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 license
- Code: Hippocratic License
- Source available in Git repository
- Can all be read online
The Author
Greg Wilson 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 and received ACM SIGSOFT's Influential Educator Award in 2020.