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Fix two live bugs reported in the PR backlog #258
Workflow file for this run
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| name: reactome_chatbot CI | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| push: | |
| branches: | |
| - main | |
| # A second push to a PR makes the first run's result irrelevant; without this | |
| # they both run to completion and queue behind each other. | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.event_name == 'pull_request' }} | |
| # Least privilege by default. id-token: write is granted only to docker-push, | |
| # which needs it to assume the AWS role. | |
| permissions: | |
| contents: read | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python and Poetry | |
| uses: ./.github/actions/install_python_poetry | |
| # ruff replaces black + isort; its `I` rules sort imports and | |
| # `ruff format` is black-compatible. Config lives in pyproject.toml. | |
| - name: Lint | |
| run: poetry run ruff check . | |
| - name: Check formatting | |
| run: poetry run ruff format --check . | |
| - name: Type check | |
| run: poetry run mypy | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python and Poetry | |
| uses: ./.github/actions/install_python_poetry | |
| - name: Run tests | |
| run: poetry run pytest | |
| poetry-check: | |
| if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-15-intel] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # need the base branch to diff against | |
| # Plain git rather than a third-party action: this workflow can reach | |
| # AWS, so every extra action is supply-chain surface for a one-line check. | |
| - name: Check poetry.lock for changes | |
| id: check-poetry-lock | |
| shell: bash | |
| run: | | |
| base="${{ github.base_ref }}" | |
| if [ -z "$base" ]; then | |
| # manual run: no base to compare against, so always verify | |
| echo "changed=true" >> "$GITHUB_OUTPUT" | |
| elif git diff --name-only "origin/$base...HEAD" -- poetry.lock | grep -q .; then | |
| echo "changed=true" >> "$GITHUB_OUTPUT" | |
| else | |
| echo "changed=false" >> "$GITHUB_OUTPUT" | |
| fi | |
| - name: Set up Python and Poetry | |
| if: steps.check-poetry-lock.outputs.changed == 'true' | |
| uses: ./.github/actions/install_python_poetry | |
| - name: Verify Python imports | |
| if: steps.check-poetry-lock.outputs.changed == 'true' | |
| env: | |
| PYTHONPATH: ./bin:./src | |
| run: | | |
| poetry check | |
| poetry run python ./.github/actions/verify_imports.py | |
| docker-build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| tags: reactome-chatbot:${{ github.sha }} | |
| outputs: type=docker,dest=/tmp/image.tar | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: image-artifact | |
| path: /tmp/image.tar | |
| docker-push: | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write # assume the AWS role via OIDC | |
| contents: read | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: image-artifact | |
| path: /tmp | |
| - id: get-hash | |
| run: | | |
| FULL_SHA=${{ github.sha }} | |
| echo "SHORT_SHA=${FULL_SHA:0:7}" >> $GITHUB_OUTPUT | |
| - env: | |
| AWS_REGION: us-east-1 | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{ vars.AWS_ROLE }} | |
| aws-region: ${{ env.AWS_REGION }} | |
| - id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| with: | |
| registry-type: public | |
| - env: | |
| AWS_REGISTRY: ${{ steps.login-ecr.outputs.registry }} | |
| AWS_REGISTRY_ALIAS: reactome | |
| AWS_REPO: reactome-chatbot | |
| IMG_TAG: ${{ steps.get-hash.outputs.SHORT_SHA }} | |
| run: | | |
| docker load --input /tmp/image.tar | |
| docker image tag reactome-chatbot:${{ github.sha }} $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:$IMG_TAG | |
| docker image tag reactome-chatbot:${{ github.sha }} $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:latest | |
| docker push $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:$IMG_TAG | |
| docker push $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:latest |