added test-coverage

.github/workflows/R-CMD-check.yml

@@ -33,7 +33,7 @@ jobs:
           r-version: "4.3.3"
           use-public-rspm: true
 
-      - name: Install dependencies
+      - name: Install R packages
         uses: r-lib/actions/setup-renv@v2
         with:
           cache-version: 1

.github/workflows/test-coverage.yml

@@ -0,0 +1,68 @@
+name: test coverage
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+
+    # env:
+    #   RENV_CONFIG_PAK_ENABLED: true
+    # with above uncommented, the workflow fails with the following error:
+    # Error in remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...),
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgit2-dev libsqliteodbc
+
+      - name: Create custom odbcinst.ini in a user-accessible directory
+        run: |
+          echo "[SQLite]" >> $HOME/odbcinst.ini
+          echo "Driver=/usr/lib/x86_64-linux-gnu/odbc/libsqlite3odbc.so" >> $HOME/odbcinst.ini
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "4.3.3"
+          use-public-rspm: true
+
+      - name: Install R packages
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          cache-version: 1
+          working-directory: phenoRankeR
+        env:
+          RENV_CONFIG_REPOS_OVERRIDE: ${{ env.RSPM }}
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
+
+
+
+