Merge branch 'main' into redesign_extraction@main

Author: gogonzo

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9014
+    rev: v0.4.3.9015
     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: 0.5.0.9003
-Date: 2025-09-23
+Version: 0.5.0.9005
+Date: 2025-10-07
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,8 @@
-# teal.modules.general 0.5.0.9003
+# teal.modules.general 0.5.0.9005
+
+### Enhancements
+
+- Modules now return a `teal_report` object that contains the data, code and reporter. All the reporter buttons were removed from the modules' UI.
 
 # teal.modules.general 0.5.0
 

R/tm_a_pca.R

@@ -351,9 +351,6 @@ ui_a_pca.default <- function(id, ...) {
           )
         )
       ),
-      forms = tagList(
-        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-      ),
       pre_output = args$pre_output,
       post_output = args$post_output
     )
@@ -1090,8 +1087,6 @@ srv_a_pca.default <- function(id, data, dat, plot_height, plot_width, ggplot2_ar
       graph_align = "center"
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)
-
     # tables ----
     output$tbl_importance <- renderTable(
       expr = {
@@ -1145,14 +1140,6 @@ srv_a_pca.default <- function(id, data, dat, plot_height, plot_width, ggplot2_ar
       )
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R Code for PCA"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q)
   })
 }

R/tm_a_regression.R

@@ -374,9 +374,6 @@ ui_a_regression.default <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -1021,22 +1018,12 @@ srv_a_regression.default <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q)
-
     output$text <- renderText({
       req(iv_r()$is_valid())
       req(iv_out$is_valid())
       paste(utils::capture.output(summary(fitted()))[-1], collapse = "\n")
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R code for the regression plot",
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q)
   })
 }

R/tm_g_association.R

@@ -307,9 +307,6 @@ ui_tm_g_association.default <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -563,18 +560,8 @@ srv_tm_g_association.default <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_grob_q)
-
     output$title <- renderText(output_q()[["title"]])
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Association Plot"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_grob_q)
   })
 }

R/tm_g_bivariate.R

@@ -464,9 +464,6 @@ ui_g_bivariate.default <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -739,18 +736,7 @@ srv_g_bivariate.default <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_q_facets)
-
-    # Render R code.
-
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Bivariate Plot"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_q_facets)
   })
 }
 

R/tm_g_distribution.R

@@ -381,9 +381,6 @@ ui_g_distribution.default <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -1276,13 +1273,13 @@ srv_g_distribution.default <- function(id,
     output_dist_q <- reactive(c(common_q(), req(dist_q())))
     output_qq_q <- reactive(c(common_q(), req(qq_q())))
 
-    # Summary table listing has to be created separately to allow for qenv join
-    q_common <- common_q()
-    teal.reporter::teal_card(q_common) <- c(
-      teal.reporter::teal_card(q_common),
-      "## Statistics table"
-    )
     output_summary_q <- reactive({
+      # Summary table listing has to be created separately to allow for qenv join
+      q_common <- common_q()
+      teal.reporter::teal_card(q_common) <- c(
+        teal.reporter::teal_card(q_common),
+        "## Statistics table"
+      )
       if (iv_r()$is_valid()) {
         within(q_common, {
           summary_table <- rtables::df_to_tt(summary_table_data)
@@ -1362,7 +1359,7 @@ srv_g_distribution.default <- function(id,
     output$summary_table <- DT::renderDataTable(summary_r())
 
     tests_r <- reactive({
-      q <- req(output_test_q())
+      q <- req(decorated_output_test_q())
       DT::datatable(q[["test_table_data"]])
     })
 
@@ -1388,7 +1385,7 @@ srv_g_distribution.default <- function(id,
 
     decorated_output_q <- reactive({
       tab <- req(input$tabs) # tab is NULL upon app launch, hence will crash without this statement
-      test_q_out <- output_test_q()
+      test_q_out <- decorated_output_test_q()
 
       out_q <- switch(tab,
         Histogram = decorated_output_dist_dims_q(),
@@ -1406,14 +1403,6 @@ srv_g_distribution.default <- function(id,
 
     output$t_stats <- DT::renderDataTable(tests_r())
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R Code for distribution"
-    )
     decorated_output_q
   })
 }

R/tm_g_response.R

@@ -344,9 +344,6 @@ ui_g_response.default <- function(id, ...) {
         )
       )
     ),
-    forms = tagList(
-      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-    ),
     pre_output = args$pre_output,
     post_output = args$post_output
   )
@@ -618,16 +615,6 @@ srv_g_response.default <- function(id,
       width = plot_width
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_plot_q)
-
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "Show R Code for Response"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_plot_q)
   })
 }

R/tm_g_scatterplot.R

@@ -466,9 +466,6 @@ ui_g_scatterplot.default <- function(id, ...) {
           )
         )
       ),
-      forms = tagList(
-        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
-      ),
       pre_output = args$pre_output,
       post_output = args$post_output
     )
@@ -1009,8 +1006,6 @@ srv_g_scatterplot.default <- function(id,
       click = TRUE
     )
 
-    decorated_output_dims_q <- set_chunk_dims(pws, decorated_output_plot_q)
-
     output$data_table <- DT::renderDataTable({
       plot_brush <- pws$brush()
 
@@ -1039,14 +1034,6 @@ srv_g_scatterplot.default <- function(id,
       }
     })
 
-    # Render R code.
-    source_code_r <- reactive(teal.code::get_code(req(decorated_output_dims_q())))
-
-    teal.widgets::verbatim_popup_srv(
-      id = "rcode",
-      verbatim_content = source_code_r,
-      title = "R Code for scatterplot"
-    )
-    decorated_output_dims_q
+    set_chunk_dims(pws, decorated_output_plot_q)
   })
 }