Allow setting document options in YAML header

.gitignore

@@ -22,6 +22,8 @@ test/**/chunk_options.jl
 doc/build
 doc/site
 stable/
+doc/Manifest.toml
+Manifest.toml
 
 tmp/
 .idea

doc/make.jl

@@ -1,11 +1,16 @@
 using Documenter, Weave
-cd("doc")
+start_dir = pwd()
+
+
 makedocs( modules = Weave, sitename="Weave.jl",
     pages = ["index.md", "getting_started.md", "usage.md",
     "publish.md", "chunk_options.md", "notebooks.md",
     "function_index.md"]
 )
+
+cd(@__DIR__)
 include("make_examples.jl")
+cd(start_dir)
 
 deploydocs(
     repo = "github.com/mpastell/Weave.jl.git",

doc/src/chunk_options.md

@@ -4,13 +4,7 @@ I've mostly followed [Knitr](http://yihui.name/knitr/options)'s naming for chunk
 
 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:
 
-
+`julia; out_width="12cm"; echo=false`
-      ```julia; out_width="12cm"; echo=false
-      using Gadfly
-      x = linspace(0, 2π, 200)
-      plot(x=x, y = sin(x), Geom.line)
-      ```
-
 
 Weave currently supports the following chunk options with the following defaults:
 
@@ -43,18 +37,16 @@ Weave currently supports the following chunk options with the following defaults
 
 ## Set default chunk options
 
-You can set or change the default chunk options for a document either before
+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:
-running weave or inside the weaved document. You can e.g. use a hidden chunk
-in the beginning of the source document to set the options:
 
-      ```julia; echo = false>>=
+```yaml
-      import Weave
+---
-      Weave.set_chunk_defaults(Dict{Symbol, Any}(
+options:
-            :out_width => "\\0.5linewidth",
+      out_width : 50%
-            :results => "tex"
+---
-            ))
+```
-      ```
 
+You can also set or change the default chunk options for a document either before weave using the `set_chunk_defaults function`.
 
 ```@docs
 set_chunk_defaults(opts)

doc/src/usage.md

@@ -123,10 +123,10 @@ added to output e.g. to include a Plots figure in markdown you can use:
 
 ## Setting document options in header
 
-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.
+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.
 
 
-```
+```yaml
 ---
 title : Weave example
 author : Matti Pastell

src/Weave.jl

@@ -38,7 +38,7 @@ function tangle(source ; out_path=:doc, informat=:auto)
     open(outname, "w") do io
     for chunk in doc.chunks
       if typeof(chunk) == CodeChunk
-          options = merge(rcParams[:chunk_defaults], chunk.options)
+          options = merge(doc.chunk_defaults, chunk.options)
           if options[:tangle]
             write(io, chunk.content*"\n")
           end
@@ -105,7 +105,7 @@ function weave(source ; doctype = :auto,
     if haskey(doc.header, "options")
         (doctype, informat, out_path, args, mod, fig_path, fig_ext,
         cache_path, cache, throw_errors, template, highlight_theme, css,
-        pandoc_options, latex_cmd) = parse_header_options(doc)
+        pandoc_options, latex_cmd) = header_args(doc)
     end
 
     highlight_theme != nothing && (doc.highlight_theme = highlight_theme)
@@ -148,13 +148,13 @@ function weave(source ; doctype = :auto,
       doc.cwd == pwd() && (outname = basename(outname))
       @info("Report weaved to $outname")
       return abspath(outname)
-    catch err
+    #catch err
-        @warn("Something went wrong during weaving")
+    #    @warn("Something went wrong during weaving")
-        @error(sprint(showerror, err))
+    #    @error(sprint(showerror, err))
-        return nothing
+    #    return nothing
     finally
         doctype == :auto && (doctype = detect_doctype(doc.source))
-        if occursin("pandoc2pdf", doctype) && cache == :off
+        if occursin("2pdf", doctype)
             rm(doc.fig_path, force = true, recursive = true)
         elseif occursin("2html", doctype)
             rm(doc.fig_path, force = true, recursive = true)

src/chunks.jl

@@ -17,11 +17,12 @@ mutable struct WeaveDoc
     css::AbstractString
     highlight_theme
     fig_path::AbstractString
+    chunk_defaults::Dict{Symbol,Any}
     function WeaveDoc(source, chunks, header)
         path, fname = splitdir(abspath(source))
         basename = splitext(fname)[1]
         new(source, basename, path, chunks, "", nothing, "", "", header,
-          "", "", Highlights.Themes.DefaultTheme, "")
+          "", "", Highlights.Themes.DefaultTheme, "", deepcopy(rcParams[:chunk_defaults]))
     end
 end
 

src/config.jl

@@ -40,15 +40,6 @@ const defaultParams =
 #This one can be changed at runtime, initially a copy of defaults
 const rcParams = deepcopy(defaultParams)
 
-#Parameters set per document
-const docParams =Dict{Symbol,Any}(
-                                :fig_path=> nothing,
-                                :fig_ext => nothing,
-                            )
-
-
-
-
 """
 `set_chunk_defaults(opts::Dict{Symbol, Any})`
 
@@ -82,7 +73,6 @@ Restore Weave.jl default chunk options
 """
 function restore_chunk_defaults()
   rcParams[:chunk_defaults] = defaultParams[:chunk_defaults]
-  merge!(rcParams[:chunk_defaults], docParams)
   return nothing
 end
 
@@ -97,7 +87,6 @@ function combine_args(args, doctype)
             common[key] = args[key]
         end
     end
-    @info specific
     haskey(specific, doctype) && merge!(common, specific[doctype])
     common
 end
@@ -105,11 +94,11 @@ end
 getvalue(d::Dict, key , default) = haskey(d, key) ? d[key] : default
 
 """
-`parse_header_options(doc::WeaveDoc)`
+header_args(doc::WeaveDoc)`
 
-Parse document options from document header
+Get weave arguments from document header
 """
-function parse_header_options(doc::WeaveDoc)
+function header_args(doc::WeaveDoc)
     args = getvalue(doc.header, "options", Dict())
     doctype = getvalue(args, "doctype", doc.doctype)
     args = combine_args(args, doctype)
@@ -132,3 +121,16 @@ function parse_header_options(doc::WeaveDoc)
       cache_path, cache, throw_errors, template, highlight_theme, css,
       pandoc_options, latex_cmd)
 end
+
+"""
+`header_chunk_defaults!(doc::WeaveDoc)`
+
+Get chunk defaults from header and update
+"""
+function header_chunk_defaults!(doc::WeaveDoc)
+    for key in keys(doc.chunk_defaults)
+        if haskey(doc.header["options"], String(key))
+             doc.chunk_defaults[key] = doc.header["options"][String(key)]
+        end
+    end
+end

src/readers.jl

@@ -56,6 +56,7 @@ function read_doc(source::AbstractString, format=:auto)
     parsed = parse_doc(document, format)
     header = parse_header(parsed[1])
     doc = WeaveDoc(source, parsed, header)
+    haskey(header, "options") && header_chunk_defaults!(doc)
     return doc
 end
 

src/run.jl

@@ -47,7 +47,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
     Sys.iswindows() && (fig_path = replace(fig_path, "\\" => "/"))
 
     doc.fig_path = fig_path
-    set_rc_params(doc.format.formatdict, fig_path, fig_ext)
+    set_rc_params(doc, fig_path, fig_ext)
 
     #New sandbox for each document with args exposed
     if mod == :sandbox
@@ -82,7 +82,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
         chunk = doc.chunks[i]
 
         if isa(chunk, CodeChunk)
-            options = merge(rcParams[:chunk_defaults], chunk.options)
+            options = merge(doc.chunk_defaults, chunk.options)
             merge!(chunk.options, options)
         end
 
@@ -91,7 +91,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
         if cached != nothing && (cache == :all || restore)
             result_chunks = restore_chunk(chunk, cached)
         else
-            result_chunks = run_chunk(chunk, report, mod)
+            result_chunks = run_chunk(chunk, doc, report, mod)
         end
 
         executed = [executed; result_chunks]
@@ -125,7 +125,7 @@ function detect_doctype(source::AbstractString)
 end
 
 
-function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
+function run_chunk(chunk::CodeChunk, doc::WeaveDoc, report::Report, SandBox::Module)
     @info("Weaving chunk $(chunk.number) from line $(chunk.start_line)")
     result_chunks = eval_chunk(chunk, report, SandBox)
     occursin("2html", report.formatdict[:doctype]) && (result_chunks = embed_figures(result_chunks, report.cwd))
@@ -163,19 +163,19 @@ function img2base64(fig, cwd)
   end
 end
 
-function run_chunk(chunk::DocChunk, report::Report, SandBox::Module)
+function run_chunk(chunk::DocChunk, doc::WeaveDoc, report::Report, SandBox::Module)
-    chunk.content =  [run_inline(c, report, SandBox) for c in chunk.content]
+    chunk.content =  [run_inline(c, doc, report, SandBox) for c in chunk.content]
     return chunk
 end
 
-function run_inline(inline::InlineText, report::Report, SandBox::Module)
+function run_inline(inline::InlineText, doc::WeaveDoc, report::Report, SandBox::Module)
     return inline
 end
 
-function run_inline(inline::InlineCode, report::Report, SandBox::Module)
+function run_inline(inline::InlineCode, doc::WeaveDoc, report::Report, SandBox::Module)
     #Make a temporary CodeChunk for running code. Collect results and don't wrap
     chunk = CodeChunk(inline.content, 0, 0, "", Dict(:hold => true, :wrap => false))
-    options = merge(rcParams[:chunk_defaults], chunk.options)
+    options = merge(doc.chunk_defaults, chunk.options)
     merge!(chunk.options, options)
 
     chunks = eval_chunk(chunk, report, SandBox)
@@ -268,7 +268,6 @@ end
 
 
 function eval_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
-
     if !chunk.options[:eval]
         chunk.output = ""
         chunk.options[:fig] = false
@@ -375,21 +374,17 @@ function get_outname(out_path::AbstractString, doc::WeaveDoc; ext = nothing)
     end
 end
 
-
+function set_rc_params(doc::WeaveDoc, fig_path, fig_ext)
-function set_rc_params(formatdict, fig_path, fig_ext)
+    formatdict = doc.format.formatdict
     if fig_ext == nothing
-        rcParams[:chunk_defaults][:fig_ext] = formatdict[:fig_ext]
+        doc.chunk_defaults[:fig_ext] = formatdict[:fig_ext]
-        docParams[:fig_ext] = formatdict[:fig_ext]
     else
-        rcParams[:chunk_defaults][:fig_ext] = fig_ext
+        doc.chunk_defaults[:fig_ext] = fig_ext
-        docParams[:fig_ext] = fig_ext
     end
-        rcParams[:chunk_defaults][:fig_path] = fig_path
+        doc.chunk_defaults[:fig_path] = fig_path
-        docParams[:fig_path] = fig_path
     return nothing
 end
 
-
 function collect_results(chunk::CodeChunk, fmt::ScriptResult)
     content = ""
     result_no = 1

test/documents/header_test.jmd

@@ -0,0 +1,12 @@
+---
+options:
+      md2html :
+            out_path : html
+      echo : false
+      out_width : 30%
+---
+
+
+```julia
+repeat("🐐", 10)
+```

test/formatter_test.jl

@@ -89,7 +89,6 @@ testcows = """
 🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄"""
 
 wcows = Weave.wrapline(cows)
-println(wcows)
 
 @test wcows == testcows
 @test length(split(wcows, "\n")[1]) == 75

test/options_test.jl

@@ -21,3 +21,6 @@ args = header["options"]
                                             "out_path" => "md/")
 @test Weave.combine_args(args, "pandoc") == Dict("fig_ext" => ".png",
                                                 "out_path" => "reports")
+doc = Weave.read_doc(joinpath(@__DIR__, "documents", "header_test.jmd"))
+@test doc.chunk_defaults[:echo] == false
+@test doc.chunk_defaults[:out_width] == "30%"