bionmf Example Website

Workshop exercise 3_Actions_Package: the bionmf package from 2_Simple_Package, extended with GitHub Actions for collaboration and CI.

GitHub Actions Workflows for bionmf

Four workflows live in .github/workflows/:

Workflow Trigger Purpose
issue-message.yml Issue opened Posts a welcome message and bug-report checklist
pull-request-message.yml PR opened / reopened Posts a contributor checklist on the PR
install-package.yml Push / PR to main Builds and installs the package on Ubuntu
run-tests.yml Push / PR to main Runs testthat via r-lib/actions

Together they cover communication (issues & PRs) and continuous integration (install + test).

Package contents

Same as step 2 — see the mapping in 2_Simple_Package/README.md. All R code, tests, and bundled data are unchanged unless you modify them during the Actions exercise.

Local development

From this directory (Exercises/3_Actions_Package):

devtools::load_all()
devtools::test()
vignette("bionmf")  # after install with vignettes built
R CMD build .
R CMD check bionmf_*.tar.gz --no-manual

Using the workflows

Standalone package repository

When bionmf is the root of your GitHub repository, copy .github/workflows/ to the repository root. GitHub only runs workflows from <repo>/.github/workflows/.

This workshop monorepo

This repository also includes mirrored workflows at the repository root:

The install, test, and PR-message workflows set working-directory: Exercises/3_Actions_Package where needed and use paths filters so they run only when this exercise changes. The issue-message workflow cannot use paths (GitHub does not support that filter on issues events); it posts only when the issue title or body mentions bionmf or 3_Actions_Package.

Try the automation

  1. Open a new issue whose title or body mentions bionmf or 3_Actions_Package — the issue workflow posts a template comment.
  2. Open a pull request that touches Exercises/3_Actions_Package/ — the PR workflow posts a checklist comment.
  3. Push a change under Exercises/3_Actions_Package/ — install and test workflows run on GitHub’s Ubuntu runners.

Check the Actions tab on GitHub for workflow run logs.

Workshop discussion points

  • Permissions — issue/PR workflows need issues: write or pull-requests: write.
  • Path filters — limit CI to the package folder in monorepos.
  • r-lib/actions — standard R setup (setup-r, setup-r-dependencies, test-package).
  • Separation of concerns — install verifies the tarball; tests verify behavior.

Prior steps