Introduction

The Problem

• Most research software engineers are self-taught programmers
• Often have gaps in their knowledge
• One of those gaps is software design
• A large program is more than just a dozen small programs

Comprehension

• Experts understand lower and higher abstraction levels than novices
• Preferred level shifts right with experience
  • Code that is optimal for one reader may not be optimal for another
• Most programming language features and programming practices exist to manage complexity

How to Learn Design

• Best way to learn design is from examples (Petre2016]
• These lessons use small versions of common research problems
  • Generally accessible to people who are programming
  • Introduce some fundamental ideas in computer science

Scenario

• Years ago, logging companies dumped toxic waste in a remote region of Vancouver Island
• As the containers leaked and the pollution spread, some of the tree snails in the region began growing unusually large
• Your team is going to collect and analyze specimens from affected regions to determine if a mutant gene makes snails more susceptible to the pollution
• Your task is to build a synthetic data generator [Alexander2023] so that the data scientists can start building and validating analysis pipelines

Who You Are

• Maya has a master's degree in genomics
  • Knows enough Python to analyze data from her experiments
  • Struggling to write code other people can use
• These lessons will teach her how to design, build, and test large programs in less time and with less pain

What You Already Know

• Write Python programs using lists, loops, conditionals, dictionaries, and functions
• Puzzle through Python programs that use classes and decorators
• Comfortable using the Unix command line (cd, ls, mv)
• Read and write a little bit of HTML
• Use Git to save and share files (add, commit, push, pull, log)

Details

• Written material: [Creative Commons - Attribution - NonCommercial][cc_by_nc] license
• Code: [Hippocratic License][hippocratic_license]
• Source available in [Git repository][lesson_repo]
• Can all be read [online][lesson_site]

The Author

[Greg Wilson][third_bit] has worked in industry and academia for 40 years, and is the author, co-author, or editor of over a dozen previous books. He was the co-founder and first Executive Director of [Software Carpentry][carpentries] and received ACM SIGSOFT's Influential Educator Award in 2020.