Merge pull request #403 from villegar/v6.3.4-dev

V6.3.4 dev - test coverage report

Author: StuartWheater

.github/workflows/dsBase_test_suite.yaml

@@ -22,6 +22,8 @@ jobs:
   dsBase_test_suite:
     runs-on: ubuntu-latest
     timeout-minutes: 120
+    permissions:
+      contents: write
 
     # These should all be constant, except TEST_FILTER. This can be used to test 
     # subsets of test files in the testthat directory. Options are like:

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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

README.md

@@ -4,6 +4,7 @@
 [![](https://www.r-pkg.org/badges/version/dsBase?color=black)](https://cran.r-project.org/package=dsBase)
 [![R build
 status](https://github.com/datashield/dsBase/workflows/R-CMD-check/badge.svg)](https://github.com/datashield/dsBase/actions)
+[![Codecov test coverage](https://codecov.io/gh/datashield/dsBase/graph/badge.svg)](https://app.codecov.io/gh/datashield/dsBase)
 
 ## Installation