Bump pycodestyle from 2.11.1 to 2.12.0 in /pipeline/seq_retrieval #497
Workflow file for this run
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| name: PR validation | |
| on: | |
| pull_request: | |
| types: [synchronize, opened, reopened, edited, labeled, unlabeled] | |
| branches: | |
| - main | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number }} | |
| cancel-in-progress: true | |
| jobs: | |
| container-build-context: | |
| name: define container image build context variables | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| tagname: ${{ steps.store_tagname.outputs.tagname }} | |
| steps: | |
| - name: Store image tag in env | |
| id: store_tagname | |
| shell: bash | |
| run: | | |
| echo "tagname=PR-${{ github.event.pull_request.number }}-validation" >> $GITHUB_OUTPUT | |
| pipeline-seq-retrieval-update-dependency-lock-files: | |
| name: pipeline/seq_retrieval update and upload dependency lock file | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./pipeline/seq_retrieval/ | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/seq_retrieval/ | |
| - name: Update lock files | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }} | |
| shell: bash | |
| run: | | |
| make pip-tools update-deps-lock update-test-deps-lock | |
| - name: Upload updated (main) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_deps_lock | |
| path: pipeline/seq_retrieval/requirements.txt | |
| if-no-files-found: error | |
| - name: Upload updated (test) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_tests_deps_lock | |
| path: pipeline/seq_retrieval/tests/requirements.txt | |
| if-no-files-found: error | |
| api-update-dependency-lock-files: | |
| name: api update and upload dependency lock file | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./api/ | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| api/ | |
| - name: Update lock files | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }} | |
| shell: bash | |
| run: | | |
| make pip-tools update-deps-lock update-test-deps-lock | |
| - name: Upload updated (main) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: api_deps_lock | |
| path: api/requirements.txt | |
| if-no-files-found: error | |
| - name: Upload updated (test) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: api_tests_deps_lock | |
| path: api/tests/requirements.txt | |
| if-no-files-found: error | |
| webui-update-dependency-lock-files: | |
| name: webui update and upload dependency lock file | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./webui/ | |
| steps: | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| webui/ | |
| - name: Update lock files | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }} | |
| shell: bash | |
| run: | | |
| make update-deps-lock | |
| - name: Upload updated lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: webui_deps_lock | |
| path: webui/package-lock.json | |
| if-no-files-found: error | |
| pipeline-aws-infra-update-dependency-lock-files: | |
| name: pipeline/aws_infra update and upload dependency lock file | |
| needs: | |
| - shared-aws-infra-package-build | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./pipeline/aws_infra/ | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/aws_infra/ | |
| - name: Download shared AWS infra package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_package | |
| path: /tmp/ | |
| - name: Update lock files | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }} | |
| shell: bash | |
| run: | | |
| make pip-tools update-deps-lock update-test-deps-lock | |
| - name: Upload updated (main) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pipeline_aws_infra_deps_lock | |
| path: pipeline/aws_infra/requirements.txt | |
| if-no-files-found: error | |
| - name: Upload updated (test) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pipeline_aws_infra_tests_deps_lock | |
| path: pipeline/aws_infra/tests/requirements.txt | |
| if-no-files-found: error | |
| api-aws-infra-update-dependency-lock-files: | |
| name: api/aws_infra update and upload dependency lock file | |
| needs: | |
| - shared-aws-infra-package-build | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./api/aws_infra/ | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| api/aws_infra/ | |
| - name: Download shared AWS infra package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_package | |
| path: /tmp/ | |
| - name: Update lock files | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }} | |
| shell: bash | |
| run: | | |
| make pip-tools update-deps-lock update-test-deps-lock | |
| - name: Upload updated (main) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: api_aws_infra_deps_lock | |
| path: api/aws_infra/requirements.txt | |
| if-no-files-found: error | |
| - name: Upload updated (test) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: api_aws_infra_tests_deps_lock | |
| path: api/aws_infra/tests/requirements.txt | |
| if-no-files-found: error | |
| shared-aws-infra-update-dependency-lock-files: | |
| name: shared_aws_infra update and upload dependency lock file | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./shared_aws_infra/ | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| shared_aws_infra/ | |
| - name: Update lock files | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }} | |
| shell: bash | |
| run: | | |
| make pip-tools update-deps-lock update-test-deps-lock | |
| - name: Upload updated (main) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: shared_aws_infra_deps_lock | |
| path: shared_aws_infra/requirements.txt | |
| if-no-files-found: error | |
| - name: Upload updated (test) lock file as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: shared_aws_infra_test_deps_lock | |
| path: shared_aws_infra/tests/requirements.txt | |
| if-no-files-found: error | |
| shared-aws-infra-code-checks: | |
| name: shared_aws_infra code checks | |
| needs: | |
| - shared-aws-infra-update-dependency-lock-files | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: ./shared_aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| shared_aws_infra/ | |
| - name: Download updated shared_aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_deps_lock | |
| path: shared_aws_infra | |
| - name: Download updated shared_aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_test_deps_lock | |
| path: shared_aws_infra/tests | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Code typing test | |
| run: | | |
| make run-type-checks | |
| - name: Code style test | |
| run: | | |
| make run-style-checks | |
| - name: Unit tests | |
| run: make run-unit-tests | |
| shared-aws-infra-package-build: | |
| name: shared_aws_infra python package build | |
| needs: | |
| - shared-aws-infra-code-checks | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: ./shared_aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| shared_aws_infra/ | |
| - name: Download updated shared_aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_deps_lock | |
| path: shared_aws_infra | |
| - name: Download updated shared_aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_test_deps_lock | |
| path: shared_aws_infra/tests | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Build package | |
| run: | | |
| make build | |
| - name: Upload package as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: shared_aws_infra_package | |
| path: shared_aws_infra/dist/pavi_shared_aws_infra-0.0.0-py3-none-any.whl | |
| pipeline-seq-retrieval-container-image-build: | |
| name: pipeline/seq_retrieval container-image build | |
| needs: | |
| - container-build-context | |
| - pipeline-seq-retrieval-update-dependency-lock-files | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/seq_retrieval/ | |
| - name: Download updated seq_retrieval (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_deps_lock | |
| path: pipeline/seq_retrieval | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-seq-retrieval-image-upload | |
| aws-region: us-east-1 | |
| - name: Amazon ECR login | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/seq_retrieval/ | |
| push: false | |
| tags: agr_pavi/pipeline_seq_retrieval:latest | |
| outputs: type=docker,dest=/tmp/pavi_seq_retrieval_docker_image.tar | |
| - name: Upload image as artifact (share between jobs) | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: seq_retrieval_image | |
| path: /tmp/pavi_seq_retrieval_docker_image.tar | |
| - name: Load, tag and push image to registry | |
| run: | | |
| docker load --input /tmp/pavi_seq_retrieval_docker_image.tar | |
| docker tag agr_pavi/pipeline_seq_retrieval:latest ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{needs.container-build-context.outputs.tagname}} | |
| docker push ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{needs.container-build-context.outputs.tagname}} | |
| pipeline-seq-retrieval-code-checks: | |
| name: pipeline/seq_retrieval code checks | |
| needs: | |
| - pipeline-seq-retrieval-update-dependency-lock-files | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./pipeline/seq_retrieval/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/seq_retrieval/ | |
| - name: Download updated seq_retrieval (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_deps_lock | |
| path: pipeline/seq_retrieval | |
| - name: Download updated seq_retrieval (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_tests_deps_lock | |
| path: pipeline/seq_retrieval/tests | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Code typing test | |
| run: | | |
| make run-type-checks | |
| - name: Code style test | |
| run: | | |
| make run-style-checks | |
| - name: Run unit tests | |
| run: | | |
| make run-unit-tests | |
| pipeline-alignment-container-image-build: | |
| name: pipeline/alignment container-image build | |
| needs: | |
| - container-build-context | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/alignment/ | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-alignment-image-upload | |
| aws-region: us-east-1 | |
| - name: Amazon ECR login | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/alignment/ | |
| push: false | |
| tags: agr_pavi/pipeline_alignment:latest | |
| outputs: type=docker,dest=/tmp/pavi_alignment_docker_image.tar | |
| - name: Upload image as artifact (share between jobs) | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: alignment_image | |
| path: /tmp/pavi_alignment_docker_image.tar | |
| - name: Load, tag and push image to registry | |
| run: | | |
| docker load --input /tmp/pavi_alignment_docker_image.tar | |
| docker tag agr_pavi/pipeline_alignment:latest ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{needs.container-build-context.outputs.tagname}} | |
| docker push ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{needs.container-build-context.outputs.tagname}} | |
| pipeline-alignment-unit-testing: | |
| name: pipeline/alignment unit testing | |
| needs: | |
| - pipeline-alignment-container-image-build | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./pipeline/alignment/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/alignment/ | |
| - name: Download alignment image artifact (from previous job) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alignment_image | |
| path: /tmp | |
| - name: Load alignment Docker image | |
| run: | | |
| docker load --input /tmp/pavi_alignment_docker_image.tar | |
| - name: Run unit test | |
| run: | | |
| make run-unit-tests | |
| pipeline-workflow-integration-testing: | |
| name: pipeline/workflow integration testing | |
| needs: | |
| - container-build-context | |
| - pipeline-seq-retrieval-container-image-build | |
| - pipeline-alignment-container-image-build | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./pipeline/workflow/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/workflow/ | |
| tests/resources/ | |
| - name: Download seq_retrieval image artifact (from previous job) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: seq_retrieval_image | |
| path: /tmp | |
| - name: Download alignment image artifact (from previous job) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alignment_image | |
| path: /tmp | |
| - name: Load seq_retrieval Docker image | |
| run: | | |
| docker load --input /tmp/pavi_seq_retrieval_docker_image.tar | |
| - name: Load alignment Docker image | |
| run: | | |
| docker load --input /tmp/pavi_alignment_docker_image.tar | |
| - name: Run local integration test | |
| run: | | |
| make run-integration-test-local | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-workflow-aws-test | |
| aws-region: us-east-1 | |
| - name: Run AWS integration test | |
| run: | | |
| make run-integration-test-aws TAG_NAME=${{needs.container-build-context.outputs.tagname}} | |
| pipeline-aws-infra-code-checks: | |
| name: pipeline/aws_infra code checks | |
| needs: | |
| - pipeline-aws-infra-update-dependency-lock-files | |
| - shared-aws-infra-package-build | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: ./pipeline/aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/aws_infra/ | |
| - name: Download updated pipeline/aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_aws_infra_deps_lock | |
| path: pipeline/aws_infra | |
| - name: Download updated aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_aws_infra_tests_deps_lock | |
| path: pipeline/aws_infra/tests | |
| - name: Download shared AWS infra package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_package | |
| path: /tmp/ | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Code typing test | |
| run: | | |
| make run-type-checks | |
| - name: Code style test | |
| run: | | |
| make run-style-checks | |
| - name: Setup node.js (CDK requirement) | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "18" | |
| - name: Install CDK CLI | |
| run: npm install -g aws-cdk | |
| - name: Install CDK stack dependencies | |
| run: pip install -r requirements.txt | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-test | |
| aws-region: us-east-1 | |
| - name: Validate production CDK stack code | |
| run: make validate | |
| api-code-checks: | |
| name: API code checks | |
| needs: | |
| - api-update-dependency-lock-files | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./api/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| api/ | |
| - name: Download updated api (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_deps_lock | |
| path: api | |
| - name: Download updated api (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_tests_deps_lock | |
| path: api/tests | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Code typing test | |
| run: | | |
| make run-type-checks | |
| - name: Code style test | |
| run: | | |
| make run-style-checks | |
| api-container-image-build: | |
| name: API container-image build | |
| needs: | |
| - api-update-dependency-lock-files | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Download updated api (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_deps_lock | |
| path: api | |
| - name: Download updated api (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_tests_deps_lock | |
| path: api/tests | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./ | |
| file: api/Dockerfile | |
| push: false | |
| tags: agr_pavi/api:latest | |
| outputs: type=docker,dest=/tmp/pavi_api_docker_image.tar | |
| - name: Upload image as artifact (share between jobs) | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: api_image | |
| path: /tmp/pavi_api_docker_image.tar | |
| api-unit-integration-testing: | |
| name: API unit and integration testing | |
| needs: | |
| - api-update-dependency-lock-files | |
| - pipeline-seq-retrieval-container-image-build | |
| - pipeline-alignment-container-image-build | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./api/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Download updated api (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_deps_lock | |
| path: api | |
| - name: Download updated api (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_tests_deps_lock | |
| path: api/tests | |
| - name: Download seq_retrieval image artifact (from previous job) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: seq_retrieval_image | |
| path: /tmp | |
| - name: Download alignment image artifact (from previous job) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alignment_image | |
| path: /tmp | |
| - name: Load seq_retrieval Docker image | |
| run: | | |
| docker load --input /tmp/pavi_seq_retrieval_docker_image.tar | |
| - name: Load alignment Docker image | |
| run: | | |
| docker load --input /tmp/pavi_alignment_docker_image.tar | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Run unit and integration tests | |
| run: | | |
| make run-tests | |
| api-container-integration-testing: | |
| name: API container integration testing (AWS batch execution) | |
| needs: | |
| - container-build-context | |
| - pipeline-seq-retrieval-container-image-build | |
| - pipeline-alignment-container-image-build | |
| - api-container-image-build | |
| - api-update-dependency-lock-files | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./api/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| api/ | |
| tests/resources/ | |
| - name: Download updated api (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_deps_lock | |
| path: api | |
| - name: Download updated api (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_tests_deps_lock | |
| path: api/tests | |
| - name: Download API image artifact (from previous job) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_image | |
| path: /tmp | |
| - name: Load API Docker image | |
| run: | | |
| docker load --input /tmp/pavi_api_docker_image.tar | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-api-aws-test | |
| aws-region: us-east-1 | |
| - name: Run container integration test (AWS execution) | |
| run: | | |
| make run-integration-test-container TAG_NAME=${{needs.container-build-context.outputs.tagname}} | |
| api-aws-infra-code-checks: | |
| name: api/aws_infra code checks | |
| needs: | |
| - api-aws-infra-update-dependency-lock-files | |
| - shared-aws-infra-package-build | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: ./api/aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| api/aws_infra/ | |
| - name: Download updated api/aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_aws_infra_deps_lock | |
| path: api/aws_infra | |
| - name: Download updated api/aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_aws_infra_tests_deps_lock | |
| path: api/aws_infra/tests | |
| - name: Download shared AWS infra package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_package | |
| path: /tmp/ | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Code typing test | |
| run: | | |
| make run-type-checks | |
| - name: Code style test | |
| run: | | |
| make run-style-checks | |
| - name: Setup node.js (CDK requirement) | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "18" | |
| - name: Install CDK CLI | |
| run: npm install -g aws-cdk | |
| - name: Install CDK stack dependencies | |
| run: pip install -r requirements.txt | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-test | |
| aws-region: us-east-1 | |
| - name: Validate production CDK stack code | |
| run: make validate-all | |
| webui-code-checks: | |
| name: webUI code checks | |
| needs: | |
| - webui-update-dependency-lock-files | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: ./webui/ | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| webui/ | |
| - name: Download updated webui dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: webui_deps_lock | |
| path: webui | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Code typing test | |
| run: | | |
| make run-type-checks | |
| - name: Code style test | |
| run: | | |
| make run-style-checks | |
| webui-container-image-build: | |
| name: webUI container-image build | |
| needs: | |
| - webui-update-dependency-lock-files | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Download updated webui dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: webui_deps_lock | |
| path: webui | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./webui/ | |
| file: webui/Dockerfile | |
| push: false | |
| tags: agr_pavi/webui:latest | |
| outputs: type=docker,dest=/tmp/pavi_webui_docker_image.tar | |
| commit-deps-lock-updates: | |
| #TODO: Moving the commit from before to after merge to prevent need for repetitive forced reruns of PR-validation. | |
| # * Convert this job into job that tars up all updated dependency files and uploads them as a single artifact. | |
| # * The new artifact should then be downloaded, unpacked and committed in the main-build-and-deploy workflow. | |
| # * PR validation should get an additional job that reports in the open PR if dependency files have been updated, | |
| # with a link to the updated files or summary report to enable inspection before merge (download and report git diff?). | |
| runs-on: ubuntu-22.04 | |
| #Only commit updated lock files on successfull validation (to prevent PR cluttering) | |
| needs: | |
| - pipeline-seq-retrieval-update-dependency-lock-files | |
| - pipeline-seq-retrieval-code-checks | |
| - shared-aws-infra-update-dependency-lock-files | |
| - shared-aws-infra-package-build | |
| - pipeline-aws-infra-update-dependency-lock-files | |
| - pipeline-aws-infra-code-checks | |
| - pipeline-workflow-integration-testing | |
| - api-aws-infra-update-dependency-lock-files | |
| - api-aws-infra-code-checks | |
| - api-update-dependency-lock-files | |
| - api-container-integration-testing | |
| - api-unit-integration-testing | |
| - api-code-checks | |
| - webui-update-dependency-lock-files | |
| - webui-code-checks | |
| - webui-container-image-build | |
| permissions: | |
| contents: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.head_ref }} | |
| - name: Download updated seq_retrieval (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_deps_lock | |
| path: pipeline/seq_retrieval | |
| - name: Download updated seq_retrieval (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_seq_retrieval_tests_deps_lock | |
| path: pipeline/seq_retrieval/tests | |
| - name: Download updated api (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_deps_lock | |
| path: api | |
| - name: Download updated api (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_tests_deps_lock | |
| path: api/tests | |
| - name: Download updated pipeline/aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_aws_infra_deps_lock | |
| path: pipeline/aws_infra | |
| - name: Download updated pipeline/aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pipeline_aws_infra_tests_deps_lock | |
| path: pipeline/aws_infra/tests | |
| - name: Download updated shared_aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_deps_lock | |
| path: shared_aws_infra | |
| - name: Download updated shared_aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: shared_aws_infra_test_deps_lock | |
| path: shared_aws_infra/tests | |
| - name: Download updated api/aws_infra (main) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_aws_infra_deps_lock | |
| path: api/aws_infra | |
| - name: Download updated api/aws_infra (test) dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: api_aws_infra_tests_deps_lock | |
| path: api/aws_infra/tests | |
| - name: Download updated webui dependencies lock file | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: webui_deps_lock | |
| path: webui | |
| # Commit all changed dependency lock files back to the open PR | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: Auto-updated deps lock files | |
| file_pattern: '*requirements.txt' | |
| disable_globbing: true |