Merge branch 'develop'

rjdverse · Jul 12, 2024 · 47bd161 · 47bd161
2 parents 32bea80 + 80dea05
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,8 +1,27 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+
 ^\.git$
 ^\.github$
+
 ^README\.Rmd$
-^_pkgdown\.yml$
+^README-.*\.png$
+
+^Meta$
 ^docs$
+^doc$
 ^pkgdown$
+^_pkgdown\.yml$
+
+^\.lintr$
+
+^appveyor\.yml$
+.travis.yml
+
+cran-comments.md
+
+^\.DS_Store$
+
+^revdep$
+^reconf\.sh$
+^pom\.xml$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,68 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - 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
+
+      - name: Set up for RProtoBuf on Windows
+        if: runner.os == 'Windows'
+        run: choco install protoc
+
+      - name: Set up for RProtoBuf on macos
+        if: runner.os == 'macOS'
+        run: brew install protobuf
+
+      - name: Set up for RProtoBuf on ubuntu
+        if: runner.os == 'Linux'
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'
diff --git a/.github/workflows/check-changelog.yml b/.github/workflows/check-changelog.yml
@@ -0,0 +1,17 @@
+name: Check changelog
+
+on: [ push, pull_request ]
+
+jobs:
+  check-changelog-job:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - uses: jbangdev/[email protected]
+        with:
+          script: com.github.nbbrd.heylogs:heylogs-cli:0.7.2:bin
+          scriptargs: "check NEWS.md"
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -0,0 +1,42 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -22,9 +22,9 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-java@v3
+      - uses: actions/setup-java@v4
         with:
           distribution: 'zulu' # See 'Supported distributions' for available options
           java-version: '17'

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,139 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Config git
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+
+      # Check if there are any changes
+      - name: Check for changes
+        id: check-changes
+        run: |
+          if git diff --quiet -- NAMESPACE man/; then
+            echo "has-changed=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "has-changed=true" >> "$GITHUB_OUTPUT"
+          fi
+          
+      - name: Commit the changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'true' }}
+        run: |
+          git add man/\* NAMESPACE
+          git commit -m '[GHA] Document package'
+
+      # Commit changes or a placeholder commit if no changes
+      - name: Commit no changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'false' }}
+        run: |
+          git commit --allow-empty -m '[GHA] Package already documented'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
+        shell: Rscript {0}
+
+      - name: Config git
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+
+      # Check if there are any changes
+      - name: Check for changes
+        id: check-changes
+        run: |
+          if git diff --quiet -- '*.R'; then
+            echo "has-changed=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "has-changed=true" >> "$GITHUB_OUTPUT"
+          fi
+          
+      - name: Commit the changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'true' }}
+        run: |
+          git add \*.R
+          git commit -m '[GHA] Style package'
+
+      # Commit changes or a placeholder commit if no changes
+      - name: Commit no changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'false' }}
+        run: |
+          git commit --allow-empty -m '[GHA] Package already styled'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,57 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_dispatch
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package