From bcdcdbc1f8eeb2b15e5110890539cec4edd3cace Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Wed, 14 Oct 2026 14:23:53 -0400
Subject: [PATCH 1/9] test: :zap: reduced `convert_output` tests to only run on
 subset of SS3 models

---
 tests/testthat/test-convert_output.R | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-convert_output.R b/tests/testthat/test-convert_output.R
index 1a546672..7d74a56b 100644
--- a/tests/testthat/test-convert_output.R
+++ b/tests/testthat/test-convert_output.R
@@ -6,11 +6,21 @@ test_that("convert_output works for SS3", {
     recursive = FALSE
   )
 
+  model_names <- c(
+    "Hake_2018",
+    "platoons",
+    "Empirical_wtatage_Age_Selex",
+    "three_area_nomove",
+    "BigSkate_2019"
+  )
+
+  models_to_test <- all_models[grepl(paste0(model_names, collapse="|"), all_models)]
+
   # Loop through each model directory and check convert_output function
-  for (i in seq_along(all_models)) {
+  for (i in seq_along(models_to_test)) {
     # Ensure no errors occur while converting SS3 output
     expect_no_error(result <- convert_output(
-      file = file.path(all_models[i], "Report.sso")
+      file = file.path(models_to_test[i], "Report.sso")
     ))
 
     # Check that the result has exactly 35 columns

From 4ed80d11c96356903e31cdc411ab961f45b1b87a Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Wed, 14 Oct 2026 14:29:41 -0400
Subject: [PATCH 2/9] test: :bug: resolve "table_biomass_abundance_catch
 generates error with incorrect module" test issue

Test would fail with original module specification ("SPR_SERIES") because labels were present for the given module. Change to new module ("DERIVED_QUANTITIES") ensures test passes.
---
 tests/testthat/test-table_biomass_abundance_catch.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-table_biomass_abundance_catch.R b/tests/testthat/test-table_biomass_abundance_catch.R
index 82b58464..6e3325cb 100644
--- a/tests/testthat/test-table_biomass_abundance_catch.R
+++ b/tests/testthat/test-table_biomass_abundance_catch.R
@@ -58,7 +58,7 @@ test_that("table_biomass_abundance_catch generates error with incorrect module",
     table_biomass_abundance_catch(
       dat = stockplotr::example_data,
       interactive = FALSE,
-      module = "SPR_SERIES",
+      module = "DERIVED_QUANTITIES",
       make_rda = FALSE,
       tables_dir = getwd()
     )

From 13859eb15fd5b1de94562d69953ba5f6ea600867 Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Wed, 14 Oct 2026 14:46:49 -0400
Subject: [PATCH 3/9] test: :zap: set interactive=FALSE on all plotting tests

this alleviates users from having to interact with the tests to confirm MODULE choices
---
 tests/testthat/test-plot_abundance_at_age.R     | 12 +++++++++++-
 tests/testthat/test-plot_biomass.R              | 11 +++++++++--
 tests/testthat/test-plot_biomass_at_age.R       | 12 ++++++++++--
 tests/testthat/test-plot_catch_comp.R           | 14 ++++++++++++--
 tests/testthat/test-plot_index.R                | 14 +++++++++++---
 tests/testthat/test-plot_landings.R             | 14 +++++++++++---
 tests/testthat/test-plot_natural_mortality.R    | 10 ++++++++--
 tests/testthat/test-plot_recruitment.R          |  9 +++++++--
 .../testthat/test-plot_recruitment_deviations.R |  9 +++++++--
 tests/testthat/test-plot_selectivity.R          | 11 +++++++----
 tests/testthat/test-plot_spawning_biomass.R     | 17 +++++++++++++----
 tests/testthat/test-plot_stock_recruitment.R    |  6 +++++-
 .../test-table_biomass_abundance_catch.R        |  1 +
 tests/testthat/test-table_index.R               |  2 ++
 tests/testthat/test-table_landings.R            |  2 ++
 tests/testthat/test-table_total_catch.R         |  2 ++
 16 files changed, 118 insertions(+), 28 deletions(-)

diff --git a/tests/testthat/test-plot_abundance_at_age.R b/tests/testthat/test-plot_abundance_at_age.R
index 8acaca51..fe225f2f 100644
--- a/tests/testthat/test-plot_abundance_at_age.R
+++ b/tests/testthat/test-plot_abundance_at_age.R
@@ -1,7 +1,10 @@
 test_that("plot_abundance_at_age generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_abundance_at_age(stockplotr::example_data)
+    plot_abundance_at_age(
+      stockplotr::example_data,
+      interactive = FALSE
+    )
   )
 
   # expect error-free plot with many arguments
@@ -11,6 +14,7 @@ test_that("plot_abundance_at_age generates plots without errors", {
       facet = "area",
       unit_label = "fish",
       scale_amount = 1000,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -22,6 +26,7 @@ test_that("plot_abundance_at_age generates plots without errors", {
       stockplotr::example_data,
       unit_label = "fish",
       scale_amount = 1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     ),
@@ -34,6 +39,7 @@ test_that("rda file made when indicated", {
   plot_abundance_at_age(
     stockplotr::example_data,
     figures_dir = getwd(),
+      interactive = FALSE,
     make_rda = TRUE
   )
 
@@ -54,6 +60,7 @@ test_that("plot_abundance_at_age generates error with scaling <1", {
       stockplotr::example_data,
       unit_label = "fish",
       scale_amount = 0.1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -131,6 +138,7 @@ test_that("plot_abundance_at_age generates error when abundance label is not fou
       sample_data,
       unit_label = "fish",
       scale_amount = 1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -143,6 +151,7 @@ test_that("plot is made proportional and does not contain a legend", {
     unit_label = "fish",
     proportional = TRUE,
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
@@ -155,6 +164,7 @@ test_that("plot contains a legend", {
     proportional = FALSE,
     unit_label = "fish",
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-plot_biomass.R b/tests/testthat/test-plot_biomass.R
index f816f763..b3e2091f 100644
--- a/tests/testthat/test-plot_biomass.R
+++ b/tests/testthat/test-plot_biomass.R
@@ -29,7 +29,10 @@
 test_that("plot_biomass generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_biomass(stockplotr::example_data)
+    plot_biomass(
+      stockplotr::example_data,
+      interactive = FALSE
+    )
   )
 
   # TODO: Update test
@@ -46,6 +49,7 @@ test_that("plot_biomass generates plots without errors", {
       unit_label = "metric tons",
       scale_amount = 1,
       relative = FALSE,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd(),
       module = "TIME_SERIES"
@@ -58,7 +62,8 @@ test_that("plot_biomass generates plots without errors", {
       stockplotr::example_data,
       unit_label = "mt",
       # scale_amount = 10,
-      relative = TRUE
+      relative = TRUE,
+      interactive = FALSE
     )
   )
 
@@ -68,6 +73,7 @@ test_that("plot_biomass generates plots without errors", {
       stockplotr::example_data,
       unit_label = "metric tons",
       scale_amount = 1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd(),
       module = "TIME_SERIES"
@@ -81,6 +87,7 @@ test_that("rda file made when indicated", {
   plot_biomass(
     stockplotr::example_data,
     figures_dir = getwd(),
+    interactive = FALSE,
     make_rda = TRUE,
     module = "TIME_SERIES"
   )
diff --git a/tests/testthat/test-plot_biomass_at_age.R b/tests/testthat/test-plot_biomass_at_age.R
index 8639736c..1cb74696 100644
--- a/tests/testthat/test-plot_biomass_at_age.R
+++ b/tests/testthat/test-plot_biomass_at_age.R
@@ -1,8 +1,10 @@
 test_that("plot_biomass_at_age generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_biomass_at_age(stockplotr::example_data,
-      module = "BIOMASS_AT_AGE"
+    plot_biomass_at_age(
+      stockplotr::example_data,
+      module = "BIOMASS_AT_AGE",
+      interactive = FALSE
     )
   )
 
@@ -14,6 +16,7 @@ test_that("plot_biomass_at_age generates plots without errors", {
       proportional = FALSE,
       scale_amount = 10,
       module = "BIOMASS_AT_AGE",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -26,6 +29,7 @@ test_that("plot_biomass_at_age generates plots without errors", {
       unit_label = "metric tons",
       scale_amount = 1,
       module = "BIOMASS_AT_AGE",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     ),
@@ -38,6 +42,7 @@ test_that("rda file made when indicated", {
   plot_biomass_at_age(
     stockplotr::example_data,
     module = "BIOMASS_AT_AGE",
+    interactive = FALSE,
     figures_dir = getwd(),
     make_rda = TRUE
   )
@@ -123,6 +128,7 @@ test_that("plot_biomass_at_age generates error when biomass label is not found",
       sample_data,
       unit_label = "fish",
       scale_amount = 1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -136,6 +142,7 @@ test_that("plot is made proportional and does not contain a legend", {
     unit_label = "fish",
     proportional = TRUE,
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
@@ -149,6 +156,7 @@ test_that("plot contains a legend", {
     proportional = FALSE,
     unit_label = "fish",
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-plot_catch_comp.R b/tests/testthat/test-plot_catch_comp.R
index d5edb287..79356c74 100644
--- a/tests/testthat/test-plot_catch_comp.R
+++ b/tests/testthat/test-plot_catch_comp.R
@@ -2,8 +2,10 @@
 test_that("plot_catch_comp generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_catch_comp(stockplotr::example_data,
-      module = "CATCH_AT_AGE"
+    plot_catch_comp(
+      stockplotr::example_data,
+      module = "CATCH_AT_AGE",
+      interactive = FALSE
     )
   )
 
@@ -15,6 +17,7 @@ test_that("plot_catch_comp generates plots without errors", {
       unit_label = "fish",
       scale_amount = 1000,
       module = "CATCH_AT_AGE",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -27,6 +30,7 @@ test_that("plot_catch_comp generates plots without errors", {
       unit_label = "fish",
       scale_amount = 1,
       module = "CATCH_AT_AGE",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     ),
@@ -39,6 +43,7 @@ test_that("rda file made when indicated", {
   plot_catch_comp(
     stockplotr::example_data,
     module = "CATCH_AT_AGE",
+    interactive = FALSE,
     figures_dir = getwd(),
     make_rda = TRUE
   )
@@ -60,6 +65,7 @@ test_that("plot_catch_comp generates error with scaling <1", {
       stockplotr::example_data,
       unit_label = "fish",
       scale_amount = 0.1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -137,6 +143,7 @@ test_that("plot_catch_comp generates error when catch label is not found", {
       sample_data,
       unit_label = "fish",
       scale_amount = 1,
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -150,6 +157,7 @@ test_that("plot is made proportional and does not contain a legend", {
     module = "CATCH_AT_AGE",
     proportional = TRUE,
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
@@ -163,6 +171,7 @@ test_that("plot contains a legend", {
     module = "CATCH_AT_AGE",
     unit_label = "fish",
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
@@ -176,6 +185,7 @@ test_that("year class lines are plotted", {
     unit_label = "fish",
     module = "CATCH_AT_AGE",
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-plot_index.R b/tests/testthat/test-plot_index.R
index 26ea0695..276c6406 100644
--- a/tests/testthat/test-plot_index.R
+++ b/tests/testthat/test-plot_index.R
@@ -1,21 +1,29 @@
 test_that("plot_index generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_index(stockplotr::example_data)
+    plot_index(
+      stockplotr::example_data,
+      interactive = FALSE
+    )
   )
 
   # expect ggplot object is returned
   expect_s3_class(
-    plot_index(stockplotr::example_data),
+    plot_index(
+      stockplotr::example_data,
+      interactive = FALSE
+    ),
     "gg"
   )
 })
 
 test_that("rda file made when indicated", {
   # export rda
-  plot_index(stockplotr::example_data,
+  plot_index(
+    stockplotr::example_data,
     make_rda = TRUE,
     unit_label = "metric tons",
+    interactive = FALSE,
     figures_dir = getwd()
   )
 
diff --git a/tests/testthat/test-plot_landings.R b/tests/testthat/test-plot_landings.R
index 12961856..cfe8bdae 100644
--- a/tests/testthat/test-plot_landings.R
+++ b/tests/testthat/test-plot_landings.R
@@ -1,20 +1,28 @@
 test_that("plot_landings generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_landings(stockplotr::example_data)
+    plot_landings(
+      stockplotr::example_data,
+      interactive = FALSE
+    )
   )
 
 
   # expect ggplot object is returned
   expect_s3_class(
-    plot_landings(stockplotr::example_data),
+    plot_landings(
+      stockplotr::example_data,
+      interactive = FALSE
+    ),
     "gg"
   )
 })
 
 test_that("rda file made when indicated", {
   # export rda
-  plot_landings(stockplotr::example_data,
+  plot_landings(
+    stockplotr::example_data,
+    interactive = FALSE,
     make_rda = TRUE,
     unit_label = "metric tons",
     figures_dir = getwd()
diff --git a/tests/testthat/test-plot_natural_mortality.R b/tests/testthat/test-plot_natural_mortality.R
index 9119ecd0..f082b2fe 100644
--- a/tests/testthat/test-plot_natural_mortality.R
+++ b/tests/testthat/test-plot_natural_mortality.R
@@ -1,7 +1,11 @@
 test_that("plot_natural_mortality generate without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_natural_mortality(stockplotr::example_data, module = "Natural_Mortality")
+    plot_natural_mortality(
+      stockplotr::example_data, 
+      module = "Natural_Mortality",
+      interactive = FALSE
+    )
   )
 
   # This check is moot with the more flextible approach and labelling?
@@ -14,7 +18,8 @@ test_that("plot_natural_mortality generate without errors", {
   expect_s3_class(
     plot_natural_mortality(
       stockplotr::example_data,
-      module = "Natural_Mortality"
+      module = "Natural_Mortality",
+      interactive = FALSE
     ),
     "gg"
   )
@@ -25,6 +30,7 @@ test_that("rda file made when indicated", {
   plot_natural_mortality(
     stockplotr::example_data,
     module = "Natural_Mortality",
+    interactive = FALSE,
     make_rda = TRUE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-plot_recruitment.R b/tests/testthat/test-plot_recruitment.R
index 545d3aac..7cbb763c 100644
--- a/tests/testthat/test-plot_recruitment.R
+++ b/tests/testthat/test-plot_recruitment.R
@@ -1,8 +1,10 @@
 test_that("plot_recruitment generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_recruitment(stockplotr::example_data,
-      module = "TIME_SERIES"
+    plot_recruitment(
+      stockplotr::example_data,
+      module = "TIME_SERIES",
+      interactive = FALSE
     )
   )
 
@@ -13,6 +15,7 @@ test_that("plot_recruitment generates plots without errors", {
       unit_label = "mt",
       scale_amount = 10,
       module = "TIME_SERIES",
+      interactive = FALSE,
       # relative = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
@@ -42,6 +45,7 @@ test_that("plot_recruitment generates plots without errors", {
       scale_amount = 10,
       # relative = TRUE,
       module = "TIME_SERIES",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     ),
@@ -54,6 +58,7 @@ test_that("rda file made when indicated", {
   plot_recruitment(
     stockplotr::example_data,
     module = "TIME_SERIES",
+    interactive = FALSE,
     figures_dir = getwd(),
     make_rda = TRUE
   )
diff --git a/tests/testthat/test-plot_recruitment_deviations.R b/tests/testthat/test-plot_recruitment_deviations.R
index ad97aad6..efa631ca 100644
--- a/tests/testthat/test-plot_recruitment_deviations.R
+++ b/tests/testthat/test-plot_recruitment_deviations.R
@@ -1,8 +1,10 @@
 test_that("plot_recruitment_deviations generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_recruitment_deviations(stockplotr::example_data,
-      module = "SPAWN_RECRUIT"
+    plot_recruitment_deviations(
+      stockplotr::example_data,
+      module = "SPAWN_RECRUIT",
+      interactive = FALSE
     )
   )
 
@@ -11,6 +13,7 @@ test_that("plot_recruitment_deviations generates plots without errors", {
     plot_recruitment_deviations(
       stockplotr::example_data,
       module = "SPAWN_RECRUIT",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -21,6 +24,7 @@ test_that("plot_recruitment_deviations generates plots without errors", {
     plot_recruitment_deviations(
       stockplotr::example_data,
       module = "SPAWN_RECRUIT",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     ),
@@ -33,6 +37,7 @@ test_that("rda file made when indicated", {
   plot_recruitment_deviations(
     stockplotr::example_data,
     module = "SPAWN_RECRUIT",
+    interactive = FALSE,
     make_rda = TRUE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-plot_selectivity.R b/tests/testthat/test-plot_selectivity.R
index 1221b0c1..8b4723ac 100644
--- a/tests/testthat/test-plot_selectivity.R
+++ b/tests/testthat/test-plot_selectivity.R
@@ -2,7 +2,8 @@ test_that("plot_selectivity generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
     plot_selectivity(
-      stockplotr::example_data
+      stockplotr::example_data,
+      interactive = FALSE
     )
   )
 
@@ -14,7 +15,7 @@ test_that("plot_selectivity generates plots without errors", {
       era = NULL,
       group = NULL,
       facet = NULL,
-      interactive = TRUE,
+      interactive = FALSE,
       module = "AGE_SELEX",
       make_rda = FALSE,
       figures_dir = getwd()
@@ -28,7 +29,7 @@ test_that("plot_selectivity generates plots without errors", {
       unit_label = "mm",
       group = NULL,
       facet = NULL,
-      interactive = TRUE,
+      interactive = FALSE,
       module = "LEN_SELEX",
       make_rda = FALSE,
       figures_dir = getwd()
@@ -38,7 +39,8 @@ test_that("plot_selectivity generates plots without errors", {
   # expect ggplot object is returned
   expect_s3_class(
     plot_selectivity(
-      stockplotr::example_data
+      stockplotr::example_data,
+      interactive = FALSE
     ),
     "gg"
   )
@@ -49,6 +51,7 @@ test_that("rda file made when indicated", {
   plot_selectivity(
     stockplotr::example_data,
     module = "AGE_SELEX",
+    interactive = FALSE,
     figures_dir = getwd(),
     make_rda = TRUE
   )
diff --git a/tests/testthat/test-plot_spawning_biomass.R b/tests/testthat/test-plot_spawning_biomass.R
index e467d648..d5194a7c 100644
--- a/tests/testthat/test-plot_spawning_biomass.R
+++ b/tests/testthat/test-plot_spawning_biomass.R
@@ -1,12 +1,18 @@
 test_that("plot_spawning_biomass generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_spawning_biomass(stockplotr::example_data)
+    plot_spawning_biomass(
+      stockplotr::example_data,
+      interactive = FALSE
+    )
   )
 
   # expect plot with warnings if ref_point not indicated
   expect_message(
-    plot_spawning_biomass(stockplotr::example_data)
+    plot_spawning_biomass(
+      stockplotr::example_data,
+      interactive = FALSE
+    )
   )
 
   # expect error-free plot with many arguments
@@ -15,7 +21,8 @@ test_that("plot_spawning_biomass generates plots without errors", {
       stockplotr::example_data,
       unit_label = "metric tons",
       scale_amount = 1,
-      ref_line = "msy"
+      ref_line = "msy",
+      interactive = FALSE
     )
   )
 
@@ -26,7 +33,8 @@ test_that("plot_spawning_biomass generates plots without errors", {
       unit_label = "metric tons",
       scale_amount = 1,
       ref_line = c("msy" = 2000000),
-      relative = FALSE
+      relative = FALSE,
+      interactive = FALSE
     ),
     "gg"
   )
@@ -40,6 +48,7 @@ test_that("rda file made when indicated", {
     scale_amount = 1,
     ref_line = "msy",
     module = "TIME_SERIES",
+    interactive = FALSE,
     make_rda = TRUE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-plot_stock_recruitment.R b/tests/testthat/test-plot_stock_recruitment.R
index 569eead4..3e63f676 100644
--- a/tests/testthat/test-plot_stock_recruitment.R
+++ b/tests/testthat/test-plot_stock_recruitment.R
@@ -2,7 +2,8 @@ test_that("plot_stock_recruitment generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
     stockplotr::plot_stock_recruitment(
-      dat = stockplotr::example_data
+      dat = stockplotr::example_data,
+      interactive = FALSE
     )
   )
 
@@ -12,6 +13,7 @@ test_that("plot_stock_recruitment generates plots without errors", {
       stockplotr::example_data,
       spawning_biomass_label = "mt",
       recruitment_label = "mt",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     )
@@ -24,6 +26,7 @@ test_that("plot_stock_recruitment generates plots without errors", {
       stockplotr::example_data,
       spawning_biomass_label = "mt",
       recruitment_label = "mt",
+      interactive = FALSE,
       make_rda = FALSE,
       figures_dir = getwd()
     ),
@@ -37,6 +40,7 @@ test_that("rda file made when indicated", {
     stockplotr::example_data,
     spawning_biomass_label = "mt",
     recruitment_label = "mt",
+    interactive = FALSE,
     make_rda = TRUE,
     figures_dir = getwd()
   )
diff --git a/tests/testthat/test-table_biomass_abundance_catch.R b/tests/testthat/test-table_biomass_abundance_catch.R
index 6e3325cb..7e3f0d3c 100644
--- a/tests/testthat/test-table_biomass_abundance_catch.R
+++ b/tests/testthat/test-table_biomass_abundance_catch.R
@@ -38,6 +38,7 @@ test_that("rda file made when indicated", {
   table_biomass_abundance_catch(
     dat = stockplotr::example_data,
     module = c("TIME_SERIES", "CATCH", "TIME_SERIES"),
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )
diff --git a/tests/testthat/test-table_index.R b/tests/testthat/test-table_index.R
index c17434e3..34f26b6f 100644
--- a/tests/testthat/test-table_index.R
+++ b/tests/testthat/test-table_index.R
@@ -37,6 +37,7 @@ test_that("rda file made when indicated", {
   # export rda
   table_index(
     dat = stockplotr::example_data,
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )
@@ -53,6 +54,7 @@ test_that("rda file made when indicated", {
   # export rda
   table_index(
     dat = stockplotr::example_data,
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )
diff --git a/tests/testthat/test-table_landings.R b/tests/testthat/test-table_landings.R
index c7c8c9d3..2459b5b7 100644
--- a/tests/testthat/test-table_landings.R
+++ b/tests/testthat/test-table_landings.R
@@ -80,6 +80,7 @@ test_that("rda file made when indicated", {
   # export rda
   table_landings(
     dat = stockplotr::example_data,
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )
@@ -96,6 +97,7 @@ test_that("rda file made when indicated", {
   # export rda
   table_landings(
     dat = stockplotr::example_data,
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )
diff --git a/tests/testthat/test-table_total_catch.R b/tests/testthat/test-table_total_catch.R
index 319771b2..bd1f73b3 100644
--- a/tests/testthat/test-table_total_catch.R
+++ b/tests/testthat/test-table_total_catch.R
@@ -81,6 +81,7 @@ test_that("rda file made when indicated", {
   table_total_catch(
     dat = stockplotr::example_data,
     module = "TIME_SERIES",
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )
@@ -99,6 +100,7 @@ test_that("rda file made when indicated", {
   table_total_catch(
     dat = stockplotr::example_data,
     module = "TIME_SERIES",
+    interactive = FALSE,
     make_rda = TRUE,
     tables_dir = getwd()
   )

From e7913ccd50b6c41c3fa1350619fa2593c85f3c02 Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Wed, 14 Oct 2026 16:02:36 -0400
Subject: [PATCH 4/9] test: :zap: clean ups to remove warnings from tests

---
 R/convert_output.R                     | 4 ++--
 R/table_total_catch.R                  | 2 +-
 tests/testthat/test-plot_biomass.R     | 2 +-
 tests/testthat/test-plot_selectivity.R | 1 -
 4 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/R/convert_output.R b/R/convert_output.R
index 62fed9e0..86285689 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -439,7 +439,7 @@ convert_output <- function(
                 for (i in intersect(tolower(fleet_names), colnames(df3))) {
                   col_name <- glue::glue("exploitation_{i}")
                   df3 <- df3 |>
-                    dplyr::rename(!!col_name := i)
+                    dplyr::rename(!!col_name := dplyr::all_of(i))
                 }
               }
             }
@@ -488,7 +488,7 @@ convert_output <- function(
               if (length(err_col_id) > 0) {
                 uncert_name <- stringr::str_extract(err_col_id, paste0(errors, collapse = "|"))
                 df3 <- df3 |>
-                  dplyr::rename(!!uncert_name := err_col_id)
+                  dplyr::rename(!!uncert_name := dplyr::all_of(err_col_id))
               }
               df4 <- df3 |>
                 tidyr::pivot_longer(
diff --git a/R/table_total_catch.R b/R/table_total_catch.R
index 8c1f79a5..bb1f3529 100644
--- a/R/table_total_catch.R
+++ b/R/table_total_catch.R
@@ -116,7 +116,7 @@ table_total_catch <- function(
   }
 
   catch <- catch |>
-    dplyr::select(-cols_to_remove)
+    dplyr::select(-dplyr::all_of(cols_to_remove))
 
   if ("uncertainty" %in% colnames(catch)) {
     catch <- catch |>
diff --git a/tests/testthat/test-plot_biomass.R b/tests/testthat/test-plot_biomass.R
index b3e2091f..915c01cb 100644
--- a/tests/testthat/test-plot_biomass.R
+++ b/tests/testthat/test-plot_biomass.R
@@ -45,7 +45,7 @@ test_that("plot_biomass generates plots without errors", {
   expect_no_error(
     plot_biomass(
       stockplotr::example_data,
-      ref_point = c("target" = 18000),
+      ref_line = c("target" = 18000),
       unit_label = "metric tons",
       scale_amount = 1,
       relative = FALSE,
diff --git a/tests/testthat/test-plot_selectivity.R b/tests/testthat/test-plot_selectivity.R
index 8b4723ac..0e9f3cfe 100644
--- a/tests/testthat/test-plot_selectivity.R
+++ b/tests/testthat/test-plot_selectivity.R
@@ -12,7 +12,6 @@ test_that("plot_selectivity generates plots without errors", {
     plot_selectivity(
       stockplotr::example_data |>
         dplyr::filter(year == 2020),
-      era = NULL,
       group = NULL,
       facet = NULL,
       interactive = FALSE,

From 89486c7aece00cdab778221fefa94ae53354fe00 Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Wed, 14 Oct 2026 16:27:45 -0400
Subject: [PATCH 5/9] refactor: :art: replaced file check calls in "rda file
 made when indicated" tests with routine function call

---
 tests/testthat/helper-test_functions.R        | 29 +++++++++++++++++++
 tests/testthat/test-plot_abundance_at_age.R   | 10 ++-----
 tests/testthat/test-plot_biomass.R            |  8 +----
 tests/testthat/test-plot_biomass_at_age.R     |  8 +----
 tests/testthat/test-plot_catch_comp.R         |  8 +----
 tests/testthat/test-plot_index.R              |  8 +----
 tests/testthat/test-plot_landings.R           |  8 +----
 tests/testthat/test-plot_natural_mortality.R  |  8 +----
 tests/testthat/test-plot_recruitment.R        |  8 +----
 .../test-plot_recruitment_deviations.R        |  8 +----
 tests/testthat/test-plot_selectivity.R        |  8 +----
 tests/testthat/test-plot_spawning_biomass.R   |  8 +----
 tests/testthat/test-plot_stock_recruitment.R  |  8 +----
 13 files changed, 42 insertions(+), 85 deletions(-)
 create mode 100644 tests/testthat/helper-test_functions.R

diff --git a/tests/testthat/helper-test_functions.R b/tests/testthat/helper-test_functions.R
new file mode 100644
index 00000000..f920f6e6
--- /dev/null
+++ b/tests/testthat/helper-test_functions.R
@@ -0,0 +1,29 @@
+#' Check for the existence and remove .rda files from test environment
+#' 
+#' Checks for the existence of `dir` and `filename` as well as the
+#' existence of "captions_alt_text.csv" and "key_quantities.csv". 
+#' Files are removed upon completion of checks. 
+#' 
+#' For testing only.
+#' 
+#' @param filename String. filename of figure/table .rda file
+#' @param dir String. directory where filename exists
+#' 
+check_and_remove_tmp_files <- function(filename, dir=fs::path(getwd())){
+    # expect that both figures dir and the abundance_at_age_figure.rda file exist
+    expect_true(dir.exists(dir)) # this check needs to exist in case save dir isnt getwd()
+    expect_true(dir.exists(fs::path(dir, "figures")))
+    expect_true(file.exists(fs::path(dir, "figures", filename)))
+
+    # erase temporary testing files
+    captions_file <- fs::path(dir, "captions_alt_text.csv")
+    keyquant_file <- fs::path(dir, "key_quantities.csv")
+
+    if(fs::file_exists(captions_file))
+        fs::file_delete(captions_file)
+
+    if(fs::file_exists(keyquant_file))
+        fs::file_delete(keyquant_file)
+
+    unlink(fs::path(dir, "figures"), recursive = T)
+}
diff --git a/tests/testthat/test-plot_abundance_at_age.R b/tests/testthat/test-plot_abundance_at_age.R
index fe225f2f..3bed4d19 100644
--- a/tests/testthat/test-plot_abundance_at_age.R
+++ b/tests/testthat/test-plot_abundance_at_age.R
@@ -39,18 +39,12 @@ test_that("rda file made when indicated", {
   plot_abundance_at_age(
     stockplotr::example_data,
     figures_dir = getwd(),
-      interactive = FALSE,
+    interactive = FALSE,
     make_rda = TRUE
   )
 
   # expect that both figures dir and the abundance_at_age_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "abundance_at_age_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("abundance_at_age_figure.rda")
 })
 
 test_that("plot_abundance_at_age generates error with scaling <1", {
diff --git a/tests/testthat/test-plot_biomass.R b/tests/testthat/test-plot_biomass.R
index 915c01cb..c4136da5 100644
--- a/tests/testthat/test-plot_biomass.R
+++ b/tests/testthat/test-plot_biomass.R
@@ -93,11 +93,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the biomass_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "biomass_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("biomass_figure.rda")
 })
diff --git a/tests/testthat/test-plot_biomass_at_age.R b/tests/testthat/test-plot_biomass_at_age.R
index 1cb74696..acb4e995 100644
--- a/tests/testthat/test-plot_biomass_at_age.R
+++ b/tests/testthat/test-plot_biomass_at_age.R
@@ -48,13 +48,7 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the biomass_at_age_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "biomass_at_age_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("biomass_at_age_figure.rda")
 })
 
 test_that("plot_biomass_at_age generates error when biomass label is not found", {
diff --git a/tests/testthat/test-plot_catch_comp.R b/tests/testthat/test-plot_catch_comp.R
index 79356c74..bcd847d7 100644
--- a/tests/testthat/test-plot_catch_comp.R
+++ b/tests/testthat/test-plot_catch_comp.R
@@ -49,13 +49,7 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the catch_comp_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "catch_comp_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("catch_comp_figure.rda")
 })
 
 test_that("plot_catch_comp generates error with scaling <1", {
diff --git a/tests/testthat/test-plot_index.R b/tests/testthat/test-plot_index.R
index 276c6406..2a190aa3 100644
--- a/tests/testthat/test-plot_index.R
+++ b/tests/testthat/test-plot_index.R
@@ -28,11 +28,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the index_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "index_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("index_figure.rda")
 })
diff --git a/tests/testthat/test-plot_landings.R b/tests/testthat/test-plot_landings.R
index cfe8bdae..f0dc9339 100644
--- a/tests/testthat/test-plot_landings.R
+++ b/tests/testthat/test-plot_landings.R
@@ -29,11 +29,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the landings_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "landings_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("landings_figure.rda")
 })
diff --git a/tests/testthat/test-plot_natural_mortality.R b/tests/testthat/test-plot_natural_mortality.R
index f082b2fe..f26efb37 100644
--- a/tests/testthat/test-plot_natural_mortality.R
+++ b/tests/testthat/test-plot_natural_mortality.R
@@ -36,11 +36,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the natural_mortality_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "natural_mortality_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("natural_mortality_figure.rda")
 })
diff --git a/tests/testthat/test-plot_recruitment.R b/tests/testthat/test-plot_recruitment.R
index 7cbb763c..d6d1dd08 100644
--- a/tests/testthat/test-plot_recruitment.R
+++ b/tests/testthat/test-plot_recruitment.R
@@ -64,11 +64,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the recruitment_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "recruitment_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("recruitment_figure.rda")
 })
diff --git a/tests/testthat/test-plot_recruitment_deviations.R b/tests/testthat/test-plot_recruitment_deviations.R
index efa631ca..69126810 100644
--- a/tests/testthat/test-plot_recruitment_deviations.R
+++ b/tests/testthat/test-plot_recruitment_deviations.R
@@ -43,11 +43,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the recruitment_deviations_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "recruitment_deviations_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("recruitment_deviations_figure.rda")
 })
diff --git a/tests/testthat/test-plot_selectivity.R b/tests/testthat/test-plot_selectivity.R
index 0e9f3cfe..ed097ffd 100644
--- a/tests/testthat/test-plot_selectivity.R
+++ b/tests/testthat/test-plot_selectivity.R
@@ -56,11 +56,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the selectivity_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "selectivity_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("selectivity_figure.rda")
 })
diff --git a/tests/testthat/test-plot_spawning_biomass.R b/tests/testthat/test-plot_spawning_biomass.R
index d5194a7c..40cc4521 100644
--- a/tests/testthat/test-plot_spawning_biomass.R
+++ b/tests/testthat/test-plot_spawning_biomass.R
@@ -54,11 +54,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the spawning_biomass_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "spawning_biomass_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("spawning_biomass_figure.rda")
 })
diff --git a/tests/testthat/test-plot_stock_recruitment.R b/tests/testthat/test-plot_stock_recruitment.R
index 3e63f676..64288b80 100644
--- a/tests/testthat/test-plot_stock_recruitment.R
+++ b/tests/testthat/test-plot_stock_recruitment.R
@@ -46,11 +46,5 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both figures dir and the sr_figure.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "stock_recruitment_figure.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "figures"), recursive = T)
+  check_and_remove_tmp_files("stock_recruitment_figure.rda")
 })

From 45ea79e174c99484d7b7dd569d905362445a4ea5 Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Wed, 14 Oct 2026 17:05:48 -0400
Subject: [PATCH 6/9] refactor: :art: updated check_and_remove_tmp_files to
 work for temporary table files from tests

---
 tests/testthat/helper-test_functions.R        | 11 +++++----
 .../test-table_biomass_abundance_catch.R      |  8 +------
 tests/testthat/test-table_index.R             | 20 +---------------
 tests/testthat/test-table_landings.R          | 21 +----------------
 tests/testthat/test-table_projections.R       |  8 +------
 tests/testthat/test-table_total_catch.R       | 23 +------------------
 6 files changed, 12 insertions(+), 79 deletions(-)

diff --git a/tests/testthat/helper-test_functions.R b/tests/testthat/helper-test_functions.R
index f920f6e6..78688e07 100644
--- a/tests/testthat/helper-test_functions.R
+++ b/tests/testthat/helper-test_functions.R
@@ -8,12 +8,15 @@
 #' 
 #' @param filename String. filename of figure/table .rda file
 #' @param dir String. directory where filename exists
+#' @param figs_or_tables String. whether check for a "figures" or "tables" internal directory
 #' 
-check_and_remove_tmp_files <- function(filename, dir=fs::path(getwd())){
+#' DEFAULT: "figures"
+#' 
+check_and_remove_tmp_files <- function(filename, dir=fs::path(getwd()), figs_or_tables="figures"){
     # expect that both figures dir and the abundance_at_age_figure.rda file exist
     expect_true(dir.exists(dir)) # this check needs to exist in case save dir isnt getwd()
-    expect_true(dir.exists(fs::path(dir, "figures")))
-    expect_true(file.exists(fs::path(dir, "figures", filename)))
+    expect_true(dir.exists(fs::path(dir, figs_or_tables)))
+    expect_true(file.exists(fs::path(dir, figs_or_tables, filename)))
 
     # erase temporary testing files
     captions_file <- fs::path(dir, "captions_alt_text.csv")
@@ -25,5 +28,5 @@ check_and_remove_tmp_files <- function(filename, dir=fs::path(getwd())){
     if(fs::file_exists(keyquant_file))
         fs::file_delete(keyquant_file)
 
-    unlink(fs::path(dir, "figures"), recursive = T)
+    unlink(fs::path(dir, figs_or_tables), recursive = T)
 }
diff --git a/tests/testthat/test-table_biomass_abundance_catch.R b/tests/testthat/test-table_biomass_abundance_catch.R
index 7e3f0d3c..6f753ac0 100644
--- a/tests/testthat/test-table_biomass_abundance_catch.R
+++ b/tests/testthat/test-table_biomass_abundance_catch.R
@@ -44,13 +44,7 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both tables dir and the biomass_abundance_catch_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "biomass_abundance_catch_table.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
+  check_and_remove_tmp_files("biomass_abundance_catch_table.rda", figs_or_tables="tables")
 })
 
 test_that("table_biomass_abundance_catch generates error with incorrect module", {
diff --git a/tests/testthat/test-table_index.R b/tests/testthat/test-table_index.R
index 34f26b6f..4946f025 100644
--- a/tests/testthat/test-table_index.R
+++ b/tests/testthat/test-table_index.R
@@ -34,23 +34,6 @@ test_that("table_index generates plots without errors", {
 })
 
 test_that("rda file made when indicated", {
-  # export rda
-  table_index(
-    dat = stockplotr::example_data,
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
-
-  # expect that both tables dir and the index_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "index_table.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
-
-
   # export rda
   table_index(
     dat = stockplotr::example_data,
@@ -75,6 +58,5 @@ test_that("rda file made when indicated", {
   expect_true(rda$caption == "Calculated index of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ")
 
   # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
+  check_and_remove_tmp_files("index_table.rda", figs_or_tables="tables")
 })
diff --git a/tests/testthat/test-table_landings.R b/tests/testthat/test-table_landings.R
index 2459b5b7..236f4c37 100644
--- a/tests/testthat/test-table_landings.R
+++ b/tests/testthat/test-table_landings.R
@@ -85,23 +85,6 @@ test_that("rda file made when indicated", {
     tables_dir = getwd()
   )
 
-  # expect that both tables dir and the landings_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "landings_table.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
-
-  # export rda
-  table_landings(
-    dat = stockplotr::example_data,
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
-
   # load the rda file and check that it contains the expected object
   load(fs::path(getwd(), "tables", "landings_table.rda"))
   # expect rda contains three objects: table, caption, and latex table
@@ -118,7 +101,5 @@ test_that("rda file made when indicated", {
   expect_true(rda$caption == "Landed catch by fleet and year in  (mt).")
 
   # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
+  check_and_remove_tmp_files("landings_table.rda", figs_or_tables="tables")
 })
diff --git a/tests/testthat/test-table_projections.R b/tests/testthat/test-table_projections.R
index 77d631d2..58ad4f1f 100644
--- a/tests/testthat/test-table_projections.R
+++ b/tests/testthat/test-table_projections.R
@@ -28,13 +28,7 @@ test_that("rda file made when indicated", {
   )
 
   # expect that both tables dir and the projections_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "projections_table.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
+  check_and_remove_tmp_files("projections_table.rda", figs_or_tables="tables")
 })
 
 test_that("table_projections generates error with incorrect module", {
diff --git a/tests/testthat/test-table_total_catch.R b/tests/testthat/test-table_total_catch.R
index bd1f73b3..8af7899d 100644
--- a/tests/testthat/test-table_total_catch.R
+++ b/tests/testthat/test-table_total_catch.R
@@ -77,25 +77,6 @@ test_that("table_total_catch generates error with incorrect module", {
 
 
 test_that("rda file made when indicated", {
-  # export rda
-  table_total_catch(
-    dat = stockplotr::example_data,
-    module = "TIME_SERIES",
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
-
-  # expect that both tables dir and the total_catch_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "total_catch_table.rda")))
-
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
-
-
   # export rda
   table_total_catch(
     dat = stockplotr::example_data,
@@ -121,7 +102,5 @@ test_that("rda file made when indicated", {
   expect_true(rda$caption == "Total catch by fleet over time.")
 
   # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
+  check_and_remove_tmp_files("total_catch_table.rda", figs_or_tables="tables")
 })

From 4e20f1e047d89596944bb346434d3fdb797343cf Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Fri, 16 Oct 2026 11:35:53 -0400
Subject: [PATCH 7/9] test: :zap: remove redundant rda generation test

plot specific tests for rda generation were redundant with the save_all_plots test
---
 tests/testthat/test-plot_abundance_at_age.R   | 22 ++++-----
 tests/testthat/test-plot_biomass.R            | 24 +++++-----
 tests/testthat/test-plot_biomass_at_age.R     | 24 +++++-----
 tests/testthat/test-plot_catch_comp.R         | 24 +++++-----
 tests/testthat/test-plot_index.R              | 24 +++++-----
 tests/testthat/test-plot_landings.R           | 24 +++++-----
 tests/testthat/test-plot_natural_mortality.R  | 24 +++++-----
 tests/testthat/test-plot_recruitment.R        | 24 +++++-----
 .../test-plot_recruitment_deviations.R        | 24 +++++-----
 tests/testthat/test-plot_selectivity.R        | 24 +++++-----
 tests/testthat/test-plot_spawning_biomass.R   | 30 ++++++------
 tests/testthat/test-plot_stock_recruitment.R  | 26 +++++-----
 .../test-table_biomass_abundance_catch.R      | 24 +++++-----
 tests/testthat/test-table_index.R             | 48 +++++++++----------
 tests/testthat/test-table_landings.R          | 38 +++++++--------
 tests/testthat/test-table_projections.R       | 22 ++++-----
 16 files changed, 213 insertions(+), 213 deletions(-)

diff --git a/tests/testthat/test-plot_abundance_at_age.R b/tests/testthat/test-plot_abundance_at_age.R
index 3bed4d19..64381c1e 100644
--- a/tests/testthat/test-plot_abundance_at_age.R
+++ b/tests/testthat/test-plot_abundance_at_age.R
@@ -34,18 +34,18 @@ test_that("plot_abundance_at_age generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_abundance_at_age(
-    stockplotr::example_data,
-    figures_dir = getwd(),
-    interactive = FALSE,
-    make_rda = TRUE
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_abundance_at_age(
+#     stockplotr::example_data,
+#     figures_dir = getwd(),
+#     interactive = FALSE,
+#     make_rda = TRUE
+#   )
 
-  # expect that both figures dir and the abundance_at_age_figure.rda file exist
-  check_and_remove_tmp_files("abundance_at_age_figure.rda")
-})
+#   # expect that both figures dir and the abundance_at_age_figure.rda file exist
+#   check_and_remove_tmp_files("abundance_at_age_figure.rda")
+# })
 
 test_that("plot_abundance_at_age generates error with scaling <1", {
   # expect error
diff --git a/tests/testthat/test-plot_biomass.R b/tests/testthat/test-plot_biomass.R
index c4136da5..67506a40 100644
--- a/tests/testthat/test-plot_biomass.R
+++ b/tests/testthat/test-plot_biomass.R
@@ -82,16 +82,16 @@ test_that("plot_biomass generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_biomass(
-    stockplotr::example_data,
-    figures_dir = getwd(),
-    interactive = FALSE,
-    make_rda = TRUE,
-    module = "TIME_SERIES"
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_biomass(
+#     stockplotr::example_data,
+#     figures_dir = getwd(),
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     module = "TIME_SERIES"
+#   )
 
-  # expect that both figures dir and the biomass_figure.rda file exist
-  check_and_remove_tmp_files("biomass_figure.rda")
-})
+#   # expect that both figures dir and the biomass_figure.rda file exist
+#   check_and_remove_tmp_files("biomass_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_biomass_at_age.R b/tests/testthat/test-plot_biomass_at_age.R
index acb4e995..a19e4e59 100644
--- a/tests/testthat/test-plot_biomass_at_age.R
+++ b/tests/testthat/test-plot_biomass_at_age.R
@@ -37,19 +37,19 @@ test_that("plot_biomass_at_age generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_biomass_at_age(
-    stockplotr::example_data,
-    module = "BIOMASS_AT_AGE",
-    interactive = FALSE,
-    figures_dir = getwd(),
-    make_rda = TRUE
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_biomass_at_age(
+#     stockplotr::example_data,
+#     module = "BIOMASS_AT_AGE",
+#     interactive = FALSE,
+#     figures_dir = getwd(),
+#     make_rda = TRUE
+#   )
 
-  # expect that both figures dir and the biomass_at_age_figure.rda file exist
-  check_and_remove_tmp_files("biomass_at_age_figure.rda")
-})
+#   # expect that both figures dir and the biomass_at_age_figure.rda file exist
+#   check_and_remove_tmp_files("biomass_at_age_figure.rda")
+# })
 
 test_that("plot_biomass_at_age generates error when biomass label is not found", {
   # generate test data set
diff --git a/tests/testthat/test-plot_catch_comp.R b/tests/testthat/test-plot_catch_comp.R
index bcd847d7..ad2e3c65 100644
--- a/tests/testthat/test-plot_catch_comp.R
+++ b/tests/testthat/test-plot_catch_comp.R
@@ -38,19 +38,19 @@ test_that("plot_catch_comp generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_catch_comp(
-    stockplotr::example_data,
-    module = "CATCH_AT_AGE",
-    interactive = FALSE,
-    figures_dir = getwd(),
-    make_rda = TRUE
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_catch_comp(
+#     stockplotr::example_data,
+#     module = "CATCH_AT_AGE",
+#     interactive = FALSE,
+#     figures_dir = getwd(),
+#     make_rda = TRUE
+#   )
 
-  # expect that both figures dir and the catch_comp_figure.rda file exist
-  check_and_remove_tmp_files("catch_comp_figure.rda")
-})
+#   # expect that both figures dir and the catch_comp_figure.rda file exist
+#   check_and_remove_tmp_files("catch_comp_figure.rda")
+# })
 
 test_that("plot_catch_comp generates error with scaling <1", {
   # expect error
diff --git a/tests/testthat/test-plot_index.R b/tests/testthat/test-plot_index.R
index 2a190aa3..2a5239a3 100644
--- a/tests/testthat/test-plot_index.R
+++ b/tests/testthat/test-plot_index.R
@@ -17,16 +17,16 @@ test_that("plot_index generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_index(
-    stockplotr::example_data,
-    make_rda = TRUE,
-    unit_label = "metric tons",
-    interactive = FALSE,
-    figures_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_index(
+#     stockplotr::example_data,
+#     make_rda = TRUE,
+#     unit_label = "metric tons",
+#     interactive = FALSE,
+#     figures_dir = getwd()
+#   )
 
-  # expect that both figures dir and the index_figure.rda file exist
-  check_and_remove_tmp_files("index_figure.rda")
-})
+#   # expect that both figures dir and the index_figure.rda file exist
+#   check_and_remove_tmp_files("index_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_landings.R b/tests/testthat/test-plot_landings.R
index f0dc9339..2ffa0e9f 100644
--- a/tests/testthat/test-plot_landings.R
+++ b/tests/testthat/test-plot_landings.R
@@ -18,16 +18,16 @@ test_that("plot_landings generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_landings(
-    stockplotr::example_data,
-    interactive = FALSE,
-    make_rda = TRUE,
-    unit_label = "metric tons",
-    figures_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_landings(
+#     stockplotr::example_data,
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     unit_label = "metric tons",
+#     figures_dir = getwd()
+#   )
 
-  # expect that both figures dir and the landings_figure.rda file exist
-  check_and_remove_tmp_files("landings_figure.rda")
-})
+#   # expect that both figures dir and the landings_figure.rda file exist
+#   check_and_remove_tmp_files("landings_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_natural_mortality.R b/tests/testthat/test-plot_natural_mortality.R
index f26efb37..fb241f72 100644
--- a/tests/testthat/test-plot_natural_mortality.R
+++ b/tests/testthat/test-plot_natural_mortality.R
@@ -25,16 +25,16 @@ test_that("plot_natural_mortality generate without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_natural_mortality(
-    stockplotr::example_data,
-    module = "Natural_Mortality",
-    interactive = FALSE,
-    make_rda = TRUE,
-    figures_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_natural_mortality(
+#     stockplotr::example_data,
+#     module = "Natural_Mortality",
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     figures_dir = getwd()
+#   )
 
-  # expect that both figures dir and the natural_mortality_figure.rda file exist
-  check_and_remove_tmp_files("natural_mortality_figure.rda")
-})
+#   # expect that both figures dir and the natural_mortality_figure.rda file exist
+#   check_and_remove_tmp_files("natural_mortality_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_recruitment.R b/tests/testthat/test-plot_recruitment.R
index d6d1dd08..03764914 100644
--- a/tests/testthat/test-plot_recruitment.R
+++ b/tests/testthat/test-plot_recruitment.R
@@ -53,16 +53,16 @@ test_that("plot_recruitment generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_recruitment(
-    stockplotr::example_data,
-    module = "TIME_SERIES",
-    interactive = FALSE,
-    figures_dir = getwd(),
-    make_rda = TRUE
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_recruitment(
+#     stockplotr::example_data,
+#     module = "TIME_SERIES",
+#     interactive = FALSE,
+#     figures_dir = getwd(),
+#     make_rda = TRUE
+#   )
 
-  # expect that both figures dir and the recruitment_figure.rda file exist
-  check_and_remove_tmp_files("recruitment_figure.rda")
-})
+#   # expect that both figures dir and the recruitment_figure.rda file exist
+#   check_and_remove_tmp_files("recruitment_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_recruitment_deviations.R b/tests/testthat/test-plot_recruitment_deviations.R
index 69126810..491ca4b5 100644
--- a/tests/testthat/test-plot_recruitment_deviations.R
+++ b/tests/testthat/test-plot_recruitment_deviations.R
@@ -32,16 +32,16 @@ test_that("plot_recruitment_deviations generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_recruitment_deviations(
-    stockplotr::example_data,
-    module = "SPAWN_RECRUIT",
-    interactive = FALSE,
-    make_rda = TRUE,
-    figures_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_recruitment_deviations(
+#     stockplotr::example_data,
+#     module = "SPAWN_RECRUIT",
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     figures_dir = getwd()
+#   )
 
-  # expect that both figures dir and the recruitment_deviations_figure.rda file exist
-  check_and_remove_tmp_files("recruitment_deviations_figure.rda")
-})
+#   # expect that both figures dir and the recruitment_deviations_figure.rda file exist
+#   check_and_remove_tmp_files("recruitment_deviations_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_selectivity.R b/tests/testthat/test-plot_selectivity.R
index ed097ffd..8244c10d 100644
--- a/tests/testthat/test-plot_selectivity.R
+++ b/tests/testthat/test-plot_selectivity.R
@@ -45,16 +45,16 @@ test_that("plot_selectivity generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_selectivity(
-    stockplotr::example_data,
-    module = "AGE_SELEX",
-    interactive = FALSE,
-    figures_dir = getwd(),
-    make_rda = TRUE
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_selectivity(
+#     stockplotr::example_data,
+#     module = "AGE_SELEX",
+#     interactive = FALSE,
+#     figures_dir = getwd(),
+#     make_rda = TRUE
+#   )
 
-  # expect that both figures dir and the selectivity_figure.rda file exist
-  check_and_remove_tmp_files("selectivity_figure.rda")
-})
+#   # expect that both figures dir and the selectivity_figure.rda file exist
+#   check_and_remove_tmp_files("selectivity_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_spawning_biomass.R b/tests/testthat/test-plot_spawning_biomass.R
index 40cc4521..dea24c82 100644
--- a/tests/testthat/test-plot_spawning_biomass.R
+++ b/tests/testthat/test-plot_spawning_biomass.R
@@ -40,19 +40,19 @@ test_that("plot_spawning_biomass generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_spawning_biomass(
-    stockplotr::example_data,
-    unit_label = "metric tons",
-    scale_amount = 1,
-    ref_line = "msy",
-    module = "TIME_SERIES",
-    interactive = FALSE,
-    make_rda = TRUE,
-    figures_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_spawning_biomass(
+#     stockplotr::example_data,
+#     unit_label = "metric tons",
+#     scale_amount = 1,
+#     ref_line = "msy",
+#     module = "TIME_SERIES",
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     figures_dir = getwd()
+#   )
 
-  # expect that both figures dir and the spawning_biomass_figure.rda file exist
-  check_and_remove_tmp_files("spawning_biomass_figure.rda")
-})
+#   # expect that both figures dir and the spawning_biomass_figure.rda file exist
+#   check_and_remove_tmp_files("spawning_biomass_figure.rda")
+# })
diff --git a/tests/testthat/test-plot_stock_recruitment.R b/tests/testthat/test-plot_stock_recruitment.R
index 64288b80..b918730f 100644
--- a/tests/testthat/test-plot_stock_recruitment.R
+++ b/tests/testthat/test-plot_stock_recruitment.R
@@ -34,17 +34,17 @@ test_that("plot_stock_recruitment generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_stock_recruitment(
-    stockplotr::example_data,
-    spawning_biomass_label = "mt",
-    recruitment_label = "mt",
-    interactive = FALSE,
-    make_rda = TRUE,
-    figures_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_stock_recruitment(
+#     stockplotr::example_data,
+#     spawning_biomass_label = "mt",
+#     recruitment_label = "mt",
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     figures_dir = getwd()
+#   )
 
-  # expect that both figures dir and the sr_figure.rda file exist
-  check_and_remove_tmp_files("stock_recruitment_figure.rda")
-})
+#   # expect that both figures dir and the sr_figure.rda file exist
+#   check_and_remove_tmp_files("stock_recruitment_figure.rda")
+# })
diff --git a/tests/testthat/test-table_biomass_abundance_catch.R b/tests/testthat/test-table_biomass_abundance_catch.R
index 6f753ac0..d4a5b1e0 100644
--- a/tests/testthat/test-table_biomass_abundance_catch.R
+++ b/tests/testthat/test-table_biomass_abundance_catch.R
@@ -33,19 +33,19 @@ test_that("table_biomass_abundance_catch generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_biomass_abundance_catch(
-    dat = stockplotr::example_data,
-    module = c("TIME_SERIES", "CATCH", "TIME_SERIES"),
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_biomass_abundance_catch(
+#     dat = stockplotr::example_data,
+#     module = c("TIME_SERIES", "CATCH", "TIME_SERIES"),
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # expect that both tables dir and the biomass_abundance_catch_table.rda file exist
-  check_and_remove_tmp_files("biomass_abundance_catch_table.rda", figs_or_tables="tables")
-})
+#   # expect that both tables dir and the biomass_abundance_catch_table.rda file exist
+#   check_and_remove_tmp_files("biomass_abundance_catch_table.rda", figs_or_tables="tables")
+# })
 
 test_that("table_biomass_abundance_catch generates error with incorrect module", {
   # expect error
diff --git a/tests/testthat/test-table_index.R b/tests/testthat/test-table_index.R
index 4946f025..9fa9563e 100644
--- a/tests/testthat/test-table_index.R
+++ b/tests/testthat/test-table_index.R
@@ -33,30 +33,30 @@ test_that("table_index generates plots without errors", {
   # )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_index(
-    dat = stockplotr::example_data,
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_index(
+#     dat = stockplotr::example_data,
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # load the rda file and check that it contains the expected object
-  load(fs::path(getwd(), "tables", "index_table.rda"))
-  # expect rda contains three objects: table, caption, and latex table
-  expect_false(
-    is.null(rda$table)
-  )
-  expect_false(
-    is.null(rda$caption)
-  )
-  expect_false(
-    is.null(rda$latex_table)
-  )
+#   # load the rda file and check that it contains the expected object
+#   load(fs::path(getwd(), "tables", "index_table.rda"))
+#   # expect rda contains three objects: table, caption, and latex table
+#   expect_false(
+#     is.null(rda$table)
+#   )
+#   expect_false(
+#     is.null(rda$caption)
+#   )
+#   expect_false(
+#     is.null(rda$latex_table)
+#   )
 
-  expect_true(rda$caption == "Calculated index of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ")
+#   expect_true(rda$caption == "Calculated index of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ")
 
-  # erase temporary testing files
-  check_and_remove_tmp_files("index_table.rda", figs_or_tables="tables")
-})
+#   # erase temporary testing files
+#   check_and_remove_tmp_files("index_table.rda", figs_or_tables="tables")
+# })
diff --git a/tests/testthat/test-table_landings.R b/tests/testthat/test-table_landings.R
index 236f4c37..1bc7df84 100644
--- a/tests/testthat/test-table_landings.R
+++ b/tests/testthat/test-table_landings.R
@@ -37,27 +37,27 @@ test_that("table_landings generates plots without errors", {
   # )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_landings(
-    dat = stockplotr::example_data,
-    unit_label = "mt",
-    era = NULL,
-    interactive = FALSE,
-    module = "CATCH",
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_landings(
+#     dat = stockplotr::example_data,
+#     unit_label = "mt",
+#     era = NULL,
+#     interactive = FALSE,
+#     module = "CATCH",
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # expect that both tables dir and the landings_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "landings_table.rda")))
+#   # expect that both tables dir and the landings_table.rda file exist
+#   expect_true(dir.exists(fs::path(getwd(), "tables")))
+#   expect_true(file.exists(fs::path(getwd(), "tables", "landings_table.rda")))
 
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
-})
+#   # erase temporary testing files
+#   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+#   file.remove(fs::path(getwd(), "key_quantities.csv"))
+#   unlink(fs::path(getwd(), "tables"), recursive = T)
+# })
 
 test_that("table_landings generates error with incorrect module", {
   # expect error
diff --git a/tests/testthat/test-table_projections.R b/tests/testthat/test-table_projections.R
index 58ad4f1f..316661cc 100644
--- a/tests/testthat/test-table_projections.R
+++ b/tests/testthat/test-table_projections.R
@@ -18,18 +18,18 @@ test_that("table_projections generates plots without errors", {
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_projections(
-    dat = stockplotr::example_data,
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_projections(
+#     dat = stockplotr::example_data,
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # expect that both tables dir and the projections_table.rda file exist
-  check_and_remove_tmp_files("projections_table.rda", figs_or_tables="tables")
-})
+#   # expect that both tables dir and the projections_table.rda file exist
+#   check_and_remove_tmp_files("projections_table.rda", figs_or_tables="tables")
+# })
 
 test_that("table_projections generates error with incorrect module", {
   # expect error

From d74aa43b7f2a11959a01c767acb69f676bd5c010 Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Fri, 16 Oct 2026 12:34:50 -0400
Subject: [PATCH 8/9] test: :zap: removed redundant "make rda" tests for select
 tables

---
 tests/testthat/test-table_landings.R    | 48 +++++++-------
 tests/testthat/test-table_total_catch.R | 88 ++++++++++++-------------
 2 files changed, 68 insertions(+), 68 deletions(-)

diff --git a/tests/testthat/test-table_landings.R b/tests/testthat/test-table_landings.R
index 1bc7df84..04f37761 100644
--- a/tests/testthat/test-table_landings.R
+++ b/tests/testthat/test-table_landings.R
@@ -76,30 +76,30 @@ test_that("table_landings generates error with incorrect module", {
 })
 
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_landings(
-    dat = stockplotr::example_data,
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_landings(
+#     dat = stockplotr::example_data,
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # load the rda file and check that it contains the expected object
-  load(fs::path(getwd(), "tables", "landings_table.rda"))
-  # expect rda contains three objects: table, caption, and latex table
-  expect_false(
-    is.null(rda$table)
-  )
-  expect_false(
-    is.null(rda$caption)
-  )
-  expect_false(
-    is.null(rda$latex_table)
-  )
+#   # load the rda file and check that it contains the expected object
+#   load(fs::path(getwd(), "tables", "landings_table.rda"))
+#   # expect rda contains three objects: table, caption, and latex table
+#   expect_false(
+#     is.null(rda$table)
+#   )
+#   expect_false(
+#     is.null(rda$caption)
+#   )
+#   expect_false(
+#     is.null(rda$latex_table)
+#   )
 
-  expect_true(rda$caption == "Landed catch by fleet and year in  (mt).")
+#   expect_true(rda$caption == "Landed catch by fleet and year in  (mt).")
 
-  # erase temporary testing files
-  check_and_remove_tmp_files("landings_table.rda", figs_or_tables="tables")
-})
+#   # erase temporary testing files
+#   check_and_remove_tmp_files("landings_table.rda", figs_or_tables="tables")
+# })
diff --git a/tests/testthat/test-table_total_catch.R b/tests/testthat/test-table_total_catch.R
index 8af7899d..dfb9f8be 100644
--- a/tests/testthat/test-table_total_catch.R
+++ b/tests/testthat/test-table_total_catch.R
@@ -37,27 +37,27 @@ test_that("table_total_catch generates plots without errors", {
   # )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_total_catch(
-    dat = stockplotr::example_data,
-    unit_label = "mt",
-    era = NULL,
-    interactive = FALSE,
-    module = "TIME_SERIES",
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_total_catch(
+#     dat = stockplotr::example_data,
+#     unit_label = "mt",
+#     era = NULL,
+#     interactive = FALSE,
+#     module = "TIME_SERIES",
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # expect that both tables dir and the total_catch_table.rda file exist
-  expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "total_catch_table.rda")))
+#   # expect that both tables dir and the total_catch_table.rda file exist
+#   expect_true(dir.exists(fs::path(getwd(), "tables")))
+#   expect_true(file.exists(fs::path(getwd(), "tables", "total_catch_table.rda")))
 
-  # erase temporary testing files
-  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-  file.remove(fs::path(getwd(), "key_quantities.csv"))
-  unlink(fs::path(getwd(), "tables"), recursive = T)
-})
+#   # erase temporary testing files
+#   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+#   file.remove(fs::path(getwd(), "key_quantities.csv"))
+#   unlink(fs::path(getwd(), "tables"), recursive = T)
+# })
 
 test_that("table_total_catch generates error with incorrect module", {
   # expect error
@@ -76,31 +76,31 @@ test_that("table_total_catch generates error with incorrect module", {
 })
 
 
-test_that("rda file made when indicated", {
-  # export rda
-  table_total_catch(
-    dat = stockplotr::example_data,
-    module = "TIME_SERIES",
-    interactive = FALSE,
-    make_rda = TRUE,
-    tables_dir = getwd()
-  )
+# test_that("rda file made when indicated", {
+#   # export rda
+#   table_total_catch(
+#     dat = stockplotr::example_data,
+#     module = "TIME_SERIES",
+#     interactive = FALSE,
+#     make_rda = TRUE,
+#     tables_dir = getwd()
+#   )
 
-  # load the rda file and check that it contains the expected object
-  load(fs::path(getwd(), "tables", "total_catch_table.rda"))
-  # expect rda contains three objects: table, caption, and latex table
-  expect_false(
-    is.null(rda$table)
-  )
-  expect_false(
-    is.null(rda$caption)
-  )
-  expect_false(
-    is.null(rda$latex_table)
-  )
+#   # load the rda file and check that it contains the expected object
+#   load(fs::path(getwd(), "tables", "total_catch_table.rda"))
+#   # expect rda contains three objects: table, caption, and latex table
+#   expect_false(
+#     is.null(rda$table)
+#   )
+#   expect_false(
+#     is.null(rda$caption)
+#   )
+#   expect_false(
+#     is.null(rda$latex_table)
+#   )
 
-  expect_true(rda$caption == "Total catch by fleet over time.")
+#   expect_true(rda$caption == "Total catch by fleet over time.")
 
-  # erase temporary testing files
-  check_and_remove_tmp_files("total_catch_table.rda", figs_or_tables="tables")
-})
+#   # erase temporary testing files
+#   check_and_remove_tmp_files("total_catch_table.rda", figs_or_tables="tables")
+# })

From 5568d3fb3b2051fcf3bc3abab76f8e3c28452283 Mon Sep 17 00:00:00 2001
From: Joshua Zahner <joshua.zahner@noaa.gov>
Date: Fri, 16 Oct 2026 12:35:54 -0400
Subject: [PATCH 9/9] chore: :zap: added support for parallel testthat

save_all_plots and convert_output tests will run first, followed by the individual plotting and table function tests
---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0b38cf27..6c7db50c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,7 +63,8 @@ VignetteBuilder:
     knitr
 Config/roxygen2/version: 8.1.0
 Config/testthat/edition: 3
-Config/testthat/parallel: false
+Config/testthat/parallel: true
+Config/testthat/start-first: save_all_plots*, convert_output*
 Encoding: UTF-8
 Language: en-US
 LazyData: true