Merge pull request #229 from atorus-research/221-dependency-cleanup

Closes #221 Removes suggested packages and update CI actions

.github/workflows/check-standard.yaml

@@ -1,21 +1,34 @@
+---
 # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 name: R-CMD-check 📦
 
 on:
+  # 'push' events are triggered when commits
+  # are pushed to one of these branches
   push:
     branches:
       - main
+    tags:
+      - "v*"
+  # 'pull_request' events are triggered when PRs are
+  # created against one of these target branches.
   pull_request:
+    types:
+    - opened
+    - synchronize
+    - reopened
+    - ready_for_review
     branches:
       - main
+  # 'workflow_dispatch' gives you the ability
+  # to run this workflow on demand, anytime
+  workflow_dispatch:
 
 jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
+  check:
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
+    runs-on: ${{ matrix.config.os }}
     strategy:
       fail-fast: false
       matrix:
@@ -25,24 +38,29 @@ jobs:
           - { 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
-
+    if: >
+      !contains(github.event.commits[0].message, '[skip checks]')
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository 🛎
+        uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Install Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Setup R 📊
+        uses: r-lib/actions/setup-r@v2
         with:
           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
+      - name: Install R package dependencies 📦
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
 
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Run R CMD check 🎯
+        uses: r-lib/actions/check-r-package@v2

.github/workflows/common.yaml

@@ -0,0 +1,113 @@
+---
+name: xportr CI/CD Workflows
+
+on:
+  # 'push' events are triggered when commits
+  # are pushed to one of these branches
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  # 'pull_request' events are triggered when PRs are
+  # created against one of these target branches.
+  pull_request:
+    types:
+    - opened
+    - synchronize
+    - reopened
+    - ready_for_review
+    branches:
+      - main
+  # 'workflow_dispatch' gives you the ability
+  # to run this workflow on demand, anytime
+  workflow_dispatch:
+
+concurrency:
+  group: common-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  R_VERSION: "release"
+
+jobs:
+  # Get R version from environmental variable
+  # and use it in downstream jobs
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
+
+  # Test code coverage of R Package
+  coverage:
+    name: Code Coverage
+    uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
+    if: >
+      github.event_name != 'release'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+      # Whether to skip code coverage badge creation
+      # Setting to 'false' will require you to create
+      # an orphan branch called 'badges' in your repository
+      skip-coverage-badges: true
+
+  # Ensure that styling guidelines are followed
+  style:
+    name: Code Style
+    uses: pharmaverse/admiralci/.github/workflows/style.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
+  # Ensure there are no broken URLs in the package documentation
+  links:
+    name: Links
+    uses: pharmaverse/admiralci/.github/workflows/links.yml@main
+    if: github.event_name == 'pull_request'
+
+  # Build the website and deploy to `gh-pages` branch
+  site:
+    name: Documentation
+    uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
+    if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
+    needs: get_r_version
+    with:
+      r-version: "release"
+      skip-multiversion-docs: true
+    secrets:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+  # Ensure there are no linter errors in the package
+  linter:
+    name: Lint
+    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
+  # Ensure there are no spelling errors in the package
+  spellcheck:
+    name: Spelling
+    uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
+  # Bumps development version of the package
+  vbump:
+    name: Version Bump 🤜🤛
+    if: github.event_name == 'push'
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+