Merge branch 'main' into poc3@spotfire_poc2

# Conflicts:
#	R/tm_data_table.R
#	R/tm_g_scatterplot.R

Author: vedhav

.lintr

@@ -1,6 +1,5 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
-  cyclocomp_linter = NULL,
   object_usage_linter = NULL,
   object_name_linter = object_name_linter(styles = c("snake_case", "symbols"), regexes = c(ANL = "^ANL_?[0-9A-Z_]*$", ADaM = "^r?AD[A-Z]{2,3}_?[0-9]*$")),
   indentation_linter = NULL

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9005
+    rev: v0.4.3.9013
     hooks:
       - id: style-files
         name: Style code with `styler`

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.4.0.9001
-Date: 2025-03-11
+Version: 0.4.1.9020
+Date: 2025-08-20
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -26,9 +26,9 @@ Depends:
     ggmosaic (>= 0.3.0),
     ggplot2 (>= 3.4.0),
     R (>= 4.1),
-    shiny (>= 1.6.0),
-    teal (>= 0.16.0.9002),
-    teal.transform (>= 0.6.0)
+    shiny (>= 1.8.1),
+    teal (>= 0.16.0.9008),
+    teal.transform (>= 0.6.0.9002)
 Imports:
     bslib (>= 0.8.0),
     checkmate (>= 2.1.0),
@@ -39,7 +39,7 @@ Imports:
     forcats (>= 1.0.0),
     generics (>= 0.1.3),
     ggExtra (>= 0.10.1),
-    ggpmisc (>= 0.4.3),
+    ggpmisc (>= 0.5.6),
     ggpp (>= 0.5.8-1),
     ggrepel (>= 0.9.6),
     goftest (>= 1.2-3),
@@ -66,19 +66,19 @@ Imports:
     sparkline (>= 2.0),
     stats,
     stringr (>= 1.4.1),
-    teal.code (>= 0.6.1),
+    teal.code (>= 0.7.0),
     teal.data (>= 0.7.0),
-    teal.logger (>= 0.3.2),
-    teal.reporter (>= 0.4.0.9004),
-    teal.widgets (>= 0.4.3.9001),
+    teal.logger (>= 0.4.0),
+    teal.reporter (>= 0.5.0),
+    teal.widgets (>= 0.4.3.9005),
     tern (>= 0.9.7),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
     tools,
     utils
 Suggests:
     knitr (>= 1.42),
-    logger (>= 0.2.0),
+    logger (>= 0.4.0),
     nestcolor (>= 0.1.0),
     pkgload,
     roxy.shinylive,
@@ -90,15 +90,15 @@ VignetteBuilder:
     knitr,
     rmarkdown
 Remotes:
-    insightsengineering/teal.reporter@main,
+    insightsengineering/teal.transform@main,
     insightsengineering/teal.widgets@main,
     insightsengineering/teal@main
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, insightsengineering/teal,
-    insightsengineering/teal.slice, insightsengineering/teal.transform,
-    mllg/checkmate, tidyverse/dplyr, rstudio/DT, tidyverse/forcats,
-    r-lib/lifecycle, r-lib/scales, daattali/shinyjs, shinyTree/shinyTree,
-    rstudio/shinyvalidate, dreamRs/shinyWidgets, tidyverse/stringr,
+    insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
+    rstudio/DT, tidyverse/forcats, r-lib/lifecycle, r-lib/scales,
+    daattali/shinyjs, shinyTree/shinyTree, rstudio/shinyvalidate,
+    dreamRs/shinyWidgets, tidyverse/stringr,
     insightsengineering/teal.code, insightsengineering/teal.data,
     insightsengineering/teal.logger, insightsengineering/teal.reporter,
     insightsengineering/teal.widgets, insightsengineering/tern,

NEWS.md

@@ -1,4 +1,25 @@
-# teal.modules.general 0.4.0.9001
+# teal.modules.general 0.4.1.9020
+
+### Breaking changes
+
+- Removed the `table` object decoration in `tm_missing_data` and `tm_outliers` (#899).
+- Removed the `summary_table` and `test_table` object decoration in `tm_g_distribution` (#897).
+
+### Bug fixes
+
+- Fixed "Add to Report" functionality in `tm_outliers`, `tm_missing_data` and `tm_g_distribution` modules (#899 and #897).
+
+### Miscellaneous
+
+- Fixed deprecation warning for `tern::stack_grobs` in `tm_g_association` (#903).
+
+# teal.modules.general 0.4.1
+
+### Bug fixes
+* Fixes output is not updated when filter is added for the modules:  `tm_a_pca`, `tm_a_regression`, `tm_g_scatterplot`, `tm_g_association`, `tm_g_bivariate`, `tm_g_distribution`, `tm_g_response`, `tm_t_crosstable` (#870)
+
+### Enhancements
+* Added `remove_zero_columns` to `tm_t_crosstable` to add an option to remove empty columns (#890)
 
 # teal.modules.general 0.4.0
 

R/tm_a_pca.R

@@ -229,14 +229,14 @@ ui_a_pca <- function(id, ...) {
   }
 
   tagList(
-    include_css_files("custom"),
     teal.widgets::standard_layout(
       output = teal.widgets::white_small_well(
         uiOutput(ns("all_plots"))
       ),
       encoding = tags$div(
         ### Reporter
-        teal.reporter::simple_reporter_ui(ns("simple_reporter")),
+        teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
+        tags$br(), tags$br(),
         ###
         tags$label("Encodings", class = "text-primary"),
         teal.transform::datanames_input(args["dat"]),
@@ -436,10 +436,12 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       selector_list = selector_list,
       datasets = data
     )
-    qenv <- teal.code::eval_code(data(), 'library("ggplot2");library("dplyr");library("tidyr")') # nolint quotes
+    qenv <- reactive(
+      teal.code::eval_code(data(), 'library("ggplot2");library("dplyr");library("tidyr")') # nolint quotes
+    )
     anl_merged_q <- reactive({
       req(anl_merged_input())
-      qenv %>%
+      qenv() %>%
         teal.code::eval_code(as.expression(anl_merged_input()$expr))
     })
 
@@ -1116,7 +1118,6 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
 
       validation()
       tags$div(
-        class = "overflow-scroll",
         uiOutput(session$ns("tbl_importance_ui")),
         uiOutput(session$ns("tbl_eigenvector_ui")),
         teal.widgets::plot_with_settings_ui(id = session$ns("pca_plot"))
@@ -1154,7 +1155,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         card$append_src(source_code_r())
         card
       }
-      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
+      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
     }
     ###
   })

R/tm_a_regression.R

@@ -286,7 +286,8 @@ ui_a_regression <- function(id, ...) {
     )),
     encoding = tags$div(
       ### Reporter
-      teal.reporter::simple_reporter_ui(ns("simple_reporter")),
+      teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
+      tags$br(), tags$br(),
       ###
       tags$label("Encodings", class = "text-primary"), tags$br(),
       teal.transform::datanames_input(args[c("response", "regressor")]),
@@ -462,14 +463,13 @@ srv_a_regression <- function(id,
       )
     })
 
-    qenv <- teal.code::eval_code(
-      data(),
-      'library("ggplot2");library("dplyr")' # nolint quotes
+    qenv <- reactive(
+      teal.code::eval_code(data(), 'library("ggplot2");library("dplyr")') # nolint quotes
     )
 
     anl_merged_q <- reactive({
       req(anl_merged_input())
-      qenv %>%
+      qenv() %>%
         teal.code::eval_code(as.expression(anl_merged_input()$expr))
     })
 
@@ -830,18 +830,15 @@ srv_a_regression <- function(id,
               color = "red",
               linetype = "dashed"
             ) +
-            ggplot2::geom_text(
-              ggplot2::aes(
-                x = 0,
-                y = mean(data$.cooksd, na.rm = TRUE),
-                label = paste("mu", "=", round(mean(data$.cooksd, na.rm = TRUE), 4)),
-                vjust = -1,
-                hjust = 0,
-                color = "red",
-                angle = 90
-              ),
-              parse = TRUE,
-              show.legend = FALSE
+            ggplot2::annotate(
+              geom = "text",
+              x = 0,
+              y = mean(data$.cooksd, na.rm = TRUE),
+              label = paste("mu", "=", round(mean(data$.cooksd, na.rm = TRUE), 4)),
+              vjust = -1,
+              hjust = 0,
+              color = "red",
+              angle = 90
             ) +
             outlier_label,
           env = list(plot = plot, outlier = input$outlier, outlier_label = outlier_label())
@@ -998,7 +995,7 @@ srv_a_regression <- function(id,
       "decorator",
       data = output_q,
       decorators = select_decorators(decorators, "plot"),
-      expr = print(plot)
+      expr = plot
     )
 
     fitted <- reactive({
@@ -1021,9 +1018,7 @@ srv_a_regression <- function(id,
     output$text <- renderText({
       req(iv_r()$is_valid())
       req(iv_out$is_valid())
-      paste(utils::capture.output(summary(teal.code::dev_suppress(fitted())))[-1],
-        collapse = "\n"
-      )
+      paste(utils::capture.output(summary(fitted()))[-1], collapse = "\n")
     })
 
     # Render R code.
@@ -1053,7 +1048,7 @@ srv_a_regression <- function(id,
         card$append_src(source_code_r())
         card
       }
-      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
+      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
     }
     ###
   })

R/tm_data_table.R

@@ -112,7 +112,7 @@ tm_data_table <- function(label = "Data Table",
     })
   }
   if (!missing(datasets_selected)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_stop(
       when = "0.4.0",
       what = "tm_data_table(datasets_selected)",
       with = "tm_data_table(datanames)",
@@ -156,7 +156,6 @@ tm_data_table <- function(label = "Data Table",
 ui_data_table <- function(id, pre_output = NULL, post_output = NULL) {
   ns <- NS(id)
   bslib::page_fluid(
-    include_css_files("custom"),
     teal.widgets::standard_layout(
       output = bslib::page_fluid(
         div(checkboxInput(ns("if_distinct"), "Show only distinct rows:", value = FALSE)),

R/tm_file_viewer.R

@@ -103,21 +103,20 @@ ui_viewer <- function(id, ...) {
   ns <- NS(id)
 
   tagList(
-    include_css_files("custom"),
     teal.widgets::standard_layout(
       output = tags$div(
         uiOutput(ns("output"))
       ),
       encoding = tags$div(
-        class = "file_viewer_encoding",
+        style = "overflow-y: hidden; overflow-x: auto;",
         tags$label("Encodings", class = "text-primary"),
         shinyTree::shinyTree(
           ns("tree"),
           dragAndDrop = FALSE,
           sort = FALSE,
-          wholerow = TRUE,
           theme = "proton",
-          multiple = FALSE
+          multiple = FALSE,
+          search = TRUE
         )
       )
     )
@@ -173,7 +172,7 @@ srv_viewer <- function(id, input_path) {
         tags$img(src = con_type$selected_path, alt = "file does not exist")
       } else if (file_extension == "pdf") {
         tags$embed(
-          class = "embed_pdf",
+          style = "height: 600px; width: 100%;",
           src = con_type$selected_path
         )
       } else if (!isFALSE(con_type$output_text[1])) {

R/tm_front_page.R

@@ -83,7 +83,7 @@ tm_front_page <- function(label = "Front page",
   checkmate::assert_multi_class(additional_tags, classes = c("shiny.tag.list", "html"))
   checkmate::assert_character(footnotes, min.len = 0, any.missing = FALSE)
   if (!missing(show_metadata)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_stop(
       when = "0.4.0",
       what = "tm_front_page(show_metadata)",
       with = "tm_front_page(datanames)",
@@ -119,33 +119,32 @@ ui_front_page <- function(id, ...) {
   ns <- NS(id)
 
   tagList(
-    include_css_files("custom"),
     tags$div(
       id = "front_page_content",
-      class = "ml-8",
+      style = "margin-left: 2rem;",
       tags$div(
         id = "front_page_headers",
         get_header_tags(args$header_text)
       ),
       tags$div(
         id = "front_page_tables",
-        class = "ml-4",
+        style = "margin-left: 2rem;",
         get_table_tags(args$tables, ns)
       ),
       tags$div(
         id = "front_page_custom_html",
-        class = "my-4",
+        style = "margin-left: 2rem;",
         args$additional_tags
       ),
       if (length(args$datanames) > 0L) {
         tags$div(
           id = "front_page_metabutton",
-          class = "m-4",
+          style = "margin: 1rem;",
           actionButton(ns("metadata_button"), "Show metadata")
         )
       },
       tags$footer(
-        class = ".small",
+        class = "small",
         get_footer_tags(args$footnotes)
       )
     )
@@ -228,7 +227,7 @@ get_table_tags <- function(tables, ns) {
       tableOutput(ns(paste0("table_", idx)))
     )
   }))
-  return(table_tags)
+  table_tags
 }
 
 get_footer_tags <- function(footnotes) {
@@ -255,11 +254,11 @@ convert_metadata_to_dataframe <- function(raw_metadata, datanames) {
     if (is.null(metadata)) {
       return(data.frame(Dataset = character(0), Name = character(0), Value = character(0)))
     }
-    return(data.frame(
+    data.frame(
       Dataset = dataname,
       Name = names(metadata),
       Value = unname(unlist(lapply(metadata, as.character)))
-    ))
+    )
   }, raw_metadata, datanames, SIMPLIFY = FALSE)
   do.call(rbind, output)
 }