Changed chunk options to follow Knitr's naming

* Implemented dpi and fig_witdth and fig_height for Gadfly and Winston

.gitignore

@@ -1,8 +1,12 @@
 
 test.jl
-examples/*/*.png
+examples/figures/
 examples/*.md
+examples/*.pdf
 examples/*.html
 tmp/
 .idea
 *.*~
+*.aux
+*.log
+*.out

examples/winston_sample.mdw

@@ -33,7 +33,7 @@ p = plot(t, sinc(t))
 
 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"; fig_width=8; fig_height=4>>=
 p = plot(cumsum(randn(1000, 1)))
 xlabel("x")
 ylabel("sinc(x)")

src/JuliaReport.jl

@@ -1,6 +1,5 @@
 module JuliaReport
 using Compat
-import Base: display, writemime
 
 #Contains report global properties
 type Report <: Display
@@ -10,15 +9,13 @@ type Report <: Display
   basename::String
   formatdict
   pending_code::String
-  figdir::String
-  executed::Array
   cur_result::String
   fignum::Int
   figures::Array
   cur_chunk::Dict
 
   function Report()
-        new("", false, "", "",  Any[], "", "", Any[], "", 1, Any[],  @compat Dict{Symbol, Any}())
+        new("", false, "", "",  Any[], "", "", 1, Any[],  @compat Dict{Symbol, Any}())
   end
 
 end
@@ -29,7 +26,7 @@ const supported_mime_types =
     [MIME"image/png",
      MIME"text/plain"]
 
-function display(doc::Report, data)
+function Base.display(doc::Report, data)
     for m in supported_mime_types
         if mimewritable(m(), data)
             display(doc, m(), data)
@@ -48,23 +45,25 @@ module ReportSandBox
 end
 
 
-function weave(source ; doctype = "pandoc", plotlib="PyPlot", informat="noweb", figdir = "figures", figformat = nothing)
+function weave(source ; doctype = "pandoc", plotlib="PyPlot", informat="noweb", fig_path = "figures", fig_ext = nothing)
 
     cwd, fname = splitdir(abspath(source))
     basename = splitext(fname)[1]
     formatdict = formats[doctype].formatdict
-    figformat == nothing || (formatdict[:figfmt] = figformat)
+    fig_ext == nothing || (rcParams[:chunk_defaults][:fig_ext] = fig_ext)
+
+
     #report = Report(source, false, cwd, basename, formatdict, "", figdir)
 
     report.source = source
     report.cwd = cwd
     report.basename = basename
-    report.figdir = figdir
+    rcParams[:chunk_defaults][:fig_path] = fig_path
     report.formatdict = formatdict
 
 
     if plotlib == nothing
-        rcParams[:chunk][:defaultoptions][:fig] = false
+        rcParams[:chunk_defaults][:fig] = false
     else
         l_plotlib = lowercase(plotlib)
         if l_plotlib == "winston"
@@ -76,6 +75,10 @@ function weave(source ; doctype = "pandoc", plotlib="PyPlot", informat="noweb",
         elseif l_plotlib == "gadfly"
             eval(parse("""include(Pkg.dir("JuliaReport","src","gadfly.jl"))"""))
             rcParams[:plotlib] = "Gadfly"
+            if rcParams[:chunk_defaults][:fig_ext] != ".png"
+              rcParams[:chunk_defaults][:fig_ext] = ".png"
+              warn("Saving figures as .png with Gadfly")
+            end
         end
     end
 
@@ -152,19 +155,19 @@ function run(parsed)
     if chunk[:type] == "code"
       #print(chunk["content"])
       info("Weaving chunk $(chunk[:number]) from line $(chunk[:start_line])")
-      defaults = copy(rcParams[:chunk][:defaultoptions])
+      defaults = copy(rcParams[:chunk_defaults])
       options = copy(chunk[:options])
       try
-        options = merge(rcParams[:chunk][:defaultoptions], options)
+        options = merge(rcParams[:chunk_defaults], options)
       catch
-        options = rcParams[:chunk][:defaultoptions]
+        options = rcParams[:chunk_defaults]
         warn("Invalid format for chunk options line: $(chunk[:start_line])")
       end
 
       merge!(chunk, options)
       delete!(chunk, :options)
 
-      chunk[:evaluate] || (chunk[:result] = ""; continue) #Do nothing if eval is false
+      chunk[:eval] || (chunk[:result] = ""; continue) #Do nothing if eval is false
 
       report.fignum = 1
       report.cur_result = ""
@@ -197,15 +200,14 @@ end
 
 function savefigs_pyplot(chunk)
     fignames = String[]
-    ext = report.formatdict[:figfmt]
+    ext = report.formatdict[:fig_ext]
-    figpath = joinpath(report.cwd, report.figdir)
+    figpath = joinpath(report.cwd, chunk[:fig_path])
     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")
+        full_name, rel_name = get_figname(report, chunk, fignum=fig)
-        rel_name = "$(report.figdir)/$(report.basename)_$(chunkid)_$fig$ext" #Relative path is used in output
+        savefig(full_name, dpi=chunk[:dpi])
-        savefig(full_name)
         push!(fignames, rel_name)
         plt.draw()
         plt.close()
@@ -215,22 +217,20 @@ end
 
 
 
-function display(report::Report, m::MIME"text/plain", data)
+function Base.display(report::Report, m::MIME"text/plain", data)
   s = reprmime(m, data)
   report.cur_result *= s
-  push!(report.executed, s)
 end
 
-function get_figname(report::Report, chunk)
+function get_figname(report::Report, chunk; fignum = nothing)
-    figpath = joinpath(report.cwd, report.figdir)
+    figpath = joinpath(report.cwd, chunk[:fig_path])
     isdir(figpath) || mkdir(figpath)
-    ext = report.formatdict[:figfmt]
+    ext = chunk[:fig_ext]
-    fig = report.fignum
+    fignum == nothing && (fignum = report.fignum)
-    chunk = report.cur_chunk
-    chunkid = (chunk[:name] == nothing) ? chunk[:number] : chunk[:name]
-    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
 
+    chunkid = (chunk[:name] == nothing) ? chunk[:number] : chunk[:name]
+    full_name = joinpath(report.cwd, chunk[:fig_path], "$(report.basename)_$(chunkid)_$(fignum)$ext")
+    rel_name = "$(chunk[:fig_path])/$(report.basename)_$(chunkid)_$(fignum)$ext" #Relative path is used in output
     return full_name, rel_name
 end
 

src/config.jl

@@ -1,25 +1,70 @@
 const rcParams =
-    @compat Dict{Symbol,Any}(:figdir=> "figures",
+    @compat Dict{Symbol,Any}(
                              :plotlib => "PyPlot",
-                             :storeresults=> false,
+                             :storeresults => false,
-                             :cachedir=> "cache",
+                             :chunk_defaults => Dict{Symbol,Any}(:echo=> true,
-                             :chunk=>
+                                                               :results=> "markup",
-                             Dict{Symbol,Any}(:defaultoptions=>
-                                              Dict{Symbol,Any}(:echo=> true,
-                                                               :results=> "verbatim",
                                                                :fig=> true,
                                                                :include=> true,
-                                                               :evaluate=> true,
+                                                               :eval => true,
-                                                               :caption=> false,
+                                                               :fig_cap=> false,
+                                                               :fig_width => 8, #Size in inches
+                                                               :fig_height => 6,
+                                                               :fig_path=> "figures",
+                                                               :out_width=> nothing, #Defined separately for each format
+                                                               :out_height=> nothing,
+                                                               :fig_ext => ".png",
+                                                               :dpi => 200,
                                                                :term=> false,
                                                                :name=> nothing,
                                                                :wrap=> true,
-                                                               :f_pos=> "htpb",
+                                                               :fig_pos=> nothing,
-                                                               :f_size=> (8, 6),
+                                                               :fig_env=> nothing,
-                                                               :f_env=> nothing,
-                                                               :f_spines=> true,
-                                                               :complete=> true,
                                                                :engine=> "julia",
                                                                :option_string=> "")
                                               )
-                             )
+
+
+
+
+# Working towards Knitr compatible options, implemented options are added to defaultoptions dictionary above
+# and work in progress stays here, options from https://github.com/yihui/knitr/blob/master/R/defaults.R
+# If you need a particular options, consider implementing it and making a pull request.
+
+#tidy = FALSE,
+#tidy.opts = NULL,
+#collapse = FALSE
+#prompt = FALSE
+#highlight = TRUE
+#strip.white = TRUE
+#size = 'normalsize'
+#background = '#F7F7F7',
+#cache = FALSE
+#cache.path = 'cache/'
+#cache.vars = NULL
+#cache.lazy = TRUE,
+#dependson = NULL
+#autodep = FALSE,
+#fig.keep = 'high'
+#fig.show = 'asis'
+#fig.align = 'default'
+#dev = NULL
+#dev.args = NULL
+#fig.ext = NULL
+#fig.scap = NULL
+#fig.lp = 'fig:'
+#fig.subcap = NULL,
+#out.extra = NULL
+#fig.retina = 1,
+#external = TRUE
+#sanitize = FALSE
+#interval = 1
+#aniopts = 'controls,loop',
+#warning = TRUE
+#error = TRUE
+#message = TRUE,
+#render = NULL,
+#ref.label = NULL
+#child = NULL
+#split = FALSE
+#purl = TRUE

src/formatters.jl

@@ -5,15 +5,27 @@ function format(executed, doctype)
   formatted = String[]
   docformat = formats[doctype]
   #@show docformat
+
+  #Complete format dictionaries with defaults
   formatdict = docformat.formatdict
   get!(formatdict, :termstart, formatdict[:codestart])
   get!(formatdict, :termend, formatdict[:codeend])
+  get!(formatdict, :out_width, nothing)
+  get!(formatdict, :out_height, nothing)
+  get!(formatdict, :fig_pos, nothing)
+  get!(formatdict, :fig_env, nothing)
+
 
   for chunk in copy(executed)
 
       if chunk[:type] == "doc"
           push!(formatted, chunk[:content])
       else
+          #Fill undefined options with format specific defaults
+          chunk[:out_width] == nothing && (chunk[:out_width] =  docformat.formatdict[:out_width])
+          chunk[:fig_env] == nothing && (chunk[:fig_env] =  docformat.formatdict[:fig_env])
+          chunk[:fig_pos] == nothing && (chunk[:fig_pos] =  docformat.formatdict[:fig_pos])
+
 
           #Format code
           result = format_codechunk(chunk, formatdict)
@@ -34,7 +46,7 @@ end
 function format_codechunk(chunk, formatdict)
 
 
-    if !chunk[:evaluate]
+    if !chunk[:eval]
         if chunk[:echo]
             result = "$(formatdict[:codestart])$(chunk[:content])$(formatdict[:codeend])"
             return result
@@ -59,10 +71,10 @@ function format_codechunk(chunk, formatdict)
 
         if (strip(chunk[:result])!= "") && (chunk[:results] != "hidden")
             #@show chunk
-            if chunk[:results] != "verbatim"
+            if chunk[:results] != "markup"
                 haskey(formatdict, :indent) && (chunk[:result] = indent(chunk[:result]))
                 result *= "$(chunk[:result])"
-            elseif chunk[:results] == "verbatim"
+            elseif chunk[:results] == "markup"
                 result *= "$(formatdict[:outputstart])$(chunk[:result])\n$(formatdict[:outputend])\n"
             end
         end
@@ -98,9 +110,11 @@ const tex = Tex(@compat Dict{Symbol,Any}(:codestart => "\\begin{juliacode}",
                                          :codeend => "\\end{juliacode}",
                                          :outputstart => "\\begin{juliaout}",
                                          :outputend => "\\end{juliaout}",
-                                         :figfmt => ".pdf",
+                                         :fig_ext => ".pdf",
                                          :extension =>"tex",
-                                         :width => "\\linewidth",
+                                         :out_width=> "\\linewidth",
+                                         :fig_env=> "figure",
+                                         :fig_pos => "htpb",
                                          :doctype => "tex"
                                          ))
 
@@ -110,9 +124,11 @@ const texminted = Tex(@compat Dict{Symbol,Any}(:codestart => "\\begin{minted}[ma
                                          :outputend => "\\end{minted}",
                                          :termstart=> "\\begin{minted}[fontsize=\\footnotesize, xleftmargin=0.5em, mathescape]{julia}",
                                          :termend => "\\end{minted}",
-                                         :figfmt => ".pdf",
+                                         :fig_ext => ".pdf",
                                          :extension =>"tex",
-                                         :width => "\\linewidth",
+                                         :out_width => "\\linewidth",
+                                         :fig_env=> "figure",
+                                         :fig_pos => "htpb",
                                          :doctype => "texminted"
                                          ))
 
@@ -124,19 +140,20 @@ const pandoc = Pandoc(@compat Dict{Symbol,Any}(:codestart => "~~~~{.julia}",
                                :codeend=>"~~~~~~~~~~~~~\n\n",
                                :outputstart=>"~~~~{.julia}",
                                :outputend=>"~~~~~~~~~~~~~\n\n",
-                               :figfmt=>".png",
+                               :fig_ext=>".png",
                                :extension=>"md",
-                               :width=>"15 cm",
                                :doctype=>"pandoc"
                                                ))
 
 
 function formatfigures(chunk, docformat::Tex)
     fignames = chunk[:figure]
-    caption = chunk[:caption]
+    caption = chunk[:fig_cap]
-    width = get!(chunk, :width, docformat.formatdict[:width])
+    width = chunk[:out_width]
-    f_pos = chunk[:f_pos]
+
-    f_env = chunk[:f_env]
+
+    f_pos = chunk[:fig_pos]
+    f_env = chunk[:fig_env]
     result = ""
     figstring = ""
 
@@ -144,6 +161,7 @@ function formatfigures(chunk, docformat::Tex)
         result *= """\\begin{$f_env}\n"""
     end
 
+
     for fig = fignames
         figstring *= "\\includegraphics[width= $width]{$fig}\n"
     end
@@ -172,8 +190,7 @@ end
 
 function formatfigures(chunk, docformat::Pandoc)
     fignames = chunk[:figure]
-    caption = chunk[:caption]
+    caption = chunk[:fig_cap]
-    width = get!(chunk, :width, docformat.formatdict[:width])
     result = ""
     figstring = ""
 

src/gadfly.jl

@@ -3,8 +3,14 @@ using Gadfly
 Gadfly.set_default_plot_format(:png)
 
 #Captures figures
-function display(report::Report, m::MIME"image/png", data)
+function Base.display(report::Report, m::MIME"image/png", p::Plot)
     chunk = report.cur_chunk
+
+    if chunk[:fig_ext] != ".png"
+      chunk[:fig_ext]
+      warn("Saving figures as .png with Gadfly")
+    end
+
     full_name, rel_name = get_figname(report, chunk)
 
     docformat = formats[report.formatdict[:doctype]]
@@ -21,7 +27,11 @@ function display(report::Report, m::MIME"image/png", data)
     end
 
     report.fignum += 1
-    out = open(full_name, "w")
+
-    writemime(out, m, data)
+    #TODO other formats
-    close(out)
+    r = chunk[:dpi]/96 #Relative to Gadfly default 96dpi
+    draw(PNG(full_name, chunk[:fig_width]inch*r, chunk[:fig_height]inch*r ), p)
+    #out = open(full_name, "w")
+    #writemime(out, m, data)
+    #close(out)
 end

src/winston.jl

@@ -1,6 +1,6 @@
 using Winston
 
-function display(report::Report, m::MIME"image/png", data)
+function Base.display(report::Report, m::MIME"image/png", data)
 
     chunk = report.cur_chunk
     full_name, rel_name = get_figname(report, chunk)
@@ -19,7 +19,7 @@ function display(report::Report, m::MIME"image/png", data)
     end
 
     #TODO get width and height from chunk options, after implementing Knitr compatible options
-    savefig(data, full_name, width=2000, height=800)
+    savefig(data, full_name, width=chunk[:fig_width]*chunk[:dpi], height=chunk[:fig_height]*chunk[:dpi])
     report.fignum += 1
     #out = open(full_name, "w")
     #writemime(out, m, data)