Merge remote-tracking branch 'origin/main' into poc3@spotfire_poc2

# Conflicts:
#	R/tm_g_scatterplot.R
#	R/utils.R

Author: vedhav

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9013
+    rev: v0.4.3.9014
     hooks:
       - id: style-files
         name: Style code with `styler`
@@ -18,33 +18,45 @@ repos:
           - ggmosaic
           - ggplot2
           - shiny
+          - insightsengineering/teal
+          - insightsengineering/teal.transform
+          - bslib
           - checkmate
+          - colourpicker
           - dplyr
           - DT
           - forcats
+          - ggExtra
+          - ggpmisc
+          - ggpp
+          - ggrepel
+          - goftest
           - grid
-          - logger
+          - gridExtra
+          - htmlwidgets
+          - jsonlite
+          - lattice
+          - lifecycle
+          - MASS
+          - rtables
           - scales
           - shinyjs
           - shinyTree
           - shinyvalidate
           - shinyWidgets
+          - sparkline
           - stats
           - stringr
-          - insightsengineering/roxy.shinylive
-          - insightsengineering/teal
-          - insightsengineering/teal.transform
           - insightsengineering/teal.code
           - insightsengineering/teal.data
           - insightsengineering/teal.logger
           - insightsengineering/teal.reporter
-          - insightsengineering/teal.slice
           - insightsengineering/teal.widgets
           - tern
           - tibble
           - tidyr
-          - utils
-
+          - insightsengineering/teal.slice
+          - insightsengineering/roxy.shinylive
       - id: spell-check
         name: Check spelling with `spelling`
         exclude: >

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.4.1.9020
-Date: 2025-08-20
+Version: 0.5.0.9001
+Date: 2025-09-09
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -27,8 +27,8 @@ Depends:
     ggplot2 (>= 3.4.0),
     R (>= 4.1),
     shiny (>= 1.8.1),
-    teal (>= 0.16.0.9008),
-    teal.transform (>= 0.6.0.9002)
+    teal (>= 1.0.0.9003),
+    teal.transform (>= 0.7.0)
 Imports:
     bslib (>= 0.8.0),
     checkmate (>= 2.1.0),
@@ -67,10 +67,10 @@ Imports:
     stats,
     stringr (>= 1.4.1),
     teal.code (>= 0.7.0),
-    teal.data (>= 0.7.0),
+    teal.data (>= 0.8.0),
     teal.logger (>= 0.4.0),
-    teal.reporter (>= 0.5.0),
-    teal.widgets (>= 0.4.3.9005),
+    teal.reporter (>= 0.5.0.9001),
+    teal.widgets (>= 0.5.0),
     tern (>= 0.9.7),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
@@ -90,9 +90,8 @@ VignetteBuilder:
     knitr,
     rmarkdown
 Remotes:
-    insightsengineering/teal.transform@main,
-    insightsengineering/teal.widgets@main,
-    insightsengineering/teal@main
+    insightsengineering/teal,
+    insightsengineering/teal.reporter
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, insightsengineering/teal,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
@@ -115,4 +114,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE, packages = c("roxy.shinylive"))
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,4 +1,6 @@
-# teal.modules.general 0.4.1.9020
+# teal.modules.general 0.5.0.9001
+
+# teal.modules.general 0.5.0
 
 ### Breaking changes
 
@@ -8,19 +10,20 @@
 ### Bug fixes
 
 - Fixed "Add to Report" functionality in `tm_outliers`, `tm_missing_data` and `tm_g_distribution` modules (#899 and #897).
+- Fixes a bug in `tm_outliers` that fails when data has no join keys (#650).
 
-### Miscellaneous
+### Enhancements
 
+- Improved the layout and appearance of the app using `bslib` components.
 - Fixed deprecation warning for `tern::stack_grobs` in `tm_g_association` (#903).
+- Allow search feature in `tm_file_viewer` (#152).
+- Added `remove_zero_columns` to `tm_t_crosstable` to add an option to remove empty columns (#890)
 
 # 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
 
 ### Enhancements

R/tm_a_pca.R

@@ -47,6 +47,8 @@
 #' To learn more please refer to the vignette
 #' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
+#' @inheritSection teal::example_module Reporting
+#'
 #' @examplesShinylive
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
@@ -234,10 +236,6 @@ ui_a_pca <- function(id, ...) {
         uiOutput(ns("all_plots"))
       ),
       encoding = tags$div(
-        ### Reporter
-        teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
-        tags$br(), tags$br(),
-        ###
         tags$label("Encodings", class = "text-primary"),
         teal.transform::datanames_input(args["dat"]),
         teal.transform::data_extract_ui(
@@ -353,9 +351,7 @@ ui_a_pca <- function(id, ...) {
 }
 
 # Server function for the PCA module
-srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, plot_width, ggplot2_args, decorators) {
-  with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
-  with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, decorators) {
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
@@ -436,9 +432,16 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       selector_list = selector_list,
       datasets = data
     )
-    qenv <- reactive(
-      teal.code::eval_code(data(), 'library("ggplot2");library("dplyr");library("tidyr")') # nolint quotes
-    )
+    qenv <- reactive({
+      obj <- data()
+      teal.reporter::teal_card(obj) <-
+        c(
+          teal.reporter::teal_card("# Principal Component Analysis"),
+          teal.reporter::teal_card(obj),
+          teal.reporter::teal_card("## Module's code")
+        )
+      teal.code::eval_code(obj, 'library("ggplot2");library("dplyr");library("tidyr")') # nolint: quotes
+    })
     anl_merged_q <- reactive({
       req(anl_merged_input())
       qenv() %>%
@@ -514,6 +517,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         )
       )
 
+      teal.reporter::teal_card(qenv) <- c(teal.reporter::teal_card(qenv), "## Principal Components Table")
+
       qenv <- teal.code::eval_code(
         qenv,
         quote({
@@ -522,6 +527,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         })
       )
 
+      teal.reporter::teal_card(qenv) <- c(teal.reporter::teal_card(qenv), "## Eigenvectors Table")
+
       teal.code::eval_code(
         qenv,
         quote({
@@ -602,7 +609,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         ),
         ggtheme = ggtheme
       )
-
+      teal.reporter::teal_card(base_q) <- c(teal.reporter::teal_card(base_q), "## Elbow plot")
       teal.code::eval_code(
         base_q,
         substitute(
@@ -679,6 +686,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         ggtheme = ggtheme
       )
 
+      teal.reporter::teal_card(base_q) <- c(teal.reporter::teal_card(base_q), "## Circle plot")
       teal.code::eval_code(
         base_q,
         substitute(
@@ -737,6 +745,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       size <- input$size
       font_size <- input$font_size
 
+      teal.reporter::teal_card(base_q) <- c(teal.reporter::teal_card(base_q), "## Biplot")
       qenv <- teal.code::eval_code(
         qenv,
         substitute(
@@ -997,6 +1006,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
         parsed_ggplot2_args$theme
       )
 
+      teal.reporter::teal_card(base_q) <- c(teal.reporter::teal_card(base_q), "## Eigenvector plot")
       teal.code::eval_code(
         base_q,
         substitute(
@@ -1038,9 +1048,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
           data = q,
           decorators = select_decorators(decorators, obj_name),
           expr = reactive({
-            substitute(print(.plot), env = list(.plot = as.name(obj_name)))
-          }),
-          expr_is_reactive = TRUE
+            substitute(.plot, env = list(.plot = as.name(obj_name)))
+          })
         )
       },
       names(output_q),
@@ -1071,6 +1080,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       graph_align = "center"
     )
 
+    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)
+
     # tables ----
     output$tbl_importance <- renderTable(
       expr = {
@@ -1132,31 +1143,6 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       verbatim_content = source_code_r,
       title = "R Code for PCA"
     )
-
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "Principal Component Analysis Plot",
-          label = label,
-          with_filter = with_filter,
-          filter_panel_api = filter_panel_api
-        )
-        card$append_text("Principal Components Table", "header3")
-        card$append_table(computation()[["tbl_importance"]])
-        card$append_text("Eigenvectors Table", "header3")
-        card$append_table(computation()[["tbl_eigenvector"]])
-        card$append_text("Plot", "header3")
-        card$append_plot(plot_r(), dim = pws$dim())
-        if (!comment == "") {
-          card$append_text("Comment", "header3")
-          card$append_text(comment)
-        }
-        card$append_src(source_code_r())
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
-    ###
+    decorated_output_dims_q
   })
 }