Merge f3e5541 into f402204

R/esqlabs-env.R

@@ -1,8 +1,3 @@
-.getPackageVersion <- function() {
-  version <- getNamespaceVersion("esqlabsR")
-  return(version)
-}
-
 # Environment that holds various global variables and settings for the esqlabsR,
 # It is not exported and should not be directly manipulated by other packages.
 esqlabsEnv <- new.env(parent = emptyenv())
@@ -11,7 +6,7 @@ esqlabsEnv <- new.env(parent = emptyenv())
 esqlabsEnv$packageName <- "esqlabsR"
 
 # Version of the package
-esqlabsEnv$packageVersion <- .getPackageVersion()
+esqlabsEnv$packageVersion <- getNamespaceVersion("esqlabsR")
 
 # Default width of a plot of a single `PlotMapping`
 esqlabsEnv$widthPerPlotMapping <- 8

R/utilities-individual.R

@@ -41,7 +41,12 @@ writeIndividualToXLS <- function(individualCharacteristics, outputXLSPath) {
     units[i] <- individual$distributedParameters$units[[i]]
   }
 
-  output <- data.frame(unlist(containerPaths, use.names = FALSE), unlist(paramNames, use.names = FALSE), unlist(as.numeric(values), use.names = FALSE), unlist(units, use.names = FALSE))
+  output <- data.frame(
+    unlist(containerPaths, use.names = FALSE),
+    unlist(paramNames, use.names = FALSE),
+    unlist(as.numeric(values), use.names = FALSE),
+    unlist(units, use.names = FALSE)
+  )
   colnames(output) <- columnNames
 
   writexl::write_xlsx(output, path = outputXLSPath, col_names = TRUE)
@@ -118,7 +123,6 @@ readIndividualCharacteristicsFromXLS <- function(XLSpath,
 #' @export
 #'
 #' @examples
-#' #'
 #' \dontrun{
 #' simulation <- loadSimulation(filePath = modelPath)
 #' humanIndividualCharacteristics <- createIndividualCharacteristics(

R/utilities-steady-state.R

@@ -94,21 +94,33 @@ exportSteadyStateToXLS <- function(simulation,
   }
 
   speciesInitVals <- data.frame(
-    unlist(moleculeContainerPath, use.names = FALSE), unlist(moleculeName, use.names = FALSE), unlist(moleculeIsPresent, use.names = FALSE), unlist(moleculeValue, use.names = FALSE),
-    unlist(moleculeUnits, use.names = FALSE), unlist(moleculeScaleDivisor, use.names = FALSE), unlist(moleculeNegValsAllowed, use.names = FALSE)
+    unlist(moleculeContainerPath, use.names = FALSE),
+    unlist(moleculeName, use.names = FALSE),
+    unlist(moleculeIsPresent, use.names = FALSE),
+    unlist(moleculeValue, use.names = FALSE),
+    unlist(moleculeUnits, use.names = FALSE),
+    unlist(moleculeScaleDivisor, use.names = FALSE),
+    unlist(moleculeNegValsAllowed, use.names = FALSE)
   )
 
   if (length(speciesInitVals) > 0) {
     colnames(speciesInitVals) <- c("Container Path", "Molecule Name", "Is Present", "Value", "Units", "Scale Divisor", "Neg. Values Allowed")
   }
 
   parameterInitVals <- data.frame(
-    unlist(parameterContainerPath, use.names = FALSE), unlist(parameterName, use.names = FALSE), unlist(parameterValue, use.names = FALSE), unlist(parameterUnits, use.names = FALSE)
+    unlist(parameterContainerPath, use.names = FALSE),
+    unlist(parameterName, use.names = FALSE),
+    unlist(parameterValue, use.names = FALSE),
+    unlist(parameterUnits, use.names = FALSE)
   )
 
   if (length(parameterInitVals) > 0) {
     colnames(parameterInitVals) <- c("Container Path", "Parameter Name", "Value", "Units")
   }
   # Write the results into an excel file.
-  writexl::write_xlsx(list("Molecules" = speciesInitVals, "Parameters" = parameterInitVals), path = resultsXLSPath, col_names = TRUE)
+  writexl::write_xlsx(
+    list("Molecules" = speciesInitVals, "Parameters" = parameterInitVals),
+    path = resultsXLSPath,
+    col_names = TRUE
+  )
 }

tests/testthat/test-esqlabsr-settings.R

@@ -1,5 +1,13 @@
 test_that("Names for settings are as expected", {
-  expect_snapshot(esqlabsRSettingNames)
+  expect_equal(
+    esqlabsRSettingNames,
+    list(
+      packageVersion = "packageVersion",
+      packageName = "packageName",
+      widthPerPlotMapping = "widthPerPlotMapping",
+      heightPerPlotMapping = "heightPerPlotMapping"
+    )
+  )
 })
 
 test_that("Check that values for package environment bindings are correct", {
@@ -9,4 +17,5 @@ test_that("Check that values for package environment bindings are correct", {
   )
 
   expect_equal(getEsqlabsRSetting("packageName"), "esqlabsR")
+  expect_type(getEsqlabsRSetting("packageVersion"), "character")
 })

tests/testthat/test-sensitivity-calculation.R

@@ -237,7 +237,7 @@ test_that("sensitivityCalculation errors if file extension is incorrect", {
 # checking `SensitivityCalculation`  object ------------------
 
 test_that("sensitivityCalculation returns the correct object", {
-  expect_s3_class(results, "SensitivityCalculation")
+  expect_true(isOfType(results, "SensitivityCalculation"))
 
   expect_equal(
     length(results$simulationResults),

tests/testthat/test-utilities-figures.R

@@ -50,15 +50,15 @@ test_that("col2hsv returns expected HSV values for a given R color name", {
 
 test_that("createEsqlabsPlotConfiguration() creates object with chosen defaults", {
   myPC <- createEsqlabsPlotConfiguration()
-  expect_s3_class(myPC, "DefaultPlotConfiguration")
+  expect_true(isOfType(myPC, "DefaultPlotConfiguration"))
   expect_equal(myPC$titleSize, 8)
 })
 
 ## context("createEsqlabsPlotGridConfiguration")
 
 test_that("createEsqlabsPlotGridConfiguration() creates object with chosen defaults", {
   myPGC <- createEsqlabsPlotGridConfiguration()
-  expect_s3_class(myPGC, "PlotGridConfiguration")
+  expect_true(isOfType(myPGC, "PlotGridConfiguration"))
   expect_equal(myPGC$tagLevels, "a")
 })
 
@@ -67,6 +67,6 @@ test_that("createEsqlabsPlotGridConfiguration() creates object with chosen defau
 test_that("createEsqlabsExportConfiguration() creates object with chosen defaults", {
   myProjConfig <- ProjectConfiguration$new()
   myEC <- createEsqlabsExportConfiguration(myProjConfig)
-  expect_s3_class(myEC, "ExportConfiguration")
+  expect_true(isOfType(myEC, "ExportConfiguration"))
   expect_equal(myEC$units, "cm")
 })

tests/testthat/test-utilities-file.R

@@ -1,8 +1,6 @@
 ##  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")
@@ -21,8 +19,6 @@ test_that("`sourceAll()` sources all files in the directory", {
 ##  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

tests/testthat/test-utilities-individual.R

@@ -50,3 +50,27 @@ test_that("It create IndividualCharacteristics when numerical values are empty",
   expect_equal(individualCharacteristics$population, "European_ICRP_2002")
   expect_equal(individualCharacteristics$gender, "MALE")
 })
+
+## context("writeIndividualToXLS")
+
+test_that("`writeIndividualToXLS()` writes correct data to a spreadsheet", {
+  withr::with_tempdir(
+    code = {
+      humanIndividualCharacteristics <- createIndividualCharacteristics(
+        species = Species$Human,
+        population = HumanPopulation$European_ICRP_2002,
+        gender = Gender$Male,
+        weight = 70
+      )
+      tmp <- writeIndividualToXLS(humanIndividualCharacteristics, "ParameterSet.xlsx")
+      df <- readxl::read_xlsx(tmp)
+
+      expect_equal(dim(df), c(96L, 4L))
+      expect_equal(colnames(df), c("Container Path", "Parameter Name", "Value", "Units"))
+      expect_equal(
+        unique(df$Units),
+        c("year(s)", "week(s)", "dm", NA, "kg", "l", "l/min/kg organ", "l/min", "min")
+      )
+    }
+  )
+})

tests/testthat/test-utilities-population.R

@@ -0,0 +1,30 @@
+## context("sampleRandomValue")
+
+test_that("`sampleRandomValue()` generates needed distribution", {
+  expect_error(
+    sampleRandomValue("xyz", 5, 2, 10),
+    messages$errorDistributionNotSupported("xyz")
+  )
+
+  set.seed(123)
+  expect_equal(
+    sampleRandomValue(Distributions$Normal, 5, 2, 10),
+    c(
+      3.87904870689558, 4.53964502103344, 8.11741662829825, 5.14101678284915,
+      5.25857547032189, 8.43012997376656, 5.9218324119784, 2.46987753078693,
+      3.62629429621295, 4.10867605980008
+    ),
+    tolerance = 0.001
+  )
+
+  set.seed(123)
+  expect_equal(
+    sampleRandomValue(Distributions$LogNormal, 5, 2, 10),
+    c(
+      3.74081271106427, 4.24843764475839, 8.46318202896501, 4.77021554349172,
+      4.87946908411847, 8.98864517081978, 5.54444951200875, 2.85153959957418,
+      3.56304555191325, 3.90999158989997
+    ),
+    tolerance = 0.001
+  )
+})

tests/testthat/test-utilities-simulation.R

@@ -0,0 +1,22 @@
+## context("initializeSimulation")
+
+test_that("`initializeSimulation()` loads a simulation at the minimum", {
+  simulation <- loadSimulation(system.file("extdata", "simple.pkml", package = "ospsuite"))
+  initializeSimulation(simulation, steadyStateTime = TRUE)
+  simulationResults <- runSimulation(simulation)
+  expect_true(isOfType(simulationResults, "SimulationResults"))
+})
+
+## context("compareSimulationParameters")
+
+test_that("`compareSimulationParameters()` produces no differences with identical simulations", {
+  simPath <- system.file("extdata", "simple.pkml", package = "ospsuite")
+  sim1 <- loadSimulation(simPath)
+  sim2 <- loadSimulation(simPath)
+
+  res <- compareSimulationParameters(sim1, sim2)
+  expect_equal(
+    res,
+    list(In1NotIn2 = list(), In2NotIn1 = list(), Different = list())
+  )
+})