From ac473666f47889c1bf3e9c1a54e07c8d48bbe7e1 Mon Sep 17 00:00:00 2001
From: John Hodrien <J.H.Hodrien@leeds.ac.uk>
Date: Mon, 8 Dec 2025 09:55:41 +0000
Subject: [PATCH] Switch from Vagrant to Codespaces

This matches the changes that were made to the Aire arcdocs.
---
 .devcontainer/CODESPACE_WELCOME.md |  36 ++++++++++++++++++++
 .devcontainer/Dockerfile           |  20 +++++++++++
 .devcontainer/devcontainer.json    |  36 ++++++++++++++++++++
 .devcontainer/open_in_browser.png  | Bin 0 -> 7006 bytes
 .gitignore                         |   3 --
 README.md                          |  51 ++++++++++++++++-------------
 Vagrantfile                        |  10 ------
 vagrant/bootstrap.sh               |  18 ----------
 8 files changed, 120 insertions(+), 54 deletions(-)
 create mode 100644 .devcontainer/CODESPACE_WELCOME.md
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/devcontainer.json
 create mode 100644 .devcontainer/open_in_browser.png
 delete mode 100644 Vagrantfile
 delete mode 100755 vagrant/bootstrap.sh

diff --git a/.devcontainer/CODESPACE_WELCOME.md b/.devcontainer/CODESPACE_WELCOME.md
new file mode 100644
index 0000000..0c0c0a6
--- /dev/null
+++ b/.devcontainer/CODESPACE_WELCOME.md
@@ -0,0 +1,36 @@
+# Welcome to the HPC2 Codespace
+
+This codespace contains everything you need to build the HPC2 website.
+
+Hit `Ctrl + Shift + V` to view this as nicely rendered Markdown.
+
+Please read our [contributing guidelines](../CONTRIBUTING.md) and [readme file](../README.md) to ensure you follow good practice (e.g. no edits to the main branch).
+
+You can use `git` as you would locally, including pushing to the remote. You won't have to authenticate, as you're already logged in to GitHub.
+
+## Quick Start
+
+You should automatically have an open terminal with the prompt `(hpc2-jb) root@codespaces-e8c8b0:/workspace#`.
+If not, open a new terminal with `Ctrl + Shift + '`; this terminal should already have the [`hpc2-jb` conda environment](../environment.yml) activated.
+
+### 1. Build the documentation
+
+```bash
+jupyter-book build book/
+```
+
+### 2. Serve locally
+
+```bash
+python -m http.server -d book/_build/html
+```
+
+Then visit the forwarded port 8000 in your browser. VSCode should prompt you to do this with a popup, providing a URL for you to visit (the rmeote-machine equivalent of [localhost:8000](http://localhost:8000/welcome.html)):
+
+![alt text](open_in_browser.png)
+
+## Useful Commands
+
+- **Build book**: `jupyter-book build book/`
+- **Clean build**: `jupyter-book clean book/`
+- **Check links**: `jupyter-book build book/ --warningiserror --keep-going`
diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 0000000..6cba73d
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,20 @@
+# Use the official miniforge image as base
+FROM condaforge/miniforge3:latest
+
+# Set working directory
+WORKDIR /workspace
+
+# Copy environment file
+COPY environment.yml .
+
+# Create conda environment from environment.yml
+RUN mamba env create -f environment.yml
+
+# Make RUN commands use the new environment
+SHELL ["conda", "run", "-n", "hpc2-jb", "/bin/bash", "-c"]
+
+# Activate environment in bashrc for interactive sessions
+RUN echo "conda activate hpc2-jb" >> ~/.bashrc
+
+# Set default command to bash
+CMD ["/bin/bash"]
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..b7734d6
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,36 @@
+{
+    "name": "HPC2 Environment",
+    "dockerFile": "Dockerfile",
+    "context": "..",
+    
+    // Configure container
+    "workspaceMount": "source=${localWorkspaceFolder},target=/workspace,type=bind",
+    "workspaceFolder": "/workspace",
+    
+    // Forward ports for Jupyter Book development
+    "forwardPorts": [8000, 8080],
+    
+    // Install VS Code extensions
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-toolsai.jupyter",
+                "yzhang.markdown-all-in-one",
+                "davidanson.vscode-markdownlint"
+            ],
+            "settings": {
+                "files.defaultLanguage": "markdown"
+            }
+        },
+        // this won't work locally - see https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/configuring-dev-containers/automatically-opening-files-in-the-codespaces-for-a-repository
+        "codespaces": {
+            "openFiles": [
+            ".devcontainer/CODESPACE_WELCOME.md"
+            ]
+        }
+    },
+    
+    // Keep container running
+    "shutdownAction": "stopContainer"
+}
diff --git a/.devcontainer/open_in_browser.png b/.devcontainer/open_in_browser.png
new file mode 100644
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diff --git a/.gitignore b/.gitignore
index 64a663a..49f44b5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,3 @@
 
 # built book
 **/_build/*
-
-# vagrant stuff
-**/.vagrant/*
diff --git a/README.md b/README.md
index c3f41fc..e58194c 100644
--- a/README.md
+++ b/README.md
@@ -18,44 +18,49 @@ The current lesson format to follow as a guide:
 * Exercises
 * Key points
 
-## Contributing to this project
+## Contributing to the documentation
+We welcome all contributions to this project via GitHub issues and pull requests. Please follow the guidelines on the [`CONTRIBUTING.md` file](CONTRIBUTING.md) to make sure your contributions can be easily integrated in the project. Edits must be approved by at least one user from the arcdocs group (generally RSEs & RIEs at Leeds). For larger issues that can't be solved quickly, or require greater input, please raise an Issue in the "Issues" tab. 
 
-### Working with this project locally
+There are two main ways to update the documentation; via GitHub codespaces (recommended) or locally on your own machine.
 
-You will need to install the [conda package management tool](https://docs.conda.io/en/latest/) before you can get this project working locally.
-You can use the `environment.yml` file included to create a conda environment that contains all the dependencies required to get started.
+### Option 1: Working with this project via GitHub Codespaces
+
+GitHub's codespace feature provides a cloud-based development environment that you can run from the repository's main page. To get started, switch to a new branch, then under the "Code" dropdown menu, select "Codespaces", then "Create codespace on \<branch-name>". The codespace will then launch in a new window, and will be ready to use after a few minutes of setup.
+
+Instructions for using the codespace are in the [codespace readme file](.devcontainer/CODESPACE_WELCOME.md); this will open automatically when you build the codespace.
+
+### Option 2: Working with this project locally
+
+> **_NOTE:_**  This documentation is based on jupyter-book, which does not support Windows. If you are working on a Windows machine, you are recommended to use Windows Subsystem for Linux 2 (WSL2).
+
+In a shell with git and conda available (we recommend Miniforge):
 
 ```{bash}
-$ git clone https://github.com/ARCTraining/template-jb-docs.git
 
+# clone repository and navigate to root
+$ git clone https://github.com/ARCTraining/hpc2-software.git
+$ cd hpc2-software
+
+# create environment
 $ conda env create -f environment.yml
 ```
 
 To build the html content locally 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/
-```
-### Windows
+# activate the conda environment 
+$ conda activate hpc2-jb
 
-Jupyterbook now supports [Windows](https://jupyterbook.org/en/stable/advanced/windows.html) so the above steps can also be used on a Windows terminal.
+# build book
+$ jupyter-book build book/
 
-#### Set up a development environment using Vagrant
 
-To aid with this we have created a `Vagrantfile` that can allow Windows users who have a virtualisation provider installed (such as [VirtualBox](https://www.virtualbox.org/)) and [Vagrant](https://www.vagrantup.com/) installed to create a headless virtual Linux machine that will build the jupyter book. You can do this with the following steps once you've installed a virtualisation provider and vagrant:
+# if necessary, old files can be removed by running:
+$ jupyter-book clean book/
 ```
-# within git-bash or powershell
-$ cd template-jb-docs
-$ vagrant up
 
-# to rebuild the site after changes with the vagrant box running
-$ vagrant reload --provision
+To preview the built html locally, you can open up a basic Python server:
 
-# don't forget to destroy the box when you're done
-$ vagrant destroy
+```bash
+python -m http.server -d book/_build/html
 ```
-
-This will build the jupyter-book html files on your Windows file system (by navigating via /vagrant) so your local build will still persist after you've destroyed your vagrant box.
diff --git a/Vagrantfile b/Vagrantfile
deleted file mode 100644
index 039f741..0000000
--- a/Vagrantfile
+++ /dev/null
@@ -1,10 +0,0 @@
-# -*- mode: ruby -*-
-# vi: set ft=ruby :
-
-Vagrant.configure("2") do |config|
-  config.vm.box = "hashicorp/bionic64"
-
-  config.vm.hostname = "arcdocsSite"
-
-  config.vm.provision :shell, path: "vagrant/bootstrap.sh"
-end
diff --git a/vagrant/bootstrap.sh b/vagrant/bootstrap.sh
deleted file mode 100755
index ff593cb..0000000
--- a/vagrant/bootstrap.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-apt-get update
-apt-get install git
-wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-chmod +x miniconda.sh
-./miniconda.sh -b -p /home/vagrant/miniconda
-# ensures conda loaded in shell
-echo "source /home/vagrant/miniconda/etc/profile.d/conda.sh" >> /home/vagrant/.bashrc
-source /home/vagrant/miniconda/etc/profile.d/conda.sh
-chown -R vagrant:vagrant /home/vagrant/miniconda
-
-# create environment and build book
-cd /vagrant
-conda env create -f environment.yml
-conda activate arcdocs-jb
-jb clean book/
-jb build book/