Merge 42548626b3 into 5047103527

Project.toml

@@ -4,6 +4,7 @@ version = "2.15.0"
 
 [deps]
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+CommonMark = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
 IOCapture = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

src/Literate.jl

@@ -6,7 +6,7 @@ https://fredrikekre.github.io/Literate.jl/ for documentation.
 """
 module Literate
 
-import JSON, REPL, IOCapture
+import JSON, REPL, IOCapture, CommonMark
 
 include("IJulia.jl")
 import .IJulia
@@ -16,6 +16,7 @@ struct DefaultFlavor <: AbstractFlavor end
 struct DocumenterFlavor <: AbstractFlavor end
 struct CommonMarkFlavor <: AbstractFlavor end
 struct FranklinFlavor <: AbstractFlavor end
+struct CarpentriesFlavor <: AbstractFlavor end
 
 # # Some simple rules:
 #
@@ -45,7 +46,7 @@ CodeChunk() = CodeChunk(String[], false)
 
 ismdline(line) = (occursin(r"^\h*#$", line) || occursin(r"^\h*# .*$", line)) && !occursin(r"^\h*##", line)
 
-function parse(content; allow_continued = true)
+function parse(content; allow_continued=true)
     lines = collect(eachline(IOBuffer(content)))
 
     chunks = Chunk[]
@@ -123,10 +124,10 @@ function parse(content; allow_continued = true)
 end
 
 function replace_default(content, sym;
-                         config::Dict,
+    config::Dict,
-                         branch = "gh-pages",
+    branch="gh-pages",
-                         commit = "master"
+    commit="master"
-                         )
+)
     repls = Pair{Any,Any}[]
 
     # add some shameless advertisement
@@ -228,7 +229,7 @@ filename(str) = first(splitext(last(splitdir(str))))
 isdocumenter(cfg) = cfg["flavor"]::AbstractFlavor isa DocumenterFlavor
 
 _DEFAULT_IMAGE_FORMATS = [(MIME("image/svg+xml"), ".svg"), (MIME("image/png"), ".png"),
-                          (MIME("image/jpeg"), ".jpeg")]
+    (MIME("image/jpeg"), ".jpeg")]
 
 # Cache of inputfile => head branch
 const HEAD_BRANCH_CACHE = Dict{String,String}()
@@ -246,7 +247,7 @@ function edit_commit(inputfile, user_config)
             readchomp(
                 pipeline(
                     setenv(`$(git) rev-parse --show-toplevel`; dir=dirname(inputfile));
-                    stderr=devnull,
+                    stderr=devnull
                 )
             )
         catch
@@ -292,15 +293,15 @@ function create_configuration(inputfile; user_config, user_kwargs, type=nothing)
     if (d = get(user_config, "documenter", nothing); d !== nothing)
         if type === :md
             Base.depwarn("The documenter=$(d) keyword to Literate.markdown is deprecated." *
-                " Pass `flavor = Literate.$(d ? "DocumenterFlavor" : "CommonMarkFlavor")()`" *
+                         " Pass `flavor = Literate.$(d ? "DocumenterFlavor" : "CommonMarkFlavor")()`" *
-                " instead.", Symbol("Literate.markdown"))
+                         " instead.", Symbol("Literate.markdown"))
             user_config["flavor"] = d ? DocumenterFlavor() : CommonMarkFlavor()
         elseif type === :nb
             Base.depwarn("The documenter=$(d) keyword to Literate.notebook is deprecated." *
-                " It is not used anymore for notebook output.", Symbol("Literate.notebook"))
+                         " It is not used anymore for notebook output.", Symbol("Literate.notebook"))
         elseif type === :jl
             Base.depwarn("The documenter=$(d) keyword to Literate.script is deprecated." *
-                " It is not used anymore for script output.", Symbol("Literate.script"))
+                         " It is not used anymore for script output.", Symbol("Literate.script"))
         end
     end
 
@@ -420,7 +421,7 @@ Available options:
   `$(_DEFAULT_IMAGE_FORMATS)`. Results which are `showable` with a MIME type are saved with
   the first match, with the corresponding extension.
 """
-const DEFAULT_CONFIGURATION=nothing # Dummy const for documentation
+const DEFAULT_CONFIGURATION = nothing # Dummy const for documentation
 
 function preprocessor(inputfile, outputdir; user_config, user_kwargs, type)
     # Create configuration by merging default and userdefined
@@ -474,7 +475,7 @@ function preprocessor(inputfile, outputdir; user_config, user_kwargs, type)
     content = replace_default(content, type; config=config)
 
     # parse the content into chunks
-    chunks = parse(content; allow_continued = type !== :nb)
+    chunks = parse(content; allow_continued=type !== :nb)
 
     return chunks, config
 end
@@ -527,6 +528,56 @@ function script(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs.
 end
 
 
+#_______________________________________________________________________________________
+# Define general functions needed for admonitions formating.
+
+function containsAdmonition(chunk)
+    for line in chunk.lines
+        if startswith(strip(line.first * line.second), "!!!")
+            return true
+        end
+    end
+    return false
+end
+
+function chunkToMD(chunk)
+    parser = CommonMark.Parser()
+    CommonMark.enable!(parser, CommonMark.AdmonitionRule())
+    buffer = IOBuffer()
+    for line in chunk.lines
+        write(buffer, line.first * line.second, '\n')
+    end
+    str = String(take!(buffer))
+    return parser(str)
+end
+
+function rewriteContent!(mdContent)
+    for (node, entering) in mdContent
+        if isa(node.t, CommonMark.Admonition)
+            admonition = node.t
+            node.t = CommonMark.Paragraph()
+            if admonition.category == "yaml"
+                node.first_child.t = CommonMark.Text()
+                node.first_child.nxt.t = CommonMark.Paragraph()
+                CommonMark.insert_after(node.first_child.nxt.last_child, CommonMark.text("\n---\n"))
+                CommonMark.insert_before(node.first_child.nxt, CommonMark.text("---\n"))
+            else
+                CommonMark.insert_before(node, CommonMark.text(""":::::: $(admonition.category)
+
+                ## $(admonition.title)
+
+                """))
+                CommonMark.insert_after(node, CommonMark.text("::::::\n\n"))
+            end
+        end
+    end
+    mdContent
+end
+
+#_______________________________________________________________________________________
+
+
+
 """
     Literate.markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwargs...)
 
@@ -540,12 +591,37 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
     # preprocessing and parsing
     chunks, config =
         preprocessor(inputfile, outputdir; user_config=config, user_kwargs=kwargs, type=:md)
-
     # create the markdown file
-    sb = sandbox()
     iomd = IOBuffer()
+
+
+    write_md_chunks!(iomd, chunks, outputdir, config)
+
+
+    # custom post-processing from user
+    content = config["postprocess"](String(take!(iomd)))
+
+    # write to file
+    outputfile = write_result(content, config)
+    return outputfile
+
+end
+
+function write_md_chunks!(iomd, chunks, outputdir, config)
+    flavor = config["flavor"]
+    sb = sandbox()
     for (chunknum, chunk) in enumerate(chunks)
         if isa(chunk, MDChunk)
+
+            if flavor isa CarpentriesFlavor
+                if containsAdmonition(chunk)
+                    md_chunk = chunkToMD(chunk)
+                    rewriteContent!(md_chunk)
+                    CommonMark.markdown(iomd, md_chunk)
+                    continue
+                end
+            end
+
             for line in chunk.lines
                 write(iomd, line.second, '\n') # skip indent here
             end
@@ -574,34 +650,30 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
             if execute
                 cd(config["literate_outputdir"]) do
                     execute_markdown!(iomd, sb, join(chunk.lines, '\n'), outputdir;
-                                      inputfile=config["literate_inputfile"],
+                        inputfile=config["literate_inputfile"],
-                                      fake_source=config["literate_outputfile"],
+                        fake_source=config["literate_outputfile"],
-                                      flavor=config["flavor"],
+                        flavor=config["flavor"],
-                                      image_formats=config["image_formats"],
+                        image_formats=config["image_formats"],
-                                      file_prefix="$(config["name"])-$(chunknum)",
+                        file_prefix="$(config["name"])-$(chunknum)"
                     )
                 end
             end
         end
         write(iomd, '\n') # add a newline between each chunk
     end
+end
 
-    # custom post-processing from user
-    content = config["postprocess"](String(take!(iomd)))
 
-    # write to file
-    outputfile = write_result(content, config)
-    return outputfile
-end
 
 function execute_markdown!(io::IO, sb::Module, block::String, outputdir;
-                           inputfile::String, fake_source::String,
+    inputfile::String, fake_source::String,
-                           flavor::AbstractFlavor, image_formats::Vector, file_prefix::String)
+    flavor::AbstractFlavor, image_formats::Vector, file_prefix::String)
     # TODO: Deal with explicit display(...) calls
     r, str, _ = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source)
     # issue #101: consecutive codefenced blocks need newline
     # issue #144: quadruple backticks allow for triple backticks in the output
-    plain_fence = "\n````\n" =>  "\n````"
+    plain_fence = "\n````$(flavor == CarpentriesFlavor() ? "output" : "")\n" => "\n````"
+    # Here CarpentiresFlavor fork...
     if r !== nothing && !REPL.ends_with_semicolon(block)
         if (flavor isa FranklinFlavor || flavor isa DocumenterFlavor) &&
            Base.invokelatest(showable, MIME("text/html"), r)
@@ -647,8 +719,8 @@ function parse_nbmeta(line)
     # Cf. https://jupytext.readthedocs.io/en/latest/formats.html#the-percent-format
     m = match(r"^%% ([^[{]+)?\s*(?:\[(\w+)\])?\s*(\{.*)?$", line)
     typ = m.captures[2]
-    name = m.captures[1] === nothing ? Dict{String, String}() : Dict("name" => m.captures[1])
+    name = m.captures[1] === nothing ? Dict{String,String}() : Dict("name" => m.captures[1])
-    meta = m.captures[3] === nothing ? Dict{String, Any}() : JSON.parse(m.captures[3])
+    meta = m.captures[3] === nothing ? Dict{String,Any}() : JSON.parse(m.captures[3])
     return typ, merge(name, meta)
 end
 line_is_nbmeta(line::Pair) = line_is_nbmeta(line.second)
@@ -671,7 +743,7 @@ function notebook(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
     nb = jupyter_notebook(chunks, config)
 
     # write to file
-    outputfile = write_result(nb, config; print = (io, c)->JSON.print(io, c, 1))
+    outputfile = write_result(nb, config; print=(io, c) -> JSON.print(io, c, 1))
     return outputfile
 end
 
@@ -690,11 +762,11 @@ function jupyter_notebook(chunks, config)
             metatype !== nothing && metatype != chunktype && error("specifying a different cell type is not supported")
             popfirst!(chunk.lines)
         else
-            metadata = Dict{String, Any}()
+            metadata = Dict{String,Any}()
         end
         lines = isa(chunk, MDChunk) ?
-                    String[x.second for x in chunk.lines] : # skip indent
+                String[x.second for x in chunk.lines] : # skip indent
-                    chunk.lines
+                chunk.lines
         @views map!(x -> x * '\n', lines[1:end-1], lines[1:end-1])
         cell["cell_type"] = chunktype
         cell["metadata"] = metadata
@@ -711,15 +783,15 @@ function jupyter_notebook(chunks, config)
     metadata = Dict()
 
     kernelspec = Dict()
-    kernelspec["language"] =  "julia"
+    kernelspec["language"] = "julia"
-    kernelspec["name"] =  "julia-$(VERSION.major).$(VERSION.minor)"
+    kernelspec["name"] = "julia-$(VERSION.major).$(VERSION.minor)"
     kernelspec["display_name"] = "Julia $(string(VERSION))"
     metadata["kernelspec"] = kernelspec
 
     language_info = Dict()
     language_info["file_extension"] = ".jl"
     language_info["mimetype"] = "application/julia"
-    language_info["name"]=  "julia"
+    language_info["name"] = "julia"
     language_info["version"] = string(VERSION)
     metadata["language_info"] = language_info
 
@@ -733,7 +805,7 @@ function jupyter_notebook(chunks, config)
         try
             cd(config["literate_outputdir"]) do
                 nb = execute_notebook(nb; inputfile=config["literate_inputfile"],
-                                          fake_source=config["literate_outputfile"])
+                    fake_source=config["literate_outputfile"])
             end
         catch err
             @error "error when executing notebook based on input file: " *
@@ -759,7 +831,7 @@ function execute_notebook(nb; inputfile::String, fake_source::String)
             stream = Dict{String,Any}()
             stream["output_type"] = "stream"
             stream["name"] = "stdout"
-            stream["text"] = collect(Any, eachline(IOBuffer(String(str)), keep = true))
+            stream["text"] = collect(Any, eachline(IOBuffer(String(str)), keep=true))
             push!(cell["outputs"], stream)
         end
 
@@ -769,7 +841,7 @@ function execute_notebook(nb; inputfile::String, fake_source::String)
         function split_mime(dict)
             for mime in ("image/svg+xml", "text/html")
                 if haskey(dict, mime)
-                    dict[mime] = collect(Any, eachline(IOBuffer(dict[mime]), keep = true))
+                    dict[mime] = collect(Any, eachline(IOBuffer(dict[mime]), keep=true))
                 end
             end
             return dict
@@ -849,7 +921,7 @@ function execute_block(sb::Module, block::String; inputfile::String, fake_source
     #  - c.output: combined stdout and stderr
     # `rethrow = Union{}` means that we try-catch all the exceptions thrown in the do-block
     # and return them via the return value (they get handled below).
-    c = IOCapture.capture(rethrow = Union{}) do
+    c = IOCapture.capture(rethrow=Union{}) do
         include_string(sb, block, fake_source)
     end
     popdisplay(disp) # IOCapture.capture has a try-catch so should always end up here