Add Genome Status Tracking

[JeanMainguy]

Add support for tracking genome statuses (representative, reference, type strain, etc.) across collection releases.

Changes

Database

• New GenomeStatus table to track genome statuses per collection release
• Migration file: 1b2d64350ce4_add_genome_status_table.py
• Indexed columns for efficient querying

API

• Updated /genomes/{genome_id} endpoint to include genome statuses
• New GenomeStatusPublic model in API responses
• Genome statuses include status_type, origin, and collection_release_id

Data Import

• Updated JSON schema to support optional genome_status_files field
• Each status file contains one genome name per line
• Example: GTDB representatives, NCBI reference genomes
• Handles duplicate statuses gracefully (skips if already exists)

CLI

• New command: pangbank_db add-genome-statuses to add statuses to existing releases
• Allows updating genome statuses without re-importing entire collections
• Useful for incremental updates when new representatives/references are announced

Testing

• All existing tests pass (57 tests)
• Functional tests verify genome status import and retrieval

Migration

Run alembic upgrade head to apply the database changes.