JupyterCon Tutorial 2020

• Website: https://jupytercon.com/
• Location: Online
• Date: 5-9 October 2020

Title: Creating a Jupyter Book with The Turing Way

• Subtitle: Create a Jupyter Book from scratch using chapters from The Turing Way on Reproducible Research.
• Duration: 2 - 4h (based on familarity)
• Audience level: Novice programmers/Intermediate GitHub users
• Prerequisite: previous experience with version control, GitHub, Markdown, Jupyter Notebooks, basic commands of bash and basic Pathon
• Tutorial files: This tutorial is organised in 7 short modules that are developed in Jupyter Notebooks and paired with introductory videos.
  • Please visit the notebooks directory to find the tutorial files (named module-wise).
  • All the introductory videos are available in this YouTube playlist (named and ordered module-wise) and the slides used in those presentations are provided in the presentation directory.

Description

Short Description:

Jupyter Book is an open source project for building publication-ready online books with computational files. The Turing Way is a community-led book project on learning computational skills, which is hosted online as a Jupyter Book. In this tutorial, you will learn about the collaborative nature of both projects and create your own Jupyter Book using files and chapters from The Turing Way as examples.

Session detail:

The topics and activities to be covered in this workshop are the following:

• We will start by introducing The Turing Way and Jupyter Book.
• The session leads will present The Turing Way as a community-developed book project on research reproducibility, project design, communication, collaboration and ethics.
• A demo of The Turing Way's GitHub repository will explain how a Jupyter book is created and how they are hosted online.
• A hands-on session will be carried out to create a Jupyter Book using The Turing Way chapters as examples.
• We will explain what Continuous Integration (CI) is and how to deploy CI tests using GitHub Actions.
• We will show the collaborative workflow of Jupyter Book that allows GitHub based contributions by the users of the book.
• The session will end with sharing details on how participants can gain further support when working with Jupyter Books and The Turing Way.

Learning outcomes

In this tutorial, our learners will:

• Get introduced to The Turing Way and Jupyter Book projects as reproducible and collaborative platforms for community-developed computational resources.
• Learn how to create and structure a Jupyter Book using example chapters from The Turing Way.
• Configure and personalise their Jupyter Book locally and connect it to an online GitHub repository.
• Learn how Jupyter Notebooks can be used as chapters and executed using Binder.
• Learn what Continuous Integration (CI) and Continuous Deployment (CD) are and how to use them with GitHub Actions.
• Get introduced to Sphinx-based features in Jupyter Book for citing external resources and cross-referencing its chapters.

Instructor details

• Name: Malvika Sharan

  • Title: Dr.
  • Organization: The Turing Way, The Alan Turing Institute, London, UK
  • Biography: Malvika is the community manager of The Turing Way at The Alan Turing Institute, UK. She works with its community of diverse members to develop resources and ways that can make data science accessible for a wider audience. Malvika has a PhD in Bioinformatics and she worked at European Molecular Biology Laboratory, Germany, that helped her solidify her values as an Open Researcher and community builder. She is a co-founder of the Open Life Science mentoring program, a fellow of the Software Sustainability Institute and a board member of Open Bioinformatics Foundation, where she focuses on training resources and fellowship programs to enhance the training, skill building and representation of marginalised groups in data science and bioinformatics.
  • Photo: LINK

• Name: Martina G. Vilas

  • Title: Ms.
  • Organization: Max Plank Institute for Empirical Aesthetics, Frankfurt, Germany
  • Biography: Martina is currently working at the Max-Planck-Institute AE, where she is conducting her research in cognitive neuroscience using computational modeling techniques. She is an open-science advocate who enjoys programming and contributing to open-source projects and communities. As a core contributor and maintainer, she provides infrastructure support for The Turing Way project.
  • Photo: LINK

• Name: Sarah Gibson

  • Title: Dr
  • Organization: The Alan Turing Institute, London, UK
  • Biography: Sarah is a Research Software Engineer at The Alan Turing Institute, UK where she implements software best practices to translate academic research into real world solutions through the Turing’s collaborative network. As a maintainer and operator of the Binder project, she operates a BinderHub cluster at the Turing. Sarah is a Software Sustainability Institute Fellow where she focuses on nurturing and diversifying the Binder community. She is also a core contributor of The Turing Way project.
  • Photo: LINK

Project Leads and video contributors for module 2

• The Turing Way: Kirstie Whitaker, head of the Tools, Practices, and Systems research programme, The Alan Turing Institute, UK.
• Jupyter Book: Chris Holdgraf, member of Project Jupyter and Binder, co-founder of The International Interactive Computing Collaboration (2i2c), USA.