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Documenter.jl 2021-04-29 11:22:01 +00:00
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// Generated by Documenter.jl
requirejs.config({
paths: {
'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.15.10/languages/julia.min',
'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.10.3/headroom.min',
'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min',
'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/contrib/auto-render.min',
'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min',
'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.10.3/jQuery.headroom.min',
'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min',
'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.15.10/highlight.min',
'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.15.10/languages/julia-repl.min',
},
shim: {
"highlight-julia": {
"deps": [
"highlight"
]
},
"katex-auto-render": {
"deps": [
"katex"
]
},
"headroom-jquery": {
"deps": [
"jquery",
"headroom"
]
},
"highlight-julia-repl": {
"deps": [
"highlight"
]
}
}
});
////////////////////////////////////////////////////////////////////////////////
require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) {
$(document).ready(function() {
renderMathInElement(
document.body,
{
"delimiters": [
{
"left": "$",
"right": "$",
"display": false
},
{
"left": "$$",
"right": "$$",
"display": true
},
{
"left": "\\[",
"right": "\\]",
"display": true
}
]
}
);
})
})
////////////////////////////////////////////////////////////////////////////////
require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($, hljs) {
$(document).ready(function() {
hljs.initHighlighting();
})
})
////////////////////////////////////////////////////////////////////////////////
require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) {
// Manages the top navigation bar (hides it when the user starts scrolling down on the
// mobile).
window.Headroom = Headroom; // work around buggy module loading?
$(document).ready(function() {
$('#documenter .docs-navbar').headroom({
"tolerance": {"up": 10, "down": 10},
});
})
})
////////////////////////////////////////////////////////////////////////////////
require(['jquery'], function($) {
// Modal settings dialog
$(document).ready(function() {
var settings = $('#documenter-settings');
$('#documenter-settings-button').click(function(){
settings.toggleClass('is-active');
});
// Close the dialog if X is clicked
$('#documenter-settings button.delete').click(function(){
settings.removeClass('is-active');
});
// Close dialog if ESC is pressed
$(document).keyup(function(e) {
if (e.keyCode == 27) settings.removeClass('is-active');
});
});
})
////////////////////////////////////////////////////////////////////////////////
require(['jquery'], function($) {
// Manages the showing and hiding of the sidebar.
$(document).ready(function() {
var sidebar = $("#documenter > .docs-sidebar");
var sidebar_button = $("#documenter-sidebar-button")
sidebar_button.click(function(ev) {
ev.preventDefault();
sidebar.toggleClass('visible');
if (sidebar.hasClass('visible')) {
// Makes sure that the current menu item is visible in the sidebar.
$("#documenter .docs-menu a.is-active").focus();
}
});
$("#documenter > .docs-main").bind('click', function(ev) {
if ($(ev.target).is(sidebar_button)) {
return;
}
if (sidebar.hasClass('visible')) {
sidebar.removeClass('visible');
}
});
})
// Resizes the package name / sitename in the sidebar if it is too wide.
// Inspired by: https://github.com/davatron5000/FitText.js
$(document).ready(function() {
e = $("#documenter .docs-autofit");
function resize() {
var L = parseInt(e.css('max-width'), 10);
var L0 = e.width();
if(L0 > L) {
var h0 = parseInt(e.css('font-size'), 10);
e.css('font-size', L * h0 / L0);
// TODO: make sure it survives resizes?
}
}
// call once and then register events
resize();
$(window).resize(resize);
$(window).on('orientationchange', resize);
});
// Scroll the navigation bar to the currently selected menu item
$(document).ready(function() {
var sidebar = $("#documenter .docs-menu").get(0);
var active = $("#documenter .docs-menu .is-active").get(0);
if(typeof active !== 'undefined') {
sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15;
}
})
})
////////////////////////////////////////////////////////////////////////////////
require(['jquery'], function($) {
function set_theme(theme) {
var active = null;
var disabled = [];
for (var i = 0; i < document.styleSheets.length; i++) {
var ss = document.styleSheets[i];
var themename = ss.ownerNode.getAttribute("data-theme-name");
if(themename === null) continue; // ignore non-theme stylesheets
// Find the active theme
if(themename === theme) active = ss;
else disabled.push(ss);
}
if(active !== null) {
active.disabled = false;
if(active.ownerNode.getAttribute("data-theme-primary") === null) {
document.getElementsByTagName('html')[0].className = "theme--" + theme;
} else {
document.getElementsByTagName('html')[0].className = "";
}
disabled.forEach(function(ss){
ss.disabled = true;
});
}
// Store the theme in localStorage
if(typeof(window.localStorage) !== "undefined") {
window.localStorage.setItem("documenter-theme", theme);
} else {
console.error("Browser does not support window.localStorage");
}
}
// Theme picker setup
$(document).ready(function() {
// onchange callback
$('#documenter-themepicker').change(function themepick_callback(ev){
var themename = $('#documenter-themepicker option:selected').attr('value');
set_theme(themename);
});
// Make sure that the themepicker displays the correct theme when the theme is retrieved
// from localStorage
if(typeof(window.localStorage) !== "undefined") {
var theme = window.localStorage.getItem("documenter-theme");
if(theme !== null) {
$('#documenter-themepicker option').each(function(i,e) {
e.selected = (e.value === theme);
})
} else {
$('#documenter-themepicker option').each(function(i,e) {
e.selected = $("html").hasClass(`theme--${e.value}`);
})
}
}
})
})
////////////////////////////////////////////////////////////////////////////////
require(['jquery'], function($) {
// update the version selector with info from the siteinfo.js and ../versions.js files
$(document).ready(function() {
var version_selector = $("#documenter .docs-version-selector");
var version_selector_select = $("#documenter .docs-version-selector select");
version_selector_select.change(function(x) {
target_href = version_selector_select.children("option:selected").get(0).value;
window.location.href = target_href;
});
// add the current version to the selector based on siteinfo.js, but only if the selector is empty
if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) {
var option = $("<option value='#' selected='selected'>" + DOCUMENTER_CURRENT_VERSION + "</option>");
version_selector_select.append(option);
}
if (typeof DOC_VERSIONS !== 'undefined') {
var existing_versions = version_selector_select.children("option");
var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
DOC_VERSIONS.forEach(function(each) {
var version_url = documenterBaseURL + "/../" + each;
var existing_id = $.inArray(each, existing_versions_texts);
// if not already in the version selector, add it as a new option,
// otherwise update the old option with the URL and enable it
if (existing_id == -1) {
var option = $("<option value='" + version_url + "'>" + each + "</option>");
version_selector_select.append(option);
} else {
var option = existing_versions[existing_id];
option.value = version_url;
option.disabled = false;
}
});
}
// only show the version selector if the selector has been populated
if (version_selector_select.children("option").length > 0) {
version_selector.toggleClass("visible");
}
})
})

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// Generated by Documenter.jl
requirejs.config({
paths: {
'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.6/lunr.min',
'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.15/lodash.min',
'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min',
}
});
////////////////////////////////////////////////////////////////////////////////
require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
$(document).ready(function() {
// parseUri 1.2.2
// (c) Steven Levithan <stevenlevithan.com>
// MIT License
function parseUri (str) {
var o = parseUri.options,
m = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
uri = {},
i = 14;
while (i--) uri[o.key[i]] = m[i] || "";
uri[o.q.name] = {};
uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
if ($1) uri[o.q.name][$1] = $2;
});
return uri;
};
parseUri.options = {
strictMode: false,
key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
q: {
name: "queryKey",
parser: /(?:^|&)([^&=]*)=?([^&]*)/g
},
parser: {
strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,
loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/
}
};
$("#search-form").submit(function(e) {
e.preventDefault()
})
// list below is the lunr 2.1.3 list minus the intersect with names(Base)
// (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with)
// ideally we'd just filter the original list but it's not available as a variable
lunr.stopWordFilter = lunr.generateStopWordFilter([
'a',
'able',
'about',
'across',
'after',
'almost',
'also',
'am',
'among',
'an',
'and',
'are',
'as',
'at',
'be',
'because',
'been',
'but',
'by',
'can',
'cannot',
'could',
'dear',
'did',
'does',
'either',
'ever',
'every',
'from',
'got',
'had',
'has',
'have',
'he',
'her',
'hers',
'him',
'his',
'how',
'however',
'i',
'if',
'into',
'it',
'its',
'just',
'least',
'like',
'likely',
'may',
'me',
'might',
'most',
'must',
'my',
'neither',
'no',
'nor',
'not',
'of',
'off',
'often',
'on',
'or',
'other',
'our',
'own',
'rather',
'said',
'say',
'says',
'she',
'should',
'since',
'so',
'some',
'than',
'that',
'the',
'their',
'them',
'then',
'there',
'these',
'they',
'this',
'tis',
'to',
'too',
'twas',
'us',
'wants',
'was',
'we',
'were',
'what',
'when',
'who',
'whom',
'why',
'will',
'would',
'yet',
'you',
'your'
])
// add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
// would not find anything if searching for "add!", only for the entire qualification
lunr.tokenizer.separator = /[\s\-\.]+/
// custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
lunr.trimmer = function (token) {
return token.update(function (s) {
return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
})
}
lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter')
lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
var index = lunr(function () {
this.ref('location')
this.field('title',{boost: 100})
this.field('text')
documenterSearchIndex['docs'].forEach(function(e) {
this.add(e)
}, this)
})
var store = {}
documenterSearchIndex['docs'].forEach(function(e) {
store[e.location] = {title: e.title, category: e.category, page: e.page}
})
$(function(){
searchresults = $('#documenter-search-results');
searchinfo = $('#documenter-search-info');
searchbox = $('#documenter-search-query');
function update_search(querystring) {
tokens = lunr.tokenizer(querystring)
results = index.query(function (q) {
tokens.forEach(function (t) {
q.term(t.toString(), {
fields: ["title"],
boost: 100,
usePipeline: true,
editDistance: 0,
wildcard: lunr.Query.wildcard.NONE
})
q.term(t.toString(), {
fields: ["title"],
boost: 10,
usePipeline: true,
editDistance: 2,
wildcard: lunr.Query.wildcard.NONE
})
q.term(t.toString(), {
fields: ["text"],
boost: 1,
usePipeline: true,
editDistance: 0,
wildcard: lunr.Query.wildcard.NONE
})
})
})
searchinfo.text("Number of results: " + results.length)
searchresults.empty()
results.forEach(function(result) {
data = store[result.ref]
link = $('<a class="docs-label">'+data.title+'</a>')
link.attr('href', documenterBaseURL+'/'+result.ref)
if (data.category != "page"){
cat = $('<span class="docs-category">('+data.category+', '+data.page+')</span>')
} else {
cat = $('<span class="docs-category">('+data.category+')</span>')
}
li = $('<li>').append(link).append(" ").append(cat)
searchresults.append(li)
})
}
function update_search_box() {
querystring = searchbox.val()
update_search(querystring)
}
searchbox.keyup(_.debounce(update_search_box, 250))
searchbox.change(update_search_box)
search_query_uri = parseUri(window.location).queryKey["q"]
if(search_query_uri !== undefined) {
search_query = decodeURIComponent(search_query_uri.replace(/\+/g, '%20'))
searchbox.val(search_query)
}
update_search_box();
})
})
})

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// Small function to quickly swap out themes. Gets put into the <head> tag..
function set_theme_from_local_storage() {
// Intialize the theme to null, which means default
var theme = null;
// If the browser supports the localstorage and is not disabled then try to get the
// documenter theme
if(window.localStorage != null) {
// Get the user-picked theme from localStorage. May be `null`, which means the default
// theme.
theme = window.localStorage.getItem("documenter-theme");
}
// Check if the browser supports user color preference
var darkPreference = false;
// Check if the users preference is for dark color scheme
if(window.matchMedia('(prefers-color-scheme: dark)').matches === true) {
darkPreference = true;
}
// Initialize a few variables for the loop:
//
// - active: will contain the index of the theme that should be active. Note that there
// is no guarantee that localStorage contains sane values. If `active` stays `null`
// we either could not find the theme or it is the default (primary) theme anyway.
// Either way, we then need to stick to the primary theme.
//
// - disabled: style sheets that should be disabled (i.e. all the theme style sheets
// that are not the currently active theme)
var active = null; var disabled = []; var darkTheme = null;
for (var i = 0; i < document.styleSheets.length; i++) {
var ss = document.styleSheets[i];
// The <link> tag of each style sheet is expected to have a data-theme-name attribute
// which must contain the name of the theme. The names in localStorage much match this.
var themename = ss.ownerNode.getAttribute("data-theme-name");
// attribute not set => non-theme stylesheet => ignore
if(themename === null) continue;
// To distinguish the default (primary) theme, it needs to have the data-theme-primary
// attribute set.
var isprimary = (ss.ownerNode.getAttribute("data-theme-primary") !== null);
// Check if the theme is primary dark theme
var isDarkTheme = (ss.ownerNode.getAttribute("data-theme-primary-dark") !== null);
// If ss is for dark theme then set the value of darkTheme to the name of the theme
if(isDarkTheme) darkTheme = themename;
// If we find a matching theme (and it's not the default), we'll set active to non-null
if(themename === theme) active = i;
// Store the style sheets of inactive themes so that we could disable them
if(themename !== theme) disabled.push(ss);
}
if(active !== null) {
// If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
document.getElementsByTagName('html')[0].className = "theme--" + theme;
// and (2) disable all the other theme stylesheets
disabled.forEach(function(ss){
ss.disabled = true;
});
}
else if(darkTheme !== null && darkPreference === true) {
// If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
document.getElementsByTagName('html')[0].className = "theme--" + darkTheme;
// and (2) disable all the other theme stylesheets
disabled.forEach(function(ss){
if (ss.ownerNode.getAttribute("data-theme-name") !== darkTheme) {
ss.disabled = true;
}
});
}
}
set_theme_from_local_storage();

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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Chunk Options · Weave.jl</title><link rel="canonical" href="http://weavejl.mpastell.com/stable/chunk_options/"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit">Weave.jl</span></div><form class="docs-search" action="../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Weave.jl - Scientific Reports Using Julia</a></li><li><a class="tocitem" href="../getting_started/">Getting started</a></li><li><a class="tocitem" href="../usage/">Using Weave</a></li><li><a class="tocitem" href="../publish/">Publishing to HTML and PDF</a></li><li class="is-active"><a class="tocitem" href>Chunk Options</a><ul class="internal"><li><a class="tocitem" href="#Syntax"><span>Syntax</span></a></li><li><a class="tocitem" href="#Weave-Chunk-Options"><span>Weave Chunk Options</span></a></li><li><a class="tocitem" href="#Default-Chunk-Options"><span>Default Chunk Options</span></a></li></ul></li><li><a class="tocitem" href="../header/">Header Configuration</a></li><li><a class="tocitem" href="../notebooks/">Working with Jupyter notebooks</a></li><li><a class="tocitem" href="../function_index/">Function index</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Chunk Options</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Chunk Options</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JunoLab/Weave.jl/blob/master/doc/src/chunk_options.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="chunk-options"><a class="docs-heading-anchor" href="#chunk-options">Chunk Options</a><a id="chunk-options-1"></a><a class="docs-heading-anchor-permalink" href="#chunk-options" title="Permalink"></a></h1><p>You can use chunk options to configure how each chunk is evaluated, rendered, etc. Most of the ideas came from <a href="http://yihui.name/knitr/options">chunk options in RMarkdown</a>.</p><h2 id="Syntax"><a class="docs-heading-anchor" href="#Syntax">Syntax</a><a id="Syntax-1"></a><a class="docs-heading-anchor-permalink" href="#Syntax" title="Permalink"></a></h2><p>Chunk options come after <a href="../usage/#code-chunks">code chunk</a> header. There are two (slightly) different syntax to write them:</p><ul><li>(Julia&#39;s toplevel expression) options are separated by semicolon (<code>;</code>)</li><li>(RMarkdown style) options are separated by comma (<code>,</code>)</li></ul><p>Let&#39;s take a look at examples. All the following code chunk header are valid, and so configured to hide the source code from generated output (<code>echo = false</code>) and displays figures with 12cm width (<code>out_width = &quot;12cm&quot;</code>):</p><pre><code class="language-md"> ```julia; echo = false; out_width = &quot;12cm&quot;
```{julia; echo = false; out_width = &quot;12cm&quot;}
```julia, echo = false, out_width = &quot;12cm&quot;
```{julia, echo = false, out_width = &quot;12cm&quot;}</code></pre><h2 id="Weave-Chunk-Options"><a class="docs-heading-anchor" href="#Weave-Chunk-Options">Weave Chunk Options</a><a id="Weave-Chunk-Options-1"></a><a class="docs-heading-anchor-permalink" href="#Weave-Chunk-Options" title="Permalink"></a></h2><p>Weave currently supports the following chunk options: we&#39;ve mostly followed <a href="http://yihui.name/knitr/options">RMarkdown&#39;s namings</a>, but not all options are implemented.</p><h3 id="Evaluation"><a class="docs-heading-anchor" href="#Evaluation">Evaluation</a><a id="Evaluation-1"></a><a class="docs-heading-anchor-permalink" href="#Evaluation" title="Permalink"></a></h3><ul><li><code>eval = true</code>: Evaluate the code chunk. If <code>false</code> the chunk won’t be executed.</li><li><code>error = true</code>: If <code>true</code> <a href="../usage/#Weave.weave"><code>weave</code></a> won&#39;t stop on errors and rather they will be included in output document. If <code>false</code>, <a href="../usage/#Weave.weave"><code>weave</code></a> will halt on any of un-caught errors.</li><li><code>cache = false</code>: Cache results, depending on <code>cache</code> parameter on <a href="../usage/#Weave.weave"><code>weave</code></a> function.</li><li><code>tangle = true</code>: Set tangle to <code>false</code> to exclude chunk from tangled code.</li></ul><h3 id="Rendering"><a class="docs-heading-anchor" href="#Rendering">Rendering</a><a id="Rendering-1"></a><a class="docs-heading-anchor-permalink" href="#Rendering" title="Permalink"></a></h3><ul><li><code>echo = true</code>: Echo the code in the output document. If <code>false</code> the source code will be hidden.</li><li><code>results = &quot;markup&quot;</code>: The output format of the printed results. <code>&quot;markup&quot;</code> for literal block, <code>&quot;hidden&quot;</code> for hidden results, or anything else for raw output (I tend to use <code>&quot;tex&quot;</code> for Latex and <code>&quot;rst&quot;</code> for rest). Raw output is useful if you want to e.g. create tables from code chunks.</li><li><code>term = false</code>: If <code>true</code> the output emulates a REPL session. Otherwise only stdout and figures will be included in output.</li><li><code>wrap = true</code>: Wrap long lines from output.</li><li><code>line_width = 75</code>: Line width for wrapped lines.</li><li><code>hold = false</code>: Hold all results until the end of the chunk.</li></ul><h3 id="Figures"><a class="docs-heading-anchor" href="#Figures">Figures</a><a id="Figures-1"></a><a class="docs-heading-anchor-permalink" href="#Figures" title="Permalink"></a></h3><ul><li><code>label = nothing</code>: Chunk label, will be used for figure labels in Latex as <code>fig:label</code>.</li><li><code>fig_width = 6</code>: Figure width passed to plotting library.</li><li><code>fig_height = 4</code>: Figure height passed to plotting library.</li><li><code>out_width</code>: Width of saved figure in output markup e.g. <code>&quot;50%&quot;</code>, <code>&quot;12cm&quot;</code>, <code>0.5\linewidth</code></li><li><code>out_height</code>: Height of saved figure in output markup</li><li><code>dpi = 96</code>: Resolution of saved figures.</li><li><code>fig_cap</code>: Figure caption.</li><li><code>fig_ext</code>: File extension (format) of saved figures.</li><li><code>fig_pos = &quot;!h&quot;</code>: Figure position in Latex, e.g.: <code>&quot;ht&quot;</code>.</li><li><code>fig_env = &quot;figure&quot;</code>: Figure environment in Latex.</li></ul><h2 id="Default-Chunk-Options"><a class="docs-heading-anchor" href="#Default-Chunk-Options">Default Chunk Options</a><a id="Default-Chunk-Options-1"></a><a class="docs-heading-anchor-permalink" href="#Default-Chunk-Options" title="Permalink"></a></h2><p>You can set the default chunk options (and <code>weave</code> arguments) for a document using <code>weave_options</code> key in YAML <a href="../header/#Header-Configuration">Header Configuration</a>. E.g. to set the default <code>out_width</code> of all figures you can use:</p><pre><code class="language-yaml">---
weave_options:
out_width : 50%
---</code></pre><p>You can also set or change the default chunk options for a document either before weave using the <code>set_chunk_defaults</code> function.</p><article class="docstring"><header><a class="docstring-binding" id="Weave.set_chunk_defaults!" href="#Weave.set_chunk_defaults!"><code>Weave.set_chunk_defaults!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">set_chunk_defaults!(k, v)
set_chunk_defaults!(kv::Pair...)
set_chunk_defaults!(opts::AbstractDict)</code></pre><p>Set default options for code chunks, use <a href="#Weave.get_chunk_defaults"><code>get_chunk_defaults</code></a> to see the current values.</p><p>E.g.: all the three examples below will set default <code>dpi</code> to <code>200</code> and <code>fig_width</code> to <code>8</code>:</p><ul><li><code>set_chunk_defaults!(:dpi, 200); set_chunk_defaults!(:fig_width, 8)</code></li><li><code>set_chunk_defaults!(:dpi =&gt; 200, :fig_width =&gt; 8)</code></li><li><code>set_chunk_defaults!(Dict(:dpi =&gt; 200, :fig_width =&gt; 8))</code></li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JunoLab/Weave.jl/blob/2b5a5f32a7083bbf4ff7be845fb162b848f5089d/src/config.jl#L30-L41">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Weave.get_chunk_defaults" href="#Weave.get_chunk_defaults"><code>Weave.get_chunk_defaults</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">get_chunk_defaults()</code></pre><p>Get default options used for code chunks.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JunoLab/Weave.jl/blob/2b5a5f32a7083bbf4ff7be845fb162b848f5089d/src/config.jl#L46-L50">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Weave.restore_chunk_defaults!" href="#Weave.restore_chunk_defaults!"><code>Weave.restore_chunk_defaults!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">restore_chunk_defaults!()</code></pre><p>Restore Weave.jl default chunk options.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JunoLab/Weave.jl/blob/2b5a5f32a7083bbf4ff7be845fb162b848f5089d/src/config.jl#L53-L57">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../publish/">« Publishing to HTML and PDF</a><a class="docs-footer-nextpage" href="../header/">Header Configuration »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Thursday 29 April 2021 11:16">Thursday 29 April 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

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---
title: FIR filter design with Julia
author: Matti Pastell
date: 21th April 2016
---
# Introduction
This an example of a julia script that can be published using
[Weave](http://weavejl.mpastell.com/dev/usage/).
The script can be executed normally using Julia
or published to HTML or pdf with Weave.
Text is written in markdown in lines starting with "`#'` " and code
is executed and results are included in the published document.
Notice that you don't need to define chunk options, but you can using
`#+`. just before code e.g. `#+ term=True, caption='Fancy plots.'`.
If you're viewing the published version have a look at the
[source](FIR_design_plots.jl) to see the markup.
<!-- this setup dependencies, but doesn't appear in the generated document -->
```julia; echo = false; results = "hidden"
using Pkg
"Plots" ∉ keys(Pkg.project().dependencies) && Pkg.add("Plots")
"DSP" ∉ keys(Pkg.project().dependencies) && Pkg.add("DSP")
```
# FIR Filter Design
We'll implement lowpass, highpass and ' bandpass FIR filters. If
you want to read more about DSP I highly recommend [The Scientist
and Engineer's Guide to Digital Signal
Processing](http://www.dspguide.com/) which is freely available
online.
## Calculating frequency response
DSP.jl package doesn't (yet) have a method to calculate the
the frequency response of a FIR filter so we define it:
```julia
using Plots, DSP
gr()
function FIRfreqz(b::Array, w = range(0, stop=π, length=1024))
n = length(w)
h = Array{ComplexF32}(undef, n)
sw = 0
for i = 1:n
for j = 1:length(b)
sw += b[j]*exp(-im*w[i])^-j
end
h[i] = sw
sw = 0
end
return h
end
```
## Design Lowpass FIR filter
Designing a lowpass FIR filter is very simple to do with DSP.jl, all you
need to do is to define the window length, cut off frequency and the
window. We will define a lowpass filter with cut off frequency at 5Hz for a signal
sampled at 20 Hz.
We will use the Hamming window, which is defined as:
$w(n) = \alpha - \beta\cos\frac{2\pi n}{N-1}$, where $\alpha=0.54$ and $\beta=0.46$
```julia
fs = 20
f = digitalfilter(Lowpass(5, fs = fs), FIRWindow(hamming(61)))
w = range(0, stop=pi, length=1024)
h = FIRfreqz(f, w)
```
## Plot the frequency and impulse response
The next code chunk is executed in term mode, see the [script](FIR_design.jl) for syntax.
```julia; term=true
h_db = log10.(abs.(h));
ws = w/pi*(fs/2)
```
```julia
plot(ws, h_db,
xlabel = "Frequency (Hz)", ylabel = "Magnitude (db)")
```
And again with default options
```julia
h_phase = unwrap(-atan.(imag.(h),real.(h)))
plot(ws, h_phase,
xlabel = "Frequency (Hz)", ylabel = "Phase (radians)")
```

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---
author: "Matti Pastell"
title: "FIR filter design with Julia"
date: "21th April 2016"
---
# Introduction
This an example of a julia script that can be published using
[Weave](http://weavejl.mpastell.com/dev/usage/).
The script can be executed normally using Julia
or published to HTML or pdf with Weave.
Text is written in markdown in lines starting with "`#'` " and code
is executed and results are included in the published document.
Notice that you don't need to define chunk options, but you can using
`#+`. just before code e.g. `#+ term=True, caption='Fancy plots.'`.
If you're viewing the published version have a look at the
[source](FIR_design_plots.jl) to see the markup.
<!-- this setup dependencies, but doesn't appear in the generated document -->
# FIR Filter Design
We'll implement lowpass, highpass and ' bandpass FIR filters. If
you want to read more about DSP I highly recommend [The Scientist
and Engineer's Guide to Digital Signal
Processing](http://www.dspguide.com/) which is freely available
online.
## Calculating frequency response
DSP.jl package doesn't (yet) have a method to calculate the
the frequency response of a FIR filter so we define it:
~~~~{.julia}
using Plots, DSP
gr()
function FIRfreqz(b::Array, w = range(0, stop=π, length=1024))
n = length(w)
h = Array{ComplexF32}(undef, n)
sw = 0
for i = 1:n
for j = 1:length(b)
sw += b[j]*exp(-im*w[i])^-j
end
h[i] = sw
sw = 0
end
return h
end
~~~~~~~~~~~~~
~~~~
FIRfreqz (generic function with 2 methods)
~~~~
## Design Lowpass FIR filter
Designing a lowpass FIR filter is very simple to do with DSP.jl, all you
need to do is to define the window length, cut off frequency and the
window. We will define a lowpass filter with cut off frequency at 5Hz for a signal
sampled at 20 Hz.
We will use the Hamming window, which is defined as:
$w(n) = \alpha - \beta\cos\frac{2\pi n}{N-1}$, where $\alpha=0.54$ and $\beta=0.46$
~~~~{.julia}
fs = 20
f = digitalfilter(Lowpass(5, fs = fs), FIRWindow(hamming(61)))
w = range(0, stop=pi, length=1024)
h = FIRfreqz(f, w)
~~~~~~~~~~~~~
~~~~
1024-element Array{Complex{Float32},1}:
1.0f0 + 0.0f0im
0.99546844f0 + 0.095055714f0im
0.98191506f0 + 0.1892486f0im
0.95946306f0 + 0.28172377f0im
0.9283168f0 + 0.37164196f0im
0.8887594f0 + 0.45818728f0im
0.84115064f0 + 0.54057467f0im
0.7859234f0 + 0.618057f0im
0.72357976f0 + 0.6899319f0im
0.65468615f0 + 0.7555481f0im
⋮
0.00043952762f0 - 0.00041908873f0im
0.0005152718f0 - 0.00040521423f0im
0.0005873293f0 - 0.00037745363f0im
0.0006531789f0 - 0.0003367371f0im
0.0007105166f0 - 0.00028444792f0im
0.0007573364f0 - 0.00022237403f0im
0.0007920005f0 - 0.00015264557f0im
0.0008132961f0 - 7.766036f-5im
0.0008204784f0 - 3.1148685f-18im
~~~~
## Plot the frequency and impulse response
The next code chunk is executed in term mode, see the [script](FIR_design.jl) for syntax.
~~~~{.julia}
julia> h_db = log10.(abs.(h));
julia> ws = w/pi*(fs/2)
0.0:0.009775171065493646:10.0
~~~~~~~~~~~~~
~~~~{.julia}
plot(ws, h_db,
xlabel = "Frequency (Hz)", ylabel = "Magnitude (db)")
~~~~~~~~~~~~~
![](figures/FIR_design_5_1.png)\
And again with default options
~~~~{.julia}
h_phase = unwrap(-atan.(imag.(h),real.(h)))
plot(ws, h_phase,
xlabel = "Frequency (Hz)", ylabel = "Phase (radians)")
~~~~~~~~~~~~~
![](figures/FIR_design_6_1.png)\

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---
author: "Matti Pastell"
title: "FIR filter design with Julia"
date: "21th April 2016"
---
# Introduction
This an example of a julia script that can be published using
[Weave](http://weavejl.mpastell.com/dev/usage/).
The script can be executed normally using Julia
or published to HTML or pdf with Weave.
Text is written in markdown in lines starting with "`#'` " and code
is executed and results are included in the published document.
Notice that you don't need to define chunk options, but you can using
`#+`. just before code e.g. `#+ term=True, caption='Fancy plots.'`.
If you're viewing the published version have a look at the
[source](FIR_design_plots.jl) to see the markup.
<!-- this setup dependencies, but doesn't appear in the generated document -->
# FIR Filter Design
We'll implement lowpass, highpass and ' bandpass FIR filters. If
you want to read more about DSP I highly recommend [The Scientist
and Engineer's Guide to Digital Signal
Processing](http://www.dspguide.com/) which is freely available
online.
## Calculating frequency response
DSP.jl package doesn't (yet) have a method to calculate the
the frequency response of a FIR filter so we define it:
~~~~{.julia}
using Plots, DSP
gr()
function FIRfreqz(b::Array, w = range(0, stop=π, length=1024))
n = length(w)
h = Array{ComplexF32}(undef, n)
sw = 0
for i = 1:n
for j = 1:length(b)
sw += b[j]*exp(-im*w[i])^-j
end
h[i] = sw
sw = 0
end
return h
end
~~~~~~~~~~~~~
~~~~
FIRfreqz (generic function with 2 methods)
~~~~
## Design Lowpass FIR filter
Designing a lowpass FIR filter is very simple to do with DSP.jl, all you
need to do is to define the window length, cut off frequency and the
window. We will define a lowpass filter with cut off frequency at 5Hz for a signal
sampled at 20 Hz.
We will use the Hamming window, which is defined as:
$w(n) = \alpha - \beta\cos\frac{2\pi n}{N-1}$, where $\alpha=0.54$ and $\beta=0.46$
~~~~{.julia}
fs = 20
f = digitalfilter(Lowpass(5, fs = fs), FIRWindow(hamming(61)))
w = range(0, stop=pi, length=1024)
h = FIRfreqz(f, w)
~~~~~~~~~~~~~
~~~~
1024-element Array{Complex{Float32},1}:
1.0f0 + 0.0f0im
0.99546844f0 + 0.095055714f0im
0.98191506f0 + 0.1892486f0im
0.95946306f0 + 0.28172377f0im
0.9283168f0 + 0.37164196f0im
0.8887594f0 + 0.45818728f0im
0.84115064f0 + 0.54057467f0im
0.7859234f0 + 0.618057f0im
0.72357976f0 + 0.6899319f0im
0.65468615f0 + 0.7555481f0im
⋮
0.00043952762f0 - 0.00041908873f0im
0.0005152718f0 - 0.00040521423f0im
0.0005873293f0 - 0.00037745363f0im
0.0006531789f0 - 0.0003367371f0im
0.0007105166f0 - 0.00028444792f0im
0.0007573364f0 - 0.00022237403f0im
0.0007920005f0 - 0.00015264557f0im
0.0008132961f0 - 7.766036f-5im
0.0008204784f0 - 3.1148685f-18im
~~~~
## Plot the frequency and impulse response
The next code chunk is executed in term mode, see the [script](FIR_design.jl) for syntax.
~~~~{.julia}
julia> h_db = log10.(abs.(h));
julia> ws = w/pi*(fs/2)
0.0:0.009775171065493646:10.0
~~~~~~~~~~~~~
~~~~{.julia}
plot(ws, h_db,
xlabel = "Frequency (Hz)", ylabel = "Magnitude (db)")
~~~~~~~~~~~~~
![](figures/FIR_design_5_1.png)\
And again with default options
~~~~{.julia}
h_phase = unwrap(-atan.(imag.(h),real.(h)))
plot(ws, h_phase,
xlabel = "Frequency (Hz)", ylabel = "Phase (radians)")
~~~~~~~~~~~~~
![](figures/FIR_design_6_1.png)\

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#' ---
#' title: FIR filter design with Julia
#' author: Matti Pastell
#' date: 21th April 2016
#' ---
#' # Introduction
#' This an example of a julia script that can be published using
#' [Weave](http://weavejl.mpastell.com/dev/usage/).
#' The script can be executed normally using Julia
#' or published to HTML or pdf with Weave.
#' Text is written in markdown in lines starting with "`#'` " and code
#' is executed and results are included in the published document.
#' Notice that you don't need to define chunk options, but you can using
#' `#+`. just before code e.g. `#+ term=True, caption='Fancy plots.'`.
#' If you're viewing the published version have a look at the
#' [source](FIR_design_plots.jl) to see the markup.
#' # FIR Filter Design
#' We'll implement lowpass, highpass and ' bandpass FIR filters. If
#' you want to read more about DSP I highly recommend [The Scientist
#' and Engineer's Guide to Digital Signal
#' Processing](http://www.dspguide.com/) which is freely available
#' online.
#' ## Calculating frequency response
#' DSP.jl package doesn't (yet) have a method to calculate the
#' the frequency response of a FIR filter so we define it:
using Plots, DSP
gr()
function FIRfreqz(b::Array, w = range(0, stop=π, length=1024))
n = length(w)
h = Array{ComplexF32}(undef, n)
sw = 0
for i = 1:n
for j = 1:length(b)
sw += b[j]*exp(-im*w[i])^-j
end
h[i] = sw
sw = 0
end
return h
end
#' ## Design Lowpass FIR filter
#' Designing a lowpass FIR filter is very simple to do with DSP.jl, all you
#' need to do is to define the window length, cut off frequency and the
#' window. We will define a lowpass filter with cut off frequency at 5Hz for a signal
#' sampled at 20 Hz.
#' We will use the Hamming window, which is defined as:
#' $w(n) = \alpha - \beta\cos\frac{2\pi n}{N-1}$, where $\alpha=0.54$ and $\beta=0.46$
fs = 20
f = digitalfilter(Lowpass(5, fs = fs), FIRWindow(hamming(61)))
w = range(0, stop=pi, length=1024)
h = FIRfreqz(f, w)
#' ## Plot the frequency and impulse response
#' The next code chunk is executed in term mode, see the [script](FIR_design.jl) for syntax.
#+ term=true
h_db = log10.(abs.(h));
ws = w/pi*(fs/2)
#+
plot(ws, h_db,
xlabel = "Frequency (Hz)", ylabel = "Magnitude (db)")
#' And again with default options
h_phase = unwrap(-atan.(imag.(h),real.(h)))
plot(ws, h_phase,
xlabel = "Frequency (Hz)", ylabel = "Phase (radians)")

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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Getting started · Weave.jl</title><link rel="canonical" href="http://weavejl.mpastell.com/stable/getting_started/"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit">Weave.jl</span></div><form class="docs-search" action="../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Weave.jl - Scientific Reports Using Julia</a></li><li class="is-active"><a class="tocitem" href>Getting started</a></li><li><a class="tocitem" href="../usage/">Using Weave</a></li><li><a class="tocitem" href="../publish/">Publishing to HTML and PDF</a></li><li><a class="tocitem" href="../chunk_options/">Chunk Options</a></li><li><a class="tocitem" href="../header/">Header Configuration</a></li><li><a class="tocitem" href="../notebooks/">Working with Jupyter notebooks</a></li><li><a class="tocitem" href="../function_index/">Function index</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Getting started</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Getting started</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JunoLab/Weave.jl/blob/master/doc/src/getting_started.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Getting-started"><a class="docs-heading-anchor" href="#Getting-started">Getting started</a><a id="Getting-started-1"></a><a class="docs-heading-anchor-permalink" href="#Getting-started" title="Permalink"></a></h1><p>The best way to get started using Weave.jl is to look at the example input and output documents. Examples for different formats are included in the package&#39;s <a href="https://github.com/JunoLab/Weave.jl/tree/master/examples"><code>examples</code></a> directory.</p><p>First have a look at source document using markdown code chunks and <a href="https://github.com/JuliaPlots/Plots.jl">Plots.jl</a> for figures:</p><p>All the different format documents below are generated from a single Weave document <a href="../examples/FIR_design.jmd"><code>FIR_design.jmd</code></a>:</p><ul><li>HTML: <a href="../examples/FIR_design.html"><code>FIR_design.html</code></a></li><li>PDF: <a href="../examples/FIR_design.pdf"><code>FIR_design.pdf</code></a></li><li>Pandoc markdown: <a href="../examples/FIR_design.txt"><code>FIR_design.txt</code></a></li></ul><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Producing PDF output requires that you have XeLateX installed.</p></div></div><p>Add dependencies for the example if needed:</p><pre><code class="language-julia">using Pkg; Pkg.add.([&quot;Plots&quot;, &quot;DSP&quot;])</code></pre><p>Weave the files to your working directory:</p><pre><code class="language-julia">using Weave
filename = normpath(Weave.EXAMPLE_FOLDER, &quot;FIR_design.jmd&quot;)
# Julia markdown to HTML
weave(filename; doctype = &quot;md2html&quot;, out_path = :pwd)
# Julia markdown to PDF
weave(filename; doctype = &quot;md2pdf&quot;, out_path = :pwd)
# Julia markdown to Pandoc markdown
weave(filename; doctype = &quot;pandoc&quot;, out_path = :pwd)</code></pre><div class="admonition is-category-tips"><header class="admonition-header">Tips</header><div class="admonition-body"><p><code>Weave.EXAMPLE_FOLDER</code> points to <a href="https://github.com/JunoLab/Weave.jl/tree/master/examples">the <code>examples</code> directory</a>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Weave.jl - Scientific Reports Using Julia</a><a class="docs-footer-nextpage" href="../usage/">Using Weave »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Thursday 29 April 2021 11:16">Thursday 29 April 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Publishing to HTML and PDF · Weave.jl</title><link rel="canonical" href="http://weavejl.mpastell.com/stable/publish/"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit">Weave.jl</span></div><form class="docs-search" action="../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Weave.jl - Scientific Reports Using Julia</a></li><li><a class="tocitem" href="../getting_started/">Getting started</a></li><li><a class="tocitem" href="../usage/">Using Weave</a></li><li class="is-active"><a class="tocitem" href>Publishing to HTML and PDF</a><ul class="internal"><li><a class="tocitem" href="#Templates"><span>Templates</span></a></li><li><a class="tocitem" href="#Supported-Markdown-syntax"><span>Supported Markdown syntax</span></a></li></ul></li><li><a class="tocitem" href="../chunk_options/">Chunk Options</a></li><li><a class="tocitem" href="../header/">Header Configuration</a></li><li><a class="tocitem" href="../notebooks/">Working with Jupyter notebooks</a></li><li><a class="tocitem" href="../function_index/">Function index</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Publishing to HTML and PDF</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Publishing to HTML and PDF</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JunoLab/Weave.jl/blob/master/doc/src/publish.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Publishing-to-HTML-and-PDF"><a class="docs-heading-anchor" href="#Publishing-to-HTML-and-PDF">Publishing to HTML and PDF</a><a id="Publishing-to-HTML-and-PDF-1"></a><a class="docs-heading-anchor-permalink" href="#Publishing-to-HTML-and-PDF" title="Permalink"></a></h1><p>You can also publish any supported input format to HTML and PDF documents.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Producing PDF output requires that you have XeLaTex installed and in your path.</p></div></div><p>You can use a YAML header in the beginning of the input document delimited with <code>---</code> to set the document title, author and date, e.g.:</p><pre><code class="language-none">---
title : Weave example
author : Matti Pastell
date: 15th December 2016
---</code></pre><p>Here are sample input and outputs:</p><ul><li>input (Julia markdown format): <a href="../examples/FIR_design_plots.jl"><code>FIR_design_plots.jl</code></a> (its path is bound to <code>Weave.SAMPLE_JL_DOC</code>)</li><li>HTML output: <a href="../examples/FIR_design_plots.html"><code>FIR_design_plots.html</code></a></li><li>PDF output: <a href="../examples/FIR_design_plots.pdf"><code>FIR_design_plots.pdf</code></a></li></ul><p>They are generated as follows:</p><pre><code class="language-julia">weave(Weave.SAMPLE_JL_DOC)) # default to md2html output format
weave(Weave.SAMPLE_JL_DOC; doctype = &quot;md2pdf&quot;)</code></pre><div class="admonition is-category-tips"><header class="admonition-header">Tips</header><div class="admonition-body"><p><code>Weave.SAMPLE_JL_DOC</code> is the path of <a href="../examples/FIR_design.jl">FIR_design.jl</a>.</p></div></div><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p><code>&quot;md2html&quot;</code> and <code>&quot;md2pdf&quot;</code> assume Julia markdown format as an input, while <code>pandoc2pdf</code> and <code>pandoc2html</code> assume Noweb input format (i.e. Pandoc markdown).</p></div></div><h2 id="Templates"><a class="docs-heading-anchor" href="#Templates">Templates</a><a id="Templates-1"></a><a class="docs-heading-anchor-permalink" href="#Templates" title="Permalink"></a></h2><p>You can use a custom template with <code>md2html</code> and <code>md2pdf</code> formats with <code>template</code> keyword option, e.g.: <code>weave(&quot;FIR_design_plots.jl&quot;, template = &quot;custom.tpl&quot;</code>.</p><p>As starting point, you can use the existing templates:</p><ul><li>HTML (<code>md2html</code>): <a href="https://github.com/JunoLab/Weave.jl/blob/master/templates/md2html.tpl"><code>md2html.tpl</code></a></li><li>LaTex (<code>md2pdf</code>): <a href="https://github.com/JunoLab/Weave.jl/blob/master/templates/md2pdf.tpl"><code>md2pdf.tpl</code></a></li></ul><p>Templates are rendered using <a href="https://github.com/jverzani/Mustache.jl">Mustache.jl</a>.</p><h2 id="Supported-Markdown-syntax"><a class="docs-heading-anchor" href="#Supported-Markdown-syntax">Supported Markdown syntax</a><a id="Supported-Markdown-syntax-1"></a><a class="docs-heading-anchor-permalink" href="#Supported-Markdown-syntax" title="Permalink"></a></h2><p>The markdown variant used by Weave is <a href="https://docs.julialang.org/en/v1/stdlib/Markdown/#">Julia markdown</a>. In addition Weave supports few additional Markdown features:</p><h3 id="Comments"><a class="docs-heading-anchor" href="#Comments">Comments</a><a id="Comments-1"></a><a class="docs-heading-anchor-permalink" href="#Comments" title="Permalink"></a></h3><p>You can add comments using html syntax: <code>&lt;!-- --&gt;</code></p><h3 id="Multiline-equations"><a class="docs-heading-anchor" href="#Multiline-equations">Multiline equations</a><a id="Multiline-equations-1"></a><a class="docs-heading-anchor-permalink" href="#Multiline-equations" title="Permalink"></a></h3><p>You can add multiline equations using:</p><pre><code class="language-none">$$
x^2 = x*x
$$</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../usage/">« Using Weave</a><a class="docs-footer-nextpage" href="../chunk_options/">Chunk Options »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Thursday 29 April 2021 11:16">Thursday 29 April 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

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