1031 drop list support (#1051)

Fixes #1031

NEWS.md

@@ -2,14 +2,14 @@
 
 ### New features
 
-* `data` argument in `init` now accepts `teal_data` and `teal_data_module`.
 * Added `landing_popup_module` function which creates a module that will display a popup when the app starts. The popup will block access to the app until it is dismissed.
 * Filter state snapshots can now be uploaded from file. See `?snapshot`.
 * Added `as_tdata` function to facilitate migration of modules to the new `teal_data` class.
 * Added `build_app_title` function to facilitate adding favicons to app title.
 
 ### Breaking changes
 
+* `data` argument in `init` now accepts only `teal_data` and `teal_data_module`.
 * `tdata` has been deprecated and replaced with `teal_data`. Support for `tdata` passed to the `data` argument in `module(server)` will be removed in the next release.
 * `module(ui)` argument no longer accepts `data` and `datasets` arguments. All data dependent logic should be set in the `server` function.
 * `module(server)` argument deprecated `datasets` argument. `teal_module`s' `server` functions should accept `data` (`teal_data`) instead.

R/init.R

@@ -14,10 +14,8 @@
 #' When initializing the `teal` app, if `datanames` are not set for the `teal_data` object,
 #' defaults from the `teal_data` environment will be used.
 #'
-#' @param data (`teal_data`, `teal_data_module`, `named list`)\cr
-#' `teal_data` object as returned by [teal.data::teal_data()] or
-#' `teal_data_module` or simply a list of a named list of objects
-#' (`data.frame` or `MultiAssayExperiment`).
+#' @param data (`teal_data`, `teal_data_module`)\cr
+#' `teal_data` object as returned by [teal.data::teal_data()] or `teal_data_module`.
 #' @param modules (`list`, `teal_modules` or `teal_module`)\cr
 #'   nested list of `teal_modules` or `teal_module` objects or a single
 #'   `teal_modules` or `teal_module` object. These are the specific output modules which
@@ -119,14 +117,7 @@ init <- function(data,
       )
     )
   }
-  checkmate::assert(
-    .var.name = "data",
-    checkmate::check_multi_class(data, c("teal_data", "teal_data_module")),
-    checkmate::check_list(data, names = "named")
-  )
-  if (is.list(data) && !inherits(data, "teal_data_module")) {
-    data <- do.call(teal.data::teal_data, data)
-  }
+  checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
 
   ## `modules`
   checkmate::assert(

R/teal_slices.R

@@ -51,7 +51,7 @@
 #' )
 #'
 #' app <- init(
-#'   data = list(iris = iris, mtcars = mtcars),
+#'   data = teal_data(iris = iris, mtcars = mtcars),
 #'   modules = list(
 #'     module("module1"),
 #'     module("module2")

R/utils.R

@@ -294,7 +294,7 @@ create_app_id <- function(data, modules) {
   checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
   checkmate::assert_class(modules, "teal_modules")
 
-  hashables <- c(data, modules)
+  hashables <- list(data = data, modules = modules)
   hashables$data <- if (inherits(hashables$data, "teal_data")) {
     as.list(hashables$data@env)
   } else if (inherits(data, "teal_data_module")) {

tests/testthat/test-init.R

@@ -1,51 +1,15 @@
+example_module <- teal:::example_module
+
+# data ----
 testthat::test_that("init data accepts teal_data object", {
   testthat::expect_no_error(
     init(
       data = teal.data::teal_data(iris = iris),
-      modules = modules(teal:::example_module())
-    )
-  )
-})
-
-testthat::test_that("init data accepts a single dataframe", {
-  testthat::expect_no_error(
-    init(data = list(iris = iris), modules = modules(example_module()))
-  )
-})
-
-testthat::test_that("init data accepts a list of single dataframe without renaming", {
-  testthat::skip("todo: should we support data as unnamed list in teal?")
-  testthat::expect_no_error(
-    init(data = list(iris, mtcars), modules = modules(example_module()))
-  )
-})
-
-testthat::test_that("init data accepts a list of single dataframe with renaming", {
-  testthat::expect_no_error(
-    init(
-      data = list(iris2 = iris),
       modules = modules(example_module())
     )
   )
 })
 
-testthat::test_that("init data accepts a single MultiAssayExperiment object", {
-  utils::data(miniACC, package = "MultiAssayExperiment")
-  testthat::expect_no_error(
-    init(data = list(MAE = miniACC), modules = modules(example_module()))
-  )
-})
-
-testthat::test_that("init data accepts a list of a single MultiAssayExperiment object with renaming", {
-  utils::data(miniACC, package = "MultiAssayExperiment")
-  testthat::expect_no_error(init(data = list(x = miniACC), modules = modules(example_module())))
-})
-
-testthat::test_that("init data acceptsa mixed list of MultiAssayExperiment object and data.frame", {
-  utils::data(miniACC, package = "MultiAssayExperiment")
-  testthat::expect_no_error(init(data = list(x = miniACC, y = head(iris)), modules = modules(example_module())))
-})
-
 testthat::test_that("init data accepts teal_data_module", {
   testthat::expect_no_error(
     init(
@@ -55,40 +19,44 @@ testthat::test_that("init data accepts teal_data_module", {
   )
 })
 
+
+# modules ----
 testthat::test_that("init modules accepts a teal_modules object", {
   mods <- modules(example_module(), example_module())
-  testthat::expect_no_error(init(data = list(iris = iris), modules = mods))
+  testthat::expect_no_error(init(data = teal_data(iris = iris), modules = mods))
 })
 
 testthat::test_that("init modules accepts a list of teal_module elements", {
   mods <- list(example_module(), example_module())
-  testthat::expect_no_error(init(data = list(iris = iris), modules = mods))
+  testthat::expect_no_error(init(data = teal_data(iris = iris), modules = mods))
 })
 
 testthat::test_that("init modules accepts a teal_module object", {
   mods <- example_module()
-  testthat::expect_no_error(init(data = list(iris = iris), modules = mods))
+  testthat::expect_no_error(init(data = teal_data(iris = iris), modules = mods))
 })
 
+# filter ----
 testthat::test_that("init filter accepts `teal_slices`", {
   fs <- teal.slice::teal_slices(
     teal.slice::teal_slice(dataname = "iris", varname = "species", selected = "setosa")
   )
-  testthat::expect_no_error(init(data = list(iris = iris), modules = modules(example_module()), filter = fs))
+  testthat::expect_no_error(init(data = teal_data(iris = iris), modules = modules(example_module()), filter = fs))
   testthat::expect_error(
-    init(data = list(iris = iris), modules = modules(example_module()), filter = unclass(fs)),
+    init(data = teal_data(iris = iris), modules = modules(example_module()), filter = unclass(fs)),
     "Assertion on 'filter' failed"
   )
 })
 
+# data + modules ----
 testthat::test_that("init throws when data has no datanames", {
   testthat::expect_error(
     init(data = teal_data(), modules = list(example_module())),
     "`data` object has no datanames and its environment is empty"
   )
 })
 
-testthat::test_that("init throws when incompatible module's datanames", {
+testthat::test_that("init throws when datanames in modules incompatible w/ datanames in data", {
   msg <- "Module 'example teal module' uses datanames not available in 'data'"
   testthat::expect_error(
     init(
@@ -99,7 +67,7 @@ testthat::test_that("init throws when incompatible module's datanames", {
   )
 })
 
-testthat::test_that("init throws when incompatible filter's datanames", {
+testthat::test_that("init throws when dataname in filter incompatible w/ datanames in data", {
   testthat::expect_warning(
     init(
       data = teal_data(mtcars = mtcars),