From 7e88052db3e9d458ab5f55f3540533cff496c289 Mon Sep 17 00:00:00 2001
From: Fredrik Bagge Carlson <baggepinnen@gmail.com>
Date: Sun, 9 Feb 2020 20:11:29 +0800
Subject: [PATCH 1/2] keep latex figures

---
 src/Weave.jl  | 70 ++++++++++++++++++++++-----------------------------
 src/pandoc.jl |  2 +-
 2 files changed, 31 insertions(+), 41 deletions(-)

diff --git a/src/Weave.jl b/src/Weave.jl
index 35eadec..aeb5de3 100644
--- a/src/Weave.jl
+++ b/src/Weave.jl
@@ -131,49 +131,39 @@ function weave(
     #theme != nothing && (doc.theme = theme) #Reserved for themes
     css != nothing && (doc.css = css)
 
-    try
-      doc = run(doc, doctype = doctype,
-              mod = mod,
-              out_path=out_path, args = args,
-              fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache,
-              throw_errors = throw_errors,latex_keep_unicode=latex_keep_unicode)
-      formatted = format(doc)
+    doc = run(doc, doctype = doctype,
+    mod = mod,
+    out_path=out_path, args = args,
+    fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache,
+    throw_errors = throw_errors,latex_keep_unicode=latex_keep_unicode)
+    formatted = format(doc)
 
-      outname = get_outname(out_path, doc)
+    outname = get_outname(out_path, doc)
 
-      open(outname, "w") do io
-          write(io, formatted)
-      end
-
-      #Special for that need external programs
-      if doc.doctype == "pandoc2html"
-          mdname = outname
-          outname = get_outname(out_path, doc, ext = "html")
-          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, pandoc_options)
-          rm(mdname)
-      elseif doc.doctype == "md2pdf"
-          success = run_latex(doc, outname, latex_cmd)
-          success && rm(doc.fig_path, force = true, recursive = true)
-          success || return
-          outname = get_outname(out_path, doc, ext = "pdf")
-      end
-
-      doc.cwd == pwd() && (outname = basename(outname))
-      @info "Report weaved to $outname"
-      return abspath(outname)
-    # catch err
-    #    @warn "Something went wrong during weaving"
-    #    @error sprint(showerror, err)
-    #    return nothing
-    finally
-        doctype == :auto && (doctype = detect_doctype(doc.source))
-        occursin(r"2(pdf|html)", doctype) && rm(doc.fig_path, force = true, recursive = true)
+    open(outname, "w") do io
+        write(io, formatted)
     end
+
+    #Special for that need external programs
+    if doc.doctype == "pandoc2html"
+        mdname = outname
+        outname = get_outname(out_path, doc, ext = "html")
+        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, pandoc_options)
+        rm(mdname)
+    elseif doc.doctype == "md2pdf"
+        success = run_latex(doc, outname, latex_cmd)
+        success || return
+        outname = get_outname(out_path, doc, ext = "pdf")
+    end
+
+    doc.cwd == pwd() && (outname = basename(outname))
+    @info("Report weaved to $outname")
+    return abspath(outname)
 end
 
 weave(doc::AbstractString, doctype::Union{Symbol,AbstractString}) =
diff --git a/src/pandoc.jl b/src/pandoc.jl
index f4b5fdb..c1870fb 100644
--- a/src/pandoc.jl
+++ b/src/pandoc.jl
@@ -108,7 +108,7 @@ function run_latex(doc::WeaveDoc, outname, latex_cmd = "xelatex")
   old_wd = pwd()
   cd(doc.cwd)
   xname = basename(outname)
-  @info("Weaved code to $outname. Running $latex_cmd")
+  @info("Weaved code to $outname . Running $latex_cmd") # space before '.' added for link to be clickable in Juno terminal
   textmp = mktempdir(".")
   try
     out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)

From f126e1c7a9898b26db1313a378a07d3d37f6f175 Mon Sep 17 00:00:00 2001
From: Fredrik Bagge Carlson <baggepinnen@gmail.com>
Date: Sun, 9 Feb 2020 20:13:37 +0800
Subject: [PATCH 2/2] fix formatting

---
 src/Weave.jl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Weave.jl b/src/Weave.jl
index aeb5de3..d6a8846 100644
--- a/src/Weave.jl
+++ b/src/Weave.jl
@@ -132,10 +132,10 @@ function weave(
     css != nothing && (doc.css = css)
 
     doc = run(doc, doctype = doctype,
-    mod = mod,
-    out_path=out_path, args = args,
-    fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache,
-    throw_errors = throw_errors,latex_keep_unicode=latex_keep_unicode)
+                mod = mod,
+                out_path=out_path, args = args,
+                fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache,
+                throw_errors = throw_errors,latex_keep_unicode=latex_keep_unicode)
     formatted = format(doc)
 
     outname = get_outname(out_path, doc)