build.yml

name: build
on: push
jobs:
  build:
    name: build
    runs-on: ubuntu-20.04
    strategy:
      matrix:
        python-version:
          - '3.9'
          - '3.10'
          - '3.11'
    services:
      postgres:
        image: postgres:16
        env:
          POSTGRES_DB: sodar
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
        options: >-
          --health-cmd "pg_isready -U postgres"
          --health-interval 10s
          --health-timeout 5s
          --health-retries 10
        ports:
          - 5432:5432
      redis:
        image: redis
        options: >-
          --health-cmd "redis-cli ping"
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 6379:6379
      irods:
        image: ghcr.io/bihealth/irods-docker:4.3.3-wip
        env:
          IRODS_AUTHENTICATION_SCHEME: native
          IRODS_DEFAULT_HASH_SCHEME: MD5
          IRODS_ICAT_DBSERVER: postgres
          IRODS_ICAT_DBUSER: postgres
          IRODS_ICAT_DBPASS: postgres
          IRODS_ZONE_NAME: sodarZone
          NO_WAIT: 1
        ports:
          - 4488:1247
    env:
      POSTGRES_HOST: 127.0.0.1
      POSTGRES_PORT: 5432
      DATABASE_URL: 'postgres://postgres:postgres@127.0.0.1/sodar'
    steps:
      - name: Install server dependencies
        run: |
          sudo apt update
          sudo apt install -qq build-essential zlib1g-dev libtiff5-dev libjpeg8-dev libfreetype6-dev
          sudo apt install -qq liblcms2-dev libwebp-dev libpq-dev graphviz-dev
      - name: Install Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Checkout repository
        uses: actions/checkout@v3
      - name: Install project Python dependencies
        run: |
          pip install wheel==0.42.0
          pip install -r requirements/local.txt
          pip install -r requirements/test.txt
      - name: Setup Node.js
        uses: actions/setup-node@v3
        with:
          node-version: 18.x
      - name: Build and run Vue app
        run: |
          npm ci --prefix samplesheets/vueapp
          nohup npm run -prefix samplesheets/vueapp serve &
      - name: Download icons
        run: python manage.py geticons
      - name: Run collectstatic
        run: python manage.py collectstatic --noinput
      # NOTE: Workaround for python-irodsclient>1.1.9 redirect issue
      - name: Add irods to /etc/hosts
        run: |
          sudo echo "127.0.0.1 irods" | sudo tee -a /etc/hosts
      - name: Run Django tests
        run: |
          coverage run --rcfile=.coveragerc manage.py test -v 2 --settings=config.settings.test
          coverage lcov
          coverage report
      - name: Run Vue app tests
        run: make test_samplesheets_vue
        if: ${{ matrix.python-version == '3.11' }}
      - name: Check Python linting
        run: flake8 .
      - name: Check Python formatting
        run: make black arg=--check
        if: ${{ matrix.python-version == '3.11' }}
      - name: Report coverage with Coveralls
        uses: coverallsapp/github-action@master
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          path-to-lcov: './coverage.lcov'
        if: ${{ matrix.python-version == '3.11' }}