cell-state-engineering/.github/workflows/ci.yml at main · arnavbathla/cell-state-engineering · GitHub

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name: CI

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

jobs:
  no-mock-evo2-check:
    name: "Verify no MockEvo2 in codebase"
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Check for MockEvo2 or mock_evo2
        run: |
          if grep -r "MockEvo2\|mock_evo2" --include="*.py" --include="*.ts" --include="*.tsx" .; then
            echo "ERROR: MockEvo2 or mock_evo2 found in codebase. Remove all mock Evo 2 adapters."
            exit 1
          fi
          echo "PASS: No mock Evo2 adapters found."

  backend-tests:
    name: Backend API tests
    runs-on: ubuntu-latest
    services:
      postgres:
        image: pgvector/pgvector:pg16
        env:
          POSTGRES_DB: test_cell_state_compiler
          POSTGRES_USER: cellcompiler
          POSTGRES_PASSWORD: cellcompiler
        ports:
          - 5432:5432
        options: >-
          --health-cmd pg_isready
          --health-interval 5s
          --health-timeout 5s
          --health-retries 10
      redis:
        image: redis:7-alpine
        ports:
          - 6379:6379
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install API deps
        working-directory: apps/api
        run: pip install -e ".[test]"
      - name: Run Alembic migrations
        working-directory: apps/api
        env:
          DATABASE_URL: postgresql+psycopg2://cellcompiler:cellcompiler@localhost:5432/test_cell_state_compiler
        run: alembic upgrade head
      - name: Run backend tests
        working-directory: apps/api
        env:
          DATABASE_URL: postgresql+psycopg2://cellcompiler:cellcompiler@localhost:5432/test_cell_state_compiler
          REDIS_URL: redis://localhost:6379/0
          JWT_SECRET: test_secret_32_chars_minimum_here_xx
          GENOME_MODEL_SERVICE_URL: http://localhost:8100
        run: pytest app/tests/ -v --tb=short

  genome-service-tests:
    name: Genome model service tests
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install genome service deps
        working-directory: apps/genome-model-service
        run: pip install -e ".[test]"
      - name: Run genome service tests
        working-directory: apps/genome-model-service
        env:
          EVO2_PROVIDER: local
          EVO2_MODEL_NAME: evo2_1b_base
          EVO2_DEVICE: cpu
          EVO2_HEALTH_RUN_SMOKE_TEST: "false"
          ENABLE_EVO2_GENERATION: "false"
          MAX_SEQUENCE_LENGTH: "8192"
          SEQUENCE_SAFETY_MODE: restricted
        run: pytest app/tests/ -v --tb=short

  frontend-type-check:
    name: Frontend TypeScript check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "20"
          cache: "npm"
          cache-dependency-path: apps/web/package-lock.json
      - name: Install deps
        working-directory: apps/web
        run: npm ci
      - name: Type check
        working-directory: apps/web
        run: npx tsc --noEmit
      - name: Lint
        working-directory: apps/web
        run: npm run lint