Implemented noweb reader in Julia

Causes changes to chunk option formatting. Updated sample accordingly.

examples/julia_sample.mdw

@@ -3,7 +3,7 @@
 
 This a sample [Julia](http://julialang.org/) noweb document that can
 be executed using JuliaReport. Output from code chunks and PyPlot
-plots will be included in the weaved document. You also need to install Pweave from Github in order to use JuliaReport. 
+plots will be included in the weaved document. You also need to install Pweave from Github in order to use JuliaReport.
 
 This documented can be turned into Pandoc markdown with captured
 result from Julia prompt.
@@ -15,7 +15,7 @@ weave("examples/julia_sample.mdw")
 
 ## Terminal chunk
 
-<<term=True>>=
+<<"term"=>true>>=
 x = 1:10
 d = {"juliareport" => "testing"}
 y = [2, 4 ,8]
@@ -35,6 +35,6 @@ ylabel("sinc(x)")
 
 You can also include a plot with caption and hide the code:
 
-<<echo=False, caption="Random walk.", label="random">>=
+<<"echo"=>false, "caption"=>"Random walk.", "label"=>"random">>=
 plot(cumsum(randn(1000, 1)))
 @

src/JuliaReport.jl

@@ -1,9 +1,8 @@
 module JuliaReport
 using PyCall
 using PyPlot
+@pyimport pweave #Output formatting uses Pweave
 
-#Parsing and formatting uses Pweave
-@pyimport pweave
 
 #Contains report global properties
 #Similar to pweave.PwebProcessor
@@ -18,7 +17,7 @@ type Report
 end
 
 
-global report = Report("", false, "", "",  {}, "", "")
+global const report = Report("", false, "", "",  {}, "", "")
 
 function listformats()
   pweave.listformats()
@@ -28,19 +27,27 @@ function weave(source ; doctype = "pandoc", informat="noweb", figdir = "figures"
     pweave.rcParams["chunk"]["defaultoptions"]["engine"] = "julia"
 
     doc = pweave.Pweb(source, doctype, shell="julia")
-    doc[:setreader](informat)
-    doc[:parse]()
+    #doc[:setreader](informat)
+    #doc[:parse]()
 
-    #Julia version of doc.run()
     cwd, fname = splitdir(abspath(source))
     basename = splitext(fname)[1]
     formatdict = doc[:formatter][:getformatdict]()
     figformat == nothing || (formatdict["figfmt"] = figformat)
     #println(formatdict["figfmt"])
-    global report = Report(source, false, cwd, basename, formatdict, "", figdir)
+    #report = Report(source, false, cwd, basename, formatdict, "", figdir)
+
+    report.source = source
+    report.cwd = cwd
+    report.basename = basename
+    report.figdir = figdir
+    report.formatdict = formatdict
+
+    parsed = read_noweb(source)
+    doc[:executed] = run(parsed)
 
     #Formatting with pweave
-    doc[:executed] = run(PyVector(doc["parsed"]))
+    #doc[:executed] = run(PyVector(doc["parsed"]))
     doc[:isexecuted] = true
     doc[:format]()
     doc[:write]()
@@ -93,11 +100,19 @@ function run(parsed)
         if chunk["type"] == "code"
             #print(chunk["content"])
             info("""Weaving chunk $(chunk["number"]) from line $(chunk["start_line"])""")
-            defaults = copy(pweave.rcParams["chunk"]["defaultoptions"])
-            merge!(defaults, chunk["options"])
-            merge!(chunk, defaults)
-            chunk["evaluate"] || (chunk["result"] = ""; continue) #Do nothing if eval is false
+            defaults = copy(rcParams["chunk"]["defaultoptions"])
+            options = copy(chunk["options"])
+            try
+              options = merge(rcParams["chunk"]["defaultoptions"], options)
+            catch
+              options = rcParams["chunk"]["defaultoptions"]
+              warn(string("Invalid format for chunk options line: ", chunk["start_line"]))
+            end
 
+            merge!(chunk, options)
+
+
+            chunk["evaluate"] || (chunk["result"] = ""; continue) #Do nothing if eval is false
             if chunk["term"]
                 chunk["result"] = run_term(chunk["content"])
             else
@@ -134,4 +149,6 @@ end
 
 export weave
 
+include("config.jl")
+include("readers.jl")
 end

src/config.jl

@@ -0,0 +1,24 @@
+rcParams = {"figdir"=> "figures",
+"usematplotlib"=> true,
+"storeresults"=> false,
+"cachedir"=> "cache",
+"chunk"=> {"defaultoptions"=> {
+"echo"=> true,
+"results"=> "verbatim",
+"fig"=> true,
+"include"=> true,
+"evaluate"=> true,
+"caption"=> false,
+"term"=> false,
+"name"=> nothing,
+"wrap"=> true,
+"f_pos"=> "htpb",
+"f_size"=> (8, 6),
+"f_env"=> nothing,
+"f_spines"=> true,
+"complete"=> true,
+"engine"=> "julia",
+"option_string"=> ""
+}
+}
+}

src/readers.jl

@@ -0,0 +1,60 @@
+function read_noweb(document)
+  doctext = readall(open(document))
+  #doctext = document #Replace with file...
+  codestart = r"^<<(.*?)>>="
+  codeend = r"^@(\s*)$"
+  state = "doc"
+
+  docno = 1
+  codeno = 1
+  content = ""
+  lineno = 0
+  start_line = 0
+
+  options = Dict()
+  optionstring = ""
+  parsed = Dict[]
+  for (lineno, line) in enumerate(split(doctext, "\n"))
+
+    if ismatch(codestart, line) && state=="doc"
+      state = "code"
+      m = match(codestart, line)
+      optionstring=m.captures[1]
+      #println(m.captures[1])
+      if strip(optionstring)==""
+        options = Dict()
+      else
+        options = eval(parse("{" * optionstring * "}"))
+      end
+      haskey(options, "label") && (options["name"] = options["label"])
+      haskey(options, "name") || (options["name"] = nothing)
+
+      chunk = {"type" => "doc", "content"=> content, "number" =>  docno, "start_line"=>start_line}
+      docno += 1
+      start_line = lineno
+      push!(parsed, chunk)
+      content = ""
+      continue
+    end
+    if ismatch(codeend, line) && state=="code"
+      chunk = {"type" => "code", "content" => content, "number" => codeno,
+      "options"=>options,"optionstring"=>optionstring, "start_line"=>start_line}
+      codeno+=1
+      start_line = lineno
+      content = ""
+      state = "doc"
+      push!(parsed, chunk)
+      continue
+    end
+
+    content *= "\n" * line  
+  end
+
+  #Remember the last chunk
+  if content != ""
+    chunk = {"type" => "doc", "content"=> content, "number" =>  docno, "start_line"=>lineno}
+    push!(parsed, chunk)
+  end
+
+  return parsed
+end