mirror of https://github.com/mpastell/Weave.jl
353 lines
14 KiB
Julia
353 lines
14 KiB
Julia
module Weave
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using Highlights, Mustache, Requires
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const PKG_DIR = normpath(@__DIR__, "..")
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const TEMPLATE_DIR = normpath(PKG_DIR, "templates")
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const STYLESHEET_DIR = normpath(PKG_DIR, "stylesheets")
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const WEAVE_OPTION_NAME = "weave_options"
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const WEAVE_OPTION_NAME_DEPRECATED = "options" # remove this when tagging v0.11
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const WEAVE_OPTION_DEPRECATE_ID = "weave_option_duplicate_id"
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# keeps paths of sample documents for easy try
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const EXAMPLE_FOLDER = normpath(PKG_DIR, "examples")
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function __init__()
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@require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" include("plots.jl")
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@require Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004" include("gadfly.jl")
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end
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@static @isdefined(isnothing) || begin
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isnothing(::Any) = false
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isnothing(::Nothing) = true
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end
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take2string!(io) = String(take!(io))
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"""
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list_out_formats()
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List supported output formats
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"""
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function list_out_formats()
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for format in keys(formats)
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println(string(format, ": ", formats[format].description))
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end
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end
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"""
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tangle(source::AbstractString; kwargs...)
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Tangle source code from input document to .jl file.
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## Keyword options
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- `informat::Union{Nothing,AbstractString} = nothing`: Input document format. By default (i.e. given `nothing`), Weave will set it automatically based on file extension. You can also specify either of `"script"`, `"markdown"`, `"notebook"`, or `"noweb"`
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- `out_path::Union{Symbol,AbstractString} = :doc`: Path where the output is generated can be either of:
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* `:doc`: Path of the source document (default)
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* `:pwd`: Julia working directory
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* `"somepath"`: `String` of output directory e.g. `"~/outdir"`, or of filename e.g. `"~/outdir/outfile.tex"`
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"""
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function tangle(
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source::AbstractString;
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out_path::Union{Symbol,AbstractString} = :doc,
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informat::Union{Nothing,AbstractString} = nothing,
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)
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doc = WeaveDoc(source, informat)
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doc.cwd = get_cwd(doc, out_path)
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outname = get_outname(out_path, doc, ext = "jl")
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open(outname, "w") do io
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for chunk in doc.chunks
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if typeof(chunk) == CodeChunk
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options = merge(doc.chunk_defaults, chunk.options)
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options[:tangle] && write(io, chunk.content * "\n")
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end
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end
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end
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doc.cwd == pwd() && (outname = basename(outname))
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@info("Writing to file $outname")
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end
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"""
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weave(source::AbstractString; kwargs...)
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Weave an input document to output file.
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## Keyword options
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- `doctype::Union{Nothing,AbstractString} = nothing`: Output document format. By default (i.e. given `nothing`), Weave will set it automatically based on file extension. You can also manually specify it; see [`list_out_formats()`](@ref) for the supported formats
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- `informat::Union{Nothing,AbstractString} = nothing`: Input document format. By default (i.e. given `nothing`), Weave will set it automatically based on file extension. You can also specify either of `"script"`, `"markdown"`, `"notebook"`, or `"noweb"`
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- `out_path::Union{Symbol,AbstractString} = :doc`: Path where the output is generated can be either of:
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* `:doc`: Path of the source document (default)
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* `:pwd`: Julia working directory
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* `"somepath"`: `String` of output directory e.g. `"~/outdir"`, or of filename e.g. `"~/outdir/outfile.tex"`
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- `args::Dict = Dict()`: Arguments to be passed to the weaved document; will be available as `WEAVE_ARGS` in the document
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- `mod::Union{Module,Nothing} = nothing`: Module where Weave `eval`s code. You can pass a `Module` object, otherwise create an new sandbox module.
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- `fig_path::AbstractString = "figures"`: Where figures will be generated, relative to `out_path`
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- `fig_ext::Union{Nothing,AbstractString} = nothing`: Extension for saved figures e.g. `".pdf"`, `".png"`. Default setting depends on `doctype`
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- `cache_path::AbstractString = "cache"`: Where of cached output will be saved
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- `cache::Symbol = :off`: Controls caching of code:
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* `:off` means no caching (default)
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* `:all` caches everything
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* `:user` caches based on chunk options
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* `:refresh` runs all code chunks and save new cache
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- `throw_errors::Bool = false`: If `false` errors are included in output document and the whole document is executed. If `true` errors are thrown when they occur
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- `template::Union{Nothing,AbstractString,Mustache.MustacheTokens} = nothing`: Template (file path) or `Mustache.MustacheTokens`s for `md2html` or `md2tex` formats
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- `css::Union{Nothing,AbstractString} = nothing`: Path of a CSS file used for md2html format
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- `highlight_theme::Union{Nothing,Type{<:Highlights.AbstractTheme}} = nothing`: Theme used for syntax highlighting (defaults to `Highlights.Themes.DefaultTheme`)
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- `pandoc_options::Vector{<:AbstractString} = String[]`: `String`s of options to pass to pandoc for `pandoc2html` and `pandoc2pdf` formats, e.g. `["--toc", "-N"]`
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- `latex_cmd::AbstractString = "xelatex"`: The command used to make PDF file from .tex
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- `keep_unicode::Bool = false`: If `true`, do not convert unicode characters to their respective latex representation. This is especially useful if a font and tex-engine with support for unicode characters are used
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!!! note
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Run Weave from terminal and try to avoid weaving from IJulia or ESS; they tend to mess with capturing output.
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"""
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function weave(
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source::AbstractString;
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doctype::Union{Nothing,AbstractString} = nothing,
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informat::Union{Nothing,AbstractString} = nothing,
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out_path::Union{Symbol,AbstractString} = :doc,
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args::Dict = Dict(),
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mod::Union{Module,Nothing} = nothing,
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fig_path::AbstractString = "figures",
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fig_ext::Union{Nothing,AbstractString} = nothing,
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cache_path::AbstractString = "cache",
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cache::Symbol = :off,
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throw_errors::Bool = false,
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template::Union{Nothing,AbstractString,Mustache.MustacheTokens} = nothing,
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css::Union{Nothing,AbstractString} = nothing, # TODO: rename to `stylesheet`
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highlight_theme::Union{Nothing,Type{<:Highlights.AbstractTheme}} = nothing,
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pandoc_options::Vector{<:AbstractString} = String[],
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latex_cmd::AbstractString = "xelatex",
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keep_unicode::Bool = false,
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)
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doc = WeaveDoc(source, informat)
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# run document
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# ------------
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# overwrites options with those specified in header, that are needed for running document
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# NOTE: these YAML options can NOT be given dynamically
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weave_options = get(doc.header, WEAVE_OPTION_NAME, nothing)
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if haskey(doc.header, WEAVE_OPTION_NAME_DEPRECATED)
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@warn "Weave: `options` key is deprecated. Use `weave_options` key instead." _id = WEAVE_OPTION_DEPRECATE_ID maxlog = 1
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weave_options = get(doc.header, WEAVE_OPTION_NAME_DEPRECATED, nothing)
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end
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if !isnothing(weave_options)
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doctype = get(weave_options, "doctype", doctype)
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specific_options!(weave_options, doctype)
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if haskey(weave_options, "out_path")
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out_path = let
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out_path = weave_options["out_path"]
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if out_path == ":doc" || out_path == ":pwd"
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Symbol(out_path)
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else
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normpath(dirname(source), out_path) # resolve relative to this document
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end
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end
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end
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mod = get(weave_options, "mod", mod)
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mod isa AbstractString && (mod = Main.eval(Meta.parse(mod)))
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fig_path = get(weave_options, "fig_path", fig_path)
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fig_ext = get(weave_options, "fig_ext", fig_ext)
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cache_path = get(weave_options, "cache_path", cache_path)
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cache = Symbol(get(weave_options, "cache", cache))
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throw_errors = get(weave_options, "throw_errors", throw_errors)
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end
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doc = run_doc(
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doc;
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doctype = doctype,
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mod = mod,
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out_path = out_path,
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args = args,
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fig_path = fig_path,
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fig_ext = fig_ext,
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cache_path = cache_path,
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cache = cache,
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throw_errors = throw_errors,
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)
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# format document
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# ---------------
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# overwrites options with those specified in header, that are needed for formatting document
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# NOTE: these YAML options can be given dynamically
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if !isnothing(weave_options)
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if haskey(weave_options, "template")
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template = weave_options["template"]
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# resolve relative to this document
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template isa AbstractString && (template = normpath(dirname(source), template))
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end
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if haskey(weave_options, "css")
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css = weave_options["css"]
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# resolve relative to this document
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css isa AbstractString && (css = normpath(dirname(source), css))
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end
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highlight_theme = get(weave_options, "highlight_theme", highlight_theme)
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pandoc_options = get(weave_options, "pandoc_options", pandoc_options)
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latex_cmd = get(weave_options, "latex_cmd", latex_cmd)
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keep_unicode = get(weave_options, "keep_unicode", keep_unicode)
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end
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get!(doc.format.formatdict, :keep_unicode, keep_unicode)
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rendered = format(doc, template, highlight_theme; css = css)
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outname = get_outname(out_path, doc)
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open(io->write(io,rendered), outname, "w")
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# document generation via external programs
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doctype = doc.doctype
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if doctype == "pandoc2html"
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mdname = outname
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outname = get_outname(out_path, doc, ext = "html")
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pandoc2html(rendered, doc, highlight_theme, outname, pandoc_options)
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rm(mdname)
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elseif doctype == "pandoc2pdf"
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mdname = outname
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outname = get_outname(out_path, doc, ext = "pdf")
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pandoc2pdf(rendered, doc, outname, pandoc_options)
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rm(mdname)
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elseif doctype == "md2pdf"
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run_latex(doc, outname, latex_cmd)
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outname = get_outname(out_path, doc, ext = "pdf")
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end
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doc.cwd == pwd() && (outname = basename(outname))
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@info "Report weaved to $outname"
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return abspath(outname)
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end
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weave(doc::AbstractString, doctype::Union{Symbol,AbstractString}; kwargs...) =
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weave(doc; doctype = doctype, kwargs...)
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function specific_options!(weave_options, doctype)
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fmts = keys(formats)
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for (k,v) in weave_options
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if k in fmts
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k == doctype && merge!(weave_options, v)
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delete!(weave_options, k)
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end
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end
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end
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"""
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notebook(source::AbstractString; kwargs...)
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Convert Weave document `source` to Jupyter Notebook and execute the code
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using [`nbconvert`](https://nbconvert.readthedocs.io/en/latest/).
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**Ignores** all chunk options.
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## Keyword options
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- `out_path::Union{Symbol,AbstractString} = :pwd`: Path where the output is generated can be either of:
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* `:doc`: Path of the source document
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* `:pwd`: Julia working directory (default)
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* `"somepath"`: `String` of output directory e.g. `"~/outdir"`, or of filename e.g. `"~/outdir/outfile.tex"`
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- `timeout = -1`: nbconvert cell timeout in seconds. Defaults to `-1` (no timeout)
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- `nbconvert_options::AbstractString = ""`: `String` of additional options to pass to nbconvert, such as `"--allow-errors"`
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- `jupyter_path::AbstractString = "jupyter"`: Path/command for the Jupyter you want to use. Defaults to `"jupyter"`, which runs whatever is linked/alias to that
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!!! warning
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The code is _**not**_ executed by Weave, but by [`nbconvert`](https://nbconvert.readthedocs.io/en/latest/).
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This means that the output doesn't necessarily always work properly; see [#116](https://github.com/mpastell/Weave.jl/issues/116).
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!!! note
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In order to _just_ convert Weave document to Jupyter Notebook,
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use [`convert_doc`](@ref) instead.
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"""
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function notebook(
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source::AbstractString;
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out_path::Union{Symbol,AbstractString} = :pwd,
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timeout = -1,
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nbconvert_options::AbstractString = "",
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jupyter_path::AbstractString = "jupyter",
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)
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doc = WeaveDoc(source)
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converted = convert_to_notebook(doc)
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doc.cwd = get_cwd(doc, out_path)
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outfile = get_outname(out_path, doc, ext = "ipynb")
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open(outfile, "w") do f
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write(f, converted)
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end
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@info "Running nbconvert"
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return read(
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`$jupyter_path nbconvert --ExecutePreprocessor.timeout=$timeout --to notebook --execute $outfile $nbconvert_options --output $outfile`,
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String,
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)
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end
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"""
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include_weave(source::AbstractString, informat::Union{Nothing,AbstractString} = nothing)
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include_weave(m::Module, source::AbstractString, informat::Union{Nothing,AbstractString} = nothing)
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Include code from Weave document calling `include_string` on all code from doc.
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Code is run in the path of the include document.
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"""
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function include_weave(
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m::Module,
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source::AbstractString,
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informat::Union{Nothing,AbstractString} = nothing,
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)
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old_path = pwd()
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doc = WeaveDoc(source, informat)
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cd(doc.path)
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try
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code = join(
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[x.content for x in filter(x -> isa(x, Weave.CodeChunk), doc.chunks)],
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"\n",
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)
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include_string(m, code)
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catch err
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throw(err)
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finally
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cd(old_path)
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end
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return nothing
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end
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include_weave(source, informat = nothing) = include_weave(Main, source, informat)
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# Hooks to run before and after chunks, this is form IJulia,
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# but note that Weave hooks take the chunk as input
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const preexecute_hooks = Function[]
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push_preexecute_hook(f::Function) = push!(preexecute_hooks, f)
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pop_preexecute_hook(f::Function) =
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splice!(preexecute_hooks, findfirst(x -> x == f, preexecute_hooks))
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const postexecute_hooks = Function[]
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push_postexecute_hook(f::Function) = push!(postexecute_hooks, f)
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pop_postexecute_hook(f::Function) =
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splice!(postexecute_hooks, findfirst(x -> x == f, postexecute_hooks))
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include("types.jl")
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include("config.jl")
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include("WeaveMarkdown/markdown.jl")
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include("display_methods.jl")
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include("reader/reader.jl")
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include("run.jl")
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include("cache.jl")
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include("formatters.jl")
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include("format.jl")
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include("pandoc.jl")
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include("converter.jl")
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export weave,
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list_out_formats,
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tangle,
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convert_doc,
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notebook,
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set_chunk_defaults!,
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get_chunk_defaults,
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restore_chunk_defaults!,
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include_weave
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end
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