.github/workflows/python-package.yml

name: Python Package

on:
  push:
    branches: [main, develop]
    paths:
      - "stem_ai/**"
      - "pyproject.toml"
      - "README.md"
      - ".github/workflows/python-package.yml"
  pull_request:
    branches: [main]
    paths:
      - "stem_ai/**"
      - "pyproject.toml"
      - "README.md"
      - ".github/workflows/python-package.yml"

jobs:
  package-smoke:
    name: Python ${{ matrix.python-version }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]

    steps:
      - name: Checkout
        uses: actions/checkout@v4

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

      - name: Install package with PDF extra
        run: |
          python -m pip install --upgrade pip
          python -m pip install -e ".[pdf]"

      - name: Compile package
        run: |
          python -m py_compile stem_ai/cli.py stem_ai/scanner.py stem_ai/render.py stem_ai/app.py

      - name: CLI help smoke test
        run: |
          stem --help
          python -m stem_ai --help

      - name: Create synthetic bio repository
        run: |
          mkdir -p /tmp/stem-target/.github/workflows /tmp/stem-target/tests
          cat > /tmp/stem-target/README.md <<'EOF'
          # Synthetic Viral Sequencing Pipeline

          Research-use-only viral sequencing workflow.
          Not for clinical use. Not for diagnostic use.
          EOF
          cat > /tmp/stem-target/requirements.txt <<'EOF'
          biopython==1.83
          EOF
          cat > /tmp/stem-target/tests/test_pipeline.py <<'EOF'
          def test_pipeline_smoke():
              assert True
          EOF
          cat > /tmp/stem-target/.github/workflows/ci.yml <<'EOF'
          name: CI
          on: [push]
          jobs:
            test:
              runs-on: ubuntu-latest
              steps:
                - uses: actions/checkout@v4
                - run: python -m pytest
          EOF

      - name: Run Level 1/2/3 CLI scans
        run: |
          stem /tmp/stem-target --level 1 --format all --out /tmp/stem-output-l1
          stem /tmp/stem-target --level 2 --format all --out /tmp/stem-output-l2
          stem /tmp/stem-target --level 3 --format all --out /tmp/stem-output-l3

      - name: Verify generated artifacts
        run: |
          test -f /tmp/stem-output-l1/stem-target_experiment_results.json
          test -f /tmp/stem-output-l1/stem-target_report.md
          test -f /tmp/stem-output-l1/stem-target_brief_1p.pdf
          test -f /tmp/stem-output-l2/stem-target_detailed_3p.pdf
          test -f /tmp/stem-output-l3/stem-target_detailed_5p.pdf

      - name: Build source and wheel distributions
        run: |
          python -m pip install build
          python -m build