[GEN-2375] Replace deprecated DataFrame.append with pandas.concat
#1163
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: | |
| push: | |
| branches: [main, develop, 'GEN*', 'gen*'] | |
| paths-ignore: | |
| - '**.md' # All Markdown files | |
| - '**/docs/**' # Documentation directory | |
| # - '.github/workflows/**' # Ignore all github workflow file changes | |
| pull_request: | |
| types: | |
| - opened | |
| - reopened | |
| paths-ignore: | |
| - '**.md' # All Markdown files | |
| - '**/docs/**' # Documentation directory | |
| # - '.github/workflows/**' # Ignore all github workflow file changes | |
| release: | |
| types: | |
| - created | |
| workflow_dispatch: | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| TEST_PROJECT_SYNID: syn7208886 # synapse_id of the test synapse project | |
| TEST_SEQ_DATE: Jul-2022 # SEQ_DATE to use for test pipeline. Should match the one used in nf-genie. | |
| jobs: | |
| determine-changes: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| non-test-changes: ${{ steps.get-changes.outputs.non-test-changes }} | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Determine Changes | |
| id: get-changes | |
| run: | | |
| if [ "${{ github.event_name }}" == "push" ]; then | |
| echo "Handling a push event..." | |
| ALL_CHANGED_FILES=$(git diff --name-only HEAD^ HEAD) | |
| elif [ "${{ github.event_name }}" == "pull_request" ]; then | |
| echo "Handling a pull request event..." | |
| git fetch origin ${{ github.base_ref }} | |
| ALL_CHANGED_FILES=$(git diff --name-only origin/${{ github.base_ref }} HEAD) | |
| fi | |
| echo "All Changed Files: $ALL_CHANGED_FILES" | |
| NON_TEST_CHANGES=$(echo "$ALL_CHANGED_FILES" | grep -v '^tests/' || true) | |
| echo "Non-Test Changes: $NON_TEST_CHANGES" | |
| echo "::set-output name=non-test-changes::$NON_TEST_CHANGES" | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', 3.11] | |
| # python-version: ['3.10', 3.11, 3.12] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install -y bedtools | |
| python -m pip install --upgrade pip | |
| pip install pytest pytest-cov | |
| pip install . | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Test with pytest | |
| run: | | |
| pytest tests/ --cov=genie --cov=genie_registry --cov-report=html | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: htmlcov | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: ${{ always() }} | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| with: | |
| version: "~=23.12" | |
| build-container: | |
| needs: [test, lint] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Docker buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log into registry ${{ env.REGISTRY }} | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract Docker metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: Format tags as registry refs | |
| id: registry_refs | |
| env: | |
| TAGS: ${{ steps.meta.outputs.json }} | |
| run: | | |
| echo "tags=$(echo $TAGS | jq -r '.tags[] | "type=registry,ref=\(.)_cache"')" >> $GITHUB_OUTPUT | |
| - name: Build and push Docker image | |
| id: build-and-push | |
| uses: docker/build-push-action@v5 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| context: . | |
| push: true | |
| provenance: false | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: ${{ steps.registry_refs.outputs.tags }},mode=max | |
| cache-to: ${{ steps.registry_refs.outputs.tags }},mode=max | |
| integration-tests: | |
| needs: [determine-changes, lint, test, build-container] | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.determine-changes.outputs.non-test-changes }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Extract Branch Name | |
| run: | | |
| if [ "$GITHUB_HEAD_REF" != "" ]; then | |
| echo "BRANCH_NAME=$GITHUB_HEAD_REF" >> $GITHUB_ENV | |
| else | |
| echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV | |
| fi | |
| - name: Pull Public Docker Image from GHCR | |
| run: | | |
| docker pull ghcr.io/sage-bionetworks/genie:${{ env.BRANCH_NAME }} | |
| - name: Start Docker Container | |
| run: | | |
| docker run -d --name genie-container \ | |
| -e SYNAPSE_AUTH_TOKEN="${{ secrets.SYNAPSE_AUTH_TOKEN }}" \ | |
| ghcr.io/sage-bionetworks/genie:${{ env.BRANCH_NAME }} \ | |
| sh -c "while true; do sleep 1; done" | |
| - name: Run validation in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/input_to_database.py \ | |
| mutation \ | |
| --project_id ${{ env.TEST_PROJECT_SYNID }} \ | |
| --onlyValidate \ | |
| --genie_annotation_pkg /root/annotation-tools | |
| - name: Run processing on mutation data in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/input_to_database.py mutation \ | |
| --project_id ${{ env.TEST_PROJECT_SYNID }} \ | |
| --genie_annotation_pkg /root/annotation-tools \ | |
| --createNewMafDatabase | |
| - name: Run processing on non-mutation data in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/input_to_database.py main \ | |
| --project_id ${{ env.TEST_PROJECT_SYNID }} | |
| - name: Run consortium release in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/database_to_staging.py ${{ env.TEST_SEQ_DATE }} ../cbioportal TEST --test | |
| - name: Run public release in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/consortium_to_public.py ${{ env.TEST_SEQ_DATE }} ../cbioportal TEST --test | |
| - name: Stop and Remove Docker Container | |
| run: docker stop genie-container && docker rm genie-container | |
| deploy: | |
| needs: [test, lint, build-container] | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel build | |
| - name: Build distributions | |
| run: python -m build | |
| - name: Publish to pypi | |
| uses: pypa/gh-action-pypi-publish@release/v1 |