Merge jupyter_update

.gitignore

@@ -1,12 +1,7 @@
-# Conda environment
+# Conda environments
 *-env
 
-# Xaringan-related files
-**/*_files
-
 # Lecture-related files
-lectures/**/*.html
-# lectures/**/*.pdf
 lectures/*/*/remark-css-0.0.1/default.css
 lectures/*/*/header-attrs-2.3/header-attrs.js
 
@@ -22,10 +17,14 @@ jupyter/.ipynb_checkpoints
 **/intermediate
 **/results
 **/work
-rmarkdown/.R*
-rmarkdown/*html
-rmarkdown/*Rproj
 snakemake/*txt
 snakemake/*png
 snakemake/*tsv
-.Rproj.user
+
+# jupyter checkpoints
+.ipynb_checkpoints
+.idea
+
+# Quarto-related files
+.quarto/
+**/*_files

lectures/.gitignore

@@ -0,0 +1 @@
+/.quarto/

lectures/README.md

@@ -1,5 +1,9 @@
 # Lectures
 
+This directory contains all the course lectures, which were created using
+[Quarto](https://quarto.org/). The directory is set up as a Quarto project,
+so as to make rendering as simple as possible.
+
 ## Requirements
 
 Install the required packages using:
@@ -10,23 +14,20 @@ conda env create -f environment.yml
 
 ## Rendering
 
-Lectures in **Rmarkdown** format can be rendered using the following from
-the command line:
+Make sure your current directory is the `lectures/` directory and run the
+following command:
 
 ```bash
-Rscript -e 'rmarkdown::render(<Rmd-file>, "xaringan::moon_reader")'
+quarto render
 ```
 
-Lectures in **Jupyter notebook** format can be rendered using:
+## Render a single lecture
+
+To render only a single, specific lecture you can execute the following command:
 
 ```bash
-jupyter nbconvert --to slides --execute <.ipynb-file>
+quarto render <lecture>
 ```
 
-## Render everything
-
-To render all lectures you can use `snakemake`:
-
-```bash
-snakemake -j 1
-```
+For example, to render the Git lecture execute `quarto render git` while inside
+the `lectures/` directory.

lectures/_extensions/NBISweden/nbis/_extension.yml

@@ -0,0 +1,23 @@
+title: NBIS Quarto Extension
+author: Erik Fasterius
+version: 1.0.0
+quarto-required: ">=1.2.0"
+contributes:
+  formats:
+    html:
+      code-fold: true
+      df-print: paged
+      embed-resources: true
+      highlight-style: nbis.theme
+      smooth-scroll: true
+      theme: [default, nbis.scss]
+      toc-location: left
+      toc-title: nbis-logo-green.svg
+      toc: true
+    revealjs:
+      code-line-numbers: false
+      embed-resources: true
+      logo: nbis-logo-green.svg
+      slide-level: 2
+      slide-number: false
+      theme: [default, nbis.scss]

lectures/_extensions/NBISweden/nbis/nbis.scss

@@ -0,0 +1,198 @@
+/*-- scss:defaults --*/
+
+$theme: "nbis" !default;
+
+// NBIS base colours
+$green:  #92BB55 !default;
+$blue:   #0093BD !default;
+$orange: #EF7C00 !default;
+
+// NBIS light colours
+$lgreen:  #F8FFE5 !default;
+$lblue:   #E5F9FF !default;
+$lorange: #FFF2E5 !default;
+
+// Extra colours
+$red:    #BB5454 !default;
+$yellow: #BBBB54 !default;
+$purple: #AF75A7 !default;
+
+// Greyscale colours
+$white:    #FFFFFF !default;
+$grey-100: #F5F5F5 !default;
+$grey-90:  #E5E5E5 !default;
+$grey-80:  #CCCCCC !default;
+$grey-70:  #B2B2B2 !default;
+$grey-60:  #999999 !default;
+$grey-50:  #7F7F7F !default;
+$grey-40:  #666666 !default;
+$grey-30:  #4C4C4C !default;
+$grey-20:  #333333 !default;
+$grey-10:  #191919 !default;
+$black:    #000000 !default;
+
+// Theme
+$primary:   $green !default;
+$secondary: $blue !default;
+$light:     $grey-100 !default;
+$dark:      $grey-30 !default;
+$success:   $green !default;
+$info:      $purple !default;
+$warning:   $yellow !default;
+$danger:    $red !default;
+
+// Code
+$code-color:    $primary !default;
+$code-bg:       $light !default;
+$code-block-bg: $light !default;
+
+// Links
+$link-color: $primary !default;
+
+// Popover
+$popover:       $light !default;
+
+// Dropdowns
+$dropdown-link-color:       $grey-30 !default;
+$dropdown-link-hover-color: $white !default;
+$dropdown-link-hover-bg:    $primary !default;
+
+// Fonts
+$font-family-sans-serif: Lato, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol" !default;
+
+// Font size for headers
+$h1-font-size: 1.75rem !default;
+$h2-font-size: 1.50rem !default;
+$h3-font-size: 1.25rem !default;
+
+// Font size base for reveal.js presentations
+$presentation-font-size-root: 35px !default;
+
+// Tables
+$table-bg-scale: 0 !default;
+
+// Navs
+$nav-link-padding-y:      .5rem !default !default;
+$nav-link-padding-x:      2rem !default;
+$nav-link-disabled-color: $grey-40 !default !default;
+$nav-tabs-border-color:   $grey-80 !default;
+
+// Navbar
+$navbar-padding-y:               1rem !default;
+$navbar-light-bg:                $primary !default;
+$navbar-light-color:             $white !default;
+$navbar-light-hover-color:       $success !default;
+$navbar-light-active-color:      $success !default;
+$navbar-light-brand-color:       $white !default;
+$navbar-light-brand-hover-color: $navbar-light-brand-color !default;
+$navbar-dark-color:              $white !default;
+$navbar-dark-hover-color:        $primary !default;
+$navbar-dark-active-color:       $primary !default;
+$navbar-dark-brand-color:        $white !default;
+$navbar-dark-brand-hover-color:  $navbar-dark-brand-color !default;
+
+// Pagination
+$pagination-color:                 $white !default;
+$pagination-bg:                    $success !default;
+$pagination-border-width:          0 !default;
+$pagination-border-color:          transparent !default;
+$pagination-hover-color:           $white !default;
+$pagination-hover-bg:              darken($success, 15%) !default;
+$pagination-hover-border-color:    transparent !default;
+$pagination-active-bg:             $pagination-hover-bg !default;
+$pagination-active-border-color:   transparent !default;
+$pagination-disabled-color:        $grey-80 !default;
+$pagination-disabled-bg:           lighten($success, 15%) !default;
+$pagination-disabled-border-color: transparent !default;
+
+// List group
+$list-group-hover-bg:    $grey-80 !default;
+$list-group-disabled-bg: $grey-80 !default;
+
+// Close
+$btn-close-color:         $white !default;
+$btn-close-opacity:       .4 !default;
+$btn-close-hover-opacity: 1 !default;
+
+/*-- scss:rules --*/
+
+// Variables
+$web-font-path: "https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;1,400&display=swap" !default;
+@if $web-font-path {
+    @import url($web-font-path);
+}
+
+// Navbar
+.bg-primary {
+    .navbar-nav .show > .nav-link,
+    .navbar-nav .nav-link.active,
+    .navbar-nav .nav-link:hover,
+    .navbar-nav .nav-link:focus {
+        color: $success !important;
+    }
+}
+
+// Navs
+.nav-tabs {
+    .nav-link.active,
+    .nav-link.active:focus,
+    .nav-link.active:hover,
+    .nav-item.open .nav-link,
+    .nav-item.open .nav-link:focus,
+    .nav-item.open .nav-link:hover {
+        color: $primary;
+    }
+}
+
+// Pagination
+.pagination {
+    a:hover {
+        text-decoration: none;
+    }
+}
+
+// Blockquotes
+.reveal .slide blockquote {
+    color: $primary;
+    border-left-color: $primary;
+}
+
+// Cell Output
+.cell-output-error > pre > code {
+    color: $red;
+}
+.cell-output-stderr > pre > code {
+    color: $yellow;
+}
+
+// Horizontally center level 1 headers
+.center h1 {
+    text-align: center
+}
+
+// Text justification
+.justify-right {
+    text-align: right
+}
+.justify-center {
+    text-align: center
+}
+
+// Custom colours
+.green {
+    color: $green;
+    font-weight: bold;
+}
+.blue {
+    color: $blue;
+    font-weight: bold;
+}
+.light-grey {
+    color: $grey-60;
+}
+.grey {
+    color: $grey-40;
+}
+.dark-grey {
+    color: $grey-20;
+}