refactor: migrate from Kubernetes to Docker Compose deployment

[SatoryKono]

Summary

Migrate BioETL deployment infrastructure from Kubernetes to Docker Compose, implementing ADR-010 (Local-Only Deployment). This change simplifies the deployment model for development and staging environments while maintaining full feature parity with the previous Kubernetes setup.

Changes

• scripts/deploy-bioetl.sh: Complete rewrite from Kubernetes-based deployment to Docker Compose orchestration

  • Replaced kubectl commands with docker compose equivalents
  • Expanded action set: added start, stop, restart, shell, run-pipeline, backup, restore commands
  • Improved error handling with set -euo pipefail and prerequisite checks
  • Added colored output for better UX (info, success, warn, error)
  • Enhanced documentation with detailed usage examples and architecture notes
  • Supports multiple compose files (infra, app, monitoring) with flexible composition
  • Added health check monitoring and service status reporting
  • Implemented data backup/restore functionality with volume snapshots

• docker-compose.app.yml: New file defining BioETL application service

  • Multi-stage Docker build with production target
  • Environment configuration via .env file
  • Volume mounts for data persistence and config
  • Health checks with configurable intervals
  • Resource limits and reservations (memory/CPU)
  • Network integration with WARP infrastructure service
  • Metrics port exposure (8000)

• Makefile: Added deployment convenience targets

  • deploy: Full stack deployment
  • deploy-status: Service status check
  • deploy-stop: Stop services (preserve data)
  • deploy-update: Rebuild and restart app only
  • deploy-teardown: Destructive cleanup
  • deploy-logs: Log streaming

Benefits

• Simplified Operations: Docker Compose is more accessible than Kubernetes for local/staging deployments
• Better DX: New commands like shell, run-pipeline, backup/restore improve developer experience
• Flexible Composition: Separate compose files allow independent scaling of infra, app, and monitoring
• Data Safety: Explicit backup/restore with volume snapshots
• Health Monitoring: Built-in health checks and status reporting
• Resource Control: Explicit memory/CPU limits prevent resource exhaustion

Checklist

• make lint passes
• make test passes (no new tests required—deployment script is operational)
• No hardcoded secrets or credentials (uses .env file)
• Architecture tests pass
• Documentation updated (inline script comments, help text, Makefile targets)
• Follows Conventional Commits format

Notes

• Kubernetes manifests (k8s-*.yaml) are no longer used; can be archived or removed in follow-up
• .env file is required; script copies from .env.example if missing
• Backward compatibility: existing docker-compose.yml and docker-compose.monitoring.yml are reused
• All data volumes are preserved across stop/start cycles; only teardown is destructive

https://claude.ai/code/session_01P4MZFVobVkix1c6FCXmu9g

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