Merge pull request #319 from JunoLab/avi/weavedoc

remove weird default constructor for `WeaveDoc`

src/Weave.jl

@@ -3,6 +3,9 @@ import Highlights
 using Mustache
 using Requires
 
+
+const WEAVE_OPTION_NAME = "options" # TODO: rename to "weave_options"
+
 function __init__()
     @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Base.include(
         Main,
@@ -123,7 +126,7 @@ function weave(
     doc.doctype = doctype
 
     # Read args from document header, overrides command line args
-    if haskey(doc.header, "options")
+    if haskey(doc.header, WEAVE_OPTION_NAME)
         (
             doctype,
             informat,
@@ -248,7 +251,7 @@ function notebook(
     end
 
     @info "Running nbconvert"
-    out = read(
+    return out = read(
         `$jupyter_path nbconvert --ExecutePreprocessor.timeout=$timeout --to notebook --execute $outfile  $nbconvert_options --output $outfile`,
         String,
     )

src/config.jl

@@ -107,7 +107,7 @@ function header_args(
     pandoc_options,
     latex_cmd,
 )
-    args = get(doc.header, "options", Dict())
+    args = get(doc.header, WEAVE_OPTION_NAME, Dict())
     doctype = get(args, "doctype", doc.doctype)
     args = combine_args(args, doctype)
     informat = get(args, "informat", :auto)
@@ -145,16 +145,3 @@ function header_args(
         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 (val = get(doc.header["options"], string(key), nothing)) !== nothing
-            doc.chunk_defaults[key] = val
-        end
-    end
-end

src/format.jl

@@ -131,7 +131,7 @@ function strip_header!(docchunk::DocChunk, doctype)
         else
             # only strips Weave headers
             header = YAML.load(m[:header])
-            delete!(header, "options")
+            delete!(header, WEAVE_OPTION_NAME)
             if isempty(header)
                 lstrip(replace(content, HEADER_REGEX => ""))
             else

src/reader/reader.jl

@@ -2,20 +2,48 @@ using JSON, YAML
 
 
 """
-    read_doc(source::AbstractString, format = :auto) -> WeaveDoc
+    read_doc(source, format = :auto)
 
 Read the input document from `source` and parse it into [`WeaveDoc`](@ref).
 """
-function read_doc(source::AbstractString, format = :auto)
+function read_doc(source, format = :auto)
     document = replace(read(source, String), "\r\n" => "\n") # fix line ending
-
     format === :auto && (format = detect_informat(source))
     chunks = parse_doc(document, format)
-    header = parse_header(first(chunks))
+    return WeaveDoc(source, chunks)
-    doc = WeaveDoc(source, chunks, header)
+end
-    haskey(header, "options") && header_chunk_defaults!(doc) # TODO: rename `options` => `weave_options`
 
-    return doc
+function WeaveDoc(source, chunks)
+    path, fname = splitdir(abspath(source))
+    basename = splitext(fname)[1]
+
+    header = parse_header(first(chunks))
+    # get chunk defaults from header and update
+    chunk_defaults = deepcopy(rcParams[:chunk_defaults])
+    if haskey(header, WEAVE_OPTION_NAME)
+        for key in keys(chunk_defaults)
+            if (val = get(header[WEAVE_OPTION_NAME], string(key), nothing)) !== nothing
+                chunk_defaults[key] = val
+            end
+        end
+    end
+
+    return WeaveDoc(
+        source,
+        basename,
+        path,
+        chunks,
+        "",
+        nothing,
+        "",
+        "",
+        header,
+        "",
+        "",
+        Highlights.Themes.DefaultTheme,
+        "",
+        chunk_defaults,
+    )
 end
 
 """
@@ -32,7 +60,7 @@ function detect_informat(source::AbstractString)
     return "noweb"
 end
 
-function parse_doc(document, format)
+function parse_doc(document, format)::Vector{WeaveChunk}
     return if format == "markdown"
         parse_markdown(document)
     elseif format == "noweb"

src/types.jl

@@ -17,26 +17,6 @@ mutable struct WeaveDoc
     highlight_theme::Type{<:Highlights.AbstractTheme}
     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,
-            "",
-            deepcopy(rcParams[:chunk_defaults]),
-        )
-    end
 end
 
 struct ChunkOutput

test/errors_test.jl

@@ -1,35 +0,0 @@
-s1= """
-
-```julia
-using NonExisting
-```
-
-```julia
-x =
-```
-
-
-```julia;term=true
-plot(x)
-y = 10
-print(y
-```
-
-"""
-
-p1 = Weave.parse_markdown(s1)
-doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
-doc1 = run_doc(doc, doctype = "pandoc")
-
-@test doc1.chunks[1].output == "Error: ArgumentError: Package NonExisting not found in current path:\n- Run `import Pkg; Pkg.add(\"NonExisting\")` to install the NonExisting package.\n\n"
-@test doc1.chunks[2].output == "Error: syntax: incomplete: premature end of input\n"
-@test doc1.chunks[3].output == "\njulia> plot(x)\nError: UndefVarError: plot not defined\n\njulia> y = 10\n10\n\njulia> print(y\nError: syntax: incomplete: premature end of input\n"
-
-@test_throws ArgumentError run_doc(doc, doctype = "pandoc", throw_errors = true)
-
-doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
-doc3 = run_doc(doc, doctype = "md2html")
-@test doc3.chunks[1].rich_output == "<pre class=\"julia-error\">\nERROR: ArgumentError: Package NonExisting not found in current path:\n- Run &#96;import Pkg; Pkg.add&#40;&quot;NonExisting&quot;&#41;&#96; to install the NonExisting package.\n\n</pre>\n"
-@test doc3.chunks[2].rich_output == "<pre class=\"julia-error\">\nERROR: syntax: incomplete: premature end of input\n</pre>\n"
-@test doc3.chunks[3].output == "\njulia> plot(x)\nError: UndefVarError: plot not defined\n\njulia> y = 10\n10\n\njulia> print(y\nError: syntax: incomplete: premature end of input\n"
-@test doc3.chunks[3].rich_output == ""

test/formatter_test.jl

@@ -127,24 +127,21 @@ pformat.formatdict[:keep_unicode] = true
 f = Weave.format_chunk(dchunk, pformat.formatdict, pformat)
 @test f == "\\section{Test chunk}\nα\n\n"
 
-function doc_from_string(str)
-    parsed = Weave.parse_markdown(str)
-    header = Weave.parse_header(parsed[1])
-    Weave.WeaveDoc("",parsed,header)
-end
 
-doc_content = """
+str = """
 ```julia
 α = 10
 ```
 """
 
-parsed = doc_from_string(doc_content)
+let
-ldoc = run_doc(parsed, doctype = "md2tex")
+    doc = run_doc(mock_doc(str), doctype = "md2tex")
-@test occursin(Weave.uc2tex("α"),Weave.format(ldoc))
+    @test occursin(Weave.uc2tex("α"), Weave.format(doc))
-@test !occursin("α",Weave.format(ldoc))
+    @test !occursin("α", Weave.format(doc))
+end
 
-parsed = doc_from_string(doc_content)
+let
-ldoc = run_doc(parsed, doctype = "md2tex",latex_keep_unicode=true)
+    doc = run_doc(mock_doc(str), doctype = "md2tex",latex_keep_unicode = true)
-@test occursin("α",Weave.format(ldoc))
+    @test occursin("α", Weave.format(doc))
-@test !occursin(Weave.uc2tex("α"),Weave.format(ldoc))
+    @test !occursin(Weave.uc2tex("α"), Weave.format(doc))
+end

test/runtests.jl

@@ -6,16 +6,15 @@ using Test
 # TODO: add test for header processsing
 # TODO: add test for `include_weave`
 
+# constructs `WeaveDoc` from `String`
+mock_doc(str, chunk_parser = Weave.parse_markdown) = Weave.WeaveDoc("dummy", chunk_parser(str))
+
 
 @testset "Weave" begin
     @testset "Chunk options" begin
         include("chunk_options.jl")
     end
 
-    @testset "Error handling " begin
-        include("errors_test.jl")
-    end
-
     @testset "module evaluation" begin
         include("test_module_evaluation.jl")
     end
@@ -24,6 +23,10 @@ using Test
         include("test_header.jl")
     end
 
+    @testset "error rendering" begin
+        include("test_error_rendering.jl")
+    end
+
     @testset "Conversions" begin
         include("convert_test.jl")
     end

test/test_error_rendering.jl

@@ -0,0 +1,49 @@
+function get_err_str(ex)
+    try
+        eval(ex)
+    catch err
+        return sprint(showerror, err)
+    end
+end
+get_err_str(str::AbstractString) = get_err_str(Meta.parse(str; raise = false))
+
+err_stmt1 = "using NonExisting"
+err_stmt2 = "x = "
+err_stmt3 = """
+plot(x)
+y = 10
+f(y
+"""
+
+str = """
+```julia
+$err_stmt1
+```
+
+```julia
+$err_stmt2
+```
+
+```julia; term=true
+$err_stmt3
+```
+"""
+
+err_str1 = get_err_str(err_stmt1)
+err_str2 = get_err_str(err_stmt2)
+err_str3_1 = get_err_str("plot(x)")
+err_str3_2 = get_err_str("f(y")
+
+
+let doc = run_doc(mock_doc(str), doctype = "pandoc")
+    get_output(i) = doc.chunks[i].output
+
+    @test occursin(err_str1, get_output(1))
+    @test occursin(err_str2, get_output(2))
+    @test occursin(err_str3_1, get_output(3))
+    @test occursin(err_str3_2, get_output(3))
+end
+
+@test_throws ArgumentError run_doc(mock_doc(str), doctype = "pandoc", throw_errors = true)
+
+# TODO: test error rendering in `rich_output`

test/test_header.jl

@@ -1,4 +1,4 @@
-using YAML
+using Weave.YAML
 
 # TODO:
 # - header stripping
@@ -19,7 +19,7 @@ options:
 ---
 """)
 
-let args = header["options"]
+let args = header[Weave.WEAVE_OPTION_NAME]
     @test Weave.combine_args(args, "md2html") == Dict("fig_ext" => ".png", "out_path" => "html/")
     @test Weave.combine_args(args, "github") == Dict("fig_ext" => ".png", "out_path" => "md/")
     @test Weave.combine_args(args, "pandoc") == Dict("fig_ext" => ".png", "out_path" => "reports")

test/test_module_evaluation.jl

@@ -1,23 +1,20 @@
 @testset "evaluation module" begin
-    function mock_output(document, mod = nothing)
+    function mock_output(str, mod = nothing)
-        parsed = Weave.parse_markdown(document)
+        result_doc = run_doc(mock_doc(str), mod = mod)
-        doc = Weave.WeaveDoc("dummy.jmd", parsed, Dict())
-        result_doc = run_doc(doc, mod = mod)
-        @test isdefined(result_doc.chunks[1], :output)
         return result_doc.chunks[1].output
     end
 
-    document = """
+    str = """
     ```julia
     @__MODULE__
     ```
     """
 
     # in sandbox
-    @test occursin(r"\#+WeaveSandBox[\#\d]+", mock_output(document))
+    @test occursin(r"\#+WeaveSandBox[\#\d]+", mock_output(str))
 
     # in Main
-    @test strip(mock_output(document, Main)) == "Main"
+    @test strip(mock_output(str, Main)) == "Main"
 end
 
 @testset "clear_module!" begin