Upgrade tests to use testthat edition 3

- close #191

- remove defunct functions, e.g., `context()`
- update deprecated functions, e.g., `expect_equivalent()` -> `expect_equal()`
- handle cases where functions issue multiple warnings/messages but testthat is now capturing only the first warning/message

DESCRIPTION

@@ -35,7 +35,7 @@ Suggests:
   rSW2exter (>= 0.1.0),
   soilDB,
   spelling (>= 2.1.0),
-  testthat
+  testthat (>= 3.0.0)
 Remotes:
     github::DrylandEcology/rSW2utils,
     github::DrylandEcology/rSW2data,
@@ -46,6 +46,7 @@ URL: https://github.com/DrylandEcology/rSOILWAT2
 BugReports: https://github.com/DrylandEcology/rSOILWAT2/issues
 Encoding: UTF-8
 RoxygenNote: 7.2.2
+Config/testthat/edition: 3
 LazyData: true
 Language: en-US
 VignetteBuilder: knitr

tests/testthat/test_DataAccess.R

@@ -1,5 +1,3 @@
-context("rSOILWAT2 data access functions")
-
 
 #--- Tests
 test_that("set_requested_flags:", {

tests/testthat/test_OutputDerived.R

@@ -1,5 +1,3 @@
-context("Derived output functions")
-
 
 # Tests
 test_that("Derived output: transpiration and evaporation", {

tests/testthat/test_SegmentationFault_v3.R

@@ -1,4 +1,3 @@
-context("rSOILWAT2 segfault")
 
 # nolint start: line_length_linter, commented_code_linter.
 # Running from command line --> segfaults
@@ -15,20 +14,24 @@ context("rSOILWAT2 segfault")
 #gctorture(FALSE) #https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-gctorture
 # nolint end
 
-# Create reference objects
-path_demo <- system.file("extdata", "example1", package = "rSOILWAT2")
 
-a <- sw_inputDataFromFiles(dir = path_demo,
-  files.in = file.path(path_demo, "files.in"))
+test_that("Test for segfault", {
+  # Create reference objects
+  path_demo <- system.file("extdata", "example1", package = "rSOILWAT2")
+
+  a <- sw_inputDataFromFiles(
+    dir = path_demo,
+    files.in = file.path(path_demo, "files.in")
+  )
+
+  # Location of segfaults with upper bound of b
+  #	- (eo/debug/!interactive()): step 2 >= 558151 > step 3 >= 558105 >
+  #                              step 4 >= 555193 > no segfault
+  b <- 1:1e6
+  b2 <- 1:1e7
+  b3 <- 1:1e7
 
-# Location of segfaults with upper bound of b
-#	- (eo/debug/!interactive()): step 2 >= 558151 > step 3 >= 558105 >
-#                              step 4 >= 555193 > no segfault
-b <- 1:1e6
-b2 <- 1:1e7
-b3 <- 1:1e7
 
-test_that("Test for segfault", {
   expect_silent({
     elems <- ls(envir = .GlobalEnv)
     if (length(elems) > 0) for (i in seq_along(elems)) x <- get(elems[i])

tests/testthat/test_Soils.R

@@ -1,4 +1,3 @@
-context("Manipulate soil")
 
 
 test_that("Manipulate soils", {

tests/testthat/test_Vegetation.R

@@ -1,4 +1,3 @@
-context("Vegetation functions")
 
 # Inputs
 utils::data("weatherData", package = "rSOILWAT2")
@@ -339,7 +338,7 @@ test_that("Vegetation: estimate land cover composition", {
   )
 
   expect_pnv(pnv[1:2])
-  expect_equivalent(pnv[["Rel_Abundance_L0"]][ibar], 1)
+  expect_equal(pnv[["Rel_Abundance_L0"]][ibar], 1, ignore_attr = "names")
 
   # Make sure `SOILWAT2` throws a warning that R, we use `sw_verbosity()`
   # to do that

tests/testthat/test_WaterBalance.R

@@ -1,4 +1,3 @@
-context("rSOILWAT2 water balance")
 
 # The 8 checks, implemented below, correspond to the checks in
 # \var{SOILWAT/test/test_WaterBalance.cc}
@@ -13,7 +12,10 @@ dir_test_data <- file.path("..", "test_data")
 temp <- list.files(dir_test_data, pattern = "Ex")
 temp <- sapply(strsplit(temp, "_", fixed = TRUE), function(x) x[[1]])
 tests <- unique(temp)
-test_that("Test data availability", expect_gt(length(tests), 0))
+test_that("Test data availability", {
+  expect_gt(length(tests), 0)
+})
+
 
 aggregate_for_each_timestep <- function(x, dyt) {
   nid <- 1:2

tests/testthat/test_WeatherData.R

@@ -1,4 +1,3 @@
-context("rSOILWAT2 weather data")
 
 
 test_that("Weather data check", {

tests/testthat/test_WeatherGenerator_functionality.R

@@ -1,48 +1,41 @@
-context("rSOILWAT2 weather generator")
 
 #---INPUTS
-path_extdata <- file.path("..", "..", "inst", "extdata")
-if (!dir.exists(path_extdata)) {
-  path_extdata <- system.file("extdata", package = "rSOILWAT2")
-}
-
-
 dir_test_data <- file.path("..", "test_data")
 temp <- list.files(dir_test_data, pattern = "Ex")
 temp <- sapply(strsplit(temp, "_", fixed = TRUE), function(x) x[[1]])
 tests <- unique(temp)
-test_that("Test data availability", expect_gt(length(tests), 0))
+test_that("Test data availability", {
+  expect_gt(length(tests), 0)
+})
 
-sw_weather <- lapply(
-  tests,
-  function(it) readRDS(file.path(dir_test_data, paste0(it, "_weather.rds")))
-)
 
 
 #---TESTS
-
-
 test_that("Weather generator: estimate input parameters", {
   for (k in seq_along(tests)) {
-    test_dat <- sw_weather[[k]]
+    test_dat <- readRDS(
+      file.path(dir_test_data, paste0(tests[k], "_weather.rds"))
+    )
+
     test_df <- data.frame(dbW_weatherData_to_dataframe(test_dat, valNA = NULL))
 
     if (anyNA(test_df)) {
-      expect_warning(
-        res <- dbW_estimate_WGen_coefs(
-          test_df,
-          propagate_NAs = TRUE
-        ),
-        "Insufficient weather data to estimate values"
+      # We have NAs that propagate
+      # --> warnings: "Insufficient weather data to estimate values [...]"
+      res <- suppressWarnings(
+        dbW_estimate_WGen_coefs(test_df, propagate_NAs = TRUE)
       )
+      expect_true(all(is.na(res[["mkv_woy"]][, -1])))
+      expect_true(all(is.na(res[["mkv_doy"]][, -1])))
 
-      expect_message(
-        res <- dbW_estimate_WGen_coefs(
+      # We have NAs that we impute
+      # --> messages: "Impute missing [...]"
+      res <- suppressMessages(
+        dbW_estimate_WGen_coefs(
           test_df,
           propagate_NAs = FALSE,
           imputation_type = "mean"
-        ),
-        "Impute missing"
+        )
       )
 
     } else {
@@ -70,25 +63,31 @@ test_that("Weather generator: estimate input parameters", {
 
 test_that("Weather generator: generate weather", {
   for (k in seq_along(tests)) {
-    test_dat <- sw_weather[[k]]
+    test_dat <- readRDS(
+      file.path(dir_test_data, paste0(tests[k], "_weather.rds"))
+    )
     years <- get_years_from_weatherData(test_dat)
     n <- length(test_dat)
 
     wout <- list()
 
     # Case 1: generate weather for dataset and impute missing values
-    wout[[1]] <- dbW_generateWeather(
-      test_dat,
-      imputation_type = "mean",
-      imputation_span = 5
+    wout[[1]] <- suppressMessages(
+      dbW_generateWeather(
+        test_dat,
+        imputation_type = "mean",
+        imputation_span = 5
+      )
     )
 
     # Case 2: generate weather based on partial dataset,
     #   use estimated weather generator coefficients from full dataset
-    wgen_coeffs <- dbW_estimate_WGen_coefs(
-      test_dat,
-      imputation_type = "mean",
-      imputation_span = 5
+    wgen_coeffs <- suppressMessages(
+      dbW_estimate_WGen_coefs(
+        test_dat,
+        imputation_type = "mean",
+        imputation_span = 5
+      )
     )
 
     wout[[2]] <- dbW_generateWeather(
@@ -143,6 +142,8 @@ test_that("Weather generator (integration tests): compare input/output", {
     )
   )
 
+  tag <- "IntegrationTest-WeatherGenerator"
+
   dir_inttests <- file.path("..", "rSOILWAT_IntegrationTestOutput")
   dir.create(dir_inttests, showWarnings = FALSE)
 
@@ -197,12 +198,21 @@ test_that("Weather generator (integration tests): compare input/output", {
 
 
   #--- Comparison
-  compare_weather(
-    ref_weather = obs_df,
-    weather = wgen_df,
-    N = N,
-    path = dir_inttests,
-    tag = "IntegrationTest-WeatherGenerator"
+  suppressMessages(
+    compare_weather(
+      ref_weather = obs_df,
+      weather = wgen_df,
+      N = N,
+      path = dir_inttests,
+      tag = tag
+    )
   )
 
+  expect_length(
+    list.files(
+      path = dir_inttests,
+      pattern = tag
+    ),
+    n = 4L
+  )
 })

tests/testthat/test_class_swCarbon.R

@@ -1,4 +1,3 @@
-context("Carbon dioxide class")
 
 #---TESTS
 test_that("Manipulate swCarbon", {

tests/testthat/test_class_swProd.R

@@ -1,29 +1,30 @@
-context("Vegetation parameters class")
-
-ids_VegType <- rSW2_glovars[["kSOILWAT2"]][["VegTypes"]]
-names_VegTypes <- tolower(
-  gsub(
-    "SW_",
-    "",
-    names(rSW2_glovars[["kSOILWAT2"]][["VegTypes"]]),
-    fixed = TRUE
-  )
-)
-
-names_VegTypes2 <- sapply(
-  names_VegTypes,
-  function(x) {
-    if (endsWith(x, "s")) {
-      if (endsWith(x, "ss")) x else substr(x, 1, nchar(x) - 1)
-    } else {
-      x
-    }
-  }
-)
+
 
 
 #---TESTS
 test_that("Manipulate 'swProd' class", {
+  ids_VegType <- rSW2_glovars[["kSOILWAT2"]][["VegTypes"]]
+  names_VegTypes <- tolower(
+    gsub(
+      "SW_",
+      "",
+      names(rSW2_glovars[["kSOILWAT2"]][["VegTypes"]]),
+      fixed = TRUE
+    )
+  )
+
+  names_VegTypes2 <- sapply(
+    names_VegTypes,
+    function(x) {
+      if (endsWith(x, "s")) {
+        if (endsWith(x, "ss")) x else substr(x, 1, nchar(x) - 1)
+      } else {
+        x
+      }
+    }
+  )
+
+
   x <- new("swProd")
   expect_s4_class(x, "swProd")
 

tests/testthat/test_class_swSite.R

@@ -1,11 +1,12 @@
-context("Site parameters class")
 
 dir_test_data <- file.path("..", "test_data")
 temp <- list.files(dir_test_data, pattern = "Ex")
 temp <- sapply(strsplit(temp, "_", fixed = TRUE), function(x) x[[1]])
 tests <- unique(temp)
 
-test_that("Test data availability", expect_gt(length(tests), 0))
+test_that("Test data availability", {
+  expect_gt(length(tests), 0)
+})
 
 
 #---TESTS

tests/testthat/test_climate_functions.R

@@ -1,4 +1,3 @@
-context("Calculations of climate variables")
 
 # Inputs
 weatherList_year1980 <- readRDS(