Tuberous Sclerosis Complex — Advanced Learning Guide

For engineers extending or operating this subject.

Source: core/disease-programs/tuberous-sclerosis · 115 Python files · 7,598 LOC · 24 test files

Registered capabilities

No capability is registered for this subject in lib/hcls_common/capabilities.json.

No service port — this subject exposes no single registered endpoint.

Principal modules

src/viz/usd_ascii.py

write_usda, write_mosaic_usda, write_atlas_usda, write_population_usda

• write_mosaic_usda — Author the mosaic 'powers-of-ten' cell field as a USD PointInstancer: exactly the

api/main.py

lifespan, create_app

src/eval/harness.py

evaluate

• evaluate — Run the full scorecard. featured defaults to the engine's featured map if present.

src/agents/trajectory_modeler/runner.py

TrajectoryModeler

src/orchestrator/graph.py

Orchestrator

Dependencies

anthropic>=0.40, fastapi>=0.109, langgraph>=0.2, minio>=7.2, numpy>=1.26, psycopg2-binary>=2.9, pydantic-settings>=2.0, pydantic>=2.0, pymilvus>=2.4, pytest>=8.0, pyyaml>=6.0, redis>=5.0, sentence-transformers>=2.2, statsmodels>=0.14

Running the tests

.venv/bin/python scripts/run_all_tests.py tuberous-sclerosis

Two traps the shared harness handles, which a hand-rolled pytest invocation will not:

1. Several subjects ship src/vector_collections.py, which shadows the Python standard library. Putting their src/ on PYTHONPATH kills the interpreter before collection.
2. structural-biology/vendor_rfdiffusion/ is vendored third-party code needing gated GPU packages and is excluded.

Operational notes

Gene-therapy correction of TSC1/TSC2 is preclinical — an open design bench, not a cure today. Pediatric caution at full force. Decision support, never prescribing.

Before changing a port, read ../../build/PORT_MAP.md. The convention is enforced by scripts/validate_registry.py, which also cross-checks health-monitor.sh — a port change in one place and not the other fails the build.

Extending it

1. Add or change code under core/disease-programs/tuberous-sclerosis.
2. Keep the capability entry in lib/hcls_common/capabilities.json truthful — a live status must answer a health probe. Two capabilities were found registered live with nothing bound to their ports; do not add a third.
3. Run the gate: ruff, pytest lib/hcls_common, validate_registry.py, run_all_tests.py.