🐛 Better error behavior for repeated calls of standardize
#9178
Workflow file for this run
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| name: build | |
| on: | |
| push: | |
| branches: [release] | |
| pull_request: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_EVENT_NAME: ${{ github.event_name }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| group: | |
| - "unit-core" | |
| - "unit-storage" | |
| - "tutorial" | |
| - "guide" | |
| - "biology" | |
| - "faq" | |
| - "storage" | |
| - "cli" | |
| timeout-minutes: 15 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| if: ${{ matrix.group == 'storage' }} | |
| with: | |
| python-version: "3.9" | |
| - uses: actions/setup-python@v5 | |
| if: ${{ matrix.group == 'unit-storage' }} | |
| with: | |
| python-version: "3.11" # there are problems with installation time with python 3.12 | |
| - uses: actions/setup-python@v5 | |
| if: ${{ matrix.group != 'storage' && matrix.group != 'unit-storage'}} | |
| with: | |
| python-version: "3.12" | |
| - name: cache pre-commit | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-${{ 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" | |
| - 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: ${{ matrix.group == 'tutorial' }} # choose a fast-running a group | |
| - run: nox -s "install_ci(group='${{ matrix.group }}')" | |
| - uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: us-east-1 | |
| - run: nox -s "build(group='${{ 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: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: us-east-1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" # use 3.10 because 3.11+ give issues (ablog lacks 3.12 support) | |
| - run: pip install "laminci@git+https://x-access-token:${{ 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/[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 }} | |
| - 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 |