r-check.yml

# Checks for the R package in `r/`.
#
# Derived from https://github.com/r-lib/actions/tree/v2/examples. Every action
# that touches the package is pointed at the `r/` subdirectory through its
# `working-directory` input, because the repository root holds the Python
# package rather than an R package.
#
# Live terminology server access: the unit suite answers every request from
# canned fixtures, so it needs no network. The one exception is
# `r/tests/testthat/test-integration.R`, which runs the README example against
# the CSIRO public Ontoserver. It skips here for two independent reasons:
#
# 1. `skip_on_cran()` skips unless `NOT_CRAN` is set. Neither `R CMD check` nor
#    covr sets it, so both jobs below skip the test on that ground alone.
# 2. It also skips whenever `CI` is set, which GitHub Actions always sets. This
#    covers anyone who later adds a job running `devtools::test()` or
#    `testthat::test_local()`, both of which do set `NOT_CRAN`.
#
# A terminology server outage or a content change on the server therefore
# cannot fail this workflow. The live check runs locally, where `CI` is unset
# and `devtools::test()` sets `NOT_CRAN`.

name: R check

on:
  push:
    branches: [main]
  pull_request:

permissions: read-all

jobs:
  check:
    runs-on: ${{ matrix.os }}
    name: R CMD check (${{ matrix.os }})

    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v4

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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          working-directory: r
          extra-packages: any::rcmdcheck
          needs: check

      - uses: r-lib/actions/check-r-package@v2
        with:
          working-directory: r
          upload-snapshots: true

  coverage:
    runs-on: ubuntu-latest
    name: Coverage

    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:
          working-directory: r
          extra-packages: any::covr
          needs: coverage

      # Results are printed to the job log. There is no external coverage
      # service; read the per-file table in the step output.
      - name: Report coverage
        run: |
          coverage <- covr::package_coverage("r", quiet = FALSE)
          print(coverage)
          uncovered <- covr::zero_coverage(coverage)
          if (nrow(uncovered) > 0) {
            print(uncovered)
            stop(sprintf("%d uncovered line(s)", nrow(uncovered)))
          }
          message("All lines covered.")
        shell: Rscript {0}