ci.yml

# AI: Claude Code | Opus 4.5 | 2026 February 12 | Purpose: CI workflow for GIGANTIC
# Human: Eric Edsinger

name: CI

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

jobs:
  validate-yaml:
    name: Validate YAML files
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install yamllint
        run: pip install yamllint

      - name: Validate YAML files
        run: |
          echo "Validating YAML configuration files..."
          find . -name "*.yml" -o -name "*.yaml" | while read file; do
            # Skip GitHub workflow files (they have special syntax)
            if [[ "$file" == *".github/workflows"* ]]; then
              continue
            fi
            echo "Checking: $file"
            yamllint -d "{extends: relaxed, rules: {line-length: disable}}" "$file" || true
          done

  validate-python:
    name: Validate Python syntax
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'

      - name: Check Python syntax
        run: |
          echo "Checking Python syntax..."
          find . -name "*.py" | while read file; do
            echo "Checking: $file"
            python -m py_compile "$file"
          done

      - name: Install flake8
        run: pip install flake8

      - name: Lint Python files (warnings only)
        run: |
          echo "Linting Python files (informational)..."
          # E501: line too long (we allow long lines for readability)
          # W503: line break before binary operator (style preference)
          # E201, E202: whitespace inside brackets (GIGANTIC style)
          flake8 --ignore=E501,W503,E201,E202,E203 --exit-zero .

  validate-shell:
    name: Validate shell scripts
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install shellcheck
        run: sudo apt-get install -y shellcheck

      - name: Check shell scripts
        run: |
          echo "Checking shell scripts..."
          find . -name "*.sh" -o -name "*.sbatch" | while read file; do
            echo "Checking: $file"
            # SC1091: Can't follow sourced files (expected for conda)
            # SC2086: Double quote to prevent globbing (sometimes intentional)
            shellcheck --severity=error --exclude=SC1091,SC2086 "$file" || true
          done

  check-structure:
    name: Check project structure
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Verify COPYME template structure
        run: |
          echo "Verifying gigantic_project-COPYME structure..."

          # Required directories
          required_dirs=(
            "gigantic_project-COPYME/INPUT_user"
            "gigantic_project-COPYME/research_notebook"
            "gigantic_project-COPYME/research_notebook/research_user"
            "gigantic_project-COPYME/research_notebook/research_ai"
            "gigantic_project-COPYME/subprojects"
            "gigantic_project-COPYME/subprojects/phylonames"
          )

          for dir in "${required_dirs[@]}"; do
            if [ -d "$dir" ]; then
              echo "✓ Found: $dir"
            else
              echo "✗ Missing: $dir"
              exit 1
            fi
          done

          # Required files
          required_files=(
            "gigantic_project-COPYME/AI_GUIDE-project.md"
            "gigantic_project-COPYME/RUN-setup_environments.sh"
            "gigantic_project-COPYME/RUN-record_project.sh"
            "README.md"
            "LICENSE"
          )

          for file in "${required_files[@]}"; do
            if [ -f "$file" ]; then
              echo "✓ Found: $file"
            else
              echo "✗ Missing: $file"
              exit 1
            fi
          done

          echo ""
          echo "All required structure verified!"

  check-docs:
    name: Check documentation
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Check for broken markdown links
        run: |
          echo "Checking for common documentation issues..."

          # Check that AI_GUIDE files exist where referenced
          echo "Verifying AI_GUIDE hierarchy..."

          if [ -f "gigantic_project-COPYME/AI_GUIDE-project.md" ]; then
            echo "✓ Project-level AI_GUIDE exists"
          fi

          if [ -f "gigantic_project-COPYME/subprojects/phylonames/AI_GUIDE-phylonames.md" ]; then
            echo "✓ Phylonames AI_GUIDE exists"
          fi

          # Count AI_GUIDE files
          ai_guide_count=$(find . -name "AI_GUIDE*.md" | wc -l)
          echo "Total AI_GUIDE files: $ai_guide_count"

  # This job runs only on main branch pushes (not PRs)
  # It's a placeholder for future demo testing
  test-demo:
    name: Test demo (placeholder)
    runs-on: ubuntu-latest
    if: github.ref == 'refs/heads/main' && github.event_name == 'push'
    steps:
      - uses: actions/checkout@v4

      - name: Demo test placeholder
        run: |
          echo "Demo testing will be implemented when demo/run_demo.sh is complete."
          echo "For now, this is a placeholder that always passes."

          if [ -f "demo/run_demo.sh" ]; then
            echo "demo/run_demo.sh exists - ready for testing when implemented"
          else
            echo "demo/run_demo.sh not yet created"
          fi