Add feature_type column to var (#1310) #2582
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| name: Python cell_census build | |
| on: | |
| pull_request: | |
| paths: | |
| - "api/python/**" | |
| - "tools/cellxgene_census_builder/**" | |
| - ".github/workflows/**" # Re-run if a workflow is modified - useful to test workflow changes in PRs | |
| push: | |
| branches: [main] | |
| workflow_dispatch: | |
| jobs: | |
| build_python_wheels: | |
| name: Build Python wheel and sdist | |
| runs-on: [self-hosted, Linux, X64] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install deps | |
| run: | | |
| python -m pip install -U pip setuptools build | |
| - name: Build | |
| run: python -m build | |
| working-directory: api/python/cellxgene_census/ | |
| - name: Upload build artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: api/python/cellxgene_census/dist/* | |
| build_docker_container: | |
| name: Build Docker image for Census Builder | |
| runs-on: [self-hosted, Linux, X64] | |
| permissions: # these permissions must be set for AWS auth to work! | |
| id-token: write | |
| contents: read | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_PROD_ROLE_TO_ASSUME }} | |
| role-session-name: PushDockerImage | |
| - name: Login to Amazon ECR | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| - name: Install up-to-date docker buildx | |
| run: | | |
| # In lieu of having docker buildx plugin installed on our base runner image, | |
| # install it manually. https://docs.docker.com/engine/install/ubuntu/ | |
| for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do | |
| sudo apt-get remove $pkg || echo "${pkg} not installed" | |
| done | |
| sudo apt-get update | |
| sudo apt-get install -y ca-certificates curl | |
| sudo install -m 0755 -d /etc/apt/keyrings | |
| sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc | |
| sudo chmod a+r /etc/apt/keyrings/docker.asc | |
| # Add the repository to Apt sources: | |
| echo \ | |
| "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \ | |
| $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \ | |
| sudo tee /etc/apt/sources.list.d/docker.list > /dev/null | |
| sudo apt-get update | |
| sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin | |
| - name: Install python deps | |
| run: | | |
| python -m pip install -U pip setuptools build | |
| - name: Build package | |
| run: python -m build | |
| working-directory: tools/cellxgene_census_builder/ | |
| - name: Build and tag docker image to Amazon ECR | |
| env: | |
| REGISTRY: ${{ secrets.ECR_PROD_REGISTRY }} | |
| REPOSITORY: cellxgene-census-builder | |
| run: | | |
| GIT_SHA=$(git rev-parse --short HEAD) | |
| docker build --build-arg=COMMIT_SHA=$GIT_SHA -t $REGISTRY/$REPOSITORY:$GIT_SHA . | |
| working-directory: tools/cellxgene_census_builder/ | |
| - name: Push docker image to Amazon ECR | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| env: | |
| REGISTRY: ${{ secrets.ECR_PROD_REGISTRY }} | |
| REPOSITORY: cellxgene-census-builder | |
| run: | | |
| GIT_SHA=$(git rev-parse --short HEAD) | |
| docker push $REGISTRY/$REPOSITORY:$GIT_SHA | |
| docker tag $REGISTRY/$REPOSITORY:$GIT_SHA $REGISTRY/$REPOSITORY:latest | |
| docker push $REGISTRY/$REPOSITORY:latest |