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<!DOCTYPE html><html><head><meta name="viewport" content="width=device-width"/><meta charSet="utf-8"/><title>The basics of org-babel</title><script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script><script id="MathJax-script" async="" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script><script type="text/x-mathjax-config">
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</script><meta name="next-head-count" content="6"/><link rel="preload" href="/wiki/_next/static/css/52fc2ba29703df73922c.css" as="style"/><link rel="stylesheet" href="/wiki/_next/static/css/52fc2ba29703df73922c.css" data-n-g=""/><noscript data-n-css=""></noscript><link rel="preload" href="/wiki/_next/static/chunks/main-ae4733327bd95c4ac325.js" as="script"/><link rel="preload" href="/wiki/_next/static/chunks/webpack-50bee04d1dc61f8adf5b.js" as="script"/><link rel="preload" href="/wiki/_next/static/chunks/framework.9d524150d48315f49e80.js" as="script"/><link rel="preload" href="/wiki/_next/static/chunks/commons.0e1c3f9aa780c2dfe9f0.js" as="script"/><link rel="preload" href="/wiki/_next/static/chunks/pages/_app-8e3d0c58a60ec788aa69.js" as="script"/><link rel="preload" href="/wiki/_next/static/chunks/940643274e605e7596ecea1f2ff8d83317a3fb76.4841a16762f602a59f00.js" as="script"/><link rel="preload" href="/wiki/_next/static/chunks/pages/%5B%5B...slug%5D%5D-1aa198f87ede1cd0e1dc.js" as="script"/></head><body><div id="__next"><main><h1>The basics of org-babel</h1><section class="post-metadata"><span>Date: <!-- -->2021-05-19 18:54:37 +08:00</span><span>Date modified: <!-- -->2021-06-04 11:11:18 +08:00</span></section><nav class="toc"><ol class="toc-level toc-level-1"><li class="toc-item toc-item-h1"><a href="/wiki/text.org-mode.babel#functional-and-scripting-mode" class="toc-link toc-link-h1">Functional and scripting mode</a></li><li class="toc-item toc-item-h1"><a href="/wiki/text.org-mode.babel#functional-mode-values-and-passing-them-around" class="toc-link toc-link-h1">Functional mode values and passing them around</a></li><li class="toc-item toc-item-h1"><a href="/wiki/text.org-mode.babel#source-code-evaluation" class="toc-link toc-link-h1">Source code evaluation</a></li><li class="toc-item toc-item-h1"><a href="/wiki/text.org-mode.babel#creating-dynamic-content-with-meta-programming" class="toc-link toc-link-h1">Creating dynamic content with meta-programming</a></li><li class="toc-item toc-item-h1"><a href="/wiki/text.org-mode.babel#executing-code-blocks-in-the-same-session" class="toc-link toc-link-h1">Executing code blocks in the same session</a></li></ol></nav><p>org-babel (see <a href="/wiki/2020-04-17-21-41-30">Org mode: Babel</a>) is the framework that enables Org mode features for reproducible research.
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It has a variety of applications that Org mode can do in this field so let's enumerate them.
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</p><h1 id="functional-and-scripting-mode">Functional and scripting mode</h1><p>Babel works in two modes: functional and scripting mode.
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</p><ul><li><p>Functional mode returns a value either from the last statement or the return statement.
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The value can then be used in other source code blocks and appropriately converted into Org mode equivalents.
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If the return value is a vector type, it will be printed as tables in Org mode which will then be rendered as a vector when used in another source code block.
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</p></li><li><p>Scripting mode simply prints the output.
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Do keep in mind different languages have different ways of capturing the output.
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</p></li></ul><p>The default mode is in functional mode but you can change it by setting <code class="inline-code">:results</code> header argument with the values from the <a href="https://orgmode.org/manual/Results-of-Evaluation.html">collection class</a>.
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</p><h1 id="functional-mode-values-and-passing-them-around">Functional mode values and passing them around</h1><p>With functional mode, the value return will appear as an appropriate element in the Org mode buffer.
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The following examples are in <a href="https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html">Python</a>.
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</p><p>Scalar values appear as strings...
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</p><pre class="src-block"><code class="language-python">return "The quick brown fox jumps over the lazy dog."
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</code></pre><pre class="fixed-width">The quick brown fox jumps over the lazy dog.</pre><p>
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...and vector values print as tables.
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</p><pre class="src-block"><code class="language-python">return [
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["Monty", 45],
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["Soup", 54],
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["Cabbages", 63]
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]
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</code></pre><table><tbody><tr><td>Monty</td><td>45</td></tr><tr><td>Soup</td><td>54</td></tr><tr><td>Cabbages</td><td>63</td></tr></tbody></table><p>To pass values between different code blocks, you have to give the blocks a name.
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The previous code block was given a name <code class="inline-verbatim">data</code> and passed it to the next block.
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</p><pre class="src-block"><code class="language-python">return o[0]
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</code></pre><table><tbody><tr><td>Monty</td><td>45</td></tr></tbody></table><h1 id="source-code-evaluation">Source code evaluation</h1><p>The header property for executing a source code block is <code class="inline-verbatim">eval</code>.
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It can accept either the following values:
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</p><ul><li><p><code class="inline-verbatim">no</code> to disable evaluation of the code block.
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</p></li><li><p><code class="inline-verbatim">query</code> will prompt to enable evaluation first.
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</p></li><li><p><code class="inline-verbatim">never-export</code> will not show the results in export but can still interact with it from the raw source.
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</p></li></ul><p>By default, it will enable evaluation so you have to explicitly define it (or set it in your Emacs config).
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</p><h1 id="creating-dynamic-content-with-meta-programming">Creating dynamic content with meta-programming</h1><p>With <a href="https://orgmode.org/worg/org-contrib/babel/intro.html">Babel</a>, you can call named code blocks anywhere from blocks to inline.
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This creates a "function" with Babel using different languages.
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The following block creates <code class="inline-code">init</code> function with a default value for its argument.
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</p><pre class="src-block"><code class="language-python">return f"Hello {name}"
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</code></pre><p>You can then call the <code class="inline-code">init</code> function inline with <code class="inline-code">call_init[${HEADER_ARGS}](${ARGS})</code> which should contain "call<sub>init</sub>[:results raw]() Hello world".
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For blocks, you can use the <code class="inline-code">#+call</code> block with a similar syntax to inline functions — i.e., <code class="inline-code">#+call: init[${HEADER_ARGS}](${ARGS})</code>.
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</p><pre class="fixed-width">Hello world</pre><p>
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You can also use it inside of code blocks with <code class="inline-code"><<init>></code> which makes it perfect for code blocks templates like configuring paper output for Lilypond blocks.
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Though, you have to set <code class="inline-code">:noweb yes</code> in the header arguments or configure it in <code class="inline-code">org-babel-default-header-args</code> as one of the default.
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</p><pre class="src-block"><code class="language-shell">echo -n <<init(name="Canavan")>>
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</code></pre><pre class="fixed-width">Hello Canavan</pre><p>
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Babel functions are commonly used for inserting dynamic values.
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Very helpful in reducing places you need to edit (not to mention less prone to errors).
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</p><h1 id="executing-code-blocks-in-the-same-session">Executing code blocks in the same session</h1><p>Each of the source code block runs on an individual session.
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However, you can connect source code blocks in the same session with <code class="inline-code">:session <SESSION NAME></code>.
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This allows you to cut code blocks and add more detailed explanations for them.
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</p><p>Let's start with a simple example where we want to demonstrate some Python shenanigans.
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Here's one Python code block.
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</p><pre class="src-block"><code class="language-python">x = 30
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print(x)
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</code></pre><pre class="fixed-width">30</pre><p>
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Then here's another code block in the same session.
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</p><pre class="src-block"><code class="language-python">for i in range(5):
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x += 5
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print(x)
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</code></pre><pre class="fixed-width">35
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40
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45
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50
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55</pre><p>
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In certain code where the output can still change (for example, try executing the previous code block again), this may not be the desired behavior.
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To correct this, simply execute <code class="inline-code">org-babel-execute-buffer</code>.
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</p><section><h2>Backlinks</h2><ul><li><a href="/wiki/2020-04-17-21-41-30">Org mode: Babel</a></li></ul></section></main></div><script id="__NEXT_DATA__" type="application/json">{"props":{"pageProps":{"metadata":{"date":"\"2021-05-19 18:54:37 +08:00\"","date_modified":"\"2021-06-04 11:11:18 +08:00\"","language":"en","source":""},"title":"The basics of org-babel","hast":{"type":"root","children":[{"type":"element","tagName":"nav","properties":{"className":"toc"},"children":[{"type":"element","tagName":"ol","properties":{"className":"toc-level toc-level-1"},"children":[{"type":"element","tagName":"li","data":{"hookArgs":[{"type":"element","tagName":"h1","properties":{"id":"functional-and-scripting-mode"},"children":[{"type":"text","value":"Functional and scripting mode"}]}]},"properties":{"className":"toc-item toc-item-h1"},"children":[{"type":"element","tagName":"a","properties":{"className":"toc-link toc-link-h1","href":"/text.org-mode.babel#functional-and-scripting-mode"},"children":[{"type":"text","value":"Functional and scripting mode"}]}]},{"type":"element","tagName":"li","data":{"hookArgs":[{"type":"element","tagName":"h1","properties":{"id":"functional-mode-values-and-passing-them-around"},"children":[{"type":"text","value":"Functional mode values and passing them around"}]}]},"properties":{"className":"toc-item toc-item-h1"},"children":[{"type":"element","tagName":"a","properties":{"className":"toc-link toc-link-h1","href":"/text.org-mode.babel#functional-mode-values-and-passing-them-around"},"children":[{"type":"text","value":"Functional mode values and passing them around"}]}]},{"type":"element","tagName":"li","data":{"hookArgs":[{"type":"element","tagName":"h1","properties":{"id":"source-code-evaluation"},"children":[{"type":"text","value":"Source code evaluation"}]}]},"properties":{"className":"toc-item toc-item-h1"},"children":[{"type":"element","tagName":"a","properties":{"className":"toc-link toc-link-h1","href":"/text.org-mode.babel#source-code-evaluation"},"children":[{"type":"text","value":"Source code evaluation"}]}]},{"type":"element","tagName":"li","data":{"hookArgs":[{"type":"element","tagName":"h1","properties":{"id":"creating-dynamic-content-with-meta-programming"},"children":[{"type":"text","value":"Creating dynamic content with meta-programming"}]}]},"properties":{"className":"toc-item toc-item-h1"},"children":[{"type":"element","tagName":"a","properties":{"className":"toc-link toc-link-h1","href":"/text.org-mode.babel#creating-dynamic-content-with-meta-programming"},"children":[{"type":"text","value":"Creating dynamic content with meta-programming"}]}]},{"type":"element","tagName":"li","data":{"hookArgs":[{"type":"element","tagName":"h1","properties":{"id":"executing-code-blocks-in-the-same-session"},"children":[{"type":"text","value":"Executing code blocks in the same session"}]}]},"properties":{"className":"toc-item toc-item-h1"},"children":[{"type":"element","tagName":"a","properties":{"className":"toc-link toc-link-h1","href":"/text.org-mode.babel#executing-code-blocks-in-the-same-session"},"children":[{"type":"text","value":"Executing code blocks in the same session"}]}]}]}]},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"org-babel (see "},{"type":"element","tagName":"a","properties":{"href":"/2020-04-17-21-41-30"},"children":[{"type":"text","value":"Org mode: Babel"}]},{"type":"text","value":") is the framework that enables Org mode features for reproducible research.\nIt has a variety of applications that Org mode can do in this field so let's enumerate them.\n"}]},{"type":"element","tagName":"h1","properties":{"id":"functional-and-scripting-mode"},"children":[{"type":"text","value":"Functional and scripting mode"}]},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Babel works in two modes: functional and scripting mode.\n"}]},{"type":"element","tagName":"ul","properties":{},"children":[{"type":"element","tagName":"li","properties":{},"children":[{"type":"element","tagName":"p","properties":{},"children":[{"type":"te
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