KANBAN-507 managed workflow implementation #33
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: PR validation | |
| on: | |
| pull_request: | |
| types: [synchronize, opened, reopened, edited] | |
| branches: | |
| - main | |
| jobs: | |
| pipeline-seq-retrieval-container-image-build: | |
| name: pipeline/seq_retrieval container-image build | |
| 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: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/seq_retrieval/ | |
| push: false | |
| tags: agr_pavi/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 | |
| pipeline-seq-retrieval-python-typing-check: | |
| name: pipeline/seq_retrieval python typing check | |
| 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/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check python typing | |
| run: | | |
| make run-python-type-check | |
| pipeline-seq-retrieval-python-style-check: | |
| name: pipeline/seq_retrieval python style check | |
| 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/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check python style | |
| run: | | |
| make run-python-style-check | |
| pipeline-seq-retrieval-unit-tests: | |
| name: pipeline/seq_retrieval unit tests | |
| 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/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Run unit tests | |
| run: | | |
| make run-unit-tests | |
| pipeline-alignment-container-image-build: | |
| name: pipeline/alignment container-image build | |
| 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 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/alignment/ | |
| push: false | |
| tags: agr_pavi/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 | |
| pipeline-workflow-integration-testing: | |
| name: pipeline/workflow integration testing | |
| needs: | |
| - pipeline-seq-retrieval-container-image-build | |
| - pipeline-alignment-container-image-build | |
| 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/ | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - 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 integration test | |
| run: | | |
| make run-integration-test |