Mostly fixed caching, echo=false needs fixing. Switched to JLD format.

src/cache.jl

@@ -1,9 +1,10 @@
-import JSON
+import JSON, JLD
 
 function write_cache(doc::WeaveDoc, cache_path)
     cache_dir = "$(doc.cwd)/$cache_path"
     isdir(cache_dir) || mkpath(cache_dir)
     name = "$cache_dir/$(doc.basename).json"
+    JLD.save("$cache_dir/$(doc.basename).jld", Dict("doc" => doc))
     open(name, "w") do io
         write(io, JSON.json(doc))
     end
@@ -11,28 +12,42 @@ function write_cache(doc::WeaveDoc, cache_path)
 end
 
 function read_cache(doc::WeaveDoc, cache_path)
-    name = "$(doc.cwd)/$cache_path/$(doc.basename).json"
+    #name = "$(doc.cwd)/$cache_path/$(doc.basename).json"
+    name = "$(doc.cwd)/$cache_path/$(doc.basename).jld"
     isfile(name) || return nothing
-    parsed = JSON.parsefile(name)
+    #parsed = JSON.parsefile(name)
+    return JLD.load(name)["doc"]
 end
 
 #read_cache returns a dictionary, parse to back to chunk
-function restore_chunk(chunk::CodeChunk, cached, idx)
-    options = Dict{Symbol, Any}()
-    for (keys,vals) = cached["chunks"][idx]["options"]
-        options[symbol(keys)] = vals
+function restore_chunk(chunk::CodeChunk, cached)
+    chunks = filter(x -> x.number == chunk.number &&
+            string(typeof(x)) == "Weave.CodeChunk", cached.chunks)
+
+    #Chunk types, don't match after loading. Need to reinitialize
+    new_chunks = Any[]
+    for c in chunks
+      newc = CodeChunk(c.content, c.number, c.start_line, c.optionstring, c.options)
+      newc.result_no = c.result_no
+      newc.figures = c.figures
+      newc.result = c.result
+      push!(new_chunks, newc)
     end
-    haskey(options, :term_state) && (options[:term_state] = symbol(options[:term_state]))
+    #options = Dict{Symbol, Any}()
+    #info(cached["chunks"][idx])
+    #for (keys,vals) = cached["chunks"][idx]["options"]
+    #    options[symbol(keys)] = vals
+    #end
+    #haskey(options, :term_state) && (options[:term_state] = symbol(options[:term_state]))
+    #chunk.options = options
+    #chunk.content = cached["chunks"][idx]["content"]
+    #chunk.output = cached["chunks"][idx]["output"]
+    #chunk.figures = cached["chunks"][idx]["figures"]
 
-    chunk.options = options
-    chunk.content = cached["chunks"][idx]["content"]
-    chunk.output = cached["chunks"][idx]["output"]
-    chunk.figures = cached["chunks"][idx]["figures"]
-
-    return chunk
+    return new_chunks
 end
 
 #Could be used to restore inline code in future
-#function restore_chunk(chunk::DocChunk, cached, idx)
-#    chunk
-#end
+function restore_chunk(chunk::DocChunk, cached)
+      return chunk
+end

src/chunks.jl

@@ -26,13 +26,13 @@ type CodeChunk
     number::Int
     result_no::Int
     start_line::Int
-    option_AbstractString::AbstractString
+    optionstring::AbstractString
     options::Dict{Symbol, Any}
     output::AbstractString
     figures::Array{AbstractString}
     result::Array{ChunkOutput}
-    function CodeChunk(content, number, start_line, option_AbstractString, options)
-        new(content, number, 0, start_line, option_AbstractString, options, "", AbstractString[], ChunkOutput[])
+    function CodeChunk(content, number, start_line, optionstring, options)
+        new(content, number, 0, start_line, optionstring, options, "", AbstractString[], ChunkOutput[])
     end
 end
 

src/formatters.jl

@@ -3,7 +3,6 @@ function format(doc::WeaveDoc)
     formatted = AbstractString[]
     docformat = doc.format
 
-
     #Complete format dictionaries with defaults
     formatdict = docformat.formatdict
     get!(formatdict, :termstart, formatdict[:codestart])

src/run.jl

@@ -53,20 +53,25 @@ function Base.run(doc::WeaveDoc; doctype = :auto, plotlib="Gadfly",
 
     for i = 1:n
         chunk = doc.chunks[i]
-        result_chunks = run_chunk(chunk, report, SandBox, cached, cache, i)
-        #push!(executed, result_chunk)
+        if cached != nothing && (cache == :all || (cache ==:user && chunk.options[:cache]))
+            result_chunks = restore_chunk(chunk, cached)
+        else
+            result_chunks = run_chunk(chunk, report, SandBox)
+        end
         executed = [executed; result_chunks]
     end
 
+
     popdisplay(report)
 
+    #Clear variables from used sandbox
+    clear_sandbox(SandBox)
+    doc.chunks = executed
+
     if cache != :off
         write_cache(doc, cache_path)
     end
 
-    #Clear variables from used sandbox
-    clear_sandbox(SandBox)
-    doc.chunks = executed
     return doc
 end
 
@@ -83,19 +88,14 @@ function detect_doctype(source::AbstractString)
 end
 
 
-function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module, cached, cache, idx)
+function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
     #Defaults, already merged before, this merges format specific things
     options = merge(rcParams[:chunk_defaults], chunk.options)
     merge!(chunk.options, options)
-
-    if cached != nothing && (cache == :all || (cache ==:user && chunk.options[:cache]))
-        result_chunk = restore_chunk(chunk, cached, idx)
-    else
-        result_chunk = eval_chunk(chunk, report, SandBox)
-    end
+    result_chunk = eval_chunk(chunk, report, SandBox)
 end
 
-function run_chunk(chunk::DocChunk, report::Report, SandBox::Module, cached, cache, idx)
+function run_chunk(chunk::DocChunk, report::Report, SandBox::Module)
     return chunk
 end
 
@@ -193,6 +193,7 @@ function eval_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
       #else
      #   chunk.options[:fig] && (chunk.figures = copy(report.figures))
     #end
+
     chunks
 end
 
@@ -281,7 +282,7 @@ function collect_results(chunk::CodeChunk, fmt::ScriptResult)
             content *= r.code
         else
             content = "\n" * content * r.code
-            rchunk = CodeChunk(content, chunk.number, chunk.start_line, chunk.option_AbstractString, copy(chunk.options))
+            rchunk = CodeChunk(content, chunk.number, chunk.start_line, chunk.optionstring, copy(chunk.options))
             content = ""
             rchunk.result_no = result_no
             result_no *=1
@@ -308,7 +309,7 @@ function collect_results(chunk::CodeChunk, fmt::TermResult)
         output *= prompt * r.code
         output *=  r.displayed * r.stdout
         if !isempty(r.figures)
-            rchunk = CodeChunk("", chunk.number, chunk.start_line, chunk.option_AbstractString, copy(chunk.options))
+            rchunk = CodeChunk("", chunk.number, chunk.start_line, chunk.optionstring, copy(chunk.options))
             rchunk.output = output
             output = ""
             rchunk.figures = r.figures
@@ -316,7 +317,7 @@ function collect_results(chunk::CodeChunk, fmt::TermResult)
         end
     end
     if output != ""
-         rchunk = CodeChunk("", chunk.number, chunk.start_line, chunk.option_AbstractString, copy(chunk.options))
+         rchunk = CodeChunk("", chunk.number, chunk.start_line, chunk.optionstring, copy(chunk.options))
          rchunk.output = output
         push!(result_chunks, rchunk)
     end