lettuce/.github/workflows/check.run-tests.yml at main · Health-Informatics-UoN/lettuce · GitHub

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name: Run Tests

permissions:
  contents: read
  code-quality: write

on:
  pull_request:
    branches:
      - main
  push:
    branches:
      - main

jobs:
  run-tests:
    name: Run Tests
    runs-on: ubuntu-latest

    env:
      SKIP_DATABASE_TESTS: false
      SKIP_LLM_TESTS: true
      DB_HOST: "localhost"
      DB_USER: "postgres"
      DB_PASSWORD: "password"
      DB_NAME: "omop"
      DB_PORT: "5432"
      DB_SCHEMA: "public"
      DB_VECTABLE: "embeddings"
      DB_VECSIZE: "384"
      AUTH_API_KEY: "test_key_123"

    steps:
      - name: Checkout omop-lite repository
        uses: actions/checkout@v7
        with:
          repository: Health-Informatics-UoN/omop-lite
          path: omop-lite
          ref: 31d6280947de78acd8a41928ef2a3da04b93cf43

      - name: Checkout lettuce repository
        uses: actions/checkout@v7
        with:
          path: lettuce
          ref: ${{ github.head_ref }}

      - name: Start omop-ts Docker services
        run: |
          docker compose -f omop-lite/docker-compose.yml --profile text-search up -d

          echo "Waiting for database to initialise..."
          sleep 15

      - name: Check DNS resolution
        run: |
          nslookup localhost || echo "Failed to resolve hostname"
          ping -c 3 localhost || echo "Failed to ping host"

      - name: Inspect Docker networks
        run: |
          docker network ls

      - name: Check running containers and their IPs
        run: |
          docker ps
          docker inspect -f '{{.Name}} - {{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' $(docker ps -q)

      - name: Setup uv
        uses: astral-sh/setup-uv@v7
        with:
          version: "0.8.15"
          enable-cache: true
          cache-dependency-glob: "lettuce/lettuce/uv.lock"

      - name: Setup musl
        run: |
          sudo apt-get install -y musl-dev
          sudo ln -s /usr/lib/x86_64-linux-musl/libc.so /lib/libc.musl-x86_64.so.1

      - name: Setup Python
        uses: actions/setup-python@v7
        with:
          python-version-file: "lettuce/lettuce/.python-version"

      - name: uv sync
        run: uv sync --extra test --extra llama-cpu
        working-directory: lettuce/lettuce

      - name: Run tests
        run: |
          set -e
          INFERENCE_TYPE="llama-cpp-python" uv run pytest tests --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=lettuce tests | tee pytest-coverage.txt
          test ${PIPESTATUS[0]} -eq 0
        working-directory: lettuce/lettuce

      - name: Cleanup Docker services
        if: always()
        run: |
          # Cleanup all services to prevent resource issues
          docker compose -f lettuce/lettuce/compose.yaml down
          docker compose -f omop-lite/docker-compose.yml down
          docker network rm omop-ts_default || true

      - name: Pytest coverage comment
        uses: MishaKav/pytest-coverage-comment@9516bf7f32a9229cf18d5e1717ae387c7154f279
        with:
          pytest-coverage-path: pytest-coverage.txt
          junitxml-path: pytest.xml