Bas training 2026

.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

exercises/dependencies_exercises.qmd

@@ -39,9 +39,7 @@ https://docs.xarray.dev/en/stable/getting-started-guide/installing.html
 - lapack library
 - blas library
 - sqlite
-- curl
 - glibc
-- gcc/gfortran
 - mpdecimal
 - libffi
 - ...

exercises/problem/climate_model.py

@@ -0,0 +1,15 @@
+solar_constant = 1370
+sigma = 5.67e-8 # Stefan-Boltzmann constant
+
+def absorbed_solar_radiation(albedo):
+    return solar_constant*(1-albedo)/4
+
+def emitted_radiation(emissivity, temperature):
+    return emissivity * sigma * temperature**4
+
+def energy_balanced_temperature(emissivity, albedo):
+    # dT/dt = 0 => in = out
+    return (solar_constant*(1-albedo)/(4*emissivity * sigma))**0.25
+
+def emissivity_given_temp(albedo, temperature):
+    return solar_constant*(1-albedo)/(4*sigma*temperature**4)

exercises/problem/plot4.py

@@ -0,0 +1,25 @@
+import climate_model
+
+import xarray
+import matplotlib.pyplot as plt
+
+global_ds = xarray.open_dataset("../data/HadCRUT.5.0.0.0_analysis_summary-series_global_annual.nc")
+
+fig, axs = plt.subplots(1, 1, figsize=(10,6), layout='constrained')
+
+# Absolute mean temperature between 1961 and 1990
+# https://crudata.uea.ac.uk/cru/data/temperature/abs_glnhsh.txt
+absolute_value = 13.974 + 273.5
+time = global_ds['time'].data
+temperature = global_ds['tas_mean'].data + absolute_value
+albedo = 0.3
+
+epsilon = climate_model.emissivity_given_temp(albedo, temperature)
+
+axs.plot(time, epsilon)
+
+axs.set_xlabel("Year")
+axs.set_ylabel("Effective emissivity of Earth")
+
+plt.show()
+

exercises/testing_exercises.qmd

@@ -0,0 +1,13 @@
+## Exercises
+
+In the example repository, there is a file called 'climate_model.py'.
+This file contains some functions that are used in 'plot4.py'
+
+Task:
+
+1. Write some basic tests for these functions (think about inputs that give known
+   outputs)
+2. Think about what properties/behaviours these functions should have, and write
+   tests for them
+3. Look at the other python files, and see if any functions can be extracted and
+   tested

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)';
+  }
+}
+
+};