ci: add copilot setup workflow and componentize install steps

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

@@ -24,25 +24,17 @@ jobs:
           - {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@v6
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
+      - uses: ./.github/workflows/install
         with:
+          token: ${{ secrets.GITHUB_TOKEN }}
           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
-        with:
-          extra-packages: any::rcmdcheck
           needs: check
+          extra-packages: any::rcmdcheck
+          cache-version: "1"
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/copilot-setup-steps.yml

@@ -0,0 +1,34 @@
+name: "Copilot Setup Steps"
+
+# Automatically run when the file changes to allow for easy validation,
+# and allow manual testing through the repository's "Actions" tab.
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Lowest permissions needed; Copilot gets its own token for its operations.
+    permissions:
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: ./.github/workflows/install
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          cache-version: copilot
+          needs: build, check, website
+          extra-packages: any::rcmdcheck any::roxygen2 any::pkgdown local::.
+
+      - name: Install air
+        uses: posit-dev/setup-air@v1

.github/workflows/install/action.yml

@@ -0,0 +1,45 @@
+name: "Install R and dependencies"
+description: "Set up pandoc, R, and package dependencies"
+inputs:
+  token:
+    description: "GitHub token, set to secrets.GITHUB_TOKEN"
+    required: true
+  r-version:
+    description: "R version, passed to r-lib/actions/setup-r@v2"
+    required: false
+    default: release
+  http-user-agent:
+    description: "HTTP user agent, passed to r-lib/actions/setup-r@v2"
+    required: false
+    default: ""
+  needs:
+    description: "Config/Needs tag(s), passed to r-lib/actions/setup-r-dependencies@v2"
+    required: false
+    default: ""
+  extra-packages:
+    description: "Extra packages, passed to r-lib/actions/setup-r-dependencies@v2"
+    required: false
+    default: any::rcmdcheck
+  cache-version:
+    description: "Cache version for r-lib/actions/setup-r-dependencies@v2"
+    required: false
+    default: "1"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: r-lib/actions/setup-pandoc@v2
+
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ inputs.r-version }}
+        http-user-agent: ${{ inputs.http-user-agent }}
+        use-public-rspm: true
+
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      env:
+        GITHUB_PAT: ${{ inputs.token }}
+      with:
+        needs: ${{ inputs.needs }}
+        extra-packages: ${{ inputs.extra-packages }}
+        cache-version: ${{ inputs.cache-version }}

.github/workflows/pkgdown.yaml

@@ -17,23 +17,17 @@ jobs:
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
       contents: write
     steps:
       - uses: actions/checkout@v6
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: ./.github/workflows/install
         with:
-          extra-packages: any::pkgdown, local::.
+          token: ${{ secrets.GITHUB_TOKEN }}
           needs: website
+          extra-packages: any::pkgdown local::.
+          cache-version: "1"
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

.github/workflows/pr-commands.yaml

@@ -11,23 +11,19 @@ jobs:
     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@v6
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: ./.github/workflows/install
         with:
-          extra-packages: any::roxygen2
+          token: ${{ secrets.GITHUB_TOKEN }}
           needs: pr-document
+          extra-packages: any::roxygen2
+          cache-version: "1"
 
       - name: Document
         run: roxygen2::roxygenise()
@@ -48,8 +44,6 @@ jobs:
     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@v6
 
@@ -59,13 +53,12 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
 
-      - name: Install dependencies
-        run: install.packages("styler")
-        shell: Rscript {0}
+      - name: Install air
+        uses: posit-dev/setup-air@v1
 
       - name: Style
-        run: styler::style_pkg()
-        shell: Rscript {0}
+        run: air format .
+        shell: bash
 
       - name: commit
         run: |

.github/workflows/test-coverage.yaml

@@ -11,35 +11,41 @@ name: test-coverage
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
     steps:
       - uses: actions/checkout@v6
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: ./.github/workflows/install
         with:
-          extra-packages: any::covr
+          token: ${{ secrets.GITHUB_TOKEN }}
           needs: coverage
+          extra-packages: any::covr
+          cache-version: "1"
 
       - name: Test coverage
         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")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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