r.yml

name: R

on:
  pull_request:
    branches:
      - "*"
  push:
    branches:
      - "master"

env:
  cache-version: "cache-v1"

jobs:
  build:
    strategy:
      max-parallel: 5
      matrix:
        config:
          - { os: ubuntu-latest }
          - { os: windows-latest }
          - { os: macos-latest }
    runs-on: ${{ matrix.config.os }}
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v4

      - name: Setup R and Bioconductor
        uses: grimbough/bioc-actions/setup-bioc@v1
        id: install-r
        with:
          bioc-version: release

      - name: Get R version
        id: R
        run: |
          R --version > VERSION
          echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT
        shell: bash -l {0}

      - name: Get Bioconductor version
        id: BIOC
        run: |
          echo "version=$R_BIOC_VERSION" >> $GITHUB_OUTPUT
        shell: bash -l {0}

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

      - name: Cache R packages
        uses: actions/cache@v4
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ steps.BIOC.outputs.version}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ steps.BIOC.outputs.version}}-r-${{ steps.R.outputs.version}}-

      - name: Install and check
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::rcmdcheck
            covr
            pkgdown
          needs: check

      - name: Test coverage
        if: github.actor == 'zktuong' && matrix.config.os == 'ubuntu-latest'
        run: |
          Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")'
        shell: bash -l {0}