This lua filter will automatically number equations

excluding ones with `\nonumber`

R/article-tools.R

@@ -124,6 +124,8 @@ convert_to_markdown <- function(article_dir) {
         "issue_checker.lua", package = "texor")
     wdtable_filter <- system.file(
         "widetable_patcher.lua", package = "texor")
+    auto_num_eq <- system.file(
+        "auto_number_equations.lua", package = "texor")
     pandoc_opt <- c("-s",
                     "--resource-path", abs_file_path,
                     "--lua-filter", error_checker_filter,
@@ -439,6 +441,8 @@ convert_to_native <- function(article_dir) {
         "bookdown_ref.lua", package = "texor")
     wdtable_filter <- system.file(
         "widetable_patcher.lua", package = "texor")
+    auto_num_eq <- system.file(
+        "auto_number_equations.lua", package = "texor")
     pandoc_opt <- c("-s",
                     "--resource-path", abs_file_path,
                     "--lua-filter", abs_filter,

inst/auto_number_equations.lua

@@ -0,0 +1,30 @@
+--[[
+AutoNumber Equation filter – tries to autonumber equations.
+Copyright: © 2023 Abhishek Ulayil
+License:   MIT – see LICENSE file for details
+--]]
+equation_counter =1
+function Math(el)
+    if el.mathtype == "DisplayMath" then
+        if el.text:match('\\#eq:')  then
+            -- skip equation numbering for equations with dedicated labels,
+            -- but also add them to the tally of equation
+            equation_counter = equation_counter + 1
+            return {pandoc.Str("\n"),el,pandoc.Str("\n")}
+        elseif el.text:match('\\nonumber') then
+              -- skip numbering equations with \nonumber
+              return {pandoc.Str("\n"),el,pandoc.Str("\n")}
+        else
+            local text = pandoc.utils.stringify(el.text)
+            -- insert a label to invoke numbering.
+            html_label = "eq:".. tostring(equation_counter)
+            --el.text = [[\label{eq:}]] .. tostring(equation_counter) .. [[}]] .. text
+            el.text = text .. [[   (\#]] .. html_label .. [[)]]
+            equation_counter = equation_counter + 1
+        end
+        return {pandoc.Str("\n"),el,pandoc.Str("\n")}
+        --return el
+    else
+        return el
+    end
+end