Improved test efficiency

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

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(

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 |>

tests/testthat/helper-test_functions.R

@@ -0,0 +1,32 @@
+#' 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
+#' @param figs_or_tables String. whether check for a "figures" or "tables" internal directory
+#' 
+#' 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, 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")
+    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, figs_or_tables), recursive = T)
+}

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

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()
     )
@@ -22,30 +26,26 @@ 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()
     ),
     "gg"
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_abundance_at_age(
-    stockplotr::example_data,
-    figures_dir = getwd(),
-    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")))
+# test_that("rda file made when indicated", {
+#   # export rda
+#   plot_abundance_at_age(
+#     stockplotr::example_data,
+#     figures_dir = getwd(),
+#     interactive = FALSE,
+#     make_rda = TRUE
+#   )
 
-  # 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)
-})
+#   # 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
@@ -54,6 +54,7 @@ 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 +132,7 @@ 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 +145,7 @@ 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 +158,7 @@ test_that("plot contains a legend", {
     proportional = FALSE,
     unit_label = "fish",
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )

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
@@ -42,10 +45,11 @@ 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,
+      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"
@@ -76,21 +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(),
-    make_rda = TRUE,
-    module = "TIME_SERIES"
-  )
-
-  # 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")))
+# 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"
+#   )
 
-  # 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)
-})
+#   # expect that both figures dir and the biomass_figure.rda file exist
+#   check_and_remove_tmp_files("biomass_figure.rda")
+# })

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()
     )
@@ -26,31 +29,27 @@ 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()
     ),
     "gg"
   )
 })
 
-test_that("rda file made when indicated", {
-  # export rda
-  plot_biomass_at_age(
-    stockplotr::example_data,
-    module = "BIOMASS_AT_AGE",
-    figures_dir = getwd(),
-    make_rda = TRUE
-  )
-
-  # 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")))
+# 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
+#   )
 
-  # 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)
-})
+#   # 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
@@ -123,6 +122,7 @@ 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 +136,7 @@ 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 +150,7 @@ test_that("plot contains a legend", {
     proportional = FALSE,
     unit_label = "fish",
     scale_amount = 1,
+    interactive = FALSE,
     make_rda = FALSE,
     figures_dir = getwd()
   )