diff --git a/030-module-2.Rmd b/030-module-2.Rmd index 398e2fe..561c932 100644 --- a/030-module-2.Rmd +++ b/030-module-2.Rmd @@ -4,10 +4,25 @@ ## Lab -put some example of producing images, show chunk options + -```{r, pressure-plot, echo=FALSE}, -plot(pressure) -``` +:::: {.blackbox data-latex=""} +::: {.center data-latex=""} +**NOTICE!** +::: -- include formatting options +TESTING CALLOUT BLOCKS +:::: + + + + + + + + + + + + + diff --git a/docs/404.html b/docs/404.html index 9103560..c9c442b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Error 404: This page does not exist. | [Name of Workshop][Year] - + diff --git a/docs/_main.epub b/docs/_main.epub index 51cb00d..6011f83 100644 Binary files a/docs/_main.epub and b/docs/_main.epub differ diff --git a/docs/_main.pdf b/docs/_main.pdf index aba1952..ed575e2 100644 Binary files a/docs/_main.pdf and b/docs/_main.pdf differ diff --git a/docs/_main.tex b/docs/_main.tex index 7a580f7..28999c4 100644 --- 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 index efb1822..58755c6 100644 --- a/docs/course-schedule.html +++ b/docs/course-schedule.html @@ -6,7 +6,7 @@ Course Schedule | [Name of Workshop][Year] - + diff --git a/docs/index.html b/docs/index.html index 6295723..c98017f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@ [Name of Workshop][Year] - + diff --git a/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js b/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js index e743148..a70f0fb 100644 --- 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 index ba5267b..cbfa0b8 100644 --- a/docs/module-1.html +++ b/docs/module-1.html @@ -6,7 +6,7 @@ Module 1 | [Name of Workshop][Year] - + diff --git a/docs/module-2.html b/docs/module-2.html index 4978c24..5f59c50 100644 --- a/docs/module-2.html +++ b/docs/module-2.html @@ -6,7 +6,7 @@ Module 2 | [Name of Workshop][Year] - + @@ -201,11 +201,20 @@

Lecture

Lab

-

put some example of producing images, show chunk options

-

{r, pressure-plot, echo=FALSE}, plot(pressure)

- + +
+
+

NOTICE!

+
+

TESTING CALLOUT BLOCKS

+
+ + + + + + + diff --git a/docs/search_index.json b/docs/search_index.json index 7a55023..aa0d11f 100644 --- 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 & 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 — support@bioinformatics.ca 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 — nia.hughes@oicr.on.ca 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 — support@bioinformatics.ca 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 — nia.hughes@oicr.on.ca 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. "]] diff --git a/docs/style.css b/docs/style.css index b71f90a..e9e3ca6 100644 --- 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 index dfd2e14..9197d9b 100644 --- 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 index b71f90a..e9e3ca6 100644 --- 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*/