blockr.ci

Reusable GitHub Actions CI workflows for the blockr ecosystem.

Usage

Replace your repo's .github/workflows/ contents with two files:

.github/workflows/ci.yaml

on:
  push:
    branches: main
  pull_request:
  merge_group:

name: ci

jobs:
  ci:
    uses: cynkra/blockr.ci/.github/workflows/ci.yaml@main
    secrets: inherit
    permissions:
      contents: write

.github/workflows/deps-rerun.yaml

on:
  pull_request:
    branches: main
    types: [edited]

name: deps-rerun

jobs:
  rerun:
    uses: cynkra/blockr.ci/.github/workflows/deps-rerun.yaml@main
    secrets: inherit

Pipeline

lint → smoke → check       (multi-platform, merge queue + push)
             → coverage
             → revdep      (if configured)
             → pkgdown

All steps are mandatory — a consumer gets the full pipeline or none of it.

Inputs

Input	Type	Default	Purpose
revdep-packages	newline-separated list	''	Downstream packages to reverse-dep check. Empty skips the job.
lintr-exclusions	newline-separated list	''	File paths to exclude from linting
skip-pkgdown	boolean	false	Skip pkgdown for repos with custom site builds
default-deps	newline-separated list	''	Extra pak refs always included in dependency resolution (e.g., cynkra/g6R). Overrides registry; overridden by PR body deps block.

Example with all inputs

jobs:
  ci:
    uses: cynkra/blockr.ci/.github/workflows/ci.yaml@main
    with:
      revdep-packages: |
        cynkra/blockr.dock
        cynkra/blockr.dag
      lintr-exclusions: |
        vignettes/foo.qmd
        vignettes/bar.qmd
      default-deps: |
        cynkra/g6R
    secrets: inherit
    permissions:
      contents: write

What's included

• Lint with a canonical lintr config (object_name_linter = NULL)
• Smoke test — single-platform R CMD check (PR gate)
• Full check — 4-platform matrix (macOS, Windows, Ubuntu devel, Ubuntu oldrel), merge queue + push
• Coverage via covr + codecov
• Reverse-dependency checks against configurable downstream packages
• pkgdown site build + deploy to gh-pages
• parse-deps — override dependency versions via a ```deps block in the PR body
• deps-rerun — automatically re-run affected jobs when the deps block changes

Dependency resolution

Dependencies on internal blockr.* packages are resolved automatically via three layers (lowest to highest priority):

1. Package registry (automatic)

A central registry file (.github/actions/registry.txt) maps R package names to GitHub refs:

blockr.core=BristolMyersSquibb/blockr.core
blockr.dock=BristolMyersSquibb/blockr.dock
blockr.dag=BristolMyersSquibb/blockr.dag

When a consumer package lists blockr.core in its DESCRIPTION Imports, Depends, or Suggests, CI automatically adds BristolMyersSquibb/blockr.core to the install list. No Remotes: field needed.

2. default-deps workflow input (per-repo)

For dependencies not in the registry (e.g., cynkra/g6R), pass them via the default-deps input:

jobs:
  ci:
    uses: cynkra/blockr.ci/.github/workflows/ci.yaml@main
    with:
      default-deps: |
        cynkra/g6R

These override registry entries for the same owner/repo.

3. PR body deps block (per-PR override)

Add a fenced deps block to the PR body to override any dependency for that specific PR:

```deps
BristolMyersSquibb/blockr.core@my-feature-branch
BristolMyersSquibb/blockr.dock#42
```

Each line is a pak ref. Two override syntaxes are supported:

• owner/repo@branch — install from a specific branch
• owner/repo#123 — install from a pull request

PR body deps override both registry and default-deps entries for the same owner/repo. These refs are passed to r-lib/actions/setup-r-dependencies as extra packages. For revdep checks, the #123 and @branch syntax also controls which ref of the downstream package gets checked out.

How it works

The parse-deps composite action resolves dependencies on every CI run using the three layers above, deduplicating by owner/repo prefix (higher-priority layers win). The deps-rerun workflow watches for PR body edits — when the deps block changes, it automatically re-runs the smoke and revdep jobs without needing a new push.

Example

You're working on blockr.dock and need it tested against an in-progress PR on blockr.core:

1. Open your PR on blockr.dock

2. blockr.core is already auto-resolved from the registry (installed from default branch)

3. To test against a specific PR, add to the PR body:

   ```deps
   BristolMyersSquibb/blockr.core#87
   ```

4. CI installs blockr.core from PR #87 instead of the default branch

5. If you later change the deps block (e.g., point to a different PR), the affected jobs re-run automatically

Secrets

• BLOCKR_PAT (optional) — GitHub PAT with access to private blockr repos. Falls back to GITHUB_TOKEN if not set, which is sufficient for public repos.
• CODECOV_TOKEN — for coverage uploads