From c0d6704fd934694da545d7145416d07e1a45fec1 Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Wed, 15 May 2024 16:47:50 +0200
Subject: [PATCH] Update actions

---
 .github/workflows/R-CMD-check.yaml   |  5 +++--
 .github/workflows/pkgdown.yaml       |  2 ++
 .github/workflows/pr-commands.yaml   |  2 ++
 .github/workflows/test-coverage.yaml | 17 ++++++++++++++---
 4 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 4ea965a..f770ae6 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -13,6 +13,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -28,8 +30,6 @@ jobs:
 
           - {os: windows-latest, r: 'release'}
           - {os: windows-latest, r: 'release', quarto: 'pre-release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
@@ -72,3 +72,4 @@ 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/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index a7276e8..c9f0165 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
index eea58c5..d1f7650 100644
--- a/.github/workflows/pr-commands.yaml
+++ b/.github/workflows/pr-commands.yaml
@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 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') }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index d74b036..b616ee8 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -8,6 +8,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -28,23 +30,32 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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