revert: remove test package scripts from dev branch #56
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| name: CI/CD Pipeline | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| unit-tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install pytest pytest-cov pytest-mock flake8 | |
| - name: Lint with flake8 | |
| run: | | |
| # Stop the build if there are Python syntax errors or undefined names | |
| flake8 scripts cdm_ontologies --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings | |
| flake8 scripts cdm_ontologies --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Run unit tests | |
| run: | | |
| pytest tests/ -v --cov=scripts --cov=cdm_ontologies --cov-report=term-missing | |
| - name: Test CLI | |
| run: | | |
| python -m cdm_ontologies --help | |
| python -m cdm_ontologies analyze-core --help | |
| build-and-push: | |
| needs: unit-tests | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Create lowercase image name for cache | |
| id: lowercase | |
| run: echo "IMAGE_NAME_LOWER=$(echo '${{ env.IMAGE_NAME }}' | tr '[:upper:]' '[:lower:]')" >> $GITHUB_OUTPUT | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ steps.lowercase.outputs.IMAGE_NAME_LOWER }} | |
| tags: | | |
| type=ref,event=branch | |
| type=ref,event=pr | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=raw,value=latest,enable={{is_default_branch}} | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ steps.lowercase.outputs.IMAGE_NAME_LOWER }}:cache | |
| cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ steps.lowercase.outputs.IMAGE_NAME_LOWER }}:cache,mode=max | |
| test-small-dataset: | |
| needs: build-and-push | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Create lowercase image name and determine tag | |
| id: lowercase-test | |
| run: | | |
| echo "IMAGE_NAME_LOWER=$(echo '${{ env.IMAGE_NAME }}' | tr '[:upper:]' '[:lower:]')" >> $GITHUB_OUTPUT | |
| # Use same tag format as docker/metadata-action: pr-{number} for PRs, branch name for pushes | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| echo "DOCKER_TAG=pr-${{ github.event.pull_request.number }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "DOCKER_TAG=${{ github.ref_name }}" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Run Docker test pipeline | |
| run: | | |
| docker run --rm \ | |
| -v ${{ github.workspace }}:/home/ontology/workspace \ | |
| -w /home/ontology/workspace \ | |
| -e DATASET_SIZE=test \ | |
| -e ONTOLOGIES_SOURCE_FILE=config/ontologies_source_test.txt \ | |
| -e ROBOT_JAVA_ARGS="-Xmx8g -XX:MaxMetaspaceSize=1g -XX:+UseG1GC" \ | |
| -e RELATION_GRAPH_JAVA_ARGS="-Xmx8g -XX:MaxMetaspaceSize=1g -XX:+UseG1GC" \ | |
| -e SEMSQL_MEMORY_LIMIT=8g \ | |
| -e PYTHON_MEMORY_LIMIT=8g \ | |
| -e JAVA_PARALLEL_GC=true \ | |
| -e ENABLE_MEMORY_MONITORING=true \ | |
| -e ENABLE_TSV_EXPORT=true \ | |
| -e ENABLE_PARQUET_EXPORT=true \ | |
| -e CREATE_UTILS_LOGS=true \ | |
| -e SKIP_RESOURCE_CHECK=true \ | |
| -e SKIP_NON_CORE_ANALYSIS=true \ | |
| -e PYTHONPATH=scripts \ | |
| -e HOST_UID=1001 \ | |
| -e HOST_GID=1001 \ | |
| ${{ env.REGISTRY }}/${{ steps.lowercase-test.outputs.IMAGE_NAME_LOWER }}:${{ steps.lowercase-test.outputs.DOCKER_TAG }} \ | |
| python -m cdm_ontologies.cli run-all |