Book Skeleton

The aim of this file is iterate/decide on:

A list of chapters
The scope of each chapter
The order of the chapters

Update from January Sprint

Completed Chapters

Version Control - @r-j-arnold
Open Research - @r-j-arnold
Reproducibility - @pherterich

WIP

Testing for research - @r-j-arnold and @annakrystalli
Continuous integration - @r-j-arnold and @annakrystalli
Reproducible Compute Environment - @r-j-arnold and @annakrystalli
Research Data Management - @pherterich and @rosiehigman

Needed

Collaborating (through Github/Gitlab) - @pherterich and @rosiehigman
Case studies - @LouiseABowler
Checklist - @annakrystalli and @KirstieJane

Desired

Working Environment and notebooks - @LouiseABowler & @sgibson91
Coding Styles and Linting - @r-j-arnold
Deep Learning
Ethics
Credit for Reproducible Research
Scoping a data project - RSEs
Similarities and differences across data science disciplines
Visualisation

Ideas from the November Sprint

Why do reproducbile research

For yourself
For everyone else

Git & Version Control

Version Control - what is it and why use it. (Or xx_final_Final.docx is version control, but you can do better.)
Your first project using Git
Accessing previous versions of your code
Branches and Merging
Semantic Versioning - Tags and releases (and how that fits in with trad publishing DOIs)

Collaborating throught Github

Commenting and documenting projects
How to write a good README
How to write good commit messages
Anatomy of a github repo
Using Pull requests
How to use cloud-based tools to power-up your repo (e.g. cloud-based CI see below)

Testing for research

Why should you test your code?
What is a good test
End-to-end testing vs. Unit Testing & other types.

Data Management

Documenting Data
Open (FAIR) Standards

Reproducible Compute Environments

Packaging code for re-use (containers)
Managing Dependences
Continuous Integration (and available tools)
Random Seeds & Dealing with Stochastic simulations (e.g. due to floating point errors)
Reproducible Research for HPC Projects

Getting Credit for Reproducible Research

Licensing For re-use

Definition of Reproducibility

How does reproducibility overlap with Open

Reproducible as a team

Roles in a reproducible project
Maintaining reproducibility as a group

Barriers to Reproducibility

A reproducible paper

Your Working Environment

Introduction to the command line
Alternatives to the Command Line
Interactive Development Environments
Jupyter Notebooks (and common issues)

Ethics

Dealing with Sensitive Data
Getting Consent for Data Sharing
Ethics Approbal @ the Turing

Scoping a data project

What makes a good data science project