Coffee and coding

Intro session

Chris Beeley

Feb 23, 2023

Welcome to coffee and coding

• Project demos, showcasing work from a particular project
• Method demos, showcasing how to use a particular method/tool/package
• Surgery and problem solving sessions
• Defining code standards and SOP

What are we trying to achieve?

• Legibility
• Reproducibility
• Accuracy
• Laziness

What are some of the fundamental principles?

• Predictability, reducing mental load, and reducing truck factor
• Making it easy to collaborate with yourself and others on different computers, in the cloud, in six months’ time…
• DRY

What is RAP

• a process in which code is used to minimise manual, undocumented steps, and a clear, properly documented process is produced in code which can reliably give the same result from the same dataset
• RAP should be:

the core working practice that must be supported by all platforms and teams; make this a core focus of NHS analyst training

Goldacre review

The road to RAP

• We’re roughly using NHS Digital’s RAP stages
• There is an incredibly large amount to learn!
• Confession time! (everything I do not know…)
• You don’t need to do it all at once
• You don’t need to do it all at all ever
• Each thing you learn will incrementally help you
• Remember- that’s why we learnt this stuff. Because it helped us. And it can help you too

Levels of RAP- Baseline

• Data produced by code in an open-source language (e.g., Python, R, SQL).
• Code is version controlled (see Git basics and using Git collaboratively guides).
• Repository includes a README.md file (or equivalent) that clearly details steps a user must follow to reproduce the code
• Code has been peer reviewed.
• Code is published in the open and linked to & from accompanying publication (if relevant).

Source: NHS Digital RAP community of practice

Levels of RAP- Silver

• Code is well-documented…
• Code is well-organised following standard directory format
• Reusable functions and/or classes are used where appropriate
• Pipeline includes a testing framework
• Repository includes dependency information (e.g. requirements.txt, PipFile, environment.yml
• Data is handled and output in a Tidy data format

Source: NHS Digital RAP community of practice

Levels of RAP- Gold

• Code is fully packaged
• Repository automatically runs tests etc. via CI/CD or a different integration/deployment tool e.g. GitHub Actions
• Process runs based on event-based triggers (e.g., new data in database) or on a schedule
• Changes to the RAP are clearly signposted. E.g. a changelog in the package, releases etc. (See gov.uk info on Semantic Versioning)

Source: NHS Digital RAP community of practice

A learning journey to get us there

• Code style, organising your files
• Functions and iteration
• Git and GitHub
• Packaging your code
• Testing
• Package management and versioning

How we can help each other get there

• Work as a team!
• Coffee and coding!
• Ask for help!
• Do pair coding!
• Get your code reviewed!
• Join the NHS-R/ NHSPycom communities