ARCTraining · jhodrien · Nov 4, 2025 · Nov 4, 2025 · Dec 5, 2025 · Nov 4, 2025
diff --git a/.github/workflows/deploy-book.yml b/.github/workflows/deploy-book.yml
@@ -19,7 +19,7 @@ jobs:
         environment-file: environment.yml
         auto-activate-base: false
         activate-environment: arcdocs-jb
-        python-version: 3.9
+        python-version: 3.14
 
     # Build the book
     - name: Build the book

diff --git a/.github/workflows/test-build.yml b/.github/workflows/test-build.yml
@@ -19,7 +19,7 @@ jobs:
         environment-file: environment.yml
         auto-activate-base: false
         activate-environment: arcdocs-jb
-        python-version: 3.9
+        python-version: 3.14
 
     # Build the book
     - name: Build the book

diff --git a/README.md b/README.md
@@ -31,13 +31,12 @@ $ git clone https://github.com/ARCTraining/template-jb-docs.git
 $ conda env create -f environment.yml
 ```
 
-To build the html content locally you can use the `jupyter-book` command line tool:
+To build the html content locally and serve on http://localhost:3000 you can use the `jupyter-book` command line tool:
 
 ```{bash}
 # navigate to the repository root
-$ cd template-jb-docs
-# sometimes worth running jupyter-book clean book/ to remove old files
-$ jupyter-book build book/
+$ cd book
+$ jupyter-book start
 ```
 ### Windows
 

diff --git a/book/_config.yml b/book/_config.yml
diff --git a/book/_toc.yml b/book/_toc.yml
diff --git a/book/course/conda.md b/book/course/conda.md
@@ -4,7 +4,7 @@ Content from this lesson has been inspired and adapted from a number of sources
 - [Conda documentation](https://docs.conda.io/en/latest/)
 - [Carpentries Incubator: Introduction to Conda for data scientists](https://carpentries-incubator.github.io/introduction-to-conda-for-data-scientists/)
 
-(introduction)=
+(intro)=
 ## Introduction
 
 Conda is an open source package management and environment management system that runs on multiple operating systems (Windows, Linux, macOS). Its features include:
@@ -450,7 +450,7 @@ We've discovered we also need the `statsmodels` package for some extra work we w
 
 ````{admonition} Searching for packages
 
-Conda has a command-line search functionality that we describe below in the section [Use Conda to search for a package](#searching-for-packages); you can also use the [`conda-forge` repository](https://anaconda.org/conda-forge) or [`bioconda` repository](https://anaconda.org/bioconda) to search for packages.
+Conda has a command-line search functionality that we describe below in the section [Using Conda to search for a package](searching-for-packages); you can also use the [`conda-forge` repository](https://anaconda.org/conda-forge) or [`bioconda` repository](https://anaconda.org/bioconda) to search for packages.
 ````
 
 Once you have the name (and possibly version) of the package you want to install, again there are two different ways to add these packages, much like there were two ways to create the environment to begin with.
@@ -459,7 +459,7 @@ Once you have the name (and possibly version) of the package you want to install
 
 You can add new packages directly from the command line using the `install` subcommand with the format `conda install PACKAGE`, where `PACKAGE` is the name of the package you wish to install.
 
-To install packages into an existing environment we need to activate it with the [subcommand shown above](activating-environments).
+To install packages into an existing environment we need to activate it with the [subcommand shown above](#activating-environments).
 
 ```bash
 $ conda activate data-sci-env
@@ -614,7 +614,7 @@ The `--prune` argument here clears out old unused libraries and is key to keepin
 ### Removing a Conda environment
 
 It is also possible to delete a Conda environment through the `remove` subcommand.
-This [command is outlined below](removing-packages) in relation to removing specific packages but can also be used to delete an entire Conda environment.
+This [command is outlined below](#removing-packages) in relation to removing specific packages but can also be used to delete an entire Conda environment.
 
 To remove the `py39-env` we created earlier we use the command:
 
@@ -1494,19 +1494,19 @@ Again, this can also be easily done by updating our `environment.yaml` file to c
 
 ```{important}
 
-- [Introduces Conda](introduction) as a cross-platform package and environment manager
-- Highlights options for [how to install Conda](installing-conda)
+- [Introduces Conda](#intro) as a cross-platform package and environment manager
+- Highlights options for [how to install Conda](#installing-conda)
 - Introduces Conda environments for separating specific package dependencies on a project-by-project basis
-  - How to [create an environment using Conda](creating-environments)
-  - How to use a created Conda environment through [environment activation](activating-environments)
-  - Leaving an environment through [deactivation](deactivating-environments)
-  - [Listing available Conda environments](listing-current-environments)
-  - [Deleting Conda environments](removing-a-conda-environment)
-  - [Exporting and sharing Conda Environments](sharing-conda-environments)
+  - How to [create an environment using Conda](#creating-environments)
+  - How to use a created Conda environment through [environment activation](#activating-environments)
+  - Leaving an environment through [deactivation](#deactivating-environments)
+  - [Listing available Conda environments](#listing-current-environments)
+  - [Deleting Conda environments](#removing-a-conda-environment)
+  - [Exporting and sharing Conda Environments](#sharing-conda-environments)
 - Shows how Conda can be used for managing packages
-  - Using Conda to [search Conda repositories for a package](searching-for-packages)
-  - Using Conda to [install a package](installing-packages)
-  - Using Conda to [remove a package](removing-packages)
-  - Using Conda to [update a package](updating-a-package)
+  - Using Conda to [search Conda repositories for a package](#searching-for-packages)
+  - Using Conda to [install a package](#installing-packages)
+  - Using Conda to [remove a package](#removing-packages)
+  - Using Conda to [update a package](#updating-a-package)
 
 ```
diff --git a/book/course/containers.md b/book/course/containers.md
@@ -319,25 +319,25 @@ You can now experiment inside this sandbox to work out what you need for your re
 ## Summary
 
 ```{important}
-- [What are containers](containers:what)?
-- [Why do I want a container](containers:why)?
-- [Can I use Docker on HPC](containers:docker-hpc)?
-- [Singularity vs Apptainer](containers:singularity-vs-apptainer)
-- [Example of running a container](containers:example) and a look into the steps involved:
-    - [Pulling a container image down from Docker Hub](containers:pulling-from-docker)
-    - [Converting it into a SIF image](containers:converting-to-sif)
-    - [Running software within a container](containers:running-within)
+- [What are containers](#containers:what)?
+- [Why do I want a container](#containers:why)?
+- [Can I use Docker on HPC](#containers:docker-hpc)?
+- [Singularity vs Apptainer](#containers:singularity-vs-apptainer)
+- [Example of running a container](#containers:example) and a look into the steps involved:
+    - [Pulling a container image down from Docker Hub](#containers:pulling-from-docker)
+    - [Converting it into a SIF image](#containers:converting-to-sif)
+    - [Running software within a container](#containers:running-within)
 - What else can I do with containers?
-  - [Access host storage within a container](containers:host-storage)
-  - [Run an alternative command within a container](containers:run-alternative-command)
-  - [Have an interactive shell inside the container](containers:shell)
-  - [Use GPUs within a container](containers:gpu)
+  - [Access host storage within a container](#containers:host-storage)
+  - [Run an alternative command within a container](#containers:run-alternative-command)
+  - [Have an interactive shell inside the container](#containers:shell)
+  - [Use GPUs within a container](#containers:gpu)
 - Building a container
-  - [Creating a recipe](containers:recipe)
-  - [Converting a Dockerfile to a Singularity recipe](containers:convert-from-dockerfile)
-  - [Generate a SIF image from a recipe](containers:generate-sif)
-  - [Test the image we've created](containers:test)
-- [Submitting jobs with containers](containers:submit-job)
+  - [Creating a recipe](#containers:recipe)
+  - [Converting a Dockerfile to a Singularity recipe](#containers:convert-from-dockerfile)
+  - [Generate a SIF image from a recipe](#containers:generate-sif)
+  - [Test the image we've created](#containers:test)
+- [Submitting jobs with containers](#containers:submit-job)
 - Bonus section
-  - [Sandboxes](containers:sandbox)
+  - [Sandboxes](#containers:sandbox)
 ```
diff --git a/book/course/spack.md b/book/course/spack.md
@@ -9,13 +9,13 @@ I'll introduce Spack by quoting the first paragraph of their documentation:
 > specific microarchitectures.
 
 So what does this mean in practice?  You've already learnt about build systems
-like [Autotools](autotools) and [CMake](cmake), and may be familiar with
+like [Autotools](./autotools) and [CMake](./cmake), and may be familiar with
 [module systems](https://arcdocs.leeds.ac.uk/aire/software/start.html#modules)
 as used on Aire.  You may also have worked through the section on
-[containers](containers) and wondered if there was an easier way of building a
+[containers](./containers) and wondered if there was an easier way of building a
 potentially deep stack of software for a particular project.
 
-You may have already tried [Conda](conda) and found it wonderful, but for the
+You may have already tried [Conda](./conda) and found it wonderful, but for the
 fact that the piece of software you want isn't built with the options you
 wanted, so you can't use it.  Or maybe you just can't make the conda installed
 version work with the MPI setup on the HPC cluster you're using.