How CI/CD Enhances the Development of R Packages in the Pharmaverse

PhUSE 2023, US Connect

March 7th, 2023

Ben Straub (GSK) & Dinakar Kulkarni (Roche)

What is CI/CD?

  • Continuous Integration (CI): Frequent merging of several small changes into a main branch
  • Continuous Delivery (CD): Repeatable deployment process when deciding to deploy

CI/CD bridges the gaps between development and operation activities and teams by enforcing automation in building, testing and deployment of {pharmaverse} R packages.

Wikipedia: CI/CD {pharmaverse}

Does it help?

…Yes! Yes, it does!!

XKCD

How does CI/CD help R packages?

  • Catch issues (bugs) early on
  • User base on multiple OSes and multiple R versions
  • Faster turnaround on Code Review
  • Multiple Contributors on your R Package
  • Enforce style conventions and preferences
  • Measure test coverage for new code
  • Keep docs up-to-date
  • And we can just keep going!

We covered a lot of custom CI/CD actions for R packages in the R/Pharma Workshop in 2022: Intro to CI/CD for R Packages

Two Case Studies

admiral

nest

Case Study - admiral

About admiral


  • Provide an open source, modularized toolbox that enables the pharmaceutical programming community to develop ADaM datasets in R.
  • ADaM is one of the required standards for data submission to FDA (U.S.) and PMDA (Japan) for clinical trials
  • Links
  • Issue 1: Checking ADaM Template code
  • Issue 2: Common CI/CD workflows for the admiral family of packages

Issue 1 - How to Check our Template Code

  • Create a reference files to build common ADaM datasets that shows users how to implement our functions
  • Way less text than a Vignette - Code is ready to go and build a dataset
  • Where we store this code is not checked by R-CMD
  • How to ensure code stays up to date with deprecated functions or unforeseen bugs get in from functions working together?
  • CI/CD for the win!

Solution 1 - CI/CD for Templates

  • Dedicated CI/CD workflow that executes the Template code
  • Once a Code Review is completed the Check Template Workflow is executed
  • If any errors or warnings are detected the CI/CD check fails and the contributor must fix the error or warning.

.github/workflows/check-templates.yml

Issue 2 - admiral upstream and downstream dependencies

  • As you can imagine there can be a lot of different types of ADaMs!
  • Extension packages focus on specific disease areas like oncology
  • The admiral family has a package for developers, template R package repo and dummy data
  • Eek!! How to keep this all in line!

Solution 2 - Common CI/CD workflows for admiral upstream and downstream dependencies

  • Using {admiralci}, we have a common set of CI/CD workflows
  • Developers moving between packages are familiar with these workflows
  • Common documentation between packages for CI/CD workflows - easy to maintain and provide to new contributors

Case Study - NEST

About NEST


  • A collection of R packages for creating TLGs/TFLs and exploratory clinical trials data visualization
  • tern and rtablesfor creating TLGs
  • teal for creating exploratory web applications for analyzing clinical trial data
  • Links

Use Case 1 - Integration Testing


  • An in-development package must be tested against the latest versions of upstream dependencies
  • Monorepo emulation via a git branch naming strategy is achieved by using
  • Testing as a cohort can be done at any stage (eg. development, pre-release, release)

Use Case 2 - Web Application Testing & Deployment


  • Analysts create Shiny web apps via the teal framework for analyzing data
  • Apps are tested via a CI pipeline that uses the shinytest2 R package
  • Apps deployed to an Posit Connect Server instance via a CD pipeline

Use Case 3 - Validating R Packages


  • R packages are validated by an internal validation team that uses CI/CD pipelines to automatically
    • accept new package submissions via a form
    • running tests against the new package to ensure package integrity
    • enforcing criteria to ensure that the package meets regulatory requirements
  • Also validated externally via an open source project called thevalidatoR

Additional Materials


<CI-CD GitHub>