From 9c9b28bc3d6c9809b9376759639b8559c81c572d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 19 Aug 2025 12:07:58 +0100
Subject: [PATCH] chore: cleanup unnecessary lintr comments

---
 .lintr                               | 1 -
 design/design_signature_module.Rmd   | 4 ++--
 tests/testthat/test-adtteSpec.R      | 4 ----
 tests/testthat/test-assaySpec.R      | 4 ----
 tests/testthat/test-barplot.R        | 4 ----
 tests/testthat/test-boxplot.R        | 4 ----
 tests/testthat/test-experimentSpec.R | 4 ----
 tests/testthat/test-forest.R         | 4 ----
 tests/testthat/test-geneSpec.R       | 9 ++++-----
 tests/testthat/test-km.R             | 4 ----
 tests/testthat/test-pca.R            | 9 ++++-----
 tests/testthat/test-quality.R        | 4 ----
 tests/testthat/test-sampleVarSpec.R  | 4 ----
 tests/testthat/test-scatterplot.R    | 4 ----
 tests/testthat/test-volcanoplot.R    | 4 ----
 15 files changed, 10 insertions(+), 57 deletions(-)

diff --git a/.lintr b/.lintr
index 34473d27..3377b646 100644
--- a/.lintr
+++ b/.lintr
@@ -1,5 +1,4 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
-  cyclocomp_linter = NULL,
   object_usage_linter = NULL
   )
diff --git a/design/design_signature_module.Rmd b/design/design_signature_module.Rmd
index c663d3e9..3689f6fa 100644
--- a/design/design_signature_module.Rmd
+++ b/design/design_signature_module.Rmd
@@ -16,11 +16,11 @@ library(checkmate)
 
 ## Objectives
 
-We need a shiny module that captures the gene signature logic. We might also need additional functions and classes which capture reused functionality. 
+We need a shiny module that captures the gene signature logic. We might also need additional functions and classes which capture reused functionality.
 
 ## Hermes Interface
 
-### Helpers 
+### Helpers
 
 ```{r}
 shorten_list <- function(x) {
diff --git a/tests/testthat/test-adtteSpec.R b/tests/testthat/test-adtteSpec.R
index 6ad128bb..5acc80f0 100644
--- a/tests/testthat/test-adtteSpec.R
+++ b/tests/testthat/test-adtteSpec.R
@@ -178,8 +178,6 @@ test_that("adtteSpecInput creates expected HTML", {
   expect_class(result, "shiny.tag")
 })
 
-# nolint start
-
 test_that("adtteSpecServer module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -242,5 +240,3 @@ test_that("adtteSpecServer module works as expected in the test app", {
   app$click(ns_fp("ADTTE-filter-ADTTE_PARAMCD-remove"))
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-assaySpec.R b/tests/testthat/test-assaySpec.R
index 382b5e7d..3ddcfd64 100644
--- a/tests/testthat/test-assaySpec.R
+++ b/tests/testthat/test-assaySpec.R
@@ -9,8 +9,6 @@ test_that("assaySpecInput creates expected HTML", {
   expect_class(result, "shiny.tag")
 })
 
-# nolint start
-
 # assaySpecServer ----
 test_that("assaySpecServer module works as expected in the test app", {
   skip_if_covr()
@@ -54,5 +52,3 @@ test_that("assaySpecServer module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-barplot.R b/tests/testthat/test-barplot.R
index 436eb420..88e2c317 100644
--- a/tests/testthat/test-barplot.R
+++ b/tests/testthat/test-barplot.R
@@ -19,8 +19,6 @@ test_that("ui_g_barplot creates expected HTML", {
 
 # tm_g_barplot ----
 
-# nolint start
-
 test_that("barplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -97,5 +95,3 @@ test_that("barplot module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-boxplot.R b/tests/testthat/test-boxplot.R
index 12fe891b..8f505de1 100644
--- a/tests/testthat/test-boxplot.R
+++ b/tests/testthat/test-boxplot.R
@@ -15,8 +15,6 @@ test_that("ui_g_boxplot creates expected HTML", {
 
 # tm_g_boxplot ----
 
-# nolint start
-
 test_that("boxplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -64,5 +62,3 @@ test_that("boxplot module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-experimentSpec.R b/tests/testthat/test-experimentSpec.R
index a1e35945..31a2a6ab 100644
--- a/tests/testthat/test-experimentSpec.R
+++ b/tests/testthat/test-experimentSpec.R
@@ -89,8 +89,6 @@ test_that("h_gene_data does not fail when object does not contain any genes", {
   expect_identical(result, expected)
 })
 
-# nolint start
-
 test_that("experimentSpec module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -170,5 +168,3 @@ test_that("experimentSpec module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-forest.R b/tests/testthat/test-forest.R
index 9a17519c..a914b863 100644
--- a/tests/testthat/test-forest.R
+++ b/tests/testthat/test-forest.R
@@ -19,8 +19,6 @@ test_that("ui_g_forest_tte creates expected HTML", {
 
 # tm_g_forest_tte ----
 
-# nolint start
-
 test_that("forest_tte module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -68,5 +66,3 @@ test_that("forest_tte module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-geneSpec.R b/tests/testthat/test-geneSpec.R
index c9bec629..18672e4b 100644
--- a/tests/testthat/test-geneSpec.R
+++ b/tests/testthat/test-geneSpec.R
@@ -32,8 +32,6 @@ test_that("h_parse_genes correctly returns empty data frame when no genes match"
 
 # geneSpecServer ----
 
-# nolint start
-
 test_that("geneSpec module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -80,7 +78,10 @@ test_that("geneSpec module works as expected in the test app", {
   ns_fp <- active_module_filter_panel_ns(app)
   app$set_inputs(!!ns_fp("MAE-MAE-hd1-row_to_add") := "chromosome", allow_no_input_binding_ = TRUE)
   app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection") := c("1", "2"))
-  app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  app$set_inputs(
+    !!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE,
+    allow_no_input_binding_ = TRUE
+  )
   app$wait_for_idle()
 
   # Confirm that gene selection was not changed.
@@ -122,5 +123,3 @@ test_that("geneSpec module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-km.R b/tests/testthat/test-km.R
index 6d7cdd8c..f5894db7 100644
--- a/tests/testthat/test-km.R
+++ b/tests/testthat/test-km.R
@@ -20,8 +20,6 @@ test_that("ui_g_km creates expected HTML", {
 
 # tm_g_km ----
 
-# nolint start
-
 test_that("km module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -66,5 +64,3 @@ test_that("km module works as expected in the test app", {
   )
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
index d4955428..13863337 100644
--- a/tests/testthat/test-pca.R
+++ b/tests/testthat/test-pca.R
@@ -14,8 +14,6 @@ test_that("ui_g_pca creates HTML", {
 
 # pca Server ----
 
-# nolint start
-
 test_that("pca module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -65,7 +63,10 @@ test_that("pca module works as expected in the test app", {
   ns_fp <- active_module_filter_panel_ns(app)
   app$set_inputs(!!ns_fp("MAE-MAE-hd1-row_to_add") := "chromosome", allow_no_input_binding_ = TRUE)
   app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection") := character())
-  app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  app$set_inputs(
+    !!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE,
+    allow_no_input_binding_ = TRUE
+  )
   app$wait_for_idle()
 
   res <- app$get_value(output = ns("test_pca"))
@@ -231,5 +232,3 @@ test_that("pca module works as expected in the test app", {
   expect_identical(res, 2500L)
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-quality.R b/tests/testthat/test-quality.R
index e51968b1..d710fea7 100644
--- a/tests/testthat/test-quality.R
+++ b/tests/testthat/test-quality.R
@@ -16,8 +16,6 @@ test_that("ui_g_quality creates expected HTML", {
 
 # tm_g_quality ----
 
-# nolint start
-
 test_that("quality module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -81,5 +79,3 @@ test_that("quality module works as expected in the test app", {
   )
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-sampleVarSpec.R b/tests/testthat/test-sampleVarSpec.R
index 71ad14f0..8ef6fade 100644
--- a/tests/testthat/test-sampleVarSpec.R
+++ b/tests/testthat/test-sampleVarSpec.R
@@ -166,8 +166,6 @@ test_that("sampleVarSpecServer only gives factor columns in col_data_vars when c
   )
 })
 
-# nolint start
-
 test_that("sampleVarSpec module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -224,5 +222,3 @@ test_that("sampleVarSpec module works as expected in the test app", {
   expect_match(res, "< 18/>= 18 \n         5 ")
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-scatterplot.R b/tests/testthat/test-scatterplot.R
index e3321ae6..83912ea6 100644
--- a/tests/testthat/test-scatterplot.R
+++ b/tests/testthat/test-scatterplot.R
@@ -19,8 +19,6 @@ test_that("ui_g_scatterplot creates expected HTML", {
 
 # tm_g_scatterplot ----
 
-# nolint start
-
 test_that("scatterplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -102,5 +100,3 @@ test_that("scatterplot module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end
diff --git a/tests/testthat/test-volcanoplot.R b/tests/testthat/test-volcanoplot.R
index aa82ab48..4cc18484 100644
--- a/tests/testthat/test-volcanoplot.R
+++ b/tests/testthat/test-volcanoplot.R
@@ -14,8 +14,6 @@ test_that("ui_g_volcanoplot creates expected HTML", {
 
 # tm_g_volcanoplot ----
 
-# nolint start
-
 test_that("volcanoplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -57,5 +55,3 @@ test_that("volcanoplot module works as expected in the test app", {
   expect_snapshot(cat(res))
   app$stop()
 })
-
-# nolint end