add test-coverage.yaml

.github/workflows/test-coverage.yaml

@@ -0,0 +1,69 @@
+# 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: devel
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-22.04
+    container: bioconductor/bioconductor_docker:devel
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout Repository
+      - uses: actions/checkout@v3
+
+      - name: Query dependencies
+        run: |
+          BiocManager::install(c("remotes", "covr"))
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-1-
+
+      - name: Install Dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          BiocManager::install("rcmdcheck", ask = FALSE, update = TRUE)
+        shell: Rscript {0}
+
+      - name: Check Package
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "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