Chore: customize github workflows to correctly install system dependencies

.github/workflows/lintr.yml

@@ -0,0 +1,149 @@
+# Source:
+# https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/lintr.yml
+# Modified to install system dependencies.
+
+name: Lint
+
+on:
+  workflow_dispatch:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: choice
+        options:
+          - devel
+          - latest
+      lint-all-files:
+        description: "Lint all files every time"
+        default: "false"
+        required: false
+        type: string
+      latest-lintr:
+        description: "Latest lintr CRAN release"
+        default: "false"
+        required: false
+        type: string
+      install-package:
+        description: "Install package locally."
+        default: "false"
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: string
+      lint-all-files:
+        description: "Lint all files every time"
+        default: "false"
+        required: false
+        type: string
+      latest-lintr:
+        description: "Latest lintr CRAN release"
+        default: "false"
+        required: false
+        type: string
+      install-package:
+        description: "Install package locally."
+        default: "false"
+        required: false
+        type: string
+
+concurrency:
+  group: lint-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
+    if: >
+      !contains(github.event.commits[0].message, '[skip lint]')
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      ##################### BEGIN boilerplate steps #####################
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/[email protected]
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/[email protected]
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install latest release of lintr
+        run: |
+          install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/")
+        shell: Rscript {0}
+        if: ${{ inputs.latest-lintr == 'true' }}
+
+      - name: Install package
+        run: renv::install(".", dependencies = "no-deps")
+        shell: Rscript {0}
+        if: ${{ inputs.install-package == 'true' }}
+      ##################### END boilerplate steps #####################
+
+      - name: Changed files
+        id: files
+        uses: Ana06/[email protected]
+        with:
+          format: "json"
+          filter: "*"
+
+      - name: Lint
+        run: |
+          exclusions_list <- NULL
+          if (!identical("${{ inputs.lint-all-files }}", "true")) {
+            changed_files <- jsonlite::fromJSON('${{ steps.files.outputs.added_modified }}')
+            all_files <- list.files(recursive = TRUE)
+            exclusions_list <- if (any(changed_files %in% c(".lintr", "renv.lock"))) {
+              as.list(setdiff(all_files, changed_files))
+            } else {
+              NULL
+            }
+          }
+          lints <- lintr::lint_package(exclusions = exclusions_list)
+          saveRDS(lints, file = "lints.rds")
+        shell: Rscript {0}
+
+      - name: Error if lints are detected
+        run: |
+          lints <- readRDS("lints.rds")
+          if (length(lints) > 0L) {
+            print(lints)
+            stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
+          }
+        shell: Rscript {0}

.github/workflows/main.yml

@@ -3,6 +3,13 @@
 # the developement process. When package is ready to
 # be published, revisit and add release-related
 # workflows.
+# Due to the need of some customization, instead of
+# referencing the workflows directly, they are copied
+# over and modified to install needed system dependencies.
+# This means that in case of an update, the changes
+# will need to be applied manually.
+#
+# Last workflow update: 2025-09-01
 name: admiral CI/CD Workflows
 
 on:
@@ -32,49 +39,42 @@ jobs:
         id: get_r_version
         run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
         shell: bash
+
   spellcheck:
     name: Spelling
-    uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
+    uses: ./.github/workflows/spellcheck.yml
     if: github.event_name == 'pull_request'
     needs: get_r_version
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
   linter:
     name: Lint
-    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    uses: ./.github/workflows/lintr.yml
     needs: get_r_version
     if: github.event_name == 'pull_request'
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
   man-pages:
     name: Man Pages
-    uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
-    if: github.event_name == 'pull_request'
+    uses: ./.github/workflows/man-pages.yml
     needs: get_r_version
+    if: github.event_name == 'pull_request'
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
   tests:
     name: Tests
-    runs-on: ubuntu-latest
+    uses: ./.github/workflows/test.yml
     needs: get_r_version
-    container:
-      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
-    steps:
-        - name: Checkout code
-          uses: actions/checkout@v2
-
-        - name: Install dependencies
-          run: |
-            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+    if: github.event_name == 'pull_request'
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
 
-        - name: Run tests
-          shell: Rscript {0}
-          run: |
-            devtools::load_all(".")
-            devtools::test()
   check:
     name: Check
-    uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+    uses: ./.github/workflows/r-cmd-check.yml
     if: github.event_name == 'pull_request'
     with:
         error-on: error

.github/workflows/man-pages.yml

@@ -0,0 +1,115 @@
+# Source:
+# https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/man-pages.yml
+# Modified to install system dependencies.
+
+name: Man Pages
+
+on:
+  workflow_dispatch:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: choice
+        options:
+          - devel
+          - latest
+  workflow_call:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: string
+
+concurrency:
+  group: roxygen-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Roxygen
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
+    if: >
+      !contains(github.event.commits[0].message, '[skip lint]')
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      ##################### BEGIN boilerplate steps #####################
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/[email protected]
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/[email protected]
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          remotes::install_local(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+        env:
+          R_REMOTES_STANDALONE: "true"
+
+      ##################### END boilerplate steps #####################
+
+      - name: Generate man pages
+        run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
+        shell: Rscript {0}
+
+      - name: Set-up safe dir
+        run: git config --global --add safe.directory "${GITHUB_WORKSPACE}"
+        shell: bash
+
+      - name: Roxygen check
+        if: "!startsWith(github.event.comment.body, '/roxygenize')"
+        run: |
+          git status -s
+          if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]]
+          then {
+            ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')"
+            echo "🙈 Manuals are not up-to-date with roxygen comments!"
+            echo "🔀 The following differences were noted:"
+            git diff man/* DESCRIPTION
+            echo -e "\n💻 Please rerun the following command on your workstation and push your changes"
+            echo "--------------------------------------------------------------------"
+            echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))"
+            echo "--------------------------------------------------------------------"
+            echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION"
+            echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version"
+            exit 1
+          } else {
+            echo "💚 Manuals are up-to-date with roxygen comments"
+          }
+          fi
+        shell: bash