Merge branch 'main' into 211_subset@main

Signed-off-by: Marcin <[email protected]>

Author: m7pr

.pre-commit-config.yaml

@@ -37,6 +37,9 @@ repos:
           - insightsengineering/teal.slice
           - insightsengineering/teal.widgets
           - utils
+          - shinytest2 # Necessary for documentation
+          - shinyvalidate # Necessary for documentation
+          - rvest # Necessary for documentation
       - id: spell-check
         name: Check spelling with `spelling`
         exclude: >

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal
 Title: Exploratory Web Apps for Analyzing Clinical Trials Data
-Version: 0.15.2.9081
-Date: 2024-11-07
+Version: 0.15.2.9082
+Date: 2024-11-08
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
@@ -37,7 +37,7 @@ BugReports: https://github.com/insightsengineering/teal/issues
 Depends:
     R (>= 4.0),
     shiny (>= 1.8.1),
-    teal.data (>= 0.6.0.9014),
+    teal.data (>= 0.6.0.9015),
     teal.slice (>= 0.5.1.9009)
 Imports:
     checkmate (>= 2.1.0),
@@ -49,7 +49,7 @@ Imports:
     rlang (>= 1.0.0),
     shinyjs,
     stats,
-    teal.code (>= 0.5.0.9011),
+    teal.code (>= 0.5.0.9012),
     teal.logger (>= 0.2.0),
     teal.reporter (>= 0.3.1.9004),
     teal.widgets (>= 0.4.0),

NEWS.md

@@ -1,4 +1,4 @@
-# teal 0.15.2.9081
+# teal 0.15.2.9082
 
 ### New features
 

R/dummy_functions.R

@@ -20,7 +20,7 @@ example_module <- function(label = "example teal module", datanames = "all", tra
     server = function(id, data) {
       checkmate::assert_class(isolate(data()), "teal_data")
       moduleServer(id, function(input, output, session) {
-        datanames_rv <- reactive(ls(teal.code::get_env((req(data())))))
+        datanames_rv <- reactive(names(req(data())))
         observeEvent(datanames_rv(), {
           selected <- input$dataname
           if (identical(selected, "")) {

R/init.R

@@ -207,16 +207,16 @@ init <- function(data,
 
   ## `data` - `modules`
   if (inherits(data, "teal_data")) {
-    if (length(ls(teal.code::get_env(data))) == 0) {
+    if (length(data) == 0) {
       stop("The environment of `data` is empty.")
     }
 
-    is_modules_ok <- check_modules_datanames(modules, ls(teal.code::get_env(data)))
+    is_modules_ok <- check_modules_datanames(modules, names(data))
     if (!isTRUE(is_modules_ok) && length(unlist(extract_transformers(modules))) == 0) {
       warning(is_modules_ok, call. = FALSE)
     }
 
-    is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data)))
+    is_filter_ok <- check_filter_datanames(filter, names(data))
     if (!isTRUE(is_filter_ok)) {
       warning(is_filter_ok)
       # we allow app to continue if applied filters are outside

R/module_data_summary.R

@@ -64,7 +64,7 @@ srv_data_summary <- function(id, teal_data) {
 
       summary_table <- reactive({
         req(inherits(teal_data(), "teal_data"))
-        if (!length(ls(teal.code::get_env(teal_data())))) {
+        if (!length(teal_data())) {
           return(NULL)
         }
         get_filter_overview_wrapper(teal_data)
@@ -142,7 +142,8 @@ srv_data_summary <- function(id, teal_data) {
 
 #' @rdname module_data_summary
 get_filter_overview_wrapper <- function(teal_data) {
-  datanames <- teal.data::datanames(teal_data())
+  # Sort datanames in topological order
+  datanames <- names(teal_data())
   joinkeys <- teal.data::join_keys(teal_data())
 
   current_data_objs <- sapply(

R/module_init_data.R

@@ -101,7 +101,7 @@ srv_init_data <- function(id, data) {
       list(code = trimws(c(teal.code::get_code(data), hashes), which = "right")),
       list(join_keys = teal.data::join_keys(data)),
       sapply(
-        ls(teal.code::get_env(data)),
+        names(data),
         teal.code::get_var,
         object = data,
         simplify = FALSE
@@ -121,7 +121,7 @@ srv_init_data <- function(id, data) {
 #' @return A character vector with the code lines.
 #' @keywords internal
 #'
-.get_hashes_code <- function(data, datanames = ls(teal.code::get_env(data))) {
+.get_hashes_code <- function(data, datanames = names(data)) {
   vapply(
     datanames,
     function(dataname, datasets) {

R/module_nested_tabs.R

@@ -364,11 +364,11 @@ srv_teal_module.teal_module <- function(id,
 .resolve_module_datanames <- function(data, modules) {
   stopifnot("data_rv must be teal_data object." = inherits(data, "teal_data"))
   if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
-    .topologically_sort_datanames(ls(teal.code::get_env(data)), teal.data::join_keys(data))
+    names(data)
   } else {
     intersect(
-      .include_parent_datanames(modules$datanames, teal.data::join_keys(data)),
-      ls(teal.code::get_env(data))
+      names(data), # Keep topological order from teal.data::names()
+      .include_parent_datanames(modules$datanames, teal.data::join_keys(data))
     )
   }
 }

R/module_teal.R

@@ -195,7 +195,7 @@ srv_teal <- function(id, data, modules, filter = teal_slices()) {
     )
     data_rv <- reactive({
       req(inherits(data_validated(), "teal_data"))
-      is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data_validated())))
+      is_filter_ok <- check_filter_datanames(filter, names(data_validated()))
       if (!isTRUE(is_filter_ok)) {
         showNotification(
           "Some filters were not applied because of incompatibility with data. Contact app developer.",

R/module_teal_data.R

@@ -223,7 +223,7 @@ srv_check_shiny_warnings <- function(id, data, modules) {
     output$message <- renderUI({
       if (inherits(data(), "teal_data")) {
         is_modules_ok <- check_modules_datanames_html(
-          modules = modules, datanames = ls(teal.code::get_env(data()))
+          modules = modules, datanames = names(data())
         )
         if (!isTRUE(is_modules_ok)) {
           tags$div(is_modules_ok, class = "teal-output-warning")