Merge branch 'use_evaluate' into teal_reportable

Author: gogonzo

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9009
+    rev: v0.4.3.9011
     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: 0.4.1.9003
-Date: 2025-06-04
+Version: 0.4.1.9005
+Date: 2025-06-23
 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 (>= 1.6.0),
-    teal (>= 0.16.0.9002),
-    teal.transform (>= 0.6.0)
+    teal (>= 0.16.0.9008),
+    teal.transform (>= 0.6.0.9002)
 Imports:
     bslib (>= 0.8.0),
     checkmate (>= 2.1.0),
@@ -38,7 +38,7 @@ 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),
@@ -60,9 +60,9 @@ Imports:
     stringr (>= 1.4.1),
     teal.code (>= 0.6.1),
     teal.data (>= 0.7.0),
-    teal.logger (>= 0.3.2),
+    teal.logger (>= 0.3.2.9001),
     teal.reporter (>= 0.4.0.9004),
-    teal.widgets (>= 0.4.3.9001),
+    teal.widgets (>= 0.4.3.9005),
     tern (>= 0.9.7),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
@@ -84,7 +84,9 @@ VignetteBuilder:
     knitr,
     rmarkdown
 Remotes:
+    insightsengineering/teal.logger@main,
     insightsengineering/teal.reporter@main,
+    insightsengineering/teal.transform@main,
     insightsengineering/teal.widgets@main,
     insightsengineering/teal@main
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.general 0.4.1.9003
+# teal.modules.general 0.4.1.9005
 
 # teal.modules.general 0.4.1
 

R/tm_a_pca.R

@@ -517,8 +517,7 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
         quote({
           tbl_importance <- dplyr::as_tibble(pca$importance, rownames = "Metric")
           tbl_importance
-        }),
-        keep_output = "tbl_importance"
+        })
       )
 
       teal.reporter::teal_card(qenv) <- append(teal.reporter::teal_card(qenv), "## Eigenvectors Table")
@@ -528,8 +527,7 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
         quote({
           tbl_eigenvector <- dplyr::as_tibble(pca$rotation, rownames = "Variable")
           tbl_eigenvector
-        }),
-        keep_output = "tbl_eigenvector"
+        })
       )
     })
 
@@ -1044,8 +1042,7 @@ srv_a_pca <- function(id, data, dat, plot_height, plot_width, ggplot2_args, deco
           decorators = select_decorators(decorators, obj_name),
           expr = reactive({
             substitute(.plot, env = list(.plot = as.name(obj_name)))
-          }),
-          keep_output = obj_name
+          })
         )
       },
       names(output_q),

R/tm_a_regression.R

@@ -536,7 +536,7 @@ srv_a_regression <- function(id,
         teal.code::eval_code(quote({
           fit_summary <- summary(fit)
           fit_summary
-        }), keep_output = "fit_summary")
+        }))
       teal.reporter::teal_card(anl_fit) <- append(teal.reporter::teal_card(anl_fit), "## Plot")
       anl_fit
     })
@@ -1000,8 +1000,7 @@ srv_a_regression <- function(id,
       "decorator",
       data = output_q,
       decorators = select_decorators(decorators, "plot"),
-      expr = quote(plot),
-      keep_output = "plot"
+      expr = quote(plot)
     )
 
     fitted <- reactive({
@@ -1024,9 +1023,7 @@ 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.

R/tm_g_association.R

@@ -492,7 +492,7 @@ srv_tm_g_association <- function(id,
             )
           )
         }
-      obj <-  merged$anl_q_r()
+      obj <- merged$anl_q_r()
       teal.reporter::teal_card(obj) <- append(teal.reporter::teal_card(obj), "## Plot")
       teal.code::eval_code(
         obj,
@@ -522,8 +522,7 @@ srv_tm_g_association <- function(id,
       id = "decorator",
       data = output_q,
       decorators = select_decorators(decorators, "plot"),
-      expr = quote(plot),
-      keep_output = "plot"
+      expr = quote(plot)
     )
 
     plot_r <- reactive({
@@ -538,9 +537,7 @@ srv_tm_g_association <- function(id,
       width = plot_width
     )
 
-    output$title <- renderText({
-      teal.code::dev_suppress(output_q()[["title"]])
-    })
+    output$title <- renderText(output_q()[["title"]])
 
     # Render R code.
     source_code_r <- reactive(teal.code::get_code(req(decorated_output_grob_q())))

R/tm_g_bivariate.R

@@ -553,16 +553,17 @@ srv_g_bivariate <- function(id,
       selector_list = selector_list,
       datasets = data
     )
-    qenv <- reactive({
-      obj <- data()
-      teal.reporter::teal_card(obj) <- append(teal.reporter::teal_card(obj), "# Bivariate Plot", after = 0)
-      teal.code::eval_code(obj, 'library("ggplot2");library("dplyr");library("teal.modules.general")') # nolint quotes
-    })
 
     anl_merged_q <- reactive({
-      req(anl_merged_input())
-      qenv() %>%
-        teal.code::eval_code(as.expression(anl_merged_input()$expr))
+      obj <- data()
+      teal.reporter::teal_card(obj) <- append(teal.reporter::teal_card(obj), "# Bivariate Plot", after = 0)
+      obj |>
+        teal.code::eval_code(
+          c(
+            expression(library(ggplot2), library(dplyr), library(teal.modules.general)),
+            as.expression(anl_merged_input()$expr)
+          )
+        )
     })
 
     merged <- list(
@@ -728,8 +729,7 @@ srv_g_bivariate <- function(id,
           )
         }
         print_call
-      }),
-      keep_output = "plot"
+      })
     )
 
     plot_r <- reactive(req(decorated_output_q_facets())[["plot"]])

R/tm_g_distribution.R

@@ -637,7 +637,7 @@ srv_distribution <- function(id,
 
       obj <- merged$anl_q_r()
       teal.reporter::teal_card(obj) <- append(teal.reporter::teal_card(obj), "# Distribution Plot", after = 0)
-      
+
       ANL <- obj[["ANL"]]
       dist_var <- merge_vars()$dist_var
       s_var <- merge_vars()$s_var
@@ -1297,32 +1297,28 @@ srv_distribution <- function(id,
       "d_density",
       data = output_dist_q,
       decorators = select_decorators(decorators, "histogram_plot"),
-      expr = quote(histogram_plot),
-      keep_output = "histogram_plot"
+      expr = quote(histogram_plot)
     )
 
     decorated_output_qq_q <- srv_decorate_teal_data(
       "d_qq",
       data = output_qq_q,
       decorators = select_decorators(decorators, "qq_plot"),
-      expr = quote(qq_plot),
-      keep_output = "qq_plot"
+      expr = quote(qq_plot)
     )
 
     decorated_output_summary_q <- srv_decorate_teal_data(
       "d_summary",
       data = output_summary_q,
       decorators = select_decorators(decorators, "summary_table"),
-      expr = quote(summary_table),
-      keep_output = "summary_table"
+      expr = quote(summary_table)
     )
 
     decorated_output_test_q <- srv_decorate_teal_data(
       "d_test",
       data = output_test_q,
       decorators = select_decorators(decorators, "test_table"),
-      expr = quote(test_table),
-      keep_output = "test_table"
+      expr = quote(test_table)
     )
 
     decorated_output_q <- reactive({

R/tm_g_response.R

@@ -576,8 +576,7 @@ srv_g_response <- function(id,
       id = "decorator",
       data = output_q,
       decorators = select_decorators(decorators, "plot"),
-      expr = quote(plot),
-      keep_output = "plot"
+      expr = quote(plot)
     )
 
     plot_r <- reactive(req(decorated_output_plot_q())[["plot"]])

R/tm_g_scatterplot.R

@@ -372,7 +372,7 @@ ui_g_scatterplot <- function(id, ...) {
         DT::dataTableOutput(ns("data_table"), width = "100%")
       ),
       encoding = tags$div(
-          tags$label("Encodings", class = "text-primary"),
+        tags$label("Encodings", class = "text-primary"),
         teal.transform::datanames_input(args[c("x", "y", "color_by", "size_by", "row_facet", "col_facet")]),
         teal.transform::data_extract_ui(
           id = ns("x"),
@@ -1020,8 +1020,7 @@ srv_g_scatterplot <- function(id,
       id = "decorator",
       data = output_q,
       decorators = select_decorators(decorators, "plot"),
-      expr = quote(plot),
-      keep_output = "plot"
+      expr = quote(plot)
     )
 
     plot_r <- reactive(req(decorated_output_plot_q())[["plot"]])
@@ -1042,7 +1041,7 @@ srv_g_scatterplot <- function(id,
         validate(need(!input$add_density, "Brushing feature is currently not supported when plot has marginal density"))
       }
 
-      merged_data <- isolate(teal.code::dev_suppress(output_q()[["ANL"]]))
+      merged_data <- isolate(output_q()[["ANL"]])
 
       brushed_df <- teal.widgets::clean_brushedPoints(merged_data, plot_brush)
       numeric_cols <- names(brushed_df)[