mirror of https://github.com/mpastell/Weave.jl
Allow setting document options in YAML header
Matti Pastell
parent
52f3a23d28
commit
6082786f92
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@ -22,6 +22,8 @@ test/**/chunk_options.jl
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doc/build
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doc/site
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stable/
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doc/Manifest.toml
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Manifest.toml
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tmp/
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.idea
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@ -1,11 +1,16 @@
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using Documenter, Weave
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cd("doc")
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start_dir = pwd()
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makedocs( modules = Weave, sitename="Weave.jl",
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pages = ["index.md", "getting_started.md", "usage.md",
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"publish.md", "chunk_options.md", "notebooks.md",
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"function_index.md"]
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)
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cd(@__DIR__)
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include("make_examples.jl")
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cd(start_dir)
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deploydocs(
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repo = "github.com/mpastell/Weave.jl.git",
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@ -4,13 +4,7 @@ I've mostly followed [Knitr](http://yihui.name/knitr/options)'s naming for chunk
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Options are separated using ";" and need to be valid Julia expressions. Example: markdown code chunk that saves and displays a 12 cm wide image and hides the source code:
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```julia; out_width="12cm"; echo=false
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using Gadfly
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x = linspace(0, 2π, 200)
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plot(x=x, y = sin(x), Geom.line)
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```
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`julia; out_width="12cm"; echo=false`
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Weave currently supports the following chunk options with the following defaults:
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@ -43,18 +37,16 @@ Weave currently supports the following chunk options with the following defaults
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## Set default chunk options
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You can set or change the default chunk options for a document either before
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running weave or inside the weaved document. You can e.g. use a hidden chunk
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in the beginning of the source document to set the options:
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You can set the default chunk options (and `weave` arguments) for a document using the YAML header `options` field. e.g to set the default `out_width` of all figures you can use:
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```julia; echo = false>>=
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import Weave
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Weave.set_chunk_defaults(Dict{Symbol, Any}(
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:out_width => "\\0.5linewidth",
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:results => "tex"
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))
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```
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```yaml
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---
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options:
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out_width : 50%
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---
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```
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You can also set or change the default chunk options for a document either before weave using the `set_chunk_defaults function`.
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```@docs
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set_chunk_defaults(opts)
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@ -123,10 +123,10 @@ added to output e.g. to include a Plots figure in markdown you can use:
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## Setting document options in header
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You can use a YAML header in the beginning of the input document delimited with "---" to set the document title, author and date e.g. and default document options. Each of Weave command line arguments can be set in header using `options` field. Below is an example that sets document `out_path` and `doctype` using the header.
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You can use a YAML header in the beginning of the input document delimited with "---" to set the document title, author and date e.g. and default document options. Each of Weave command line arguments and chunk options can be set in header using `options` field. Below is an example that sets document `out_path` and `doctype` using the header.
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```
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```yaml
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---
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title : Weave example
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author : Matti Pastell
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14
src/Weave.jl
14
src/Weave.jl
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@ -38,7 +38,7 @@ function tangle(source ; out_path=:doc, informat=:auto)
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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(rcParams[:chunk_defaults], chunk.options)
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options = merge(doc.chunk_defaults, chunk.options)
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if options[:tangle]
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write(io, chunk.content*"\n")
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end
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@ -105,7 +105,7 @@ function weave(source ; doctype = :auto,
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if haskey(doc.header, "options")
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(doctype, informat, out_path, args, mod, fig_path, fig_ext,
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cache_path, cache, throw_errors, template, highlight_theme, css,
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pandoc_options, latex_cmd) = parse_header_options(doc)
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pandoc_options, latex_cmd) = header_args(doc)
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end
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highlight_theme != nothing && (doc.highlight_theme = highlight_theme)
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@ -148,13 +148,13 @@ function weave(source ; doctype = :auto,
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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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catch err
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@warn("Something went wrong during weaving")
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@error(sprint(showerror, err))
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return nothing
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#catch err
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# @warn("Something went wrong during weaving")
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# @error(sprint(showerror, err))
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# return nothing
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finally
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doctype == :auto && (doctype = detect_doctype(doc.source))
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if occursin("pandoc2pdf", doctype) && cache == :off
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if occursin("2pdf", doctype)
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rm(doc.fig_path, force = true, recursive = true)
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elseif occursin("2html", doctype)
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rm(doc.fig_path, force = true, recursive = true)
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@ -17,11 +17,12 @@ mutable struct WeaveDoc
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css::AbstractString
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highlight_theme
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fig_path::AbstractString
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chunk_defaults::Dict{Symbol,Any}
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function WeaveDoc(source, chunks, header)
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path, fname = splitdir(abspath(source))
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basename = splitext(fname)[1]
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new(source, basename, path, chunks, "", nothing, "", "", header,
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"", "", Highlights.Themes.DefaultTheme, "")
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"", "", Highlights.Themes.DefaultTheme, "", deepcopy(rcParams[:chunk_defaults]))
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end
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end
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@ -40,15 +40,6 @@ const defaultParams =
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#This one can be changed at runtime, initially a copy of defaults
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const rcParams = deepcopy(defaultParams)
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#Parameters set per document
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const docParams =Dict{Symbol,Any}(
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:fig_path=> nothing,
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:fig_ext => nothing,
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)
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"""
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`set_chunk_defaults(opts::Dict{Symbol, Any})`
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@ -82,7 +73,6 @@ Restore Weave.jl default chunk options
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"""
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function restore_chunk_defaults()
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rcParams[:chunk_defaults] = defaultParams[:chunk_defaults]
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merge!(rcParams[:chunk_defaults], docParams)
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return nothing
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end
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@ -97,7 +87,6 @@ function combine_args(args, doctype)
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common[key] = args[key]
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end
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end
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@info specific
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haskey(specific, doctype) && merge!(common, specific[doctype])
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common
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end
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@ -105,11 +94,11 @@ end
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getvalue(d::Dict, key , default) = haskey(d, key) ? d[key] : default
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"""
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`parse_header_options(doc::WeaveDoc)`
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header_args(doc::WeaveDoc)`
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Parse document options from document header
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Get weave arguments from document header
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"""
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function parse_header_options(doc::WeaveDoc)
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function header_args(doc::WeaveDoc)
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args = getvalue(doc.header, "options", Dict())
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doctype = getvalue(args, "doctype", doc.doctype)
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args = combine_args(args, doctype)
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@ -132,3 +121,16 @@ function parse_header_options(doc::WeaveDoc)
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cache_path, cache, throw_errors, template, highlight_theme, css,
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pandoc_options, latex_cmd)
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end
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"""
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`header_chunk_defaults!(doc::WeaveDoc)`
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Get chunk defaults from header and update
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"""
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function header_chunk_defaults!(doc::WeaveDoc)
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for key in keys(doc.chunk_defaults)
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if haskey(doc.header["options"], String(key))
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doc.chunk_defaults[key] = doc.header["options"][String(key)]
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end
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end
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end
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@ -56,6 +56,7 @@ function read_doc(source::AbstractString, format=:auto)
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parsed = parse_doc(document, format)
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header = parse_header(parsed[1])
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doc = WeaveDoc(source, parsed, header)
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haskey(header, "options") && header_chunk_defaults!(doc)
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return doc
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end
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33
src/run.jl
33
src/run.jl
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@ -47,7 +47,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
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Sys.iswindows() && (fig_path = replace(fig_path, "\\" => "/"))
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doc.fig_path = fig_path
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set_rc_params(doc.format.formatdict, fig_path, fig_ext)
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set_rc_params(doc, fig_path, fig_ext)
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#New sandbox for each document with args exposed
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if mod == :sandbox
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@ -82,7 +82,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
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chunk = doc.chunks[i]
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if isa(chunk, CodeChunk)
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options = merge(rcParams[:chunk_defaults], chunk.options)
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options = merge(doc.chunk_defaults, chunk.options)
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merge!(chunk.options, options)
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end
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@ -91,7 +91,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
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if cached != nothing && (cache == :all || restore)
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result_chunks = restore_chunk(chunk, cached)
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else
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result_chunks = run_chunk(chunk, report, mod)
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result_chunks = run_chunk(chunk, doc, report, mod)
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end
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executed = [executed; result_chunks]
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@ -125,7 +125,7 @@ function detect_doctype(source::AbstractString)
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end
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function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
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function run_chunk(chunk::CodeChunk, doc::WeaveDoc, report::Report, SandBox::Module)
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@info("Weaving chunk $(chunk.number) from line $(chunk.start_line)")
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result_chunks = eval_chunk(chunk, report, SandBox)
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occursin("2html", report.formatdict[:doctype]) && (result_chunks = embed_figures(result_chunks, report.cwd))
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@ -163,19 +163,19 @@ function img2base64(fig, cwd)
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end
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end
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function run_chunk(chunk::DocChunk, report::Report, SandBox::Module)
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chunk.content = [run_inline(c, report, SandBox) for c in chunk.content]
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function run_chunk(chunk::DocChunk, doc::WeaveDoc, report::Report, SandBox::Module)
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chunk.content = [run_inline(c, doc, report, SandBox) for c in chunk.content]
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return chunk
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end
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function run_inline(inline::InlineText, report::Report, SandBox::Module)
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function run_inline(inline::InlineText, doc::WeaveDoc, report::Report, SandBox::Module)
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return inline
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end
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function run_inline(inline::InlineCode, report::Report, SandBox::Module)
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function run_inline(inline::InlineCode, doc::WeaveDoc, report::Report, SandBox::Module)
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#Make a temporary CodeChunk for running code. Collect results and don't wrap
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chunk = CodeChunk(inline.content, 0, 0, "", Dict(:hold => true, :wrap => false))
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options = merge(rcParams[:chunk_defaults], chunk.options)
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options = merge(doc.chunk_defaults, chunk.options)
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merge!(chunk.options, options)
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chunks = eval_chunk(chunk, report, SandBox)
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@ -268,7 +268,6 @@ end
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function eval_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
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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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@ -375,21 +374,17 @@ function get_outname(out_path::AbstractString, doc::WeaveDoc; ext = nothing)
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end
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end
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function set_rc_params(formatdict, fig_path, fig_ext)
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function set_rc_params(doc::WeaveDoc, fig_path, fig_ext)
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formatdict = doc.format.formatdict
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if fig_ext == nothing
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rcParams[:chunk_defaults][:fig_ext] = formatdict[:fig_ext]
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docParams[:fig_ext] = formatdict[:fig_ext]
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doc.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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docParams[:fig_ext] = fig_ext
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doc.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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docParams[:fig_path] = fig_path
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doc.chunk_defaults[:fig_path] = fig_path
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return nothing
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end
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function collect_results(chunk::CodeChunk, fmt::ScriptResult)
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content = ""
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result_no = 1
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@ -0,0 +1,12 @@
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---
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options:
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md2html :
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out_path : html
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echo : false
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out_width : 30%
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---
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```julia
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repeat("🐐", 10)
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```
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@ -89,7 +89,6 @@ testcows = """
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🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄"""
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wcows = Weave.wrapline(cows)
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println(wcows)
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@test wcows == testcows
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@test length(split(wcows, "\n")[1]) == 75
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@ -21,3 +21,6 @@ args = header["options"]
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"out_path" => "md/")
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@test Weave.combine_args(args, "pandoc") == Dict("fig_ext" => ".png",
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"out_path" => "reports")
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doc = Weave.read_doc(joinpath(@__DIR__, "documents", "header_test.jmd"))
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@test doc.chunk_defaults[:echo] == false
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@test doc.chunk_defaults[:out_width] == "30%"
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