Add bibtex support to md2pdf

src/Weave.jl

@@ -122,8 +122,6 @@ function weave(source ; doctype = :auto,
           write(io, formatted)
       end
 
-      WeaveMarkdown.reset_parser()
-
       #Special for that need external programs
       if doc.doctype == "pandoc2html"
           mdname = outname
@@ -148,6 +146,7 @@ function weave(source ; doctype = :auto,
     #    @warn("Something went wrong during weaving")
     #    println(e)
     finally
+        WeaveMarkdown.reset_parser()
         doctype == :auto && (doctype = detect_doctype(doc.source))
         if occursin("pandoc2pdf", doctype) && cache == :off
             rm(doc.fig_path, force = true, recursive = true)

src/WeaveMarkdown/bibliography.jl

@@ -7,7 +7,6 @@ function list_references(m::MIME"text/html")
         refs[CITATIONS[:refnumbers][key]] = key
     end
     io = IOBuffer()
-    write(io, "<h3>References</h3>")
     write(io, "<ol>")
     for i in 1:length(refs)
         ref = CITATIONS[:references][refs[i]]

src/WeaveMarkdown/latex.jl

@@ -24,5 +24,5 @@ function latexinline(io, citations::Citations)
     for c in citations.content
         push!(cites, c.key)
     end
-    write(io, string("\\cite{", join(cites, ", "), "}"))
+    write(io, string("\\citep{", join(cites, ", "), "}"))
 end

src/format.jl

@@ -99,9 +99,9 @@ function render_doc(formatted, doc::WeaveDoc, format::JMarkdown2tex)
 
   references = ""
   if !isempty(WeaveMarkdown.CITATIONS[:references])
-      bibfile = splitext(joinpath(dirname(doc.source), doc.header["bibliography"]))[1]
+      bibfile = splitext(abspath(joinpath(dirname(doc.source), doc.header["bibliography"])))[1]
+      bibfile = replace(bibfile, "\\" => "/")
       references = """
-      \\section*{References}
       \\bibliographystyle{unsrt}
       \\bibliography{$bibfile}
       """

src/pandoc.jl

@@ -1,4 +1,4 @@
-
+import .WeaveMarkdown
 
 """
 `pandoc2html(formatted::AbstractString, doc::WeaveDoc)`
@@ -108,9 +108,17 @@ function run_latex(doc::WeaveDoc, outname, latex_cmd = "xelatex")
   old_wd = pwd()
   cd(doc.cwd)
   xname = basename(outname)
+  bibname = splitext(xname)[1]
   @info("Weaved code to $outname. Running $latex_cmd")
   textmp = mktempdir(".")
   try
+    out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)
+    if !isempty(WeaveMarkdown.CITATIONS[:references])
+       cd(textmp)
+       out = read(`bibtex $bibname`, String)
+       cd("..")
+       out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)
+    end
     out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)
     out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)
     rm(xname)
@@ -118,9 +126,11 @@ function run_latex(doc::WeaveDoc, outname, latex_cmd = "xelatex")
     cd(old_wd)
     return true
   catch e
-    @warn("Error converting document to pdf. Try running latex manually")
+    @info(e)
+    @warn("Error converting document to pdf. Try running with md2tex format and using latex manually")
     cd(old_wd)
-    rm(textmp)
+    rm(xname)
+    rm(textmp, recursive=true)
     return false
   end
 end

templates/julia_tex.tpl

@@ -5,6 +5,7 @@
 \usepackage{amssymb,amsmath}
 \usepackage{bm}
 \usepackage{graphicx}
+\usepackage{natbib}
 \usepackage{microtype}
 \usepackage{hyperref}
 \setlength{\parindent}{0pt}