prep for eric test commit

cbw-dev · Dec 9, 2024 · c91c715 · c91c715
1 parent d5de48a
commit c91c715
Show file tree

Hide file tree

Showing 14 changed files with 87 additions and 47 deletions.
diff --git a/030-module-2.Rmd b/030-module-2.Rmd
@@ -4,10 +4,25 @@
 
 ## Lab
 
-put some example of producing images, show chunk options
+<!-- ERIC TEST -->
 
-```{r, pressure-plot, echo=FALSE}, 
-plot(pressure)
-```
+:::: {.blackbox data-latex=""}
+::: {.center data-latex=""}
+**NOTICE!**
+:::
 
-- include formatting options
+TESTING CALLOUT BLOCKS
+::::
+
+<!-- Test: Go to preamble.tex, and comment out lines 2-9,  ctrl+shift+c-->
+
+
+<!-- Additional Notes for Julia provided below, can ignore -->
+
+<!-- put some example of producing images, show chunk options -->
+
+<!-- ```{r, pressure-plot, echo=FALSE},  -->
+<!-- plot(pressure) -->
+<!-- ``` -->
+
+<!-- - include formatting options -->
diff --git a/docs/404.html b/docs/404.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Error 404: This page does not exist. | [Name of Workshop][Year]</title>
   <meta name="description" content="CBW’s Bookdown Template for Workshops" />
-  <meta name="generator" content="bookdown 0.41.1 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Error 404: This page does not exist. | [Name of Workshop][Year]" />
   <meta property="og:type" content="book" />

diff --git a/docs/_main.epub b/docs/_main.epub
diff --git a/docs/_main.pdf b/docs/_main.pdf
diff --git a/docs/_main.tex b/docs/_main.tex
@@ -104,6 +104,14 @@
   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 \setcounter{secnumdepth}{5}
 \usepackage{booktabs}
+\usepackage{tcolorbox}
+
+\newtcolorbox{blackbox}{
+  colback=black,
+  colframe=orange,
+  coltext=white,
+  boxsep=5pt,
+  arc=4pt}
 \ifLuaTeX
   \usepackage{selnolig}  % disable illegal ligatures
 \fi
@@ -281,15 +289,16 @@ \section{Lecture}\label{lecture-1}
 
 \section{Lab}\label{lab-1}
 
-put some example of producing images, show chunk options
+\begin{blackbox}
 
-\texttt{\{r,\ pressure-plot,\ echo=FALSE\},\ \ plot(pressure)}
+\begin{center}
+\textbf{NOTICE!}
 
-\begin{itemize}
-\tightlist
-\item
-  include formatting options
-\end{itemize}
+\end{center}
+
+TESTING CALLOUT BLOCKS
+
+\end{blackbox}
 
   \bibliography{book.bib,packages.bib}
 

diff --git a/docs/course-schedule.html b/docs/course-schedule.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Course Schedule | [Name of Workshop][Year]</title>
   <meta name="description" content="CBW’s Bookdown Template for Workshops" />
-  <meta name="generator" content="bookdown 0.41.1 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Course Schedule | [Name of Workshop][Year]" />
   <meta property="og:type" content="book" />

diff --git a/docs/index.html b/docs/index.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>[Name of Workshop][Year]</title>
   <meta name="description" content="CBW’s Bookdown Template for Workshops" />
-  <meta name="generator" content="bookdown 0.41.1 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="[Name of Workshop][Year]" />
   <meta property="og:type" content="book" />

diff --git a/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js b/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js
@@ -60,13 +60,6 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
         saveFontSettings();
     };
 
-    // Increase or decrease line spacing
-    function changeSpacing(e, inc = true) {
-        e.preventDefault();
-        inc ? fontState.spacing++ : (fontState.spacing > 10 && fontState.spacing--);
-        saveFontSettings();
-    }
-
     function update() {
         var $book = gitbook.state.$book;
 
@@ -81,9 +74,6 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
             $book[0].className = $book[0].className.replace(/\bcolor-theme-\S+/g, '');
             $book.addClass("color-theme-"+fontState.theme);
         }
-        var lineHeight = fontState.spacing / 10;
-        $book.find('section').css('line-height', lineHeight);
-        $('.font-settings .spacing-reduce').prop('disabled', lineHeight <= 1);
     };
 
     function init(config) {
@@ -97,8 +87,7 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
         fontState = gitbook.storage.get("fontState", {
             size: config.size || 2,
             family: FAMILY[config.family || "sans"],
-            theme: THEMES[config.theme || "white"],
-            spacing: config.spacing || 17,
+            theme: THEMES[config.theme || "white"]
         });
 
         update();
@@ -150,18 +139,6 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
                         text: 'Night',
                         onClick: _.partial(changeColorTheme, 2)
                     }
-
-                ],
-                [
-                    {
-                    className: 'spacing-reduce',
-                    text: 'Spacing -',
-                    onClick: e => changeSpacing(e, false)
-                    },
-                    {
-                    text: 'Spacing +',
-                    onClick: changeSpacing
-                    }
                 ]
             ]
         });

diff --git a/docs/module-1.html b/docs/module-1.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Module 1 | [Name of Workshop][Year]</title>
   <meta name="description" content="CBW’s Bookdown Template for Workshops" />
-  <meta name="generator" content="bookdown 0.41.1 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Module 1 | [Name of Workshop][Year]" />
   <meta property="og:type" content="book" />

diff --git a/docs/module-2.html b/docs/module-2.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Module 2 | [Name of Workshop][Year]</title>
   <meta name="description" content="CBW’s Bookdown Template for Workshops" />
-  <meta name="generator" content="bookdown 0.41.1 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Module 2 | [Name of Workshop][Year]" />
   <meta property="og:type" content="book" />
@@ -201,11 +201,20 @@ <h2>Lecture<a href="module-2.html#lecture-1" class="anchor-section" aria-label="
 </div>
 <div id="lab-1" class="section level2 hasAnchor">
 <h2>Lab<a href="module-2.html#lab-1" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<p>put some example of producing images, show chunk options</p>
-<p><code>{r, pressure-plot, echo=FALSE},  plot(pressure)</code></p>
-<ul>
-<li>include formatting options</li>
-</ul>
+<!-- ERIC TEST -->
+<div class="blackbox">
+<div class="center">
+<p><strong>NOTICE!</strong></p>
+</div>
+<p>TESTING CALLOUT BLOCKS</p>
+</div>
+<!-- Test: Go to preamble.tex, and comment out lines 2-9,  ctrl+shift+c-->
+<!-- Additional Notes for Julia provided below, can ignore -->
+<!-- put some example of producing images, show chunk options -->
+<!-- ```{r, pressure-plot, echo=FALSE},  -->
+<!-- plot(pressure) -->
+<!-- ``` -->
+<!-- - include formatting options -->
 
 </div>
 </div>

diff --git a/docs/search_index.json b/docs/search_index.json
@@ -1 +1 @@
-[["index.html", "[Name of Workshop][Year] Welcome", " [Name of Workshop][Year] Instructors: [list instructor names here] [Insert dates of the workshop] Welcome Welcome to CBW’s [workshop name, year] Workshop! Put some introductory content here. (ex. links to bioinformatics.ca, general info) "],["course-schedule.html", "Course Schedule Pre-workshop Materials Computing Setup &amp; Downloads Meet Your Faculty Class Photo", " Course Schedule Copy paste a table into https://www.tablesgenerator.com/markdown_tables (select convert to markdown) to create a table in markdown. Pre-workshop Materials Click here for your prework! Computing Setup &amp; Downloads Insert downloads (ex. datasets) or other tech instructions here (ex. AWS Instructions) Meet Your Faculty Here’s your team! Instructor, TA, … Job Title Company/University/… Location — contact information [insert description of the person] Michelle Brazas, PhD Scientific Director Canadian Bioinformatics Workshops (CBW) Toronto, ON, CA — [email protected] Dr. Michelle Brazas is the Associate Director for Adaptive Oncology at the Ontario Institute for Cancer Research (OICR), and acting Scientific Director at Bioinformatics.ca. Previously, Dr. Brazas was the Program Manager for Bioinformatics.ca and a faculty member in Biotechnology at BCIT. Michelle co-founded and runs the Toronto Bioinformatics User Group (TorBUG) now in its 11th season, and plays an active role in the International Society of Computational Biology where she sits on the Board of Directors and Executive Board. Nia Hughes (she/her) Program Manager, Bioinformatics.ca Ontario Institute for Cancer Research Toronto, ON, Canada — [email protected] Nia is the Program Manager for Bioinformatics.ca, where she coordinates the Canadian Bioinformatics Workshop Series. Prior to starting at OICR, she completed her M.Sc. in Bioinformatics from the University of Guelph in 2020 before working there as a bioinformatician studying epigenetic and transcriptomic patterns across maize varieties. Class Photo &lt;- Replace the file address to your actual class photo file location "],["module-1.html", "Module 1 Lecture Lab", " Module 1 Welcome to module 1! Lecture Here is an example of a pdf embedded:   Here is an example of a YouTube video embedded: ^ HEIGHT HAS A BUG Downloads [insert your downloads for this module here (ex. datasets)] Lab [Your lab here] # Your R code here # For example: x &lt;- 42 x ## [1] 42 # Your python code here # For example: print(&quot;hello world&quot;) ## hello world # Your bash code here # For example: pwd ## /Users/jqiu/Documents/CBWgithub/cbw-dev-templates-docs/bookdown-template Try running these code “chunks” by pressing the green (left-pointing) triangle next to your code chunks. You will see the code run in the console and the output provided below the code chunk. The output of the code will also be produced under the code chunk on your website page. "],["module-2.html", "Module 2 Lecture Lab", " Module 2 Lecture Lab put some example of producing images, show chunk options {r, pressure-plot, echo=FALSE}, plot(pressure) include formatting options "],["404.html", "Error 404: This page does not exist.", " Error 404: This page does not exist. This page does not exist anymore! Try going back to the workshop homepage or the bioinformatics.ca homepage. You must update these pages for new workshops. "]]
+[["index.html", "[Name of Workshop][Year] Welcome", " [Name of Workshop][Year] Instructors: [list instructor names here] [Insert dates of the workshop] Welcome Welcome to CBW’s [workshop name, year] Workshop! Put some introductory content here. (ex. links to bioinformatics.ca, general info) "],["course-schedule.html", "Course Schedule Pre-workshop Materials Computing Setup &amp; Downloads Meet Your Faculty Class Photo", " Course Schedule Copy paste a table into https://www.tablesgenerator.com/markdown_tables (select convert to markdown) to create a table in markdown. Pre-workshop Materials Click here for your prework! Computing Setup &amp; Downloads Insert downloads (ex. datasets) or other tech instructions here (ex. AWS Instructions) Meet Your Faculty Here’s your team! Instructor, TA, … Job Title Company/University/… Location — contact information [insert description of the person] Michelle Brazas, PhD Scientific Director Canadian Bioinformatics Workshops (CBW) Toronto, ON, CA — [email protected] Dr. Michelle Brazas is the Associate Director for Adaptive Oncology at the Ontario Institute for Cancer Research (OICR), and acting Scientific Director at Bioinformatics.ca. Previously, Dr. Brazas was the Program Manager for Bioinformatics.ca and a faculty member in Biotechnology at BCIT. Michelle co-founded and runs the Toronto Bioinformatics User Group (TorBUG) now in its 11th season, and plays an active role in the International Society of Computational Biology where she sits on the Board of Directors and Executive Board. Nia Hughes (she/her) Program Manager, Bioinformatics.ca Ontario Institute for Cancer Research Toronto, ON, Canada — [email protected] Nia is the Program Manager for Bioinformatics.ca, where she coordinates the Canadian Bioinformatics Workshop Series. Prior to starting at OICR, she completed her M.Sc. in Bioinformatics from the University of Guelph in 2020 before working there as a bioinformatician studying epigenetic and transcriptomic patterns across maize varieties. Class Photo &lt;- Replace the file address to your actual class photo file location "],["module-1.html", "Module 1 Lecture Lab", " Module 1 Welcome to module 1! Lecture Here is an example of a pdf embedded:   Here is an example of a YouTube video embedded: ^ HEIGHT HAS A BUG Downloads [insert your downloads for this module here (ex. datasets)] Lab [Your lab here] # Your R code here # For example: x &lt;- 42 x ## [1] 42 # Your python code here # For example: print(&quot;hello world&quot;) ## hello world # Your bash code here # For example: pwd ## /Users/jqiu/Documents/CBWgithub/cbw-dev-templates-docs/bookdown-template Try running these code “chunks” by pressing the green (left-pointing) triangle next to your code chunks. You will see the code run in the console and the output provided below the code chunk. The output of the code will also be produced under the code chunk on your website page. "],["module-2.html", "Module 2 Lecture Lab", " Module 2 Lecture Lab NOTICE! TESTING CALLOUT BLOCKS "],["404.html", "Error 404: This page does not exist.", " Error 404: This page does not exist. This page does not exist anymore! Try going back to the workshop homepage or the bioinformatics.ca homepage. You must update these pages for new workshops. "]]
diff --git a/docs/style.css b/docs/style.css
@@ -21,4 +21,15 @@ pre code {
   text-align: center;
 }
 
+.blackbox {
+  padding: 1em;
+  background: black;
+  color: white;
+  border: 2px solid orange;
+  border-radius: 10px;
+}
+.center {
+  text-align: center;
+}
+
 /* Insert any of your specific css additions below*/
diff --git a/preamble.tex b/preamble.tex
@@ -1 +1,9 @@
 \usepackage{booktabs}
+\usepackage{tcolorbox}
+
+\newtcolorbox{blackbox}{
+  colback=black,
+  colframe=orange,
+  coltext=white,
+  boxsep=5pt,
+  arc=4pt}
diff --git a/style.css b/style.css
@@ -21,4 +21,15 @@ pre code {
   text-align: center;
 }
 
+.blackbox {
+  padding: 1em;
+  background: black;
+  color: white;
+  border: 2px solid orange;
+  border-radius: 10px;
+}
+.center {
+  text-align: center;
+}
+
 /* Insert any of your specific css additions below*/
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		[["index.html", "[Name of Workshop][Year] Welcome", " [Name of Workshop][Year] Instructors: [list instructor names here] [Insert dates of the workshop] Welcome Welcome to CBW’s [workshop name, year] Workshop! Put some introductory content here. (ex. links to bioinformatics.ca, general info) "],["course-schedule.html", "Course Schedule Pre-workshop Materials Computing Setup & Downloads Meet Your Faculty Class Photo", " Course Schedule Copy paste a table into https://www.tablesgenerator.com/markdown_tables (select convert to markdown) to create a table in markdown. Pre-workshop Materials Click here for your prework! Computing Setup & Downloads Insert downloads (ex. datasets) or other tech instructions here (ex. AWS Instructions) Meet Your Faculty Here’s your team! Instructor, TA, … Job Title Company/University/… Location — contact information [insert description of the person] Michelle Brazas, PhD Scientific Director Canadian Bioinformatics Workshops (CBW) Toronto, ON, CA — [email protected] Dr. Michelle Brazas is the Associate Director for Adaptive Oncology at the Ontario Institute for Cancer Research (OICR), and acting Scientific Director at Bioinformatics.ca. Previously, Dr. Brazas was the Program Manager for Bioinformatics.ca and a faculty member in Biotechnology at BCIT. Michelle co-founded and runs the Toronto Bioinformatics User Group (TorBUG) now in its 11th season, and plays an active role in the International Society of Computational Biology where she sits on the Board of Directors and Executive Board. Nia Hughes (she/her) Program Manager, Bioinformatics.ca Ontario Institute for Cancer Research Toronto, ON, Canada — [email protected] Nia is the Program Manager for Bioinformatics.ca, where she coordinates the Canadian Bioinformatics Workshop Series. Prior to starting at OICR, she completed her M.Sc. in Bioinformatics from the University of Guelph in 2020 before working there as a bioinformatician studying epigenetic and transcriptomic patterns across maize varieties. Class Photo <- Replace the file address to your actual class photo file location "],["module-1.html", "Module 1 Lecture Lab", " Module 1 Welcome to module 1! Lecture Here is an example of a pdf embedded: Here is an example of a YouTube video embedded: ^ HEIGHT HAS A BUG Downloads [insert your downloads for this module here (ex. datasets)] Lab [Your lab here] # Your R code here # For example: x <- 42 x ## [1] 42 # Your python code here # For example: print("hello world") ## hello world # Your bash code here # For example: pwd ## /Users/jqiu/Documents/CBWgithub/cbw-dev-templates-docs/bookdown-template Try running these code “chunks” by pressing the green (left-pointing) triangle next to your code chunks. You will see the code run in the console and the output provided below the code chunk. The output of the code will also be produced under the code chunk on your website page. "],["module-2.html", "Module 2 Lecture Lab", " Module 2 Lecture Lab put some example of producing images, show chunk options {r, pressure-plot, echo=FALSE}, plot(pressure) include formatting options "],["404.html", "Error 404: This page does not exist.", " Error 404: This page does not exist. This page does not exist anymore! Try going back to the workshop homepage or the bioinformatics.ca homepage. You must update these pages for new workshops. "]]
		[["index.html", "[Name of Workshop][Year] Welcome", " [Name of Workshop][Year] Instructors: [list instructor names here] [Insert dates of the workshop] Welcome Welcome to CBW’s [workshop name, year] Workshop! Put some introductory content here. (ex. links to bioinformatics.ca, general info) "],["course-schedule.html", "Course Schedule Pre-workshop Materials Computing Setup & Downloads Meet Your Faculty Class Photo", " Course Schedule Copy paste a table into https://www.tablesgenerator.com/markdown_tables (select convert to markdown) to create a table in markdown. Pre-workshop Materials Click here for your prework! Computing Setup & Downloads Insert downloads (ex. datasets) or other tech instructions here (ex. AWS Instructions) Meet Your Faculty Here’s your team! Instructor, TA, … Job Title Company/University/… Location — contact information [insert description of the person] Michelle Brazas, PhD Scientific Director Canadian Bioinformatics Workshops (CBW) Toronto, ON, CA — [email protected] Dr. Michelle Brazas is the Associate Director for Adaptive Oncology at the Ontario Institute for Cancer Research (OICR), and acting Scientific Director at Bioinformatics.ca. Previously, Dr. Brazas was the Program Manager for Bioinformatics.ca and a faculty member in Biotechnology at BCIT. Michelle co-founded and runs the Toronto Bioinformatics User Group (TorBUG) now in its 11th season, and plays an active role in the International Society of Computational Biology where she sits on the Board of Directors and Executive Board. Nia Hughes (she/her) Program Manager, Bioinformatics.ca Ontario Institute for Cancer Research Toronto, ON, Canada — [email protected] Nia is the Program Manager for Bioinformatics.ca, where she coordinates the Canadian Bioinformatics Workshop Series. Prior to starting at OICR, she completed her M.Sc. in Bioinformatics from the University of Guelph in 2020 before working there as a bioinformatician studying epigenetic and transcriptomic patterns across maize varieties. Class Photo <- Replace the file address to your actual class photo file location "],["module-1.html", "Module 1 Lecture Lab", " Module 1 Welcome to module 1! Lecture Here is an example of a pdf embedded: Here is an example of a YouTube video embedded: ^ HEIGHT HAS A BUG Downloads [insert your downloads for this module here (ex. datasets)] Lab [Your lab here] # Your R code here # For example: x <- 42 x ## [1] 42 # Your python code here # For example: print("hello world") ## hello world # Your bash code here # For example: pwd ## /Users/jqiu/Documents/CBWgithub/cbw-dev-templates-docs/bookdown-template Try running these code “chunks” by pressing the green (left-pointing) triangle next to your code chunks. You will see the code run in the console and the output provided below the code chunk. The output of the code will also be produced under the code chunk on your website page. "],["module-2.html", "Module 2 Lecture Lab", " Module 2 Lecture Lab NOTICE! TESTING CALLOUT BLOCKS "],["404.html", "Error 404: This page does not exist.", " Error 404: This page does not exist. This page does not exist anymore! Try going back to the workshop homepage or the bioinformatics.ca homepage. You must update these pages for new workshops. "]]