Lua: ensure we're using Custom-aware walkers everywhere (#4622)

* Lua filters - :walk() must be _quarto.ast.walk() for custom AST nodes

* smoke test

Author: cscheid

src/resources/filters/ast/customnodes.lua

@@ -17,7 +17,7 @@ function resolve_custom_node(node)
   end
 end
 
-function run_emulated_filter(doc, filter)
+function run_emulated_filter(doc, filter, top_level)
   local wrapped_filter = {}
   for k, v in pairs(filter) do
     wrapped_filter[k] = v
@@ -132,7 +132,7 @@ function run_emulated_filter(doc, filter)
   end
 
   local result = doc:walk(wrapped_filter)
-  if filter._filter_name ~= nil then
+  if top_level and filter._filter_name ~= nil then
     add_trace(result, filter._filter_name)
   end
   return result

src/resources/filters/ast/runemulation.lua

@@ -8,7 +8,7 @@ local function run_emulated_filter_chain(doc, filters, afterFilterPass)
   if tisarray(filters) then
     for i, v in ipairs(filters) do
       local function callback()
-        doc = run_emulated_filter(doc, v)
+        doc = run_emulated_filter(doc, v, true)
       end
       if v.scriptFile then
         _quarto.withScriptFile(v.scriptFile, callback)
@@ -20,7 +20,7 @@ local function run_emulated_filter_chain(doc, filters, afterFilterPass)
       end
     end
   elseif type(filters) == "table" then
-    doc = run_emulated_filter(doc, filters)
+    doc = run_emulated_filter(doc, filters, true)
     if afterFilterPass then
       afterFilterPass()
     end

src/resources/filters/common/refs.lua

@@ -78,7 +78,7 @@ function hasSubRefs(divEl, type)
 
       end
     end
-    pandoc.walk_block(divEl, {
+    _quarto.ast.walk(divEl, {
       Div = checkForParent,
       Image = checkForParent
     })

src/resources/filters/common/tables.lua

@@ -115,7 +115,7 @@ end
 
 function countTables(div)
   local tables = 0
-  pandoc.walk_block(div, {
+  _quarto.ast.walk(div, {
     Table = function(table)
       tables = tables + 1
     end,

src/resources/filters/common/wrapped-filter.lua

@@ -195,7 +195,7 @@ function filterSeq(filters)
         if filter.filter ~= nil then
           filter = filter.filter
         end
-        local r = run_emulated_filter(doc, filter)
+        local r = run_emulated_filter(doc, filter, true)
         if r ~= nil then
           doc = r
           result = r

src/resources/filters/crossref/format.lua

@@ -61,7 +61,7 @@ function refPrefix(type, upper)
   if upper then
     local el = pandoc.Plain(prefix)
     local firstStr = true
-    el = pandoc.walk_block(el, {
+    el = _quarto.ast.walk(el, {
       Str = function(str)
         if firstStr then
           local strText = pandoc.text.upper(pandoc.text.sub(str.text, 1, 1)) .. pandoc.text.sub(str.text, 2, -1)

src/resources/filters/crossref/preprocess.lua

@@ -37,7 +37,7 @@ function crossrefPreprocess()
                 if isTableRef(el.attr.identifier) then
                   el.attr.classes:insert("tbl-parent")
                 end
-                el = pandoc.walk_block(el, walkRefs(el.attr.identifier))
+                el = _quarto.ast.walk(el, walkRefs(el.attr.identifier))
               end
             end
             return el
@@ -100,7 +100,7 @@ function crossrefPreprocess()
               el.content:insert(err)
             end
           end
-          doc.blocks[i] = pandoc.walk_block(el, walkRefs(parentId))
+          doc.blocks[i] = _quarto.ast.walk(el, walkRefs(parentId))
         end
       end
 

src/resources/filters/crossref/theorems.lua

@@ -8,7 +8,7 @@ function crossrefPreprocessTheorems()
     Div = function(el)
       local type = refType(el.attr.identifier)
       if types[type] ~= nil or proofType(el) ~= nil then
-        return pandoc.walk_block(el, {
+        return _quarto.ast.walk(el, {
           Header = function(el)
             el.classes:insert("unnumbered")
             return el

src/resources/filters/layout/cites.lua

@@ -7,7 +7,7 @@ function citesPreprocess()
 
     Note = function(note) 
       if _quarto.format.isLatexOutput() and marginCitations() then
-        return pandoc.walk_inline(note, {
+        return _quarto.ast.walk(note, {
           Inlines = walkUnresolvedCitations(function(citation, appendInline, appendAtEnd)
             appendAtEnd(citePlaceholderInline(citation))
           end)
@@ -21,7 +21,7 @@ function citesPreprocess()
         if hasMarginColumn(figure) or hasMarginCaption(figure) then
           -- This is a figure in the margin itself, we need to append citations at the end of the caption
           -- without any floating
-          para.content[1] = pandoc.walk_inline(figure, {
+          para.content[1] = _quarto.ast.walk(figure, {
               Inlines = walkUnresolvedCitations(function(citation, appendInline, appendAtEnd)
                 appendAtEnd(citePlaceholderInlineWithProtection(citation))
               end)
@@ -30,7 +30,7 @@ function citesPreprocess()
         elseif marginCitations() then
           -- This is a figure is in the body, but the citation should be in the margin. Use 
           -- protection to shift any citations over
-          para.content[1] = pandoc.walk_inline(figure, {
+          para.content[1] = _quarto.ast.walk(figure, {
             Inlines = walkUnresolvedCitations(function(citation, appendInline, appendAtEnd)
               appendInline(marginCitePlaceholderWithProtection(citation))
             end)
@@ -56,7 +56,7 @@ function citesPreprocess()
             end
           end  
         else
-          return pandoc.walk_block(div, {
+          return _quarto.ast.walk(div, {
             Inlines = walkUnresolvedCitations(function(citation, appendInline, appendAtEnd)
               if hasMarginColumn(div) then
                 appendAtEnd(citePlaceholderInline(citation))

src/resources/filters/layout/jats.lua

@@ -5,7 +5,7 @@
 function jatsDivFigure(divEl)
 
   -- ensure that only valid elements are permitted
-  local filteredEl = pandoc.walk_block(divEl, {
+  local filteredEl = _quarto.ast.walk(divEl, {
     Header = function(el)
       return pandoc.Strong(el.content)
     end