test-coverage.yaml

# 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: test-coverage

jobs:
  test-coverage:
    runs-on: ubuntu-latest
    env:
      NOT_CRAN: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      REDCAP_URI: ${{ secrets.REDCAP_URI }}
      REDCAPTIDIER_CLASSIC_API: ${{ secrets.REDCAPTIDIER_CLASSIC_API }}
      REDCAPTIDIER_LONGITUDINAL_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_API }}
      REDCAPTIDIER_LONGITUDINAL_NOARMS_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_NOARMS_API }}
      SUPERHEROES_REDCAP_API: ${{ secrets.SUPERHEROES_REDCAP_API }}
      REDCAPTIDIER_RESTRICTED_ACCESS_API: ${{ secrets.REDCAPTIDIER_RESTRICTED_ACCESS_API }}
      REDCAPTIDIER_CLASSIC_NOREPEAT_API: ${{ secrets.REDCAPTIDIER_CLASSIC_NOREPEAT_API }}
      REDCAPTIDIER_LONGITUDINAL_NOREPEAT_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_NOREPEAT_API }}
      REDCAPTIDIER_REPEAT_FIRST_INSTRUMENT_API: ${{ secrets.REDCAPTIDIER_REPEAT_FIRST_INSTRUMENT_API }}
      REDCAPTIDIER_DEEP_DIVE_VIGNETTE_API: ${{ secrets.REDCAPTIDIER_DEEP_DIVE_VIGNETTE_API }}
      REDCAPTIDIER_REPEATING_EVENT_API: ${{ secrets.REDCAPTIDIER_REPEATING_EVENT_API }}
      REDCAPTIDIER_LARGE_SPARSE_API: ${{ secrets.REDCAPTIDIER_LARGE_SPARSE_API }}
      REDCAPTIDIER_DAG_API: ${{ secrets.REDCAPTIDIER_DAG_API }}
      REDCAPTIDIER_LONGITUDINAL_DAG_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_DAG_API }}
      REDCAPTIDIER_MDC_API: ${{ secrets.REDCAPTIDIER_MDC_API }}
    steps:
      - name: Update Ubuntu, Install cURL Headers, add Libraries
        run: |
         sudo apt-get update
         sudo apt-get install libcurl4-openssl-dev libxml2-dev

      - uses: actions/checkout@v3

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

      - name: Install pak dependency
        run: |
          install.packages("pak")
        shell: Rscript {0}

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::covr, any::xml2
          needs: coverage

      - name: Test coverage
        run: covr::codecov(quiet = FALSE)
        shell: Rscript {0}