no weird Base.run overload

src/Weave.jl

@@ -152,12 +152,12 @@ function weave(
         )
     end
 
-    template != nothing && (doc.template = template)
-    highlight_theme != nothing && (doc.highlight_theme = highlight_theme)
+    template !== nothing && (doc.template = template)
+    highlight_theme !== nothing && (doc.highlight_theme = highlight_theme)
     # theme != nothing && (doc.theme = theme) # Reserved for themes
-    css != nothing && (doc.css = css)
+    css !== nothing && (doc.css = css)
 
-    doc = run(
+    doc = run_doc(
         doc,
         doctype = doctype,
         mod = mod,

src/run.jl

@@ -1,7 +1,7 @@
 using Base64
 
 """
-    run(doc::WeaveDoc; kwargs...)
+    run_doc(doc::WeaveDoc; kwargs...)
 
 Run code chunks and capture output from the parsed document.
 
@@ -28,7 +28,7 @@ Run code chunks and capture output from the parsed document.
 !!! note
     Run Weave from terminal and try to avoid weaving from IJulia or ESS; they tend to mess with capturing output.
 """
-function Base.run(
+function run_doc(
     doc::WeaveDoc;
     doctype::Union{Symbol,AbstractString} = :auto,
     out_path::Union{Symbol,AbstractString} = :doc,
@@ -44,6 +44,7 @@ function Base.run(
     # cache :all, :user, :off, :refresh
 
     doc.cwd = get_cwd(doc, out_path)
+    # doctype detection is unnecessary here, but existing unit test requires this.
     doctype == :auto && (doctype = detect_doctype(doc.source))
     doc.doctype = doctype
     doc.format = formats[doctype]

test/errors_test.jl

@@ -1,4 +1,5 @@
 using Weave
+using Weave: run_doc
 using Test
 
 s1= """
@@ -22,7 +23,7 @@ print(y
 
 p1 = Weave.parse_doc(s1, "markdown")
 doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
-doc1 = Weave.run(doc, doctype = "pandoc")
+doc1 = run_doc(doc, doctype = "pandoc")
 
 doc1.chunks[1].output
 
@@ -30,10 +31,10 @@ doc1.chunks[1].output
 @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 Weave.run(doc, doctype = "pandoc", throw_errors = true)
+@test_throws ArgumentError run_doc(doc, doctype = "pandoc", throw_errors = true)
 
 doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
-doc3 = Weave.run(doc, doctype = "md2html")
+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/formatter_test.jl

@@ -1,4 +1,5 @@
 using Weave
+using Weave: run_doc
 using Test
 
 # Test rendering of doc chunks
@@ -22,7 +23,7 @@ f = Weave.format_chunk(dchunk, docformat.formatdict, docformat)
 # Test with actual doc
 
 parsed = Weave.read_doc("documents/chunk_options.noweb")
-doc = Weave.run(parsed, doctype = "md2html")
+doc = run_doc(parsed, doctype = "md2html")
 
 c_check = "<pre class='hljl'>\n<span class='hljl-n'>x</span><span class='hljl-t'> </span><span class='hljl-oB'>=</span><span class='hljl-t'> </span><span class='hljl-p'>[</span><span class='hljl-ni'>12</span><span class='hljl-p'>,</span><span class='hljl-t'> </span><span class='hljl-ni'>10</span><span class='hljl-p'>]</span><span class='hljl-t'>\n</span><span class='hljl-nf'>println</span><span class='hljl-p'>(</span><span class='hljl-n'>y</span><span class='hljl-p'>)</span>\n</pre>\n"
 doc.format.formatdict[:theme] = doc.highlight_theme
@@ -39,7 +40,7 @@ rendered = Weave.render_doc("Hello", doc, doc.format)
 
 # Tex format
 parsed = Weave.read_doc("documents/chunk_options.noweb")
-doc = Weave.run(parsed, doctype = "md2tex")
+doc = run_doc(parsed, doctype = "md2tex")
 
 c_check = "\\begin{lstlisting}\n(*@\\HLJLnf{println}@*)(*@\\HLJLp{(}@*)(*@\\HLJLn{x}@*)(*@\\HLJLp{)}@*)\n\\end{lstlisting}\n"
 doc.format.formatdict[:theme] = doc.highlight_theme
@@ -101,15 +102,15 @@ tfied = "\\ensuremath{\\bm{\\mathrm{L}}} \\ensuremath{\\bm{\\mathfrak{F}}} \\ens
 
 # Test markdown output from chunks
 parsed = Weave.read_doc("documents/markdown_output.jmd")
-doc = Weave.run(parsed, doctype = "md2html")
+doc = run_doc(parsed, doctype = "md2html")
 @test doc.chunks[1].rich_output == "\n<div class=\"markdown\"><h3>Small markdown sample</h3>\n<p><strong>Hello</strong> from <code>code</code> block.</p>\n</div>"
 @test doc.chunks[2].rich_output == "\n<div class=\"markdown\"><ul>\n<li><p>one</p>\n</li>\n<li><p>two</p>\n</li>\n<li><p>three</p>\n</li>\n</ul>\n</div>"
 
-ldoc = Weave.run(parsed, doctype = "md2tex")
+ldoc = run_doc(parsed, doctype = "md2tex")
 @test ldoc.chunks[1].rich_output == "\n\\subsubsection{Small markdown sample}\n\\textbf{Hello} from \\texttt{code} block.\n\n"
 @test ldoc.chunks[2].rich_output == "\n\\begin{itemize}\n\\item one\n\n\n\\item two\n\n\n\\item three\n\n\\end{itemize}\n"
 
-mdoc = Weave.run(parsed, doctype = "github")
+mdoc = run_doc(parsed, doctype = "github")
 @test mdoc.chunks[1].rich_output == "\n\n### Small markdown sample\n\n**Hello** from `code` block.\n\n"
 @test mdoc.chunks[2].rich_output == "\n\n* one\n* two\n* three\n\n"
 
@@ -143,11 +144,11 @@ doc_content = """
 """
 
 parsed = doc_from_string(doc_content)
-ldoc = Weave.run(parsed, doctype = "md2tex")
+ldoc = run_doc(parsed, doctype = "md2tex")
 @test occursin(Weave.uc2tex("α"),Weave.format(ldoc))
 @test !occursin("α",Weave.format(ldoc))
 
 parsed = doc_from_string(doc_content)
-ldoc = Weave.run(parsed, doctype = "md2tex",latex_keep_unicode=true)
+ldoc = run_doc(parsed, doctype = "md2tex",latex_keep_unicode=true)
 @test occursin("α",Weave.format(ldoc))
 @test !occursin(Weave.uc2tex("α"),Weave.format(ldoc))

test/sandbox_test.jl

@@ -1,10 +1,11 @@
 using Weave
+using Weave: run_doc
 using Test
 
 function weavestring(source; doctype = "pandoc", informat="markdown", mod=Main)
     p1 = Weave.parse_doc(source, informat)
     doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
-    return Weave.run(doc, doctype=doctype, mod=mod)
+    return run_doc(doc, doctype=doctype, mod=mod)
 end
 
 smod = """