Fix CODECOV_TOKEN and improve dependency installation

Updated CODECOV_TOKEN reference and adjusted installation commands for BiocManager and phyloseq.

Author: adw96

.github/workflows/test-coverage.yaml

@@ -13,7 +13,7 @@ jobs:
     runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN_tinyvamp }} 
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     steps:
       - uses: actions/checkout@v3
 
@@ -38,17 +38,12 @@ jobs:
       - name: Install dependencies
         run: |
           install.packages(c("remotes"))
-          if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install(c("phyloseq"), ask = FALSE)
+          if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
+          BiocManager::install("phyloseq", ask = FALSE)
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}
-
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v5
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: statdivlab/tinyvamp