just throwing stuff against the wall to try to make code coverage work

Author: adw96

.github/workflows/test-coverage.yaml

@@ -13,12 +13,11 @@ jobs:
     runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v3
-
       - uses: r-lib/actions/setup-r@v2
-
       - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
@@ -42,20 +41,14 @@ jobs:
           BiocManager::install("phyloseq", ask = FALSE)
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
-          install.packages("xml2")
         shell: Rscript {0}
 
-      - name: Build coverage report
+      - name: Debug token presence
         run: |
-          cov <- covr::package_coverage()
-          print(cov)
-          covr::to_cobertura(cov, filename = "coverage.xml")
+          cat("Has token? ", nzchar(Sys.getenv("CODECOV_TOKEN")), "\n", sep = "")
+          cat("Token chars: ", nchar(Sys.getenv("CODECOV_TOKEN")), "\n", sep = "")
         shell: Rscript {0}
 
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v5
-        with:
-          token: ${{ secrets.CODECOV_TOKEN_tinyvamp }}
-          files: coverage.xml
-          slug: statdivlab/tinyvamp
-          fail_ci_if_error: true
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}