Add tests for utilities

DESCRIPTION

@@ -35,10 +35,12 @@ Imports:
     stringr,
     labeling
 Suggests: 
+    clipr,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
-    vdiffr (>= 1.0.0)
+    vdiffr (>= 1.0.0),
+    withr
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

R/error-checks.R

@@ -1 +0,0 @@
-

R/utilities-file.R

@@ -1,9 +1,9 @@
 #' Source all .R files located in a specific folder
 #'
 #' @param folderPath Path to the folder where .R files are located
-#' @param recursive If TRUE, the contents of the sub-folders are also sourced,
+#' @param recursive If `TRUE`, the contents of the sub-folders are also sourced,
 #' otherwise only the files located directly in the directory are considered.
-#' Default is FALSE.
+#' Default is `FALSE`.
 #' @export
 sourceAll <- function(folderPath, recursive = FALSE) {
   filesPaths <- list.files(folderPath, recursive = recursive)
@@ -18,15 +18,15 @@ sourceAll <- function(folderPath, recursive = FALSE) {
   invisible(lapply(file.path(folderPath, filesPaths), sourceFile))
 }
 
-#' pathFromClipboard
+#' Convert Windows filepaths for R
 #'
-#' Converts the windows-like path (using `\`) from the clipboard to the form
+#' Converts the Windows-like path (using `\`) from the clipboard to the form
 #' readable by R (using` /`).
 #'
-#' @param path Path that will be converted. If "clipboard" (default), path is
+#' @param path Path that will be converted. If `"clipboard"` (default), path is
 #'   queried from clipboard.
 #'
-#' @return String representation of a file path with `/` as separator
+#' @return String representation of a file path with `/` as separator.
 #' @export
 pathFromClipboard <- function(path = "clipboard") {
   y <- if (path == "clipboard") {

R/utilities.R

@@ -114,14 +114,14 @@ removeFromList <- function(entry, listArg) {
   return(listArg)
 }
 
-#' Compare values including NA
+#' Compare values including `NA`
 #'
-#' @param v1 Value or a list of values to compare. May include NA.
-#' @param v2 Value or a list of values to compare. May include NA.
+#' @param v1 Value or a list of values to compare. May include `NA`.
+#' @param v2 Value or a list of values to compare. May include `NA`.
 #' @details From http://www.cookbook-r.com/Manipulating_data/Comparing_vectors_or_factors_with_NA/
 #'
-#' @return TRUE wherever elements are the same, including NA's,
-# and FALSE everywhere else.
+#' @return `TRUE` wherever elements are the same, including `NA`'s,
+# and `FALSE` everywhere else.
 #' @export
 compareWithNA <- function(v1, v2) {
   same <- (v1 == v2) | (is.na(v1) & is.na(v2))

appveyor.yml

@@ -56,7 +56,10 @@ build_script:
   - travis-tool.sh r_binary_install curl
   - Rscript -e "install.packages('https://github.com/Open-Systems-Pharmacology/rClr/releases/download/v0.9.2/rClr_0.9.2.zip', repos = NULL, type = 'binary')"
   - Rscript -e "install.packages('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-r/artifacts/ospsuite.zip', repos = NULL, type = 'binary')"
-  - Rscript -e "install.packages(c('covr', 'FME', 'readr', 'tidyr', 'ggplot2', 'patchwork', 'vdiffr'), repos = 'http://cran.us.r-project.org')"
+  # hard dependencies (Imports)
+  - Rscript -e "install.packages(c('FME', 'readr', 'tidyr', 'ggplot2', 'patchwork'), repos = 'http://cran.us.r-project.org')"
+  # soft dependencies (Suggests)
+  - Rscript -e "install.packages(c('covr', 'clipr', 'vdiffr', 'withr'), repos = 'http://cran.us.r-project.org')"
   - Rscript -e "install.packages('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-rutils/artifacts/ospsuite.utils.zip', repos = NULL, type = 'binary')"
   - Rscript -e "install.packages('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/tlf-library/artifacts/tlf.zip', repos = NULL, type = 'binary')"
   - Rscript -e "install.packages('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-parameteridentification/artifacts/ospsuite.parameteridentification.zip', repos = NULL, type = 'binary')"

tests/testthat/_snaps/scenario-configuration.md

@@ -0,0 +1,33 @@
+# `ScenarioConfiguration` defaults are as expected
+
+    Code
+      mySC <- ScenarioConfiguration$new(projectConfiguration = ProjectConfiguration$
+        new())
+      mySC
+    Output
+      ProjectConfiguration: 
+         Model folder: 
+         Parameters folder: 
+         Parameters file name: 
+         Individual parameters file name: 
+         Individual physiology file name: 
+         Population parameters file name: 
+         Scenario definitions file name: 
+         Scenario applications definitions file name: 
+         Experimental data folder: 
+         Experimental data file: 
+         Data importer configuration: 
+         Output folder: 
+         Output device: 
+      ScenarioConfiguration: 
+         Model file name: 
+         Scenario name: 
+         Parameters sheets: 
+         Individual Id: 
+         Application protocol: 
+         Simulation time: 
+         Points per minute: 1 
+         Simulate steady-state: FALSE 
+         Steady-state time: 1000 
+         Set test parameters: FALSE 
+

tests/testthat/test-scenario-configuration.R

@@ -0,0 +1,8 @@
+##  context("ScenarioConfiguration")
+
+test_that("`ScenarioConfiguration` defaults are as expected", {
+  expect_snapshot({
+    mySC <- ScenarioConfiguration$new(projectConfiguration = ProjectConfiguration$new())
+    mySC
+  })
+})

tests/testthat/test-utilities-file.R

@@ -0,0 +1,38 @@
+##  context("sourceAll")
+
+test_that("`sourceAll()` sources all files in the directory", {
+  skip_if_not_installed("withr")
+
+  withr::with_tempdir(
+    code = {
+      f1 <- file.create("f1.R")
+      f2 <- file.create("f2.R")
+      writeLines("var1 <- 1 + 1", "f1.R")
+      writeLines("var2 <- paste0('a', 'b')", "f2.R")
+
+      sourceAll(".")
+
+      expect_true(exists("var1"))
+      expect_true(exists("var2"))
+    }
+  )
+})
+
+##  context("pathFromClipboard")
+
+test_that("`pathFromClipboard()` converts paths as expected", {
+  skip_if_not_installed("clipr")
+
+  # This will work only in interactive mode, i.e. with
+  # `devtools::test_active_file()` or `devtools::test()`, but not during R CMD
+  # Check on CRAN or AppVeyor where the system clipboard is not available
+  if (clipr::clipr_available()) {
+    path <- "C:\\Users\\Documents"
+    clipr::write_clip(path, allow_non_interactive = TRUE)
+
+    expect_equal(
+      pathFromClipboard(),
+      "C:/Users/Documents"
+    )
+  }
+})

tests/testthat/test-utilities.R

@@ -138,3 +138,14 @@ test_that("It finds a 0 with relative threshold", {
 test_that("Escape a string for possible regular expression match", {
   expect_equal(escapeForRegex("C:/Downloads"), "\\QC:/Downloads\\E")
 })
+
+##  context("compareWithNA")
+
+test_that("`compareWithNA()` works as expected", {
+  res <- compareWithNA(
+    c(NA, "a", "b", NA),
+    c(NA, "c", "b", "a")
+  )
+
+  expect_equal(res, c(TRUE, FALSE, TRUE, FALSE))
+})