test-coverage.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
on:
  push:
    branches: main
  pull_request:
    branches: main
  workflow_dispatch:

name: test-coverage

jobs:
  test-coverage:
    runs-on: ubuntu-latest
    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:
          extra-packages: |
            covr
            pkgdown
            remotes

      - name: Checkout FAIRDataPipeline/FAIR-CLI
        uses: actions/checkout@v4
        with:
          repository: FAIRDataPipeline/FAIR-CLI
          path: FAIR-CLI
      - name: Move FAIR-CLI
        run: mv FAIR-CLI ../FAIR-CLI
      - name: Install Poetry
        uses: snok/install-poetry@v1
        with:
          virtualenvs-create: true
          virtualenvs-in-project: true

      - name: Install and initialise FAIR CLI
        run: |
          cd ../FAIR-CLI
          poetry install
          source $VENV
          cd '${{ github.workspace }}'
          fair registry install --version main
          fair registry start
        shell: bash

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        shell: Rscript {0}

      - name: Restore R package cache
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}

      - name: Install package
        run: R CMD INSTALL .

      - name: init
        run: |
          rDataPipeline::fair_init(
            name = "Sonia Mitchell",
            identifier = "https://orcid.org/0000-0003-1536-2066",
            endpoint = "http://127.0.0.1:8000/api/")
        shell: Rscript {0}
      - name: Test coverage
        env:
          _RUN_TESTS_: true
        run: covr::codecov()
        shell: Rscript {0}