From 9fe5b8d4c32955bc69382f4c80fa38ac234f7e3e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 09:45:31 +0100
Subject: [PATCH 1/8] test: merge all tests for `foreign.R` into one test file

---
 tests/testthat/{test-read_graph.R => test-foreign.R} | 12 ++++++++++++
 tests/testthat/test-pajek.R                          | 11 -----------
 2 files changed, 12 insertions(+), 11 deletions(-)
 rename tests/testthat/{test-read_graph.R => test-foreign.R} (54%)
 delete mode 100644 tests/testthat/test-pajek.R

diff --git a/tests/testthat/test-read_graph.R b/tests/testthat/test-foreign.R
similarity index 54%
rename from tests/testthat/test-read_graph.R
rename to tests/testthat/test-foreign.R
index 2f671f872e..169eae2f7c 100644
--- a/tests/testthat/test-read_graph.R
+++ b/tests/testthat/test-foreign.R
@@ -1,3 +1,15 @@
+test_that("writing Pajek files works", {
+  g <- make_ring(9)
+  V(g)$color <- rep(c("red", "green", "yellow"), 3)
+
+  tc <- rawConnection(raw(0), "w")
+  write_graph(g, format = "pajek", file = tc)
+  out <- rawToChar(rawConnectionValue(tc))
+  close(tc)
+
+  expect_equal(out, "*Vertices 9\n1 \"1\" ic \"red\"\n2 \"2\" ic \"green\"\n3 \"3\" ic \"yellow\"\n4 \"4\" ic \"red\"\n5 \"5\" ic \"green\"\n6 \"6\" ic \"yellow\"\n7 \"7\" ic \"red\"\n8 \"8\" ic \"green\"\n9 \"9\" ic \"yellow\"\n*Edges\n1 2\n2 3\n3 4\n4 5\n5 6\n6 7\n7 8\n8 9\n1 9\n")
+})
+
 test_that("reading GraphML file works", {
   skip_if_no_graphml()
 
diff --git a/tests/testthat/test-pajek.R b/tests/testthat/test-pajek.R
deleted file mode 100644
index 8a44c41f97..0000000000
--- a/tests/testthat/test-pajek.R
+++ /dev/null
@@ -1,11 +0,0 @@
-test_that("writing Pajek files works", {
-  g <- make_ring(9)
-  V(g)$color <- rep(c("red", "green", "yellow"), 3)
-
-  tc <- rawConnection(raw(0), "w")
-  write_graph(g, format = "pajek", file = tc)
-  out <- rawToChar(rawConnectionValue(tc))
-  close(tc)
-
-  expect_equal(out, "*Vertices 9\n1 \"1\" ic \"red\"\n2 \"2\" ic \"green\"\n3 \"3\" ic \"yellow\"\n4 \"4\" ic \"red\"\n5 \"5\" ic \"green\"\n6 \"6\" ic \"yellow\"\n7 \"7\" ic \"red\"\n8 \"8\" ic \"green\"\n9 \"9\" ic \"yellow\"\n*Edges\n1 2\n2 3\n3 4\n4 5\n5 6\n6 7\n7 8\n8 9\n1 9\n")
-})

From c19d47d776d5c4f3cf198cb738c0f839e6cc4b3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 09:47:13 +0100
Subject: [PATCH 2/8] refactor: use `rep_len()` -- more readable?

---
 tests/testthat/test-foreign.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-foreign.R b/tests/testthat/test-foreign.R
index 169eae2f7c..0798df75f1 100644
--- a/tests/testthat/test-foreign.R
+++ b/tests/testthat/test-foreign.R
@@ -1,6 +1,6 @@
 test_that("writing Pajek files works", {
   g <- make_ring(9)
-  V(g)$color <- rep(c("red", "green", "yellow"), 3)
+  V(g)$color <- rep_len(c("red", "green", "yellow"), length.out = 9)
 
   tc <- rawConnection(raw(0), "w")
   write_graph(g, format = "pajek", file = tc)

From a4a56c90203fff25d64df00f5a14b2ab86f3cad4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 09:47:58 +0100
Subject: [PATCH 3/8] chore: multiline

---
 tests/testthat/test-foreign.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-foreign.R b/tests/testthat/test-foreign.R
index 0798df75f1..d33ccbb0bf 100644
--- a/tests/testthat/test-foreign.R
+++ b/tests/testthat/test-foreign.R
@@ -7,7 +7,10 @@ test_that("writing Pajek files works", {
   out <- rawToChar(rawConnectionValue(tc))
   close(tc)
 
-  expect_equal(out, "*Vertices 9\n1 \"1\" ic \"red\"\n2 \"2\" ic \"green\"\n3 \"3\" ic \"yellow\"\n4 \"4\" ic \"red\"\n5 \"5\" ic \"green\"\n6 \"6\" ic \"yellow\"\n7 \"7\" ic \"red\"\n8 \"8\" ic \"green\"\n9 \"9\" ic \"yellow\"\n*Edges\n1 2\n2 3\n3 4\n4 5\n5 6\n6 7\n7 8\n8 9\n1 9\n")
+  expect_equal(
+    out,
+    "*Vertices 9\n1 \"1\" ic \"red\"\n2 \"2\" ic \"green\"\n3 \"3\" ic \"yellow\"\n4 \"4\" ic \"red\"\n5 \"5\" ic \"green\"\n6 \"6\" ic \"yellow\"\n7 \"7\" ic \"red\"\n8 \"8\" ic \"green\"\n9 \"9\" ic \"yellow\"\n*Edges\n1 2\n2 3\n3 4\n4 5\n5 6\n6 7\n7 8\n8 9\n1 9\n"
+  )
 })
 
 test_that("reading GraphML file works", {

From ed8ea42206d8af2b6d746520844d679a19229707 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 09:51:52 +0100
Subject: [PATCH 4/8] refactor: use `withr::local_connection()`

---
 tests/testthat/test-foreign.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/testthat/test-foreign.R b/tests/testthat/test-foreign.R
index d33ccbb0bf..f48f569aa7 100644
--- a/tests/testthat/test-foreign.R
+++ b/tests/testthat/test-foreign.R
@@ -2,10 +2,9 @@ test_that("writing Pajek files works", {
   g <- make_ring(9)
   V(g)$color <- rep_len(c("red", "green", "yellow"), length.out = 9)
 
-  tc <- rawConnection(raw(0), "w")
+  tc <- withr::local_connection(rawConnection(raw(0), "w"))
   write_graph(g, format = "pajek", file = tc)
   out <- rawToChar(rawConnectionValue(tc))
-  close(tc)
 
   expect_equal(
     out,

From 6c8d9a0429d3c41cc2b088c8e5648930ea360fea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 09:52:13 +0100
Subject: [PATCH 5/8] chore: simpler

---
 tests/testthat/test-foreign.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-foreign.R b/tests/testthat/test-foreign.R
index f48f569aa7..78c75161d1 100644
--- a/tests/testthat/test-foreign.R
+++ b/tests/testthat/test-foreign.R
@@ -3,11 +3,11 @@ test_that("writing Pajek files works", {
   V(g)$color <- rep_len(c("red", "green", "yellow"), length.out = 9)
 
   tc <- withr::local_connection(rawConnection(raw(0), "w"))
+
   write_graph(g, format = "pajek", file = tc)
-  out <- rawToChar(rawConnectionValue(tc))
 
   expect_equal(
-    out,
+    rawToChar(rawConnectionValue(tc)),
     "*Vertices 9\n1 \"1\" ic \"red\"\n2 \"2\" ic \"green\"\n3 \"3\" ic \"yellow\"\n4 \"4\" ic \"red\"\n5 \"5\" ic \"green\"\n6 \"6\" ic \"yellow\"\n7 \"7\" ic \"red\"\n8 \"8\" ic \"green\"\n9 \"9\" ic \"yellow\"\n*Edges\n1 2\n2 3\n3 4\n4 5\n5 6\n6 7\n7 8\n8 9\n1 9\n"
   )
 })

From 879a9ca3d4d7045f0c817ac2faeb3736acb0904f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 09:56:39 +0100
Subject: [PATCH 6/8] test: isomorphic expectations helpers

---
 tests/testthat/helper.R           |  8 ++++++--
 tests/testthat/test-components.R  |  6 +++---
 tests/testthat/test-conversion.R  |  8 ++++----
 tests/testthat/test-foreign.R     |  2 +-
 tests/testthat/test-isomorphism.R | 16 ++++++++--------
 tests/testthat/test-operators.R   |  2 +-
 tests/testthat/test-trees.R       |  8 ++++----
 7 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index c0d7e6309c..03a7eabe58 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -20,8 +20,12 @@ local_rng_version <- function(version, .local_envir = parent.frame()) {
   orig
 }
 
-expect_isomorphic <- function(g1, g2) {
-  expect_true(isomorphic(g1, g2))
+expect_isomorphic <- function(g1, g2, ...) {
+  expect_true(isomorphic(g1, g2, ...))
+}
+
+expect_not_isomorphic <- function(g1, g2, ...) {
+  expect_false(isomorphic(g1, g2, ...))
 }
 
 expect_vcount <- function(graph, expected, ...) {
diff --git a/tests/testthat/test-components.R b/tests/testthat/test-components.R
index 50733ffd31..a30bde3338 100644
--- a/tests/testthat/test-components.R
+++ b/tests/testthat/test-components.R
@@ -111,7 +111,7 @@ test_that("largest strongly and weakly components are correct", {
     B - +C,
     C - +A
   )
-  expect_true(isomorphic(largest_component(g, "strong"), strongly))
+  expect_isomorphic(largest_component(g, "strong"), strongly)
 
   weakly <- graph_from_literal(
     A - +B,
@@ -119,13 +119,13 @@ test_that("largest strongly and weakly components are correct", {
     C - +A,
     C - +D
   )
-  expect_true(isomorphic(largest_component(g, "weak"), weakly))
+  expect_isomorphic(largest_component(g, "weak"), weakly)
 })
 
 test_that("the largest component of a null graph is a valid null graph", {
   nullgraph <- make_empty_graph(0)
 
-  expect_true(isomorphic(largest_component(make_empty_graph(0)), nullgraph))
+  expect_isomorphic(largest_component(make_empty_graph(0)), nullgraph)
 })
 
 test_that("articulation_points works", {
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index 93016bde07..f127975035 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -306,11 +306,11 @@ test_that("as_adj_list works", {
   expect_s3_class(adj_list[[1]], "igraph.vs")
   g_same <- graph_from_adj_list(adj_list, mode = "all")
   expect_isomorphic(g, g_same)
-  expect_true(isomorphic(g, g_same,
+  expect_isomorphic(g, g_same,
     method = "vf2",
     vertex.color1 = seq_len(vcount(g)),
     vertex.color2 = seq_len(vcount(g_same))
-  ))
+  )
 
   adj_el_list <- as_adj_edge_list(g)
   expect_s3_class(adj_el_list[[1]], "igraph.es")
@@ -345,11 +345,11 @@ test_that("as_adj_list works when return.vs.es is FALSE", {
   expect_s3_class(adj_list[[1]], NA)
   g2 <- graph_from_adj_list(adj_list, mode = "all")
   expect_isomorphic(g, g2)
-  expect_true(isomorphic(g, g2,
+  expect_isomorphic(g, g2,
     method = "vf2",
     vertex.color1 = 1:vcount(g),
     vertex.color2 = 1:vcount(g2)
-  ))
+  )
 
   adj_el_list <- as_adj_edge_list(g)
   for (i in seq_len(vcount(g))) {
diff --git a/tests/testthat/test-foreign.R b/tests/testthat/test-foreign.R
index 78c75161d1..bbb1a39420 100644
--- a/tests/testthat/test-foreign.R
+++ b/tests/testthat/test-foreign.R
@@ -18,7 +18,7 @@ test_that("reading GraphML file works", {
   g <- read_graph(f <- gzfile("zachary.graphml.gz"), format = "graphml")
   g2 <- make_graph("zachary")
 
-  expect_true(isomorphic(g2, g))
+  expect_isomorphic(g2, g)
 })
 
 test_that("reading graph in NCOL format", {
diff --git a/tests/testthat/test-isomorphism.R b/tests/testthat/test-isomorphism.R
index cbb2b6cf11..c4a867d6da 100644
--- a/tests/testthat/test-isomorphism.R
+++ b/tests/testthat/test-isomorphism.R
@@ -1,15 +1,15 @@
 test_that("isomorphic", {
   g <- graph_from_literal(A - B - C - A)
-  expect_true(isomorphic(g, g))
-  expect_true(isomorphic(g, g, method = "direct"))
-  expect_true(isomorphic(g, g, method = "vf2"))
-  expect_true(isomorphic(g, g, method = "bliss"))
+  expect_isomorphic(g, g)
+  expect_isomorphic(g, g, method = "direct")
+  expect_isomorphic(g, g, method = "vf2")
+  expect_isomorphic(g, g, method = "bliss")
 
   g2 <- graph_from_literal(A - B - C)
-  expect_false(isomorphic(g, g2))
-  expect_false(isomorphic(g, g2, method = "direct"))
-  expect_false(isomorphic(g, g2, method = "vf2"))
-  expect_false(isomorphic(g, g2, method = "bliss"))
+  expect_not_isomorphic(g, g2)
+  expect_not_isomorphic(g, g2, method = "direct")
+  expect_not_isomorphicg, g2, method = "vf2")
+  expect_not_isomorphic(g, g2, method = "bliss")
 })
 
 test_that("subgraph_isomorphic", {
diff --git a/tests/testthat/test-operators.R b/tests/testthat/test-operators.R
index 28a7020b5a..6821d69b23 100644
--- a/tests/testthat/test-operators.R
+++ b/tests/testthat/test-operators.R
@@ -87,7 +87,7 @@ test_that("edge reversal works", {
   directed_graph <- make_graph(~ 1 -+ 2, 1 -+ 3, 1 -+ 4, 2 -+ 3, 3 -+ 4)
   reverse_directed_graph <- reverse_edges(directed_graph, 1:3)
   expected <- make_graph(~ 1 +- 2, 1 +- 3, 1 +- 4, 2 -+ 3, 3 -+ 4)
-  expect_true(isomorphic(reverse_directed_graph, expected))
+  expect_isomorphic(reverse_directed_graph, expected)
 
   reverse_all_directed_graph <- reverse_edges(directed_graph)
   expect_vcount(reverse_all_directed_graph, vcount(directed_graph))
diff --git a/tests/testthat/test-trees.R b/tests/testthat/test-trees.R
index 1dba898ba5..b02ee6a4d7 100644
--- a/tests/testthat/test-trees.R
+++ b/tests/testthat/test-trees.R
@@ -73,26 +73,26 @@ test_that("to_prufer and make_from_prufer works for trees", {
   g <- make_tree(13, 3, mode = "undirected")
   seq <- to_prufer(g)
   g2 <- make_from_prufer(seq)
-  expect_true(isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 
   g <- make_tree(13, 3, mode = "out")
   seq <- to_prufer(g)
   g2 <- make_from_prufer(seq)
   g3 <- as_undirected(g)
-  expect_true(isomorphic(g2, g3))
+  expect_isomorphic(g2, g3)
 
   g <- make_tree(13, 3, mode = "in")
   seq <- to_prufer(g)
   g2 <- make_from_prufer(seq)
   g3 <- as_undirected(g)
-  expect_true(isomorphic(g2, g3))
+  expect_isomorphic(g2, g3)
 })
 
 test_that("make_(from_prufer(...)) works", {
   g <- make_tree(13, 3, mode = "undirected")
   seq <- to_prufer(g)
   g2 <- make_(from_prufer(seq))
-  expect_true(isomorphic(g, g2))
+  expect_isomorphic(g, g2)
 })
 
 test_that("to_prufer prints an error for non-trees", {

From 6124395d3223374bf0a1f81311fad8f2e1ae7098 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 10:00:54 +0100
Subject: [PATCH 7/8] test: we can expect more than no error, and we can use
 withr

---
 tests/testthat/_snaps/foreign.md | 20 ++++++++++++++++++++
 tests/testthat/test-foreign.R    | 12 ++++++++----
 2 files changed, 28 insertions(+), 4 deletions(-)
 create mode 100644 tests/testthat/_snaps/foreign.md

diff --git a/tests/testthat/_snaps/foreign.md b/tests/testthat/_snaps/foreign.md
new file mode 100644
index 0000000000..1f4d040c57
--- /dev/null
+++ b/tests/testthat/_snaps/foreign.md
@@ -0,0 +1,20 @@
+# reading graph in NCOL format
+
+    Code
+      read_graph(ncol_path, "ncol")
+    Output
+      IGRAPH UN-- 3 2 -- 
+      + attr: name (v/c)
+      + edges (vertex names):
+      [1] 0--1 1--2
+
+# reading graph in LGL format
+
+    Code
+      read_graph(lgl_path, "lgl")
+    Output
+      IGRAPH UN-- 3 2 -- 
+      + attr: name (v/c)
+      + edges (vertex names):
+      [1] 0--1 1--2
+
diff --git a/tests/testthat/test-foreign.R b/tests/testthat/test-foreign.R
index bbb1a39420..31713d0d00 100644
--- a/tests/testthat/test-foreign.R
+++ b/tests/testthat/test-foreign.R
@@ -22,15 +22,19 @@ test_that("reading GraphML file works", {
 })
 
 test_that("reading graph in NCOL format", {
-  ncol_path <- tempfile("testfile", fileext = ".ncol")
+  local_igraph_options(print.id = FALSE)
+
+  ncol_path <- withr::local_tempfile(pattern = "testfile", fileext = ".ncol")
   g <- make_graph(c(1, 2, 2, 3))
   write_graph(g, ncol_path, "ncol")
-  expect_no_error(g2 <- read_graph(ncol_path, "ncol"))
+  expect_snapshot(read_graph(ncol_path, "ncol"))
 })
 
 test_that("reading graph in LGL format", {
-  lgl_path <- tempfile("testfile", fileext = ".lgl")
+  local_igraph_options(print.id = FALSE)
+
+  lgl_path <- withr::local_tempfile(pattern = "testfile", fileext = ".lgl")
   g <- make_graph(c(1, 2, 2, 3))
   write_graph(g, lgl_path, "lgl")
-  expect_no_error(g2 <- read_graph(lgl_path, "lgl"))
+  expect_snapshot(read_graph(lgl_path, "lgl"))
 })

From 1fd4e63c4f9e5bd4e39b3fc7418110ce6cc4ce3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Mon, 24 Feb 2025 10:22:04 +0100
Subject: [PATCH 8/8] oops

---
 tests/testthat/test-isomorphism.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-isomorphism.R b/tests/testthat/test-isomorphism.R
index c4a867d6da..4fb497ccfa 100644
--- a/tests/testthat/test-isomorphism.R
+++ b/tests/testthat/test-isomorphism.R
@@ -8,7 +8,7 @@ test_that("isomorphic", {
   g2 <- graph_from_literal(A - B - C)
   expect_not_isomorphic(g, g2)
   expect_not_isomorphic(g, g2, method = "direct")
-  expect_not_isomorphicg, g2, method = "vf2")
+  expect_not_isomorphic(g, g2, method = "vf2")
   expect_not_isomorphic(g, g2, method = "bliss")
 })