Merge pull request #481 from dlfivefifty/patch-2

Mention Quarto in Related Packages

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false # don't stop CI even when one of them fails
       matrix:
         version:
-          - '1.4'
+          - '1.5'
         os:
           - ubuntu-latest
           - macOS-latest

.travis.yml

@@ -3,7 +3,7 @@ language: julia
 jobs:
   include:
     - stage: "Documentation"
-      julia: 1
+      julia: 1.5
       os: linux
       script:
         - julia --project=doc/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'

NEWS.md

@@ -1,6 +1,19 @@
 ## Release notes for Weave.jl
 
-### v0.10 - 2020/05/18
+### v0.10.6 – 2020/10/03
+
+improvements:
+- cleaned up chunk rendering (removed unnecessary extra newlines): #401
+- `WEAVE_ARGS` now can take arbitrary objects: https://github.com/JunoLab/Weave.jl/commit/c24a2621359b5d0af1bb6825f488e58cc11b8a9e
+- improved docs: #397 by @baggepinnen
+
+bug fixes
+- fixed #398: #399
+- removed unnecessary quote for markdown output: https://github.com/JunoLab/Weave.jl/commit/a1830e05029f33195627ec5dedbacb30af23947e
+- fixed #386: #396 by @torfjelde
+
+
+### v0.10 – 2020/05/18
 
 improvements:
 - `weave` is now integrated with Juno's progress bar; just call `weave` function inside Juno or use `julia-client: weave-to-html(pdf)` command (#331)

Project.toml

@@ -1,6 +1,6 @@
 name = "Weave"
 uuid = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"
-version = "0.10.3"
+version = "0.10.12"
 
 [deps]
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -12,15 +12,17 @@ Mustache = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+RelocatableFolders = "05181044-ff0b-4ac5-8273-598c1e38db00"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
-Highlights = "0.3.1, 0.4"
+Highlights = "0.3.1, 0.4, 0.5"
 JSON = "0.21"
 Mustache = "0.4.1, 0.5, 1"
 Plots = "0.28, 0.29, 1.0"
+RelocatableFolders = "0.1,0.2,0.3,1"
 Requires = "1.0"
 YAML = "0.3, 0.4"
 julia = "1.2"

README.md

@@ -97,3 +97,8 @@ Thanks for the important additions, fixes and comments.
 
 - [DiffEqTutorials.jl](https://github.com/JuliaDiffEq/DiffEqTutorials.jl) uses Weave to output tutorials (`.jmd` documents) to html, pdf and Jupyter notebooks.
 - [TuringTutorials](https://github.com/TuringLang/TuringTutorials) uses Weave to convert notebooks to html.
+
+## Related packages
+
+- [Literate.jl](https://github.com/fredrikekre/Literate.jl) can be used to generate Markdown and Jupyter notebooks directly from Julia source files with markdown in comments.
+- [Quarto](https://quarto.org) can generate Jupyter notebooks, HTML, or PDF directly from a Markdown format containing Julia code blocks, and also works with R and Python.

doc/src/header.md

@@ -39,11 +39,11 @@ Note that `Date` is available since the chunk is evaluated first.
  ---
  title : Header Example
  author : Shuhei Kadowaki
- date: `j Date(now())`
+ date: `j import Dates; Dates.Date(Dates.now())`
  ---
 
  ```julia; echo = false
- using Datas
+ using Dates
  ```
 ```
 

doc/src/usage.md

@@ -130,7 +130,7 @@ e.g. to include a Plots figure in markdown you can use:
 ```
 or to produce any HTML output:
 ```
-! display("text/html", "Header from julia");
+! display("text/html", HTML("Header from julia"));
 ```
 
 ### Script Format
@@ -165,29 +165,12 @@ See [Header Configuration](@ref) section for more details.
 
 ## Passing Runtime Arguments to Documents
 
-You can pass arguments as `Dict` to the weaved document using the `args` argument
+You can pass arbitrary object to the weaved document using [`weave`](@ref)'s optional argument `args`.
-to `weave`. The arguments will be available as `WEAVE_ARGS` variable in the document.
+It will be available as `WEAVE_ARGS` variable in the `weave`d document.
 
-This makes it possible to create the same report easily for e.g. different
+This makes it possible to create the same report easily for e.g. different date ranges of input data from a database or from files with similar format giving the filename as input.
-date ranges of input data from a database or from files with similar format giving the
-filename as input.
 
-In order to pass a filename to a document you need call `weave` using:
+E.g. if you call `weave("weavefile.jmd", args = (datalocation = "somedata.h5",))`, and then you can retrieve the `datalocation` in `weavefile.jmd` as follows: `WEAVE_ARGS.datalocation`
-
-```julia
-weave("mydoc.jmd", args = Dict("filename" => "somedata.h5"))
-```
-
-and you can access the filename from document as follows:
-
-```
-    ```julia
-    print(WEAVE_ARGS["filename"])
-    ```
-```
-
-You can use the `out_path` argument to control the name of the
-output document.
 
 
 ## `include_weave`

src/Weave.jl

@@ -1,14 +1,13 @@
 module Weave
 
-using Highlights, Mustache, Requires, Pkg, REPL
+using Highlights, Mustache, Requires, Pkg, REPL, RelocatableFolders, Base64
-
 
 # directories
 const PKG_DIR = normpath(@__DIR__, "..")
-const TEMPLATE_DIR = normpath(PKG_DIR, "templates")
+const TEMPLATE_DIR = @path joinpath(PKG_DIR, "templates")
-const STYLESHEET_DIR = normpath(PKG_DIR, "stylesheets")
+const STYLESHEET_DIR = @path joinpath(PKG_DIR, "stylesheets")
 # keeps paths of sample documents for easy try
-const EXAMPLE_FOLDER = normpath(PKG_DIR, "examples")
+const EXAMPLE_FOLDER = @path joinpath(PKG_DIR, "examples")
 
 # constant names
 const WEAVE_OPTION_NAME = "weave_options"
@@ -102,7 +101,7 @@ Weave an input document to output file.
   * `:doc`: Path of the source document (default)
   * `:pwd`: Julia working directory
   * `"somepath"`: `String` of output directory e.g. `"~/outdir"`, or of filename e.g. `"~/outdir/outfile.tex"`
-- `args::Dict = Dict()`: Arguments to be passed to the weaved document; will be available as `WEAVE_ARGS` in the document
+- `args::Any = Dict()`: A runtime object that is available as `WEAVE_ARGS` while `weave`ing
 - `mod::Union{Module,Nothing} = nothing`: Module where Weave `eval`s code. You can pass a `Module` object, otherwise create an new sandbox module.
 - `fig_path::Union{Nothing,AbstractString} = nothing`: Where figures will be generated, relative to `out_path`. By default (i.e. given `nothing`), Weave will automatically create `$(DEFAULT_FIG_PATH)` directory.
 - `fig_ext::Union{Nothing,AbstractString} = nothing`: Extension for saved figures e.g. `".pdf"`, `".png"`. Default setting depends on `doctype`
@@ -127,7 +126,7 @@ function weave(
     doctype::Union{Nothing,AbstractString} = nothing,
     informat::Union{Nothing,AbstractString} = nothing,
     out_path::Union{Symbol,AbstractString} = :doc,
-    args::Dict = Dict(),
+    args::Any = Dict(),
     mod::Union{Module,Nothing} = nothing,
     fig_path::Union{Nothing,AbstractString} = nothing,
     fig_ext::Union{Nothing,AbstractString} = nothing,
@@ -244,8 +243,16 @@ function specific_options!(weave_options, doctype)
 end
 
 get_out_path(doc, out_path, ext::Nothing = nothing) = get_out_path(doc, out_path, doc.format.extension)
-get_out_path(doc, out_path, ext) = abspath(get_cwd(doc, out_path), string(doc.basename , '.', ext))
+function get_out_path(doc, out_path, ext)
-
+    if (out_path === :doc) || (out_path === :pwd)
+        abspath(get_cwd(doc, out_path), string(doc.basename, '.', ext))
+    elseif isempty(splitext(out_path)[2]) # directory given
+        abspath(get_cwd(doc, out_path), string(doc.basename, '.', ext))
+    else
+        # out_path is given, but if extension is explitly provided override this will override the extension
+        abspath(string(splitext(out_path)[1], '.', ext))
+    end
+end
 """
     notebook(source::AbstractString; kwargs...)
 

src/WeaveMarkdown/markdown.jl

@@ -5,9 +5,11 @@ using ..Weave: isnothing, take2string!
 using Markdown
 import Markdown: @trigger, @breaking, Code, MD, withstream, startswith, LaTeX
 
-# Note that this definition causes a "Method overwritten" warning,
+# HACK: that this definition is type-piracy. It is required since `Markdown`
-# but defining this function in __init__() is not legal in julia v1.5
+# does not have a built in system for contextual rendering by users. `io` here
-function Markdown.latex(io::IO, tex::Markdown.LaTeX)
+# should always be either `IOBuffer` or `IOContext` since it is reached via
+# `sprint` in all user-facing code paths in `Markdown`.
+function Markdown.latex(io::Union{IOBuffer,IOContext}, tex::Markdown.LaTeX)
     math_envs = ["align", "equation", "eqnarray"]
     use_dollars =
         !any([occursin("\\begin{$me", tex.formula) for me in math_envs])

src/plots.jl

@@ -1,6 +1,6 @@
 module WeavePlots
 
-using Base64, ..Plots, ..Weave
+using ..Base64, ..Plots, ..Weave
 
 
 # Pre-execute hooks to set the plot size for the chunk
@@ -17,7 +17,7 @@ function Base.display(
     report::Weave.Report,
     m::MIME"image/svg+xml",
     data::Plots.Plot{Plots.PlotlyBackend},
-)#
+)
     # Remove extra spaces from start of line for pandoc
     s = repr(MIME("text/html"), data)
     splitted = split(s, "\n")
@@ -39,7 +39,7 @@ function Base.display(
     report::Weave.Report,
     m::MIME"image/png",
     data::Plots.Plot{Plots.PlotlyBackend},
-)#
+)
     display(report, MIME("image/svg+xml"), data)
 end
 

src/reader/markdown.jl

@@ -5,7 +5,7 @@ function parse_markdown(document_body; is_pandoc = false)
         r"^<<(?<options>.*?)>>=\s*$",
         r"^@\s*$"
     else
-        r"^[`~]{3}(\{?)julia\s*([;,]?)\s*(?<options>.*?)(\}|\s*)$",
+        r"^[`~]{3}(\{?)julia\s*([;,\{]?)\s*(?<options>.*?)(\}|\s*)$",
         r"^[`~]{3}\s*$"
     end
     return header, parse_markdown_body(document_body, code_start, code_end, offset)

src/rendering/common.jl

@@ -44,18 +44,14 @@ function render_chunk(docformat::WeaveFormat, chunk::CodeChunk)
 
     chunk.content = render_code(docformat, chunk.content)
 
-    if !chunk.options[:eval]
+    echo = chunk.options[:echo]
-        return if chunk.options[:echo]
+
-            string(docformat.codestart, '\n', chunk.content, docformat.codeend)
+    chunk.options[:eval] || return echo ? string(docformat.codestart, chunk.content, docformat.codeend) : ""
-        else
-            ""
-        end
-    end
 
     if chunk.options[:term]
         result = render_termchunk(docformat, chunk)
     else
-        result = if chunk.options[:echo]
+        result = if echo
             # Convert to output format and highlight (html, tex...) if needed
             string(docformat.codestart, chunk.content, docformat.codeend, '\n')
         else
@@ -126,7 +122,7 @@ render_output(docformat::WeaveFormat, output) = output
 
 function render_termchunk(docformat::WeaveFormat, chunk)
     return if should_render(chunk)
-        string(docformat.termstart, chunk.output, '\n', docformat.termend, '\n')
+        string(docformat.termstart, chunk.output, docformat.termend)
     else
         ""
     end

src/rendering/exportformat.jl

@@ -0,0 +1,24 @@
+abstract type ExportFormat <: WeaveFormat end
+
+function Base.getproperty(sf::T, s::Symbol) where {T<:ExportFormat}
+    hasfield(T, s) && return getfield(sf, s)
+    return getproperty(sf.primaryformat, s)
+end
+function Base.setproperty!(sf::T, s::Symbol, v) where {T<:ExportFormat}
+    if hasfield(T, s)
+        setfield!(sf, s, v)
+    else
+        setproperty!(sf.primaryformat, s, v)
+    end
+end
+function Base.hasproperty(sf::T, s::Symbol) where {T<:ExportFormat}
+    hasfield(T, s) || hasproperty(sf.primaryformat, s)
+end
+
+render_doc(df::ExportFormat, body, doc) = render_doc(df.primaryformat, body, doc)
+
+render_chunk(df::ExportFormat, chunk) = render_chunk(df.primaryformat, chunk)
+# Need to define these to avoid ambiguities
+render_chunk(df::ExportFormat, chunk::DocChunk) = render_chunk(df.primaryformat, chunk)
+render_chunk(df::ExportFormat, chunk::CodeChunk) = render_chunk(df.primaryformat, chunk)
+render_output(df::ExportFormat, output) = render_output(df.primaryformat, output)

src/rendering/htmlformats.jl

@@ -15,8 +15,8 @@ render_termchunk(docformat::HTMLFormat, chunk) =
 Base.@kwdef mutable struct WeaveHTML <: HTMLFormat
     description = "Weave-style HTML"
     extension = "html"
-    codestart = "\n"
+    codestart = '\n'
-    codeend = "\n"
+    codeend = '\n'
     termstart = codestart
     termend = codeend
     outputstart = "<pre class=\"output\">"
@@ -124,23 +124,9 @@ end
 # Pandoc
 # ------
 
-Base.@kwdef mutable struct Pandoc2HTML <: HTMLFormat
+Base.@kwdef mutable struct Pandoc2HTML <: ExportFormat
     description = "HTML via intermediate Pandoc Markdown (requires Pandoc 2)"
-    extension = "md"
+    primaryformat = Pandoc()
-    codestart = "\n"
-    codeend = "\n"
-    termstart = codestart
-    termend = codeend
-    outputstart = "\n"
-    outputend = "\n"
-    mimetypes = ["image/png", "image/svg+xml", "image/jpg", "text/html", "text/markdown", "text/plain"]
-    fig_ext = ".png"
-    out_width = nothing
-    out_height = nothing
-    fig_pos = nothing
-    fig_env = nothing
-    # specials
-    preserve_header = true
     template_path = nothing
     stylesheet_path = nothing
     highlight_theme = nothing

src/rendering/miscformats.jl

@@ -4,12 +4,12 @@
 Base.@kwdef mutable struct GitHubMarkdown <: WeaveFormat
     description = "GitHub Markdown"
     extension = "md"
-    codestart = "````julia"
+    codestart = "```julia"
-    codeend = "````\n\n"
+    codeend = "```\n"
     termstart = codestart
     termend = codeend
-    outputstart = "````"
+    outputstart = "```"
-    outputend = "````\n\n"
+    outputend = "```\n\n"
     fig_ext = ".png"
     mimetypes = ["image/png", "image/svg+xml", "image/jpg",
                 "text/markdown", "text/plain"]
@@ -50,12 +50,12 @@ end
 Base.@kwdef mutable struct Hugo <: WeaveFormat
     description = "Hugo Markdown (using shortcodes)"
     extension = "md"
-    codestart = "````julia"
+    codestart = "```julia"
-    codeend = "````\n\n"
+    codeend = "```\n"
     termstart = codestart
     termend = codeend
-    outputstart = "````"
+    outputstart = "```"
-    outputend = "````\n\n"
+    outputend = "```\n\n"
     mimetypes = default_mime_types
     fig_ext = ".png"
     out_width = nothing
@@ -88,12 +88,12 @@ end
 Base.@kwdef mutable struct MultiMarkdown <: WeaveFormat
     description = "MultiMarkdown"
     extension = "md"
-    codestart = "````julia"
+    codestart = "```julia"
-    codeend = "````\n\n"
+    codeend = "```\n"
     termstart = codestart
     termend = codeend
-    outputstart = "````"
+    outputstart = "```"
-    outputend = "````\n\n"
+    outputend = "```\n\n"
     mimetypes = default_mime_types
     fig_ext = ".png"
     out_width = nothing
@@ -143,7 +143,7 @@ Base.@kwdef mutable struct Rest <: WeaveFormat
     description = "reStructuredText and Sphinx"
     extension = "rst"
     codestart = ".. code-block:: julia\n"
-    codeend = "\n\n"
+    codeend = "\n"
     termstart = codestart
     termend = codeend
     outputstart = "::\n"
@@ -190,7 +190,7 @@ Base.@kwdef mutable struct AsciiDoc <: WeaveFormat
     description = "AsciiDoc"
     extension = "txt"
     codestart = "[source,julia]\n--------------------------------------"
-    codeend = "--------------------------------------\n\n"
+    codeend = "--------------------------------------\n"
     termstart = codestart
     termend = codeend
     outputstart = "--------------------------------------"

src/rendering/pandocformats.jl

@@ -37,7 +37,7 @@ Base.@kwdef mutable struct Pandoc <: PandocFormat
     description = "Pandoc Markdown"
     extension = "md"
     codestart = "~~~~{.julia}"
-    codeend = "~~~~~~~~~~~~~\n\n"
+    codeend = "~~~~~~~~~~~~~\n"
     termstart = codestart
     termend = codeend
     outputstart = "~~~~"
@@ -54,28 +54,14 @@ Base.@kwdef mutable struct Pandoc <: PandocFormat
 end
 register_format!("pandoc", Pandoc())
 
+
 const DEFAULT_PANDOC_OPTIONS = String[]
 
-Base.@kwdef mutable struct Pandoc2PDF <: PandocFormat
+Base.@kwdef mutable struct Pandoc2PDF <: ExportFormat
     description = "PDF via intermediate Pandoc Markdown"
-    extension = "md"
+    primaryformat = Pandoc()
-    codestart = "~~~~{.julia}"
-    codeend = "~~~~~~~~~~~~~\n\n"
-    termstart = codestart
-    termend = codeend
-    outputstart = "~~~~"
-    outputend = "~~~~\n\n"
-    # Prefer png figures for markdown conversion, svg doesn't work with latex
-    mimetypes = ["image/png", "image/jpg", "image/svg+xml", "text/markdown", "text/plain"]
-    fig_ext = ".png"
-    out_width = nothing
-    out_height = nothing
-    fig_pos = nothing
-    fig_env = nothing
-    # specials
-    preserve_header = true
-    header_template = normpath(TEMPLATE_DIR, "pandoc2pdf_header.txt")
     pandoc_options = DEFAULT_PANDOC_OPTIONS
+    header_template = normpath(TEMPLATE_DIR, "pandoc2pdf_header.txt")
 end
 register_format!("pandoc2pdf", Pandoc2PDF())
 

src/rendering/rendering.jl

@@ -23,9 +23,9 @@ function render_doc(doc::WeaveDoc)
     return render_doc(docformat, body, doc)
 end
 
-
+include("exportformat.jl")
 include("common.jl")
+include("pandocformats.jl")
 include("htmlformats.jl")
 include("texformats.jl")
-include("pandocformats.jl")
 include("miscformats.jl")

src/rendering/texformats.jl

@@ -34,7 +34,10 @@ render_output(docformat::LaTeXFormat, output) = unicode2latex(docformat, output,
 
 render_code(docformat::LaTeXFormat, code) = unicode2latex(docformat, code, true)
 
-render_termchunk(docformat::LaTeXFormat, chunk) = string(docformat.termstart, chunk.output, docformat.termend, "\n")
+render_termchunk(docformat::LaTeXFormat, chunk) =
+    string(docformat.termstart,
+            unicode2latex(docformat, chunk.output, true),
+            docformat.termend, "\n")
 
 # from julia symbols (e.g. "\bfhoge") to valid latex
 const UNICODE2LATEX = let
@@ -149,11 +152,11 @@ end
 Base.@kwdef mutable struct LaTeXMinted <: LaTeXFormat
     description = "LaTeX using minted package for code highlighting"
     extension = "tex"
-    codestart = "\\begin{minted}[escapeinside=||, mathescape, fontsize=\\small, xleftmargin=0.5em]{julia}"
+    codestart = "\\begin{minted}[texcomments = true, mathescape, fontsize=\\small, xleftmargin=0.5em]{julia}"
     codeend = "\\end{minted}"
-    termstart = "\\begin{minted}[escapeinside=||, mathescape, fontsize=\\footnotesize, xleftmargin=0.5em]{jlcon}"
+    termstart = "\\begin{minted}[texcomments = true, mathescape, fontsize=\\footnotesize, xleftmargin=0.5em]{jlcon}"
     termend = "\\end{minted}"
-    outputstart = "\\begin{minted}[escapeinside=||, mathescape, fontsize=\\small, xleftmargin=0.5em, frame = leftline]{text}"
+    outputstart = "\\begin{minted}[texcomments = true, mathescape, fontsize=\\small, xleftmargin=0.5em, frame = leftline]{text}"
     outputend = "\\end{minted}"
     mimetypes = ["application/pdf", "image/png", "text/latex", "text/plain"]
     fig_ext = ".pdf"
@@ -198,8 +201,14 @@ function render_code(docformat::WeaveLaTeXFormat, code)
     unicode2latex(docformat, ret, false)
 end
 
-render_termchunk(docformat::WeaveLaTeXFormat, chunk) =
+function render_termchunk(docformat::WeaveLaTeXFormat, chunk)
-    should_render(chunk) ? highlight_term(MIME("text/latex"), chunk.output, docformat.highlight_theme) : ""
+    if should_render(chunk)
+        ret = highlight_term(MIME("text/latex"), chunk.output, docformat.highlight_theme)
+        unicode2latex(docformat, ret, true)
+    else
+        ""
+    end
+end
 
 function render_doc(docformat::WeaveLaTeXFormat, body, doc)
     return Mustache.render(
@@ -233,44 +242,23 @@ Base.@kwdef mutable struct WeaveLaTeX <: WeaveLaTeXFormat
     tex_deps = ""
     # how to escape latex in verbatim/code environment
     escape_starter = "(*@"
-    escape_closer = reverse(escape_starter)
+    escape_closer = "@*)"
 end
 register_format!("md2tex", WeaveLaTeX())
 
 # will be used by `write_doc`
 const DEFAULT_LATEX_CMD = ["xelatex", "-shell-escape", "-halt-on-error"]
 
-Base.@kwdef mutable struct WeaveLaTeX2PDF <: WeaveLaTeXFormat
-    description = "PDF via Weave-styled LaTeX"
-    extension = "tex"
-    codestart = ""
-    codeend = ""
-    termstart = codestart
-    termend = codeend
-    outputstart = "\\begin{lstlisting}"
-    outputend = "\\end{lstlisting}\n"
-    mimetypes = ["application/pdf", "image/png", "image/jpg", "text/latex", "text/markdown", "text/plain"]
-    fig_ext = ".pdf"
-    out_width = "\\linewidth"
-    out_height = nothing
-    fig_pos = nothing
-    fig_env = nothing
-    # specials
-    highlight_theme = nothing
-    template = nothing
-    keep_unicode = false
-    tex_deps = ""
-    latex_cmd = DEFAULT_LATEX_CMD
-    # how to escape latex in verbatim/code environment
-    escape_starter = "(*@"
-    escape_closer = reverse(escape_starter)
-end
-register_format!("md2pdf", WeaveLaTeX2PDF())
 
-function set_format_options!(docformat::WeaveLaTeX2PDF; template = nothing, highlight_theme = nothing, keep_unicode = false, latex_cmd = DEFAULT_LATEX_CMD, _kwargs...)
+Base.@kwdef mutable struct LaTeX2PDF <: ExportFormat
-    docformat.template =
+    primaryformat = WeaveLaTeX()
-        get_mustache_template(isnothing(template) ? normpath(TEMPLATE_DIR, "md2pdf.tpl") : template)
+    description = "PDF via LaTeX"
-    docformat.highlight_theme = get_highlight_theme(highlight_theme)
+    latex_cmd = DEFAULT_LATEX_CMD
-    docformat.keep_unicode |= keep_unicode
+end
-    docformat.latex_cmd = latex_cmd
+register_format!("md2pdf", LaTeX2PDF())
+register_format!("minted2pdf", LaTeX2PDF(primaryformat=LaTeXMinted()))
+
+function set_format_options!(docformat::LaTeX2PDF; latex_cmd = DEFAULT_LATEX_CMD, _kwargs...)
+    docformat.latex_cmd = latex_cmd
+    set_format_options!(docformat.primaryformat; _kwargs...)
 end

src/run.jl

@@ -7,7 +7,7 @@ function run_doc(
     doc::WeaveDoc;
     doctype::Union{Nothing,AbstractString} = nothing,
     out_path::Union{Symbol,AbstractString} = :doc,
-    args::Dict = Dict(),
+    args::Any = Dict(),
     mod::Union{Module,Nothing} = nothing,
     fig_path::Union{Nothing,AbstractString} = nothing,
     fig_ext::Union{Nothing,AbstractString} = nothing,
@@ -20,8 +20,9 @@ function run_doc(
     doc.format = deepcopy(get_format(doctype))
 
     cwd = doc.cwd = get_cwd(doc, out_path)
-    isdir(cwd) || mkdir(cwd)
+    mkpath(cwd)
 
+    # TODO: provide a way not to create `fig_path` ?
     if isnothing(fig_path)
         fig_path = if (endswith(doctype, "2pdf") && cache === :off) || endswith(doctype, "2html")
             basename(mktempdir(abspath(cwd)))
@@ -29,7 +30,7 @@ function run_doc(
             DEFAULT_FIG_PATH
         end
     end
-    let d = normpath(cwd, fig_path); isdir(d) || mkdir(d); end
+    mkpath(normpath(cwd, fig_path))
     # This is needed for latex and should work on all output formats
     @static Sys.iswindows() && (fig_path = replace(fig_path, "\\" => "/"))
     set_rc_params(doc, fig_path, fig_ext)
@@ -38,7 +39,7 @@ function run_doc(
 
     # New sandbox for each document with args exposed
     isnothing(mod) && (mod = sandbox = Core.eval(Main, :(module $(gensym(:WeaveSandBox)) end))::Module)
-    @eval mod WEAVE_ARGS = $args
+    Core.eval(mod, :(WEAVE_ARGS = $(args)))
 
     mimetypes = doc.format.mimetypes
 
@@ -89,6 +90,8 @@ function run_doc(
         @info "Weaved all chunks" progress=1 _id=PROGRESS_ID
         cd_back()
         popdisplay(report) # ensure display pops out even if internal error occurs
+        # Temporary fig_path is not automatically removed because it contains files so...
+        !isnothing(fig_path) && startswith(fig_path, "jl_") && rm(normpath(cwd, fig_path), force=true, recursive=true)
     end
 
     return doc
@@ -139,27 +142,17 @@ function embed_figures!(chunk::CodeChunk, cwd)
         chunk.figures[i] = img2base64(fig, cwd)
     end
 end
-
+embed_figures!(chunks, cwd) = embed_figures!.(chunks, Ref(cwd))
-function embed_figures!(chunks::Vector{CodeChunk}, cwd)
-    for chunk in chunks
-        embed_figures!(chunk, cwd)
-    end
-end
 
 function img2base64(fig, cwd)
     ext = splitext(fig)[2]
     f = open(joinpath(cwd, fig), "r")
     raw = read(f)
     close(f)
-    if ext == ".png"
+    return ext == ".png" ? "data:image/png;base64," * stringmime(MIME("image/png"), raw) :
-        return "data:image/png;base64," * stringmime(MIME("image/png"), raw)
+           ext == ".svg" ? "data:image/svg+xml;base64," * stringmime(MIME("image/svg"), raw) :
-    elseif ext == ".svg"
+           ext == ".gif" ? "data:image/gif;base64," * stringmime(MIME("image/gif"), raw) :
-        return "data:image/svg+xml;base64," * stringmime(MIME("image/svg"), raw)
+           fig
-    elseif ext == ".gif"
-        return "data:image/gif;base64," * stringmime(MIME("image/gif"), raw)
-    else
-        return (fig)
-    end
 end
 
 function run_chunk(chunk::DocChunk, doc, report, mod)
@@ -225,7 +218,7 @@ function capture_output(code, mod, path, error, report)
     task_local_storage(:SOURCE_PATH, path) do
         try
             obj = include_string(mod, code, path) # TODO: fix line number
-            !isnothing(obj) && display(obj)
+            !isnothing(obj) && !REPL.ends_with_semicolon(code) && display(obj)
         catch _err
             err = unwrap_load_err(_err)
             error || throw(err)
@@ -273,15 +266,9 @@ function eval_chunk(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module
 
     execute_posthooks!(chunk)
 
-    chunks = if chunk.options[:term]
+    return chunk.options[:term] ? collect_term_results(chunk) :
-        collect_term_results(chunk)
+           chunk.options[:hold] ? collect_hold_results(chunk) :
-    elseif chunk.options[:hold]
+           collect_results(chunk)
-        collect_hold_results(chunk)
-    else
-        collect_results(chunk)
-    end
-
-    return chunks
 end
 
 # Hooks to run before and after chunks, this is form IJulia,
@@ -292,7 +279,11 @@ function pop_preexecution_hook!(f::Function)
     isnothing(i) && error("this function has not been registered in the pre-execution hook yet")
     return splice!(preexecution_hooks, i)
 end
-execute_prehooks!(chunk::CodeChunk) = for prehook in preexecution_hooks; Base.invokelatest(prehook, chunk); end
+function execute_prehooks!(chunk::CodeChunk)
+    for prehook in preexecution_hooks
+        Base.invokelatest(prehook, chunk)
+    end
+end
 
 const postexecution_hooks = Function[]
 push_postexecution_hook!(f::Function) = push!(postexecution_hooks, f)
@@ -301,7 +292,11 @@ function pop_postexecution_hook!(f::Function)
     isnothing(i) && error("this function has not been registered in the post-execution hook yet")
     return splice!(postexecution_hooks, i)
 end
-execute_posthooks!(chunk::CodeChunk) = for posthook in postexecution_hooks; Base.invokelatest(posthook, chunk); end
+function execute_posthooks!(chunk::CodeChunk)
+    for posthook in postexecution_hooks
+        Base.invokelatest(posthook, chunk)
+    end
+end
 
 """
     clear_module!(mod::Module)
@@ -340,11 +335,7 @@ function get_figname(report::Report, chunk; fignum = nothing, ext = nothing)
 end
 
 function set_rc_params(doc::WeaveDoc, fig_path, fig_ext)
-    if isnothing(fig_ext)
+    doc.chunk_defaults[:fig_ext] = isnothing(fig_ext) ? doc.format.fig_ext : fig_ext
-        doc.chunk_defaults[:fig_ext] = doc.format.fig_ext
-    else
-        doc.chunk_defaults[:fig_ext] = fig_ext
-    end
     doc.chunk_defaults[:fig_path] = fig_path
 end
 
@@ -352,11 +343,9 @@ function collect_results(chunk::CodeChunk)
     content = ""
     result_chunks = CodeChunk[]
     for r in chunk.result
+        content *= r.code
         # Check if there is any output from chunk
-        if strip(r.stdout) == "" && isempty(r.figures) && strip(r.rich_output) == ""
+        if any(!isempty ∘ strip, (r.stdout, r.rich_output)) || !isempty(r.figures)
-            content *= r.code
-        else
-            content = "\n" * content * r.code
             rchunk = CodeChunk(
                 content,
                 chunk.number,
@@ -364,15 +353,14 @@ function collect_results(chunk::CodeChunk)
                 chunk.optionstring,
                 copy(chunk.options),
             )
-            content = ""
-            rchunk.figures = r.figures
             rchunk.output = r.stdout
             rchunk.rich_output = r.rich_output
+            rchunk.figures = r.figures
             push!(result_chunks, rchunk)
+            content = ""
         end
     end
     if !isempty(content)
-        startswith(content, "\n") || (content = "\n" * content)
         rchunk = CodeChunk(
             content,
             chunk.number,

src/writer/latex.jl

@@ -1,4 +1,4 @@
-function write_doc(docformat::WeaveLaTeX2PDF, doc, rendered, out_path)
+function write_doc(docformat::LaTeX2PDF, doc, rendered, out_path)
     cd_back = let d = pwd(); () -> cd(d); end
     cd(doc.cwd)
     try

src/writer/pandoc.jl

@@ -61,7 +61,7 @@ function write_doc(docformat::Pandoc2PDF, doc, rendered, out_path)
         cmd = `pandoc -f markdown+raw_tex -s  --pdf-engine=xelatex --highlight-style=tango
          $filt $citeproc $(docformat.pandoc_options)
          --include-in-header=$(docformat.header_template)
-         -V fontsize=12pt -o $(out)`
+         -o $(out)`
         proc = open(cmd, "r+")
         println(proc.in, rendered)
         close(proc.in)

test/end2end/test_simple.jl

@@ -3,7 +3,7 @@ using Weave.Dates
 
 test_doctypes = filter(first.(Weave.list_out_formats())) do doctype
     # don't test doctypes which need external programs
-    doctype ∉ ("pandoc2html", "pandoc2pdf", "md2pdf")
+    doctype ∉ ("pandoc2html", "pandoc2pdf", "md2pdf", "minted2pdf")
 end
 
 function test_func(body)
@@ -24,7 +24,6 @@ using Dates
 Date(now())
 ```
 """
-
 for doctype in test_doctypes
     test_mock_weave(test_func, julia_markdown_body; informat = "markdown", doctype = doctype)
 end

test/reader/test_chunk_options.jl

@@ -72,6 +72,10 @@ let opts = get_options("```julia, opt1 = 1, opt2 = \"2\"\n```")
     @test (:opt1 => 1) in opts
     @test (:opt2 => "2") in opts
 end
+let opts = get_options("```julia{opt1 = 1, opt2 = \"2\"}\n```")
+    @test (:opt1 => 1) in opts
+    @test (:opt2 => "2") in opts
+end
 
 end
 

test/run/test_module.jl

@@ -46,4 +46,14 @@ Core.eval(m, :(const a = $ary))
 Weave.clear_module!(m)
 @test_broken Base.summarysize(m) < size
 
+julia_markdown_body = """
+this is just to test the `out_path` option
+"""
+
+f_in = tempname()
+f_out = tempname() * ".md"
+write(f_in, julia_markdown_body)
+f = weave(f_in; out_path=f_out)
+@test isfile(f_out)
+
 end # @testset "clear_module!"

test/test_display.jl

@@ -6,18 +6,18 @@
 doc = mock_run("""
 ```julia
 using DataFrames
-DataFrame(rand(10,3))
+DataFrame(a=rand(10))
 ```
 """; doctype = "md2html")
 @test isdefined(doc.chunks[1], :rich_output)
-@test count("<tr>", doc.chunks[1].rich_output) == 12 # additonal 2 for name and type row
+@test count("<tr", doc.chunks[1].rich_output) == 12 # additonal 2 for name and type row
 
 # limit
 n = 100000
 doc = mock_run("""
 ```julia
 using DataFrames
-DataFrame(rand($n,3))
+DataFrame(a=rand($n))
 ```
 """; doctype = "md2html")
 @test isdefined(doc.chunks[1], :rich_output)