R-CMD-check.yaml

on:
  push:
    branches: [main]
  pull_request:
    branches: [main, development]

name: CI/CD

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macos-latest,   r: 'release'}
          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
          - {os: ubuntu-latest,   r: 'release'}
          - {os: ubuntu-latest,   r: 'oldrel-1'}

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

    steps:
      - uses: actions/checkout@v4

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

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

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

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

  Test-Docker-Build:
    # needs: R-CMD-check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v1

      - name: Get TAG from DESCRIPTION
        run: |
          TAG=$(grep  'Version:' DESCRIPTION  | grep -oE '[0-9]+(\.[0-9]+)*')
          echo "TAG=$TAG" >> $GITHUB_ENV

      - name: Set up QEMU
        uses: docker/setup-qemu-action@v3

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3
      
      - name: Test Docker Build
        uses: docker/build-push-action@v5
        with:
          context: .
          platforms: linux/amd64
          file: ./Dockerfile
          push: false

  Code-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: any::covr
          needs: coverage

      - name: Test coverage
        run: |
          covr::codecov(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
            token = "${{ secrets.CODECOV_TOKEN }}"
          )
        shell: Rscript {0}

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

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

      

  Upload-Docker:
    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/newAnnotationGx'
    # needs: R-CMD-check
    needs: R-CMD-check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v1

      - name: Get TAG from DESCRIPTION
        run: |
          TAG=$(grep  'Version:' DESCRIPTION  | grep -oE '[0-9]+(\.[0-9]+)*')
          echo "TAG=$TAG" >> $GITHUB_ENV

      - name: Set up QEMU
        uses: docker/setup-qemu-action@v3

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Login to Docker Hub
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.BHKLAB_DOCKERHUB_USERNAME }}
          password: ${{ secrets.BHKLAB_DOCKERHUB_ACCESS_KEY }}

      - name: Login to the GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Extract metadata (tags, labels) for Docker
        id: meta
        uses: docker/metadata-action@v3
        with:
          images: |
            bhklab/annotationgx-r:${{ env.TAG }}
            bhklab/annotationgx-r:latest

      - name: Build
        uses: docker/build-push-action@v5
        with:
          context: .
          platforms: linux/amd64,linux/arm64
          file: ./Dockerfile
          push: true
          tags: |
            bhklab/annotationgx-r:${{ env.TAG }}
            bhklab/annotationgx-r:latest