Update test coverage workflow

.github/workflows/test-coverage.yaml

@@ -1,10 +1,8 @@
 on:
   push:
-    branches:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
@@ -14,24 +12,58 @@ permissions:
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 'release'
+          use-public-rspm: true
 
-      - name: Install dependencies
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Install package dependencies
         run: |
           install.packages("pak")
           pak::pkg_install(".", dependencies = TRUE)
-          pak::pkg_install("covr")
         shell: Rscript {0}
 
       - 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")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tailor
 Type: Package
 Title: Tool for Adapter-domain Identification and Linking Of RBPs
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
     person("András", "Asbóth", role = c("aut", "cre"),
         email = "sbthandras+bioinfo@gmail.com",
@@ -29,6 +29,8 @@ Imports:
     reshape2,
     tibble,
     tidyr
+Suggests:
+    testthat
 Remotes:
     stitam/breakpoint
 License: GPL (>= 3)