Cambridge-ICCS · jackdfranklin · Jul 17, 2026 · Jul 13, 2026 · Jul 14, 2026 · Jul 14, 2026
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -18,6 +18,13 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Setup python env
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+          cache: `pip`
+        run: pip install -r requirements.txt
+
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
 

diff --git a/exercises/dependencies_exercises.qmd b/exercises/dependencies_exercises.qmd
@@ -2,13 +2,61 @@
 
 Returning to the Python scripts, try to answer the following questions:
 
-1. What are the python dependencies? 
-2. What are the system dependencies?
-3. What are the data dependencies?
+::: {.panel-tabset}
+
+### What are the python dependencies?
+
+:::: {.columns}
+
+::::: {.incremental .column width=40%}
+  - `xarray`
+  - `matplotlib`
+  - `numpy`
+  - `netcdf4` / `h5netcdf`!
+:::::
+
+::::: {.fragment .column width=60%}
+The last dependency is tricky, because it is not required by `xarray`, unless you
+want to read/write `netcdf` files!
+If we include the dependecies of the dependencies, the list is even longer!
+```
+ValueError: found the following matches with the input file in xarray's IO backends: ['netcdf4', 'h5netcdf']. But their dependencies may not be installed, see:
+https://docs.xarray.dev/en/stable/user-guide/io.html
+https://docs.xarray.dev/en/stable/getting-started-guide/installing.html
+```
+:::::
+
+::::
+
+:::: {.fragment}
+
+::::
+
+### What are the system dependencies?
+
+- python3
+- netcdf
+- lapack library
+- blas library
+- sqlite
+- curl
+- glibc
+- gcc/gfortran
+- mpdecimal
+- libffi
+- ...
+
+### What are the data dependencies?
+
+- HadCRUT 5.0.0, specifically:
+  - `HadCRUT.5.0.0.0_analysis_summary-series_global_annual.nc`
+  - `HadCRUT.5.0.0.0_analysis_summary-series_northern-hemisphere_annual.nc`
+  - `HadCRUT.5.0.0.0_analysis_summary-series_southern-hemisphere_annual.nc`
+  - `HadCRUT.5.0.0.0_analysis_summary-series_global_monthly.nc`
 
 ### Extension
 
-Using your favourite dependency management tool (e.g. Conda, Nix), create a
+1. Using your favourite dependency management tool (e.g. Conda, Nix), create a
 reproducible environment configuration to handle the python and system dependencies.
-
-Create a way to automatically fetch the data dependencies when using the scripts.
+2. Create a way to automatically fetch the data dependencies when using the scripts.
+:::
diff --git a/exercises/version_control_exercises.qmd b/exercises/version_control_exercises.qmd
@@ -12,5 +12,5 @@ Specifically in the directory `exercises/problem`.
 Tasks:
 
 1. Download the Python scripts from the GitHub repository
-2. Create a new git repository on your local machine
-3. Add the Python scripts to git for version control!
+2. Create a new `git` repository on your local machine
+3. Add the Python scripts to `git` for version control!
diff --git a/flake.nix b/flake.nix
@@ -0,0 +1,14 @@
+{
+  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; };
+        }
+      );
+}
diff --git a/shell.nix b/shell.nix
@@ -0,0 +1,14 @@
+{ pkgs ? import <nixpkgs> { } }:
+pkgs.mkShell {
+  packages = [
+    pkgs.quarto
+    (pkgs.python3.withPackages (python-pkgs: with python-pkgs; [
+      # select Python packages here
+      pandas
+      numpy
+      matplotlib
+      jupyter
+      jupyter-cache
+    ]))
+  ];
+}
diff --git a/src/dependencies.qmd b/src/dependencies.qmd
@@ -2,56 +2,69 @@
 
 ## Dependencies
 
+\
+
 - All software has dependencies
 - Some are more obvious than others:
   - Data/input
-  - Packages/libraries e.g. numpy, Eigen
+  - Packages/libraries e.g. `numpy`, `Eigen`
   - System libraries
   - Compiler/Interpreter
 - If your code can't run without it, it's a dependency!
 
 ## How to discover dependencies
 
+\
+
 - Some dependencies may be "implicit"
 - For example, you may have a library installed on your system
 - Since the code "just works", you may not be aware of the dependency
 - To find these, try running on a different system (or multiple) and see what breaks
 
 ## How to declare dependencies
 
+\
+
 - List them in a tracked file in the repository
   - e.g. add a "Dependencies" section to your README.md
 - Specify:
-  - Versions of each dependency e.g. numpy 2.3.9
+  - Versions of each dependency e.g. `numpy` 2.3.9
   - Where/how to aquire the dependency
 
 ## How to declare data dependencies
 
+\
+
 :::{.columns}
-:::{.column width="30%"}
+:::{.column width="60%"}
 - Links to publicly accessible data dependencies
   - Zenodo or some other long term solution
 - Reference specific versions of the data
+  - Use DOI from hosting platform
 - Ideally automate the fetching of the data
 :::
-:::{.column width="70%"}
-![Example of a zenodo listing. Note how each version of the dataset has a different reference](img/zenodo.jpg)
+:::{.column width="40%"}
+![Example of a zenodo listing. Note how each version of the dataset has a different reference](img/zenodo.png)
 :::
 :::
 
 ## Dependency metadata
 
+\
+
 - There are automated ways of resolving dependencies
 - Usually language/tool specific
 - Some tools automatically update dependency metadata
-  - e.g. Rust's cargo, Julia's Pkg, uv for Python
+  - e.g. Rust's `cargo`, Julia's `Pkg`, `uv` for Python
   - Project file: Depencies and compatible versions
   - Lock file: Write exact version (plus other metadata e.g. source) of *every* 
     dependency you are using
   - Important to track both - lock files record the exact environment you use
 
 ## System dependencies - Conda
 
+\
+
 - Python centric package manager
 - Can be used for installing python packages
 - Also able to manage environments
@@ -60,9 +73,12 @@
   - even different python versions!
 - Available on most HPC systems (usually as Miniconda)
 - Can export environments to text-based files
+- There are other alternatives, e.g. `pixi`, but `conda` is most available
 
 ## System dependencies - Containers
 
+\
+
 :::{.columns}
 :::{.column width="60%"}
 - Containers package up code and all dependencies
@@ -83,13 +99,15 @@
 
 ## System dependencies - Nix/Guix
 
+\
+
 :::{.columns}
 :::{.column width="60%"}
-What they have in common:
 
 - Declarative package managers
 - Use pure functional languages to create environments
   - same inputs = same outputs
+  - Useful for caching artifacts 
 - Packages are hashed
   - can lookup if package already exists locally
 - Publicly hosted and *versioned* package repository

diff --git a/src/documentation.qmd b/src/documentation.qmd
@@ -9,11 +9,23 @@
 
 ## README
 
+:::{.columns}
+
+::::{.column width=50%}
+
+&nbsp;
+
 - Markdown file at the project root
 - Should contain:
   - Description of project
   - Dependencies
   - Instructions on building/running
+::::
+
+::::{.column width=50%}
+![](img/ftorch-readme.png)
+::::
+:::
 
 ## Comments
 
@@ -28,3 +40,12 @@
 - Single source of truth
 - Comments/Docstrings embedded in code
 - Reduce separation between code and docs
+
+## Licences
+
+- Licences are necessary for reproducibility!
+- They define how code can be used/reused
+- Enforce openness of code and data
+  - FOSS licenses eg. GPL, MIT, BSD, etc
+- Many explanations of which licence to use exist (and I'm not a lawyer!)
+- [choosealicense.com](https://choosealicense.com/)
diff --git a/src/figs/perception.csv b/src/figs/perception.csv
@@ -0,0 +1,5 @@
+question,strongly disagree,disagree,rather disagree,don't know,rather agree,agree,strongly agree
+Most published science in my field is reproducible,8,29,24,2,24,11,3
+Reproducibility is a major problem in my field,4,15,20,2,16,29,15
+A lack of reproducibility is jepoardizing the trust in our results,6,13,20,2,24,27,10
+My own scientific work is reproducible,1,6,11,2,27,38,15
diff --git a/src/figs/reasons.csv b/src/figs/reasons.csv
@@ -0,0 +1,7 @@
+question,strongly disagree,disagree,rather disagree,don't know,rather agree,agree,strongly agree
+Workflow is poorly documented, 2, 6, 12, 3, 26, 34, 17
+Code is poorly documented, 2, 6, 11, 5, 24, 33, 19
+Code is too complex, 4, 11, 20, 6, 25, 22, 11
+Input data is not available, 3, 7, 13, 2, 16, 32, 27
+Code is not available, 2, 8, 12, 3, 20, 27, 28
+Code is written in a language I don't know, 10, 17, 21, 7, 17, 18, 10
diff --git a/src/img/ftorch-readme.png b/src/img/ftorch-readme.png
diff --git a/src/img/reprohack-hub.png b/src/img/reprohack-hub.png
diff --git a/src/img/zenodo.jpg b/src/img/zenodo.jpg
diff --git a/src/img/zenodo.png b/src/img/zenodo.png