, n1, n2, as.logical(directed), mode1)
+  res <- full_bipartite_impl(n1 = n1, n2 = n2, directed = directed, mode = mode)
   if (igraph_opt("add.params")) {
     res$graph$name <- "Full bipartite graph"
     res$n1 <- n1
@@ -644,13 +636,8 @@ graph.extended.chordal.ring <- function(n, w, directed = FALSE) {
 graph.empty <- function(n = 0, directed = TRUE) {
   # nocov start
   lifecycle::deprecate_soft("2.1.0", "graph.empty()", "make_empty_graph()")
-  # Argument checks
-  n <- as.numeric(n)
-  directed <- as.logical(directed)
-
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_empty, n, directed)
+  res <- empty_impl(n = n, directed = directed)
 
   res
 } # nocov end
@@ -672,8 +659,7 @@ graph.de.bruijn <- function(m, n) {
     "graph.de.bruijn()",
     "make_de_bruijn_graph()"
   )
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_de_bruijn, as.numeric(m), as.numeric(n))
+  res <- de_bruijn_impl(m = m, n = n)
   if (igraph_opt("add.params")) {
     res$name <- sprintf("De-Bruijn graph %i-%i", m, n)
     res$m <- m
@@ -743,8 +729,7 @@ graph.bipartite <- function(types, edges, directed = FALSE) {
 graph.atlas <- function(n) {
   # nocov start
   lifecycle::deprecate_soft("2.1.0", "graph.atlas()", "graph_from_atlas()")
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_atlas, as.numeric(n))
+  res <- atlas_impl(number = n)
   if (igraph_opt("add.params")) {
     res$name <- sprintf("Graph from the Atlas #%i", n)
     res$n <- n
@@ -2214,8 +2199,7 @@ from_prufer <- function(...) constructor_spec(make_from_prufer, ...)
 #' graph_from_atlas(sample(0:1252, 1))
 #' graph_from_atlas(sample(0:1252, 1))
 graph_from_atlas <- function(n) {
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_atlas, as.numeric(n))
+  res <- atlas_impl(number = n)
   if (igraph_opt("add.params")) {
     res$name <- sprintf("Graph from the Atlas #%i", n)
     res$n <- n
@@ -2311,8 +2295,7 @@ chordal_ring <- function(...) constructor_spec(make_chordal_ring, ...)
 make_line_graph <- function(graph) {
   ensure_igraph(graph)
 
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_linegraph, graph)
+  res <- linegraph_impl(graph = graph)
   if (igraph_opt("add.params")) {
     res$name <- "Line graph"
   }
@@ -2358,8 +2341,7 @@ line_graph <- function(...) constructor_spec(make_line_graph, ...)
 #' make_de_bruijn_graph(2, 2)
 #' make_line_graph(g)
 make_de_bruijn_graph <- function(m, n) {
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_de_bruijn, as.numeric(m), as.numeric(n))
+  res <- de_bruijn_impl(m = m, n = n)
   if (igraph_opt("add.params")) {
     res$name <- sprintf("De-Bruijn graph %i-%i", m, n)
     res$m <- m
@@ -2403,8 +2385,7 @@ de_bruijn_graph <- function(...) constructor_spec(make_de_bruijn_graph, ...)
 #' make_kautz_graph(2, 2)
 #'
 make_kautz_graph <- function(m, n) {
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_kautz, as.numeric(m), as.numeric(n))
+  res <- kautz_impl(m = m, n = n)
   if (igraph_opt("add.params")) {
     res$name <- sprintf("Kautz graph %i-%i", m, n)
     res$m <- m
@@ -2466,8 +2447,7 @@ make_full_bipartite_graph <- function(
     "total" = 3
   )
 
-  on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(R_igraph_full_bipartite, n1, n2, as.logical(directed), mode1)
+  res <- full_bipartite_impl(n1 = n1, n2 = n2, directed = directed, mode = mode)
   if (igraph_opt("add.params")) {
     res$graph$name <- "Full bipartite graph"
     res$n1 <- n1
@@ -2581,13 +2561,8 @@ bipartite_graph <- function(...) constructor_spec(make_bipartite_graph, ...)
 #' @examples
 #' print_all(make_full_citation_graph(10))
 make_full_citation_graph <- function(n, directed = TRUE) {
-  # Argument checks
-  n <- as.numeric(n)
-  directed <- as.logical(directed)
-
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_full_citation, n, directed)
+  res <- full_citation_impl(n = n, directed = directed)
 
   res <- set_graph_attr(res, "name", "Full citation graph")
   res

R/sgm.R

@@ -24,8 +24,7 @@ solve_LSAP <- function(x, maximum = FALSE) {
   if (maximum) {
     x <- max(x) - x
   }
-  storage.mode(x) <- "double"
-  out <- .Call(R_igraph_solve_lsap, x, as.numeric(nc)) + 1L
+  out <- solve_lsap_impl(c = x, n = as.numeric(nc)) + 1L
   out[seq_len(nr)]
 }
 

R/simple.R

@@ -118,9 +118,8 @@ simplify_and_colorize <- function(graph) {
   # Argument checks
   ensure_igraph(graph)
 
-  on.exit(.Call(R_igraph_finalizer))
   # Function call
-  res <- .Call(R_igraph_simplify_and_colorize, graph)
+  res <- simplify_and_colorize_impl(graph = graph)
 
   V(res$res)$color <- res$vertex_color
   E(res$res)$color <- res$edge_color