Merge pull request #139 from openpharma/ls_update_codecov

Fix codecov uploads

.github/workflows/test-coverage.yaml

@@ -15,7 +15,6 @@ jobs:
     env:
       RENV_PROFILE: "full"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       RENV_CONFIG_SANDBOX_ENABLED: false
 
     steps:
@@ -39,21 +38,28 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          packages: any::covr
+          packages: any::covr any::xml2
           needs: coverage 
-
-      - name: Install clinsight
-        shell: bash
-        run: R CMD INSTALL --preclean .
 
       - name: Test coverage
-        run: covr::codecov(
-           quiet = FALSE,
-           clean = FALSE,
-           install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"),
-           token = Sys.getenv("CODECOV_TOKEN")
-           )
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            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()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.0.9009
+Version: 0.1.0.9010
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),

NEWS.md

@@ -12,6 +12,7 @@
 
 ## Bug fixes
 
+- The test-coverage GHA workflow is updated so that codecov uploads work again.
 
 # clinsight 0.1.1
 

inst/golem-config.yml

@@ -1,6 +1,6 @@
 default:
   golem_name: clinsight
-  golem_version: 0.1.0.9009
+  golem_version: 0.1.0.9010
   app_prod: no
   user_identification: test_user
   study_data: !expr clinsight::clinsightful_data