Merge branch 'main' into register_handlers

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.3.0.9000
-Date: 2024-03-05
+Version: 0.3.0.9003
+Date: 2024-03-18
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -71,7 +71,8 @@ Suggests:
     rlang (>= 1.0.0),
     rtables (>= 0.6.6),
     sparkline,
-    testthat (>= 3.0.4)
+    testthat (>= 3.0.4),
+    withr (>= 2.0.0)
 VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
@@ -89,7 +90,7 @@ Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     jeroen/jsonlite, yihui/knitr, deepayan/lattice, daroczig/logger, MASS,
     insightsengineering/nestcolor, r-lib/rlang,
     insightsengineering/rtables, sparkline, insightsengineering/teal.data,
-    r-lib/testthat
+    r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.general 0.3.0.9000
+# teal.modules.general 0.3.0.9003
 
 # teal.modules.general 0.3.0
 

R/tm_a_pca.R

@@ -191,13 +191,13 @@ ui_a_pca <- function(id, ...) {
     color_selector[[i]]$select$selected <- NULL
   }
 
-  shiny::tagList(
+  tagList(
     include_css_files("custom"),
     teal.widgets::standard_layout(
       output = teal.widgets::white_small_well(
         uiOutput(ns("all_plots"))
       ),
-      encoding = div(
+      encoding = tags$div(
         ### Reporter
         teal.reporter::simple_reporter_ui(ns("simple_reporter")),
         ###
@@ -986,11 +986,11 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
     output$tbl_importance_ui <- renderUI({
       req("importance" %in% input$tables_display)
-      div(
+      tags$div(
         align = "center",
         tags$h4("Principal components importance"),
         tableOutput(session$ns("tbl_importance")),
-        hr()
+        tags$hr()
       )
     })
 
@@ -1006,11 +1006,11 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
     output$tbl_eigenvector_ui <- renderUI({
       req("eigenvector" %in% input$tables_display)
-      div(
+      tags$div(
         align = "center",
         tags$h4("Eigenvectors"),
         tableOutput(session$ns("tbl_eigenvector")),
-        hr()
+        tags$hr()
       )
     })
 

R/tm_a_regression.R

@@ -254,7 +254,7 @@ ui_a_regression <- function(id, ...) {
       teal.widgets::plot_with_settings_ui(id = ns("myplot")),
       tags$div(verbatimTextOutput(ns("text")))
     )),
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -284,12 +284,12 @@ ui_a_regression <- function(id, ...) {
         ns = ns,
         teal.widgets::optionalSliderInput(
           ns("outlier"),
-          div(
+          tags$div(
             class = "teal-tooltip",
             tagList(
               "Outlier definition:",
               icon("circle-info"),
-              span(
+              tags$span(
                 class = "tooltiptext",
                 paste(
                   "Use the slider to choose the cut-off value to define outliers.",
@@ -314,12 +314,12 @@ ui_a_regression <- function(id, ...) {
           teal.widgets::optionalSliderInputValMinMax(ns("size"), "Points size:", args$size, ticks = FALSE),
           teal.widgets::optionalSliderInputValMinMax(
             inputId = ns("label_min_segment"),
-            label = div(
+            label = tags$div(
               class = "teal-tooltip",
               tagList(
                 "Label min. segment:",
                 icon("circle-info"),
-                span(
+                tags$span(
                   class = "tooltiptext",
                   paste(
                     "Use the slider to choose the cut-off value to define minimum distance between label and point",

R/tm_data_table.R

@@ -141,7 +141,7 @@ ui_page_data_table <- function(id,
                                post_output = NULL) {
   ns <- NS(id)
 
-  shiny::tagList(
+  tagList(
     include_css_files("custom"),
     teal.widgets::standard_layout(
       output = teal.widgets::white_small_well(
@@ -220,7 +220,7 @@ srv_page_data_table <- function(id,
               title = x,
               column(
                 width = 12,
-                div(
+                tags$div(
                   class = "mt-4",
                   ui_data_table(
                     id = session$ns(x),

R/tm_file_viewer.R

@@ -97,13 +97,13 @@ ui_viewer <- function(id, ...) {
   args <- list(...)
   ns <- NS(id)
 
-  shiny::tagList(
+  tagList(
     include_css_files("custom"),
     teal.widgets::standard_layout(
-      output = div(
+      output = tags$div(
         uiOutput(ns("output"))
       ),
-      encoding = div(
+      encoding = tags$div(
         class = "file_viewer_encoding",
         tags$label("Encodings", class = "text-primary"),
         shinyTree::shinyTree(

R/tm_g_association.R

@@ -202,7 +202,7 @@ ui_tm_g_association <- function(id, ...) {
       tags$br(),
       teal.widgets::plot_with_settings_ui(id = ns("myplot"))
     ),
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -488,8 +488,8 @@ srv_tm_g_association <- function(id,
         )
     })
 
-    plot_r <- shiny::reactive({
-      shiny::req(iv_r()$is_valid())
+    plot_r <- reactive({
+      req(iv_r()$is_valid())
       output_q()[["p"]]
     })
 

R/tm_g_bivariate.R

@@ -313,7 +313,7 @@ ui_g_bivariate <- function(id, ...) {
     output = teal.widgets::white_small_well(
       tags$div(teal.widgets::plot_with_settings_ui(id = ns("myplot")))
     ),
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -344,13 +344,13 @@ ui_g_bivariate <- function(id, ...) {
         )
       ),
       if (!is.null(args$row_facet) || !is.null(args$col_facet)) {
-        div(
+        tags$div(
           class = "data-extract-box",
           tags$label("Facetting"),
           shinyWidgets::switchInput(inputId = ns("facetting"), value = args$facet, size = "mini"),
           conditionalPanel(
             condition = paste0("input['", ns("facetting"), "']"),
-            div(
+            tags$div(
               if (!is.null(args$row_facet)) {
                 teal.transform::data_extract_ui(
                   id = ns("row_facet"),
@@ -375,13 +375,13 @@ ui_g_bivariate <- function(id, ...) {
       },
       if (args$color_settings) {
         # Put a grey border around the coloring settings
-        div(
+        tags$div(
           class = "data-extract-box",
           tags$label("Color settings"),
           shinyWidgets::switchInput(inputId = ns("coloring"), value = TRUE, size = "mini"),
           conditionalPanel(
             condition = paste0("input['", ns("coloring"), "']"),
-            div(
+            tags$div(
               teal.transform::data_extract_ui(
                 id = ns("color"),
                 label = "Outline color by variable",
@@ -394,7 +394,7 @@ ui_g_bivariate <- function(id, ...) {
                 data_extract_spec = args$fill,
                 is_single_dataset = is_single_dataset_value
               ),
-              div(
+              tags$div(
                 id = ns("size_settings"),
                 teal.transform::data_extract_ui(
                   id = ns("size"),
@@ -674,7 +674,7 @@ srv_g_bivariate <- function(id,
         teal.code::eval_code(print_call)
     })
 
-    plot_r <- shiny::reactive({
+    plot_r <- reactive({
       output_q()[["p"]]
     })
 

R/tm_g_distribution.R

@@ -206,12 +206,12 @@ ui_distribution <- function(id, ...) {
         tabPanel("Histogram", teal.widgets::plot_with_settings_ui(id = ns("hist_plot"))),
         tabPanel("QQplot", teal.widgets::plot_with_settings_ui(id = ns("qq_plot")))
       ),
-      h3("Statistics Table"),
+      tags$h3("Statistics Table"),
       DT::dataTableOutput(ns("summary_table")),
-      h3("Tests"),
+      tags$h3("Tests"),
       DT::dataTableOutput(ns("t_stats"))
     ),
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -274,12 +274,12 @@ ui_distribution <- function(id, ...) {
             "Theoretical Distribution",
             teal.widgets::optionalSelectInput(
               ns("t_dist"),
-              div(
+              tags$div(
                 class = "teal-tooltip",
                 tagList(
                   "Distribution:",
                   icon("circle-info"),
-                  span(
+                  tags$span(
                     class = "tooltiptext",
                     "Default parameters are optimized with MASS::fitdistr function."
                   )
@@ -291,7 +291,7 @@ ui_distribution <- function(id, ...) {
             ),
             numericInput(ns("dist_param1"), label = "param1", value = NULL),
             numericInput(ns("dist_param2"), label = "param2", value = NULL),
-            span(actionButton(ns("params_reset"), "Reset params")),
+            tags$span(actionButton(ns("params_reset"), "Reset params")),
             collapsed = FALSE
           )
         )

R/tm_g_response.R

@@ -229,7 +229,7 @@ ui_g_response <- function(id, ...) {
     output = teal.widgets::white_small_well(
       teal.widgets::plot_with_settings_ui(id = ns("myplot"))
     ),
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###

R/tm_g_scatterplot.R

@@ -329,7 +329,7 @@ ui_g_scatterplot <- function(id, ...) {
     args$x, args$y, args$color_by, args$size_by, args$row_facet, args$col_facet
   )
 
-  shiny::tagList(
+  tagList(
     include_css_files("custom"),
     teal.widgets::standard_layout(
       output = teal.widgets::white_small_well(
@@ -338,7 +338,7 @@ ui_g_scatterplot <- function(id, ...) {
         teal.widgets::get_dt_rows(ns("data_table"), ns("data_table_rows")),
         DT::dataTableOutput(ns("data_table"), width = "100%")
       ),
-      encoding = div(
+      encoding = tags$div(
         ### Reporter
         teal.reporter::simple_reporter_ui(ns("simple_reporter")),
         ###
@@ -432,19 +432,19 @@ ui_g_scatterplot <- function(id, ...) {
             shinyjs::hidden(checkboxInput(ns("show_form"), "Show formula", value = TRUE)),
             shinyjs::hidden(checkboxInput(ns("show_r2"), "Show adj-R Squared", value = TRUE)),
             uiOutput(ns("num_na_removed")),
-            div(
+            tags$div(
               id = ns("label_pos"),
-              div(strong("Stats position")),
-              div(class = "inline-block w-10", helpText("Left")),
-              div(
+              tags$div(tags$strong("Stats position")),
+              tags$div(class = "inline-block w-10", helpText("Left")),
+              tags$div(
                 class = "inline-block w-70",
                 teal.widgets::optionalSliderInput(
                   ns("pos"),
                   label = NULL,
                   min = 0, max = 1, value = .99, ticks = FALSE, step = .01
                 )
               ),
-              div(class = "inline-block w-10", helpText("Right"))
+              tags$div(class = "inline-block w-10", helpText("Right"))
             ),
             teal.widgets::optionalSliderInput(
               ns("label_size"), "Stats font size",
@@ -599,7 +599,7 @@ srv_g_scatterplot <- function(id,
         x_var <- as.vector(merged$anl_input_r()$columns_source$x)
         y_var <- as.vector(merged$anl_input_r()$columns_source$y)
         if ((num_total_na <- nrow(ANL) - nrow(stats::na.omit(ANL[, c(x_var, y_var)]))) > 0) {
-          shiny::tags$div(paste(num_total_na, "row(s) with missing values were removed"), shiny::tags$hr())
+          tags$div(paste(num_total_na, "row(s) with missing values were removed"), tags$hr())
         }
       }
     })

R/tm_g_scatterplotmatrix.R

@@ -209,10 +209,10 @@ ui_g_scatterplotmatrix <- function(id, ...) {
   teal.widgets::standard_layout(
     output = teal.widgets::white_small_well(
       textOutput(ns("message")),
-      br(),
+      tags$br(),
       teal.widgets::plot_with_settings_ui(id = ns("myplot"))
     ),
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -224,7 +224,7 @@ ui_g_scatterplotmatrix <- function(id, ...) {
         data_extract_spec = args$variables,
         is_single_dataset = is_single_dataset_value
       ),
-      hr(),
+      tags$hr(),
       teal.widgets::panel_group(
         teal.widgets::panel_item(
           title = "Plot settings",
@@ -419,7 +419,7 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
 
     # show a message if conversion to factors took place
     output$message <- renderText({
-      shiny::req(iv_r()$is_valid())
+      req(iv_r()$is_valid())
       req(selector_list()$variables())
       ANL <- merged$anl_q_r()[["ANL"]]
       cols_names <- unique(unname(do.call(c, merged$anl_input_r()$columns_source)))