Updated docs, added convert_doc

README.md

@@ -12,10 +12,11 @@ You can write your documentation and code in input document using Nowed or Markd
 
 * Noweb, markdown or script syntax for input documents.
 * Execute code as terminal or "script" chunks.
-* Capture Gadfly, PyPlot and Winston figures.
+* Capture Plots, Gadfly, PyPlot and Winston figures.
 * Supports LaTex, Pandoc, Github markdown, MultiMarkdown, Asciidoc and reStructuredText output
 * Publish markdown directly to html and pdf using Pandoc.
 * Simple caching of results
+* Convert to and from IJulia notebooks
 
 ## Usage
 

doc/mkdocs.yml

@@ -31,4 +31,5 @@ pages:
   - Using Weave: usage.md
   - Publishing scripts: publish.md
   - Chunk options: chunk_options.md
+  - Working with Jupyter notebooks: notebooks.md
   - Function index: function_index.md

doc/src/index.md

@@ -10,14 +10,18 @@ and Sweave.
 
 * Noweb, markdown or script syntax for input documents.
 * Execute code as terminal or "script" chunks.
-* Capture Gadfly, PyPlot and Winston figures.
+* Capture Plots, Gadfly, PyPlot and Winston figures.
 * Supports LaTex, Pandoc, Github markdown, MultiMarkdown, Asciidoc and reStructuredText output
 * Publish markdown directly to html and pdf using Pandoc.
 * Simple caching of results
+* Convert to and from IJulia notebooks
 
 ![Weave code and output](http://mpastell.com/images/weave_demo.png)
 
 ## Contents
 
 ```@contents
+Pages = ["getting_started.md", "usage.md",
+"publish.md", "chunk_options.md", "notebooks.md",
+"function_index.md"]
 ```

doc/src/notebooks.md

@@ -0,0 +1,34 @@
+
+# Working with Jupyter notebooks
+
+## Weaving
+
+Weave supports using Jupyter notebooks as input format, this means you can weave notebooks to any supported formats. You can't use chunk options with notebooks.
+
+```
+weave("notebook.ipynb")
+```
+
+In order to output notebooks from other formats you need to convert the
+document to a notebook and run the code using IJulia.
+
+## Converting between formats
+
+You can convert between all supported input formats using the `convert_doc`
+function.
+
+To convert from script to notebook:
+
+```
+convert_doc("examples/FIR_design.jl", "FIR_design.ipynb")
+```
+
+and from notebooks to markdown use:
+
+```
+convert_doc("FIR_design.ipynb", "FIR_design.jmd")
+```
+
+```@docs
+convert_doc(infile::String, outfile::String)
+```

doc/src/publish.md

@@ -5,7 +5,7 @@ documents from Julia scripts with a specific format. Producing HTML and pdf outp
 requires that you have Pandoc and XeLatex (for pdf) installed and in your path.
 
 These scripts can be executed normally using Julia or published with Weave.
-Documentation is written in markdown in lines starting with ``#'``, ``#%%`` or ``# %%`` ,
+Documentation is written in markdown in lines starting with `#'`, `#%%` or `# %%`,
 and code is executed and results are included in the published document.
 
 The format is identical to [Pweave](http://mpastell.com/pweave/pypublish.html)
@@ -14,10 +14,9 @@ using Knitr's [spin](http://yihui.name/knitr/demo/stitch/).
 Weave will remove the first empty space from each line of documentation.
 
 All lines that are not documentation are treated as code. You can set chunk options
-using lines starting with ``#+``, ``#%%`` or ``# %%`` just before code
-e.g. ``#+ term=True, caption='Fancy plots.'``. See the example below for the markup.
+using lines starting with `#+` just before code
+e.g. `#+ term=true`. See the example below for the markup.
 
-The scripts can be published using the `pypublish` scipts:
 
 [FIR_design.jl](examples/FIR_design.jl), [FIR_design.html](examples/FIR_design.html) , [FIR_design.pdf](examples/FIR_design.pdf).
 

doc/src/usage.md

@@ -78,19 +78,17 @@ list_out_formats()
 ## Document syntax
 
 Weave uses noweb, markdown or script syntax for defining the code chunks and
-documentation chunks. The format is detected based on the file extension, but
-you can also set it manually using the `informat` parameter.
+documentation chunks. You can also weave Jupyter notebooks. The format is detected based on the file extension, but you can also set it manually using the `informat` parameter.
 
 The rules for autodetection are:
 
 ```
 ext == ".jl" && return "script"
 ext == ".jmd" && return "markdown"
+ext == ".ipynb" && return "notebook"
 return "noweb"
 ```
 
-
-
 ## Noweb
 
 ### Code chunks
@@ -104,4 +102,4 @@ Are the rest of the document (between `@` and `<<>>=` lines and the first chunk
 
 ## Markdown
 
-Markdown code chunks are defined using fenced code blocks. [See sample document:](https://github.com/mpastell/Weave.jl/blob/master/examples/gadfly_sample.jmd)
+Markdown code chunks are defined using fenced code blocks. [See sample document:](https://github.com/mpastell/Weave.jl/blob/master/examples/gadfly_md_sample.jmd)

src/Weave.jl

@@ -109,11 +109,6 @@ const postexecute_hooks = Function[]
 push_postexecute_hook(f::Function) = push!(postexecute_hooks, f)
 pop_postexecute_hook(f::Function) = splice!(postexecute_hooks, findfirst(postexecute_hooks, f))
 
-
-
-export weave, list_out_formats, tangle, convert_doc,
-        set_chunk_defaults, get_chunk_defaults, restore_chunk_defaults
-
 include("config.jl")
 include("chunks.jl")
 include("display_methods.jl")
@@ -123,4 +118,7 @@ include("cache.jl")
 include("formatters.jl")
 include("pandoc.jl")
 include("writers.jl")
+
+export weave, list_out_formats, tangle, convert_doc,
+        set_chunk_defaults, get_chunk_defaults, restore_chunk_defaults
 end

src/writers.jl

@@ -29,14 +29,23 @@ function detect_outformat(outfile::String)
   return "noweb"
 end
 
-"""Convert Weave documents between different formats"""
+"""
+`convert_doc(infile::AbstractString, outfile::AbstractString; format = nothing)`
+
+Convert Weave documents between different formats
+
+* `infile` = Name of the input document
+* `outfile` = Name of the output document
+* `format` = Output format (optional). Detected from outfile extension, but can
+  be set to `"script"`, `"markdown"`, `"notebook"` or `"noweb"`.
+"""
 function convert_doc(infile::AbstractString, outfile::AbstractString; format = nothing)
   doc = read_doc(infile)
 
   if format == nothing
     format = detect_outformat(outfile)
   end
-  
+
   converted = convert_doc(doc, output_formats[format])
 
   open(outfile, "w") do f