Manual updates for use

.Rbuildignore

@@ -11,3 +11,7 @@
 ^data-raw$
 ^_beekeeper_rapid\.rds$
 ^_beekeeper\.yml$
+^\.positai$
+^\.claude$
+^[.]?air[.]toml$
+^\.vscode$

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

@@ -4,48 +4,40 @@ on:
   push:
     branches: [main, master]
   pull_request:
+    branches: [main, master]
 
-name: R-CMD-check.yaml
-
-permissions: read-all
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
+    container: ${{ matrix.config.container }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         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'}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
+          # - {os: macos-latest,   r: 'release'}
+          # - {os: windows-latest, r: 'release'}
+          # - {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@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v6
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: api2r/actions/install@v1
         with:
+          use-container: "${{ matrix.config.container != '' }}"
+          token: ${{ secrets.GITHUB_TOKEN }}
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
           needs: check
+          extra-packages: any::rcmdcheck
+          cache-version: "1"
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/format-suggest.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  # Using `pull_request_target` over `pull_request` for elevated `GITHUB_TOKEN`
+  # privileges, otherwise we can't set `pull-requests: write` when the pull
+  # request comes from a fork, which is our main use case (external contributors).
+  #
+  # `pull_request_target` runs in the context of the target branch (`main`, usually),
+  # rather than in the context of the pull request like `pull_request` does. Due
+  # to this, we must explicitly checkout `ref: ${{ github.event.pull_request.head.sha }}`.
+  # This is typically frowned upon by GitHub, as it exposes you to potentially running
+  # untrusted code in a context where you have elevated privileges, but they explicitly
+  # call out the use case of reformatting and committing back / commenting on the PR
+  # as a situation that should be safe (because we aren't actually running the untrusted
+  # code, we are just treating it as passive data).
+  # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
+  pull_request_target:
+
+name: format-suggest.yaml
+
+jobs:
+  format-suggest:
+    name: format-suggest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # Required to push suggestion comments to the PR
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: Suggest
+        uses: reviewdog/action-suggester@v1
+        with:
+          level: error
+          fail_level: error
+          tool_name: air

.github/workflows/pkgdown-cleanup.yaml

@@ -0,0 +1,33 @@
+# This workflow removes the pkgdown preview directory when a PR is closed.
+name: Clean up pkgdown preview
+
+on:
+  pull_request:
+    types: [closed]
+
+permissions:
+  contents: write
+
+jobs:
+  clean-pr-preview:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ github.repository }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ref: gh-pages
+
+      - name: Remove PR preview directory
+        run: |
+          pr_dir="pr/${{ github.event.number }}"
+          if [ -d "$pr_dir" ]; then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+            git rm -rf "$pr_dir"
+            git commit -m "Remove preview for PR #${{ github.event.number }}"
+            git push
+          else
+            echo "Directory $pr_dir does not exist, skipping cleanup."
+          fi

.github/workflows/pkgdown.yaml

@@ -2,47 +2,70 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
+    branches: [main]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown.yaml
-
-permissions: read-all
+name: pkgdown
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
       contents: write
+      pull-requests: write
     steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - uses: actions/checkout@v6
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: api2r/actions/install@v1
         with:
-          extra-packages: any::pkgdown, local::.
+          use-container: "true"
+          token: ${{ secrets.GITHUB_TOKEN }}
           needs: website
+          extra-packages: any::pkgdown gilead-biostats/qcthat local::. any::glue
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      - name: Deploy PR preview 🧪
+        if: github.event_name == 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+          target-folder: pr/${{ github.event.number }}
+
+      - name: Comment with PR site URL 🌐
+        if: github.event_name == 'pull_request'
+        run: |
+          intPRNumber <- ${{ github.event.pull_request.number }}
+          strOwner <- tolower(qcthat::GetGHOwner())
+          strRepo <- qcthat::GetGHRepo()
+          strURL <- glue::glue(
+            "https://{strOwner}.github.io/{strRepo}/pr/{intPRNumber}/dev"
+          )
+          print(paste("🌐 URL:", strURL))
+          qcthat::CommentIssue(
+            intPRNumber,
+            glue::glue("🌐 [PR pkgdown deployed]({strURL})"),
+            NULL
+          )
+        shell: Rscript {0}
+
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4.8.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -4,34 +4,30 @@ on:
   issue_comment:
     types: [created]
 
-name: pr-commands.yaml
-
-permissions: read-all
+name: Commands
 
 jobs:
   document:
     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
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: api2r/actions/install@v1
         with:
-          extra-packages: any::roxygen2
+          use-container: "true"
+          token: ${{ secrets.GITHUB_TOKEN }}
           needs: pr-document
+          extra-packages: any::roxygen2
 
       - name: Document
         run: roxygen2::roxygenise()
@@ -47,39 +43,3 @@ jobs:
       - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-
-  style:
-    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
-    name: style
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/pr-fetch@v2
-        with:
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-
-      - uses: r-lib/actions/setup-r@v2
-
-      - name: Install dependencies
-        run: install.packages("styler")
-        shell: Rscript {0}
-
-      - name: Style
-        run: styler::style_pkg()
-        shell: Rscript {0}
-
-      - name: commit
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          git add \*.R
-          git commit -m 'Style'
-
-      - uses: r-lib/actions/pr-push@v2
-        with:
-          repo-token: ${{ secrets.GITHUB_TOKEN }}