update workflows

wjakethompson · Jan 7, 2025 · e96015e · e96015e
1 parent af13f2d
commit e96015e
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,10 +1,13 @@
+# 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, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -16,25 +19,24 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: 'release', rtools: ''}
-          - {os: windows-latest, r: 'release', rtools: '43'}
-          - {os: ubuntu-latest, r: 'devel', rtools: '', http-user-agent: 'release'}
-          - {os: ubuntu-latest, r: 'release', rtools: ''}
-          - {os: ubuntu-latest, r: 'oldrel-1', rtools: ''}
+          - {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@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          rtools-version: ${{ matrix.config.rtools }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
           extra-repositories: https://mc-stan.org/r-packages/
@@ -57,3 +59,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/lint.yaml b/.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, master]
   pull_request:
-    branches: [main, master]
 
-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:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,13 +1,16 @@
+# 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, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -17,9 +20,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -43,7 +47,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -1,8 +1,12 @@
+# 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
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -11,9 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -22,7 +27,6 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -50,9 +54,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,19 +1,22 @@
+# 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, master]
   pull_request:
-    branches: [main, master]
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     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:
@@ -25,6 +28,7 @@ jobs:
           cache-version: 3
           extra-packages: |
             any::covr
+            any::xml2
             github::stan-dev/cmdstanr
           upgrade: 'TRUE'
           needs: coverage
@@ -37,7 +41,7 @@ jobs:
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             line_exclusions = list("src/stanExports_gqs_loglik.h",
@@ -50,6 +54,15 @@ jobs:
           )
         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: |
@@ -59,7 +72,7 @@ jobs:
 
       - 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
diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml
@@ -18,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with: