Initial commit

.github/workflows/deploy-book.yml

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+# copied from https://jupyterbook.org/publish/gh-pages.html?highlight=github%20pages
+
+name: deploy-book
+
+# Only run this when the master branch changes
+on:
+  push:
+    branches:
+    - main
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        environment-file: environment.yml
+        auto-activate-base: false
+        activate-environment: arcdocs-jb
+
+    # Build the book
+    - name: Build the book
+      shell: bash -l {0}
+      run: |
+        conda activate arcdocs-jb
+        jupyter-book build ./book/
+    # Push the book's HTML to master branch (because this is an organisation homepage)
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./book/_build/html
+        publish_branch: gh-pages

.github/workflows/test-build.yml

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+# copied from https://jupyterbook.org/publish/gh-pages.html?highlight=github%20pages
+
+name: test-build
+
+# Only run this when a PR suggests changes to main branch
+on:
+  pull_request:
+    branches:
+      - main
+
+# This job installs dependencies and builds the book
+jobs:
+  deploy-book:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      # test build on multiple OS
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        environment-file: environment.yml
+        auto-activate-base: false
+        activate-environment: arcdocs-jb
+
+    # Build the book
+    - name: Build the book
+      shell: bash -l {0}
+      run: |
+        conda activate arcdocs-jb
+        jupyter-book build ./book/
+

.gitignore

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+# gitignore for template-jb-docs
+
+# built book
+**/_build/*
+
+# vagrant stuff
+**/.vagrant/*

CODE_OF_CONDUCT.md

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+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [email protected].
+
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

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+# Contributing to the template jupyter book docs repository
+
+:tada: **Welcome to the template jupyter book docs GitHub repository!** :tada:
+
+_Thank you for wanting to contribute to this project!_
+
+We hope that this guideline document will make it as easy as possible for you to get involved.
+
+We welcome all contributions to this project via GitHub issues and pull requests.
+Please follow these guidelines to make sure your contributions can be easily integrated in the project.
+
+If you have any questions that aren't discussed below, please let us know through one of the many ways to [get in touch](#get-in-touch).
+
+## Pull Request Process
+
+1. Ensure the site builds fully on your local system within the conda environment provided
+2. Your pull request will be test built locally by one of the maintainers
+3. Any Continuous Integration steps must complete successfully
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Get in touch
+
+You can get in touch with the Research Computing Team at Leeds via the following channels:
+- Open an [issue](https://github.com/ARCTraining/template-jb-docs/issues)
+- Email the Research Computing Team via [[email protected]](mailto:[email protected])
+

README.md

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+# A template jupyter book documentation repository
+
+This is a template repository that can be used when generating documentation using [Jupyter-books](https://github.com/executablebooks/jupyter-book) and hosting the site via GitHub pages.
+
+## Working with this project locally
+
+You can get this project working locally by using the environment.yml file to create a conda environment that contains all the dependencies required to get started.
+
+```{bash}
+$ 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:
+
+```{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
+
+Jupyterbook now supports [Windows](https://jupyterbook.org/en/stable/advanced/windows.html) although the steps for configuring a development environment using Vagrant are available below:
+
+#### 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:
+```
+# 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
+
+# don't forget to destroy the box when you're done
+$ vagrant destroy
+```
+
+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.

Vagrantfile

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+# -*- 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

book/_config.yml

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+# Book settings
+title: Template documentation jupyter book
+author: University of Leeds Research Computing Team
+logo: ./assets/img/logo/logo.png
+email: [email protected]
+copyright: "2020"
+
+# execute settings
+execute:
+  execute_notebooks: auto
+
+# HTML-specific settings
+html:
+  favicon                   : "./assets/img/logo/favicon-32x32.png"  # A path to a favicon image
+  navbar_number_sections    : False  # Add a number to each section in your left navbar
+  google_analytics_id       : ""  # A GA id that can be used to track book views.
+  home_page_in_navbar       : true  # Whether to include your home page in the left Navigation Bar
+  use_repository_button: true
+  use_issues_button: true
+  use_edit_page_button: true
+  baseurl                   : "https://arctraining.github.io/template-jb-docs"  # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/
+  navbar_footer_text        :
+    'Visit the <a href="https://arcleeds.github.io/">Research Computing Home Site</a>
+    <div>
+    This book is powered by <a href="https://jupyterbook.org">Jupyter Book</a>
+    </div>'  # Will be displayed underneath the left navbar.
+
+
+# Launch button settings
+launch_buttons:
+  notebook_interface        : "classic"  # The interface interactive links will activate ["classic", "jupyterlab"]
+  binderhub_url             : "https://mybinder.org"  # The URL of the BinderHub (e.g., https://mybinder.org)
+  jupyterhub_url            : ""  # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu)
+  thebelab                  : false  # Add a thebelab button to pages (requires the repository to run on Binder)
+
+repository:
+  url                       : https://github.com/ARCTraining/template-jb-docs  # The URL to your book's repository
+  path_to_book              : "book/"  # A path to your book's folder, relative to the repository root.
+  branch                    : gh-pages  # Which branch of the repository should be used when creating links
+
+
+latex:
+  latex_documents:
+    targetname: leedsarcdocs.tex

book/_toc.yml

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+# these comments are borrowed from https://github.com/alan-turing-institute/the-turing-way/blob/master/book/website/_toc.yml
+# Each entry has the following schema:
+#
+# - title: mytitle   # Title of chapter or subchapter
+#   file: myfile  # filename relative to the  folder.
+#   sections:  # Contains a list of more entries that make up the chapter's subchapters
+#
+# Below are some special values that trigger specific behavior:
+# - header: My Header  # Will insert a header with no link in the sidebar
+
+# ===== Main Landing Page ========================================
+- file: welcome
+
+# ===== Getting started ==========================================
+- file: example_section/start
+  sections:
+    - file: example_section/example

book/example_section/example.md

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+# Foo
+
+Bar bar foo foo 

book/example_section/start.md

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+# Example section

book/welcome.md

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+# Welcome
+
+Welcome to a template Documentation site for the [Research Computing Team](https://arcleeds.github.io) at the [University of Leeds](https://www.leeds.ac.uk).

environment.yml

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+name: arcdocs-jb
+channels:
+  - defaults
+dependencies:
+  - python=3.7.6
+  - jinja2=3.0.3
+  - pip=20
+  - pip:
+    - jupyter-book==0.9.1

vagrant/bootstrap.sh

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+#!/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/