Phase 4: Update Docker for Namespace Packages

[lsetiawan]

Parent Issue: #54

Goal

Update Docker Compose and Dockerfile to install and run namespace packages.

Tasks

Step 4.1: Update Pixi configuration

• Update pixi.toml to add editable installs for all namespace packages
• Remove root pyproject.toml if it exists

Step 4.2: Update Dockerfile for namespace packages

• Modify Dockerfile to install packages in dependency order:
  • Install datamodels first (no internal dependencies)
  • Install webservice (depends on datamodels)
  • Install pipeline (depends on datamodels)
• Copy remaining files (alembic, configs)

Step 4.3: Refactor docker-compose.yml services

• Keep db service (PostgreSQL)
• Keep prefect-server service
• Rename app service to prefect-worker
  • Runs Prefect worker for pipeline tasks
  • Command: pixi run prefect worker start --pool default-pool
• Add new api service
  • Runs FastAPI application
  • Command: pixi run uvicorn ca_biositing.webservice.main:app --host 0.0.0.0 --port 8000
  • Exposes port 8000
  • Depends on db service
• Ensure proper networking between all services
• Add volume mounts for development

Step 4.4: Create docker-compose overrides

• Create docker-compose.dev.yml
  • Enable hot reload for API
  • Mount volumes for live code changes
  • Enable debug mode
• Create docker-compose.prod.yml (future)
  • Production optimizations

Step 4.5: Update .dockerignore

• Create/update .dockerignore with appropriate exclusions

Step 4.6: Update environment configuration

• Update .env.example with all required variables:
  • Database configuration
  • API configuration
  • Prefect configuration
  • Google Sheets credentials

Step 4.7: Test full stack with namespace packages

• Build containers: docker-compose build
• Start all services: docker-compose up -d
• Verify namespace package imports work
• Check service health:
  • Database
  • Prefect server
  • API
  • Prefect worker
• Run database migrations: docker-compose exec api alembic upgrade head
• Test running a flow: docker-compose exec prefect-worker python run_prefect_flow.py
• Update documentation with new Docker commands

Success Criteria

• All services start with docker-compose up
• Database health check passes
• Prefect server and worker connect successfully
• API accessible on configured port
• Pipeline can execute flows in container
• Namespace packages import correctly in all containers

Dependencies

• Depends on: Phase 1: Create Namespace Package Structure #56 (Phase 1) - namespace packages
• Depends on: Phase 3: Create Webservice Namespace Package #58 (Phase 3) - webservice package

Labels

Sub-task, phase-4, docker, infrastructure

[lsetiawan]

This is partially done in #66