Added shortcut method for weave, cleaned obsolete code

src/Weave.jl

@@ -130,7 +130,9 @@ function Base.display(report::Report, m::MIME"text/plain", data)
   end
 end
 
-
+function weave(doc::String, doctype::String)
+    weave(doc, doctype=doctype)
+end
 
 export weave, list_out_formats, tangle
 

src/run.jl

@@ -71,19 +71,9 @@ function Base.run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat=
 end
 
 function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module, cached, cache, idx)
-    defaults = copy(rcParams[:chunk_defaults])
-    options = copy(chunk.options)
-    try
-        options = merge(rcParams[:chunk_defaults], options)
-    catch
-        options = rcParams[:chunk_defaults]
-        warn("Invalid format for chunk options line: $(chunk.start_line)")
-    end
-
+    options = merge(rcParams[:chunk_defaults], chunk.options)
     merge!(chunk.options, options)
 
-    delete!(chunk.options, :options)
-
     if cached != nothing && (cache == :all || (cache ==:user && chunk.options[:cache]))
         result_chunk = restore_chunk(chunk, cached, idx)
     else

test/gadfly_formats.jl

@@ -3,7 +3,7 @@ using Weave
 using Base.Test
 
 
-weave("documents/gadfly_formats_test.txt", doctype="tex", plotlib="gadfly")
+weave("documents/gadfly_formats_test.txt", "tex")
 result = readall(open("documents/gadfly_formats_test.tex"))
 ref = readall(open("documents/gadfly_formats_test_ref.tex"))
 @test result == ref