mirror of https://github.com/mpastell/Weave.jl
Changed chunk options to follow Knitr's naming
* Implemented dpi and fig_witdth and fig_height for Gadfly and Winstonpull/17/head
Matti Pastell
parent
60b29e751e
commit
e20025315d
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@ -1,8 +1,12 @@
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test.jl
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examples/*/*.png
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examples/figures/
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examples/*.md
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examples/*.pdf
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examples/*.html
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tmp/
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.idea
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*.*~
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*.aux
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*.log
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*.out
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@ -33,7 +33,7 @@ p = plot(t, sinc(t))
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You can also include a plot with caption and hide the code:
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<<echo=false; caption="Random walk."; label="random">>=
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<<echo=false; caption="Random walk."; label="random"; fig_width=8; fig_height=4>>=
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p = plot(cumsum(randn(1000, 1)))
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xlabel("x")
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ylabel("sinc(x)")
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Binary file not shown.
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@ -1,6 +1,5 @@
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module JuliaReport
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using Compat
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import Base: display, writemime
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#Contains report global properties
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type Report <: Display
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@ -10,15 +9,13 @@ type Report <: Display
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basename::String
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formatdict
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pending_code::String
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figdir::String
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executed::Array
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cur_result::String
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fignum::Int
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figures::Array
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cur_chunk::Dict
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function Report()
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new("", false, "", "", Any[], "", "", Any[], "", 1, Any[], @compat Dict{Symbol, Any}())
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new("", false, "", "", Any[], "", "", 1, Any[], @compat Dict{Symbol, Any}())
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end
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end
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@ -29,7 +26,7 @@ const supported_mime_types =
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[MIME"image/png",
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MIME"text/plain"]
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function display(doc::Report, data)
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function Base.display(doc::Report, data)
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for m in supported_mime_types
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if mimewritable(m(), data)
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display(doc, m(), data)
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@ -48,23 +45,25 @@ module ReportSandBox
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end
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function weave(source ; doctype = "pandoc", plotlib="PyPlot", informat="noweb", figdir = "figures", figformat = nothing)
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function weave(source ; doctype = "pandoc", plotlib="PyPlot", informat="noweb", fig_path = "figures", fig_ext = nothing)
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cwd, fname = splitdir(abspath(source))
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basename = splitext(fname)[1]
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formatdict = formats[doctype].formatdict
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figformat == nothing || (formatdict[:figfmt] = figformat)
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fig_ext == nothing || (rcParams[:chunk_defaults][:fig_ext] = fig_ext)
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#report = Report(source, false, cwd, basename, formatdict, "", figdir)
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report.source = source
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report.cwd = cwd
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report.basename = basename
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report.figdir = figdir
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rcParams[:chunk_defaults][:fig_path] = fig_path
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report.formatdict = formatdict
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if plotlib == nothing
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rcParams[:chunk][:defaultoptions][:fig] = false
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rcParams[:chunk_defaults][:fig] = false
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else
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l_plotlib = lowercase(plotlib)
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if l_plotlib == "winston"
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@ -76,6 +75,10 @@ function weave(source ; doctype = "pandoc", plotlib="PyPlot", informat="noweb",
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elseif l_plotlib == "gadfly"
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eval(parse("""include(Pkg.dir("JuliaReport","src","gadfly.jl"))"""))
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rcParams[:plotlib] = "Gadfly"
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if rcParams[:chunk_defaults][:fig_ext] != ".png"
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rcParams[:chunk_defaults][:fig_ext] = ".png"
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warn("Saving figures as .png with Gadfly")
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end
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end
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end
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@ -152,19 +155,19 @@ function run(parsed)
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if chunk[:type] == "code"
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#print(chunk["content"])
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info("Weaving chunk $(chunk[:number]) from line $(chunk[:start_line])")
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defaults = copy(rcParams[:chunk][:defaultoptions])
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defaults = copy(rcParams[:chunk_defaults])
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options = copy(chunk[:options])
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try
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options = merge(rcParams[:chunk][:defaultoptions], options)
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options = merge(rcParams[:chunk_defaults], options)
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catch
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options = rcParams[:chunk][:defaultoptions]
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options = rcParams[:chunk_defaults]
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warn("Invalid format for chunk options line: $(chunk[:start_line])")
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end
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merge!(chunk, options)
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delete!(chunk, :options)
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chunk[:evaluate] || (chunk[:result] = ""; continue) #Do nothing if eval is false
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chunk[:eval] || (chunk[:result] = ""; continue) #Do nothing if eval is false
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report.fignum = 1
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report.cur_result = ""
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@ -197,15 +200,14 @@ end
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function savefigs_pyplot(chunk)
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fignames = String[]
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ext = report.formatdict[:figfmt]
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figpath = joinpath(report.cwd, report.figdir)
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ext = report.formatdict[:fig_ext]
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figpath = joinpath(report.cwd, chunk[:fig_path])
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isdir(figpath) || mkdir(figpath)
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chunkid = (chunk[:name] == nothing) ? chunk[:number] : chunk[:name]
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#Iterate over all open figures, save them and store names
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for fig = plt.get_fignums()
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full_name = joinpath(report.cwd, report.figdir, "$(report.basename)_$(chunkid)_$fig$ext")
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rel_name = "$(report.figdir)/$(report.basename)_$(chunkid)_$fig$ext" #Relative path is used in output
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savefig(full_name)
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full_name, rel_name = get_figname(report, chunk, fignum=fig)
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savefig(full_name, dpi=chunk[:dpi])
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push!(fignames, rel_name)
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plt.draw()
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plt.close()
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@ -215,22 +217,20 @@ end
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function display(report::Report, m::MIME"text/plain", data)
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function Base.display(report::Report, m::MIME"text/plain", data)
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s = reprmime(m, data)
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report.cur_result *= s
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push!(report.executed, s)
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end
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function get_figname(report::Report, chunk)
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figpath = joinpath(report.cwd, report.figdir)
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function get_figname(report::Report, chunk; fignum = nothing)
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figpath = joinpath(report.cwd, chunk[:fig_path])
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isdir(figpath) || mkdir(figpath)
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ext = report.formatdict[:figfmt]
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fig = report.fignum
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chunk = report.cur_chunk
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chunkid = (chunk[:name] == nothing) ? chunk[:number] : chunk[:name]
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full_name = joinpath(report.cwd, report.figdir, "$(report.basename)_$(chunkid)_$fig$ext")
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rel_name = "$(report.figdir)/$(report.basename)_$(chunkid)_$fig$ext" #Relative path is used in output
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ext = chunk[:fig_ext]
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fignum == nothing && (fignum = report.fignum)
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chunkid = (chunk[:name] == nothing) ? chunk[:number] : chunk[:name]
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full_name = joinpath(report.cwd, chunk[:fig_path], "$(report.basename)_$(chunkid)_$(fignum)$ext")
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rel_name = "$(chunk[:fig_path])/$(report.basename)_$(chunkid)_$(fignum)$ext" #Relative path is used in output
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return full_name, rel_name
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end
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@ -1,25 +1,70 @@
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const rcParams =
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@compat Dict{Symbol,Any}(:figdir=> "figures",
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@compat Dict{Symbol,Any}(
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:plotlib => "PyPlot",
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:storeresults=> false,
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:cachedir=> "cache",
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:chunk=>
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Dict{Symbol,Any}(:defaultoptions=>
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Dict{Symbol,Any}(:echo=> true,
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:results=> "verbatim",
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:storeresults => false,
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:chunk_defaults => Dict{Symbol,Any}(:echo=> true,
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:results=> "markup",
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:fig=> true,
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:include=> true,
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:evaluate=> true,
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:caption=> false,
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:eval => true,
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:fig_cap=> false,
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:fig_width => 8, #Size in inches
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:fig_height => 6,
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:fig_path=> "figures",
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:out_width=> nothing, #Defined separately for each format
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:out_height=> nothing,
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:fig_ext => ".png",
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:dpi => 200,
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:term=> false,
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:name=> nothing,
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:wrap=> true,
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:f_pos=> "htpb",
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:f_size=> (8, 6),
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:f_env=> nothing,
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:f_spines=> true,
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:complete=> true,
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:fig_pos=> nothing,
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:fig_env=> nothing,
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:engine=> "julia",
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:option_string=> "")
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)
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)
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# Working towards Knitr compatible options, implemented options are added to defaultoptions dictionary above
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# and work in progress stays here, options from https://github.com/yihui/knitr/blob/master/R/defaults.R
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# If you need a particular options, consider implementing it and making a pull request.
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#tidy = FALSE,
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#tidy.opts = NULL,
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#collapse = FALSE
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#prompt = FALSE
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#highlight = TRUE
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#strip.white = TRUE
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#size = 'normalsize'
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#background = '#F7F7F7',
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#cache = FALSE
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#cache.path = 'cache/'
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#cache.vars = NULL
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#cache.lazy = TRUE,
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#dependson = NULL
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#autodep = FALSE,
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#fig.keep = 'high'
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#fig.show = 'asis'
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#fig.align = 'default'
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#dev = NULL
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#dev.args = NULL
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#fig.ext = NULL
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#fig.scap = NULL
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#fig.lp = 'fig:'
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#fig.subcap = NULL,
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#out.extra = NULL
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#fig.retina = 1,
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#external = TRUE
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#sanitize = FALSE
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#interval = 1
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#aniopts = 'controls,loop',
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#warning = TRUE
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#error = TRUE
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#message = TRUE,
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#render = NULL,
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#ref.label = NULL
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#child = NULL
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#split = FALSE
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#purl = TRUE
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@ -5,15 +5,27 @@ function format(executed, doctype)
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formatted = String[]
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docformat = formats[doctype]
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#@show docformat
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#Complete format dictionaries with defaults
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formatdict = docformat.formatdict
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get!(formatdict, :termstart, formatdict[:codestart])
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get!(formatdict, :termend, formatdict[:codeend])
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get!(formatdict, :out_width, nothing)
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get!(formatdict, :out_height, nothing)
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get!(formatdict, :fig_pos, nothing)
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get!(formatdict, :fig_env, nothing)
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for chunk in copy(executed)
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if chunk[:type] == "doc"
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push!(formatted, chunk[:content])
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else
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#Fill undefined options with format specific defaults
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chunk[:out_width] == nothing && (chunk[:out_width] = docformat.formatdict[:out_width])
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chunk[:fig_env] == nothing && (chunk[:fig_env] = docformat.formatdict[:fig_env])
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chunk[:fig_pos] == nothing && (chunk[:fig_pos] = docformat.formatdict[:fig_pos])
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#Format code
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result = format_codechunk(chunk, formatdict)
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@ -34,7 +46,7 @@ end
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function format_codechunk(chunk, formatdict)
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if !chunk[:evaluate]
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if !chunk[:eval]
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if chunk[:echo]
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result = "$(formatdict[:codestart])$(chunk[:content])$(formatdict[:codeend])"
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return result
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@ -59,10 +71,10 @@ function format_codechunk(chunk, formatdict)
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if (strip(chunk[:result])!= "") && (chunk[:results] != "hidden")
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#@show chunk
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if chunk[:results] != "verbatim"
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if chunk[:results] != "markup"
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haskey(formatdict, :indent) && (chunk[:result] = indent(chunk[:result]))
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result *= "$(chunk[:result])"
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elseif chunk[:results] == "verbatim"
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elseif chunk[:results] == "markup"
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result *= "$(formatdict[:outputstart])$(chunk[:result])\n$(formatdict[:outputend])\n"
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end
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end
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@ -98,9 +110,11 @@ const tex = Tex(@compat Dict{Symbol,Any}(:codestart => "\\begin{juliacode}",
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:codeend => "\\end{juliacode}",
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:outputstart => "\\begin{juliaout}",
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:outputend => "\\end{juliaout}",
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:figfmt => ".pdf",
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:fig_ext => ".pdf",
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:extension =>"tex",
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:width => "\\linewidth",
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:out_width=> "\\linewidth",
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:fig_env=> "figure",
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:fig_pos => "htpb",
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:doctype => "tex"
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))
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@ -110,9 +124,11 @@ const texminted = Tex(@compat Dict{Symbol,Any}(:codestart => "\\begin{minted}[ma
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:outputend => "\\end{minted}",
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:termstart=> "\\begin{minted}[fontsize=\\footnotesize, xleftmargin=0.5em, mathescape]{julia}",
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:termend => "\\end{minted}",
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:figfmt => ".pdf",
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:fig_ext => ".pdf",
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:extension =>"tex",
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:width => "\\linewidth",
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:out_width => "\\linewidth",
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:fig_env=> "figure",
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:fig_pos => "htpb",
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:doctype => "texminted"
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))
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@ -124,19 +140,20 @@ const pandoc = Pandoc(@compat Dict{Symbol,Any}(:codestart => "~~~~{.julia}",
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:codeend=>"~~~~~~~~~~~~~\n\n",
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:outputstart=>"~~~~{.julia}",
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:outputend=>"~~~~~~~~~~~~~\n\n",
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:figfmt=>".png",
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:fig_ext=>".png",
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:extension=>"md",
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:width=>"15 cm",
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:doctype=>"pandoc"
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))
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function formatfigures(chunk, docformat::Tex)
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fignames = chunk[:figure]
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caption = chunk[:caption]
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width = get!(chunk, :width, docformat.formatdict[:width])
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f_pos = chunk[:f_pos]
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f_env = chunk[:f_env]
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caption = chunk[:fig_cap]
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width = chunk[:out_width]
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f_pos = chunk[:fig_pos]
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f_env = chunk[:fig_env]
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result = ""
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figstring = ""
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@ -144,6 +161,7 @@ function formatfigures(chunk, docformat::Tex)
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result *= """\\begin{$f_env}\n"""
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end
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for fig = fignames
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figstring *= "\\includegraphics[width= $width]{$fig}\n"
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end
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@ -172,8 +190,7 @@ end
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function formatfigures(chunk, docformat::Pandoc)
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fignames = chunk[:figure]
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caption = chunk[:caption]
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width = get!(chunk, :width, docformat.formatdict[:width])
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caption = chunk[:fig_cap]
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result = ""
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figstring = ""
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@ -3,8 +3,14 @@ using Gadfly
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Gadfly.set_default_plot_format(:png)
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#Captures figures
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function display(report::Report, m::MIME"image/png", data)
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function Base.display(report::Report, m::MIME"image/png", p::Plot)
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chunk = report.cur_chunk
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if chunk[:fig_ext] != ".png"
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chunk[:fig_ext]
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warn("Saving figures as .png with Gadfly")
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end
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full_name, rel_name = get_figname(report, chunk)
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docformat = formats[report.formatdict[:doctype]]
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@ -21,7 +27,11 @@ function display(report::Report, m::MIME"image/png", data)
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end
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report.fignum += 1
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out = open(full_name, "w")
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writemime(out, m, data)
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close(out)
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#TODO other formats
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r = chunk[:dpi]/96 #Relative to Gadfly default 96dpi
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draw(PNG(full_name, chunk[:fig_width]inch*r, chunk[:fig_height]inch*r ), p)
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#out = open(full_name, "w")
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#writemime(out, m, data)
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#close(out)
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end
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@ -1,6 +1,6 @@
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using Winston
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function display(report::Report, m::MIME"image/png", data)
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function Base.display(report::Report, m::MIME"image/png", data)
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chunk = report.cur_chunk
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full_name, rel_name = get_figname(report, chunk)
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@ -19,7 +19,7 @@ function display(report::Report, m::MIME"image/png", data)
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end
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#TODO get width and height from chunk options, after implementing Knitr compatible options
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savefig(data, full_name, width=2000, height=800)
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savefig(data, full_name, width=chunk[:fig_width]*chunk[:dpi], height=chunk[:fig_height]*chunk[:dpi])
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report.fignum += 1
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#out = open(full_name, "w")
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#writemime(out, m, data)
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