This lesson is still being designed and assembled (Pre-Alpha version)

Intermediate Research Software Development in Python

This course aims to teach a core set of established, intermediate-level software development skills and best practices for working as part of a team in a research environment using Python as an example programming language (see detailed learning objectives below). The core set of skills we teach is not a comprehensive set of all-encompassing skills, but a selective set of tried-and-tested collaborative development skills that forms a firm foundation for continuing on your learning journey.

A typical learner for this course may be someone who is working in academic research and, needing to write some code, has gained basic software development skills either by self-learning or attending, e.g., a novice Software Carpentry Python course. They have been applying those skills in their domain of work by writing code for some time, e.g. half a year or more. However, their software development-related projects are now becoming larger and are involving more researchers and other stakeholders (e.g. users), for example:

They now need more intermediate software engineering skills to help them design more robust software code, automate the process of testing and verifying its correctness and support collaborations with others.

Target Audience

This course is for you if:

This course is not for you if:

Prerequisites

To attend this course you should meet the following criteria. You can also test your prerequisite knowledge by taking this short quiz.

Git

  • You are familiar with the concept of version control
  • You have experience configuring Git for the first time and creating a local repository
  • You have experience using Git to create and clone a repository and add/commit changes to it and to push to/pull from a remote repository
  • Optionally, you have experience comparing various versions of tracked files or ignoring specific files

Python

  • You have a basic knowledge of programming in Python (using variables, lists, conditional statements, functions and importing external libraries)
  • You have previously written Python scripts or iPython/Jupyter notebooks to accomplish tasks in your domain of work

Shell

  • You have experience using a command line interface, such as Bash, to navigate a UNIX-style file system and run commands with arguments
  • Optionally, you have experience redirecting inputs and outputs from a command

Learning Objectives for the Workshop

  • Use a virtual environment and a set of tools (command line shell, Pip, Venv, Git, GitHub, PyCharm IDE) to develop software collaboratively
  • Use a test framework to verify the correct behaviour of code
  • Design robust, extensible software
  • Release your software for reuse by others

Schedule

Setup Download the software required for the lesson
00:00 Setting the Scene For the Workshop What are we going to teach in this workshop?
What different software development tools will we be using?
Day 1 00:00 Section 1: Environment For Collaborative Code Development What tools are needed to collaborate on code development effectively?
00:10 Introduction to Software Design and Development Why is splitting code into smaller functional units (modules) good when designing software?
What is Model-View-Controller design architecture?
00:40 Integrated Software Development Environments What are Integrated Development Environments (IDEs)?
What are the advantages of using IDEs for software development?
01:10 Virtual Environments For Software Development What are virtual environments in software design?
What are the advantages of using virtual environments?
How to set up and manage a Python virtual environment?
How to install and manage Python third party packages?
01:40 Python Coding Conventions Why should you follow software coding conventions?
Who is setting coding conventions?
What coding conventions exist for Python?
02:10 Collaborative Software Development Using Git and GitHub What are Git branches and why are they useful?
What are best practices when developing software collaboratively using Git?
02:55 Section end
Day 2 00:00 Section 2: Ensuring Correctness of Software at Scale TODO
00:05 Automatically Testing your Software Does the code we develop work the way it should do?
Can we (and others) verify these assertions for themselves?
To what extent are we confident of the accuracy of results that appear in publications?
00:55 Scaling Up Unit Testing How do we scale up the number of tests we want to run?
How can we know how much of our code is being tested?
01:10 Continuous Integration for Automated Testing How can I apply automated repository testing to scale with development activity?
01:55 Diagnosing Issues and Improving Robustness Once we know our program has errors, how can we locate them in the code?
How can we make our programs more resilient to failure?
02:45 Section end
Day 3 00:00 Section 3: Software Architecture and Design What architectural and software design paradigms exist to help us design our software?
00:05 Programming Paradigms How does the structure of a problem affect the structure of our code?
00:20 Object Oriented Programming How can we use code to describe the structure of data?
How should the relationships between structures be described?
01:10 Functional Programming What is a function really?
How can we be sure our code does the same thing every time?
What is the difference between data and code?
What do we need to do differently when working with Big Data?
01:50 Software Design Where do we start when beginning a new software project?
How do people use software?
How can we make sure the components of our software are reusable?
What should we do when our requirements change?
02:25 Persistence How can we store and transfer structured data?
How can we make it easier to substitute new components into our software?
03:15 Section end
Day 4 00:00 Section 4: Developing Software In a Team and Releasing It TODO
00:05 Preparing Software for Reuse What can we do to make our programs reusable by others?
How should we document and license our code?
01:00 Assessing Software for Suitability and Improvement What makes good code actually good?
What should we look for when selecting software to reuse?
01:45 Software Improvement Through Feedback How should we handle feedback on our software?
How, and to what extent, should we provide support to our users?
02:35 Workshop Wrap-up Looking back at what was covered and how different pieces fit together
Where are some advanced topics and further reading available?
02:50 Workshop end

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.