Weave

Weave is a scientific report generator/literate programming tool for Julia. It resembles Pweave and, Knitr and Sweave.

Current features

Noweb or markdown syntax for input documents.
Execute code as terminal or "script" chunks.
Capture PyPlot, Gadfly or Winston figures.
Supports LaTex, Pandoc and Github markdown and reStructuredText output

Chunk options

I've tried to follow Knitr's naming for chunk options, but not all options are implemented. You can see src/config.jl for the current situation.

Options are separated using ";" and need to be valid Julia expressions. e.g.

<<term=true; fig_width=6; fig_height=4>>=

File formats

You can get a list of supported output formats:

julia> list_out_formats()
pandoc: Pandoc markdown
rst: reStructuredText and Sphinx
texminted: Latex using minted for highlighting
github: Github markdown
tex: Latex with custom code environments

Usage

Run from julia:

using Weave
weave(Pkg.dir("Weave","examples","julia_sample.mdw")

Using Winston for plots (Julia 0.3 only):

weave(Pkg.dir("Weave","examples","winston_sample.mdw"),
plotlib="Winston", doctype="pandoc")

Using Gadfly (Julia 0.3 only):

weave(Pkg.dir("Weave","examples","gadfly_sample.mdw"), plotlib="Gadfly")

The signature of weave functions is:

function weave(source ; doctype = "pandoc", plotlib="Gadfly", informat="noweb", out_path=:doc, fig_path = "figures", fig_ext = nothing)

doctype: see list_out_formats()
plotlib: "PyPlot", "Gadfly", or "Winston"
informat: "noweb" of "markdown"
out_path: Path where the output is generated:
- :doc: Path of the source document.
- :pwd: Julia working directory
- "somepath": Path as a string e.g "/home/mpastell/weaveout"
fig_path: where figures will be generated, relative to out_path
fig_ext: Extension for saved figures e.g. ".pdf", ".png". Default setting depends on doctype.

Note: Run Weave from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.

Contributing

I will probably add new features to Weave when I need them myself or if they are requested and not too difficult to implement. You can contribute by opening issues on Github or implementing things yourself and making a pull request. I'd also appreciate example documents written using Weave to add to examples.

Contributors