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