update GHA workflows (#164)

* update style workflow

* update document worflow

* update `R CMD check` workflow

* update coverage workflow

* update lint workflow

* update CITATION.cff on all branches

* add rhub worflow

* update NEWS

.github/workflows/R-CMD-check.yaml

@@ -7,7 +7,9 @@ on:
     branches:
       - main
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -30,7 +32,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -50,3 +52,4 @@ jobs:
           OPENCAGE_KEY: ${{ secrets[matrix.config.oc_auth] }}
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/document.yaml

@@ -4,16 +4,20 @@ on:
   push:
     paths: ["R/**"]
 
-name: Document
+name: document.yaml
+
+permissions: read-all
 
 jobs:
   document:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/lint.yaml

@@ -1,19 +1,21 @@
 # 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
   pull_request:
-    branches: main
 
-name: lint
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,3 +29,5 @@ jobs:
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: rhub.yaml
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.github/workflows/style.yaml

@@ -4,16 +4,20 @@ on:
   push:
     paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
 
-name: Style
+name: style.yaml
+
+permissions: read-all
 
 jobs:
   style:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -46,7 +50,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache styler
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.styler-location.outputs.location }}
           key: ${{ runner.os }}-styler-${{ github.sha }}
@@ -60,9 +64,14 @@ jobs:
 
       - name: Commit and push changes
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          git add \*.[rR] \*.[qrR]md \*.[rR]markdown \*.[rR]nw \*.[rR]profile
-          git commit -m "Style code" || echo "No changes to commit"
-          git pull --ff-only
-          git push origin
+          if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
+              | egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
+          then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git commit ${FILES_TO_COMMIT[*]} -m "Style code (GHA)"
+            git pull --ff-only
+            git push origin
+          else
+            echo "No changes to commit."
+          fi

.github/workflows/test-coverage.yaml

@@ -1,13 +1,14 @@
 # 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
   pull_request:
-    branches:
-      - main
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -19,38 +20,48 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         env:
           OPENCAGE_KEY: ${{ secrets.OPENCAGE_KEY }}
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.github/workflows/update-citation-cff.yaml

@@ -8,13 +8,14 @@ on:
   release:
     types: [published]
   push:
-    branches: main
     paths:
       - DESCRIPTION
       - inst/CITATION
   workflow_dispatch:
 
-name: Update CITATION.cff
+name: update-citation-cff.yaml
+
+permissions: read-all
 
 jobs:
   update-citation-cff:

NEWS.md

@@ -10,7 +10,7 @@
 ## Internals
 
 * {opencage} now uses [{testthat} 3e](https://testthat.r-lib.org/articles/third-edition.html) for unit tests ([#141](https://github.com/ropensci/opencage/issues/141)).
-* GitHub action workflows have been updated ([#142](https://github.com/ropensci/opencage/issues/142),  [#149](https://github.com/ropensci/opencage/pull/149), [#152](https://github.com/ropensci/opencage/pull/152)). Styler and document workflows have been added ([#153](https://github.com/ropensci/opencage/pull/153)).
+* GitHub action workflows have been updated ([#142](https://github.com/ropensci/opencage/issues/142),  [#149](https://github.com/ropensci/opencage/pull/149), [#152](https://github.com/ropensci/opencage/pull/152)), [#164](https://github.com/ropensci/opencage/pull/164)). Styler, document, and rhub workflows have been added ([#153](https://github.com/ropensci/opencage/pull/153), [#164](https://github.com/ropensci/opencage/pull/164)).
 * Use [{lintr} version 3.0](https://www.tidyverse.org/blog/2022/07/lintr-3-0-0/) and add "package development" linters ([#144](https://github.com/ropensci/opencage/pull/144)).
 * `countrycodes` source and script were moved to `data-raw` ([#146](https://github.com/ropensci/opencage/pull/146)).
 * Add CITATION.cff and a corresponding GitHub action ([#148](https://github.com/ropensci/opencage/pull/148)).