First version of documentation with Documenter.jl and mkdocs. Remove Docile depency

.gitignore

@@ -19,7 +19,9 @@ test/documents/*.pdf
 test/documents/chunk_options.jl
 !test/documents/*ref.*
 
-
+doc/build
+doc/site
+stable/
 
 tmp/
 .idea

README.md

@@ -26,7 +26,9 @@ weave(Pkg.dir("Weave","examples","gadfly_sample.mdw"))
 
 ## Documentation
 
-Lexicon.jl generated documentation for [v0.0.4](http://mpastell.github.io/Weave.jl/v0.0.4/) and [master](http://mpastell.github.io/Weave.jl/master/).
+Documenter.jl with MKdDocs generated documentation:
+
+[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://mpastell.github.io/Weave.jl/stable)
 
 ## Contributing
 

REQUIRE

@@ -1,5 +1,4 @@
 julia 0.4
 Compat
 ArgParse
-Docile
 JSON

doc/make.jl

@@ -0,0 +1,3 @@
+using Documenter, Weave
+
+makedocs(modules = Weave)

doc/mkdocs.yml

@@ -0,0 +1,29 @@
+site_name: Weave.jl - Scientific Reports Using Julia
+site_author: Matti Pastell
+copyright: Matti Pastell 2016
+repo_url: https://github.com/mpastell/Weave.jl
+
+theme: material
+
+extra:
+  palette:
+    primary: 'indigo'
+    accent:  'blue'
+
+extra_css:
+  - assets/Documenter.css
+
+extra_javascript:
+  - https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
+  - assets/mathjaxhelper.js
+
+markdown_extensions:
+  - extra
+  - tables
+  - fenced_code
+  - mdx_math
+
+docs_dir: 'build'
+
+pages:
+  - Home: index.md

doc/src/index.md

@@ -1,4 +1,6 @@
 
+# Intro
+
 This is the documentation of [Weave.jl](http://github.com/mpastell/weave.jl). Weave is a scientific report generator/literate programming tool
 for Julia. It resembles [Pweave](http://mpastell.com/pweave) and, Knitr
 and Sweave.
@@ -9,9 +11,13 @@ You can write your documentation and code in input document using Nowed or Markd
 
 * Noweb or markdown syntax for input documents.
 * Execute code as terminal or "script" chunks.
-* Capture PyPlot, Gadfly or Winston figures.
+* Capture PyPlot or Gadfly figures.
 * Supports LaTex, Pandoc and Github markdown and reStructuredText output
 
+    {contents}
+
+
+
 # Document syntax
 
 Weave uses noweb or markdown syntax for defining the code chunks and documentation chunks.
@@ -76,6 +82,8 @@ Weave currently supports the following chunk options with the following defaults
 
 # Usage
 
+## Weave
+
 Run from julia using Gadfly for plots:
 
 ```julia
@@ -83,28 +91,38 @@ using Weave
 weave(Pkg.dir("Weave","examples","gadfly_sample.mdw"))
 ```
 
-Using Winston for plots (Julia 0.3 and Weave.jl 0.04 only):
-
-```julia
-weave(Pkg.dir("Weave","examples","winston_sample.mdw"),
-plotlib="Winston", doctype="pandoc")
-```
-
 Using PyPlot:
 
 ```julia
 weave(Pkg.dir("Weave","examples","julia_sample.mdw"), plotlib="PyPlot")
 ```
 
-## File formats
+    {docs}
+      weave(source)
+
+## Tangle
+
+Tangling extracts the code from document:
+
+    {docs}
+      tangle(source)
+
+
+
+## Supported formats
 
 You can get a list of supported output formats:
 
-```julia
+```
 julia> list_out_formats()
 pandoc: Pandoc markdown
 rst: reStructuredText and Sphinx
 texminted: Latex using minted for highlighting
 github: Github markdown
+asciidoc: AsciiDoc
 tex: Latex with custom code environments
 ```
+
+# Index
+
+    {index}

src/Weave.jl

@@ -1,8 +1,5 @@
 module Weave
 using Compat
-using Docile
-
-@docstrings(manual = ["../doc/manual.md"])
 
 #Contains report global properties
 type Report <: Display
@@ -37,7 +34,11 @@ function Base.display(doc::Report, data)
     end
 end
 
-@doc "List supported output formats" ->
+"""
+list_out_formats()
+
+List supported output formats
+"""
 function list_out_formats()
   for format = keys(formats)
       println(string(format,": ",  formats[format].description))
@@ -45,18 +46,15 @@ function list_out_formats()
 end
 
 
-@doc """
+"""
-Tangle source code from input document to .jl file.
-
-**parameters:**
-```julia
 tangle(source ; out_path=:doc, informat="noweb")
-```
+
+Tangle source code from input document to .jl file.
 
 * `informat`: `"noweb"` of `"markdown"`
 * `out_path`: Path where the output is generated. Can be: `:doc`: Path of the source document, `:pwd`: Julia working directory,
 `"somepath"`: Path as a AbstractString e.g `"/home/mpastell/weaveout"`
-"""->
+"""
 function tangle(source ; out_path=:doc, informat="noweb")
     doc = read_doc(source, informat)
     cwd = get_cwd(doc, out_path)
@@ -74,14 +72,11 @@ function tangle(source ; out_path=:doc, informat="noweb")
     info("Writing to file $(doc.basename).jl")
 end
 
-@doc """
+"""
-Weave an input document to output file.
-
-**parameters:**
-```julia
 weave(source ; doctype = "pandoc", plotlib="Gadfly",
     informat="noweb", out_path=:doc, fig_path = "figures", fig_ext = nothing)
-```
+
+Weave an input document to output file.
 
 * `doctype`: see `list_out_formats()`
 * `plotlib`: `"PyPlot"`, `"Gadfly"`, or `"Winston"`
@@ -95,7 +90,7 @@ weave(source ; doctype = "pandoc", plotlib="Gadfly",
   `:user` = cache based on chunk options, `:refresh`, run all code chunks and save new cache.
 
 **Note:** Run Weave from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.
-""" ->
+"""
 function weave(source ; doctype = "pandoc", plotlib="Gadfly",
         informat="noweb", out_path=:doc, fig_path = "figures", fig_ext = nothing,
         cache_path = "cache", cache=:off)

src/readers.jl

@@ -13,14 +13,14 @@ const input_formats = @compat Dict{AbstractString, Any}(
         )
 
 
-@doc "Read and parse input document" ->
+"""Read and parse input document"""
 function read_doc(source::AbstractString, format="noweb"::AbstractString)
     document = readall(source)
     parsed = parse_doc(document, format)
     doc = WeaveDoc(source, parsed)
 end
 
-@doc "Parse chunks from AbstractString" ->
+"""Parse chunks from AbstractString"""
 function parse_doc(document::AbstractString, format="noweb"::AbstractString)
   #doctext = readall(open(document))
   lines = split(document, "\n")

src/run.jl

@@ -1,11 +1,9 @@
-@doc """
+"""
-Run code chunks and capture output from parsed document.
+run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="noweb",
-
-```julia
-function run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="noweb",
     out_path=:doc, fig_path = "figures", fig_ext = nothing,
     cache_path = "cache", cache = :off)
-```
+
+Run code chunks and capture output from parsed document.
 
 * `doctype`: see `list_out_formats()`
 * `plotlib`: `"PyPlot"`, `"Gadfly"`, or `"Winston"`
@@ -19,7 +17,7 @@ function run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="nowe
  `:user` = cache based on chunk options, `:refresh`, run all code chunks and save new cache.
 
 **Note:** Run command from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.
-""" ->
+"""
 function Base.run(doc::WeaveDoc; doctype = "pandoc", plotlib="Gadfly", informat="noweb",
         out_path=:doc, fig_path = "figures", fig_ext = nothing,
         cache_path = "cache", cache = :off)