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

…-dependencies
insightsengineering · Sep 9, 2024 · 1aad0ff · 1aad0ff
1 parent 6a624d9
commit 1aad0ff
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diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
@@ -53,6 +53,19 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-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
+        default: ""
 
 concurrency:
   group: bioccheck-${{ github.event.pull_request.number || github.ref }}
@@ -122,12 +135,16 @@ 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 +154,14 @@ 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 }}
+
       - name: Run BiocCheck ☣️
         uses: insightsengineering/bioc-check-action@v1
         with:

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
@@ -126,9 +126,23 @@ 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?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-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
+        default: ""
       unit-test-report-brand:
         description: Image URL to use in unit test report for branding. If empty, the default xunit-viewer brand will be used.
         required: false
@@ -177,6 +191,8 @@ 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
@@ -373,6 +389,7 @@ jobs:
         if: >-
           env.enable_sd == 'true'
             && inputs.install-deps-from-package-repositories == ''
+            && inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -382,6 +399,15 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+          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 }}
+
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
         run: |

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -120,6 +120,19 @@ on:
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-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
+        default: ""
 
 concurrency:
   group: docs-${{ github.event.pull_request.number || github.ref }}
@@ -194,12 +207,16 @@ 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 +226,14 @@ 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 }}
+
       - name: Install R package 🚧
         run: |
           if (file.exists("renv.lock")) renv::restore()

diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
@@ -41,6 +41,19 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-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
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -109,12 +122,16 @@ jobs:
           SKIP_INSTRUCTION: "[skip roxygen]"
 
       - 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 }}
@@ -124,6 +141,14 @@ 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: ${{ steps.github-token.outputs.token }}
+
       - name: Generate man pages 📄
         run: |
           logfile <- "roxygen_${{ github.event.repository.name }}.log"

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -82,6 +82,19 @@ on:
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-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
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -207,12 +220,16 @@ 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 +239,14 @@ 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 }}
+
       - name: Install R package 🚧
         run: |
           if (file.exists("renv.lock")) renv::restore()

diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
@@ -38,6 +38,19 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-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
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -111,12 +124,16 @@ 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 +143,14 @@ 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 }}
+
       - name: Build report 🏗
         uses: insightsengineering/thevalidatoR@v2
         env: