🐛 Sample level metadata is now optional in SpatialDataCurator & UX improvements #9672
Workflow file for this run
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| name: build | |
| on: | |
| push: | |
| branches: [release] | |
| pull_request: | |
| jobs: | |
| pre-filter: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: dorny/paths-filter@v3 | |
| id: changes | |
| if: github.event_name != 'push' | |
| with: | |
| filters: | | |
| curator: | |
| - 'lamindb/curators/**' | |
| - 'tests/curators/test_curator.py' | |
| - id: set-matrix | |
| shell: bash | |
| run: | | |
| BASE_GROUPS=$(jq -n -c '["unit-core", "unit-storage", "tutorial", "guide", "biology", "faq", "storage", "cli"]') | |
| if [[ "${{ github.event_name }}" == "push" || "${{ steps.changes.outputs.curator }}" == "true" ]]; then | |
| # Run everything on push or when curator paths change | |
| MATRIX=$(jq -n -c --argjson groups "$BASE_GROUPS" '{group: ($groups + ["curator"])}') | |
| else | |
| # Otherwise only run base groups | |
| MATRIX=$(jq -n -c --argjson groups "$BASE_GROUPS" '{group: $groups}') | |
| fi | |
| # Output as single line for GitHub Actions | |
| echo "matrix=$(echo "$MATRIX" | jq -c .)" >> $GITHUB_OUTPUT | |
| # Pretty print for debugging | |
| echo "Generated matrix:" | |
| echo "$MATRIX" | jq . | |
| test: | |
| needs: pre-filter | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{fromJson(needs.pre-filter.outputs.matrix)}} | |
| timeout-minutes: 15 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: | | |
| ${{ matrix.group == 'storage' && '3.10' || | |
| '3.12' | |
| }} | |
| - name: cache pre-commit | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }} | |
| - name: cache postgres | |
| if: ${{ matrix.group == 'faq' || matrix.group == 'unit-core' || matrix.group == 'unit-storage' }} | |
| id: cache-postgres | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/postgres.tar | |
| key: cache-postgres-0 | |
| - name: cache postgres miss | |
| if: ${{ steps.cache-postgres.outputs.cache-hit != 'true' }} | |
| run: docker pull postgres:latest && docker image save postgres:latest --output ~/postgres.tar | |
| - name: cache postgres use | |
| if: ${{ steps.cache-postgres.outputs.cache-hit == 'true' }} | |
| run: docker image load --input ~/postgres.tar | |
| - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci" | |
| - run: nox -s configure_coverage -- '${{needs.pre-filter.outputs.matrix}}' | |
| - name: install postgres | |
| if: ${{ matrix.group == 'faq' }} | |
| run: sudo apt-get install libpq-dev | |
| - name: install graphviz | |
| if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' }} | |
| run: sudo apt-get -y install graphviz | |
| - run: nox -s lint | |
| if: ${{ matrix.group == 'tutorial' }} | |
| - run: nox -s "install_ci(group='${{ matrix.group }}')" | |
| - uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: us-east-1 | |
| - run: nox -s "test(group='${{ matrix.group }}')" | |
| - name: upload coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage--${{ matrix.group }} | |
| path: .coverage | |
| include-hidden-files: true | |
| - name: upload docs | |
| if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' || matrix.group == 'faq' || matrix.group == 'storage' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docs-${{ matrix.group }} | |
| path: ./docs/${{ matrix.group }} | |
| docs: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - 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 | |
| - uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: us-east-1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci" | |
| - run: nox -s "install_ci(group='docs')" | |
| - uses: actions/download-artifact@v4 | |
| - run: nox -s docs | |
| - uses: nwtgck/actions-netlify@v1.2 | |
| 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 }} | |
| - uses: peter-evans/repository-dispatch@v2 | |
| if: ${{ github.event_name == 'push' }} | |
| with: | |
| token: ${{ secrets.LAMIN_BUILD_DOCS }} | |
| repository: "laminlabs/lamin-docs" | |
| event-type: build | |
| coverage: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - run: | | |
| python -m pip install -U uv | |
| uv pip install --system coverage[toml] | |
| uv pip install --system --no-deps . | |
| - uses: actions/download-artifact@v4 | |
| - 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 }} | |
| dispatch: | |
| if: ${{ github.event_name == 'push' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: peter-evans/repository-dispatch@v2 | |
| with: | |
| token: ${{ secrets.LAMIN_BUILD_DOCS }} | |
| repository: "laminlabs/lamindb-dispatch" | |
| event-type: build |