docker-publish.yml

name: Docker

on:
  push:
    branches:
      - main
      - dev
      - release
    tags: [ 'v*.*.*' ]
  pull_request:
    branches:
      - main
      - dev

env:
  REGISTRY: docker.io
  IMAGE_NAME: thomasenzlein/m2ara
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

jobs:
  build:

    runs-on: ubuntu-latest
    permissions:
      contents: read
      packages: write
      id-token: write

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      # Set up R environment
      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.3.2'

      # Install system dependencies for R packages
      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get -y install libcurl4-openssl-dev libssl-dev libxml2-dev build-essential libxml2-dev libgit2-dev libudunits2-dev librsvg2-dev tk libharfbuzz-dev libfribidi-dev

      # Install R package dependencies from req.txt
      - name: Install R packages from req.txt
        run: |
          R -e "install.packages('pak')"
          R -e "packages <- readLines('req.txt'); pak::pkg_install(packages)"

       # Install R package dependencies from req.txt
      - name: Install MALDIcellassay
        run: |
          R -e "pak::pkg_install('CeMOS-Mannheim/MALDIcellassay')"

      # Install testthat if it's not listed in req.txt
      - name: Install testthat
        run: R -e "if (!require('testthat')) pak::pkg_install('testthat')"

      # Run tests
      - name: Run tests
        run: R -e "source('tests/testthat.R')"

      # This step will be skipped if the tests fail
      # Set up Docker Buildx
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3.3.0

      - name: Log into registry ${{ env.REGISTRY }}
        if: github.event_name != 'pull_request'
        uses: docker/login-action@v3.1.0
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ secrets.dockeriouser }}
          password: ${{ secrets.dockeriopwd }}

      - name: Create cache directory
        run: mkdir -p /tmp/.buildx-cache

      - name: Cache Docker layers
        id: cache-docker-layers
        uses: actions/cache@v4.0.2
        with:
          path: /tmp/.buildx-cache
          key: ${{ runner.os }}-buildx-${{ github.sha }}
          restore-keys: |
           ${{ runner.os }}-buildx-

      - name: Extract Docker metadata
        id: meta
        uses: docker/metadata-action@v5.5.1
        with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}

      - name: Build and push Docker image
        id: build-and-push
        uses: docker/build-push-action@v5.3.0
        with:
          context: .
          push: ${{ github.event_name != 'pull_request' }}
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}
          cache-from: type=gha
          cache-to: type=gha,mode=max