First version

README.md

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 # JuliaReport
 
 [![Build Status](https://travis-ci.org/mpastell/JuliaReport.jl.svg?branch=master)](https://travis-ci.org/mpastell/JuliaReport.jl)
+
+JuliaReport is a scientific report generator/literate programming tool
+for Julia. It is based on [Pweave](http://mpastell.com/pweave) and
+resembles Knitr and Sweave. Actually JuliaReport relies on Pweave for
+document parsing and formatting.
+
+**Current features**
+
+* Pweave Noweb or script syntax for documents.
+* Execute code as terminal or "script" chunks.
+* Capture PyPlot figures.
+* All Pweave output formats supported. Including, Latex, Markdown, Sphinx etc.
+
+**Not implemented**
+
+* Inline code
+* Caching
+
+## Usage
+
+Run from julia:
+
+    using JuliaReport
+    weave("examples/julia_sample.mdw")
+
+
+
+
+

examples/julia_sample.mdw

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+
+# Introducion to JuliaReport
+
+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. 
+
+This documented can be turned into Pandoc markdown with captured
+result from Julia prompt.
+
+~~~~{.julia}
+using JuliaReport
+weave("examples/julia_sample.mdw")
+~~~~
+
+## Terminal chunk
+
+<<term=True>>=
+x = 1:10
+d = {"juliareport" => "testing"}
+y = [2, 4 ,8]
+@
+
+## Capturing figures
+
+The figures and code can be included in the output.
+
+<<>>=
+using PyPlot
+t = linspace(0, 2*pi, 100)
+plot(t, sinc(t))
+xlabel("x")
+ylabel("sinc(x)")
+@
+
+You can also include a plot with caption and hide the code:
+
+<<echo=False, caption="Random walk.", label="random">>=
+plot(cumsum(randn(1000, 1)))
+@

src/JuliaReport.jl

@@ -1,5 +1,137 @@
 module JuliaReport
+using PyCall
+using PyPlot
 
-# package code goes here
+#Parsing and formatting uses Pweave
+@pyimport pweave
 
-end # module
+#Contains report global properties
+#Similar to pweave.PwebProcessor
+type Report
+  source::String
+  documentationmode::Bool
+  cwd::String
+  basename::String
+  formatdict
+  pending_code::String
+  figdir::String
+end
+
+
+global report = Report("", false, "", "",  {}, "", "")
+
+function listformats()
+  pweave.listformats()
+end
+
+function weave(source ; doctype = "pandoc", informat="noweb", figdir = "figures", figformat = nothing)
+    pweave.rcParams["chunk"]["defaultoptions"]["engine"] = "julia"
+
+    doc = pweave.Pweb(source, doctype, shell="julia")
+    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)
+
+    #Formatting with pweave
+    doc[:executed] = run(PyVector(doc["parsed"]))
+    doc[:isexecuted] = true
+    doc[:format]()
+    doc[:write]()
+end
+
+
+function run_block(code_str)
+    oldSTDOUT = STDOUT
+    #If there is nothing to read code will hang
+    println()
+    rw, wr = redirect_stdout()
+    include_string(code_str)
+    redirect_stdout(oldSTDOUT)
+    close(wr)
+    result = readall(rw)
+    close(rw)
+    return string("\n", result)
+end
+
+function run_term(code_str)
+    oldSTDOUT = STDOUT
+    #If there is nothing to read code will hang
+    println()
+    rw, wr = redirect_stdout()
+
+
+    #Emulate terminal
+    n = length(code_str)
+    pos = 2 #The first character is extra line end
+    while pos < n
+        oldpos = pos
+        code, pos = parse(code_str, pos)
+        println(string("\njulia> ", rstrip(code_str[oldpos:(pos-1)])))
+        s = eval(code)
+        s == nothing || (smime = reprmime(MIME("text/plain"), s))  #display(s)
+        println(smime)
+    end
+
+    redirect_stdout(oldSTDOUT)
+    close(wr)
+    result = readall(rw)
+    close(rw)
+    return string(result)
+end
+
+
+function run(parsed)
+    i = 1
+    for chunk = copy(parsed)
+        if chunk["type"] == "code"
+            #print(chunk["content"])
+            info("""Weaving chunk $(chunk["number"]) from line $(chunk["start_line"])""")
+            defaults = copy(pweave.rcParams["chunk"]["defaultoptions"])
+            merge!(defaults, chunk["options"])
+            merge!(chunk, defaults)
+            chunk["evaluate"] || (chunk["result"] = ""; continue) #Do nothing if eval is false
+
+            if chunk["term"]
+                chunk["result"] = run_term(chunk["content"])
+            else
+                chunk["result"] = run_block(chunk["content"])
+            end
+
+            chunk["fig"] && (chunk["figure"] = savefigs(chunk))
+
+        end
+        parsed[i] = copy(chunk)
+        i += 1
+    end
+  return parsed
+end
+
+function savefigs(chunk)
+    fignames = String[]
+    ext = report.formatdict["figfmt"]
+    figpath = joinpath(report.cwd, report.figdir)
+    isdir(figpath) || mkdir(figpath)
+
+    chunkid = ((chunk["name"] == nothing) ? chunk["number"] : chunk["name"])
+    #Iterate over all open figures, save them and store names
+    for fig = plt.get_fignums()
+        full_name = joinpath(report.cwd, report.figdir, "$(report.basename)_$(chunkid)_$fig$ext")
+        rel_name = "$(report.figdir)/$(report.basename)_$(chunkid)_$fig$ext" #Relative path is used in output
+        savefig(full_name)
+        push!(fignames, rel_name)
+        plt.draw()
+        plt.close()
+    end
+    return fignames
+end
+
+export weave
+
+end