test: create and use expect_isomorphic()

maelle · aviator-bot · commit 4959fcefb681 · 2024-05-20T17:10:19.000Z
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
@@ -25,3 +25,7 @@ expect_that <- function(object, condition, info = NULL, label = NULL) {
     condition(object)
   )
 }
+
+expect_isomorphic <- function(g1, g2) {
+  expect_true(graph.isomorphic(g1, g2))
+}
diff --git a/tests/testthat/test-as.directed.R b/tests/testthat/test-as.directed.R
@@ -10,10 +10,10 @@ test_that("as.directed works", {
   expect_that(degree(g), equals(degree(g4)))
   expect_that(degree(g), equals(degree(g5)))
 
-  expect_true(graph.isomorphic(g, as.undirected(g2)))
-  expect_true(graph.isomorphic(g, as.undirected(g3)))
-  expect_true(graph.isomorphic(g, as.undirected(g4)))
-  expect_true(graph.isomorphic(g, as.undirected(g5)))
+  expect_isomorphic(g, as.undirected(g2))
+  expect_isomorphic(g, as.undirected(g3))
+  expect_isomorphic(g, as.undirected(g4))
+  expect_isomorphic(g, as.undirected(g5))
 })
 
 test_that("as.directed keeps attributes", {
diff --git a/tests/testthat/test-ba.game.R b/tests/testthat/test-ba.game.R
@@ -43,7 +43,7 @@ test_that("sample_pa can start from a graph", {
   expect_true(sum(is_degree_two_or_three) %in% 0:4)
 
   g6 <- sample_pa(10, m = 1, algorithm = "bag", start.graph = make_star(10))
-  expect_true(graph.isomorphic(g6, make_star(10)))
+  expect_isomorphic(g6, make_star(10))
 
   g7 <- sample_pa(10,
     m = 3, algorithm = "psumtree-multiple",
@@ -56,21 +56,21 @@ test_that("sample_pa can start from a graph", {
     start.graph = make_star(5)
   )
   expect_that(degree(g8, mode = "out"), equals(c(0, 1, 1, 1, 1, 3, 3, 3, 3, 3)))
-  expect_true(graph.isomorphic(induced_subgraph(g8, 1:5), make_star(5)))
+  expect_isomorphic(induced_subgraph(g8, 1:5), make_star(5))
 
   g9 <- sample_pa(10,
     m = 3, algorithm = "psumtree-multiple",
     start.graph = make_star(10)
   )
-  expect_true(graph.isomorphic(g9, make_star(10)))
+  expect_isomorphic(g9, make_star(10))
 
   g10 <- sample_pa(10, m = 3, start.graph = make_empty_graph(5))
   expect_that(degree(g10, mode = "out"), equals(c(0, 0, 0, 0, 0, 3, 3, 3, 3, 3)))
 
   g11 <- sample_pa(10, m = 3, start.graph = make_star(5))
   expect_that(degree(g11, mode = "out"), equals(c(0, 1, 1, 1, 1, 3, 3, 3, 3, 3)))
-  expect_true(graph.isomorphic(induced_subgraph(g11, 1:5), make_star(5)))
+  expect_isomorphic(induced_subgraph(g11, 1:5), make_star(5))
 
   g12 <- sample_pa(10, m = 3, start.graph = make_star(10))
-  expect_true(graph.isomorphic(g12, make_star(10)))
+  expect_isomorphic(g12, make_star(10))
 })
diff --git a/tests/testthat/test-bipartite.projection.R b/tests/testthat/test-bipartite.projection.R
@@ -4,8 +4,8 @@ test_that("bipartite_projection works", {
 
   g <- make_full_bipartite_graph(10, 5)
   proj <- bipartite_projection(g)
-  expect_true(graph.isomorphic(proj[[1]], make_full_graph(10)))
-  expect_true(graph.isomorphic(proj[[2]], make_full_graph(5)))
+  expect_isomorphic(proj[[1]], make_full_graph(10))
+  expect_isomorphic(proj[[2]], make_full_graph(5))
 
   M <- matrix(0, nrow = 5, ncol = 3)
   rownames(M) <- c("Alice", "Bob", "Cecil", "Dan", "Ethel")
@@ -47,8 +47,8 @@ test_that("bipartite_projection can calculate only one projection", {
   proj1 <- bipartite_projection(g, which = "false")
   proj2 <- bipartite_projection(g, which = "true")
 
-  expect_true(graph.isomorphic(proj$proj1, proj1))
-  expect_true(graph.isomorphic(proj$proj2, proj2))
+  expect_isomorphic(proj$proj1, proj1)
+  expect_isomorphic(proj$proj2, proj2)
   expect_that(vertex.attributes(proj$proj1), equals(vertex.attributes(proj1)))
   expect_that(vertex.attributes(proj$proj2), equals(vertex.attributes(proj2)))
   expect_that(edge_attr(proj$proj1), equals(edge_attr(proj1)))
diff --git a/tests/testthat/test-delete.vertices.R b/tests/testthat/test-delete.vertices.R
@@ -5,5 +5,5 @@ test_that("delete_vertices works", {
   expect_equal(V(g2)$name, c("B", "C", "D", "E", "F"))
 
   g3 <- delete_vertices(g, match("A", V(g)$name))
-  expect_true(graph.isomorphic(g2, g3))
+  expect_isomorphic(g2, g3)
 })
diff --git a/tests/testthat/test-get.adjacency.R b/tests/testthat/test-get.adjacency.R
@@ -2,24 +2,24 @@ test_that("as_adj works", {
   g <- sample_gnp(50, 1 / 50)
   A <- as_adj(g, sparse = FALSE)
   g2 <- graph_from_adjacency_matrix(A, mode = "undirected")
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   ###
 
   A <- as_adj(g, sparse = TRUE)
   g2 <- graph_from_adjacency_matrix(A, mode = "undirected")
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   ###
 
   g <- sample_gnp(50, 2 / 50, directed = TRUE)
   A <- as_adj(g, sparse = FALSE)
   g2 <- graph_from_adjacency_matrix(A)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   ###
 
   A <- as_adj(g, sparse = TRUE)
   g2 <- graph_from_adjacency_matrix(A)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 })
diff --git a/tests/testthat/test-get.adjlist.R b/tests/testthat/test-get.adjlist.R
@@ -2,7 +2,7 @@ test_that("as_adj_list works", {
   g <- sample_gnp(50, 2 / 50)
   al <- as_adj_list(g)
   g2 <- graph_from_adj_list(al, mode = "all")
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
   expect_true(graph.isomorphic.vf2(g, g2,
     vertex.color1 = 1:vcount(g),
     vertex.color2 = 1:vcount(g2)
diff --git a/tests/testthat/test-get.edge.R b/tests/testthat/test-get.edge.R
@@ -2,5 +2,5 @@ test_that("ends works", {
   g <- sample_gnp(100, 3 / 100)
   edges <- unlist(lapply(seq_len(ecount(g)), ends, graph = g))
   g2 <- make_graph(edges, dir = FALSE, n = vcount(g))
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 })
diff --git a/tests/testthat/test-get.edgelist.R b/tests/testthat/test-get.edgelist.R
@@ -2,5 +2,5 @@ test_that("as_edgelist works", {
   g <- sample_gnp(100, 3 / 100)
   e <- as_edgelist(g)
   g2 <- make_graph(t(e), n = vcount(g), dir = FALSE)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 })
diff --git a/tests/testthat/test-graph.adjlist.R b/tests/testthat/test-graph.adjlist.R
@@ -2,12 +2,12 @@ test_that("graph_from_adj_list works", {
   g <- sample_gnp(100, 3 / 100)
   al <- as_adj_list(g)
   g2 <- graph_from_adj_list(al, mode = "all")
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   ##
 
   g <- sample_gnp(100, 3 / 100, directed = TRUE)
   al <- as_adj_list(g, mode = "out")
   g2 <- graph_from_adj_list(al, mode = "out")
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 })
diff --git a/tests/testthat/test-graph.atlas.R b/tests/testthat/test-graph.atlas.R
@@ -1,11 +1,11 @@
 test_that("graph.atlas works", {
   g124 <- graph_from_atlas(124)
-  expect_true(graph.isomorphic(g124, make_graph(c(1, 2, 2, 3, 3, 4, 4, 5, 1, 5, 1, 3, 2, 6),
+  expect_isomorphic(g124, make_graph(c(1, 2, 2, 3, 3, 4, 4, 5, 1, 5, 1, 3, 2, 6),
     directed = FALSE
-  )))
+  ))
   g234 <- graph_from_atlas(234)
-  expect_true(graph.isomorphic(g234, make_graph(c(1, 6, 2, 6, 3, 6, 4, 6, 5, 6),
+  expect_isomorphic(g234, make_graph(c(1, 6, 2, 6, 3, 6, 4, 6, 5, 6),
     n = 7,
     directed = FALSE
-  )))
+  ))
 })
diff --git a/tests/testthat/test-graph.complementer.R b/tests/testthat/test-graph.complementer.R
@@ -2,5 +2,5 @@ test_that("complementer works", {
   g <- sample_gnp(50, 3 / 50)
   g2 <- complementer(g)
   g3 <- complementer(g2)
-  expect_true(graph.isomorphic(g, g3))
+  expect_isomorphic(g, g3)
 })
diff --git a/tests/testthat/test-graph.compose.R b/tests/testthat/test-graph.compose.R
@@ -5,6 +5,6 @@ test_that("compose works", {
   g2 <- compose(g1, gi)
   g3 <- compose(gi, g1)
 
-  expect_true(graph.isomorphic(g1, g2))
-  expect_true(graph.isomorphic(g1, g3))
+  expect_isomorphic(g1, g2)
+  expect_isomorphic(g1, g3)
 })
diff --git a/tests/testthat/test-graph.de.bruijn.R b/tests/testthat/test-graph.de.bruijn.R
@@ -3,9 +3,9 @@ test_that("make_de_bruijn_graph works", {
   g2 <- make_de_bruijn_graph(2, 2)
   g3 <- make_line_graph(g)
 
-  expect_true(graph.isomorphic(g3, make_graph(c(
+  expect_isomorphic(g3, make_graph(c(
     1, 1, 3, 1, 1, 2, 3, 2, 2, 3,
     4, 3, 2, 4, 4, 4
-  ))))
-  expect_true(graph.isomorphic(g2, g3))
+  )))
+  expect_isomorphic(g2, g3)
 })
diff --git a/tests/testthat/test-graph.edgelist.R b/tests/testthat/test-graph.edgelist.R
@@ -4,14 +4,14 @@ test_that("graph_from_edgelist works", {
   g <- sample_gnp(50, 5 / 50)
   el <- as_edgelist(g)
   g2 <- graph_from_edgelist(el, directed = FALSE)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   ####
 
   g <- sample_gnp(50, 5 / 50, directed = TRUE)
   el <- as_edgelist(g)
   g2 <- graph_from_edgelist(el, directed = TRUE)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   ####
 
@@ -22,5 +22,5 @@ test_that("graph_from_edgelist works", {
   mode(el) <- "character"
   el[] <- n[el]
   g2 <- graph_from_edgelist(el, directed = TRUE)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 })
diff --git a/tests/testthat/test-graphNEL.R b/tests/testthat/test-graphNEL.R
@@ -19,7 +19,7 @@ test_that("graphNEL conversion works", {
 
   N <- as_graphnel(g)
   g2 <- graph_from_graphnel(N)
-  expect_true(graph.isomorphic(g, g2))
+  expect_isomorphic(g, g2)
   expect_that(V(g)$name, equals(V(g2)$name))
 
   A <- as_adj(g, attr = "weight", sparse = FALSE)
diff --git a/tests/testthat/test-neighborhood.R b/tests/testthat/test-neighborhood.R
@@ -12,7 +12,7 @@ test_that("ego works", {
   v <- sample(vcount(g), 1)
   g1 <- make_ego_graph(g, 2, v)[[1]]
   g2 <- neig(g, 2, v)
-  expect_true(graph.isomorphic(g1, g2))
+  expect_isomorphic(g1, g2)
 
   #########
 
diff --git a/tests/testthat/test-operators.R b/tests/testthat/test-operators.R
@@ -22,18 +22,18 @@ test_that("operators work", {
 
   ####
 
-  expect_true(graph.isomorphic(difference(gu, g1), g2))
+  expect_isomorphic(difference(gu, g1), g2)
 
   ####
 
-  expect_true(graph.isomorphic(intersection(gu, g2), g2))
+  expect_isomorphic(intersection(gu, g2), g2)
 
-  expect_true(graph.isomorphic(
+  expect_isomorphic(
     intersection(gu, g1,
       keep.all.vertices = FALSE
     ),
     g1
-  ))
+  )
 
   ####
 
diff --git a/tests/testthat/test-operators3.R b/tests/testthat/test-operators3.R
@@ -6,34 +6,34 @@ test_that("infix operators work", {
   g <- g - c("a", "b")
   expect_that(vcount(g), equals(8))
   expect_that(ecount(g), equals(7))
-  expect_true(graph.isomorphic(g, make_lattice(8)))
+  expect_isomorphic(g, make_lattice(8))
 
   g <- g - edge("e|f")
-  expect_true(graph.isomorphic(g, make_lattice(5) + make_lattice(3)))
+  expect_isomorphic(g, make_lattice(5) + make_lattice(3))
 
   g <- g - edge("H")
-  expect_true(graph.isomorphic(g, graph_from_literal(a - b - c, d - e - f, g - h)))
+  expect_isomorphic(g, graph_from_literal(a - b - c, d - e - f, g - h))
 
   g <- make_ring(10)
   V(g)$name <- letters[1:10]
   g <- g - path("a", "b")
-  expect_true(graph.isomorphic(g, graph_from_literal(a, b - c - d - e - f - g - h - i - j - a)))
+  expect_isomorphic(g, graph_from_literal(a, b - c - d - e - f - g - h - i - j - a))
   g <- g + path("a", "b")
-  expect_true(graph.isomorphic(g, make_ring(10)))
+  expect_isomorphic(g, make_ring(10))
 
   g <- make_ring(10)
   V(g)$name <- letters[1:10]
 
   g <- g - path("a", "b", "c", "d")
-  expect_true(graph.isomorphic(g, make_lattice(8) + 2))
+  expect_isomorphic(g, make_lattice(8) + 2)
 
-  expect_true(graph.isomorphic(
+  expect_isomorphic(
     g - V(g)[c("d", "g")],
     make_lattice(4) + make_lattice(2) + 2
-  ))
+  )
 
-  expect_true(graph.isomorphic(
+  expect_isomorphic(
     g - E(g)["f" %--% "g"],
     make_lattice(5) + make_lattice(3) + 2
-  ))
+  )
 })
diff --git a/tests/testthat/test-sbm.game.R b/tests/testthat/test-sbm.game.R
@@ -5,7 +5,7 @@ test_that("Generating stochastic block models works", {
     pref.matrix = pm, block.sizes = bs,
     directed = FALSE, loops = FALSE
   )
-  expect_true(graph.isomorphic(g1, make_full_graph(10, directed = FALSE, loops = FALSE)))
+  expect_isomorphic(g1, make_full_graph(10, directed = FALSE, loops = FALSE))
 
   g2 <- sample_sbm(10,
     pref.matrix = pm, block.sizes = bs,
diff --git a/tests/testthat/test-unfold.tree.R b/tests/testthat/test-unfold.tree.R
@@ -2,9 +2,9 @@ test_that("unfold_tree works", {
   g <- make_tree(7, 2)
   g <- add_edges(g, c(2, 7, 1, 4))
   g2 <- unfold_tree(g, roots = 1)
-  expect_true(graph.isomorphic(g2$tree, make_graph(c(
+  expect_isomorphic(g2$tree, make_graph(c(
     1, 2, 1, 3, 2, 8, 2, 5, 3, 6,
     3, 9, 2, 7, 1, 4
-  ))))
+  )))
   expect_that(g2$vertex_index, equals(c(1, 2, 3, 4, 5, 6, 7, 4, 7)))
 })

Original file line number	Diff line number	Diff line change
`@@ -25,3 +25,7 @@ expect_that <- function(object, condition, info = NULL, label = NULL) {`
`25`	`25`	`condition(object)`
`26`	`26`	`)`
`27`	`27`	`}`
	`28`	`+`
	`29`	`+expect_isomorphic <- function(g1, g2) {`
	`30`	`+ expect_true(graph.isomorphic(g1, g2))`
	`31`	`+}`