fix: use canonical structure() attribute names

R/plot.common.R

@@ -4841,7 +4841,7 @@ curve_multiple <- function(graph, start = 0.5) {
       16777215L,
       16777215L
     ),
-    .Dim = c(64L, 64L),
+    dim = c(64L, 64L),
     class = "nativeRaster",
     channels = 4L
   )

tests/testthat/helper-test-functions.R

@@ -243,7 +243,7 @@ karate_oldstyle <- structure(
           Citation = "Wayne W. Zachary. An Information Flow Model for Conflict and Fission in Small Groups. Journal of Anthropological Research Vol. 33, No. 4 452-473",
           Author = "Wayne W. Zachary"
         ),
-        .Names = c("name", "Citation", "Author")
+        names = c("name", "Citation", "Author")
       ),
       structure(
         list(
@@ -254,7 +254,7 @@ karate_oldstyle <- structure(
           ),
           name = karate_oldstyle_names
         ),
-        .Names = c("Faction", "name")
+        names = c("Faction", "name")
       ),
       structure(
         list(
@@ -266,7 +266,7 @@ karate_oldstyle <- structure(
             2, 7, 4, 2, 4, 2, 2, 4, 2, 3, 3, 4, 4, 5
           )
         ),
-        .Names = "weight"
+        names = "weight"
       )
     )
   ),

tests/testthat/test-attributes.R

@@ -71,7 +71,7 @@ test_that("bracketing works with shortcuts (not changing attribute of similar gr
 test_that("we can query all attributes at once", {
   g <- make_graph(c(1, 2, 1, 3, 2, 4))
 
-  expect_equal(graph_attr(g), structure(list(), .Names = character(0)))
+  expect_equal(graph_attr(g), structure(list(), names = character(0)))
   expect_equal(unname(vertex_attr(g)), list())
   expect_equal(unname(edge_attr(g)), list())
 

tests/testthat/test-centrality.R

@@ -573,7 +573,7 @@ test_that("eigen_centrality() works", {
     evc,
     structure(
       c(0.732, 0.732, 0.594, 1, 0.827, 0.594, 0.827, 0.407, 0.1, 0.023),
-      .Names = c("Andre", "Beverly", "Carol", "Diane", "Fernando", "Ed", "Garth", "Heather", "Ike", "Jane")
+      names = c("Andre", "Beverly", "Carol", "Diane", "Fernando", "Ed", "Garth", "Heather", "Ike", "Jane")
     )
   )
 
@@ -857,7 +857,7 @@ test_that("arpack works for non-symmetric matrices", {
       1, -4, 9, -2, 10, 1, -7, 7, 6, 7, -3, 0, 9, -5, -8, 1, -3,
       -3, -8, -7, -8, 10, 8, 7, 0, 6, -7, -8, 10, 10, 1, 0, -2, 6
     ),
-    .Dim = c(10L, 10L)
+    dim = c(10L, 10L)
   )
 
   f <- function(x, extra = NULL) A %*% x

tests/testthat/test-community.R

@@ -100,8 +100,8 @@ test_that("communities function works", {
         `3` = c(9L, 10L, 15L, 16L, 19L, 21L, 23L, 27L, 30L, 31L, 33L, 34L),
         `4` = c(24L, 25L, 26L, 28L, 29L, 32L)
       ),
-      .Dim = 4L,
-      .Dimnames = list(c("1", "2", "3", "4"))
+      dim = 4L,
+      dimnames = list(c("1", "2", "3", "4"))
     )
   )
 
@@ -116,8 +116,8 @@ test_that("communities function works", {
         `1` = letters[1:5],
         `2` = letters[6:10]
       ),
-      .Dim = 2L,
-      .Dimnames = list(c("1", "2"))
+      dim = 2L,
+      dimnames = list(c("1", "2"))
     )
   )
 })
@@ -249,10 +249,10 @@ test_that("cluster_leading_eigen works", {
     sizes(karate_lc),
     structure(
       c(7L, 12L, 9L, 6L),
-      .Dim = 4L,
-      .Dimnames = structure(
+      dim = 4L,
+      dimnames = structure(
         list(`Community sizes` = c("1", "2", "3", "4")),
-        .Names = "Community sizes"
+        names = "Community sizes"
       ),
       class = "table"
     )
@@ -421,10 +421,10 @@ test_that("cluster_leiden works", {
     sizes(karate_leiden),
     structure(
       c(17L, 17L),
-      .Dim = 2L,
-      .Dimnames = structure(
+      dim = 2L,
+      dimnames = structure(
         list(`Community sizes` = c("1", "2")),
-        .Names = "Community sizes"
+        names = "Community sizes"
       ),
       class = "table"
     )
@@ -445,10 +445,10 @@ test_that("cluster_leiden works", {
     sizes(karate_leiden_mod),
     structure(
       c(11L, 5L, 12L, 6L),
-      .Dim = 4L,
-      .Dimnames = structure(
+      dim = 4L,
+      dimnames = structure(
         list(`Community sizes` = c("1", "2", "3", "4")),
-        .Names = "Community sizes"
+        names = "Community sizes"
       ),
       class = "table"
     )
@@ -525,10 +525,10 @@ test_that("cluster_optimal works", {
     sizes(karate_optimal),
     structure(
       c(11L, 5L, 12L, 6L),
-      .Dim = 4L,
-      .Dimnames = structure(
+      dim = 4L,
+      dimnames = structure(
         list(`Community sizes` = c("1", "2", "3", "4")),
-        .Names = "Community sizes"
+        names = "Community sizes"
       ),
       class = "table"
     )
@@ -569,10 +569,10 @@ test_that("cluster_walktrap works", {
     sizes(karate_walktrap),
     structure(
       c(9L, 7L, 9L, 4L, 5L),
-      .Dim = 5L,
-      .Dimnames = structure(
+      dim = 5L,
+      dimnames = structure(
         list(`Community sizes` = c("1", "2", "3", "4", "5")),
-        .Names = "Community sizes"
+        names = "Community sizes"
       ),
       class = "table"
     )
@@ -608,8 +608,8 @@ test_that("groups works", {
     gr,
     structure(
       list(`1` = 1:10, `2` = 11:15),
-      .Dim = 2L,
-      .Dimnames = list(c("1", "2"))
+      dim = 2L,
+      dimnames = list(c("1", "2"))
     )
   )
 
@@ -620,8 +620,8 @@ test_that("groups works", {
     gr,
     structure(
       list(`1` = letters[1:10], `2` = letters[11:15]),
-      .Dim = 2L,
-      .Dimnames = list(c("1", "2"))
+      dim = 2L,
+      dimnames = list(c("1", "2"))
     )
   )
 })

tests/testthat/test-conversion.R

@@ -805,7 +805,7 @@ test_that("edge names work", {
   g2 <- delete_edges(g, c("b", "d", "e"))
   expect_equal(
     as_edgelist(g2),
-    structure(c(1, 3, 6, 7, 8, 9, 1, 2, 4, 7, 8, 9, 10, 10), .Dim = c(7L, 2L))
+    structure(c(1, 3, 6, 7, 8, 9, 1, 2, 4, 7, 8, 9, 10, 10), dim = c(7L, 2L))
   )
 
   ## named vertices
@@ -816,7 +816,7 @@ test_that("edge names work", {
     as_edgelist(g3),
     structure(
       c("c", "d", "e", "g", "h", "i", "a", "d", "e", "f", "h", "i", "j", "j"),
-      .Dim = c(7L, 2L)
+      dim = c(7L, 2L)
     )
   )
 
@@ -825,7 +825,7 @@ test_that("edge names work", {
   g4 <- delete_edges(g, c("1|2", "8|7", "1|10"))
   expect_equal(
     as_edgelist(g4),
-    structure(c(2, 3, 4, 5, 6, 8, 9, 3, 4, 5, 6, 7, 9, 10), .Dim = c(7L, 2L))
+    structure(c(2, 3, 4, 5, 6, 8, 9, 3, 4, 5, 6, 7, 9, 10), dim = c(7L, 2L))
   )
 
   ## mix edge names and vertex names
@@ -837,7 +837,7 @@ test_that("edge names work", {
     as_edgelist(g5),
     structure(
       c("b", "c", "d", "e", "g", "h", "a", "c", "d", "e", "f", "h", "i", "j"),
-      .Dim = c(7L, 2L)
+      dim = c(7L, 2L)
     )
   )
 })

tests/testthat/test-flow.R

@@ -271,7 +271,7 @@ test_that("dominator_tree works -- legacy", {
     as_edgelist(dtree$domtree),
     structure(
       c("R", "R", "R", "R", "R", "C", "C", "D", "R", "R", "G", "R", "A", "B", "C", "D", "E", "F", "G", "L", "H", "I", "J", "K"),
-      .Dim = c(12L, 2L)
+      dim = c(12L, 2L)
     )
   )
 })

tests/testthat/test-indexing.R

@@ -54,8 +54,8 @@ test_that("[ indexing works with logical vectors", {
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0
     ),
-    .Dim = c(2L, 20L),
-    .Dimnames = list(
+    dim = c(2L, 20L),
+    dimnames = list(
       c("b", "c"),
       c(
       "a", "b", "c",
@@ -77,8 +77,8 @@ test_that("[ indexing works with negative indices", {
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0
     ),
-    .Dim = c(2L, 19L),
-    .Dimnames = list(
+    dim = c(2L, 19L),
+    dimnames = list(
       c("b", "c"),
       c(
         "b", "c", "d", "e", "f", "g", "h", "i", "j",

tests/testthat/test-make.R

@@ -440,7 +440,7 @@ test_that("make_kautz_graph works", {
       20, 21, 22, 23, 24, 1, 2, 3, 4, 5, 6, 7,
       8, 9, 10, 11, 12, 13, 14, 15, 16
     ),
-      .Dim = c(48L, 2L)
+      dim = c(48L, 2L)
     )
   )
 })

tests/testthat/test-structural-properties.R

@@ -513,7 +513,7 @@ test_that("transitivity() works", {
   t33 <- transitivity(g, type = "local")
   est3 <- structure(
     c(0, 0.06667, 0.1028, 0.1016, 0.1333, 0.2222),
-    .Names = c(
+    names = c(
       "Min.",
       "1st Qu.",
       "Median",
@@ -1058,7 +1058,7 @@ test_that("knn works", {
         knn = c(1, rep(9, 9)),
         knnk = c(9, NaN, NaN, NaN, NaN, NaN, NaN, NaN, 1)
       ),
-      .Names = c("knn", "knnk")
+      names = c("knn", "knnk")
     )
   )
 })