Add ES-based metadata retrieval #280
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| --- | |
| name: Code Checks | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| jobs: | |
| lint-format: | |
| name: Linting and Formatting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout the repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Set up workspace | |
| uses: ./.github/actions/setup-workspace | |
| - name: Lint | |
| run: ruff check --output-format=github src | |
| shell: bash | |
| - name: Check formatting | |
| run: ruff format --check --diff | |
| - name: Check dependencies | |
| run: deptry src | |
| typing: | |
| name: Static Typing | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout the repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Set up workspace | |
| uses: ./.github/actions/setup-workspace | |
| - name: Check static typing | |
| run: basedpyright src | |
| shell: bash | |
| tests: | |
| name: Tests and coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout the repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Set up workspace | |
| uses: ./.github/actions/setup-workspace | |
| - name: Test with pytest | |
| run: pytest --junitxml=junit/test-results.xml --cov=src --cov-config=pyproject.toml | |
| - name: Test summary | |
| uses: test-summary/action@v2 | |
| with: | |
| paths: junit/test-results.xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: BioPack-team/retriever | |
| docker: | |
| name: Dockerfile builds | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout the repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Test building container | |
| run: docker build -t biopack-team/retriever . |