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Man Pages

Source: vignettes/man-pages.Rmd
man-pages.Rmd

Man Pages Workflow

This GitHub Actions workflow is designed for generating and checking man pages in an R package using Roxygen. It uses a matrix strategy to test different versions of R.

Inputs

r-version

  • Description: The version of R to use for testing.
  • Default: ‘4.1’
  • Options: ‘4.1’, ‘4.2’, ‘4.3’
  • Required: No

Workflow Triggers

This workflow is triggered in two ways:

  1. Manual Dispatch: You can manually trigger the workflow using the “workflow_dispatch” event. When triggered manually, you can specify the R version.

  2. Workflow Call: The workflow can also be triggered by another workflow using the “workflow_call” event. The R version is an input for this event.

Workflow Setup

  • Name: Man Pages
  • Concurrency: Man page jobs are organized by the pull request number or branch.
  • Cancel-in-progress: Allows canceling in-progress man page jobs.

Job: lint

This job runs Roxygen to generate and check man pages in the R package. It runs on a docker container instance using admiralci images (ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest) for the R environment.

Steps

Boilerplate Steps

  1. Get branch names: Retrieves branch names for further processing.

  2. Checkout repo (PR): Checks out the repository for pull requests.

  3. Checkout repository: Checks out the repository for non-pull request events.

  4. Normalize inputs: Normalizes input values, including determining the R version.

  5. Restore cache: Restores the cache for staged dependencies.

  6. Run Staged dependencies: Runs the staged dependencies action.

  7. Install dependencies from DESCRIPTION: install dependencies from DESCRIPTION (in case of missing dependencies in parent admiralci docker image)

Roxygen Workflow
  1. Generate man pages: Runs roxygen2::roxygenize() to generate man pages.
  2. Set-up safe dir: Sets up a safe directory for git configuration.
  3. Roxygen check: Checks if manuals are up-to-date with Roxygen comments and provides guidance if differences are found. If differences are found, the workflow will fail, giving the cmd to run to the admiral devs : roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))