Merge pull request #323 from mixOmicsTeam/configure-codecov3

Configure codecov3

.Rbuildignore

@@ -26,3 +26,4 @@ Library
 ignore
 .Renviron
 ^codecov\.yml$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/actions.yml

@@ -205,20 +205,4 @@ jobs:
           password: ${{ secrets.DOCKER_PASSWORD }}
           repository: mixomicsteam/mixomics
           tags: ${{ needs.versions.outputs.docker_tag }}
-          build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} 
-
-      - name: Test coverage 🔍
-        if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
-        # the commands between 'set +e' and 'set -e' are run without throwing any error
-        run: |
-          set +e
-          Rscript -e "covr::codecov(type = c('tests', 'examples'))"
-          set -e
-
-      # - name: Notify Slack 📣
-      #   uses: 8398a7/action-slack@v3
-      #   with:
-      #     status: ${{ job.status }}
-      #     fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message)
-      #   env:
-      #     SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets
+          build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} 

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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:
+    branches: [main, master]
+
+name: Code Coverage
+
+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")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: 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