From 030a6c0b19ad31a2a9b37420c4a3415c3eebe242 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Thu, 28 May 2026 16:14:35 -0400
Subject: [PATCH 1/2] Create function that checks for duplicated chunk labels
 in fig/table docs, and if present, comments out duplicates (as per
 https://github.com/nmfs-ost/asar/issues/451)

---
 R/create_figures_doc.R | 41 +++++------------
 R/create_tables_doc.R  | 42 +++++-------------
 R/utils.R              | 99 ++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 122 insertions(+), 60 deletions(-)

diff --git a/R/create_figures_doc.R b/R/create_figures_doc.R
index f22ee745..cc003bd5 100644
--- a/R/create_figures_doc.R
+++ b/R/create_figures_doc.R
@@ -215,33 +215,14 @@ rm(rda)\n
   )
 
   # Read through figures doc and warn about identical labels
-  new_figs_doc <- readLines(
-    ifelse(
-      any(grepl("_figures.qmd$", list.files(subdir))),
-      fs::path(subdir, list.files(subdir)[grep("_figures.qmd", list.files(subdir))]),
-      fs::path(subdir, "09_figures.qmd")
-    )
-  ) |>
-    suppressWarnings() |>
-    as.list()
-
-  label_line_nums <- grep("\\label", new_figs_doc)
-  labels <- new_figs_doc[label_line_nums]
-  names(labels) <- label_line_nums
-  labels <- lapply(labels, function(x) {
-    gsub("#\\| label: ", "", x)
-  })
-
-  repeated_labels <- labels[duplicated(labels)]
-  repeated_labels <- as.vector(unlist(repeated_labels))
-
-  if (length(repeated_labels) > 0) {
-    cli::cli_alert_danger("Figures doc contains chunks with identical labels: {repeated_labels}.")
-    cli::cli_alert_info("Open figures doc and check for:")
-    cli::cli_bullets(c(
-      "*" = "Identical, repeated figures",
-      "*" = "Different figures with identical labels"
-    ))
-    cli::cli_alert_warning("Figures doc will not render if chunks have identical labels.")
-  }
-}
+  doc_path <- ifelse(
+    any(grepl("_figures.qmd$", list.files(subdir))),
+    fs::path(subdir, list.files(subdir)[grep("_figures.qmd", list.files(subdir))]),
+    fs::path(subdir, "09_figures.qmd")
+  )
+  
+  fix_duplicate_chunks(
+    doc_path = doc_path,
+    doc_type = "Figures"
+  )
+}
\ No newline at end of file
diff --git a/R/create_tables_doc.R b/R/create_tables_doc.R
index 903f9c1e..f1bfdc79 100644
--- a/R/create_tables_doc.R
+++ b/R/create_tables_doc.R
@@ -554,33 +554,15 @@ load(file.path(tables_dir, '", stringr::str_remove(tab, "_split"), "'))\n
   )
 
   # Read through tables doc and warn about identical labels
-  new_tables_doc <- readLines(
-    ifelse(
-      any(grepl("_tables.qmd$", list.files(subdir))),
-      fs::path(subdir, list.files(subdir)[grep("_tables.qmd", list.files(subdir))]),
-      fs::path(subdir, "08_tables.qmd")
-    )
-  ) |>
-    suppressWarnings() |>
-    as.list()
-
-  label_line_nums <- grep("\\label", new_tables_doc)
-  labels <- new_tables_doc[label_line_nums]
-  names(labels) <- label_line_nums
-  labels <- lapply(labels, function(x) {
-    gsub("#\\| label: ", "", x)
-  })
-
-  repeated_labels <- labels[duplicated(labels)]
-  repeated_labels <- as.vector(unlist(repeated_labels))
-
-  if (length(repeated_labels) > 0) {
-    cli::cli_alert_danger("Tables doc contains chunks with identical labels: {repeated_labels}.")
-    cli::cli_alert_info("Open tables doc and check for:")
-    cli::cli_bullets(c(
-      "*" = "Identical, repeated tables",
-      "*" = "Different tables with identical labels"
-    ))
-    cli::cli_alert_warning("Tables doc will not render if chunks have identical labels.")
-  }
-}
+  doc_path <- ifelse(
+    any(grepl("_tables.qmd$", list.files(subdir))),
+    fs::path(subdir, list.files(subdir)[grep("_tables.qmd", list.files(subdir))]),
+    fs::path(subdir, "08_tables.qmd")
+  )
+  
+  fix_duplicate_chunks(
+    doc_path = doc_path,
+    doc_type = "Tables"
+  )
+
+}
\ No newline at end of file
diff --git a/R/utils.R b/R/utils.R
index 6caa2385..0eb5d20b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -372,3 +372,102 @@ gt_split <- function(
 
   gt_group
 }
+
+#----Fix figures/tables docs with duplicate chunks----
+fix_duplicate_chunks <- function(doc_path,
+                                 doc_type){
+  
+  new_figs_doc <- readLines(doc_path) |>
+    suppressWarnings() |>
+    as.list()
+  
+  label_line_nums <- grep("\\label", new_figs_doc)
+  labels <- new_figs_doc[label_line_nums]
+  names(labels) <- label_line_nums
+  labels <- lapply(labels, function(x) {
+    gsub("#\\| label: ", "", x)
+  })
+  
+  repeated_labels <- labels[duplicated(labels)]
+  repeated_labels <- as.vector(unlist(repeated_labels))
+  
+  if (length(repeated_labels) > 0) {
+    cli::cli_alert_warning("{doc_type} doc contains chunks with identical labels: {repeated_labels}.")
+    cli::cli_alert_warning("{doc_type} doc will not render if chunks have identical labels.")
+    cli::cli_alert_info("The duplicate chunks will be commented out.")
+    
+    in_chunk <- FALSE
+    current_chunk_start <- NA
+    current_chunk_label <- NULL
+    
+    chunks_list <- list()
+    
+    for (i in seq_along(new_figs_doc)) {
+      line <- new_figs_doc[i]
+      
+      # get code chunk start
+      if (!in_chunk && grepl("^\\s*```\\s*\\{[a-zA-Z]", line)) {
+        in_chunk <- TRUE
+        current_chunk_start <- i
+        current_chunk_label <- NULL
+        
+        # Handle inline label format: e.g., ```{r my-label}
+        inline_match <- regmatches(line, regexec("^\\s*```\\s*\\{[a-zA-Z]+\\s+([^, }]+)", line))[[1]]
+        if (length(inline_match) > 1) {
+          current_chunk_label <- trimws(inline_match[2])
+        }
+      } 
+      # get label
+      else if (in_chunk && is.null(current_chunk_label) && grepl("^\\s*#\\|\\s*label:", line)) {
+        # extract everything after "label:"
+        label_match <- regmatches(line, regexec("^\\s*#\\|\\s*label:\\s*(.*)", line))[[1]]
+        if (length(label_match) > 1) {
+          current_chunk_label <- trimws(label_match[2])
+          # strip outer quotes
+          current_chunk_label <- gsub("^['\"]|['\"]$", "", current_chunk_label)
+        }
+      }
+      # find end of code chunk
+      else if (in_chunk && grepl("^\\s*```\\s*$", line)) {
+        in_chunk <- FALSE
+        
+        # get chunk label
+        if (!is.null(current_chunk_label)) {
+          chunks_list[[length(chunks_list) + 1]] <- tidyr::tibble(
+            start = current_chunk_start,
+            end = i,
+            label = current_chunk_label
+          )
+        }
+      }
+    }
+    
+    # Combine list elements into a df
+    chunks_df <- dplyr::bind_rows(chunks_list)
+    
+    # Find duplicate occurrences
+    duplicates <- chunks_df |>
+      dplyr::group_by(label) |>
+      dplyr::mutate(occurrence = dplyr::row_number()) |>
+      dplyr::ungroup() |>
+      dplyr::filter(occurrence > 1) |>
+      dplyr::arrange(dplyr::desc(start))
+    
+    modified_doc <- new_figs_doc
+    
+    # Loop over duplicate chunks and comment out every line in range
+    for (row_idx in seq_len(nrow(duplicates))) {
+      label <- duplicates$label[row_idx]
+      start <- duplicates$start[row_idx]
+      end <- duplicates$end[row_idx]
+      
+      cli::cli_alert_info(sprintf("Commenting out duplicate chunk '%s' (Lines %d to %d)", label, start, end))
+      
+      # comment out each line
+      modified_doc[start:end] <- paste0("<!-- ", modified_doc[start:end], " -->")
+    }
+    
+    writeLines(as.character(unlist(modified_doc)), doc_path)
+    cli::cli_alert_success(sprintf("Successfully resolved %d duplicate chunk label issues in {doc_type} doc.", nrow(duplicates)))
+  } 
+}
\ No newline at end of file

From 266ba383ee05fc0ec13a235db06855c89d171fc9 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Thu, 28 May 2026 16:29:21 -0400
Subject: [PATCH 2/2] Update tests

---
 tests/testthat/test-create_figures_doc.R |   3 +-
 tests/testthat/test-create_tables_doc.R  | 239 ++++++++++++-----------
 2 files changed, 123 insertions(+), 119 deletions(-)

diff --git a/tests/testthat/test-create_figures_doc.R b/tests/testthat/test-create_figures_doc.R
index 0f3d4a7d..4de11a61 100644
--- a/tests/testthat/test-create_figures_doc.R
+++ b/tests/testthat/test-create_figures_doc.R
@@ -108,7 +108,6 @@ test_that("Formerly empty figures doc renders correctly", {
   )
 
   # erase temporary testing files
-  file.remove(fs::path(getwd(), "09_figures.qmd"))
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
   file.remove(fs::path(getwd(), "key_quantities.csv"))
   unlink(fs::path(getwd(), "figures"), recursive = T)
@@ -139,7 +138,7 @@ test_that("Throws warning if chunks with identical labels", {
       subdir = getwd(),
       figures_dir = getwd()
     ),
-    "Figures doc will not render if chunks have identical labels."
+    "Figures doc contains chunks with identical labels:"
   )
 
   # erase temporary testing files
diff --git a/tests/testthat/test-create_tables_doc.R b/tests/testthat/test-create_tables_doc.R
index 7a097702..8e114ca5 100644
--- a/tests/testthat/test-create_tables_doc.R
+++ b/tests/testthat/test-create_tables_doc.R
@@ -1,3 +1,5 @@
+library(stockplotr)
+
 test_that("Creates expected start of nearly empty tables doc", {
   # create tables doc
   create_tables_doc(
@@ -27,120 +29,123 @@ test_that("Creates expected start of nearly empty tables doc", {
   file.remove(fs::path(getwd(), "08_tables.qmd"))
 })
 
-# test_that("Creates expected start of tables doc with table", {
-#   # load sample dataset
-#   load(file.path(
-#     "fixtures", "ss3_models_converted", "Hake_2018",
-#     "std_output.rda"
-#   ))
-#
-#   stockplotr::table_landings(out_new,
-#     make_rda = TRUE
-#   )
-#
-#   # create tables doc
-#   create_tables_doc(
-#     subdir = getwd(),
-#     tables_dir = getwd()
-#   )
-#
-#   # read in tables doc
-#   table_content <- readLines("08_tables.qmd")
-#   # extract first 7 lines
-#   head_table_content <- head(table_content, 7)
-#   # remove line numbers and collapse
-#   fc_pasted <- paste(head_table_content, collapse = "")
-#
-#   # expected tables doc head
-#   expected_head_table_content <- "# Tables {#sec-tables} ```{r} #| label: 'set-rda-dir-tbls'#| echo: false #| warning: false #| include: false"
-#
-#   # test expectation of start of tables doc
-#   testthat::expect_equal(
-#     fc_pasted,
-#     expected_head_table_content
-#   )
-#
-#   # erase temporary testing files
-#   file.remove(fs::path(getwd(), "08_tables.qmd"))
-#   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-#   file.remove(fs::path(getwd(), "key_quantities.csv"))
-#   unlink(fs::path(getwd(), "tables"), recursive = T)
-# })
-#
-# test_that("Throws warning if chunks with identical labels", {
-#   # load sample dataset
-#   load(file.path(
-#     "fixtures", "ss3_models_converted", "Hake_2018",
-#     "std_output.rda"
-#   ))
-#
-#   stockplotr::table_landings(out_new,
-#     make_rda = TRUE
-#   )
-#
-#   # create tables doc
-#   create_tables_doc(
-#     subdir = getwd(),
-#     tables_dir = getwd()
-#   )
-#
-#   expect_message(
-#     create_tables_doc(
-#       subdir = getwd(),
-#       tables_dir = getwd()
-#     ),
-#     "Tables doc will not render if chunks have identical labels."
-#   )
-#
-#   # erase temporary testing files
-#   file.remove(fs::path(getwd(), "08_tables.qmd"))
-#   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-#   file.remove(fs::path(getwd(), "key_quantities.csv"))
-#   unlink(fs::path(getwd(), "tables"), recursive = T)
-# })
-#
-# test_that("Formerly empty tables doc renders correctly", {
-#   # create empty tables doc
-#   create_template()
-#
-#   # load sample dataset
-#   load(file.path(
-#     "fixtures", "ss3_models_converted", "Hake_2018",
-#     "std_output.rda"
-#   ))
-#
-#   stockplotr::table_landings(
-#     dat = out_new,
-#     make_rda = TRUE,
-#     module = "CATCH"
-#   )
-#
-#   # rerender tables doc, appending new table
-#   create_tables_doc(
-#     subdir = file.path(getwd(), "report"),
-#     tables_dir = getwd()
-#   )
-#
-#   # read in tables doc
-#   table_content <- readLines(file.path(getwd(), "report", "08_tables.qmd"))
-#   # extract first 8 lines
-#   head_table_content <- head(table_content, 8)
-#   # remove line numbers and collapse
-#   fc_pasted <- paste(head_table_content, collapse = "")
-#
-#   # expected tables doc head
-#   expected_head_table_content <- "# Tables {#sec-tables} ```{r} #| label: 'set-rda-dir-tbls'#| echo: false #| warning: false #| include: false"
-#
-#   # test expectation of start of tables doc
-#   expect_equal(
-#     fc_pasted,
-#     expected_head_table_content
-#   )
-#
-#   # erase temporary testing files
-#   file.remove(fs::path(getwd(), "08_tables.qmd"))
-#   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
-#   file.remove(fs::path(getwd(), "key_quantities.csv"))
-#   unlink(fs::path(getwd(), "tables"), recursive = T)
-#   unlink(fs::path(getwd(), "report"), recursive = T)
-# })
+test_that("Creates expected start of tables doc with table", {
+  # load sample dataset
+  load(file.path(
+    "fixtures", "ss3_models_converted", "Hake_2018",
+    "std_output.rda"
+  ))
+
+  table_landings(out_new,
+    make_rda = TRUE,
+    interactive = FALSE
+  )
+
+  # create tables doc
+  create_tables_doc(
+    subdir = getwd(),
+    tables_dir = getwd()
+  )
+
+  # read in tables doc
+  table_content <- readLines("08_tables.qmd")
+  # extract first 7 lines
+  head_table_content <- head(table_content, 7)
+  # remove line numbers and collapse
+  fc_pasted <- paste(head_table_content, collapse = "")
+
+  # expected tables doc head
+  expected_head_table_content <- "# Tables {#sec-tables} ```{r} #| label: 'set-rda-dir-tbls'#| echo: false #| warning: false #| include: false"
+
+  # test expectation of start of tables doc
+  testthat::expect_equal(
+    fc_pasted,
+    expected_head_table_content
+  )
+
+  # erase temporary testing files
+  file.remove(fs::path(getwd(), "08_tables.qmd"))
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  file.remove(fs::path(getwd(), "key_quantities.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+})
+
+test_that("Throws warning if chunks with identical labels", {
+  # load sample dataset
+  load(file.path(
+    "fixtures", "ss3_models_converted", "Hake_2018",
+    "std_output.rda"
+  ))
+
+  table_landings(out_new,
+    make_rda = TRUE,
+    interactive = FALSE
+  )
+
+  # create tables doc
+  create_tables_doc(
+    subdir = getwd(),
+    tables_dir = getwd()
+  )
+
+  expect_message(
+    create_tables_doc(
+      subdir = getwd(),
+      tables_dir = getwd()
+    ),
+    "Tables doc contains chunks with identical labels:"
+  )
+
+  # erase temporary testing files
+  file.remove(fs::path(getwd(), "08_tables.qmd"))
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  file.remove(fs::path(getwd(), "key_quantities.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+})
+
+test_that("Formerly empty tables doc renders correctly", {
+  # create empty tables doc
+  create_template()
+
+  # load sample dataset
+  load(file.path(
+    "fixtures", "ss3_models_converted", "Hake_2018",
+    "std_output.rda"
+  ))
+
+  table_landings(
+    dat = out_new,
+    interactive = FALSE,
+    make_rda = TRUE,
+    module = "CATCH"
+  )
+
+  # rerender tables doc, appending new table
+  create_tables_doc(
+    subdir = file.path(getwd(), "report"),
+    tables_dir = getwd()
+  )
+
+  # read in tables doc
+  table_content <- readLines(file.path(getwd(), "report", "08_tables.qmd"))
+  # extract first 8 lines
+  head_table_content <- head(table_content, 8)
+  # remove line numbers and collapse
+  fc_pasted <- paste(head_table_content, collapse = "")
+
+  # expected tables doc head
+  expected_head_table_content <- "# Tables {#sec-tables} ```{r} #| label: 'set-rda-dir-tbls'#| echo: false #| warning: false #| include: false"
+
+  # test expectation of start of tables doc
+  expect_equal(
+    fc_pasted,
+    expected_head_table_content
+  )
+
+  # erase temporary testing files
+ # file.remove(fs::path(getwd(), "08_tables.qmd"))
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  file.remove(fs::path(getwd(), "key_quantities.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+  unlink(fs::path(getwd(), "report"), recursive = T)
+})