ci.yml

name: CI
permissions:
  contents: write

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

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pydantic omegaconf hydra-core
        pip install -e .
        pip install -e ".[dev]"
        pip install pytest pytest-cov

    - name: Run tests with coverage (branch-specific)
      run: |
        # Run tests with branch-specific marker filtering
        # For main branch: run all tests (including optional tests)
        # For dev branch: exclude optional tests (docker, llm, performance, pydantic_ai)
        if [ "${{ github.ref }}" = "refs/heads/main" ]; then
          echo "Running all tests including optional tests for main branch"
          pytest tests/ -m "not containerized" --cov=DeepResearch --cov-report=xml --cov-report=term-missing --junitxml=junit.xml -o junit_family=legacy
        else
          echo "Running tests excluding optional tests for dev branch"
          pytest tests/ -m "not optional and not containerized" --cov=DeepResearch --cov-report=xml --cov-report=term-missing --junitxml=junit.xml -o junit_family=legacy
        fi

    - name: Run bioinformatics unit tests (all branches)
      run: |
        echo "Running bioinformatics unit tests..."
        pytest tests/test_bioinformatics_tools/ -m "not containerized" --cov=DeepResearch --cov-append --cov-report=xml --cov-report=term-missing --junitxml=junit-bioinformatics.xml -o junit_family=legacy

    - name: Run bioinformatics containerized tests (main branch only)
      if: github.ref == 'refs/heads/docker'
      run: |
        echo "Running bioinformatics containerized tests..."
        # Check if Docker is available and bioinformatics images exist
        if docker --version >/dev/null 2>&1; then
          make test-bioinformatics-containerized || echo "Containerized tests failed, but continuing..."
        else
          echo "Docker not available, skipping containerized tests"
        fi

    - name: Debug coverage files
      run: |
        echo "Checking for coverage files..."
        ls -la coverage.xml junit.xml junit-bioinformatics.xml || echo "Some files missing"
        head -20 coverage.xml || echo "Coverage file not readable"

    # Codecov upload steps - These steps will NOT fail the CI even if uploads fail
    # Tests will pass regardless of Codecov upload status
    - name: Configure Codecov repository setup
      run: |
        # Check if CODECOV_TOKEN is available and set HAS_CODECOV_TOKEN flag
        if [ -n "${CODECOV_TOKEN}" ]; then
          echo "📊 Codecov token found - uploads will be enabled"
          echo "🔗 Repository: ${{ github.repository }}"
          echo "📈 Coverage reports will be uploaded to Codecov"
          echo "✅ Codecov uploads enabled for this run"
          echo "HAS_CODECOV_TOKEN=true" >> $GITHUB_ENV
        else
          echo "⚠️ CODECOV_TOKEN not found - uploads will be skipped"
          echo "💡 To enable Codecov uploads:"
          echo "   1. Go to https://codecov.io/gh/${{ github.repository }}/settings"
          echo "   2. Generate a repository upload token"
          echo "   3. Add it as CODECOV_TOKEN secret in repository settings"
          echo "   4. Repository will be auto-detected on first upload"
          echo "HAS_CODECOV_TOKEN=false" >> $GITHUB_ENV
        fi
      env:
        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

    - name: Display coverage summary
      run: |
        echo "📈 Local Coverage Summary:"
        echo "=========================="
        if command -v coverage >/dev/null 2>&1; then
          python -m coverage report --include="DeepResearch/*" --omit="*/tests/*,*/test_*" || echo "Coverage report generation failed"
        else
          echo "Coverage.py not available for summary"
        fi
        echo ""
        echo "📁 Coverage files generated:"
        ls -lh *.xml 2>/dev/null || echo "No XML coverage files found"
        echo ""
        echo "💡 To view detailed coverage: python -m coverage html && open htmlcov/index.html"

    - name: Upload coverage to Codecov
      if: env.HAS_CODECOV_TOKEN == 'true'
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml
        fail_ci_if_error: false
        verbose: true
        slug: ${{ github.repository }}
        name: "${{ github.ref_name }} - Python ${{ matrix.python-version || '3.11' }}"
      continue-on-error: true

    - name: Upload test results to Codecov
      if: env.HAS_CODECOV_TOKEN == 'true' && !cancelled()
      uses: codecov/test-results-action@v1
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./junit.xml
        verbose: true
        slug: ${{ github.repository }}
      continue-on-error: true

    - name: Upload bioinformatics test results to Codecov
      if: env.HAS_CODECOV_TOKEN == 'true' && !cancelled()
      uses: codecov/test-results-action@v1
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./junit-bioinformatics.xml
        verbose: true
        slug: ${{ github.repository }}
      continue-on-error: true

    - name: Codecov upload summary
      if: env.HAS_CODECOV_TOKEN == 'false'
      run: |
        echo "ℹ️ Codecov uploads were skipped because CODECOV_TOKEN is not configured"
        echo ""
        echo "📋 Setup Instructions:"
        echo "======================"
        echo "1. Visit: https://codecov.io/gh/${{ github.repository }}"
        echo "2. Sign in with GitHub"
        echo "3. Repository should auto-appear"
        echo "4. Go to Settings → Repository Upload Token"
        echo "5. Generate and copy the token"
        echo "6. Go to GitHub repo Settings → Secrets and variables → Actions"
        echo "7. Add new repository secret: CODECOV_TOKEN"
        echo "8. Paste the token value"
        echo "9. Codecov uploads will work on next run"
        echo ""
        echo "✅ CI will pass regardless of Codecov upload status"
        echo "📊 Coverage reports were still generated locally for inspection"

    - name: Run VLLM tests (optional, manual trigger only)
      if: github.event_name == 'workflow_dispatch' || contains(github.event.head_commit.message, '[vllm-tests]')
      run: |
        # Install VLLM test dependencies with Hydra
        pip install testcontainers omegaconf hydra-core
        # Run VLLM tests with Hydra configuration (single instance optimization)
        python scripts/run_vllm_tests.py --no-hydra
      continue-on-error: true  # VLLM tests are allowed to fail in CI

  lint:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'

    - name: Install linting tools
      run: |
        python -m pip install --upgrade pip
        pip install ruff>=0.15.1

    - name: Run linting (Ruff)
      run: |
        ruff --version
        ruff check DeepResearch/ tests/ --extend-ignore=EXE001 --output-format=github

    - name: Check formatting (Ruff)
      run: |
        ruff format --check DeepResearch/ tests/

  types:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python

      uses: actions/setup-python@v4
      with:
        python-version: '3.11'

    - name: Set up uv
      uses: astral-sh/setup-uv@v5

    - name: Create venv and install deps
      run: |
        python -m venv .venv
        source .venv/bin/activate
        python -m pip install --upgrade pip
        pip install -e .
        pip install -e ".[dev]"

    - name: Run ty type check
      env:
        VIRTUAL_ENV: .venv
      run: |
        uvx ty --version
        uvx ty check