This repository has been archived by the owner on Aug 7, 2024. It is now read-only.
✨ New ontology: CellType-cl-2024-02-13 #1761
Workflow file for this run
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| name: build | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main, staging] | |
| workflow_dispatch: | |
| env: | |
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | |
| jobs: | |
| test: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| GITHUB_EVENT_NAME: ${{ github.event_name }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11"] | |
| group: ["bionty-unit", "bionty-docs"] | |
| timeout-minutes: 25 | |
| steps: | |
| - name: Checkout main | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Checkout lndocs | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: laminlabs/lndocs | |
| ssh-key: ${{ secrets.READ_LNDOCS }} | |
| path: lndocs | |
| ref: main | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache pre-commit | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install -U pip uv | |
| python -m uv pip install --system -U laminci | |
| python -m uv pip install --system rich | |
| python -m uv pip install --system ipywidgets | |
| - name: Configure AWS | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: eu-central-1 | |
| - name: Lint | |
| if: matrix.python-version == '3.11' && matrix.group == 'bionty-unit' | |
| run: | | |
| nox -s lint | |
| - name: Build | |
| run: | | |
| nox -s "build(group='${{ matrix.group }}')" | |
| - name: upload coverage | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: coverage--${{ matrix.group }} | |
| path: .coverage | |
| - name: Deploy docs | |
| if: ${{ matrix.python-version == '3.11' && matrix.group == 'bionty-docs' }} | |
| id: netlify | |
| uses: nwtgck/[email protected] | |
| with: | |
| publish-dir: "_build/html" | |
| production-deploy: ${{ github.event_name == 'push' }} | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| enable-commit-comment: false | |
| env: | |
| NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} | |
| NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }} | |
| coverage: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - run: | | |
| python -m pip install -U pip uv | |
| uv pip install --system coverage[toml] | |
| uv pip install --system --no-deps . | |
| - uses: actions/download-artifact@v2 | |
| - name: run coverage | |
| run: | | |
| coverage combine coverage--*/.coverage* | |
| coverage report --fail-under=0 | |
| coverage xml | |
| - uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |