Close leftover panel tabsets when knitr chunks error

CHANGELOG.md

@@ -8,6 +8,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- Unclosed Quarto panel tabsets after a knitr chunk error no longer break later report sections. `open_tabset()` tracks depth, and `register_tabset_chunk_hooks()` closes leftover fences when a chunk fails.
+
 ### Changed
 
 - Colocalization heatmap text now explains that proteins are selected by mean abundance (up to 40 markers), globally across samples or within each cell type.

DEVELOPERS.md

@@ -333,6 +333,8 @@ Tab UI is created with Quarto fenced divs:
 
 The `tabset_*` helpers write these divs for you. Tab titles come from markdown headings (`#` level set by the `level` argument). Use `level` consistently within a section so tab nesting matches the surrounding heading hierarchy (e.g. `level = 5` under a `####` markdown heading).
 
+Report setup calls `register_tabset_chunk_hooks()`. If a knitr chunk errors after `open_tabset()` or a `tabset_*` helper has written an opening fence, the hook appends the missing `:::` so later sections still parse. In `.qmd` chunks, call `open_tabset()` instead of writing the opening fence with `cat()`. Markdown tabsets written outside R chunks are unchanged.
+
 ### `tabset_plotlist()`
 
 Renders a **named list of plots** as a tabset — one tab per plot.
@@ -409,10 +411,10 @@ Often used inside a manually opened tabset:
 
 ```r
 #| results: 'asis'
-cat("::: {.panel-tabset .nav-pills}\n")
+open_tabset()
 section_table(key_tables$pool, "Hash pool metrics", 3)
 section_table(key_tables$sample, "Sample metrics", 3)
-cat(":::\n")
+close_tabset()
 ```
 
 ### `style_table()`

NAMESPACE

@@ -65,6 +65,7 @@ export(merge_cell_types)
 export(merge_data)
 export(merged_cell_types)
 export(order_cd_markers)
+export(open_tabset)
 export(order_sample_alias_factors)
 export(plot_embedding)
 export(plot_embeddings_samplewise)
@@ -80,6 +81,7 @@ export(process_data)
 export(read_qc_files)
 export(read_samplesheet)
 export(register_es_data_workflow)
+export(register_tabset_chunk_hooks)
 export(run_abundance_anova)
 export(run_proximity_anova)
 export(section_intro)

R/plot_helpers.R

@@ -5,6 +5,134 @@ plot_anchor_slug <- function(...) {
   gsub("^-+|-+$", "", x)
 }
 
+.tabset_state <- new.env(parent = emptyenv())
+.tabset_state$depth <- 0L
+.tabset_state$stack <- integer(0)
+
+#' Reset tracked Quarto tabset depth
+#'
+#' Intended for tests. Report rendering resets state when
+#' [register_tabset_chunk_hooks()] is called.
+#'
+#' @return `NULL`, invisibly.
+#'
+#' @noRd
+reset_tabset_state <- function() {
+  .tabset_state$depth <- 0L
+  .tabset_state$stack <- integer(0)
+  invisible(NULL)
+}
+
+#' Current number of opened tabsets that have not been closed
+#'
+#' @return Integer depth.
+#'
+#' @noRd
+tabset_depth <- function() {
+  .tabset_state$depth
+}
+
+#' Markdown fences that close leftover tabsets down to a depth
+#'
+#' Updates the tracked depth. Does not print; callers that run during knitr
+#' chunk evaluation should `cat()` the result, while knitr output hooks should
+#' return it so it is appended to the chunk markdown.
+#'
+#' @param until Integer depth to restore. Tabsets opened above this depth are
+#'   closed.
+#'
+#' @return A string of `:::` fences, or `""` when nothing is unclosed.
+#'
+#' @noRd
+unclosed_tabset_fences <- function(until = 0L) {
+  until <- as.integer(until)
+  if (length(until) != 1L || is.na(until) || until < 0L) {
+    until <- 0L
+  }
+
+  n <- .tabset_state$depth - until
+  if (n <= 0L) {
+    return("")
+  }
+
+  .tabset_state$depth <- until
+  paste(rep(":::", n), collapse = "\n")
+}
+
+#' Open a Quarto panel tabset
+#'
+#' Emits the fenced div that starts a `{.panel-tabset}` and records it so
+#' leftover tabsets can be closed if a knitr chunk errors. Prefer this over
+#' writing the fence with `cat()` in `.qmd` files.
+#'
+#' @return The new tabset depth, invisibly.
+#'
+#' @export
+open_tabset <- function() {
+  cat("::: {.panel-tabset .nav-pills}\n")
+  .tabset_state$depth <- .tabset_state$depth + 1L
+  invisible(.tabset_state$depth)
+}
+
+#' Close Tabset
+#'
+#' Closes a tabset opened with [open_tabset()] or [tabset_figure_table()].
+#' Does nothing when no tracked tabset is open.
+#'
+#' @return The remaining tabset depth, invisibly.
+#'
+#' @export
+close_tabset <- function() {
+  fence <- unclosed_tabset_fences(until = max(0L, .tabset_state$depth - 1L))
+  if (nzchar(fence)) {
+    cat(fence, "\n", sep = "")
+  }
+  invisible(.tabset_state$depth)
+}
+
+#' Register knitr hooks that close leftover panel tabsets
+#'
+#' When Quarto is run with `execute: error: true`, a chunk can fail after
+#' [open_tabset()] (or a `tabset_*` helper) has written an opening fence.
+#' This hook restores the tabset depth from the start of the chunk by appending
+#' the missing `:::` fences so later sections of the report still parse.
+#'
+#' Call once during report setup (see `inst/quarto/shared/preprocessing.qmd`).
+#'
+#' @return `NULL`, invisibly.
+#'
+#' @export
+register_tabset_chunk_hooks <- function() {
+  reset_tabset_state()
+  knitr::opts_chunk$set(pixelatorES_tabset_guard = TRUE)
+  knitr::knit_hooks$set(
+    pixelatorES_tabset_guard = function(before, options, envir) {
+      if (before) {
+        .tabset_state$stack <- c(.tabset_state$stack, .tabset_state$depth)
+        return(NULL)
+      }
+
+      n_stack <- length(.tabset_state$stack)
+      start <- if (n_stack > 0L) {
+        .tabset_state$stack[[n_stack]]
+      } else {
+        0L
+      }
+      if (n_stack > 0L) {
+        .tabset_state$stack <- .tabset_state$stack[-n_stack]
+      }
+
+      fences <- unclosed_tabset_fences(until = start)
+      if (!nzchar(fences)) {
+        return(NULL)
+      }
+
+      paste0("\n\n", fences, "\n\n")
+    }
+  )
+  invisible(NULL)
+}
+
 resolve_anchor_prefix <- function(anchor_prefix = NULL) {
   if (is.null(anchor_prefix)) {
     label <- knitr::opts_current$get("label")
@@ -89,13 +217,12 @@ tabset_plotlist <-
 
     prefix <- resolve_anchor_prefix(anchor_prefix)
 
-    # Start the tabset
-    cat("::: {.panel-tabset .nav-pills}\n")
+    open_tabset()
+    if (close) {
+      on.exit(close_tabset(), add = TRUE)
+    }
 
     title_plotlist(plots, level, anchor_prefix = prefix)
-
-    # Close the tabset
-    if (close) cat(":::\n")
   }
 
 
@@ -133,9 +260,11 @@ tabset_nested_plotlist <-
 
     prefix <- resolve_anchor_prefix(anchor_prefix)
 
-    # Start the tabset
     cat("\n\n")
-    cat("::: {.panel-tabset .nav-pills}\n")
+    open_tabset()
+    if (close) {
+      on.exit(close_tabset(), add = TRUE)
+    }
 
     for (tab in seq_along(plots)) {
       if (inherits(plots[[tab]], "list")) {
@@ -163,15 +292,14 @@ tabset_nested_plotlist <-
         )
       }
     }
-    # Close the tabset
-    if (close) cat(":::\n")
   }
 
 
 #' Tabset a figure and a table
 #'
 #' Tabset a figure and a table at a given header level. After using this
-#' function, you should close the tabset with `close_tabset()`.
+#' function, you should close the tabset with [close_tabset()]. If the chunk
+#' errors before that call, [register_tabset_chunk_hooks()] closes the fence.
 #'
 #' @param figure A ggplot object representing the figure to be tabsetted or a list of ggplot objects to be tabsetted as
 #' nested tabs.
@@ -194,8 +322,7 @@ tabset_figure_table <- function(figure, table, level = 2,
       title = title_plotlist
     )
 
-  # Start the tabset
-  cat("::: {.panel-tabset .nav-pills}\n")
+  open_tabset()
 
   cat(paste0(strrep("#", level), " Figure\n\n"))
 
@@ -211,19 +338,6 @@ tabset_figure_table <- function(figure, table, level = 2,
   return(table)
 }
 
-#' Close Tabset
-#'
-#' Closes the tabset that was opened with `tabset_figure_table`.
-#'
-#' @return Nothing.
-#'
-#' @export
-#'
-close_tabset <-
-  function() {
-    cat(":::\n")
-  }
-
 #' Create a Void Plot
 #'
 #' Creates a ggplot object with no data and a void theme.

inst/quarto/pixelatorES.qmd

@@ -22,6 +22,7 @@ params:
 #| include: false
 
 library(pixelatorES)
+register_tabset_chunk_hooks()
 report <- get_es_workflow_report(params$workflow)
 ```
 
@@ -41,12 +42,12 @@ for (child in report$preamble) {
 #| echo: false
 
 cat("\n# \n\n")
-cat("::: {.panel-tabset .nav-pills}\n\n")
+open_tabset()
 for (section in report$sections) {
   # Two newlines so the heading starts a new block even when the preceding
   # child ends with a list or paragraph
   cat("\n\n## ", section$title, "\n\n", sep = "")
   cat(knitr::knit_child(section$child, quiet = TRUE))
 }
-cat("\n:::\n")
+close_tabset()
 ```

inst/quarto/shared/preprocessing.qmd

@@ -24,6 +24,9 @@ library(knitr)
 
 # Hook to convert PNG -> WebP after each plot is saved
 knit_hooks$set(plot = convert_png_to_webp)
+
+# Close leftover panel-tabset fences when a chunk errors
+register_tabset_chunk_hooks()
 ```
 
 ```{r}

inst/quarto/workflows/amplicon_demux/quality_metrics.qmd

@@ -19,14 +19,14 @@ eval_standard_key_metrics <-
 #| label: key_metrics_pool
 #| eval: !expr eval_hashed_key_metrics
 #| results: 'asis'
-cat("::: {.panel-tabset .nav-pills}\n")
+open_tabset()
 if (!is.null(key_tables$pool)) {
   section_table(key_tables$pool, "Hash pool metrics", 3)
 }
 if (!is.null(key_tables$sample)) {
   section_table(key_tables$sample, "Sample metrics", 3)
 }
-cat(":::\n")
+close_tabset()
 ```
 
 ```{r}