dynamic YAML option specification

src/format.jl

@@ -18,7 +18,7 @@ function format(doc::WeaveDoc)
     docformat.formatdict[:cwd] = doc.cwd # pass wd to figure formatters
     docformat.formatdict[:theme] = doc.highlight_theme
 
-    strip_header!(doc)
+    restore_header!(doc)
 
     for chunk in copy(doc.chunks)
         result = format_chunk(chunk, formatdict, docformat)
@@ -111,27 +111,20 @@ function render_doc(formatted, doc, format::JMarkdown2tex)
     )
 end
 
-strip_header!(doc::WeaveDoc) = strip_header!(doc.chunks[1], doc.doctype)
-function strip_header!(docchunk::DocChunk, doctype)
-    doctype == "pandoc" && return
-    content = docchunk.content[1].content
-    if (m = match(HEADER_REGEX, content)) !== nothing
-        # TODO: is there other format where we want to keep headers ?
-        docchunk.content[1].content = if doctype != "github"
-            lstrip(replace(content, HEADER_REGEX => ""))
-        else
-            # only strips Weave headers
-            header = YAML.load(m[:header])
-            delete!(header, WEAVE_OPTION_NAME)
-            if isempty(header)
-                lstrip(replace(content, HEADER_REGEX => ""))
-            else
-                lstrip(replace(content, HEADER_REGEX => "---\n$(YAML.write(header))---"))
-            end
-        end
-    end
+function restore_header!(doc)
+    doctype = doc.doctype
+
+    # TODO: is there any other format where we want to restore headers ?
+    doctype ≠ "github" && return
+
+    # only strips Weave headers
+    delete!(doc.header, WEAVE_OPTION_NAME)
+    isempty(doc.header) && return
+
+    # restore remained headers as `DocChunk`
+    header_text = "---\n$(YAML.write(doc.header))---"
+    pushfirst!(doc.chunks, DocChunk(header_text, 0, 0))
 end
-strip_header!(codechunk::CodeChunk, doctype) = return
 
 function format_chunk(chunk::DocChunk, formatdict, docformat)
     return join([format_inline(c) for c in chunk.content], "")

src/reader/reader.jl

@@ -2,18 +2,13 @@ using JSON, YAML
 
 
 function WeaveDoc(source, format::Union{Nothing,AbstractString} = nothing)
-    document = replace(read(source, String), "\r\n" => "\n") # normalize line ending
-    isnothing(format) && (format = detect_informat(source))
-    chunks = parse_doc(document, format)
-    return WeaveDoc(source, chunks)
-end
-
-function WeaveDoc(source, chunks::Vector{WeaveChunk})
     path, fname = splitdir(abspath(source))
     basename = splitext(fname)[1]
 
-    header = parse_header(first(chunks))
-    # get chunk defaults from header and update
+    isnothing(format) && (format = detect_informat(source))
+    header, chunks = parse_doc(read(source, String), format)
+
+    # update default chunk options from header
     chunk_defaults = deepcopy(get_chunk_defaults())
     if haskey(header, WEAVE_OPTION_NAME)
         for key in keys(chunk_defaults)
@@ -55,18 +50,17 @@ function detect_informat(source::AbstractString)
     return "noweb"
 end
 
-function parse_doc(document, format)::Vector{WeaveChunk}
-    return if format == "markdown"
-        parse_markdown(document)
-    elseif format == "noweb"
-        parse_markdown(document, true)
-    elseif format == "script"
-        parse_script(document)
-    elseif format == "notebook"
-        parse_notebook(document)
-    else
+function parse_doc(document, format)
+    document = replace(document, "\r\n" => "\n") # normalize line ending
+
+    header_text, document = separete_header_text(document)
+
+    return parse_header(header_text),
+        format == "markdown" ? parse_markdown(document) :
+        format == "noweb" ? parse_markdown(document, true) :
+        format == "script" ? parse_script(document) :
+        format == "notebook" ? parse_notebook(document) :
         error("unsupported format given: $(format)")
-    end
 end
 
 function pushopt(options::Dict, expr::Expr)
@@ -84,12 +78,13 @@ function DocChunk(text::AbstractString, number, start_line; notebook = false)
     return DocChunk(content, number, start_line)
 end
 
-const INLINE_REGEX = r"`j\s+(.*?)`|^!\s(.*)$"m
+const   INLINE_REGEX = r"`j\s+(.*?)`"
+const INLINE_REGEXES = r"`j\s+(.*?)`|^!\s(.*)$"m
 
 function parse_inlines(text)::Vector{Inline}
-    occursin(INLINE_REGEX, text) || return parse_inline(text)
+    occursin(INLINE_REGEXES, text) || return parse_inline(text)
 
-    inline_chunks = eachmatch(INLINE_REGEX, text)
+    inline_chunks = eachmatch(INLINE_REGEXES, text)
     s = 1
     e = 1
     res = Inline[]
@@ -118,20 +113,28 @@ parse_inline(text) = Inline[InlineText(text, 1, length(text), 1)]
 # headers
 # -------
 
-parse_header(chunk::CodeChunk) = Dict()
-
 const HEADER_REGEX = r"^---$(?<header>((?!---).)+)^---$"ms
 
-function parse_header(chunk::DocChunk)
-    m = match(HEADER_REGEX, chunk.content[1].content)
-    if m !== nothing
-        header = YAML.load(string(m[:header]))
-    else
-        header = Dict()
-    end
-    return header
+# TODO: non-Weave headers should keep live in a doc
+# separates header section from `text`
+function separete_header_text(text)
+    m = match(HEADER_REGEX, text)
+    isnothing(m) && return "", text
+    return m[:header], replace(text, HEADER_REGEX => "")
 end
 
+# HACK:
+# YAML.jl can't parse text including ``` characters, so first replace all the inline code
+# with these temporary code start/end string
+const HEADER_INLINE_START = "<weave_header_inline_start>"
+const   HEADER_INLINE_END = "<weave_header_inline_end>"
+
+function parse_header(header_text)
+    isempty(header_text) && return Dict()
+    pat = INLINE_REGEX => SubstitutionString("$(HEADER_INLINE_START)\\1$(HEADER_INLINE_END)")
+    header_text = replace(header_text, pat)
+    return YAML.load(header_text)
+end
 
 include("markdown.jl")
 include("script.jl")

src/run.jl

@@ -100,6 +100,8 @@ function run_doc(
             executed = [executed; result_chunks]
         end
 
+        replace_header_inline!(doc, report, mod) # evaluate and replace inline code in header
+
         doc.header_script = report.header_script
         doc.chunks = executed
 
@@ -237,17 +239,11 @@ function capture_output(expr, SandBox::Module, term, disp, lastline, throw_error
     reader = @async read(rw, String)
     try
         obj = Core.eval(SandBox, expr)
-        if (term || disp) && (typeof(expr) != Expr || expr.head != :toplevel)
-            isnothing(obj) || display(obj)
-            # This shows images and lone variables, result can
-            # Handle last line sepately
-        elseif lastline && !isnothing(obj)
-            (typeof(expr) != Expr || expr.head != :toplevel) && display(obj)
-        end
-    catch E
-        throw_errors && throw(E)
-        display(E)
-        @warn("ERROR: $(typeof(E)) occurred, including output in Weaved document")
+        !isnothing(obj) && ((term || disp) || lastline) && display(obj)
+    catch err
+        throw_errors && throw(err)
+        display(err)
+        @warn "ERROR: $(typeof(err)) occurred, including output in Weaved document"
     finally
         redirect_stdout(oldSTDOUT)
         close(wr)
@@ -486,3 +482,25 @@ function collect_results(chunk::CodeChunk, fmt::CollectResult)
     end
     return [chunk]
 end
+
+const HEADER_INLINE = Regex("$(HEADER_INLINE_START)(?<code>.+)$(HEADER_INLINE_END)")
+
+replace_header_inline!(doc, report, mod) = _replace_header_inline!(doc, doc.header, report, mod)
+
+function _replace_header_inline!(doc, header, report, mod)
+    replace!(header) do (k,v)
+        return k => v isa Dict ?
+            _replace_header_inline!(doc, v, report, mod) :
+            replace(v, HEADER_INLINE => s -> begin
+                m = match(HEADER_INLINE, s)
+                run_inline_code(m[:code], doc, report, mod)
+            end)
+    end
+    return header
+end
+
+function run_inline_code(s, doc, report, mod)
+    inline = InlineCode(s, 1, 1, 1, :inline)
+    inline = run_inline(inline, doc, report, mod)
+    return strip(inline.output, '"')
+end

test/documents/inline/markdown_beamer.html.ref

@@ -1,7 +1,6 @@
 
 
 
-
 <div class="Random plot">
 
 <p>Some inline output</p>

test/documents/inline/markdown_beamer.tex.ref

@@ -1,7 +1,6 @@
 
 
 
-
 \begin{frame}[fragile]
 \frametitle{Random plot}
 

test/formatter_test.jl

@@ -51,33 +51,6 @@ doc.template = "templates/mini.tpl"
 rendered = Weave.render_doc("Hello", doc)
 @test rendered == "\nHello\n"
 
-# Test header parsing and stripping
-header = """
----
-title : Test block
-author : Matti Pastell
----
-
-# Actual header
-
-and some text
-
-"""
-
-dchunk = Weave.DocChunk(header, 1, 1)
-h = Weave.parse_header(dchunk)
-h_ref = Dict("author" => "Matti Pastell", "title" => "Test block")
-@test h_ref == h
-
-Weave.strip_header!(dchunk, "md2html")
-h_ref = """
-# Actual header
-
-and some text
-
-"""
-@test dchunk.content[1].content == h_ref
-
 # Test wrapping
 
 cows = repeat("🐄", 100)

test/inline_test.jl

@@ -12,7 +12,7 @@ Some markdown with inline stuff and `j code`
 
 """
 
-ms = collect(eachmatch(Weave.INLINE_REGEX, doc))
+ms = collect(eachmatch(Weave.INLINE_REGEXES, doc))
 @test ms[1][2] == "println(\"Something\")"
 @test ms[2][1] == "code"
 @test ms[3][1] == "show(\"is\")"

test/runtests.jl

@@ -6,7 +6,11 @@ using Weave: run_doc
 # TODO: add test for `include_weave`
 
 # constructs `WeaveDoc` from `String`
-mock_doc(str, chunk_parser = Weave.parse_markdown) = Weave.WeaveDoc("dummy", chunk_parser(str))
+function mock_doc(str, format = "markdown")
+    f = tempname()
+    write(f, str)
+    return Weave.WeaveDoc(f, format)
+end
 
 
 @testset "Weave" begin