Updates Lesson 09 (semantic similarity)

Duke-GCB · Nov 28, 2023 · 5dad6c3 · 5dad6c3
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diff --git a/Lesson-09.qmd b/Lesson-09.qmd
@@ -2,7 +2,7 @@
 title: "Biostat 823 - Semantic Similarity"
 author: "Hilmar Lapp"
 institute: "Duke University, Department of Biostatistics & Bioinformatics"
-date: "Fall 2022"
+date: "Nov 28, 2023"
 format:
   revealjs:
     slide-number: true

diff --git a/pub/Lesson-09.html b/pub/Lesson-09.html
diff --git a/pub/Lesson-09_files/libs/clipboard/clipboard.min.js b/pub/Lesson-09_files/libs/clipboard/clipboard.min.js
diff --git a/pub/Lesson-09_files/libs/quarto-html/light-border.css b/pub/Lesson-09_files/libs/quarto-html/light-border.css
diff --git a/pub/Lesson-09_files/libs/quarto-html/quarto-syntax-highlighting.css b/pub/Lesson-09_files/libs/quarto-html/quarto-syntax-highlighting.css
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/reveal.css b/pub/Lesson-09_files/libs/revealjs/dist/reveal.css
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/reveal.esm.js b/pub/Lesson-09_files/libs/revealjs/dist/reveal.esm.js
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/reveal.esm.js.map b/pub/Lesson-09_files/libs/revealjs/dist/reveal.esm.js.map
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/reveal.js b/pub/Lesson-09_files/libs/revealjs/dist/reveal.js
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/reveal.js.map b/pub/Lesson-09_files/libs/revealjs/dist/reveal.js.map
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.eot b/pub/Lesson-09_files/libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.eot
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.ttf b/pub/Lesson-09_files/libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.ttf
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.woff b/pub/Lesson-09_files/libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.woff
diff --git a/...Lesson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot b/...Lesson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot
diff --git a/...esson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff b/...esson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff
diff --git a/...esson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot b/...esson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot
diff --git a/...sson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff b/...sson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff
diff --git a/...sson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot b/...sson-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot
diff --git a/...son-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff b/...son-09_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff
diff --git a/...9_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot b/...9_files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot
diff --git a/..._files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff b/..._files/libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff
diff --git a/pub/Lesson-09_files/libs/revealjs/dist/theme/quarto.css b/pub/Lesson-09_files/libs/revealjs/dist/theme/quarto.css
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/highlight/plugin.js b/pub/Lesson-09_files/libs/revealjs/plugin/highlight/plugin.js
@@ -106,7 +106,7 @@ const Plugin = {
 
 			var scrollState = { currentBlock: block };
 
-			// If there is at least one highlight step, generate
+			// If there is more than one highlight step, generate
 			// fragments
 			var highlightSteps = Plugin.deserializeHighlightSteps( block.getAttribute( 'data-line-numbers' ) );
 			if( highlightSteps.length > 1 ) {
@@ -142,7 +142,7 @@ const Plugin = {
 
 				} );
 
-				block.removeAttribute( 'data-fragment-index' )
+				block.removeAttribute( 'data-fragment-index' );
 				block.setAttribute( 'data-line-numbers', Plugin.serializeHighlightSteps( [ highlightSteps[0] ] ) );
 
 			}

diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/markdown/markdown.esm.js b/pub/Lesson-09_files/libs/revealjs/plugin/markdown/markdown.esm.js
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/markdown/markdown.js b/pub/Lesson-09_files/libs/revealjs/plugin/markdown/markdown.js
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/markdown/plugin.js b/pub/Lesson-09_files/libs/revealjs/plugin/markdown/plugin.js
@@ -4,7 +4,7 @@
  * of external markdown documents.
  */
 
-import marked from 'marked'
+import { marked } from 'marked';
 
 const DEFAULT_SLIDE_SEPARATOR = '\r?\n---\r?\n',
 	  DEFAULT_NOTES_SEPARATOR = 'notes?:',

diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/math/katex.js b/pub/Lesson-09_files/libs/revealjs/plugin/math/katex.js
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/math/math.esm.js b/pub/Lesson-09_files/libs/revealjs/plugin/math/math.esm.js
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/math/math.js b/pub/Lesson-09_files/libs/revealjs/plugin/math/math.js
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/math/mathjax3.js b/pub/Lesson-09_files/libs/revealjs/plugin/math/mathjax3.js
@@ -56,7 +56,7 @@ export const MathJax3 = () => {
             let revealOptions = deck.getConfig().mathjax3 || {};
             let options = {...defaultOptions, ...revealOptions};
             options.tex = {...defaultOptions.tex, ...revealOptions.tex}
-            options.options = {...options.options, ...defaultOptions.options}
+            options.options = {...defaultOptions.options, ...revealOptions.options}
             options.startup = {...defaultOptions.startup, ...revealOptions.startup}
 
             let url = options.mathjax || 'https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js';

diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/notes/notes.esm.js b/pub/Lesson-09_files/libs/revealjs/plugin/notes/notes.esm.js
diff --git a/pub/Lesson-09_files/libs/revealjs/plugin/notes/notes.js b/pub/Lesson-09_files/libs/revealjs/plugin/notes/notes.js