[WIP] Fix functions ignoring return.vs.es option

R/basic.R

@@ -77,13 +77,19 @@ get.edge <- function(graph, id) {
 #'
 #' @param graph The input graph.
 #' @param es The edges to query.
-#' @return A vertex sequence with the head(s) of the edge(s).
+#' @return A vertex sequence with the head(s) of the edge(s) if
+#'   the `return.vs.es` igraph option is true (the default), or a numeric
+#'   vector of vertex IDs otherwise.
 #'
 #' @family structural queries
 #'
 #' @export
 head_of <- function(graph, es) {
-  create_vs(graph, ends(graph, es, names = FALSE)[, 2])
+  res <- ends(graph, es, names = FALSE)[, 2]
+  if (igraph_opt("return.vs.es")) {
+    res <- create_vs(graph, res)
+  }
+  res
 }
 
 #' Tails of the edge(s) in a graph
@@ -94,11 +100,17 @@ head_of <- function(graph, es) {
 #'
 #' @param graph The input graph.
 #' @param es The edges to query.
-#' @return A vertex sequence with the tail(s) of the edge(s).
+#' @return A vertex sequence with the tail(s) of the edge(s) if
+#'   the `return.vs.es` igraph option is true (the default), or a numeric
+#'   vector of vertex IDs otherwise.
 #'
 #' @family structural queries
 #'
 #' @export
 tail_of <- function(graph, es) {
-  create_vs(graph, ends(graph, es, names = FALSE)[, 1])
+  res <- ends(graph, es, names = FALSE)[, 1]
+  if (igraph_opt("return.vs.es")) {
+    res <- create_vs(graph, res)
+  }
+  res
 }

R/conversion.R

@@ -651,7 +651,9 @@ as_undirected <- function(
 #'
 #' `as_adj_edge_list()` returns a list of numeric vectors, which include the
 #' ids of adjacent edges (according to the `mode` argument) of all
-#' vertices.
+#' vertices. The return type depends on the `return.vs.es` option: if true
+#' (default), a list of `igraph.es` is returned; if false, a list of numeric
+#' vectors is returned.
 #'
 #' @param graph The input graph.
 #' @param mode Character scalar, it gives what kind of adjacent edges/vertices
@@ -663,7 +665,8 @@ as_undirected <- function(
 #'   is not allowed for directed graphs and will be replaced with `"once"`.
 #' @param multiple Logical scalar, set to `FALSE` to use only one representative
 #'   of each set of parallel edges.
-#' @return A list of `igraph.vs` or a list of numeric vectors depending on
+#' @return A list of `igraph.vs` (for `as_adj_list()`) or `igraph.es`
+#'   (for `as_adj_edge_list()`), or a list of numeric vectors depending on
 #'   the value of `igraph_opt("return.vs.es")`, see details for performance
 #'   characteristics.
 #' @details If `igraph_opt("return.vs.es")` is true (default), the numeric
@@ -730,7 +733,11 @@ as_adj_edge_list <- function(
 
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(R_igraph_get_adjedgelist, graph, mode, loops)
-  res <- lapply(res, function(.x) E(graph)[.x + 1])
+  if (igraph_opt("return.vs.es")) {
+    res <- lapply(res, function(.x) E(graph)[.x + 1])
+  } else {
+    res <- lapply(res, `+`, 1)
+  }
   if (is_named(graph)) {
     names(res) <- V(graph)$name
   }

R/topology.R

@@ -192,7 +192,12 @@ graph.get.isomorphisms.vf2 <- function(
     edge.color2
   )
 
-  lapply(res, function(.x) V(graph2)[.x + 1])
+  if (igraph_opt("return.vs.es")) {
+    res <- lapply(res, function(.x) V(graph2)[.x + 1])
+  } else {
+    res <- lapply(res, `+`, 1)
+  }
+  res
 }
 
 #' @export
@@ -260,7 +265,12 @@ graph.get.subisomorphisms.vf2 <- function(
     edge.color2
   )
 
-  lapply(res, function(.x) V(graph1)[.x + 1])
+  if (igraph_opt("return.vs.es")) {
+    res <- lapply(res, function(.x) V(graph1)[.x + 1])
+  } else {
+    res <- lapply(res, `+`, 1)
+  }
+  res
 }
 
 #' @export
@@ -330,7 +340,11 @@ graph.subisomorphic.lad <- function(
     }
   }
   if (all.maps) {
-    res$maps <- lapply(res$maps, function(.x) V(target)[.x + 1])
+    if (igraph_opt("return.vs.es")) {
+      res$maps <- lapply(res$maps, function(.x) V(target)[.x + 1])
+    } else {
+      res$maps <- lapply(res$maps, `+`, 1)
+    }
   }
 
   res
@@ -854,8 +868,10 @@ graph.count.subisomorphisms.vf2 <- function(
 #' @param method Currently only \sQuote{vf2} is supported, see
 #'   [isomorphic()] for details about it and extra arguments.
 #' @param ... Extra arguments, passed to the various methods.
-#' @return A list of vertex sequences, corresponding to all
-#'   mappings from the first graph to the second.
+#' @return A list of vertex sequences (if the `return.vs.es` igraph option is
+#'   true, the default), or a list of numeric vectors of vertex IDs (if
+#'   `return.vs.es` is false), corresponding to all mappings from the first
+#'   graph to the second.
 #'
 #' @aliases graph.get.isomorphisms.vf2
 #'
@@ -920,8 +936,10 @@ isomorphisms <- function(graph1, graph2, method = "vf2", ...) {
 #' @param method The method to use. Possible values: \sQuote{auto},
 #'   \sQuote{lad}, \sQuote{vf2}. See their details below.
 #' @param ... Additional arguments, passed to the various methods.
-#' @return A list of vertex sequences, corresponding to all
-#'   mappings from the first graph to the second.
+#' @return A list of vertex sequences (if the `return.vs.es` igraph option is
+#'   true, the default), or a list of numeric vectors of vertex IDs (if
+#'   `return.vs.es` is false), corresponding to all mappings from the first
+#'   graph to the second.
 #'
 #' @aliases graph.get.subisomorphisms.vf2
 #'

tests/testthat/test-conversion.R

@@ -444,6 +444,24 @@ test_that("as_adj_list works when return.vs.es is FALSE", {
   }
 })
 
+test_that("as_adj_edge_list respects return.vs.es option", {
+  g <- make_tree(6, children = 2)
+  V(g)$name <- paste0("V", 1:6)
+
+  # Test with return.vs.es = TRUE (default)
+  local_igraph_options(return.vs.es = TRUE)
+  adj_el_list <- as_adj_edge_list(g)
+  expect_s3_class(adj_el_list[[1]], "igraph.es")
+  expect_length(adj_el_list[[1]], 2)
+
+  # Test with return.vs.es = FALSE
+  local_igraph_options(return.vs.es = FALSE)
+  adj_el_list <- as_adj_edge_list(g)
+  expect_type(adj_el_list[[1]], "integer")
+  expect_length(adj_el_list[[1]], 2)
+  expect_equal(as.numeric(adj_el_list[[1]]), c(1, 2))
+})
+
 test_that("as_edgelist works", {
   g <- sample_gnp(100, 3 / 100)
   el <- as_edgelist(g)

tests/testthat/test-interface.R

@@ -222,3 +222,39 @@ test_that("get_edge_id() errors correctly for wrong matrices", {
   mat <- matrix(c(1, 2, 1, 3, 1, 4), nrow = 2, ncol = 3)
   lifecycle::expect_deprecated(get_edge_ids(g, mat))
 })
+
+test_that("head_of respects return.vs.es option", {
+  g <- make_tree(6, children = 2)
+  V(g)$name <- paste0("V", 1:6)
+
+  # Test with return.vs.es = TRUE (default)
+  local_igraph_options(return.vs.es = TRUE)
+  result <- head_of(g, E(g)[c(1, 4)])
+  expect_s3_class(result, "igraph.vs")
+  expect_length(result, 2)
+
+  # Test with return.vs.es = FALSE
+  local_igraph_options(return.vs.es = FALSE)
+  result <- head_of(g, E(g)[c(1, 4)])
+  expect_type(result, "integer")
+  expect_length(result, 2)
+  expect_equal(as.numeric(result), c(2, 5))
+})
+
+test_that("tail_of respects return.vs.es option", {
+  g <- make_tree(6, children = 2)
+  V(g)$name <- paste0("V", 1:6)
+
+  # Test with return.vs.es = TRUE (default)
+  local_igraph_options(return.vs.es = TRUE)
+  result <- tail_of(g, E(g)[c(1, 4)])
+  expect_s3_class(result, "igraph.vs")
+  expect_length(result, 2)
+
+  # Test with return.vs.es = FALSE
+  local_igraph_options(return.vs.es = FALSE)
+  result <- tail_of(g, E(g)[c(1, 4)])
+  expect_type(result, "integer")
+  expect_length(result, 2)
+  expect_equal(as.numeric(result), c(1, 2))
+})

tests/testthat/test-topology.R

@@ -361,3 +361,52 @@ test_that("subgraph_isomorphisms, vf2", {
   g3 <- graph_from_literal(X - Y - Z - X)
   expect_equal(subgraph_isomorphisms(g3, g1, method = "vf2"), list())
 })
+
+test_that("graph.get.isomorphisms.vf2 respects return.vs.es option", {
+  g <- make_tree(6, children = 2)
+  V(g)$name <- paste0("V", 1:6)
+
+  # Test with return.vs.es = TRUE (default)
+  local_igraph_options(return.vs.es = TRUE)
+  result <- graph.get.isomorphisms.vf2(g, g)
+  expect_s3_class(result[[1]], "igraph.vs")
+  expect_length(result[[1]], 6)
+
+  # Test with return.vs.es = FALSE
+  local_igraph_options(return.vs.es = FALSE)
+  result <- graph.get.isomorphisms.vf2(g, g)
+  expect_type(result[[1]], "integer")
+  expect_length(result[[1]], 6)
+})
+
+test_that("graph.get.subisomorphisms.vf2 respects return.vs.es option", {
+  g <- make_tree(6, children = 2)
+
+  # Test with return.vs.es = TRUE (default)
+  local_igraph_options(return.vs.es = TRUE)
+  result <- graph.get.subisomorphisms.vf2(g, g)
+  expect_s3_class(result[[1]], "igraph.vs")
+  expect_length(result[[1]], 6)
+
+  # Test with return.vs.es = FALSE
+  local_igraph_options(return.vs.es = FALSE)
+  result <- graph.get.subisomorphisms.vf2(g, g)
+  expect_type(result[[1]], "integer")
+  expect_length(result[[1]], 6)
+})
+
+test_that("graph.subisomorphic.lad respects return.vs.es option", {
+  g <- make_tree(6, children = 2)
+
+  # Test with return.vs.es = TRUE (default)
+  local_igraph_options(return.vs.es = TRUE)
+  result <- graph.subisomorphic.lad(g, g, all.maps = TRUE)
+  expect_s3_class(result$maps[[1]], "igraph.vs")
+  expect_length(result$maps[[1]], 6)
+
+  # Test with return.vs.es = FALSE
+  local_igraph_options(return.vs.es = FALSE)
+  result <- graph.subisomorphic.lad(g, g, all.maps = TRUE)
+  expect_type(result$maps[[1]], "integer")
+  expect_length(result$maps[[1]], 6)
+})