test-coverage.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Test coverage via covr, uploaded to Codecov. Python is provided the same way
# R-CMD-check.yaml does -- through nat.python's own simple_python() engine -- so
# coverage exercises the exact provisioning path nat.python ships.
on:
  push:
    branches: [main, master]
  pull_request:
  workflow_dispatch:

name: test-coverage

permissions: read-all

jobs:
  test-coverage:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CODECOV_TOKEN: ${{ secrets.CODECOV_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: Install nat.python and provision Python via simple_python()
        # Mirrors R-CMD-check.yaml's default leg, but provisions through
        # nat.python's own simple_python(): miniconda + r-reticulate + pandas
        # (via pip). pyarrow is added so the use_arrow = TRUE conversion path is
        # exercised. RETICULATE_PYTHON is then pinned to that interpreter for the
        # coverage run.
        shell: Rscript {0}
        run: |
          pak::local_install()
          library(nat.python)
          simple_python("minimal", pkgs = "pyarrow")
          print(py_module_info(c("numpy", "pandas", "pyarrow")))
          cat(sprintf("RETICULATE_PYTHON=%s\n", reticulate::py_config()$python),
              file = Sys.getenv("GITHUB_ENV"), append = TRUE)

      - name: Test coverage
        shell: Rscript {0}
        run: |
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
          )
          covr::to_cobertura(cov)

      - uses: codecov/codecov-action@v4
        with:
          fail_ci_if_error: false
          file: ./cobertura.xml
          plugin: noop
          disable_search: true
          token: ${{ secrets.CODECOV_TOKEN }}

      - name: Show testthat output
        if: always()
        shell: bash
        run: |
          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true

      - name: Upload test results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: coverage-test-failures
          path: ${{ runner.temp }}/package