Add security updates

.github/CODEOWNERS

@@ -0,0 +1,5 @@
+# require core team member review for updates to GitHub workflows
+/.github/CODEOWNERS @hubverse-org/hubverse-developers
+/.github/actions/ @hubverse-org/hubverse-developers
+/.github/shared/ @hubverse-org/hubverse-developers
+/.github/workflows/ @hubverse-org/hubverse-developers

.github/dependabot.yaml

@@ -0,0 +1,16 @@
+# instruct GitHub dependabot to scan github actions for dependency updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    # dependabot automatically checks .github/workflows/ and .github/actions/
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # group all run-of-the mill updates into a single pull request
+    groups:
+      gha-updates:
+        applies-to: version-updates
+        update-types:
+          - patch
+          - minor

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

@@ -11,6 +11,9 @@ on:
 
 name: R-CMD-check
 
+permissions:
+  contents: read
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -44,23 +47,23 @@ jobs:
           sed -i -e '/  hubverse-org/d' DESCRIPTION
 
       - id: setup-pandoc
-        uses: r-lib/actions/setup-pandoc@v2
+        uses: r-lib/actions/setup-pandoc@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
 
       - id: setup-r
-        uses: r-lib/actions/setup-r@v2
+        uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
           extra-repositories: https://hubverse-org.r-universe.dev
 
       - id: fetch-dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
+        uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
       - id: check
-        uses: r-lib/actions/check-r-package@v2
+        uses: r-lib/actions/check-r-package@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           upload-snapshots: true

.github/workflows/lint.yaml

@@ -8,6 +8,9 @@ on:
 
 name: lint
 
+permissions:
+  contents: read
+
 jobs:
   lint:
     runs-on: ubuntu-latest
@@ -16,11 +19,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::lintr, local::.
           needs: lint

.github/workflows/pkgdown-netlify-preview.yaml

@@ -8,6 +8,12 @@ on:
   release:
     types: [published]
   workflow_dispatch:
+    inputs:
+      publish:
+        description: "Publish Site (uncheck for a dry run)"
+        type: boolean
+        required: false
+        default: true
 
 name: pkgdown-pr-preview
 
@@ -22,22 +28,22 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
       NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
-      isPush: ${{ github.event_name == 'push' || github.event_name == 'workflow_dispatch' }}
+      PUBLISH: ${{ github.event_name == 'push' || github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.publish) }}
     permissions:
       contents: write
       pull-requests: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: r-lib/actions/setup-tinytex@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-pandoc@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
@@ -47,19 +53,26 @@ jobs:
         shell: Rscript {0}
 
       - name: Deploy production to GitHub pages 🚀
-        if: contains(env.isPush, 'true')
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        if: contains(env.PUBLISH, 'true')
+        uses: JamesIves/github-pages-deploy-action@6c2d9db40f9296374acc17b90404b6e8864128c8 #v4.7.3
         with:
           clean: false
           branch: gh-pages
           folder: docs
-
+      - id: deploy-dir 
+        name: Determine dev status
+        run: |
+          if [[ $(grep -c -E 'sion. ([0-9]*\.){3}' ${{ github.workspace }}/DESCRIPTION) == 1 ]]; then
+            echo 'dir=./docs/dev' >> $GITHUB_OUTPUT
+          else
+            echo 'dir=./docs' >> $GITHUB_OUTPUT
+          fi
       - name: Deploy PR preview to Netlify
-        if: contains(env.isPush, 'false')
+        if: contains(env.PUBLISH, 'false')
         id: netlify-deploy
-        uses: nwtgck/actions-netlify@v2
+        uses: nwtgck/actions-netlify@4cbaf4c08f1a7bfa537d6113472ef4424e4eb654 #v3.0.0
         with:
-          publish-dir: './docs'
+          publish-dir: '${{ steps.deploy-dir.outputs.dir }}'
           production-branch: main
           github-token: ${{ secrets.GITHUB_TOKEN }}
           deploy-message:

.github/workflows/test-coverage.yaml

@@ -8,6 +8,9 @@ on:
 
 name: test-coverage
 
+permissions:
+  contents: read
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -17,12 +20,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           use-public-rspm: true
           extra-repositories: https://hubverse-org.r-universe.dev
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::covr
           needs: coverage