1298 enhancement/cleanup code quality

.gitignore

@@ -15,4 +15,5 @@ inst/shiny/log/*
 .DS_Store
 # {shinytest2}: Ignore new debug snapshots for `$expect_values()`
 *_.new.png
-desktop.ini
+desktop.ini
+tests/testthat/Rplots.pdf

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: aNCA
 Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9177
+Version: 0.1.0.9178
 Authors@R: c(
     person("Ercan", "Suekuer", email = "ercan.suekuer@roche.com", role = "aut",
            comment = c(ORCID = "0009-0001-1626-1526")),

NEWS.md

@@ -68,6 +68,15 @@
 ### Documentation & UI
 * UI consistency pass: standardized dropdown labels to "Select the...", help button placement to right-aligned, "colour" to "color", renamed Save to "Export as ZIP", simplified download button text, and added "Short Parameter"/"Specimen" columns to Units table (#1333)
 * Searchable PK parameter reference table in NCA > Setup (#1023)
+
+### Code Quality
+* Removed debug `print()` statements from TLG module and replaced with proper logging (#1320)
+* Removed unused `require(magrittr)` and `require(stats)` calls from `app.R` (#1320)
+* Replaced deprecated HTML `align` attributes with inline CSS in TLG module (#1320)
+* Standardized button CSS classes: removed redundant `btn` prefix where duplicate with `btn-*` (#1320)
+* Replaced `label = "Help"` with `tooltip = tooltipOptions(title = "Help")` on all help dropdown buttons for accessibility (#1320)
+* Removed redundant `disabled = FALSE` default from units table actionButton (#1320)
+* Extracted inline hex colors to shared `colors.R` constants and SCSS variables (#1320)
 * R Script Walkthrough vignette added to pkgdown website (#1090)
 * Ratio Calculations vignette documenting all ratio types (#1251)
 * "About" tab with links, citation, authors, license, version, and "Copy session info" button (#1015)
@@ -82,6 +91,7 @@
 * Last dose interval end time extends to last observed sample instead of being cut off at tau (#1235)
 * Interval creation reworked to prevent doses being combined when no post-dose samples exist (#963)
 * DOSNOA computation fixed for specimen-level grouping — urine-only data no longer gets incorrect dose numbering (#1116)
+* `pkcg02` example wrapped in `\donttest{}` to avoid Windows CI timing failure (#1320)
 * Dose-aware AUCint parameters now share the same PPTESTCD as their non-dose-aware counterparts in CDISC exports, with `PPANMETH` indicating the analytical method. Internal PPTESTCDs renamed from misleading `D` suffix (e.g. `AUCINTD`) to lowercase `da` suffix (e.g. `AUCINTda`). Fixed wrong PPTEST label for `AUCINTD` which said "Normalized by Dose" (#1242)
 * Optional settings (`slope_rules`, `int_parameters`, `ratio_table`) are now normalized to `NULL` when empty, instead of persisting as 0-row data frames throughout the app and settings pipeline (#1262)
 * Interval-specific parameters (`aucint.*`, `cav.int.*`) excluded from the Parameter Selection matrix — they require finite sub-intervals and must be configured via Partial Interval Calculations (#1309)

R/g_pkcg.R

@@ -393,6 +393,7 @@ g_pkcg02_log <- function(data, ...) {
 #' @importFrom stats setNames
 
 #' @examples
+#' \donttest{
 #' # Make an example small dataset
 #' adnca <- adnca_example
 #' adnca <- adnca[adnca$USUBJID %in% unique(adnca$USUBJID)[c(1, 2)],]
@@ -403,7 +404,7 @@ g_pkcg02_log <- function(data, ...) {
 #' plots <- pkcg02(adnca)
 #' plots_log <- pkcg02(adnca, scale = "LOG")
 #' plotly::plotly_build(plots[[1]]) # View the first plot
-#'
+#' }
 #' @export
 #' @author Kezia Kobana
 pkcg02 <- function(

inst/WORDLIST

@@ -115,6 +115,7 @@ RefParameter
 Req
 Roadmap
 SBS
+SCSS
 SDTM
 SDTMIG
 SMS
@@ -144,6 +145,7 @@ Walkthrough
 XPT
 YAML
 aNCA's
+actionButton
 adnca
 analysing
 analyte

inst/shiny/app.R

@@ -5,7 +5,6 @@ require(dplyr)
 require(htmlwidgets)
 require(logger)
 require(formatters)
-require(magrittr)
 require(plotly)
 require(purrr)
 require(reactable)
@@ -15,7 +14,6 @@ require(shinycssloaders)
 require(shinyjs)
 require(shinyjqui)
 require(shinyWidgets)
-require(stats)
 
 require(tidyr)
 require(tools)

inst/shiny/functions/colors.R

@@ -0,0 +1,26 @@
+# Color constants — keep in sync with inst/shiny/www/styles/modules/_colors.scss
+# See https://github.com/pharmaverse/aNCA/issues/1298
+
+# Backgrounds
+BG_GREY_LIGHT     <- "#eeeeee"
+BG_GREY_HEADER    <- "#e9e9e9"
+BG_HIGHLIGHT_BLUE <- "#CCE5FF"
+BG_BLUE_LIGHT     <- "#e6f2ff"
+ANCA_WHITE        <- "#ffffff"
+
+# Text
+TEXT_MUTED        <- "#999999"
+TEXT_DIM          <- "#888888"
+TEXT_SUBTLE       <- "#777777"
+TEXT_SECONDARY    <- "#666666"
+TEXT_HEADING      <- "#555555"
+
+# Borders
+BORDER_LIGHT      <- "#dddddd"
+BORDER_MUTED      <- "#cccccc"
+BORDER_PANEL      <- "#dee2e6"
+
+# Accent
+ACCENT_BLUE       <- "#0d6efd"
+ACCENT_ORANGE     <- "#ffa62d"
+ACCENT_DANGER     <- "#dc3545"

inst/shiny/functions/utils-exclusions.R

@@ -9,9 +9,9 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
 .legend_swatch <- function(color, label) {
   div(
     style = "display:flex; align-items:center; gap:6px;",
-    div(style = paste0(
-      "width:14px; height:14px; background:", color,
-      "; border:1px solid #ddd;"
+    div(style = glue::glue(
+      "width:14px; height:14px; background:{color}",
+      "; border:1px solid {BORDER_LIGHT};"
     )),
     span(label, style = "font-size:0.9em;")
   )
@@ -167,7 +167,8 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
             ns(value),
             label = NULL,
             icon = shiny::icon("times"),
-            class = "btn btn-link btn-sm",
+            `aria-label` = "Remove exclusion",
+            class = "btn-link btn-sm",
             style = "padding:2px 6px;"
           )
         )
@@ -196,7 +197,7 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
     pagination = FALSE,
     defaultPageSize = nrow(df),
     theme = reactable::reactableTheme(
-      headerStyle = list(background = "#e9e9e9")
+      headerStyle = list(background = BG_GREY_HEADER)
     ),
     columns = cols
   )

inst/shiny/modules/tab_about.R

@@ -154,7 +154,9 @@ tab_about_server <- function(id) {
         }
       )
       tags$blockquote(
-        style = "border-left: 3px solid #ccc; padding-left: 1em; color: #555;",
+        style = glue::glue(
+          "border-left: 3px solid {BORDER_MUTED}; padding-left: 1em; color: {TEXT_HEADING};"
+        ),
         tags$p(cit_text)
       )
     })
@@ -163,7 +165,9 @@ tab_about_server <- function(id) {
       cit <- utils::citation("PKNCA")
       cit_text <- paste(format(cit, style = "text"), collapse = "\n\n")
       tags$blockquote(
-        style = "border-left: 3px solid #ccc; padding-left: 1em; color: #555;",
+        style = glue::glue(
+          "border-left: 3px solid {BORDER_MUTED}; padding-left: 1em; color: {TEXT_HEADING};"
+        ),
         tags$p(cit_text)
       )
     })
@@ -255,7 +259,7 @@ tab_about_server <- function(id) {
     style = "margin-bottom: 0.3em;",
     tags$a(href = url, target = "_blank", label),
     tags$span(
-      style = "color: #999; font-size: 0.85em; margin-left: 0.5em;",
+      style = glue::glue("color: {TEXT_MUTED}; font-size: 0.85em; margin-left: 0.5em;"),
       url
     )
   )

inst/shiny/modules/tab_data/data_mapping.R

@@ -535,7 +535,7 @@ data_mapping_server <- function(id, adnca_data, imported_mapping, trigger) {
           if (dup_data[index, ".dup_group"] %% 2 == 0) {
             list(background = "white")
           } else {
-            list(background = "#e6f2ff")
+            list(background = BG_BLUE_LIGHT)
           }
         },
         selection = "multiple",

inst/shiny/modules/tab_data/data_upload.R

@@ -225,8 +225,8 @@ data_upload_server <- function(id) {
     defaultPageSize = 10,
     theme = reactableTheme(
       rowSelectedStyle = list(
-        backgroundColor = "#CCE5FF",
-        boxShadow = "inset 2px 0 0 0 #0d6efd"
+        backgroundColor = BG_HIGHLIGHT_BLUE,
+        boxShadow = paste0("inset 2px 0 0 0 ", ACCENT_BLUE)
       )
     ),
     columns = list(

inst/shiny/modules/tab_explore.R

@@ -219,7 +219,7 @@ tab_explore_server <- function(id, pknca_data, extra_group_vars) {
         footer = tagList(
           modalButton("Cancel"),
           actionButton(ns("confirm_add_to_exports"), "Save",
-                       class = "btn btn-primary")
+                       class = "btn-primary")
         ),
         size = "s",
         easyClose = TRUE

inst/shiny/modules/tab_explore/plot_sidebar.R

@@ -17,7 +17,7 @@ plot_sidebar_ui <- function(id, is_mean_plot = FALSE, extra_ui = NULL) {
       ns("add_to_exports"),
       label = "Add to Exports",
       icon = icon("plus"),
-      class = "btn btn-primary btn-sm",
+      class = "btn-primary btn-sm",
       width = "100%"
     ),
     extra_ui,

inst/shiny/modules/tab_explore/qc_plot.R

@@ -23,7 +23,7 @@ pk_dose_qc_plot_ui <- function(id, extra_ui = NULL) {
         ns("add_to_exports"),
         label = "Add to Exports",
         icon = icon("plus"),
-        class = "btn btn-primary btn-sm",
+        class = "btn-primary btn-sm",
         width = "100%"
       ),
       extra_ui,

inst/shiny/modules/tab_explore/saved_outputs.R

@@ -59,7 +59,7 @@ saved_outputs_ui <- function(id) {
     ns("view_exports"),
     label = "View Exports",
     icon = icon("eye"),
-    class = "btn btn-primary btn-sm",
+    class = "btn-primary btn-sm",
     width = "100%"
   )
 }
@@ -168,7 +168,7 @@ saved_outputs_server <- function(id, saved_plots_metadata, get_plot_obj,
           "No plots saved yet. Use ",
           tags$strong("Add to Exports"),
           " to save plots.",
-          style = "color: #888; font-style: italic; margin: 16px 0;"
+          style = glue::glue("color: {TEXT_DIM}; font-style: italic; margin: 16px 0;")
         ))
       }
 
@@ -186,9 +186,9 @@ saved_outputs_server <- function(id, saved_plots_metadata, get_plot_obj,
         )
 
         tags$div(
-          style = paste0(
-            "border: 1px solid #dee2e6; border-radius: 6px; ",
-            "padding: 12px; margin-bottom: 16px; background: #fff;"
+          style = glue::glue(
+            "border: 1px solid {BORDER_PANEL}; border-radius: 6px; ",
+            "padding: 12px; margin-bottom: 16px; background: {ANCA_WHITE};"
           ),
           tags$div(
             style = paste0(
@@ -199,16 +199,17 @@ saved_outputs_server <- function(id, saved_plots_metadata, get_plot_obj,
               tags$strong(plot_name, style = "font-size: 1.1em;"),
               tags$span(
                 paste0(" \u2014 ", plot_type, " \u00b7 ", plot_ts),
-                style = "color: #666; font-size: 0.9em;"
+                style = glue::glue("color: {TEXT_SECONDARY}; font-size: 0.9em;")
               )
             ),
             tags$a(
               href = "#",
               onclick = paste0(remove_js, "return false;"),
-              style = paste0(
-                "color: #dc3545; font-size: 1.2em; ",
+              style = glue::glue(
+                "color: {ACCENT_DANGER}; font-size: 1.2em; ",
                 "text-decoration: none;"
               ),
+              `aria-label` = "Remove from exports",
               title = "Remove from exports",
               icon("times")
             )

inst/shiny/modules/tab_nca.R

@@ -32,7 +32,7 @@ tab_nca_ui <- function(id) {
         inputId = ns("run_nca"),
         label = "Run NCA",
         icon = icon("play"),
-        class = "btn btn-primary",
+        class = "btn-primary",
         width = "100%"
       ),
       nca_setup_ui(ns("nca_setup")),

inst/shiny/modules/tab_nca/excretion_analysis.R

@@ -273,7 +273,7 @@ excretion_help_ui <- function() {
       )
     ),
     style = "unite",
-    icon = icon("question"),
+    icon = icon("question"), tooltip = tooltipOptions(title = "Help"),
     status = "primary"
   )
 }

inst/shiny/modules/tab_nca/nca_results.R

@@ -33,7 +33,9 @@ nca_results_ui <- function(id) {
         span("MISSING", style = "font-size:0.9em;")
       ),
       div(style = "display:flex; align-items:center; gap:6px;",
-        div(style = "width:14px; height:14px; background:#ffffff; border:1px solid #ddd;"),
+        div(style = glue::glue(
+          "width:14px; height:14px; background:{ANCA_WHITE}; border:1px solid {BORDER_LIGHT};"
+        )),
         span("ACCEPTED", style = "font-size:0.9em;")
       )
     ),

inst/shiny/modules/tab_nca/non_nca_ratios.R

@@ -127,7 +127,10 @@ non_nca_ratio_server <- function(id, data, grouping_vars) {
         ),
         div(
           class = "ratio-remove-btn-wrapper",
-          actionButton(ns(paste0("remove_", count)), "", icon = icon("trash-alt"))
+          actionButton(
+            ns(paste0("remove_", count)), "",
+            `aria-label` = "Remove ratio pair", icon = icon("trash-alt")
+          )
         )
       )
 
@@ -243,7 +246,7 @@ non_nca_ratio_help_ui <- function(title) {
     ),
     style = "unite",
     placement = "left",
-    icon = icon("question"),
+    icon = icon("question"), tooltip = tooltipOptions(title = "Help"),
     status = "primary"
   )
 }

inst/shiny/modules/tab_nca/setup/data_imputation.R

@@ -53,7 +53,7 @@ data_imputation_ui <- function(id) {
           ),
           style = "unite",
           right = TRUE,
-          icon = icon("question"),
+          icon = icon("question"), tooltip = tooltipOptions(title = "Help"),
           status = "primary",
           width = "500px"
         )
@@ -123,7 +123,7 @@ data_imputation_ui <- function(id) {
           ),
           style = "unite",
           right = TRUE,
-          icon = icon("question"),
+          icon = icon("question"), tooltip = tooltipOptions(title = "Help"),
           status = "primary",
           width = "500px"
         )