update coverage workflow

.github/workflows/cover.yaml

@@ -4,19 +4,19 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: cover
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
-  cover:
+  test-coverage:
     runs-on: ubuntu-latest
     env:
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: system dependencies
         if: runner.os == 'Linux'
@@ -26,35 +26,40 @@ jobs:
         with:
           use-public-rspm: true
 
-      - name: Add r-universe to repos
-        run: |
-          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',wlandau='https://wlandau.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
-        shell: Rscript {0}
-
       - 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(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