Gregor metadata airtable update #3265
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| name: Unit Tests | |
| # Run the test suite on pushes (incl. merges) to master and dev | |
| # Run the test suite when a PR is opened, pushed to, or reopened | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| jobs: | |
| python: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| services: | |
| # Label used to access the service container | |
| postgres: | |
| # Docker Hub image | |
| image: postgres | |
| # Provide the password for postgres | |
| env: | |
| POSTGRES_PASSWORD: "pgtest" | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # Maps tcp port 5432 on service container to the host | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/setup-java@v1 | |
| with: | |
| java-version: "8" # The JDK version needed by hail | |
| java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk | |
| architecture: x64 # (x64 or x86) - defaults to x64 | |
| - name: Use pip cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| pip- | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Run coverage tests | |
| run: | | |
| coverage run --source="./matchmaker","./seqr","./reference_data","./panelapp" --omit="*/migrations/*","*/apps.py" manage.py test -p '*_tests.py' -v 2 reference_data seqr matchmaker panelapp | |
| coverage report --fail-under=99 | |
| hail_search: | |
| runs-on: ubuntu-latest | |
| container: hailgenetics/hail:0.2.115 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip wheel | |
| pip install -r hail_search/requirements-test.txt | |
| - name: Run coverage tests | |
| run: | | |
| export DATASETS_DIR=./hail_search/fixtures | |
| coverage run --source="./hail_search" --omit="./hail_search/__main__.py","./hail_search/test_utils.py" -m pytest hail_search/ | |
| coverage report --fail-under=99 | |
| nodejs: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| node-version: [14] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Use Node.js ${{ matrix.node-version }} | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: ${{ matrix.node-version }} | |
| cache: "npm" | |
| cache-dependency-path: ui/package-lock.json | |
| - run: npm install -g [email protected] | |
| - run: npm ci | |
| working-directory: ./ui | |
| - run: npm test | |
| working-directory: ./ui |