Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

api/alembic/env.py

@@ -0,0 +1,32 @@
+import asyncio
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy.ext.asyncio import async_engine_from_config
+from sqlalchemy import pool
+
+from app.config import settings
+from app.models import Base
+
+config = context.config
+config.set_main_option("sqlalchemy.url", settings.database_url)
+if config.config_file_name:
+    fileConfig(config.config_file_name)
+target_metadata = Base.metadata
+
+
+def run_migrations(connection):
+    context.configure(connection=connection, target_metadata=target_metadata)
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_async():
+    engine = async_engine_from_config(
+        config.get_section(config.config_ini_section, {}), poolclass=pool.NullPool
+    )
+    async with engine.connect() as conn:
+        await conn.run_sync(run_migrations)
+
+
+asyncio.run(run_async())