Merge pull request #252 from NBISweden/devel

Merge `devel` into `main`

.github/workflows/docker-slim.yml

@@ -17,16 +17,16 @@ jobs:
       nbisweden/workshop-reproducible-research:slim
     strategy:
       matrix:
-        env: [ snakemake, nextflow, jupyter, rmarkdown ]
+        env: [ snakemake, nextflow, jupyter, quarto ]
         include:
           - env: snakemake
             cmd: snakemake -c 1 -d tutorials/snakemake/ -s tutorials/snakemake/snakefile_mrsa.smk
           - env: nextflow
             cmd: cd tutorials/nextflow && nextflow run main_mrsa.nf
           - env: jupyter
             cmd: jupyter nbconvert --to HTML tutorials/jupyter/supplementary_material.ipynb
-          - env: rmarkdown
-            cmd: mamba install --force-reinstall -y pandoc && cd tutorials/rmarkdown && echo 'rmarkdown::render("code/supplementary_material.Rmd", output_file="supplementary.html")' | R --vanilla
+          - env: quarto
+            cmd: mamba install -c conda-forge quarto && mamba install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html
     steps:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2.2.0

.github/workflows/setup.yml

@@ -15,16 +15,16 @@ jobs:
     strategy:
       matrix:
         os: [ macos-latest, ubuntu-latest ]
-        env: [snakemake, nextflow, jupyter, rmarkdown]
+        env: [snakemake, nextflow, jupyter, quarto]
         include:
           - env: snakemake
             cmd: snakemake -c 1 -d tutorials/snakemake/ -s tutorials/snakemake/snakefile_mrsa.smk
           - env: nextflow
             cmd: cd tutorials/nextflow && nextflow run main_mrsa.nf
           - env: jupyter
             cmd: jupyter nbconvert --to HTML tutorials/jupyter/supplementary_material.ipynb
-          - env: rmarkdown
-            cmd: cd tutorials/rmarkdown && echo 'rmarkdown::render("code/supplementary_material.Rmd", output_file="supplementary.html")' | R --vanilla
+          - env: quarto
+            cmd: mamba install -c conda-forge quarto && mamba install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html
     steps:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2.2.0
@@ -39,4 +39,4 @@ jobs:
         shell: bash -l {0}
         run: |
           conda list
-          ${{ matrix.cmd }}
+          ${{ matrix.cmd }}

.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]