Software-Carpentry-Inspired Book: Released and On Sale!

What's On It?

The creature on the cover is the adorable and fascinating Bobtail Squid.

The Cover

In addition to being adorned by the bobtail squid, the book is emblazoned with the kind words of two of our mentors. First and foremost, upon handling the book, the reader will encounter a quotation from Fernando Perez on the back cover. Additionally, the first few pages contain a foreword by Greg Wilson. Anthony and I are humbled and proud to have the kind support of these two extraordinary individuals, without whom this book could not have existed. To read what they said, you'll have to get your hands on a book. All I'll say here is that both were kinder than we could have dreamed.

What's In It?

Since different scientists struggle in different ways at each stage of the research game, we wanted to cover the whole playbook of scientific computing best practices. Thus, we formed this book around the idea of a soup-to-nuts, idea-to-publication scientific research workflow, split into four parts:

Getting Started
Getting It Done
Getting It Right
Getting It Out There

Getting Started

Software Carpentry instructors, students, and community members will recognize the motivation to introduce basic features of the bash shell and Python before diving in. That's exactly what we do in this book as well, preparing the reader for some computational thinking using plenty of examples and exercises.

Chapter 1 - Introduction to the Command Line
Chapter 2 - Programming Blast Off with Python
Chapter 3 - Essential Containers
Chapter 4 - Flow Control and Logic
Chapter 5 - Operating with Functions
Chapter 6 - Classes and Objects

Getting it Done

Equipped with the basic concepts, the reader is now ready to build the software. This part focuses on the details of handling and analyzing data, key data structures, data storage, parallelization, and package deployment. We think of these skills as core to the generation of software in the physical sciences, so readers from other scientific disciplines may not find this part of the book as relevant to their work as the other parts.

Chapter 7 - Analysis and Visualization
Chapter 8 - Regular Expressions
Chapter 9 - NumPy: Thinking in Arrays
Chapter 10 - Storing Data: Files and HDF5
Chapter 11 - Important Data Structures in Physics
Chapter 12 - Performing in Parallel
Chapter 13 - Deploying Software

Getting It Right

In this part of the book, notions of reproducibility and defensive programming reign. These chapters make the case and provide a foundation for producing automated, version controlled, verified, and validated software.

Chapter 14 - Building Software Pipelines
Chapter 15 - Local Version Control
Chapter 16 - Remote Version Control
Chapter 17 - Debugging
Chapter 18 - Testing

Getting It Out There

Of course, science unshared is not science. Thus, we share tools for automating documentation and publication and have chapters focused on the people-related issues encountered in collaborative, open-source work.

Chapter 19 - Documentation
Chapter 20 - Publication
Chapter 21 - Collaboration
Chapter 22 - Licenses, Ownership, and Copyright
Chapter 23 - Further Musings on Computational Physics

Where To Get It

The book can be acquired in many ways. Through Safari Books Online, O'Reilly books are free for K-12 students. But, don't worry - even if high school is long past, you can still get a discount until July 17th using the discount code: WKPYDP on the O'Reilly website. The book can also be found on Amazon and in many other places where books are lent or sold. We hope you enjoy it and that you'll post a review or tweet us @physics_codes if you like it!