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Continuous Integration

This page describes the continuous integration (CI) setup for PBPKO, including automated testing, validation, and deployment processes.

Overview

PBPKO uses GitHub Actions for continuous integration to ensure: - Automated testing on every commit - Ontology validation - Documentation deployment - Release automation

CI Workflows

1. Build and Test Workflow

File: .github/workflows/build.yml

Triggers: - Push to main branch - Pull requests - Manual trigger

Steps: 1. Checkout code 2. Setup Java (for ROBOT) 3. Download ROBOT 4. Run ontology build 5. Validate ontology 6. Run tests 7. Generate reports

Example: 

name: Build and Test
on: [push, pull_request]
jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Setup Java
        uses: actions/setup-java@v2
        with:
          java-version: '11'
      - name: Download ROBOT
        run: wget https://github.com/ontodev/robot/releases/download/v1.8.1/robot.jar
      - name: Build ontology
        run: ./scripts/build.sh
      - name: Validate ontology
        run: robot validate --input Robot/ontologies/pbpko.owl

2. Documentation Deployment

File: .github/workflows/docs.yml

Triggers: - Push to main branch - Manual trigger

Steps: 1. Checkout code 2. Setup Python 3. Install MkDocs 4. Build documentation 5. Deploy to GitHub Pages

Example: 

name: Deploy Documentation
on:
  push:
    branches: [ main ]
jobs:
  deploy:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: 3.x
      - name: Install dependencies
        run: pip install mkdocs mkdocs-material
      - name: Deploy
        run: mkdocs gh-deploy --force

3. Release Workflow

File: .github/workflows/release.yml

Triggers: - Tag creation - Manual trigger

Steps: 1. Checkout code 2. Setup Java 3. Download ROBOT 4. Build ontology 5. Generate release files 6. Create GitHub release

Example: 

name: Release
on:
  push:
    tags: ['v*']
jobs:
  release:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Setup Java
        uses: actions/setup-java@v2
        with:
          java-version: '11'
      - name: Download ROBOT
        run: wget https://github.com/ontodev/robot/releases/download/v1.8.1/robot.jar
      - name: Build ontology
        run: ./scripts/build.sh
      - name: Create release
        uses: actions/create-release@v1
        with:
          tag_name: ${{ github.ref }}
          release_name: Release ${{ github.ref }}
          draft: false
          prerelease: false

Automated Testing

Ontology Validation

ROBOT Validation: 

robot validate --input Robot/ontologies/pbpko.owl

Checks performed: - OWL syntax validation - Logical consistency - Property restrictions - Class hierarchy validation

Template Validation

Template Checking: 

robot template --template Robot/templates/vocab.tsv --check

Checks performed: - TSV format validation - Required column validation - ID uniqueness - Reference validation

Build Testing

Complete Build Test: 

./scripts/build.sh

Tests performed: - Template processing - Import merging - Ontology generation - Output validation

Quality Assurance

Code Quality

Automated Checks: - Syntax validation - Format checking - Linting - Security scanning

Documentation Quality

Documentation Checks: - Link validation - Markdown syntax - Image optimization - Accessibility testing

Performance Testing

Performance Checks: - Build time monitoring - Memory usage tracking - Output size validation - Processing speed testing

Deployment Automation

GitHub Pages Deployment

Automatic deployment: - Triggers on main branch push - Builds MkDocs site - Deploys to GitHub Pages - Updates live documentation

Release Automation

Release process: - Tag-based triggering - Automated build - Release file generation - GitHub release creation

Monitoring and Alerts

Build Status

Status Monitoring: - GitHub Actions status badges - Build success/failure notifications - Performance metrics tracking - Error reporting

Notification System

Alerts: - Email notifications for failures - Slack integration for team updates - GitHub issue creation for errors - Status page updates

Configuration Management

Environment Variables

Secrets Management: - GitHub secrets for sensitive data - Environment-specific configurations - API key management - Access token handling

Build Configuration

Configuration Files: - mkdocs.yml - Documentation configuration - robot-config.yaml - ROBOT configuration - .github/workflows/ - CI workflow definitions - scripts/ - Build script configurations

Troubleshooting

Common Issues

Build Failures: - Check ROBOT version compatibility - Verify template format - Validate import URLs - Check Java version

Deployment Issues: - Verify GitHub Pages settings - Check repository permissions - Validate MkDocs configuration - Review deployment logs

Debug Mode

Enable Debug Output: 

- name: Debug build
  run: |
    echo "Debug information"
    ls -la Robot/ontologies/
    robot --verbose validate --input Robot/ontologies/pbpko.owl

Best Practices

Workflow Design

Design Principles: - Keep workflows simple and focused - Use reusable workflow components - Implement proper error handling - Include comprehensive logging

Security

Security Measures: - Use GitHub secrets for sensitive data - Implement proper access controls - Regular security updates - Vulnerability scanning

Performance

Performance Optimization: - Use caching for dependencies - Parallel job execution - Optimize build scripts - Monitor resource usage

Maintenance

Regular Updates

Update Schedule: - Monthly dependency updates - Quarterly workflow reviews - Annual security audits - Continuous monitoring

Monitoring

Monitoring Tasks: - Build success rates - Performance metrics - Error frequency - Resource usage

Resources

Documentation

Tools

Examples