Fix pandoc support, add raw options to pandoc requires pandoc 2. Closes #132.

src/Weave.jl

@@ -56,7 +56,8 @@ end
         mod::Union{Module, Symbol} = Main,
         fig_path = "figures", fig_ext = nothing,
         cache_path = "cache", cache=:off,
-        template = nothing, highlight_theme = nothing, css = nothing
+        template = nothing, highlight_theme = nothing, css = nothing,
+        pandoc_options = "",
         latex_cmd = "xelatex")
 
 Weave an input document to output file.
@@ -80,6 +81,8 @@ Weave an input document to output file.
 * `template` : Template (file path) for md2html or md2tex formats.
 * `highlight_theme` : Theme (Highlights.AbstractTheme) for used syntax highlighting
 * `css` : CSS (file path) used for md2html format
+* `pandoc_options` = String array of options to pass to pandoc for `pandoc2html` and
+   `pandoc2pdf` formats e.g. ["--toc", "-N"]
 * `latex_cmd` the command used to make pdf from .tex
 
 **Note:** Run Weave from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.
@@ -91,6 +94,7 @@ function weave(source ; doctype = :auto,
         cache_path = "cache", cache=:off,
         throw_errors = false,
         template = nothing, highlight_theme = nothing, css = nothing,
+        pandoc_options = String[]::Array{String},
         latex_cmd = "xelatex")
 
     doc = read_doc(source, informat)
@@ -117,12 +121,12 @@ function weave(source ; doctype = :auto,
       if doc.doctype == "pandoc2html"
           mdname = outname
           outname = get_outname(out_path, doc, ext = "html")
-          pandoc2html(formatted, doc, outname)
+          pandoc2html(formatted, doc, outname, pandoc_options)
           rm(mdname)
       elseif doc.doctype == "pandoc2pdf"
           mdname = outname
           outname = get_outname(out_path, doc, ext = "pdf")
-          pandoc2pdf(formatted, doc, outname)
+          pandoc2pdf(formatted, doc, outname, pandoc_options)
           rm(mdname)
       elseif doc.doctype == "md2pdf"
           success = run_latex(doc, outname, latex_cmd)
@@ -133,14 +137,14 @@ function weave(source ; doctype = :auto,
 
       doc.cwd == pwd() && (outname = basename(outname))
       @info("Report weaved to $outname")
-    catch e
-        @warn("Something went wrong during weaving")
-        println(e)
+    #    catch err
+    #    @warn("Something went wrong during weaving")
+    #    println(e)
     finally
         doctype == :auto && (doctype = detect_doctype(doc.source))
         if occursin("pandoc2pdf", doctype) && cache == :off
             rm(doc.fig_path, force = true, recursive = true)
-    elseif occursin("2html", doctype)
+        elseif occursin("2html", doctype)
             rm(doc.fig_path, force = true, recursive = true)
         end
     end

src/formatters.jl

@@ -63,12 +63,12 @@ struct Pandoc2HTML
     formatdict::Dict{Symbol,Any}
 end
 
-const pdoc2html = Pandoc2HTML("Markdown to HTML (requires Pandoc)",
+const pdoc2html = Pandoc2HTML("Markdown to HTML (requires Pandoc 2)",
                       Dict{Symbol,Any}(
                               :codestart => "\n",
                               :codeend=> "\n",
-                              :outputstart=> "````",
-                              :outputend=> "````\n\n",
+                              :outputstart=> "\n",
+                              :outputend=> "\n",
                               :fig_ext=> ".png",
                               :extension=> "md",
                               :mimetypes => ["image/png", "image/svg+xml", "image/jpg",
@@ -368,6 +368,7 @@ function formatfigures(chunk, docformat::JMarkdown2tex)
   return result
 end
 
+formatfigures(chunk, docformat::Pandoc2HTML) = formatfigures(chunk, pandoc)
 
 function formatfigures(chunk, docformat::Pandoc)
     fignames = chunk.figures

src/pandoc.jl

@@ -5,7 +5,7 @@
 
 Convert output from pandoc markdown to html using Weave.jl template
 """
-function pandoc2html(formatted::AbstractString, doc::WeaveDoc, outname::AbstractString)
+function pandoc2html(formatted::AbstractString, doc::WeaveDoc, outname::AbstractString, pandoc_options)
   weavedir = dirname(@__FILE__)
   html_template = joinpath(weavedir, "../templates/pandoc_skeleton.html")
   css_template = joinpath(weavedir, "../templates/pandoc_skeleton.css")
@@ -18,12 +18,7 @@ function pandoc2html(formatted::AbstractString, doc::WeaveDoc, outname::Abstract
 
   #Header is inserted from displayed plots
   header_script = doc.header_script
-
-  if header_script ≠ ""
-    self_contained = []
-  else
-    self_contained = "--self-contained"
-  end
+  self_contained = (header_script ≠ "") ? [] : "--self-contained"
 
   if haskey(doc.header, "bibliography")
     filt = "--filter"
@@ -39,18 +34,23 @@ function pandoc2html(formatted::AbstractString, doc::WeaveDoc, outname::Abstract
   html =""
   outname = basename(outname)
 
+  open("temp.md", "w") do io
+    println(io, formatted)
+  end
+
   try
-    pandoc_out, pandoc_in, proc = readandwrite(`pandoc -R -s --mathjax=""
-    $filt $citeproc
+    cmd = `pandoc -f markdown+raw_html -s --mathjax=""
+    $filt $citeproc $pandoc_options
     --template $html_template -H $css_template $self_contained
      -V wversion=$wversion -V wtime=$wtime -V wsource=$wsource
      -V highlightcss=$css
      -V headerscript=$header_script
-     -o $outname`)
-    println(pandoc_in, formatted)
-    close(pandoc_in)
-    proc_output = read(pandoc_out, String)
-    cd(old_wd)
+     -o $outname`
+     proc = open(cmd, "r+")
+     println(proc.in, formatted)
+     close(proc.in)
+     proc_output = read(proc.out, String)
+     cd(old_wd)
   catch e
     cd(old_wd)
     @warn("Error converting document to HTML")
@@ -63,7 +63,7 @@ end
 
 Convert output from pandoc markdown to pdf using Weave.jl template
 """
-function pandoc2pdf(formatted::AbstractString, doc::WeaveDoc, outname::AbstractString)
+function pandoc2pdf(formatted::AbstractString, doc::WeaveDoc, outname::AbstractString, pandoc_options)
   weavedir = dirname(@__FILE__)
   header_template = joinpath(weavedir, "../templates/pandoc_header.txt")
 
@@ -88,14 +88,14 @@ function pandoc2pdf(formatted::AbstractString, doc::WeaveDoc, outname::AbstractS
 
   @info("Done executing code. Running xelatex")
   try
-    pandoc_out, pandoc_in, proc = readandwrite(`pandoc -R -s  --latex-engine=xelatex --highlight-style=tango
-     $filt $citeproc
+    cmd = `pandoc -f markdown+raw_tex -s  --pdf-engine=xelatex --highlight-style=tango
+     $filt $citeproc $pandoc_options
      --include-in-header=$header_template
-     -V fontsize=12pt -o $outname`)
-    println(pandoc_in, formatted)
-
-    close(pandoc_in)
-    proc_output = read(pandoc_out, String)
+     -V fontsize=12pt -o $outname`
+    proc = open(cmd, "r+")
+    println(proc.in, formatted)
+    close(proc.in)
+    proc_output = read(proc.out, String)
     cd(old_wd)
   catch e
     cd(old_wd)
@@ -111,19 +111,13 @@ function run_latex(doc::WeaveDoc, outname, latex_cmd = "xelatex")
   @info("Weaved code to $outname. Running $latex_cmd")
   try
     textmp = mktempdir(".")
-    #out = readstring(`$latex_cmd -shell-escape --output-directory=$textmp $xname`)
     out = read(`$latex_cmd -shell-escape $xname`, String)
-    #info(out)
-    #pdf = joinpath(textmp, "$(doc.basename).pdf")
-    #cp(pdf, "$(doc.basename).pdf", remove_destination=true)
-    #rm(textmp, recursive=true)
     rm(xname)
     cd(old_wd)
     return true
   catch e
-    cd(old_wd)
     @warn("Error converting document to pdf. Try running latex manually")
+    cd(old_wd)
     return false
-    #throw(e)
   end
 end