feat: added simple check to graph_from_literal()

R/make.R

@@ -1819,7 +1819,7 @@ graph_from_literal_i <- function(mf) {
   ids <- seq(along.with = v)
   names(ids) <- v
   res <- make_graph(unname(ids[edges]), n = length(v), directed = directed)
-  if (simplify) {
+  if (simplify && !is_simple(res)) {
     res <- simplify(res)
   }
   res <- set_vertex_attr(res, "name", value = v)

tests/testthat/_snaps/aaa-auto.md

@@ -10983,24 +10983,24 @@
       community_edge_betweenness_impl(graph = g, directed = FALSE)
     Output
       $removed_edges
-      [1] 2 0 1 3 4 5 6
+      [1] 6 0 1 2 3 4 5
 
       $edge_betweenness
       [1] 9 1 2 1 1 2 1
 
       $merges
            [,1] [,2]
-      [1,]    5    4
-      [2,]    6    3
-      [3,]    2    1
-      [4,]    8    0
+      [1,]    5    3
+      [2,]    6    4
+      [3,]    2    0
+      [4,]    8    1
       [5,]    7    9
 
       $bridges
       [1] 7 6 4 3 1
 
       $modularity
-      [1] -0.17346939 -0.07142857  0.09183673  0.19387755  0.35714286  0.00000000
+      [1] -0.17346939 -0.09183673  0.09183673  0.17346939  0.35714286  0.00000000
 
       $membership
       [1] 0 0 0 1 1 1

tests/testthat/_snaps/make.md

@@ -63,7 +63,7 @@
       IGRAPH UN-- 3 3 -- 
       + attr: name (v/c)
       + edges (vertex names):
-      [1] A--B A--C B--C
+      [1] A--B B--C A--C
 
 # graph_from_literal() and undirected explosion
 
@@ -112,7 +112,7 @@
       IGRAPH DN-- 3 3 -- 
       + attr: name (v/c)
       + edges (vertex names):
-      [1] A->B C->A C->B
+      [1] A->B C->B C->A
 
 # graph_from_literal() and directed explosion
 
@@ -129,7 +129,7 @@
       IGRAPH DN-- 13 19 -- 
       + attr: name (v/c)
       + edges (vertex names):
-       [1] A->D A->E B->D B->E C->D C->E F->D F->E F->I G->D G->E G->I H->D H->E H->I
+       [1] A->D A->E B->D B->E C->D C->E F->D G->D H->D F->E G->E H->E F->I G->I H->I
       [16] J->I K->I L->I M->I
 
 # graph_from_literal(simplify = FALSE)

tests/testthat/_snaps/structural-properties.md

@@ -10,7 +10,8 @@
 # bfs() works
 
     Code
-      g <- graph_from_literal(a - +b - +c, z - +a, d)
+      el <- structure(c("a", "b", "z", "b", "c", "a"), dim = 3:2)
+      g <- graph_from_edgelist(el) + vertex("d")
       bfs(g, root = 2, mode = "out", unreachable = FALSE, order = TRUE, rank = TRUE,
         parent = TRUE, pred = TRUE, succ = TRUE, dist = TRUE)
     Output

tests/testthat/test-conversion.R

@@ -18,7 +18,8 @@ test_that("as_directed works", {
 })
 
 test_that("as_directed keeps attributes", {
-  g <- graph_from_literal(A - B - C, D - A, E)
+  el <- structure(c("A", "A", "B", "B", "D", "C"), dim = 3:2)
+  g <- graph_from_edgelist(el, directed = FALSE) + vertex("E")
   g$name <- "Small graph"
   g_mutual <- as_directed(g, mode = "mutual")
   expect_equal(g_mutual$name, g$name)
@@ -59,7 +60,11 @@ test_that("as.undirected() deprecation", {
 })
 
 test_that("as_undirected() keeps attributes", {
-  g <- graph_from_literal(A +-+ B, A --+ C, C +-+ D)
+  el <- structure(
+    c("A", "A", "B", "C", "D", "B", "C", "A", "D", "C"),
+    dim = c(5L, 2L)
+  )
+  g <- graph_from_edgelist(el, directed = TRUE)
   g$name <- "Tiny graph"
   E(g)$weight <- seq_len(ecount(g))
 

tests/testthat/test-flow.R

@@ -50,7 +50,13 @@ test_that("st_cuts() works", {
   expect_equal(unvs(all_cuts_path$cuts), list(1, 2, 3, 4))
   expect_equal(unvs(all_cuts_path$partition1s), list(1, 1:2, 1:3, 1:4))
 
-  g_star_v7 <- graph_from_literal(s -+ a:b -+ t, a -+ 1:2:3 -+ b)
+  el <- structure(
+    c(
+      "s", "s", "a", "a", "a", "a", "b", "1", "2", "3", 
+      "a", "b", "t", "1", "2", "3", "t", "b", "b", "b"),
+    dim = c(10L, 2L)
+  )
+  g_star_v7 <- graph_from_edgelist(el)
   all_cuts_star_v7 <- st_cuts(g_star_v7, source = "s", target = "t")
   expect_equal(
     unvs(all_cuts_star_v7$cuts),
@@ -84,8 +90,13 @@ test_that("st_cuts() works", {
       c(1, 2, 5, 6, 7, 3)
     )
   )
-
-  g_star_v9 <- graph_from_literal(s -+ a:b -+ t, a -+ 1:2:3:4:5 -+ b)
+  el <- structure(
+    c("s", "s", "a", "a", "a", "a", "a", "a", "b", "1", 
+  "2", "3", "4", "5", "a", "b", "t", "1", "2", "3", "4", "5", "t", 
+  "b", "b", "b", "b", "b"),
+    dim = c(14L, 2L)
+  )
+  g_star_v9 <- graph_from_edgelist(el)
   all_cuts_star_v9 <- st_min_cuts(g_star_v9, source = "s", target = "t")
   expect_equal(all_cuts_star_v9$value, 2)
   expect_equal(unvs(all_cuts_star_v9$cuts), list(c(1, 2), c(1, 9), c(3, 9)))

tests/testthat/test-operators.R

@@ -108,8 +108,15 @@ test_that("compose() works", {
 })
 
 test_that("compose works for named graphs", {
-  g1 <- graph_from_literal(A - B:D:E, B - C:D, C - D, D - E)
-  g2 <- graph_from_literal(A - B - E - A)
+  el1 <- structure(
+    c(
+      "A", "A", "A", "B", "B", "D", "D", "B", "D", "E", 
+      "D", "C", "E", "C"),
+    dim = c(7L, 2L)
+  )
+  el2 <- structure(c("A", "A", "B", "B", "E", "E"), dim = 3:2)
+  g1 <- graph_from_edgelist(el1, directed = FALSE)
+  g2 <- graph_from_edgelist(el2, directed = FALSE)
 
   V(g1)$bar1 <- seq_len(vcount(g1))
   V(g2)$bar2 <- seq_len(vcount(g2))

tests/testthat/test-structural-properties.R

@@ -216,7 +216,8 @@ test_that("bfs() works", {
   local_igraph_options(print.id = FALSE)
 
   expect_snapshot({
-    g <- graph_from_literal(a -+ b -+ c, z -+ a, d)
+    el <- structure(c("a", "b", "z", "b", "c", "a"), dim = 3:2)
+    g <- graph_from_edgelist(el) + vertex("d")
     bfs(
       g,
       root = 2,