Precision Autoimmune — Advanced Learning Guide

For engineers extending or operating this subject.

Source: core/agents/precision-autoimmune · 45 Python files · 20,427 LOC · 9 test files

Registered capabilities

Capability	Type	Status	Endpoint
precision-autoimmune-agent	agent	live	localhost:8531

UI :8531 · API :8532 (platform convention: registry endpoint is the UI, API is UI + 1)

Principal modules

app/autoimmune_ui.py

init_services, render_sidebar

• init_services — Initialize all backend services (cached).

scripts/patient_maya.py

generate

• generate — Generate all clinical documents for Maya Rodriguez.

scripts/patient_sarah.py

generate

• generate — Generate all clinical documents for Sarah Mitchell.

src/knowledge.py

no public symbols

scripts/patients_dismissals.py

generate_maya_dismissals, generate_sarah_dismissals, generate_linda_dismissals, generate_david_dismissals

• generate_maya_dismissals — Generate dismissal documents for Maya Rodriguez.
• generate_sarah_dismissals — Generate dismissal documents for Sarah Mitchell.
• generate_linda_dismissals — Generate dismissal documents for Linda Chen.
• generate_david_dismissals — Generate dismissal documents for David Park.

Dependencies

PyPDF2>=3.0.0, anthropic>=0.18.0, fastapi>=0.109.0, httpx>=0.25.0, loguru>=0.7.0, numpy>=1.24.0, pandas>=2.0.0, plotly>=5.18.0, prometheus-client>=0.20.0, pydantic-settings>=2.7, pydantic>=2.0, pymilvus>=2.4.0, python-dotenv>=1.0.0, python-multipart>=0.0.6

Running the tests

.venv/bin/python scripts/run_all_tests.py precision-autoimmune

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

Decision support only; autoimmune management is highly individual and specialist-led.

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/agents/precision-autoimmune.
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.