feat: add an option to choose between staged-dependencies and setup-r-dependencies

.github/workflows/bioccheck.yaml

@@ -53,6 +53,20 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
+        default: staged-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        type: string
+        default: ""
 
 concurrency:
   group: bioccheck-${{ github.event.pull_request.number || github.ref }}
@@ -122,12 +136,16 @@ jobs:
           SKIP_INSTRUCTION: "[skip bioccheck]"
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -137,6 +155,15 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ github.event.repository.name }}
+
       - name: Run BiocCheck ☣️
         uses: insightsengineering/bioc-check-action@v1
         with:

.github/workflows/build-check-install.yaml

@@ -126,6 +126,21 @@ on:
         description: |
           Set this to a comma-separated named list of R packages repositories to use for installing dependencies.
           Example: "R-universe=https://insightsengineering.r-universe.dev/,CRAN=https://cloud.r-project.org/"
+          If the value is non-empty, it takes precedence over deps-installation-method.
+        required: false
+        type: string
+        default: ""
+      deps-installation-method:
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
+        default: staged-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
         type: string
         default: ""
@@ -177,6 +192,8 @@ on:
       enable-sd:
         description: |
           Whether the installation of package dependencies via staged.dependencies should be enabled.
+          Has no effect if deps-installation-method == 'setup-r-dependencies' or
+          install-deps-from-package-repositories is set to non-empty value.
         required: false
         type: boolean
         default: true
@@ -319,12 +336,14 @@ jobs:
           junit_xml_positive_threshold="${{ inputs.junit-xml-positive-threshold }}"
           junit_xml_negative_threshold="${{ inputs.junit-xml-negative-threshold }}"
           enable_sd="${{ inputs.enable-sd }}"
+          deps_installation_method="${{ inputs.deps-installation-method }}"
           echo "junit_xml_storage=${junit_xml_storage_input:-_junit_xml_reports}" >> $GITHUB_ENV
           echo "junit_xml_diff_branch=${junit_xml_diff_branch_input:-main}" >> $GITHUB_ENV
           echo "junit_xml_comparison=${junit_xml_comparison_input:-true}" >> $GITHUB_ENV
           echo "junit_xml_positive_threshold=${junit_xml_positive_threshold:-1.0}" >> $GITHUB_ENV
           echo "junit_xml_negative_threshold=${junit_xml_negative_threshold:-1.0}" >> $GITHUB_ENV
           echo "enable_sd=${enable_sd:-true}" >> $GITHUB_ENV
+          echo "deps_installation_method=${deps_installation_method:-staged-dependencies}" >> $GITHUB_ENV
         shell: bash
 
       - name: Restore npm cache 💰
@@ -356,7 +375,9 @@ jobs:
         shell: bash
 
       - name: Restore SD cache 💰
-        if: inputs.install-deps-from-package-repositories == ''
+        if: >-
+          inputs.install-deps-from-package-repositories == ''
+            && env.deps_installation_method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
@@ -373,6 +394,7 @@ jobs:
         if: >-
           env.enable_sd == 'true'
             && inputs.install-deps-from-package-repositories == ''
+            && env.deps_installation_method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -382,6 +404,16 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          env.deps_installation_method == 'setup-r-dependencies'
+          && inputs.install-deps-from-package-repositories == ''
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ github.event.repository.name }}
+
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
         run: |

.github/workflows/pkgdown.yaml

@@ -120,6 +120,20 @@ on:
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
+        default: staged-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        type: string
+        default: ""
 
 concurrency:
   group: docs-${{ github.event.pull_request.number || github.ref }}
@@ -194,12 +208,16 @@ jobs:
           SKIP_INSTRUCTION: "[skip docs]"
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -209,6 +227,15 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ github.event.repository.name }}
+
       - name: Install R package 🚧
         run: |
           if (file.exists("renv.lock")) renv::restore()

.github/workflows/roxygen.yaml

@@ -41,6 +41,20 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
+        default: staged-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        type: string
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -108,13 +122,23 @@ jobs:
         env:
           SKIP_INSTRUCTION: "[skip roxygen]"
 
+      - name: Normalize variables 📏
+        run: |
+          deps_installation_method="${{ inputs.deps-installation-method }}"
+          echo "deps_installation_method=${deps_installation_method:-staged-dependencies}" >> $GITHUB_ENV
+        shell: bash
+
       - name: Restore SD cache 💰
+        if: >-
+          env.deps_installation_method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          env.deps_installation_method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -124,6 +148,22 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          env.deps_installation_method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ github.event.repository.name }}
+
+      # setup-r-dependencies makes modifications to DESCRIPTION which
+      # should not be committed during Roxygen auto-update.
+      - name: Restore DESCRIPTION ⚙️
+        run: git restore DESCRIPTION
+        working-directory: ${{ github.event.repository.name }}
+        shell: bash
+
       - name: Generate man pages 📄
         run: |
           logfile <- "roxygen_${{ github.event.repository.name }}.log"

.github/workflows/test-coverage.yaml

@@ -82,6 +82,20 @@ on:
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
+        default: staged-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        type: string
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -207,12 +221,16 @@ jobs:
           fi
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
@@ -222,6 +240,15 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ github.event.repository.name }}
+
       - name: Install R package 🚧
         run: |
           if (file.exists("renv.lock")) renv::restore()

.github/workflows/validation.yaml

@@ -38,6 +38,20 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
+        default: staged-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        type: string
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -111,12 +125,16 @@ jobs:
         shell: bash
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -126,6 +144,15 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ env.package_subdirectory }}
+
       - name: Build report 🏗
         uses: insightsengineering/thevalidatoR@v2
         env: