Common Structure

Common structure of the workflows

R-version input

For most of the workflows, we need to select a specific R version. That’s why most of the actions have a r-version input:

inputs:
    r-version:
      description: 'The version of R to use'
      default: 'release'
      required: false
      type: choice
      options:
        - devel
        - oldrel

By default, we have r-version=release, and users can also use devel and latest versions.

• release means we are using latest stable version of R.
• oldrel means we are using previous release of R (for example if current release is 4.4, oldrel will be 4.3).
• devel refers to the development version of R, which contains the latest changes and features that are still under development. This version is typically used by developers who want to test new features. The “devel” version may be less stable.

Use of admiralci docker images

Once the r-version is picked, the worfklows will run inside a docker container instance. Indeed, admiralci contains an action push-docker-image, to be able to build rocker:rstudio images for each available version of R :

• admiralci-oldrelease
• admiralci-release
• admiralci-devel

These images are stored in admiralci ghcr (Github Container Registry - Place to store docker images), and are then reused to execute the workflows in docker container instances like this :

container:
    image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"

(For more details on docker images creation process, please read Push Docker Images) workflow documentation).

Checkout repository

This action is used to checkout on the right repository. This is a step commonly used in github actions to be able to access a repository tree.

- name: Checkout repository
  uses: actions/checkout@v3

Staged dependencies

The staged dependencies action allow to install every necessary upstream dependencies for admiral package, such as :

• pharmaversesdtm (SDTM test data)
• admiraldev (utilities functions for the Admiral package family)

(note that these dependencies are refered inside staged_dependencies.yml file)

For more details about staged.dependencies, please visit these links :

• Staged Dependencies Package
• Staged Dependencies Action (Github action to use Staged Dependencies package through github workflows)

- name: Run Staged dependencies
    uses: insightsengineering/staged-dependencies-action@v1
    with:
        run-system-dependencies: false
        renv-restore: false
    env:
        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

Note : the user can specify some parameters depending on the use case : - run-system-dependencies : install or not sys dependencies - renv-restore : restore or not renv.lock dependencies (and many other options you can find on Staged Dependencies Action documentation).