ci.yml

name: CI

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

permissions:
  contents: write

jobs:
  test:
    name: test (py${{ matrix.python-version }}, numpy${{ matrix.numpy-version }})
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.10', '3.11', '3.12', '3.13']
        numpy-version: ['1.26.4', '2.2.0']
    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Free disk space
        run: |
          sudo rm -rf /usr/local/lib/android
          sudo rm -rf /usr/share/dotnet
          sudo rm -rf /opt/ghc
          sudo rm -rf /usr/local/share/powershell
          sudo rm -rf /usr/local/share/chromium
          sudo rm -rf /usr/local/.ghcup

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          
      - name: Install uv
        run: curl -LsSf https://astral.sh/uv/install.sh | sh
        
      - name: Cache uv dependencies
        uses: actions/cache@v4
        with:
          path: ~/.cache/uv
          key: ${{ runner.os }}-uv-${{ hashFiles('**/pyproject.toml') }}
          restore-keys: |
            ${{ runner.os }}-uv-

      - name: Create virtual environment and install dependencies
        env:
          UV_HTTP_TIMEOUT: 300
          UV_CONCURRENT_DOWNLOADS: 4
        run: |
          uv venv
          uv pip install -e ".[test,dev]"

      - name: Install specific numpy version
        run: |
          source .venv/bin/activate
          uv pip install "numpy==${{ matrix.numpy-version }}"

      - name: Run linting and code quality checks with Ruff
        run: |
          source .venv/bin/activate
          # Check formatting
          ruff format --check .
          # Check linting
          ruff check . --statistics
          
      - name: Run fast tests
        run: |
          source .venv/bin/activate
          pytest tests/ -v -m "not slow" --cov=dnallm --cov-report=xml --cov-report=term-missing --tb=short

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
          file: ./coverage.xml
          fail_ci_if_error: false

      - name: Run slow tests
        continue-on-error: true
        run: |
          source .venv/bin/activate
          pytest tests/ -v -m "slow" --cov=dnallm --cov-report=xml --cov-report=term-missing --tb=short --cov-append

      - name: Run type checking
        run: |
          source .venv/bin/activate
          mypy dnallm/ --show-error-codes --pretty --exclude=dnallm/tasks/metrics/ || true
          
  test-cuda:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.11']
        cuda-version: ['12.1', '12.4']
    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Free disk space
        run: |
          sudo rm -rf /usr/local/lib/android
          sudo rm -rf /usr/share/dotnet
          sudo rm -rf /opt/ghc
          sudo rm -rf /usr/local/share/powershell
          sudo rm -rf /usr/local/share/chromium
          sudo rm -rf /usr/local/.ghcup

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install CUDA dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y nvidia-cuda-toolkit

      - name: Install uv
        run: curl -LsSf https://astral.sh/uv/install.sh | sh

      - name: Cache uv dependencies
        uses: actions/cache@v4
        with:
          path: ~/.cache/uv
          key: ${{ runner.os }}-uv-cuda-${{ matrix.cuda-version }}-${{ hashFiles('**/pyproject.toml') }}
          restore-keys: |
            ${{ runner.os }}-uv-cuda-${{ matrix.cuda-version }}-
            ${{ runner.os }}-uv-

      - name: Create virtual environment and install CUDA dependencies
        env:
          UV_HTTP_TIMEOUT: 300
          UV_CONCURRENT_DOWNLOADS: 4
        run: |
          uv venv
          if [ "${{ matrix.cuda-version }}" = "12.1" ]; then
            uv pip install -e ".[test,dev,cuda121]"
          elif [ "${{ matrix.cuda-version }}" = "12.4" ]; then
            uv pip install -e ".[test,dev,cuda124]"
          fi
          
      - name: Run GPU-enabled tests
        run: |
          source .venv/bin/activate
          pytest tests/ -v -m "not slow" --tb=short
          
  test-mamba:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.11']
    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Check for GPU
        id: gpu-check
        run: |
          if command -v nvidia-smi &> /dev/null && nvidia-smi > /dev/null 2>&1; then
            echo "has_gpu=true" >> $GITHUB_OUTPUT
            echo "GPU detected, will run mamba tests"
          else
            echo "has_gpu=false" >> $GITHUB_OUTPUT
            echo "No GPU detected, skipping mamba tests"
          fi

      - name: Set up Python ${{ matrix.python-version }}
        if: steps.gpu-check.outputs.has_gpu == 'true'
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install uv
        if: steps.gpu-check.outputs.has_gpu == 'true'
        run: curl -LsSf https://astral.sh/uv/install.sh | sh

      - name: Create virtual environment and install mamba dependencies
        if: steps.gpu-check.outputs.has_gpu == 'true'
        run: |
          uv venv
          uv pip install -e ".[test,dev]"
          uv pip install -e ".[mamba]" --no-cache-dir --no-build-isolation

      - name: Run mamba-specific tests
        if: steps.gpu-check.outputs.has_gpu == 'true'
        continue-on-error: true
        run: |
          source .venv/bin/activate
          pytest tests/ -v -m "not slow" --tb=short

      - name: Upload mamba test logs on failure
        if: steps.gpu-check.outputs.has_gpu == 'true' && failure()
        uses: actions/upload-artifact@v4
        with:
          name: mamba-test-logs-${{ matrix.python-version }}
          path: |
            pytest.log
            /tmp/mamba-build.log
          
  deploy:
    needs: [test, test-cuda, test-mamba]
    runs-on: ubuntu-latest
    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
        
      - name: Configure Git credentials
        run: |
          git config user.name github-actions[bot]
          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
          
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.11
          
      - name: Cache mkdocs dependencies
        uses: actions/cache@v3
        with:
          key: mkdocs-material-${{ github.run_number }}
          path: .cache
          restore-keys: |
            mkdocs-material-
            
      - name: Install uv
        run: curl -LsSf https://astral.sh/uv/install.sh | sh
        
      - name: Create virtual environment and install documentation dependencies
        env:
          UV_HTTP_TIMEOUT: 120
          UV_CONCURRENT_DOWNLOADS: 1
        run: |
          uv venv
          uv pip install -e ".[base,docs]"
          
      - name: Deploy documentation to GitHub Pages
        run: |
          source .venv/bin/activate
          mkdocs gh-deploy --force