Update to reveal.js 4.1.2 (#136)

- New tools/ script to manually keep step for updates
- Plugins are all updated
- Template update following latest Pandoc version
- updated README for documentation
- Help page updated 
- See other change in NEWS file
diff --git a/inst/reveal.js-4.1.2/plugin/highlight/plugin.js b/inst/reveal.js-4.1.2/plugin/highlight/plugin.js
new file mode 100644
index 0000000..ff2ac8b
--- /dev/null
+++ b/inst/reveal.js-4.1.2/plugin/highlight/plugin.js
@@ -0,0 +1,430 @@
+import hljs from 'highlight.js'
+
+/* highlightjs-line-numbers.js 2.6.0 | (C) 2018 Yauheni Pakala | MIT License | github.com/wcoder/highlightjs-line-numbers.js */
+/* Edited by Hakim for reveal.js; removed async timeout */
+!function(n,e){"use strict";function t(){var n=e.createElement("style");n.type="text/css",n.innerHTML=g(".{0}{border-collapse:collapse}.{0} td{padding:0}.{1}:before{content:attr({2})}",[v,L,b]),e.getElementsByTagName("head")[0].appendChild(n)}function r(t){"interactive"===e.readyState||"complete"===e.readyState?i(t):n.addEventListener("DOMContentLoaded",function(){i(t)})}function i(t){try{var r=e.querySelectorAll("code.hljs,code.nohighlight");for(var i in r)r.hasOwnProperty(i)&&l(r[i],t)}catch(o){n.console.error("LineNumbers error: ",o)}}function l(n,e){"object"==typeof n&&f(function(){n.innerHTML=s(n,e)})}function o(n,e){if("string"==typeof n){var t=document.createElement("code");return t.innerHTML=n,s(t,e)}}function s(n,e){e=e||{singleLine:!1};var t=e.singleLine?0:1;return c(n),a(n.innerHTML,t)}function a(n,e){var t=u(n);if(""===t[t.length-1].trim()&&t.pop(),t.length>e){for(var r="",i=0,l=t.length;i<l;i++)r+=g('<tr><td class="{0}"><div class="{1} {2}" {3}="{5}"></div></td><td class="{4}"><div class="{1}">{6}</div></td></tr>',[j,m,L,b,p,i+1,t[i].length>0?t[i]:" "]);return g('<table class="{0}">{1}</table>',[v,r])}return n}function c(n){var e=n.childNodes;for(var t in e)if(e.hasOwnProperty(t)){var r=e[t];h(r.textContent)>0&&(r.childNodes.length>0?c(r):d(r.parentNode))}}function d(n){var e=n.className;if(/hljs-/.test(e)){for(var t=u(n.innerHTML),r=0,i="";r<t.length;r++){var l=t[r].length>0?t[r]:" ";i+=g('<span class="{0}">{1}</span>\n',[e,l])}n.innerHTML=i.trim()}}function u(n){return 0===n.length?[]:n.split(y)}function h(n){return(n.trim().match(y)||[]).length}function f(e){e()}function g(n,e){return n.replace(/\{(\d+)\}/g,function(n,t){return e[t]?e[t]:n})}var v="hljs-ln",m="hljs-ln-line",p="hljs-ln-code",j="hljs-ln-numbers",L="hljs-ln-n",b="data-line-number",y=/\r\n|\r|\n/g;hljs?(hljs.initLineNumbersOnLoad=r,hljs.lineNumbersBlock=l,hljs.lineNumbersValue=o,t()):n.console.error("highlight.js not detected!")}(window,document);
+
+/*!
+ * reveal.js plugin that adds syntax highlight support.
+ */
+
+const Plugin = {
+
+	id: 'highlight',
+
+	HIGHLIGHT_STEP_DELIMITER: '|',
+	HIGHLIGHT_LINE_DELIMITER: ',',
+	HIGHLIGHT_LINE_RANGE_DELIMITER: '-',
+
+	hljs: hljs,
+
+	/**
+	 * Highlights code blocks withing the given deck.
+	 *
+	 * Note that this can be called multiple times if
+	 * there are multiple presentations on one page.
+	 *
+	 * @param {Reveal} reveal the reveal.js instance
+	 */
+	init: function( reveal ) {
+
+		// Read the plugin config options and provide fallbacks
+		let config = reveal.getConfig().highlight || {};
+		config.highlightOnLoad = typeof config.highlightOnLoad === 'boolean' ? config.highlightOnLoad : true;
+		config.escapeHTML = typeof config.escapeHTML === 'boolean' ? config.escapeHTML : true;
+
+		Array.from( reveal.getRevealElement().querySelectorAll( 'pre code' ) ).forEach( block => {
+
+			block.parentNode.className = 'code-wrapper';
+
+			// Code can optionally be wrapped in script template to avoid
+			// HTML being parsed by the browser (i.e. when you need to
+			// include <, > or & in your code).
+			let substitute = block.querySelector( 'script[type="text/template"]' );
+			if( substitute ) {
+				// textContent handles the HTML entity escapes for us
+				block.textContent = substitute.innerHTML;
+			}
+
+			// Trim whitespace if the "data-trim" attribute is present
+			if( block.hasAttribute( 'data-trim' ) && typeof block.innerHTML.trim === 'function' ) {
+				block.innerHTML = betterTrim( block );
+			}
+
+			// Escape HTML tags unless the "data-noescape" attrbute is present
+			if( config.escapeHTML && !block.hasAttribute( 'data-noescape' )) {
+				block.innerHTML = block.innerHTML.replace( /</g,"&lt;").replace(/>/g, '&gt;' );
+			}
+
+			// Re-highlight when focus is lost (for contenteditable code)
+			block.addEventListener( 'focusout', function( event ) {
+				hljs.highlightElement( event.currentTarget );
+			}, false );
+
+			if( config.highlightOnLoad ) {
+				Plugin.highlightBlock( block );
+			}
+
+		} );
+
+		// If we're printing to PDF, scroll the code highlights of
+		// all blocks in the deck into view at once
+		reveal.on( 'pdf-ready', function() {
+			[].slice.call( reveal.getRevealElement().querySelectorAll( 'pre code[data-line-numbers].current-fragment' ) ).forEach( function( block ) {
+				Plugin.scrollHighlightedLineIntoView( block, {}, true );
+			} );
+		} );
+
+	},
+
+	/**
+	 * Highlights a code block. If the <code> node has the
+	 * 'data-line-numbers' attribute we also generate slide
+	 * numbers.
+	 *
+	 * If the block contains multiple line highlight steps,
+	 * we clone the block and create a fragment for each step.
+	 */
+	highlightBlock: function( block ) {
+
+		hljs.highlightElement( block );
+
+		// Don't generate line numbers for empty code blocks
+		if( block.innerHTML.trim().length === 0 ) return;
+
+		if( block.hasAttribute( 'data-line-numbers' ) ) {
+			hljs.lineNumbersBlock( block, { singleLine: true } );
+
+			var scrollState = { currentBlock: block };
+
+			// If there is at least one highlight step, generate
+			// fragments
+			var highlightSteps = Plugin.deserializeHighlightSteps( block.getAttribute( 'data-line-numbers' ) );
+			if( highlightSteps.length > 1 ) {
+
+				// If the original code block has a fragment-index,
+				// each clone should follow in an incremental sequence
+				var fragmentIndex = parseInt( block.getAttribute( 'data-fragment-index' ), 10 );
+
+				if( typeof fragmentIndex !== 'number' || isNaN( fragmentIndex ) ) {
+					fragmentIndex = null;
+				}
+
+				// Generate fragments for all steps except the original block
+				highlightSteps.slice(1).forEach( function( highlight ) {
+
+					var fragmentBlock = block.cloneNode( true );
+					fragmentBlock.setAttribute( 'data-line-numbers', Plugin.serializeHighlightSteps( [ highlight ] ) );
+					fragmentBlock.classList.add( 'fragment' );
+					block.parentNode.appendChild( fragmentBlock );
+					Plugin.highlightLines( fragmentBlock );
+
+					if( typeof fragmentIndex === 'number' ) {
+						fragmentBlock.setAttribute( 'data-fragment-index', fragmentIndex );
+						fragmentIndex += 1;
+					}
+					else {
+						fragmentBlock.removeAttribute( 'data-fragment-index' );
+					}
+
+					// Scroll highlights into view as we step through them
+					fragmentBlock.addEventListener( 'visible', Plugin.scrollHighlightedLineIntoView.bind( Plugin, fragmentBlock, scrollState ) );
+					fragmentBlock.addEventListener( 'hidden', Plugin.scrollHighlightedLineIntoView.bind( Plugin, fragmentBlock.previousSibling, scrollState ) );
+
+				} );
+
+				block.removeAttribute( 'data-fragment-index' )
+				block.setAttribute( 'data-line-numbers', Plugin.serializeHighlightSteps( [ highlightSteps[0] ] ) );
+
+			}
+
+			// Scroll the first highlight into view when the slide
+			// becomes visible. Note supported in IE11 since it lacks
+			// support for Element.closest.
+			var slide = typeof block.closest === 'function' ? block.closest( 'section:not(.stack)' ) : null;
+			if( slide ) {
+				var scrollFirstHighlightIntoView = function() {
+					Plugin.scrollHighlightedLineIntoView( block, scrollState, true );
+					slide.removeEventListener( 'visible', scrollFirstHighlightIntoView );
+				}
+				slide.addEventListener( 'visible', scrollFirstHighlightIntoView );
+			}
+
+			Plugin.highlightLines( block );
+
+		}
+
+	},
+
+	/**
+	 * Animates scrolling to the first highlighted line
+	 * in the given code block.
+	 */
+	scrollHighlightedLineIntoView: function( block, scrollState, skipAnimation ) {
+
+		cancelAnimationFrame( scrollState.animationFrameID );
+
+		// Match the scroll position of the currently visible
+		// code block
+		if( scrollState.currentBlock ) {
+			block.scrollTop = scrollState.currentBlock.scrollTop;
+		}
+
+		// Remember the current code block so that we can match
+		// its scroll position when showing/hiding fragments
+		scrollState.currentBlock = block;
+
+		var highlightBounds = this.getHighlightedLineBounds( block )
+		var viewportHeight = block.offsetHeight;
+
+		// Subtract padding from the viewport height
+		var blockStyles = getComputedStyle( block );
+		viewportHeight -= parseInt( blockStyles.paddingTop ) + parseInt( blockStyles.paddingBottom );
+
+		// Scroll position which centers all highlights
+		var startTop = block.scrollTop;
+		var targetTop = highlightBounds.top + ( Math.min( highlightBounds.bottom - highlightBounds.top, viewportHeight ) - viewportHeight ) / 2;
+
+		// Account for offsets in position applied to the
+		// <table> that holds our lines of code
+		var lineTable = block.querySelector( '.hljs-ln' );
+		if( lineTable ) targetTop += lineTable.offsetTop - parseInt( blockStyles.paddingTop );
+
+		// Make sure the scroll target is within bounds
+		targetTop = Math.max( Math.min( targetTop, block.scrollHeight - viewportHeight ), 0 );
+
+		if( skipAnimation === true || startTop === targetTop ) {
+			block.scrollTop = targetTop;
+		}
+		else {
+
+			// Don't attempt to scroll if there is no overflow
+			if( block.scrollHeight <= viewportHeight ) return;
+
+			var time = 0;
+			var animate = function() {
+				time = Math.min( time + 0.02, 1 );
+
+				// Update our eased scroll position
+				block.scrollTop = startTop + ( targetTop - startTop ) * Plugin.easeInOutQuart( time );
+
+				// Keep animating unless we've reached the end
+				if( time < 1 ) {
+					scrollState.animationFrameID = requestAnimationFrame( animate );
+				}
+			};
+
+			animate();
+
+		}
+
+	},
+
+	/**
+	 * The easing function used when scrolling.
+	 */
+	easeInOutQuart: function( t ) {
+
+		// easeInOutQuart
+		return t<.5 ? 8*t*t*t*t : 1-8*(--t)*t*t*t;
+
+	},
+
+	getHighlightedLineBounds: function( block ) {
+
+		var highlightedLines = block.querySelectorAll( '.highlight-line' );
+		if( highlightedLines.length === 0 ) {
+			return { top: 0, bottom: 0 };
+		}
+		else {
+			var firstHighlight = highlightedLines[0];
+			var lastHighlight = highlightedLines[ highlightedLines.length -1 ];
+
+			return {
+				top: firstHighlight.offsetTop,
+				bottom: lastHighlight.offsetTop + lastHighlight.offsetHeight
+			}
+		}
+
+	},
+
+	/**
+	 * Visually emphasize specific lines within a code block.
+	 * This only works on blocks with line numbering turned on.
+	 *
+	 * @param {HTMLElement} block a <code> block
+	 * @param {String} [linesToHighlight] The lines that should be
+	 * highlighted in this format:
+	 * "1" 		= highlights line 1
+	 * "2,5"	= highlights lines 2 & 5
+	 * "2,5-7"	= highlights lines 2, 5, 6 & 7
+	 */
+	highlightLines: function( block, linesToHighlight ) {
+
+		var highlightSteps = Plugin.deserializeHighlightSteps( linesToHighlight || block.getAttribute( 'data-line-numbers' ) );
+
+		if( highlightSteps.length ) {
+
+			highlightSteps[0].forEach( function( highlight ) {
+
+				var elementsToHighlight = [];
+
+				// Highlight a range
+				if( typeof highlight.end === 'number' ) {
+					elementsToHighlight = [].slice.call( block.querySelectorAll( 'table tr:nth-child(n+'+highlight.start+'):nth-child(-n+'+highlight.end+')' ) );
+				}
+				// Highlight a single line
+				else if( typeof highlight.start === 'number' ) {
+					elementsToHighlight = [].slice.call( block.querySelectorAll( 'table tr:nth-child('+highlight.start+')' ) );
+				}
+
+				if( elementsToHighlight.length ) {
+					elementsToHighlight.forEach( function( lineElement ) {
+						lineElement.classList.add( 'highlight-line' );
+					} );
+
+					block.classList.add( 'has-highlights' );
+				}
+
+			} );
+
+		}
+
+	},
+
+	/**
+	 * Parses and formats a user-defined string of line
+	 * numbers to highlight.
+	 *
+	 * @example
+	 * Plugin.deserializeHighlightSteps( '1,2|3,5-10' )
+	 * // [
+	 * //   [ { start: 1 }, { start: 2 } ],
+	 * //   [ { start: 3 }, { start: 5, end: 10 } ]
+	 * // ]
+	 */
+	deserializeHighlightSteps: function( highlightSteps ) {
+
+		// Remove whitespace
+		highlightSteps = highlightSteps.replace( /\s/g, '' );
+
+		// Divide up our line number groups
+		highlightSteps = highlightSteps.split( Plugin.HIGHLIGHT_STEP_DELIMITER );
+
+		return highlightSteps.map( function( highlights ) {
+
+			return highlights.split( Plugin.HIGHLIGHT_LINE_DELIMITER ).map( function( highlight ) {
+
+				// Parse valid line numbers
+				if( /^[\d-]+$/.test( highlight ) ) {
+
+					highlight = highlight.split( Plugin.HIGHLIGHT_LINE_RANGE_DELIMITER );
+
+					var lineStart = parseInt( highlight[0], 10 ),
+						lineEnd = parseInt( highlight[1], 10 );
+
+					if( isNaN( lineEnd ) ) {
+						return {
+							start: lineStart
+						};
+					}
+					else {
+						return {
+							start: lineStart,
+							end: lineEnd
+						};
+					}
+
+				}
+				// If no line numbers are provided, no code will be highlighted
+				else {
+
+					return {};
+
+				}
+
+			} );
+
+		} );
+
+	},
+
+	/**
+	 * Serializes parsed line number data into a string so
+	 * that we can store it in the DOM.
+	 */
+	serializeHighlightSteps: function( highlightSteps ) {
+
+		return highlightSteps.map( function( highlights ) {
+
+			return highlights.map( function( highlight ) {
+
+				// Line range
+				if( typeof highlight.end === 'number' ) {
+					return highlight.start + Plugin.HIGHLIGHT_LINE_RANGE_DELIMITER + highlight.end;
+				}
+				// Single line
+				else if( typeof highlight.start === 'number' ) {
+					return highlight.start;
+				}
+				// All lines
+				else {
+					return '';
+				}
+
+			} ).join( Plugin.HIGHLIGHT_LINE_DELIMITER );
+
+		} ).join( Plugin.HIGHLIGHT_STEP_DELIMITER );
+
+	}
+
+}
+
+// Function to perform a better "data-trim" on code snippets
+// Will slice an indentation amount on each line of the snippet (amount based on the line having the lowest indentation length)
+function betterTrim(snippetEl) {
+	// Helper functions
+	function trimLeft(val) {
+		// Adapted from https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/Trim#Polyfill
+		return val.replace(/^[\s\uFEFF\xA0]+/g, '');
+	}
+	function trimLineBreaks(input) {
+		var lines = input.split('\n');
+
+		// Trim line-breaks from the beginning
+		for (var i = 0; i < lines.length; i++) {
+			if (lines[i].trim() === '') {
+				lines.splice(i--, 1);
+			} else break;
+		}
+
+		// Trim line-breaks from the end
+		for (var i = lines.length-1; i >= 0; i--) {
+			if (lines[i].trim() === '') {
+				lines.splice(i, 1);
+			} else break;
+		}
+
+		return lines.join('\n');
+	}
+
+	// Main function for betterTrim()
+	return (function(snippetEl) {
+		var content = trimLineBreaks(snippetEl.innerHTML);
+		var lines = content.split('\n');
+		// Calculate the minimum amount to remove on each line start of the snippet (can be 0)
+		var pad = lines.reduce(function(acc, line) {
+			if (line.length > 0 && trimLeft(line).length > 0 && acc > line.length - trimLeft(line).length) {
+				return line.length - trimLeft(line).length;
+			}
+			return acc;
+		}, Number.POSITIVE_INFINITY);
+		// Slice each line with this amount
+		return lines.map(function(line, index) {
+			return line.slice(pad);
+		})
+		.join('\n');
+	})(snippetEl);
+}
+
+export default () => Plugin;