annotations: reformat Annotation_Definitions to 'definition ==accession' #121
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| # 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 |