feat: make graph constructors default to undirected for consistency

R/make.R

@@ -13,7 +13,7 @@ graph <- function(
   ...,
   n = max(edges),
   isolates = NULL,
-  directed = TRUE,
+  directed = FALSE,
   dir = directed,
   simplify = TRUE
 ) {
@@ -97,9 +97,7 @@ graph <- function(
       if (!missing(n)) {
         args <- c(args, list(n = n))
       }
-      if (!missing(directed)) {
-        args <- c(args, list(directed = directed))
-      }
+      args <- c(args, list(directed = directed))
 
       do.call(old_graph, args)
     } else if (is.character(edges)) {
@@ -222,9 +220,7 @@ graph.famous <- function(
       if (!missing(n)) {
         args <- c(args, list(n = n))
       }
-      if (!missing(directed)) {
-        args <- c(args, list(directed = directed))
-      }
+      args <- c(args, list(directed = directed))
 
       do.call(old_graph, args)
     } else if (is.character(edges)) {
@@ -309,7 +305,7 @@ graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) {
 #' @inheritParams make_tree
 #' @keywords internal
 #' @export
-graph.tree <- function(n, children = 2, mode = c("out", "in", "undirected")) {
+graph.tree <- function(n, children = 2, mode = c("undirected", "out", "in")) {
   # nocov start
   lifecycle::deprecate_warn("2.1.0", "graph.tree()", "make_tree()")
   mode <- igraph_match_arg(mode)
@@ -339,7 +335,7 @@ graph.tree <- function(n, children = 2, mode = c("out", "in", "undirected")) {
 #' @export
 graph.star <- function(
   n,
-  mode = c("in", "out", "mutual", "undirected"),
+  mode = c("undirected", "in", "out", "mutual"),
   center = 1
 ) {
   # nocov start
@@ -1429,7 +1425,7 @@ make_graph <- function(
   ...,
   n = max(edges),
   isolates = NULL,
-  directed = TRUE,
+  directed = FALSE,
   dir = directed,
   simplify = TRUE
 ) {
@@ -1511,9 +1507,7 @@ make_graph <- function(
       if (!missing(n)) {
         args <- c(args, list(n = n))
       }
-      if (!missing(directed)) {
-        args <- c(args, list(directed = directed))
-      }
+      args <- c(args, list(directed = directed))
 
       do.call(old_graph, args)
     } else if (is.character(edges)) {
@@ -1926,7 +1920,7 @@ from_literal <- function(...) {
 make_star <- function(
   n,
   ...,
-  mode = c("in", "out", "mutual", "undirected"),
+  mode = c("undirected", "in", "out", "mutual"),
   center = 1
 ) {
   # BEGIN GENERATED ARG_HANDLE: make_star, do not edit, see tools/generate-migrations.R
@@ -1939,7 +1933,7 @@ make_star <- function(
       match_names = c("mode", "center"),
       match_to = c("mode", "center"),
       defaults = list(
-        mode = c("in", "out", "mutual", "undirected"),
+        mode = c("undirected", "in", "out", "mutual"),
         center = 1
       ),
       head_args = c("n"),
@@ -2407,7 +2401,7 @@ make_tree <- function(
   n,
   children = 2,
   ...,
-  mode = c("out", "in", "undirected")
+  mode = c("undirected", "out", "in")
 ) {
   # BEGIN GENERATED ARG_HANDLE: make_tree, do not edit, see tools/generate-migrations.R
   if (...length() > 0L) {
@@ -2418,7 +2412,7 @@ make_tree <- function(
       recover_old = c("mode"),
       match_names = c("mode"),
       match_to = c("mode"),
-      defaults = list(mode = c("out", "in", "undirected")),
+      defaults = list(mode = c("undirected", "out", "in")),
       head_args = c("n", "children"),
       fn_name = "make_tree"
     )

tests/testthat/_snaps/aaa-auto.md

@@ -10523,9 +10523,9 @@
       union_impl(left = g1, right = g2)
     Output
       $res
-      IGRAPH D--- 4 4 -- 
+      IGRAPH U--- 4 4 -- 
       + edges:
-      [1] 1->2 1->3 2->3 3->4
+      [1] 1--2 1--3 2--3 3--4
 
       $edge_map_left
       [1] 1 3
@@ -10548,9 +10548,9 @@
       intersection_impl(left = g1, right = g2)
     Output
       $res
-      IGRAPH D--- 3 2 -- 
+      IGRAPH U--- 3 2 -- 
       + edges:
-      [1] 1->2 2->3
+      [1] 1--2 2--3
 
       $edge_map_left
       [1] 1 2

tests/testthat/_snaps/conversion.md

@@ -358,9 +358,9 @@
     Output
       3 x 3 sparse Matrix of class "dgCMatrix"
 
-      [1,] .   2.1 3.2
-      [2,] 2.1 .   4.3
-      [3,] 3.2 4.3 .  
+      [1,] .   2.1 4.3
+      [2,] 2.1 .   3.2
+      [3,] 4.3 3.2 .  
 
 ---
 
@@ -369,8 +369,8 @@
     Output
       3 x 3 sparse Matrix of class "dgCMatrix"
 
-      [1,] . 2.1 3.2
-      [2,] . .   4.3
+      [1,] . 2.1 4.3
+      [2,] . .   3.2
       [3,] . .   .  
 
 ---
@@ -382,7 +382,7 @@
 
       [1,] .   .   .
       [2,] 2.1 .   .
-      [3,] 3.2 4.3 .
+      [3,] 4.3 3.2 .
 
 ---
 
@@ -391,28 +391,28 @@
     Output
       3 x 3 sparse Matrix of class "dgCMatrix"
 
-      [1,] .   2.1 3.2
-      [2,] 2.1 .   4.3
-      [3,] 3.2 4.3 .  
+      [1,] .   2.1 4.3
+      [2,] 2.1 .   3.2
+      [3,] 4.3 3.2 .  
 
 ---
 
     Code
       as_adjacency_matrix(g_undir_wt, weights = "weight", sparse = FALSE)
     Output
            [,1] [,2] [,3]
-      [1,]  0.0  2.1  3.2
-      [2,]  2.1  0.0  4.3
-      [3,]  3.2  4.3  0.0
+      [1,]  0.0  2.1  4.3
+      [2,]  2.1  0.0  3.2
+      [3,]  4.3  3.2  0.0
 
 ---
 
     Code
       as_adjacency_matrix(g_undir_wt, weights = "weight", type = "upper", sparse = FALSE)
     Output
            [,1] [,2] [,3]
-      [1,]    0  2.1  3.2
-      [2,]    0  0.0  4.3
+      [1,]    0  2.1  4.3
+      [2,]    0  0.0  3.2
       [3,]    0  0.0  0.0
 
 ---
@@ -423,17 +423,17 @@
            [,1] [,2] [,3]
       [1,]  0.0  0.0    0
       [2,]  2.1  0.0    0
-      [3,]  3.2  4.3    0
+      [3,]  4.3  3.2    0
 
 ---
 
     Code
       as_adjacency_matrix(g_undir_wt, weights = "weight", type = "both", sparse = FALSE)
     Output
            [,1] [,2] [,3]
-      [1,]  0.0  2.1  3.2
-      [2,]  2.1  0.0  4.3
-      [3,]  3.2  4.3  0.0
+      [1,]  0.0  2.1  4.3
+      [2,]  2.1  0.0  3.2
+      [3,]  4.3  3.2  0.0
 
 ---
 

tests/testthat/helper-indexing.R

@@ -10,13 +10,13 @@ as_unnamed_dense_matrix <- function(x) {
 }
 
 make_test_named_tree <- function() {
-  g <- make_tree(20)
+  g <- make_tree(20, mode = "out")
   V(g)$name <- letters[1:vcount(g)]
   g
 }
 
 make_test_weighted_tree <- function() {
-  g <- make_tree(20)
+  g <- make_tree(20, mode = "out")
   V(g)$name <- letters[1:vcount(g)]
   el <- as_edgelist(g, names = FALSE)
   E(g)$weight <- el[, 1] * el[, 2]

tests/testthat/test-aaa-auto.R

@@ -6426,7 +6426,7 @@ test_that("hrg_predict_impl errors", {
 
 test_that("hrg_create_impl basic", {
   igraph_local_seed(20250909)
-  g <- make_tree(5)
+  g <- make_tree(5, mode = "out")
   expect_snapshot(hrg_create_impl(
     graph = g,
     prob = rep(0.5, 2)

tests/testthat/test-attributes.R

@@ -211,7 +211,7 @@ test_that("cannot use vs/es from another graph", {
 })
 
 test_that("attribute combinations handle errors correctly", {
-  g <- make_graph(c(1, 2, 2, 1))
+  g <- make_graph(c(1, 2, 2, 1), directed = TRUE)
   E(g)$weight <- c("a", "b")
   expect_error(
     as_undirected(g, edge.attr.comb = list(weight = "sum")),