mirror of https://github.com/mpastell/Weave.jl
262 lines
7.7 KiB
Julia
262 lines
7.7 KiB
Julia
@doc """
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Run code chunks and capture output from parsed document.
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```julia
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function run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="noweb",
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out_path=:doc, fig_path = "figures", fig_ext = nothing,
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cache_path = "cache", cache = :off)
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```
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* `doctype`: see `list_out_formats()`
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* `plotlib`: `"PyPlot"`, `"Gadfly"`, or `"Winston"`
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* `informat`: `"noweb"` of `"markdown"`
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* `out_path`: Path where the output is generated. Can be: `:doc`: Path of the source document, `:pwd`: Julia working directory,
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`"somepath"`: Path as a string e.g `"/home/mpastell/weaveout"`
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* `fig_path`: where figures will be generated, relative to out_path
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* `fig_ext`: Extension for saved figures e.g. `".pdf"`, `".png"`. Default setting depends on `doctype`.
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* `cache_path`: where of cached output will be saved.
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* `cache`: controls caching of code: `:off` = no caching, `:all` = cache everything,
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`:user` = cache based on chunk options, `:refresh`, run all code chunks and save new cache.
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**Note:** Run command from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.
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""" ->
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function Base.run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="noweb",
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out_path=:doc, fig_path = "figures", fig_ext = nothing,
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cache_path = "cache", cache = :off)
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#cache :all, :user, :off, :refresh
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doc.cwd = get_cwd(doc, out_path)
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doc.doctype = doctype
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doc.format = formats[doctype]
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set_rc_params(doc.format.formatdict, fig_path, fig_ext)
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#New sandbox for each document
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sandbox = "ReportSandBox$(rcParams[:doc_number])"
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eval(parse("module $sandbox\nend"))
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SandBox = eval(parse(sandbox))
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rcParams[:doc_number] += 1
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init_plotting(plotlib)
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report = Report(doc.cwd, doc.basename, doc.format.formatdict)
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pushdisplay(report)
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if cache != :off || cache != :refresh
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cached = read_cache(doc, cache_path)
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cached == nothing && info("No cached results found, running code")
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else
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cached = nothing
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end
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executed = Any[]
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n = length(doc.chunks)
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for i = 1:n
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chunk = doc.chunks[i]
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result_chunk = run_chunk(chunk, report, SandBox, cached, cache, i)
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push!(executed, result_chunk)
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end
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popdisplay(report)
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if cache != :off
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write_cache(doc, cache_path)
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end
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#Clear variables from used sandbox
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clear_sandbox(SandBox)
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doc.chunks = executed
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return doc
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end
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function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module, cached, cache, idx)
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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_defaults], options)
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catch
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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, options)
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delete!(chunk.options, :options)
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if cached != nothing && (cache == :all || (cache ==:user && chunk.options[:cache]))
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result_chunk = restore_chunk(chunk, cached, idx)
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else
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result_chunk = eval_chunk(chunk, report, SandBox)
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end
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end
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function run_chunk(chunk::DocChunk, report::Report, SandBox::Module, cached, cache, idx)
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return chunk
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end
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function run_block(code_str, report::Report, SandBox::Module)
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oldSTDOUT = STDOUT
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result = ""
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rw, wr = redirect_stdout()
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#If there is nothing to read code will hang
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println()
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try
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n = length(code_str)
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pos = 1 #The first character is extra line end
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while pos < n
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oldpos = pos
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code, pos = parse(code_str, pos)
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s = eval(SandBox, code)
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if rcParams[:plotlib] == "Gadfly"
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s != nothing && display(s)
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end
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end
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finally
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redirect_stdout(oldSTDOUT)
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close(wr)
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result = readall(rw)
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close(rw)
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end
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return string("\n", result)
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end
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function run_term(code_str, report::Report, SandBox::Module)
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prompt = "\njulia> "
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codestart = "\n\n"*report.formatdict[:codestart]
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if haskey(report.formatdict, :indent)
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prompt = indent(prompt, report.formatdict[:indent])
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end
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#Emulate terminal
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n = length(code_str)
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pos = 2 #The first character is extra line end
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while pos < n
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oldpos = pos
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code, pos = parse(code_str, pos)
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report.term_state == :fig && (report.cur_result*= codestart)
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prompts = string(prompt, rstrip(code_str[oldpos:(pos-1)]), "\n")
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report.cur_result *= prompts
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report.term_state = :text
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s = eval(SandBox, code)
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s != nothing && display(s)
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end
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return string(report.cur_result)
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end
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function eval_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
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info("Weaving chunk $(chunk.number) from line $(chunk.start_line)")
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if !chunk.options[:eval]
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chunk.output = ""
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chunk.options[:fig] = false
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return chunk
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end
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report.fignum = 1
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report.cur_result = ""
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report.figures = String[]
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report.cur_chunk = chunk
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report.term_state = :text
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if haskey(report.formatdict, :out_width) && chunk.options[:out_width] == nothing
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chunk.options[:out_width] = report.formatdict[:out_width]
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end
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if chunk.options[:term]
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chunk.output = run_term(chunk.content, report, SandBox)
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chunk.options[:term_state] = report.term_state
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else
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chunk.output = run_block(chunk.content, report, SandBox)
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end
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if rcParams[:plotlib] == "PyPlot"
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chunk.options[:fig] && (chunk.figures = savefigs_pyplot(chunk, report::Report))
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else
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chunk.options[:fig] && (chunk.figures = copy(report.figures))
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end
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chunk
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end
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function eval_chunk(chunk::DocChunk, report::Report, SandBox)
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chunk
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end
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#Set all variables to nothing
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function clear_sandbox(SandBox::Module)
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for name = names(SandBox, true)
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if name != :eval && name != names(SandBox)[1]
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eval(SandBox, parse(string(string(name), "=nothing")))
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end
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end
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end
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function get_figname(report::Report, chunk; fignum = nothing)
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figpath = joinpath(report.cwd, chunk.options[:fig_path])
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isdir(figpath) || mkpath(figpath)
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ext = chunk.options[:fig_ext]
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fignum == nothing && (fignum = report.fignum)
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chunkid = (chunk.options[:name] == nothing) ? chunk.number : chunk.options[:name]
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full_name = joinpath(report.cwd, chunk.options[:fig_path],
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"$(report.basename)_$(chunkid)_$(fignum)$ext")
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rel_name = "$(chunk.options[: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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function init_plotting(plotlib)
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if plotlib == nothing
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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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rcParams[:chunk_defaults][:fig] = true
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if l_plotlib == "winston"
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eval(parse("""include(Pkg.dir("Weave","src","winston.jl"))"""))
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rcParams[:plotlib] = "Winston"
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elseif l_plotlib == "pyplot"
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eval(parse("""include(Pkg.dir("Weave","src","pyplot.jl"))"""))
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rcParams[:plotlib] = "PyPlot"
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elseif l_plotlib == "gadfly"
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eval(parse("""include(Pkg.dir("Weave","src","gadfly.jl"))"""))
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rcParams[:plotlib] = "Gadfly"
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end
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end
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return nothing
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end
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function get_cwd(doc::WeaveDoc, out_path)
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#Set the output directory
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if out_path == :doc
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cwd = doc.path
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elseif out_path == :pwd
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cwd = pwd()
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else
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cwd = out_path
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end
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return cwd
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end
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function set_rc_params(formatdict, fig_path, fig_ext)
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if fig_ext == nothing
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rcParams[:chunk_defaults][:fig_ext] = formatdict[:fig_ext]
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else
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rcParams[:chunk_defaults][:fig_ext] = fig_ext
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end
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rcParams[:chunk_defaults][:fig_path] = fig_path
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return nothing
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end
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