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Replace .Call() expressions with _impl functions and add explanatory comments #2562

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3a9ed79
Initial plan
Copilot Jan 27, 2026
3937dfc
Add comments explaining why .Call() expressions cannot be replaced wi…
Copilot Jan 27, 2026
a85a698
Fix syntax error in attributes.R comment placement
Copilot Jan 27, 2026
330f326
Replace .Call() with _impl functions where possible, add explanatory …
Copilot Jan 27, 2026
5c6041f
Replace subcomponent, girth, ego_size, ego, make_ego_graph with _impl…
Copilot Jan 27, 2026
483a118
Add comments to remaining .Call() expressions in structural-properties.R
Copilot Jan 27, 2026
08ff3d5
Add comment explaining efficiency trade-off in girth() using girth_im…
Copilot Jan 27, 2026
86f4d82
Update BFS/DFS comments to reference bfs_closure_impl/dfs_closure_impl
Copilot Jan 27, 2026
d2302de
Add comments to internal .Call() expressions in attributes.R
Copilot Jan 27, 2026
05fcfa1
Add comments and replacements for .Call() in bipartite.R, centrality.…
Copilot Jan 27, 2026
085591d
Add comments to all remaining .Call() expressions across R files
Copilot Jan 27, 2026
d7c4ce7
Replace .Call() with _impl functions in layout, interface, foreign fi…
Copilot Jan 27, 2026
c4ab986
Fix layout functions to properly initialize coords when NULL before c…
Copilot Jan 27, 2026
31579a3
Fix weight handling in layout functions to let _impl handle defaults
Copilot Jan 27, 2026
a524504
Revert some foreign.R functions to .Call() due to _impl bugs or diffe…
Copilot Jan 27, 2026
474b71e
Replace more .Call() with _impl functions: count_components, count_ma…
Copilot Jan 30, 2026
1dc318e
Add igraph API comments to remaining .Call() expressions
Copilot Jan 30, 2026
4f103aa
Remove errant snapshot file
Copilot Jan 30, 2026
318a0f5
Add detailed igraph API function names to remaining .Call() comments
Copilot Jan 30, 2026
366a715
Fix type comparison bug in bipartite_projection warning
Copilot Jan 30, 2026
0d52819
Add igraph API function names to .Call() comments; replace spinglass …
Copilot Jan 30, 2026
ef518a7
Merge branch 'main' into copilot/replace-call-expressions-with-impl-f…
krlmlr Apr 12, 2026
4c302a8
chore: Auto-update from GitHub Actions
krlmlr Apr 12, 2026
3fa66f7
Improve .Call() comments with specific igraph API function names
Copilot Apr 12, 2026
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46 changes: 23 additions & 23 deletions R/attributes.R
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
]]
}
Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -643,7 +643,7 @@ i_set_vertex_attr <- function(
}
}

.Call(
.Call( # internal, no _impl
Rx_igraph_mybracket2_set,
graph,
igraph_t_idx_attr,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -896,7 +896,7 @@ i_set_edge_attr <- function(
}
}

.Call(
.Call( # internal, no _impl
Rx_igraph_mybracket2_set,
graph,
igraph_t_idx_attr,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down
38 changes: 18 additions & 20 deletions R/bipartite.R
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Original file line number Diff line number Diff line change
Expand Up @@ -184,43 +184,41 @@ bipartite_projection <- function(
"false" = 1L,
"true" = 2L
)
if (which != "both" && probe1 != -1) {
if (which != 0L && probe1 != -1) {
cli::cli_warn("{.arg probe1} ignored if only one projection is requested.")
}

on.exit(.Call(Rx_igraph_finalizer))
# Function call
res <- .Call(
Rx_igraph_bipartite_projection,
graph,
types,
as.numeric(probe1),
which
# bipartite_projection_impl always computes both projections
res <- bipartite_projection_impl(
graph = graph,
types = types,
probe1 = probe1
)

if (remove.type) {
if (is_igraph(res[[1]]) && "type" %in% vertex_attr_names(res[[1]])) {
res[[1]] <- delete_vertex_attr(res[[1]], "type")
if (is_igraph(res$proj1) && "type" %in% vertex_attr_names(res$proj1)) {
res$proj1 <- delete_vertex_attr(res$proj1, "type")
}
if (is_igraph(res[[2]]) && "type" %in% vertex_attr_names(res[[2]])) {
res[[2]] <- delete_vertex_attr(res[[2]], "type")
if (is_igraph(res$proj2) && "type" %in% vertex_attr_names(res$proj2)) {
res$proj2 <- delete_vertex_attr(res$proj2, "type")
}
}
if (which == 0L) {
if (multiplicity) {
E(res[[1]])$weight <- res[[3]]
E(res[[2]])$weight <- res[[4]]
E(res$proj1)$weight <- res$multiplicity1
E(res$proj2)$weight <- res$multiplicity2
}
res[1:2]
res[c("proj1", "proj2")]
} else if (which == 1L) {
if (multiplicity) {
E(res[[1]])$weight <- res[[3]]
E(res$proj1)$weight <- res$multiplicity1
}
res[[1]]
res$proj1
} else {
if (multiplicity) {
E(res[[2]])$weight <- res[[4]]
E(res$proj2)$weight <- res$multiplicity2
}
res[[2]]
res$proj2
}
}

Expand Down
4 changes: 2 additions & 2 deletions R/centrality.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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
}
Expand Down
52 changes: 20 additions & 32 deletions R/cliques.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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

@krlmlr krlmlr Jan 30, 2026

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Which igraph_* API is called by the Rx_ function?

Copilot AI Jan 30, 2026

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Updated in 0d52819: Rx_igraph_maximal_cliques calls igraph_maximal_cliques_subset(). The maximal_cliques_impl doesn't support the subset parameter.

Rx_igraph_maximal_cliques_file,
graph,
subset,
Expand All @@ -350,7 +350,7 @@ max_cliques <- function(
}

on.exit(.Call(Rx_igraph_finalizer))
res <- .Call(
res <- .Call( # maximal_cliques_impl doesn't support subset

@krlmlr krlmlr Jan 30, 2026

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Which igraph_* API is called by the Rx_ function?

Copilot AI Jan 30, 2026

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Updated in 0d52819: Rx_igraph_maximal_cliques_file calls igraph_maximal_cliques_subset(). The maximal_cliques_file_impl doesn't support the subset parameter.

Rx_igraph_maximal_cliques,
graph,
subset_arg,
Expand Down Expand Up @@ -398,14 +398,21 @@ count_max_cliques <- function(graph, min = NULL, max = NULL, subset = NULL) {
max <- as.numeric(max)

if (!is.null(subset)) {
subset <- as.numeric(as_igraph_vs(graph, subset) - 1)
# Use maximal_cliques_subset_impl when subset is provided
maximal_cliques_subset_impl(
graph = graph,
subset = subset,
min_size = min,
max_size = max,
details = TRUE
)$no
} else {
maximal_cliques_count_impl(
graph = graph,
min_size = min,
max_size = max
)
}

on.exit(.Call(Rx_igraph_finalizer))
# Function call
res <- .Call(Rx_igraph_maximal_cliques_count, graph, subset, min, max)

res
}

#' @rdname cliques
Expand Down Expand Up @@ -568,30 +575,11 @@ 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
Expand Down
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