Expand on version control section

.github/workflows/deploy.yml

@@ -17,6 +17,8 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
+        with:
+          submodules: 'true'
 
       - uses: actions/setup-python@v6
         with:

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "src/Summer-school-Intro-Git"]
+	path = src/Summer-school-Intro-Git
+	url = git@github.com:Cambridge-ICCS/Summer-school-Intro-Git.git

flake.nix

@@ -1,14 +1,40 @@
 {
   description = "Reproducibility in Scientific Software environment";
-
-  inputs.flake-utils.url = "github:numtide/flake-utils";
-
-  outputs = { self, nixpkgs, flake-utils }:
-    flake-utils.lib.eachDefaultSystem
-      (system:
-        let pkgs = nixpkgs.legacyPackages.${system}; in
-        {
-          devShells.default = import ./shell.nix { inherit pkgs; };
-        }
-      );
+  inputs = {
+    nixpkgs.url = "github:Nixos/nixpkgs/nixos-unstable";
+  };
+  outputs = { self, nixpkgs }:
+    let
+      system = "x86_64-linux";
+      pkgs = nixpkgs.legacyPackages.${system};
+      myPythonPackages = ps: with ps; [ 
+        pandas
+        numpy
+        matplotlib
+        jupyter
+        jupyter-cache
+      ];
+      pythonEnv = pkgs.python3.withPackages myPythonPackages;
+    in
+    {
+      devShells.${system}.default = pkgs.mkShell {
+        packages = [
+          ((pkgs.quarto.override {
+            extraPythonPackages = myPythonPackages;
+          }).overrideAttrs (oldAttrs: {
+            # Remove this overrideAttrs patch when fixed.
+            # See https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454
+            postPatch = (oldAttrs.postPatch or "") + ''
+              substituteInPlace bin/quarto.js \
+                --replace-fail "syntax-highlighting" "highlight-style"
+            '';
+          }))
+          pythonEnv
+        ];
+        shellHook = ''
+          echo "Quarto Environment Active (Pure Flake)"
+          echo "Quickstart: run 'quarto render document.qmd'"
+        '';
+      };
+    };
 }

src/_extensions/quarto-ext/attribution/_extension.yml

@@ -0,0 +1,14 @@
+title: Attribution
+author:  Roland Schmehl
+version: 0.1.1
+quarto-required: ">=1.2.198"
+contributes:
+  revealjs-plugins:
+    - name: RevealAttribution
+      script:
+        - attribution.js
+      stylesheet:
+        - attribution.css
+
+
+

src/_extensions/quarto-ext/attribution/attribution.css

@@ -0,0 +1,19 @@
+/* Attribution plugin: text along the right edge of the viewport */
+.attribution{
+  position: absolute;
+  top: 50%;
+  bottom: auto;
+  left: 50%;
+  right: auto;
+  font-size: 0.4em;
+  pointer-events: none;
+  text-align: center;
+  writing-mode: vertical-lr;
+  transform: translate( -50%, -50% ) scale( 100% ) rotate(-180deg);
+  text-orientation: sideways;
+}
+
+/* Attribution plugin: activate pointer events for attribution text only */
+.attribution .content{
+  pointer-events: auto;
+}

src/_extensions/quarto-ext/attribution/attribution.js

@@ -0,0 +1,75 @@
+/*****************************************************************
+** Author: Roland Schmehl, r.schmehl@tudelft.nl
+**
+** A plugin for displaying attribution texts sideways along the right
+** edge of the viewport. When resizing the viewport or toggling full
+** screen mode, the attribution text sticks persistently to the right
+** edge of the viewport.
+**
+** The dynamic scaling of the attribution text via CSS transform
+** is adopted from the fullscreen plugin.
+**
+** Version: 1.0
+**
+** License: MIT license (see file LICENSE)
+**
+******************************************************************/
+
+window.RevealAttribution = window.RevealAttribution || {
+  id: 'RevealAttribution',
+  init: function(deck) {
+      initAttribution(deck);
+  }
+};
+
+const initAttribution = function(Reveal){
+
+var ready = false;
+var resize = false;
+var scale = 1;
+
+window.addEventListener( 'ready', function( event ) {
+
+  var content;
+
+  // Remove configured margin of the presentation
+  var attribution = document.getElementsByClassName("attribution");
+  var width = window.innerWidth;
+  var configuredWidth = Reveal.getConfig().width;
+  var configuredHeight = Reveal.getConfig().height;
+
+  scale = 1/(1-Reveal.getConfig().margin);
+
+  for (var i = 0; i < attribution.length; i++) {
+    content = attribution[i].innerHTML;
+    attribution[i].style.width = configuredWidth + "px";
+    attribution[i].style.height = configuredHeight + "px";
+    attribution[i].innerHTML = "<span class='content'>" + content + "</span>";
+    attribution[i].style.transform = 'translate( -50%, -50% ) scale( ' + scale*100 + '% ) rotate(-180deg)';
+  }
+
+  // Scale with cover class to mimic backgroundSize cover
+  resizeCover();
+
+});
+
+window.addEventListener( 'resize', resizeCover );
+
+function resizeCover() {
+
+  // Scale to mimic backgroundSize cover
+  var attribution = document.getElementsByClassName("attribution");
+  var xScale = window.innerWidth / Reveal.getConfig().width;
+  var yScale = window.innerHeight / Reveal.getConfig().height;
+  var s = 1;
+
+  if (xScale > yScale) {
+      // The div fits perfectly in x axis, stretched in y
+      s = xScale/yScale;
+  }
+  for (var i = 0; i < attribution.length; i++) {
+    attribution[i].style.transform = 'translate( -50%, -50% ) scale( ' + s*scale*100 + '% ) rotate(-180deg)';
+  }
+}
+
+};

src/custom.scss

@@ -1,9 +1,106 @@
 /*-- scss:defaults --*/
 
-$presentation-font-size-root: 1.5em;
-$presentation-line-height: 1.5em;
+// FONTS
+@import url('https://fonts.googleapis.com/css2?family=Montserrat:wght@500;600;700&display=swap');
 
-ul {
+$presentation-heading-font: 'Montserrat', sans-serif;
+
+$accent: #0c4e8a;
+/*-- scss:rules --*/
+
+// Title and headings styling
+#title-slide {
+  text-align: center;
+
+  .title {
+    font-family: $presentation-heading-font;
+    font-weight: 400;
+    font-size: 2.5em;
+    color: #0c4e8a;
+  }
+
+  .subtitle {
+    color: $accent;
+    font-style: italic;
+  }
+
+  .author,
+  .quarto-title-author-name {
+    color: $body-color;
+    font-size: 1.2em;
+  }
+
+  .quarto-title-authors {
+    display: flex;
+    justify-content: center;
+    flex-direction: row; // Ensure horizontal layout
+    flex-wrap: wrap;
+    gap: 2em; // Space between authors
+    // display: flex;
+    // flex-direction: row;
+    // flex-wrap: wrap;
+
+    .quarto-title-author {
+      padding-left: 0em;
+      padding-right: 0em;
+      width: auto; // Allow variable width based on content
+      max-width: 30%; // Limit width so multiple fit on one row
+      flex: 0 0 auto; // Don't grow or shrink
+    }
+  }
+
+  .institute,
+  .quarto-title-affiliation,
+  .quarto-title-author-email {
+    font-style: italic;
+    font-size: 80%;
+    // color: #fffafa;
+  }
+
+  .date {
+    font-weight: 400; // Set your desired font weight (100-900)
+    font-size: 1em;   // Optionally adjust the size
+    color: $body-color; // Use the default text color or set your own
+    margin-top: 1em;  // Add some space above the date
+  }
+
+
+}
+
+// Control heading size and weight for non-title slides
+.reveal h1:not(#title-slide h1) {
+  font-size: 2.0em;
+  font-weight: 600;
+}
+
+.reveal h2:not(#title-slide h2) {
+  font-size: 1.7em;
+  font-weight: 550;
+}
+
+.reveal h3:not(#title-slide h3) {
+  font-size: 1.3em;
+  font-weight: 500;
+}
+
+/*-- vertically center columns (or any container) --*/
+.v-center-container {
   display: flex;
+  justify-content: center;
   align-items: center;
+  height: 90%;
+}
+
+/*-- Get rid of column margins - quarto revealjs has strange behaviour --*/
+.reveal .columns> {
+
+  .column,
+  .column:last-child {
+
+    > :not(ul, ol) {
+
+      margin-left: 0em;
+      margin-right: 0em;
+    }
+  }
 }

src/dependencies.qmd

@@ -44,7 +44,7 @@
 - Ideally automate the fetching of the data
 :::
 :::{.column width="40%"}
-![Example of a zenodo listing. Note how each version of the dataset has a different reference](img/zenodo.png)
+![Example of a zenodo listing. Note how each version of the dataset has a different reference](images/zenodo.png)
 :::
 :::
 
@@ -91,9 +91,9 @@
 - Portable and cross-platform
 :::
 :::{.column width="40%"}
-![](img/docker-logo-ocean-blue.svg)
-![](img/apptainer.svg)
-![](img/podman-logo-source.svg)
+![](images/docker-logo-ocean-blue.svg)
+![](images/apptainer.svg)
+![](images/podman-logo-source.svg)
 :::
 :::
 

src/documentation.qmd

@@ -23,7 +23,7 @@
 ::::
 
 ::::{.column width=50%}
-![](img/ftorch-readme.png)
+![](images/ftorch-readme.png)
 ::::
 :::