Weave.jl/doc/src/usage.md

Using Weave

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

weave

Weave document with markup and julia code using Plots.jl for plots, out_path = :pwd makes the results appear in the current working directory.

A prepared example

# First add depencies for the example
using Pkg; Pkg.add.(["Plots", "DSP"])
using Weave
weave(joinpath(dirname(pathof(Weave)), "../examples", "FIR_design.jmd"), out_path=:pwd)

weave

tangle

Tangling extracts the code from document:

tangle

Supported Output Formats

Weave automatically detects the output format based on the file extension. The auto output format detection is handled by detect_doctype(path::AbstractString):

function detect_doctype(path::AbstractString)
    _, ext = lowercase.(splitext(path))

    match(r"^\.(jl|.?md|ipynb)", ext) !== nothing && return "md2html"
    ext == ".rst" && return "rst"
    ext == ".tex" && return "texminted"
    ext == ".txt"  && return "asciidoc"

    return "pandoc"
end

You can also manually specify it using the doctype keyword option. You can get a list of supported output formats:

list_out_formats

using Weave # hide
list_out_formats()

[Document Syntax](@id document-syntax)

Weave uses markdown, Noweb or script syntax for defining the code chunks and 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"

Documentation Chunks

In markdown and Noweb input formats documentation chunks are the parts that aren't inside code delimiters. Documentation chunks can be written with several different markup languages.

Code Chunks

Markdown Format

Markdown code chunks are defined using fenced code blocks with options following on the same line. e.g. to hide code from output you can use:

 ```julia; echo=false

Sample document

[Inline Code](@id inline-code)

You can also add inline code to your documents using

`j juliacode`

or

! juliacode

syntax. Using the j code syntax you can insert code anywhere in a line and with the ! syntax the whole line after ! will be executed. The code will be replaced with captured output in the weaved document.

If the code produces figures the filename or base64 encoded string will be added to output e.g. to include a Plots figure in markdown you can use:

![A plot](`j plot(1:10)`)

or to produce any html output:

! display("text/html", "Header from julia");

Noweb Format

Code 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 chunk options.

Script Format

Weave also support script input format with a markup in comments. These scripts can be executed normally using Julia or published with Weave.

Lines starting with #', #%% or # %% are treated as document.

All non-document lines are treated as code. You can set chunk options using lines starting with #+ just before code e.g:

#+ term=true
hoge # some code comes here

The format is identical to Pweave and the concept is similar to publishing documents with MATLAB or using Knitr's spin. Weave will remove the first empty space from each line of documentation.

See sample document:

Configuration via YAML Header

When weaveing markdown files, you can use YAML header to provide additional metadata and configuration options. See Header Configuration section for more details.

Passing Runtime Arguments to Documents

You can pass arguments as Dict to the weaved document using the args argument to weave. The arguments will be available as WEAVE_ARGS variable in the document.

This makes it possible to create the same report easily for e.g. different date ranges of input data from a database or from files with similar format giving the filename as input.

In order to pass a filename to a document you need call weave using:

weave("mydoc.jmd", args = Dict("filename" => "somedata.h5"))

and you can access the filename from document as follows:

    ```julia
    print(WEAVE_ARGS["filename"])
    ```

You can use the out_path argument to control the name of the output document.

include_weave

You can call include_weave on a Weave document and run all code chunks within in the current session.

include_weave