Skip tests/examples when packages in Suggest section are not installed (

#518) - Part of pre-release activities #506 (base branch for this PR is `pre-release-cleanup@main`) - Rationale on insightsengineering/idr-tasks#713 ### Changes description - [x] Handles `@examples` - with `@examplesIf requireNamespace("MultiAssayExperiment")` as suggested [here](https://indrajeetpatil.github.io/preventive-r-package-care/#/soft-dependency-hygiene) - Conditional clause replacing `miniACC` with empty data.frame - [x] Skips tests that use {MAE} or {SE} - [x] Skips tests that use {withr} #### Discussions - > That's not a reason to skip tests. MAE is in Suggests so installing is the responsibility of the person who wants to run tests, i.e. not the end user. If someone uses teal with MAE data, they most likely have the package installed. - Some generic tests and examples for `filter_state_api` are complex cases that join together normal data frames with MAE - These could be broken down to 2 examples. - If we merge this it also means tests using {withr} should be skipped - Seems silly, but necessary to be a complete compliance WDYT?
insightsengineering · Jan 17, 2024 · 3220aac · 3220aac
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diff --git a/R/FilteredData.R b/R/FilteredData.R
@@ -52,7 +52,7 @@
 #' isolate(datasets$get_filter_state())
 #' isolate(datasets$get_call("iris"))
 #' isolate(datasets$get_call("mtcars"))
-#'
+#' @examplesIf requireNamespace("MultiAssayExperiment")
 #' ### set_filter_state
 #'
 #' utils::data(miniACC, package = "MultiAssayExperiment")

diff --git a/R/FilteredDataset-utils.R b/R/FilteredDataset-utils.R
@@ -40,6 +40,7 @@
 #'   shinyApp(ui, server)
 #' }
 #'
+#' @examplesIf requireNamespace("MultiAssayExperiment")
 #' # MAEFilteredDataset example
 #' library(MultiAssayExperiment)
 #' data(miniACC)

diff --git a/R/FilteredDatasetMAE.R b/R/FilteredDatasetMAE.R
@@ -2,7 +2,7 @@
 
 #' @title `MAEFilteredDataset` `R6` class
 #' @keywords internal
-#' @examples
+#' @examplesIf requireNamespace("MultiAssayExperiment")
 #' # use non-exported function from teal.slice
 #' MAEFilteredDataset <- getFromNamespace("MAEFilteredDataset", "teal.slice")
 #'

diff --git a/R/filter_panel_api.R b/R/filter_panel_api.R
@@ -23,18 +23,53 @@
 #' @seealso [`teal_slice`]
 #'
 #' @examples
-#' library(MultiAssayExperiment)
-#' data(miniACC)
-#'
 #' datasets <- init_filtered_data(
 #'   x = list(
 #'     iris = list(dataset = iris),
-#'     mae = list(dataset = miniACC)
+#'     mtcars = list(dataset = mtcars)
 #'   )
 #' )
 #' fs <- teal_slices(
 #'   teal_slice(dataname = "iris", varname = "Species", selected = c("setosa", "versicolor")),
 #'   teal_slice(dataname = "iris", varname = "Sepal.Length", selected = c(5.1, 6.4)),
+#'   teal_slice(dataname = "mtcars", varname = "gear", selected = c(4, 5)),
+#'   teal_slice(dataname = "mtcars", varname = "carb", selected = c(4, 10))
+#' )
+#'
+#' # set initial filter state
+#' set_filter_state(datasets, filter = fs)
+#'
+#' # get filter state
+#' get_filter_state(datasets)
+#'
+#' # modify filter state
+#' set_filter_state(
+#'   datasets,
+#'   teal_slices(
+#'     teal_slice(dataname = "iris", varname = "Species", selected = "setosa", keep_na = TRUE)
+#'   )
+#' )
+#'
+#' # remove specific filters
+#' remove_filter_state(
+#'   datasets,
+#'   teal_slices(
+#'     teal_slice(dataname = "iris", varname = "Species"),
+#'     teal_slice(dataname = "mtcars", varname = "gear"),
+#'     teal_slice(dataname = "mtcars", varname = "carb")
+#'   )
+#' )
+#'
+#' # remove all states
+#' clear_filter_states(datasets)
+#' @examplesIf requireNamespace("MultiAssayExperiment")
+#'
+#' # Requires MultiAssayExperiment from Bioconductor
+#' library(MultiAssayExperiment)
+#' data(miniACC)
+#'
+#' datasets <- init_filtered_data(x = list(mae = list(dataset = miniAcc)))
+#' fs <- teal_slices(
 #'   teal_slice(
 #'     dataname = "mae", varname = "years_to_birth", selected = c(30, 50),
 #'     keep_na = TRUE, keep_inf = FALSE
@@ -63,15 +98,14 @@
 #' set_filter_state(
 #'   datasets,
 #'   teal_slices(
-#'     teal_slice(dataname = "iris", varname = "Species", selected = "setosa", keep_na = TRUE)
+#'     teal_slice(dataname = "mae", varname = "years_to_birth", selected = c(40, 60))
 #'   )
 #' )
 #'
 #' # remove specific filters
 #' remove_filter_state(
 #'   datasets,
 #'   teal_slices(
-#'     teal_slice(dataname = "iris", varname = "Species"),
 #'     teal_slice(dataname = "mae", varname = "years_to_birth"),
 #'     teal_slice(dataname = "mae", varname = "vital_status")
 #'   )

diff --git a/man/FilteredData.Rd b/man/FilteredData.Rd
diff --git a/man/MAEFilteredDataset.Rd b/man/MAEFilteredDataset.Rd
diff --git a/man/filter_state_api.Rd b/man/filter_state_api.Rd
diff --git a/man/init_filtered_dataset.Rd b/man/init_filtered_dataset.Rd
diff --git a/tests/testthat/test-FilteredData.R b/tests/testthat/test-FilteredData.R
@@ -1,5 +1,6 @@
 # initialize ----
 testthat::test_that("constructor accepts all types of datasets", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
 
   testthat::expect_no_error(FilteredData$new(list("logical" = c(TRUE, FALSE))))
@@ -718,6 +719,8 @@ testthat::test_that("srv_active - clicking remove_all button clears filters", {
 
 # get_filter_count
 testthat::test_that("get_filter_count properly tallies active filter states", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   test_class <- R6::R6Class(
     classname = "test_class",
     inherit = FilteredData,
@@ -753,6 +756,8 @@ testthat::test_that("get_filter_count properly tallies active filter states for
       }
     )
   )
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   datasets <- test_class$new(
     list(
       iris = list(dataset = iris),

diff --git a/tests/testthat/test-MAEFilterStates.R b/tests/testthat/test-MAEFilterStates.R
@@ -1,7 +1,7 @@
-utils::data(miniACC, package = "MultiAssayExperiment")
-
 # initialize ----
 testthat::test_that("constructor accepts a MultiAssayExperiment", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   testthat::expect_no_error(
     MAEFilterStates$new(data = miniACC, dataname = "miniACC")
   )
@@ -13,6 +13,8 @@ testthat::test_that("constructor accepts a MultiAssayExperiment", {
 
 # get_filter_state ----
 testthat::test_that("get_filter_state returns `teal_slices` with include_varname by default and count_type=none", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   filter_states <- MAEFilterStates$new(data = miniACC, dataname = "miniACC")
   fs <- teal_slices(
     count_type = "none",
@@ -27,6 +29,8 @@ testthat::test_that("get_filter_state returns `teal_slices` with include_varname
 
 # get_call ----
 testthat::test_that("get_call returns subsetByColData call with varnames prefixed by dataname$", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   filter_states <- MAEFilterStates$new(data = miniACC, dataname = "miniacc")
   filter_states$set_filter_state(
     teal_slices(

diff --git a/tests/testthat/test-MAEFilteredDataset.R b/tests/testthat/test-MAEFilteredDataset.R
@@ -1,5 +1,6 @@
 # initialize ----
 testthat::test_that("constructor accepts a MultiAssayExperiment object", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   testthat::expect_no_error(MAEFilteredDataset$new(dataset = miniACC, dataname = "miniACC"))
   testthat::expect_error(
@@ -13,6 +14,7 @@ testthat::test_that("constructor accepts a MultiAssayExperiment object", {
 })
 
 testthat::test_that("filter_states list is initialized with names of experiments", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   testfd <- R6::R6Class(
     "testfd",
     inherit = MAEFilteredDataset,
@@ -30,6 +32,7 @@ testthat::test_that("filter_states list is initialized with names of experiments
 
 # format ---
 testthat::test_that("format returns properly formatted string", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -59,6 +62,7 @@ testthat::test_that("format returns properly formatted string", {
 
 # print ---
 testthat::test_that("print returns properly formatted string", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -88,13 +92,15 @@ testthat::test_that("print returns properly formatted string", {
 
 # get_call ----
 testthat::test_that("get_call returns NULL when no filter applied", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniACC")
   get_call_output <- shiny::isolate(filtered_dataset$get_call())
   testthat::expect_null(get_call_output)
 })
 
 testthat::test_that("get_call returns a call with applying filter", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -131,6 +137,7 @@ testthat::test_that("get_call returns a call with applying filter", {
 
 # get_filter_overview ----
 testthat::test_that("get_filter_overview_info returns overview matrix for MAEFilteredDataset without filtering", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniACC")
   testthat::expect_equal(
@@ -146,6 +153,7 @@ testthat::test_that("get_filter_overview_info returns overview matrix for MAEFil
 })
 
 testthat::test_that("get_filter_overview_info returns overview matrix for MAEFilteredDataset with filtering", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -177,6 +185,7 @@ testthat::test_that("get_filter_overview_info returns overview matrix for MAEFil
 testthat::test_that(
   "MAEFilteredDataset$set_filter_state sets filters in `FilterStates` specified by `teal_slices",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -217,6 +226,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$set_filter_state only acceps `teal_slices",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- list(
@@ -236,6 +246,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$get_filter_state returns list identical to input",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -268,6 +279,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$remove_filter_state removes desired filter",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -297,6 +309,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$remove_filter_state only accepts `teal_slices",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -318,6 +331,7 @@ testthat::test_that(
 
 # UI actions ----
 testthat::test_that("remove_filters button removes all filters", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(