Analyze rapid DNA sequencing

.github/CI_CD_SETUP_SUMMARY.md

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+# CI/CD Pipeline Setup Summary
+
+## Overview
+
+Comprehensive CI/CD pipeline successfully configured for the `genomic-vector-analysis` package with 5 GitHub Actions workflows, quality gates, security scanning, and automated release management.
+
+## Quick Reference
+
+### Workflows Created
+
+| Workflow | File | Trigger | Purpose |
+|----------|------|---------|---------|
+| **Test** | `test.yml` | Push/PR + Daily | Matrix testing, coverage, performance benchmarks |
+| **Build** | `build.yml` | Push/PR | TypeScript + Rust/WASM builds, bundle analysis |
+| **Publish** | `publish.yml` | Git tags + Manual | NPM publishing, GitHub releases, Docker images |
+| **Docs** | `docs.yml` | Push to main | API docs generation, GitHub Pages deployment |
+| **Quality** | `quality.yml` | Push/PR + Weekly | ESLint, Prettier, security scans, CodeQL |
+
+### Configuration Files
+
+| File | Location | Purpose |
+|------|----------|---------|
+| `.prettierrc` | `packages/genomic-vector-analysis/` | Code formatting rules |
+| `.eslintrc.json` | `packages/genomic-vector-analysis/` | Linting configuration |
+| `.nvmrc` | `packages/genomic-vector-analysis/` | Node version (20.10.0) |
+| `dependabot.yml` | `.github/` | Automated dependency updates |
+| `markdown-link-check-config.json` | `.github/` | Documentation link validation |
+
+### Package Configuration
+
+**Updated `package.json` with:**
+- Enhanced description with SEO keywords
+- Repository, homepage, and bug tracker links
+- Funding information
+- NPM publish configuration with provenance
+- Additional keywords for NPM discovery
+- OS compatibility specifications
+- Engine requirements (Node >=18.0.0, npm >=9.0.0)
+- Proper `files` field for published package
+- Additional scripts: `lint:fix`, `format:check`, `build:wasm`, `prepublishOnly`
+
+## Quality Gates
+
+### Testing Thresholds
+- Code Coverage: ≥90% (statements, functions, lines)
+- Branch Coverage: ≥85%
+- Performance: Query latency p95 <1ms, Throughput >50k var/sec
+- Bundle Size: <512KB
+
+### Security Measures
+- npm audit (moderate threshold)
+- Snyk security scanning (high severity)
+- CodeQL analysis
+- Dependency review on PRs
+- License compliance checking
+
+## Setup Checklist
+
+### Required GitHub Secrets
+
+Set these secrets in GitHub repository settings (`Settings → Secrets and variables → Actions`):
+
+- [ ] `NPM_TOKEN` - For publishing to NPM registry
+- [ ] `SNYK_TOKEN` - For Snyk security scanning (optional but recommended)
+
+**Note:** `GITHUB_TOKEN` is automatically provided by GitHub Actions.
+
+### NPM Token Setup
+
+```bash
+# 1. Log in to npm
+npm login
+
+# 2. Generate access token
+# Go to: https://www.npmjs.com/settings/YOUR_USERNAME/tokens
+# Click "Generate New Token" → "Automation" or "Publish"
+# Copy the token
+
+# 3. Add to GitHub
+# Repository → Settings → Secrets → New repository secret
+# Name: NPM_TOKEN
+# Value: [paste token]
+```
+
+### Snyk Token Setup (Optional)
+
+```bash
+# 1. Sign up at https://snyk.io
+# 2. Go to Account Settings → API Token
+# 3. Copy your token
+# 4. Add to GitHub secrets as SNYK_TOKEN
+```
+
+### GitHub Pages Setup
+
+Enable GitHub Pages for documentation:
+
+1. Go to `Settings → Pages`
+2. Source: `GitHub Actions`
+3. Documentation will be deployed automatically on push to main
+
+## Usage
+
+### Running Tests Locally
+
+```bash
+cd packages/genomic-vector-analysis
+
+# All tests
+npm test
+
+# Specific test suites
+npm run test:unit
+npm run test:integration
+npm run test:performance
+npm run test:coverage
+
+# Watch mode
+npm run test:watch
+```
+
+### Code Quality Checks
+
+```bash
+# Linting
+npm run lint              # Check for errors
+npm run lint:fix          # Auto-fix errors
+
+# Formatting
+npm run format            # Format all files
+npm run format:check      # Check formatting
+
+# Type checking
+npm run typecheck         # TypeScript strict mode
+```
+
+### Building
+
+```bash
+# TypeScript build
+npm run build
+
+# Rust/WASM build
+npm run build:wasm
+
+# Clean build artifacts
+npm run clean
+```
+
+### Documentation
+
+```bash
+# Generate API docs
+npm run docs
+
+# Watch mode (auto-regenerate)
+npm run docs:serve
+
+# Export as JSON
+npm run docs:json
+
+# Export as Markdown
+npm run docs:markdown
+```
+
+### Publishing a New Version
+
+#### Automated (Recommended)
+
+```bash
+# 1. Update CHANGELOG.md with changes
+
+# 2. Create and push a version tag
+git tag v1.2.3
+git push origin v1.2.3
+
+# 3. GitHub Actions will automatically:
+#    - Run all quality gates
+#    - Publish to NPM
+#    - Create GitHub release
+#    - Build Docker image (optional)
+```
+
+#### Manual
+
+```bash
+# 1. Update version in package.json
+npm version patch   # 1.0.0 → 1.0.1
+npm version minor   # 1.0.0 → 1.1.0
+npm version major   # 1.0.0 → 2.0.0
+
+# 2. Run quality checks
+npm run test:ci
+npm run lint
+npm run typecheck
+
+# 3. Build
+npm run build
+
+# 4. Publish
+npm publish --access public
+```
+
+## Workflow Triggers
+
+### Automatic Triggers
+
+| Event | Workflows |
+|-------|-----------|
+| Push to main/develop | Test, Build, Quality |
+| Pull request | Test, Build, Quality, Docs |
+| Git tag (v*.*.*) | Publish |
+| Daily (2 AM UTC) | Test |
+| Weekly (Mon 9 AM UTC) | Quality |
+
+### Manual Triggers
+
+All workflows can be manually triggered via:
+- GitHub UI: `Actions → [Workflow] → Run workflow`
+- GitHub CLI: `gh workflow run [workflow-name]`
+
+## Monitoring
+
+### GitHub Actions Dashboard
+
+Monitor workflow runs:
+- `Actions` tab in repository
+- Filter by workflow, branch, or event
+- Download logs and artifacts
+
+### PR Comments
+
+Automated comments posted on PRs:
+- Performance benchmark results
+- Bundle size analysis
+- Test coverage reports
+
+### GitHub Security Tab
+
+Security alerts:
+- `Security → Dependabot alerts`
+- `Security → Code scanning alerts`
+
+## Next Steps
+
+### Immediate Actions
+
+1. **Set NPM_TOKEN secret** (required for publishing)
+2. **Enable GitHub Pages** (for documentation)
+3. **Set SNYK_TOKEN secret** (recommended for enhanced security)
+4. **Review and customize thresholds** in workflow files if needed
+
+### Recommended Setup
+
+1. **Branch Protection Rules:**
+   ```
+   Settings → Branches → Add rule
+   - Branch name pattern: main
+   - Require status checks to pass before merging
+   - Require branches to be up to date before merging
+   - Select: Test, Build, Quality workflows
+   ```
+
+2. **CODEOWNERS File:**
+   ```bash
+   # Create .github/CODEOWNERS
+   * @ruvnet
+   /.github/ @ruvnet
+   /packages/genomic-vector-analysis/ @ruvnet
+   ```
+
+3. **Issue Templates:**
+   Create issue templates for bug reports and feature requests
+
+4. **Pull Request Template:**
+   Create PR template with checklist
+
+### Future Enhancements
+
+- [ ] Add end-to-end tests
+- [ ] Implement visual regression testing
+- [ ] Add performance regression detection
+- [ ] Set up staging environment
+- [ ] Implement canary deployments
+- [ ] Add Slack/Discord notifications
+- [ ] Configure custom domain for docs
+- [ ] Add badge.fury.io badges to README
+- [ ] Implement changelog automation with conventional commits
+
+## Troubleshooting
+
+### Common Issues
+
+**Tests pass locally but fail in CI:**
+```bash
+# Run in CI mode locally
+npm run test:ci
+
+# Check Node version matches
+node --version  # Should be 20.10.0
+```
+
+**Bundle size exceeds threshold:**
+```bash
+# Check bundle size
+npm run build && du -sh dist/
+
+# Review dependencies
+npm ls --depth=0
+```
+
+**Coverage below threshold:**
+```bash
+# Generate coverage report
+npm run test:coverage
+
+# Open HTML report
+open coverage/lcov-report/index.html
+```
+
+**Publishing fails:**
+- Verify NPM_TOKEN is set correctly
+- Check version doesn't already exist on NPM
+- Ensure tag format is correct (v1.2.3)
+
+## Documentation
+
+- **Full CI/CD Guide:** `.github/CI_CD_GUIDE.md`
+- **Package README:** `packages/genomic-vector-analysis/README.md`
+- **Architecture:** `packages/genomic-vector-analysis/ARCHITECTURE.md`
+- **Contributing:** `packages/genomic-vector-analysis/CONTRIBUTING.md`
+
+## Support
+
+- **Issues:** https://github.com/ruvnet/ruvector/issues
+- **Email:** support@ruv.io
+
+---
+
+**Setup Date:** 2025-11-23
+**Version:** 1.0.0
+**Status:** ✅ Complete and Ready for Use