diff --git a/docs/lectures/README.md b/docs/lectures/README.md
deleted file mode 100644
index 2cd669839d4efad84250dcf0aabc9ed6360d36bd..0000000000000000000000000000000000000000
--- a/docs/lectures/README.md
+++ /dev/null
@@ -1,48 +0,0 @@
-# Lectures
-
-## Requirements
-
-Install the required packages using:
-
-```bash
-conda env create -f environment.yml
-```
-
-## Rendering in html
-
-Lectures in **Rmarkdown** format can be rendered using the following from
-the command line:
-
-```bash
-Rscript -e 'rmarkdown::render("<Rmd-file>", "xaringan::moon_reader")'
-```
-
-Lectures in **Jupyter notebook** format can be rendered using:
-
-```bash
-jupyter nbconvert <.ipynb-file> --to slides --debug --allow-chromium-download
-```
-
-## Rendering in pdf
-
-Lectures in **Rmarkdown** format can be rendered using the following from
-the command line:
-
-```bash
-Rscript -e 'library(webshot); webshot("<Rmd-file>", "<pdf-file-output>")'
-```
-
-Lectures in **Jupyter notebook** format can be rendered using:
-
-```bash
-jupyter nbconvert <.ipynb-file> --to webpdf --debug --allow-chromium-download
-```
-
-
-## Render everything
-
-To render all lectures you can use `snakemake`:
-
-```bash
-snakemake -j 1
-```
diff --git a/docs/lectures/Snakefile b/docs/lectures/Snakefile
deleted file mode 100644
index 338ce41326107046ad47fc33ff0062ef4f6e257b..0000000000000000000000000000000000000000
--- a/docs/lectures/Snakefile
+++ /dev/null
@@ -1,55 +0,0 @@
-# A snakefile used to render all lectures in one go
-
-from glob import glob
-import os.path as path
-
-rmd_files = glob("*/*.Rmd")
-ipy_files = glob("*/*.ipynb")
-
-ruleorder: render_jupyter_pdf > render_pdf
-
-rule all:
- input:
- ["{}.html".format(path.splitext(x)[0]) for x in rmd_files + ipy_files],
- ["{}.pdf".format(path.splitext(x)[0]) for x in rmd_files + ipy_files]
-
-rule render_rmarkdown:
- input:
- "{f}.Rmd"
- output:
- "{f}.html"
- shell:
- """
- Rscript -e 'rmarkdown::render("{input}", "xaringan::moon_reader")'
- """
-
-rule render_pdf:
- input:
- "{f}.html"
- output:
- "{f}.pdf"
- shell:
- """
- Rscript -e 'library(webshot); webshot("{input[0]}", "{output[0]}")'
- """
-
-rule render_jupyter:
- input:
- "{f}.ipynb"
- output:
- "{f}.html"
- shell:
- """
- jupyter nbconvert --to slides --execute {input}
- mv {wildcards.f}.slides.html {output}
- """
-
-rule render_jupyter_pdf:
- input:
- "{f}.ipynb"
- output:
- "{f}.pdf"
- shell:
- """
- jupyter nbconvert --to webpdf {input} --allow-chromium-download
- """
diff --git a/docs/lectures/environment.yml b/docs/lectures/environment.yml
deleted file mode 100644
index 1a7ff761210c340ea860a93ccd3f6acec864de7f..0000000000000000000000000000000000000000
--- a/docs/lectures/environment.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-# conda env create -f environment.yml
-
-name: lecture-env
-channels:
- - r
- - conda-forge
- - bioconda
- - defaults
-dependencies:
-
- # Snakemake
- - snakemake-minimal=6.0.5
-
- # Jupyter
- - python=3.8
- - numpy<1.20
- - jupyter=1.0
- - pandas=1.0
- - jupyter_contrib_nbextensions=0.5.1
- - nbconvert=6.1.0
- - rise=5.6
- - seaborn=0.10
- - rpy2=3.1
- - pyppeteer=0.2.2
- - jinja2<=3.0.3
-
- # R and Xaringan
- - phantomjs=2.1.1
- - r-base=3.6.3
- - r-ggplot2=3.3.3
- - r-kableextra=1.1.0
- - r-palmerpenguins=0.1.0
- - r-stringi=1.4.6
- - r-tidyr=0.8.3
- - r-xaringan=0.15
- - r-webshot=0.5.2
diff --git a/docs/lectures/git/git.Rmd b/docs/lectures/git/git.Rmd
deleted file mode 100644
index 7551207631e7ca6351700d162c068d702c295268..0000000000000000000000000000000000000000
--- a/docs/lectures/git/git.Rmd
+++ /dev/null
@@ -1,132 +0,0 @@
----
-title: "Version control with Git"
-subtitle: "Tools for Reproducible Research NBIS course"
-output:
- xaringan::moon_reader:
- self-contained: true
- seal: false
- css: ["default", "../template.css"]
- nature:
- slideNumberFormat: ""
----
-
-layout: true
-<div class="ird-logo"></div>
-<div class="mivegec-logo"></div>
-
----
-
-class: center, middle
-
-*Version control with*
-
-<img src="https://git-scm.com/images/logos/downloads/Git-Logo-2Color.png" style="width:50%;"/>
-
----
-
-# What is Git?
-
---
-
-* A widely used system for distributed .green[version control]
-
---
-
-* Keeps a .green[complete history] of the changes you make to your files
-
---
-
-* Each point in the history can be re-visited and compared with others
-
---
-
-* Git tracks .green[who contributed what] to your code
-
---
-
-* Git can help you .green[version, backup and share] your code and documents
-
---
-
-* Kind of like Dropbox, but you decide when each version is saved (plus a lot
- of more advanced features)
-
---
-
-* Git is mainly used for .green[text files], not large or binary files
-
----
-
-# Git nomenclature
-
---
-
-* A .green[repository] is a collection that encompasses all the files and
- directories of a project
-
---
-
-* A .green[commit] is a snapshot of a repository's history, *i.e.* a point
- in development time
-
---
-
-* Development can be separated into .green[branches], allowing for concurrent
- work on the same repository with simple transitions between functional and
- work-in-progress code
-
---
-
-* Uploading changes to a remote repository is called .green[pushing], while
- downloading changes is called .green[pulling]
-
----
-
-# Tracking code in three steps
-
-<br>
-<center>
-<img src="git_overview_local.png" style="width:50%"/>
-</center>
-<br>
-
---
-
-1. Do some .green[coding] (*i.e.* add or change contents of files)
-
---
-
-2. .green[Stage] the changes (*i.e.* specify which changes should be stored)
-
---
-
-3. .green[Commit] the changes (storing them in the repository's history)
-
----
-
-# Git is highly versatile
-
-* Ensures .green[reproducibility] of your analyses, regardless of whether you’ve
- made additional changes to your code after the analysis is run
-
---
-
-* Easily .green[fix mistakes] by reverting files to previous versions
-
---
-
-* Improves your coding by giving you .green[additional structure]
-
---
-
-* Your code has a .green[backup] in your remote repository
-
---
-
-* Easily .green[share your code] and collaborate with your colleagues
-
----
-
-class: center, middle
-
-# Questions?
diff --git a/docs/lectures/git/git.html b/docs/lectures/git/git.html
deleted file mode 100644
index 7c1cd0f16a94e17bc9b834a5dafbf9fddc519aaf..0000000000000000000000000000000000000000
--- a/docs/lectures/git/git.html
+++ /dev/null
@@ -1,246 +0,0 @@
-<!DOCTYPE html>
-<html lang="" xml:lang="">
- <head>
- <title>Version control with Git</title>
- <meta charset="utf-8" />
- <link href="git_files/remark-css-0.0.1/default.css" rel="stylesheet" />
- <link rel="stylesheet" href="../template.css" type="text/css" />
- </head>
- <body>
- <textarea id="source">
-
-
-layout: true
-<div class="ird-logo"></div>
-<div class="mivegec-logo"></div>
-
----
-
-class: center, middle
-
-*Version control with*
-
-<img src="https://git-scm.com/images/logos/downloads/Git-Logo-2Color.png" style="width:50%;"/>
-
----
-
-# What is Git?
-
---
-
-* A widely used system for distributed .green[version control]
-
---
-
-* Keeps a .green[complete history] of the changes you make to your files
-
---
-
-* Each point in the history can be re-visited and compared with others
-
---
-
-* Git tracks .green[who contributed what] to your code
-
---
-
-* Git can help you .green[version, backup and share] your code and documents
-
---
-
-* Kind of like Dropbox, but you decide when each version is saved (plus a lot
- of more advanced features)
-
---
-
-* Git is mainly used for .green[text files], not large or binary files
-
----
-
-# Git nomenclature
-
---
-
-* A .green[repository] is a collection that encompasses all the files and
- directories of a project
-
---
-
-* A .green[commit] is a snapshot of a repository's history, *i.e.* a point
- in development time
-
---
-
-* Development can be separated into .green[branches], allowing for concurrent
- work on the same repository with simple transitions between functional and
- work-in-progress code
-
---
-
-* Uploading changes to a remote repository is called .green[pushing], while
- downloading changes is called .green[pulling]
-
----
-
-# Tracking code in three steps
-
-<br>
-<center>
-<img src="git_overview_local.png" style="width:50%"/>
-</center>
-<br>
-
---
-
-1. Do some .green[coding] (*i.e.* add or change contents of files)
-
---
-
-2. .green[Stage] the changes (*i.e.* specify which changes should be stored)
-
---
-
-3. .green[Commit] the changes (storing them in the repository's history)
-
----
-
-# Git is highly versatile
-
-* Ensures .green[reproducibility] of your analyses, regardless of whether you’ve
- made additional changes to your code after the analysis is run
-
---
-
-* Easily .green[fix mistakes] by reverting files to previous versions
-
---
-
-* Improves your coding by giving you .green[additional structure]
-
---
-
-* Your code has a .green[backup] in your remote repository
-
---
-
-* Easily .green[share your code] and collaborate with your colleagues
-
----
-
-class: center, middle
-
-# Questions?
- </textarea>
-<style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
-<script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
-<script>var slideshow = remark.create({
-"slideNumberFormat": ""
-});
-if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
- window.dispatchEvent(new Event('resize'));
-});
-(function(d) {
- var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
- if (!r) return;
- s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
- d.head.appendChild(s);
-})(document);
-
-(function(d) {
- var el = d.getElementsByClassName("remark-slides-area");
- if (!el) return;
- var slide, slides = slideshow.getSlides(), els = el[0].children;
- for (var i = 1; i < slides.length; i++) {
- slide = slides[i];
- if (slide.properties.continued === "true" || slide.properties.count === "false") {
- els[i - 1].className += ' has-continuation';
- }
- }
- var s = d.createElement("style");
- s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
- d.head.appendChild(s);
-})(document);
-// delete the temporary CSS (for displaying all slides initially) when the user
-// starts to view slides
-(function() {
- var deleted = false;
- slideshow.on('beforeShowSlide', function(slide) {
- if (deleted) return;
- var sheets = document.styleSheets, node;
- for (var i = 0; i < sheets.length; i++) {
- node = sheets[i].ownerNode;
- if (node.dataset["target"] !== "print-only") continue;
- node.parentNode.removeChild(node);
- }
- deleted = true;
- });
-})();
-(function() {
- "use strict"
- /* Replace <script> tags in slides area to make them executable
- *
- * Runs after post-processing of markdown source into slides and replaces only
- * <script>s on the last slide of continued slides using the .has-continuation
- * class added by xaringan. Finally, any <script>s in the slides area that
- * aren't executed are commented out.
- */
- var scripts = document.querySelectorAll(
- '.remark-slides-area .remark-slide-container:not(.has-continuation) script'
- );
- if (!scripts.length) return;
- for (var i = 0; i < scripts.length; i++) {
- var s = document.createElement('script');
- var code = document.createTextNode(scripts[i].textContent);
- s.appendChild(code);
- scripts[i].parentElement.replaceChild(s, scripts[i]);
- }
- var scriptsNotExecuted = document.querySelectorAll(
- '.remark-slides-area .remark-slide-container.has-continuation script'
- );
- if (!scriptsNotExecuted.length) return;
- for (var i = 0; i < scriptsNotExecuted.length; i++) {
- var comment = document.createComment(scriptsNotExecuted[i].outerHTML)
- scriptsNotExecuted[i].parentElement.replaceChild(comment, scriptsNotExecuted[i])
- }
-})();
-(function() {
- var links = document.getElementsByTagName('a');
- for (var i = 0; i < links.length; i++) {
- if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
- links[i].target = '_blank';
- }
- }
-})();</script>
-
-<script>
-slideshow._releaseMath = function(el) {
- var i, text, code, codes = el.getElementsByTagName('code');
- for (i = 0; i < codes.length;) {
- code = codes[i];
- if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
- text = code.textContent;
- if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
- /^\$\$(.|\s)+\$\$$/.test(text) ||
- /^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
- code.outerHTML = code.innerHTML; // remove <code></code>
- continue;
- }
- }
- i++;
- }
-};
-slideshow._releaseMath(document);
-</script>
-<!-- dynamically load mathjax for compatibility with self-contained -->
-<script>
-(function () {
- var script = document.createElement('script');
- script.type = 'text/javascript';
- script.src = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
- if (location.protocol !== 'file:' && /^https?:/.test(script.src))
- script.src = script.src.replace(/^https?:/, '');
- document.getElementsByTagName('head')[0].appendChild(script);
-})();
-</script>
- </body>
-</html>
diff --git a/docs/lectures/git/git.pdf b/docs/lectures/git/git.pdf
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similarity index 100%
rename from docs/lectures/pptx/git_2023.pdf
rename to docs/lectures/git_2023.pdf
diff --git a/docs/lectures/pptx/git_2023.pptx b/docs/lectures/git_2023.pptx
similarity index 100%
rename from docs/lectures/pptx/git_2023.pptx
rename to docs/lectures/git_2023.pptx
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diff --git a/docs/lectures/images/reproducibility-overview.png b/docs/lectures/images/reproducibility-overview.png
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diff --git a/docs/lectures/template.css b/docs/lectures/template.css
deleted file mode 100644
index ee9501b04b7db504fa15c24d657af287e38008f4..0000000000000000000000000000000000000000
--- a/docs/lectures/template.css
+++ /dev/null
@@ -1,125 +0,0 @@
-/* CSS style general NBIS presentations using Xaringen and RMarkdown */
-
-/* Import Google font */
-@import url('https://fonts.googleapis.com/css?family=Open+Sans&display=swap');
-
-/* Fonts */
-body,p,h1,h2,h3,h4,h5,h6 {
- font-family: 'Open Sans', sans-serif;
- font-weight: 400;
- font-size: 20px;
- color: #333333;
-}
-
-/* Header 1 font size */
-h1 {
- font-size: 1.7em !important;
-}
-
-/* Header 2 font size */
-h2 {
- font-size: 1.2em !important;
-}
-
-/* Header 3 font size */
-h3 {
- font-size: 0.9em !important;
-}
-
-/* Custom font sizes */
-.micro { font-size: 25% }
-.tiny { font-size: 50% }
-.small { font-size: 75% }
-.large { font-size: 125% }
-.huge { font-size: 150% }
-.Huge { font-size: 200% }
-.HUGE { font-size: 250% }
-
-.remark-code { font-size: 50% }
-
-/* Custom colours */
-.green { color: #85be42; font-weight: bold }
-.dark-green { color: #487a2d; font-weight: bold }
-.blue { color: #0099c2; font-weight: bold }
-.dark-blue { color: #015491; font-weight: bold }
-.light-grey { color: #999999 }
-.grey { color: #666666 }
-.dark-grey { color: #333333 }
-
-/* Set the maximum figure size to 100% of the slide */
-img, video, iframe {
- max-width: 100%;
- max-height: 100%;
-}
-
-table_rot {
- color: black;
- text-transform: uppercase;
- @include transform(rotate(270deg))
- @include transform-origin(0 0);
-}
-
-/* SciLifeLab logo in bottom left corner */
-div.ird-logo {
- content: "";
- background-image: url("images/IRD.png");
- background-repeat: no-repeat;
- background-size: contain;
- position: absolute;
- bottom: 0px;
- left: 15px;
- height: 70px;
- width: 200px;
-}
-
-/* logo in bottom right corner */
-div.mivegec-logo {
- content: "";
- background-image: url("images/MIVEGEC.png");
- background-repeat: no-repeat;
- background-size: contain;
- position: absolute;
- bottom: 20px;
- right: -70px;
- height: 70px;
- width: 200px;
-}
-
-
-/* Blockquotes */
-blockquote {
- border-left: 5px solid #85be42;
- background: #f9f9f9;
- font-style: italic;
- padding: 0.01em;
- padding-left: 12px;
- padding-right: 12px;
- margin-left: 12px;
- margin-right: 12px;
- border-radius: 0 5px 5px 0;
-}
-
-/* Link colour */
-a {
- color: #85be42;
- text-decoration: none;
-}
-
-/* Underline links when hovering */
-a:hover {
- text-decoration: underline;
-}
-
-/* Inline code color and border */
-.remark-inline-code {
- background: #f2f2f2;
- border-radius: 3px;
- margin-right: 2px;
- padding: 2px 3px 1px;
- font-size: 80% !important;
-}
-
-.image-with-text {
- display: inline-block;
- vertical-align: middle;
-}