infra: use pkgskills containers

.github/workflows/R-CMD-check.yaml

@@ -11,6 +11,7 @@ name: R-CMD-check
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
+    container: ${{ matrix.config.container }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
@@ -20,15 +21,16 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'devel',    http-user-agent: 'release', container: 'ghcr.io/api2r/pkgskills-ci:devel'}
+          - {os: ubuntu-latest,  r: 'release',  container: 'ghcr.io/api2r/pkgskills-ci:release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1', container: 'ghcr.io/api2r/pkgskills-ci:oldrel-1'}
 
     steps:
       - uses: actions/checkout@v6
 
       - uses: ./.github/workflows/install
         with:
+          use-container: "${{ matrix.config.container != '' }}"
           token: ${{ secrets.GITHUB_TOKEN }}
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}

.github/workflows/copilot-setup-steps.yml

@@ -29,8 +29,8 @@ jobs:
           needs: build, check, website
           # Extra packages include things referenced in skills, to make sure the
           # agent has them available.
+          optional-packages: any::astgrepr
           extra-packages: >-
-            any::astgrepr
             any::cli
             any::covr
             any::devtools
@@ -44,6 +44,7 @@ jobs:
             any::testthat
             any::usethis
             any::withr
+            gilead-biostats/qcthat
             local::.
 
       - name: Install air

.github/workflows/install/action.yml

@@ -20,26 +20,102 @@ inputs:
     description: "Extra packages, passed to r-lib/actions/setup-r-dependencies@v2"
     required: false
     default: any::rcmdcheck
+  optional-packages:
+    description: "Optional extra packages; installed individually, warn (not error) on failure"
+    required: false
+    default: ""
   cache-version:
     description: "Cache version for r-lib/actions/setup-r-dependencies@v2"
     required: false
     default: "1"
+  use-container:
+    description: "Set to 'true' when running inside a pre-warmed container (skips R and pandoc setup)"
+    required: false
+    default: "false"
 
 runs:
   using: "composite"
   steps:
-    - uses: r-lib/actions/setup-pandoc@v2
+    - if: inputs.use-container != 'true'
+      uses: r-lib/actions/setup-pandoc@v2
 
     - uses: r-lib/actions/setup-r@v2
       with:
+        install-r: ${{ inputs.use-container != 'true' }}
         r-version: ${{ inputs.r-version }}
         http-user-agent: ${{ inputs.http-user-agent }}
         use-public-rspm: true
 
-    - uses: r-lib/actions/setup-r-dependencies@v2
+    # In pre-warmed containers every package may already be in the system
+    # library, so nothing is ever written to R_LIBS_USER.  Ensure the
+    # directory exists with a sentinel so the actions/cache glob matches
+    # and the "Path Validation Error" warning doesn't fire at cache-save.
+    - if: inputs.use-container == 'true'
+      name: Ensure R_LIBS_USER exists
+      shell: bash
+      run: |
+        lib="$(Rscript -e 'cat(Sys.getenv("R_LIBS_USER"))')"
+        mkdir -p "$lib"
+        touch "$lib/.keep"
+
+    # Container path: call pak::pak() directly so it checks .libPaths() and
+    # only installs/updates packages that are genuinely missing or outdated.
+    # setup-r-dependencies always runs a full lockfile-create → lockfile-install
+    # cycle which reinstalls everything even when the container already has it.
+    - if: inputs.use-container == 'true'
+      name: Update R package dependencies (container)
+      shell: Rscript {0}
+      env:
+        GITHUB_PAT: ${{ inputs.token }}
+      run: |
+        # *Remove* this package from the container if present. Only relevant for stbl.
+        try(remove.packages("stbl"), silent = TRUE)
+
+        # Replicate needs → Config/Needs/<field> expansion from r-lib/actions
+        needs_parts <- strsplit("${{ inputs.needs }}", "[[:space:],]+")[[1]]
+        needs_parts <- needs_parts[nzchar(needs_parts)]
+        needs <- sprintf("Config/Needs/%s", needs_parts)
+
+        extra_deps <- strsplit("${{ inputs.extra-packages }}", "[[:space:],]+")[[1]]
+        extra_deps <- extra_deps[nzchar(extra_deps)]
+
+        # Over-protect for strangeness in the container
+        if (!requireNamespace("pak", quietly = TRUE)) {
+          install.packages("pak")
+        }
+
+        pak::pak(
+          c("deps::.", extra_deps),
+          dependencies = c(needs, "all"),
+          upgrade = TRUE,
+          ask = FALSE
+        )
+
+    # Non-container path: standard setup-r-dependencies flow with caching.
+    - if: inputs.use-container != 'true'
+      uses: r-lib/actions/setup-r-dependencies@v2
       env:
         GITHUB_PAT: ${{ inputs.token }}
       with:
         needs: ${{ inputs.needs }}
         extra-packages: ${{ inputs.extra-packages }}
         cache-version: ${{ inputs.cache-version }}
+
+    - if: inputs.optional-packages != ''
+      name: Install optional packages
+      shell: Rscript {0}
+      env:
+        GITHUB_PAT: ${{ inputs.token }}
+      run: |
+        pkgs <- strsplit("${{ inputs.optional-packages }}", "\\s+")[[1]]
+        pkgs <- pkgs[nzchar(pkgs)]
+        for (pkg in pkgs) {
+          tryCatch(
+            pak::pak(pkg),
+            error = function(e) {
+              msg <- sprintf("Failed to install optional package %s: %s", pkg, conditionMessage(e))
+              msg <- gsub("[\r\n]+", " ", msg)
+              cat("::warning::", msg, "\n", sep = "")
+            }
+          )
+        }

.github/workflows/pkgdown.yaml

@@ -14,6 +14,8 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
@@ -25,18 +27,12 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - name: Set Development Mode Env Var
-        if: github.ref_name != 'main'
-        run: |
-          echo "Ref is '${{ github.ref_name }}', setting PKGDOWN_DEV_MODE=devel"
-          echo "PKGDOWN_DEV_MODE=devel" >> $GITHUB_ENV
-
       - uses: ./.github/workflows/install
         with:
+          use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}
           needs: website
           extra-packages: any::pkgdown gilead-biostats/qcthat local::.
-          cache-version: "1"
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

.github/workflows/pr-commands.yaml

@@ -11,6 +11,8 @@ jobs:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
     name: document
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
     permissions:
       contents: write
     steps:
@@ -22,10 +24,10 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
+          use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}
           needs: pr-document
           extra-packages: any::roxygen2
-          cache-version: "1"
 
       - name: Document
         run: roxygen2::roxygenise()

.github/workflows/qcthat.yaml

@@ -48,6 +48,8 @@ env:
 jobs:
   qcthat:
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
     if: >-
       (github.event_name == 'issues' && contains(github.event.issue.labels.*.name, 'qcthat-uat')) ||
       github.event_name != 'issues'
@@ -58,9 +60,9 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
+          use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}
           extra-packages: Gilead-BioStats/qcthat@main local::.
-          cache-version: "1"
 
       - name: Manage User Acceptance Testing
         if: >-

.github/workflows/test-coverage.yaml

@@ -11,15 +11,17 @@ name: test-coverage
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
     steps:
       - uses: actions/checkout@v6
 
       - uses: ./.github/workflows/install
         with:
+          use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}
           needs: coverage
           extra-packages: any::covr any::xml2
-          cache-version: "1"
 
       - name: Test coverage
         run: |