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Weave

Scientific reports/literate programming for Julia

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Weave

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

You can write your documentation and code in input document using Noweb, Markdown, Script syntax and use weave function to execute to document to capture results and figures.

Current features

  • Noweb, markdown or script syntax for input documents.
  • Execute code as terminal or "script" chunks.
  • Capture Plots, Gadfly and PyPlot figures.
  • Supports LaTex, Pandoc, Github markdown, MultiMarkdown, Asciidoc and reStructuredText output
  • Publish markdown directly to html and pdf using Julia or Pandoc markdown.
  • Simple caching of results
  • Convert to and from IJulia notebooks

Citing Weave: Pastell, Matti. 2017. Weave.jl: Scientific Reports Using Julia. The Journal of Open Source Software. http://dx.doi.org/10.21105/joss.00204

Note about Julia 0.6: Weave has been updated to support 0.6. PyPlot, Gadfly and Plots now all work, tests still need to be updated (15th May 2017).

Weave code and output

Installation

You can install the latest release using Julia package manager:

Pkg.add("Weave")

Usage

Run from julia using Gadfly for plots:

#First add depencies for the example
Pkg.add.(["Cairo", "Fontconfig", "Gadfly"])
#Use Weave
using Weave
weave(Pkg.dir("Weave","examples","gadfly_sample.mdw"))

If you have Pandoc installed you can also weave directly to html and pdf.

weave(Pkg.dir("Weave","examples","gadfly_md_sample.jmd"), informat="markdown",
  out_path = :pwd, doctype = "md2html")

Documentation

Documenter.jl with MKDocs generated documentation:

Editor support

I have made language-weave package for Atom to do the syntax highlighting correctly.

Noweb documents work well with ESS as well, to set doc-mode for .mdw files to markdown and code to Julia you can do:

(defun mdw-mode ()
       (ess-noweb-mode)
       (setq ess-noweb-default-code-mode 'ess-julia-mode)
       (setq ess-noweb-doc-mode 'markdown-mode))

(setq auto-mode-alist (append (list (cons "\\.mdw$" 'mdw-mode))
                   auto-mode-alist))

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

You can see the list of contributors on Github: https://github.com/mpastell/Weave.jl/graphs/contributors. Thanks for the important additions, fixes and comments.

First Commit

11/24/2014

Last Touched

1 day ago

Commits

414 commits

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