upgrade to irods v4.3.3 in ci (#1815) #1063
Workflow file for this run
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| 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:[email protected]/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 | |
| - 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' }} |