Working on caching. Saving and restoring added, problems with formatting

REQUIRE

@@ -2,4 +2,4 @@ julia 0.3
 Compat
 ArgParse
 Docile
-JSON
+HDF5

src/Weave.jl

@@ -100,7 +100,7 @@ function weave(source ; doctype = "pandoc", plotlib="Gadfly",
     doc = read_doc(source, informat) #Reader toimii, muuten kesken...
     doc = run(doc, doctype = doctype, plotlib=plotlib,
             informat = informat, out_path=out_path,
-            fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path)    
+            fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path)
     formatted = format(doc)
 
     outname = "$(doc.cwd)/$(doc.basename).$(doc.format.formatdict[:extension])"
@@ -131,9 +131,10 @@ end
 
 export weave, list_out_formats, tangle
 
-include("chunks.jl")
-include("run.jl")
 include("config.jl")
+include("chunks.jl")
 include("readers.jl")
+include("run.jl")
+include("cache.jl")
 include("formatters.jl")
 end

src/cache.jl

@@ -1,10 +1,25 @@
-import JSON
-
-function cache(doc::WeaveDoc, cache_path)
-    
+import HDF5, JLD
 
+function write_cache(doc::WeaveDoc, cache_path)
+    isdir(cache_path) || mkdir(cache_path)
+    name = "$cache_path/$(doc.basename).jld"
+    JLD.save(name, "doc", doc)
+    #open(name, "w") do io
+    #    write(io, JSON.json(doc))
+    #end
+    return nothing
 end
 
+function read_cache(doc::WeaveDoc, cache_path)
+    name = "$cache_path/$(doc.basename).jld"
+    isfile(name) || return nothing
+    return JLD.load(name, "doc")
+    #parsed = JSON.parsefile(name)
+    #doc = WeaveDoc(parsed["source"], parsed["chunks"],
+    #parsed["cwd"], parsed["doctype"])
+end
+
+
 
 #Todo caching of data, can get the contents of module using:
 #names(ReportSandBox, all=true)

src/chunks.jl

@@ -6,10 +6,18 @@ type WeaveDoc
     chunks::Array
     cwd::String
     format
+    doctype::String
     function WeaveDoc(source, chunks)
         path, fname = splitdir(abspath(source))
         basename = splitext(fname)[1]
-        new(source, basename, path, chunks, "", nothing)
+        new(source, basename, path, chunks, "", nothing, "")
+    end
+
+    function WeaveDoc(source, chunks, cwd, doctype)
+        path, fname = splitdir(abspath(source))
+        basename = splitext(fname)[1]
+        format = formats[doctype]
+        new(source, basename, path, chunks, cwd, format, doctype)
     end
 end
 

src/config.jl

@@ -10,6 +10,7 @@ const rcParams =
                                 :fig=> true,
                                 :include=> true,
                                 :eval => true,
+                                :cache => false,
                                 :fig_cap=> nothing,
                                 #Size in inches
                                 :fig_width => 6,

src/run.jl

@@ -2,8 +2,13 @@
 
 
 function run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="noweb",
-        out_path=:doc, fig_path = "figures", fig_ext = nothing, cache_path = "cache")
+        out_path=:doc, fig_path = "figures", fig_ext = nothing,
+        cache_path = "cache", cache = :off)
+    #cache :all, :user, :off
+
+
     doc.cwd = get_cwd(doc, out_path)
+    doc.doctype = doctype
     doc.format = formats[doctype]
     set_rc_params(doc.format.formatdict, fig_path, fig_ext)
 
@@ -18,13 +23,32 @@ function run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="nowe
     report = Report(doc.cwd, doc.basename, doc.format.formatdict)
     pushdisplay(report)
 
+    if cache != :off
+        cached = read_cache(doc, cache_path)
+        cached == nothing && info("No cached results found, running code")
+    else
+        cached = nothing
+    end
+
     executed = Any[]
-    for chunk in copy(doc.chunks)
-        result_chunk = eval_chunk(chunk, report, SandBox)
+    n = length(doc.chunks)
+
+    for i = 1:n
+        chunk = doc.chunks[i]
+        if cached != nothing && (cache == :all || (cache ==:user && chunk.options.cache))
+            result_chunk = cached.chunks[i]
+        else
+            result_chunk = eval_chunk(chunk, report, SandBox)
+        end
         push!(executed, result_chunk)
     end
+
     popdisplay(report)
 
+    if cache != :off
+        write_cache(doc, cache_path)
+    end
+
     #Clear variables from used sandbox
     clear_sandbox(SandBox)
     doc.chunks = executed
@@ -136,6 +160,8 @@ function eval_chunk(chunk::DocChunk, report::Report, SandBox)
     chunk
 end
 
+
+
 #Set all variables to nothing
 function clear_sandbox(SandBox::Module)
     for name = names(SandBox, true)