Support inline code

doc/src/usage.md

@@ -120,3 +120,20 @@ Weave will remove the first empty space from each line of documentation.
 
 
 [See sample document:](https://github.com/mpastell/Weave.jl/blob/master/examples/FIR_design.jl)
+
+## Inline code
+
+You can also add inline code to your documents using
+
+```
+`j juliacode`
+``` 
+
+syntax. The code will be replaced with the output of running the code. 
+If the code produces figures the filename or base64 encoded string will be 
+added to output e.g. to include a Plots figure in markdown you can use:
+
+```
+![A plot](`j plot(1:10)`)
+```
+

src/Weave.jl

@@ -87,46 +87,49 @@ function weave(source ; doctype = :auto, plotlib=:auto,
     css != nothing && (doc.css = css)
     template != nothing && (doc.template = template)
 
+    try
+      doc = run(doc, doctype = doctype, plotlib=plotlib,
+              out_path=out_path, args = args,
+              fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache)
+      formatted = format(doc)
 
-    doc = run(doc, doctype = doctype, plotlib=plotlib,
-            out_path=out_path, args = args,
-            fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache)
-    formatted = format(doc)
+      outname = get_outname(out_path, doc)
 
-    outname = get_outname(out_path, doc)
+      open(outname, "w") do io
+          write(io, formatted)
+      end
 
-    open(outname, "w") do io
-        write(io, formatted)
-    end
+      #Special for that need external programs
+      if doc.doctype == "pandoc2html"
+          mdname = outname
+          outname = get_outname(out_path, doc, ext = "html")
+          pandoc2html(formatted, doc, outname)
+          rm(mdname)
+      elseif doc.doctype == "pandoc2pdf"
+          mdname = outname
+          outname = get_outname(out_path, doc, ext = "pdf")
+          pandoc2pdf(formatted, doc, outname)
+          rm(mdname)
+      elseif doc.doctype == "md2pdf"
+          success = run_latex(doc, outname, latex_cmd)
+          success || return
+          outname = get_outname(out_path, doc, ext = "pdf")
+      end
 
-    #Special for that need external programs
-    if doc.doctype == "pandoc2html"
-        mdname = outname
-        outname = get_outname(out_path, doc, ext = "html")
-        pandoc2html(formatted, doc, outname)
-        rm(mdname)
-    elseif doc.doctype == "pandoc2pdf"
-        mdname = outname
-        outname = get_outname(out_path, doc, ext = "pdf")
-        pandoc2pdf(formatted, doc, outname)
-        rm(mdname)
-    elseif doc.doctype == "md2pdf"
-        success = run_latex(doc, outname, latex_cmd)
-        success || return
-        outname = get_outname(out_path, doc, ext = "pdf")
-    end
 
-    doctype == :auto && (doctype = detect_doctype(doc.source))
-
-    if contains(doctype, "2pdf") && cache == :off
-      rm(doc.fig_path, force = true, recursive = true)
-    elseif contains(doctype, "2html")
-      rm(doc.fig_path, force = true, recursive = true)
+      doc.cwd == pwd() && (outname = basename(outname))
+      info("Report weaved to $outname")
+    catch e
+      warn("Something went wrong during weaving")
+      print(e)
+    finally
+      doctype == :auto && (doctype = detect_doctype(doc.source))    
+      if contains(doctype, "2pdf") && cache == :off
+        rm(doc.fig_path, force = true, recursive = true)
+      elseif contains(doctype, "2html")
+        rm(doc.fig_path, force = true, recursive = true)
+      end
     end
-
-    doc.cwd == pwd() && (outname = basename(outname))
-
-    info("Report weaved to $outname")
 end
 
 function weave(doc::AbstractString, doctype::AbstractString)

src/cache.jl

@@ -33,7 +33,28 @@ function restore_chunk(chunk::CodeChunk, cached)
     return new_chunks
 end
 
-#Could be used to restore inline code in future
-function restore_chunk(chunk::DocChunk, cached)
-      return chunk
+#Restore inline code
+function restore_chunk(chunk::DocChunk, cached::WeaveDoc)
+    #Get chunk from cached doc
+    c_chunk = filter(x -> x.number == chunk.number && 
+                    isa(x,  DocChunk), cached.chunks)
+    isempty(c_chunk) && return chunk
+    c_chunk = c_chunk[1]
+
+    #Collect cached code
+    c_inline = filter(x -> isa(x, InlineCode), c_chunk.content)
+    isempty(c_inline) && return chunk
+
+    #Restore cached results for Inline code
+    n = length(chunk.content)    
+    for i in 1:n
+        if isa(chunk.content[i], InlineCode)
+            ci = filter(x -> x.number == chunk.content[i].number, c_inline)
+            isempty(ci) && continue
+            chunk.content[i].output = ci[1].output
+            chunk.content[i].rich_output = ci[1].rich_output
+            chunk.content[i].figures = ci[1].figures
+        end
+    end
+    return chunk
 end

src/chunks.jl

@@ -1,9 +1,12 @@
 
+abstract WeaveChunk
+abstract Inline
+
 type WeaveDoc
     source::AbstractString
     basename::AbstractString
     path::AbstractString
-    chunks::Array
+    chunks::Array{WeaveChunk}
     cwd::AbstractString
     format
     doctype::AbstractString
@@ -29,7 +32,7 @@ immutable ChunkOutput
     figures::Array{AbstractString}
 end
 
-type CodeChunk
+type CodeChunk <: WeaveChunk
     content::AbstractString
     number::Int
     result_no::Int
@@ -45,10 +48,34 @@ type CodeChunk
     end
 end
 
-type DocChunk
-    content::AbstractString
+type DocChunk <: WeaveChunk
+    content::Array{Inline}
     number::Int
     start_line::Int
+    function DocChunk(text::AbstractString, number::Int, start_line::Int, inline_regex = nothing)
+        chunks = parse_inline(text, inline_regex)
+        new(chunks, number, start_line)
+    end
+end
+
+type InlineText <: Inline
+    content::AbstractString
+    si::Int
+    ei::Int
+    number::Int
+end
+
+type InlineCode <: Inline
+    content::AbstractString
+    si::Int
+    ei::Int
+    number::Int
+    output::AbstractString
+    rich_output::AbstractString
+    figures::Array{AbstractString}
+    function InlineCode(content, si, ei, number)
+        new(content, si, ei, number, "", "", AbstractString[])
+    end
 end
 
 type TermResult

src/format.jl

@@ -105,22 +105,32 @@ function get_titleblock(doc::WeaveDoc)
 end
 
 function strip_header(chunk::DocChunk)
-  if ismatch(r"^---$(?<header>.+)^---$"ms, chunk.content)
-    chunk.content = lstrip(replace(chunk.content, r"^---$(?<header>.+)^---$"ms, ""))
+  if ismatch(r"^---$(?<header>.+)^---$"ms, chunk.content[1].content)
+    chunk.content[1].content = lstrip(replace(chunk.content[1].content, r"^---$(?<header>.+)^---$"ms, ""))
   end
   return chunk
 end
 
 function format_chunk(chunk::DocChunk, formatdict, docformat)
-    return chunk.content
+    return join([format_inline(c) for c in chunk.content], "")
+end
+
+function format_inline(inline::InlineText) 
+    return inline.content
+end
+
+function format_inline(inline::InlineCode)
+    isempty(inline.rich_output) || return inline.rich_output
+    isempty(inline.figures) || return inline.figures[end]
+    isempty(inline.output) || return inline.output
 end
 
 function format_chunk(chunk::DocChunk, formatdict, docformat::JMarkdown2HTML)
-    m = Base.Markdown.parse(chunk.content)
+    text = format_chunk(chunk, formatdict, nothing) 
+    m = Base.Markdown.parse(text)
     return string(Documenter.Writers.HTMLWriter.mdconvert(m))
 end
 
-
 #Fixes to Base latex writer
 function Base.Markdown.latex(io::IO, md::Base.Markdown.Paragraph)
     println(io)
@@ -144,7 +154,8 @@ end
 
 
 function format_chunk(chunk::DocChunk, formatdict, docformat::JMarkdown2tex)
-    m = Base.Markdown.parse(chunk.content)
+    text = format_chunk(chunk, formatdict, nothing) 
+    m = Base.Markdown.parse(text)
     return Base.Markdown.latex(m)
 end
 

src/readers.jl

@@ -5,30 +5,37 @@ pushopt(options::Dict,expr::Expr) = Base.Meta.isexpr(expr,:(=)) && (options[expr
 type MarkupInput
     codestart::Regex
     codeend::Regex
+    inline::Regex
 end
 
 type ScriptInput
   doc_line::Regex
   doc_start::Regex
   opt_line::Regex
   opt_start::Regex
+  inline::Regex
 end
 
 type NotebookInput
+  inline
 end
 
 const input_formats = Dict{AbstractString, Any}(
         "noweb" => MarkupInput(r"^<<(.*?)>>=\s*$",
-                    r"^@\s*$"),
+                    r"^@\s*$",
+                    r"`j\s+(.*?)`"s
+                    ),
         "markdown" => MarkupInput(
                       r"^[`~]{3,}(?:\{|\{\.|)julia(?:;|)\s*(.*?)(\}|\s*)$",
-                      r"^[`~]{3,}\s*$"),
+                      r"^[`~]{3,}\s*$",
+                      r"`j\s+(.*?)`"s),
         "script" => ScriptInput(
           r"(^#'.*)|(^#%%.*)|(^# %%.*)",
           r"(^#')|(^#%%)|(^# %%)",
           r"(^#\+.*$)|(^#%%\+.*$)|(^# %%\+.*$)",
-          r"(^#\+)|(^#%%\+)|(^# %%\+)"),
-        "notebook" => NotebookInput()
+          r"(^#\+)|(^#%%\+)|(^# %%\+)",
+          r"`j\s+(.*?)`"s),
+        "notebook" => NotebookInput(nothing) #Don't parse inline code from notebooks
         )
 
 """Detect the input format based on file extension"""
@@ -59,7 +66,7 @@ function parse_header(chunk::CodeChunk)
 end
 
 function parse_header(chunk::DocChunk)
-  m = match(r"^---$(?<header>.+)^---$"ms, chunk.content)
+  m = match(r"^---$(?<header>.+)^---$"ms, chunk.content[1].content)
   if m !== nothing
     header = YAML.load(string(m[:header]))
   else
@@ -109,7 +116,7 @@ function parse_doc(document::AbstractString, format::MarkupInput)
       haskey(options, :name) || (options[:name] = nothing)
 
       if !isempty(strip(content))
-        chunk = DocChunk(content, docno, start_line)
+        chunk = DocChunk(content, docno, start_line, format.inline)
         docno += 1
         push!(parsed, chunk)
       end
@@ -143,7 +150,7 @@ function parse_doc(document::AbstractString, format::MarkupInput)
 
   #Remember the last chunk
   if strip(content) != ""
-    chunk = DocChunk(content, docno, start_line)
+    chunk = DocChunk(content, docno, start_line, format.inline)
     #chunk =  Dict{Symbol,Any}(:type => "doc", :content => content,
     #                                 :number =>  docno, :start_line => start_line)
     push!(parsed, chunk)
@@ -223,7 +230,7 @@ function parse_doc(document::AbstractString, format::ScriptInput)
     elseif state == "doc" && strip(line) != "" && strip(read) != ""
       state = "code"
       (docno > 1) && (read = "\n" * read) # Add whitespace to doc chunk. Needed for markdown output
-      chunk = DocChunk(read, docno, start_line)
+      chunk = DocChunk(read, docno, start_line, format.inline)
       push!(parsed, chunk)
       options = Dict{Symbol,Any}()
       start_line = lineno
@@ -244,7 +251,7 @@ function parse_doc(document::AbstractString, format::ScriptInput)
     chunk = CodeChunk("\n" * strip(read), codeno, start_line, optionString, options)
     push!(parsed, chunk)
   else
-    chunk = DocChunk(read, docno, start_line)
+    chunk = DocChunk(read, docno, start_line, format.inline)
     push!(parsed, chunk)
   end
 
@@ -277,3 +284,32 @@ function parse_doc(document::String, format::NotebookInput)
 
 return parsed
 end
+
+#Use this if regex is undefined
+function parse_inline(text, noex)
+    return Inline[InlineText(text, 1, length(text), 1)]
+end
+
+function parse_inline(text::AbstractString, inline_ex::Regex)
+    ismatch(inline_ex, text) || return Inline[InlineText(text, 1, length(text), 1)]
+
+    inline_chunks = eachmatch(inline_ex, text)
+    s = 1
+    e = 1
+    res = Inline[]
+    textno = 1
+    codeno = 1
+
+    for ic in inline_chunks
+        s = ic.offset
+        doc = InlineText(text[e:(s-1)], e, s-1, textno)
+        textno += 1
+        push!(res, doc)
+        e = s + length(ic.match)
+        push!(res, InlineCode(ic.captures[1], s, e, codeno))
+        codeno += 1
+    end
+    push!(res, InlineText(text[e:end], e, length(text), textno))
+
+    return res
+end