test-coverage.yaml

name: test-coverage

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]

jobs:
  coverage:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      _R_CHECK_FORCE_SUGGESTS_: false
    steps:
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-pandoc@v2

      - name: Install system dependencies
        run: sudo apt-get update && sudo apt-get install -y libhdf5-dev

      # Build the standalone scconvert CLI binary and install it to inst/bin/
      # so it ships with the package that covr installs. Without this step,
      # sc_find_cli() returns NULL during covr and test-cli-integration.R
      # is entirely skipped -- C code never contributes to coverage.
      - name: Build CLI binary
        run: |
          cd src
          make -f Makefile.cli
          make -f Makefile.cli install-bin

      # Install the scverse Python stack so test-python-validation.R runs
      # in CI instead of skipping. micromamba is faster than full conda and
      # supports activation via setup-micromamba's built-in shell hook.
      - uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: '1.5.10-0'
          environment-file: tests/scverse-env.yml
          environment-name: scverse
          cache-environment: true
          init-shell: bash

      - name: Export RETICULATE_PYTHON and threading env
        shell: bash
        run: |
          echo "RETICULATE_PYTHON=${MAMBA_ROOT_PREFIX}/envs/scverse/bin/python" >> "$GITHUB_ENV"
          echo "NUMBA_THREADING_LAYER=tbb" >> "$GITHUB_ENV"
          echo "OMP_NUM_THREADS=1" >> "$GITHUB_ENV"
          echo "OPENBLAS_NUM_THREADS=1" >> "$GITHUB_ENV"
          echo "MKL_NUM_THREADS=1" >> "$GITHUB_ENV"

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: 'release'
          use-public-rspm: true

      - name: Pre-install BPCells from r-universe
        shell: Rscript {0}
        run: |
          install.packages(
            "BPCells",
            repos = c(
              bnprks = "https://bnprks.r-universe.dev",
              CRAN   = "https://cloud.r-project.org"
            )
          )

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          dependencies: 'c("Depends", "Imports", "LinkingTo", "Suggests")'
          extra-packages: any::covr any::reticulate
          cache-version: 1

      # install_path must live outside the R session tempdir: R deletes its
      # own Rtmp* directory when the process exits (clean = FALSE does not
      # prevent that), which used to take testthat.Rout.fail with it.
      - name: Run test coverage
        shell: Rscript {0}
        run: |
          covr::codecov(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "covr-install")
          )

      # covr runs the test suite via tools::testInstalledPackage, which writes
      # test output only to testthat.Rout(.fail) inside its install library --
      # the job log otherwise shows nothing but "running the tests failed",
      # making CI failures undiagnosable. Surface the file on failure.
      - name: Show testthat output on failure
        if: failure()
        shell: bash
        run: |
          found=0
          while IFS= read -r f; do
            found=1
            echo "=== $f ==="
            tail -n 500 "$f"
          done < <(find "$RUNNER_TEMP/covr-install" /tmp -name 'testthat.Rout*' 2>/dev/null)
          if [ "$found" -eq 0 ]; then
            echo "No testthat.Rout* files found"
          fi