List supported output formats
This is the documentation of Weave.jl. Weave is a scientific report generator/literate programming tool for Julia. It resembles Pweave and, Knitr and Sweave.
You can write your documentation and code in input document using Nowed or Markdown syntax and use weave
function to execute to document to capture results and figures.
Current features
Weave uses noweb or markdown syntax for defining the code chunks and documentation chunks.
start with a line marked with <<>>=
or <<options>>=
and end with line marked with @
. The code between the start and end markers is executed and the output is captured to the output document. See for options below.
Are the rest of the document (between @
and <<>>=
lines and the first chunk be default) and can be written with several different markup languages.
Markdown code chunks are defined using fenced code blocks. See sample document:
I've tried to follow Knitr's naming for chunk options, but not all options are implemented.
Options are separated using ";" and need to be valid Julia expressions. Example: A code chunk that saves and displays a 12 cm wide image and hides the source code:
<<fig_width=5; echo=false >>=
using Gadfly
x = linspace(0, 2π, 200)
plot(x=x, y = sin(x), Geom.line)
@
Weave currently supports the following chunk options with the following defaults:
Options for code
echo = true
. Echo the code in the output document. If false
the source code will be hidden.
results = "markup"
. The output format of the printed results. "markup" for literal block, "hidden" for hidden results or anything else for raw output (I tend to use ‘tex’ for Latex and ‘rst’ for rest. Raw output is useful if you wan’t to e.g. create tables from code chunks.
eval = true
. Evaluate the code chunk. If false the chunk won’t be executed.
term=false
. If true the output emulates a REPL session. Otherwise only stdout and figures will be included in output.
label
. Chunk label, will be used for figure labels in Latex as fig:label
wrap=true
. Wrap long lines from output.
Options for figures
fig_width
. Figure width defined in markup, default depends on the output format.
out_width
. Width of saved figure.
out_height
. Height of saved figure.
dpi
=96. Resolution of saved figures.
fig_cap
. Figure caption.
label
. Chunk label, will be used for figure labels in Latex as fig:label
fig_ext
. File extension (format) of saved figures.
fig_pos="htpb"
. Figure position in Latex.
fig_env="figure"
. Figure environment in Latex.
Run from julia using Gadfly for plots:
using Weave
weave(Pkg.dir("Weave","examples","gadfly_sample.mdw"))
Using Winston for plots (Julia 0.3 only):
weave(Pkg.dir("Weave","examples","winston_sample.mdw"),
plotlib="Winston", doctype="pandoc")
Using PyPlot:
weave(Pkg.dir("Weave","examples","julia_sample.mdw"), plotlib="PyPlot")
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
List supported output formats
Tangle source code from input document to .jl file.
parameters:
tangle(source ; out_path=:doc, informat="noweb")
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 string e.g "/home/mpastell/weaveout"
Weave an input document to output file.
parameters:
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. Can be: :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.