Merge branch 'main' into in_teal.reporter@custom_card_functions@main

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>

.pre-commit-config.yaml

@@ -24,7 +24,6 @@ repos:
           - dplyr
           - DT
           - forcats
-          - ggrepel
           - grid
           - logger
           - scales

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.3.0.9029
-Date: 2024-04-29
+Version: 0.3.0.9038
+Date: 2024-06-27
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"),
@@ -45,10 +45,10 @@ Imports:
     stringr (>= 1.4.1),
     teal.code (>= 0.5.0),
     teal.data (>= 0.5.0),
-    teal.logger (>= 0.1.3.9013),
+    teal.logger (>= 0.2.0.9004),
     teal.reporter (>= 0.3.0),
     teal.widgets (>= 0.4.0),
-    tern (>= 0.9.3),
+    tern (>= 0.9.5),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
     tools,
@@ -70,11 +70,12 @@ Suggests:
     MASS,
     nestcolor (>= 0.1.0),
     pkgload,
-    rtables (>= 0.6.6),
+    rmarkdown (>= 2.23),
+    rtables (>= 0.6.8),
     rvest,
     shinytest2,
     sparkline,
-    testthat (>= 3.0.4),
+    testthat (>= 3.1.9),
     withr (>= 2.0.0)
 VignetteBuilder:
     knitr
@@ -90,8 +91,8 @@ Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     tidymodels/broom, daattali/colourpicker, daattali/ggExtra,
     aphalo/ggpmisc, aphalo/ggpp, slowkow/ggrepel, baddstats/goftest,
     gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite, yihui/knitr,
-    deepayan/lattice, daroczig/logger, MASS,
-    insightsengineering/nestcolor, r-lib/rlang,
+    daroczig/logger, deepayan/lattice, MASS,
+    insightsengineering/nestcolor, r-lib/rlang, rstudio/rmarkdown,
     insightsengineering/rtables, tidyverse/rvest, sparkline,
     rstudio/shinytest2, insightsengineering/teal.data, r-lib/testthat,
     r-lib/withr

NEWS.md

@@ -1,4 +1,9 @@
-# teal.modules.general 0.3.0.9029
+# teal.modules.general 0.3.0.9038
+
+* Removed `Show Warnings` modals from modules.
+
+### Enhancements
+* Added `teal.logger` functionality for logging changes in shiny inputs in all modules.
 
 * Users can now provide their own card functions to specify the content that modules send to reports.
 
@@ -38,6 +43,7 @@
 * Removed `scda` package dependency from examples.
 * Replaced deprecated `ggplot2` functions `..count..`, `..density..` and `..prop..`.
 * Version bump on `forcats` dependency.
+* Replaced `scda` data generation functions with `random.cdisc.data`
 
 # teal.modules.general 0.2.15
 

R/tm_a_pca.R

@@ -282,7 +282,6 @@ ui_a_pca <- function(id, ...) {
         )
       ),
       forms = tagList(
-        teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
         teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
       ),
       pre_output = args$pre_output,
@@ -298,6 +297,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     response <- dat
 
     for (i in seq_along(response)) {
@@ -1033,13 +1034,6 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       )
     })
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_a_regression.R

@@ -348,7 +348,6 @@ ui_a_regression <- function(id, ...) {
       )
     ),
     forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
     ),
     pre_output = args$pre_output,
@@ -372,6 +371,8 @@ srv_a_regression <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     rule_rvr1 <- function(value) {
@@ -1000,13 +1001,6 @@ srv_a_regression <- function(id,
       )
     })
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_data_table.R

@@ -182,6 +182,8 @@ srv_page_data_table <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     if_filtered <- reactive(as.logical(input$if_filtered))
     if_distinct <- reactive(as.logical(input$if_distinct))
 

R/tm_file_viewer.R

@@ -124,6 +124,8 @@ ui_viewer <- function(id, ...) {
 # Server function for the file viewer module
 srv_viewer <- function(id, input_path) {
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     temp_dir <- tempfile()
     if (!dir.exists(temp_dir)) {
       dir.create(temp_dir, recursive = TRUE)

R/tm_front_page.R

@@ -137,6 +137,8 @@ srv_front_page <- function(id, data, tables, show_metadata) {
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     setBookmarkExclude("metadata_button")

R/tm_g_association.R

@@ -262,7 +262,6 @@ ui_tm_g_association <- function(id, ...) {
       )
     ),
     forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
     ),
     pre_output = args$pre_output,
@@ -286,6 +285,8 @@ srv_tm_g_association <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(ref = ref, vars = vars),
       datasets = data,
@@ -506,13 +507,6 @@ srv_tm_g_association <- function(id,
       teal.code::dev_suppress(output_q()[["title"]])
     })
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_g_bivariate.R

@@ -431,7 +431,6 @@ ui_g_bivariate <- function(id, ...) {
       )
     ),
     forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
     ),
     pre_output = args$pre_output,
@@ -460,6 +459,8 @@ srv_g_bivariate <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     data_extract <- list(
@@ -689,13 +690,6 @@ srv_g_bivariate <- function(id,
       width = plot_width
     )
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_g_distribution.R

@@ -340,7 +340,6 @@ ui_distribution <- function(id, ...) {
       )
     ),
     forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
     ),
     pre_output = args$pre_output,
@@ -365,6 +364,8 @@ srv_distribution <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     setBookmarkExclude("params_reset")
 
     ns <- session$ns
@@ -1275,13 +1276,6 @@ srv_distribution <- function(id,
       rownames = FALSE
     )
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_g_response.R

@@ -289,7 +289,6 @@ ui_g_response <- function(id, ...) {
       )
     ),
     forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
     ),
     pre_output = args$pre_output,
@@ -314,6 +313,8 @@ srv_g_response <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     data_extract <- list(response = response, x = x, row_facet = row_facet, col_facet = col_facet)
 
     rule_diff <- function(other) {
@@ -547,13 +548,6 @@ srv_g_response <- function(id,
       width = plot_width
     )
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_g_scatterplot.R

@@ -466,7 +466,6 @@ ui_g_scatterplot <- function(id, ...) {
         )
       ),
       forms = tagList(
-        teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
         teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
       ),
       pre_output = args$pre_output,
@@ -495,6 +494,8 @@ srv_g_scatterplot <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     data_extract <- list(
       x = x,
       y = y,
@@ -1022,13 +1023,6 @@ srv_g_scatterplot <- function(id,
       }
     })
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_g_scatterplotmatrix.R

@@ -252,7 +252,6 @@ ui_g_scatterplotmatrix <- function(id, ...) {
       )
     ),
     forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
     ),
     pre_output = args$pre_output,
@@ -267,6 +266,8 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(variables = variables),
       datasets = data,
@@ -441,13 +442,6 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
       }
     })
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(output_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

R/tm_missing_data.R

@@ -170,6 +170,8 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   moduleServer(id, function(input, output, session) {
+    teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     datanames <- isolate(teal.data::datanames(data()))
     datanames <- Filter(function(name) {
       is.data.frame(isolate(data())[[name]])
@@ -228,7 +230,6 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
         conditionalPanel(
           is_tab_active_js(ns("dataname_tab"), x),
           tagList(
-            teal.widgets::verbatim_popup_ui(dataname_ns("warning"), "Show Warnings"),
             teal.widgets::verbatim_popup_ui(dataname_ns("rcode"), "Show R code")
           )
         )
@@ -1269,13 +1270,6 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
       }
     })
 
-    teal.widgets::verbatim_popup_srv(
-      id = "warning",
-      verbatim_content = reactive(teal.code::get_warnings(final_q())),
-      title = "Warning",
-      disabled = reactive(is.null(teal.code::get_warnings(final_q())))
-    )
-
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(final_q())),