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Using Weave
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Using Weave
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Weave
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Weave from shell
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Tangle
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<a title="Supported formats" href="#supported-formats">
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Supported formats
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Document syntax
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Noweb
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<p><a id='Using-Weave-1'></a></p>
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<h1 id="using-weave">Using Weave</h1>
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<p>You can write your documentation and code in input document using Noweb or Markdown syntax and use <code>weave</code> function to execute to document to capture results and figures.</p>
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<p><a id='Weave-1'></a></p>
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<h2 id="weave">Weave</h2>
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<p>Weave document with markup and julia code using Gadfly for plots, <code>out_path = :pwd</code> makes the results appear in the current working directory.</p>
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<div class="code"><pre><span></span><span class="k">using</span> <span class="n">Weave</span>
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<span class="n">weave</span><span class="p">(</span><span class="n">Pkg</span><span class="o">.</span><span class="n">dir</span><span class="p">(</span><span class="s">"Weave"</span><span class="p">,</span><span class="s">"examples"</span><span class="p">,</span><span class="s">"gadfly_sample.mdw"</span><span class="p">),</span> <span class="n">out_path</span> <span class="o">=</span> <span class="p">:</span><span class="n">pwd</span><span class="p">)</span>
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</pre></div>
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<p>Using PyPlot:</p>
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<div class="code"><pre><span></span><span class="n">weave</span><span class="p">(</span><span class="n">Pkg</span><span class="o">.</span><span class="n">dir</span><span class="p">(</span><span class="s">"Weave"</span><span class="p">,</span><span class="s">"examples"</span><span class="p">,</span><span class="s">"julia_sample.mdw"</span><span class="p">),</span> <span class="n">plotlib</span><span class="o">=</span><span class="s">"PyPlot"</span><span class="p">,</span> <span class="n">out_path</span> <span class="o">=</span> <span class="p">:</span><span class="n">pwd</span><span class="p">)</span>
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</pre></div>
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<p><a id='Weave.weave-Tuple{Any}' href='#Weave.weave-Tuple{Any}'>#</a>
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<strong><code>Weave.weave</code></strong> — <em>Method</em>.</p>
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<p><code>function weave(source ; doctype = :auto, plotlib="Gadfly", informat=:auto, out_path=:doc, fig_path = "figures", fig_ext = nothing, cache_path = "cache", cache=:off)</code></p>
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<p>Weave an input document to output file.</p>
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<ul>
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<li><code>doctype</code>: :auto = set based on file extension or specify one of the supported formats. See <code>list_out_formats()</code></li>
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<li><code>plotlib</code>: <code>"PyPlot"</code>, <code>"Gadfly"</code> or <code>nothing</code></li>
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<li><code>informat</code>: :auto = set based on file extension or set to <code>"noweb"</code>, <code>"markdown"</code> or <code>script</code></li>
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<li><code>out_path</code>: Path where the output is generated. Can be: <code>:doc</code>: Path of the source document, <code>:pwd</code>: Julia working directory, <code>"somepath"</code>: output directory as a String e.g <code>"/home/mpastell/weaveout"</code> or filename as string e.g. ~/outpath/outfile.tex.</li>
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<li><code>fig_path</code>: where figures will be generated, relative to out_path</li>
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<li><code>fig_ext</code>: Extension for saved figures e.g. <code>".pdf"</code>, <code>".png"</code>. Default setting depends on <code>doctype</code>.</li>
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<li><code>cache_path</code>: where of cached output will be saved.</li>
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<li><code>cache</code>: controls caching of code: <code>:off</code> = no caching, <code>:all</code> = cache everything, <code>:user</code> = cache based on chunk options, <code>:refresh</code>, run all code chunks and save new cache.</li>
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</ul>
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<p><strong>Note:</strong> Run Weave from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.</p>
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<p><a id='Weave-from-shell-1'></a></p>
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<h2 id="weave-from-shell">Weave from shell</h2>
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<p>You can also use the <code>weave.jl</code> script under bin directory to weave documents from the shell:</p>
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<div class="code"><pre><span></span>$ ./weave.jl
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usage: weave.jl <span class="o">[</span>--doctype DOCTYPE<span class="o">]</span> <span class="o">[</span>--plotlib PLOTLIB<span class="o">]</span>
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<span class="o">[</span>--informat INFORMAT<span class="o">]</span> <span class="o">[</span>--out_path OUT_PATH<span class="o">]</span>
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<span class="o">[</span>--fig_path FIG_PATH<span class="o">]</span> <span class="o">[</span>--fig_ext FIG_EXT<span class="o">]</span> source...
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</pre></div>
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<p><a id='Tangle-1'></a></p>
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<h2 id="tangle">Tangle</h2>
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<p>Tangling extracts the code from document:</p>
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<p><a id='Weave.tangle-Tuple{Any}' href='#Weave.tangle-Tuple{Any}'>#</a>
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<strong><code>Weave.tangle</code></strong> — <em>Method</em>.</p>
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<p><code>tangle(source ; out_path=:doc, informat="noweb")</code></p>
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<p>Tangle source code from input document to .jl file.</p>
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<ul>
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<li><code>informat</code>: <code>"noweb"</code> of <code>"markdown"</code></li>
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<li><code>out_path</code>: Path where the output is generated. Can be: <code>:doc</code>: Path of the source document, <code>:pwd</code>: Julia working directory, <code>"somepath"</code>, directory name as a string e.g <code>"/home/mpastell/weaveout"</code></li>
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</ul>
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<p>or filename as string e.g. ~/outpath/outfile.jl.</p>
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<p><a id='Supported-formats-1'></a></p>
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<h2 id="supported-formats">Supported formats</h2>
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<p>Weave sets the output format based on the file extension, but you can also set it using <code>doctype</code> option. The rules for detecting the format are:</p>
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<div class="code"><pre><span></span><span class="n">ext</span> <span class="o">==</span> <span class="s">".jl"</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"md2html"</span>
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<span class="n">contains</span><span class="p">(</span><span class="n">ext</span><span class="p">,</span> <span class="s">".md"</span><span class="p">)</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"md2html"</span>
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<span class="n">contains</span><span class="p">(</span><span class="n">ext</span><span class="p">,</span> <span class="s">".rst"</span><span class="p">)</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"rst"</span>
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<span class="n">contains</span><span class="p">(</span><span class="n">ext</span><span class="p">,</span> <span class="s">".tex"</span><span class="p">)</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"texminted"</span>
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<span class="n">contains</span><span class="p">(</span><span class="n">ext</span><span class="p">,</span> <span class="s">".txt"</span><span class="p">)</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"asciidoc"</span>
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<span class="k">return</span> <span class="s">"pandoc"</span>
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</pre></div>
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<p>You can get a list of supported output formats:</p>
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<div class="code"><pre><span></span><span class="n">julia</span><span class="o">></span> <span class="n">list_out_formats</span><span class="p">()</span>
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<span class="n">pandoc</span><span class="p">:</span> <span class="n">Pandoc</span> <span class="n">markdown</span>
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<span class="n">rst</span><span class="p">:</span> <span class="n">reStructuredText</span> <span class="n">and</span> <span class="n">Sphinx</span>
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<span class="n">texminted</span><span class="p">:</span> <span class="n">Latex</span> <span class="k">using</span> <span class="n">minted</span> <span class="k">for</span> <span class="n">highlighting</span>
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<span class="n">github</span><span class="p">:</span> <span class="n">Github</span> <span class="n">markdown</span>
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<span class="n">md2html</span><span class="p">:</span> <span class="n">Markdown</span> <span class="n">to</span> <span class="n">HTML</span> <span class="p">(</span><span class="n">requires</span> <span class="n">Pandoc</span><span class="p">)</span>
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<span class="n">md2pdf</span><span class="p">:</span> <span class="n">Markdown</span> <span class="n">to</span> <span class="n">pdf</span> <span class="p">(</span><span class="n">requires</span> <span class="n">Pandoc</span> <span class="n">and</span> <span class="n">xelatex</span><span class="p">)</span>
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<span class="n">asciidoc</span><span class="p">:</span> <span class="n">AsciiDoc</span>
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<span class="n">tex</span><span class="p">:</span> <span class="n">Latex</span> <span class="n">with</span> <span class="n">custom</span> <span class="n">code</span> <span class="n">environments</span>
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</pre></div>
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<p><a id='Weave.list_out_formats-Tuple{}' href='#Weave.list_out_formats-Tuple{}'>#</a>
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<strong><code>Weave.list_out_formats</code></strong> — <em>Method</em>.</p>
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<p><code>list_out_formats()</code></p>
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<p>List supported output formats</p>
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<p><a id='Document-syntax-1'></a></p>
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<h2 id="document-syntax">Document syntax</h2>
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<p>Weave uses noweb, markdown 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 <code>informat</code> parameter.</p>
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<p>The rules for autodetection are:</p>
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<div class="code"><pre><span></span><span class="n">ext</span> <span class="o">==</span> <span class="s">".jl"</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"script"</span>
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<span class="n">ext</span> <span class="o">==</span> <span class="s">".jmd"</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"markdown"</span>
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<span class="n">ext</span> <span class="o">==</span> <span class="s">".ipynb"</span> <span class="o">&&</span> <span class="k">return</span> <span class="s">"notebook"</span>
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<span class="k">return</span> <span class="s">"noweb"</span>
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</pre></div>
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<p><a id='Noweb-1'></a></p>
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<h2 id="noweb">Noweb</h2>
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<p><a id='Code-chunks-1'></a></p>
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<h3 id="code-chunks">Code chunks</h3>
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<p>start with a line marked with <code><<>>=</code> or <code><<options>>=</code> and end with line marked with <code>@</code>. The code between the start and end markers is executed and the output is captured to the output document. See for options below.</p>
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<p><a id='Documentation-chunks-1'></a></p>
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<h3 id="documentation-chunks">Documentation chunks</h3>
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<p>Are the rest of the document (between <code>@</code> and <code><<>>=</code> lines and the first chunk be default) and can be written with several different markup languages.</p>
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<p><a href="https://github.com/mpastell/Weave.jl/blob/master/examples/julia_sample.mdw">Sample document</a></p>
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<p><a id='Markdown-1'></a></p>
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<h2 id="markdown">Markdown</h2>
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<p>Markdown code chunks are defined using fenced code blocks. <a href="https://github.com/mpastell/Weave.jl/blob/master/examples/gadfly_md_sample.jmd">See sample document:</a></p>
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<aside class="copyright" role="note">
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Matti Pastell 2016 –
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Documentation built with
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<a href="http://www.mkdocs.org" target="_blank">MkDocs</a>
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using the
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<a href="http://squidfunk.github.io/mkdocs-material/" target="_blank">
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Material
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</a>
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theme.
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</aside>
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<footer class="footer">
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<nav class="pagination" aria-label="Footer">
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Previous
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Publishing scripts
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