Merge pull request #807 from pharmaR/jt-800-fix_codecov

Fix test-coverage workflow

.github/workflows/test-coverage.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -9,6 +9,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -24,21 +26,45 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y texlive-xetex
       
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          use-public-rspm: true
+          use-public-rspm: false
           r-version: 'renv'
 
       - uses: r-lib/actions/setup-renv@v2
 
-      - name: Install riskassessment
-        shell: bash
-        run: R CMD INSTALL --preclean .
-
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

manifest.json

@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <[email protected]>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-09 17:38:19 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-10 13:11:46 UTC; unix"
       }
     },
     "reprex": {
@@ -6175,7 +6175,7 @@
       "checksum": "d74482ddef0a4941a51c077f5ea60e10"
     },
     ".github/workflows/test-coverage.yaml": {
-      "checksum": "c0baef024db9ec1299aae4098e904e9c"
+      "checksum": "a854cdb9e1cfbcbbf5ccffdf4755606b"
     },
     ".github/workflows/write-manifest.yaml": {
       "checksum": "cdfc1470af653982867daed2b99d5b97"