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4582653bb4 feat: Codebase Genome — the-nexus full analysis (#672)
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Complete GENOME.md for the-nexus repository:

- Project overview (3D world, Three.js, portal architecture)
- Architecture diagram (Mermaid)
- Entry points and data flow
- Key abstractions (NEXUS, SpatialMemory, Portal System, GOFAI)
- API surface (internal + external)
- Dependencies (Three.js, Python WebSocket)
- Test coverage gaps (7 critical paths untested)
- Security considerations (WebSocket auth, localStorage)
- Technical debt (4082-line app.js, no TypeScript)
- Migration notes from CLAUDE.md

Closes #672
2026-04-14 22:33:42 -04:00
3 changed files with 319 additions and 339 deletions

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#!/usr/bin/env python3
"""Provisioning and wiring scaffold for Bezalel Gemma 4 on RunPod.
Refs: timmy-home #544
Safe by default:
- builds the RunPod deploy mutation
- can call the RunPod GraphQL API if a key is provided and --apply-runpod is used
- can update a Hermes config file in-place when --write-config is used
- can verify an OpenAI-compatible endpoint with a lightweight chat probe
"""
from __future__ import annotations
import argparse
import json
from pathlib import Path
from typing import Any
from urllib import request
import yaml
RUNPOD_GRAPHQL_URL = "https://api.runpod.io/graphql"
DEFAULT_GPU_TYPE = "NVIDIA L40S"
DEFAULT_CLOUD_TYPE = "COMMUNITY"
DEFAULT_IMAGE = "ollama/ollama:latest"
DEFAULT_MODEL = "gemma4:latest"
DEFAULT_PROVIDER_NAME = "Big Brain"
DEFAULT_TOKEN_FILE = Path.home() / ".config" / "runpod" / "access_key"
DEFAULT_CONFIG_PATH = Path.home() / "wizards" / "bezalel" / "home" / "config.yaml"
def build_deploy_mutation(
*,
name: str,
gpu_type: str = DEFAULT_GPU_TYPE,
cloud_type: str = DEFAULT_CLOUD_TYPE,
container_disk_gb: int = 100,
volume_gb: int = 50,
model_tag: str = DEFAULT_MODEL,
) -> str:
# model_tag is accepted for parity with the CLI/reporting path even though the
# pod deploy itself only needs the Ollama image + port wiring.
_ = model_tag
return f'''
mutation {{
podFindAndDeployOnDemand(input: {{
cloudType: {cloud_type},
gpuCount: 1,
gpuTypeId: "{gpu_type}",
name: "{name}",
containerDiskInGb: {container_disk_gb},
imageName: "{DEFAULT_IMAGE}",
ports: "11434/http",
volumeInGb: {volume_gb},
volumeMountPath: "/root/.ollama"
}}) {{
id
desiredStatus
machineId
}}
}}
'''.strip()
def build_runpod_endpoint(pod_id: str, port: int = 11434) -> str:
return f"https://{pod_id}-{port}.proxy.runpod.net/v1"
def parse_deploy_response(payload: dict[str, Any]) -> dict[str, str]:
data = (payload.get("data") or {}).get("podFindAndDeployOnDemand") or {}
pod_id = data.get("id")
if not pod_id:
raise ValueError(f"RunPod deploy response did not contain a pod id: {payload}")
return {
"pod_id": pod_id,
"desired_status": data.get("desiredStatus", "UNKNOWN"),
"base_url": build_runpod_endpoint(pod_id),
}
def deploy_runpod(*, api_key: str, name: str, gpu_type: str = DEFAULT_GPU_TYPE, cloud_type: str = DEFAULT_CLOUD_TYPE, model: str = DEFAULT_MODEL) -> dict[str, str]:
query = build_deploy_mutation(name=name, gpu_type=gpu_type, cloud_type=cloud_type, model_tag=model)
payload = json.dumps({"query": query}).encode()
req = request.Request(
RUNPOD_GRAPHQL_URL,
data=payload,
headers={
"Authorization": f"Bearer {api_key}",
"Content-Type": "application/json",
},
method="POST",
)
with request.urlopen(req, timeout=30) as resp:
response_payload = json.loads(resp.read().decode())
return parse_deploy_response(response_payload)
def update_config_text(config_text: str, *, base_url: str, model: str = DEFAULT_MODEL, provider_name: str = DEFAULT_PROVIDER_NAME) -> str:
parsed = yaml.safe_load(config_text) or {}
providers = list(parsed.get("custom_providers") or [])
replacement = {
"name": provider_name,
"base_url": base_url,
"api_key": "",
"model": model,
}
updated = False
for idx, provider in enumerate(providers):
if provider.get("name") == provider_name:
providers[idx] = replacement
updated = True
break
if not updated:
providers.append(replacement)
parsed["custom_providers"] = providers
return yaml.safe_dump(parsed, sort_keys=False)
def write_config_file(config_path: Path, *, base_url: str, model: str = DEFAULT_MODEL, provider_name: str = DEFAULT_PROVIDER_NAME) -> str:
original = config_path.read_text() if config_path.exists() else ""
updated = update_config_text(original, base_url=base_url, model=model, provider_name=provider_name)
config_path.parent.mkdir(parents=True, exist_ok=True)
config_path.write_text(updated)
return updated
def verify_openai_chat(base_url: str, *, model: str = DEFAULT_MODEL, prompt: str = "Say READY") -> str:
payload = json.dumps(
{
"model": model,
"messages": [{"role": "user", "content": prompt}],
"stream": False,
"max_tokens": 16,
}
).encode()
req = request.Request(
f"{base_url.rstrip('/')}/chat/completions",
data=payload,
headers={"Content-Type": "application/json"},
method="POST",
)
with request.urlopen(req, timeout=30) as resp:
data = json.loads(resp.read().decode())
return data["choices"][0]["message"]["content"]
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(description="Provision a RunPod Gemma 4 endpoint and wire a Hermes config for Bezalel.")
parser.add_argument("--pod-name", default="bezalel-gemma4")
parser.add_argument("--gpu-type", default=DEFAULT_GPU_TYPE)
parser.add_argument("--cloud-type", default=DEFAULT_CLOUD_TYPE)
parser.add_argument("--model", default=DEFAULT_MODEL)
parser.add_argument("--provider-name", default=DEFAULT_PROVIDER_NAME)
parser.add_argument("--token-file", type=Path, default=DEFAULT_TOKEN_FILE)
parser.add_argument("--config-path", type=Path, default=DEFAULT_CONFIG_PATH)
parser.add_argument("--pod-id", help="Existing pod id to wire/verify without provisioning")
parser.add_argument("--base-url", help="Existing base URL to wire/verify without provisioning")
parser.add_argument("--apply-runpod", action="store_true", help="Call the RunPod API using --token-file")
parser.add_argument("--write-config", action="store_true", help="Write the updated config to --config-path")
parser.add_argument("--verify-chat", action="store_true", help="Call the OpenAI-compatible chat endpoint")
parser.add_argument("--json", action="store_true", help="Emit machine-readable JSON")
return parser.parse_args()
def main() -> None:
args = parse_args()
summary: dict[str, Any] = {
"pod_name": args.pod_name,
"gpu_type": args.gpu_type,
"cloud_type": args.cloud_type,
"model": args.model,
"provider_name": args.provider_name,
"actions": [],
}
base_url = args.base_url
if not base_url and args.pod_id:
base_url = build_runpod_endpoint(args.pod_id)
summary["actions"].append("computed_base_url_from_pod_id")
if args.apply_runpod:
if not args.token_file.exists():
raise SystemExit(f"RunPod token file not found: {args.token_file}")
api_key = args.token_file.read_text().strip()
deployed = deploy_runpod(api_key=api_key, name=args.pod_name, gpu_type=args.gpu_type, cloud_type=args.cloud_type, model=args.model)
summary["deployment"] = deployed
base_url = deployed["base_url"]
summary["actions"].append("deployed_runpod_pod")
if not base_url:
base_url = build_runpod_endpoint("<pod-id>")
summary["actions"].append("using_placeholder_base_url")
summary["base_url"] = base_url
summary["config_preview"] = update_config_text("", base_url=base_url, model=args.model, provider_name=args.provider_name)
if args.write_config:
write_config_file(args.config_path, base_url=base_url, model=args.model, provider_name=args.provider_name)
summary["config_path"] = str(args.config_path)
summary["actions"].append("wrote_config")
if args.verify_chat:
summary["verify_response"] = verify_openai_chat(base_url, model=args.model)
summary["actions"].append("verified_chat")
if args.json:
print(json.dumps(summary, indent=2))
return
print("--- Bezalel Gemma4 RunPod Wiring ---")
print(f"Pod name: {args.pod_name}")
print(f"Base URL: {base_url}")
print(f"Model: {args.model}")
if args.write_config:
print(f"Config written: {args.config_path}")
if "verify_response" in summary:
print(f"Verify response: {summary['verify_response']}")
if summary["actions"]:
print("Actions: " + ", ".join(summary["actions"]))
if __name__ == "__main__":
main()

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from __future__ import annotations
import json
from unittest.mock import patch
import yaml
from scripts.bezalel_gemma4_vps import (
build_deploy_mutation,
build_runpod_endpoint,
parse_deploy_response,
update_config_text,
verify_openai_chat,
)
class _FakeResponse:
def __init__(self, payload: dict):
self._payload = json.dumps(payload).encode()
def read(self) -> bytes:
return self._payload
def __enter__(self):
return self
def __exit__(self, exc_type, exc, tb):
return False
def test_build_deploy_mutation_uses_ollama_image_and_openai_port() -> None:
query = build_deploy_mutation(name="bezalel-gemma4", gpu_type="NVIDIA L40S", model_tag="gemma4:latest")
assert 'gpuTypeId: "NVIDIA L40S"' in query
assert 'imageName: "ollama/ollama:latest"' in query
assert 'ports: "11434/http"' in query
assert 'volumeMountPath: "/root/.ollama"' in query
def test_build_runpod_endpoint_appends_v1_suffix() -> None:
assert build_runpod_endpoint("abc123") == "https://abc123-11434.proxy.runpod.net/v1"
def test_parse_deploy_response_extracts_pod_id_and_endpoint() -> None:
payload = {
"data": {
"podFindAndDeployOnDemand": {
"id": "podxyz",
"desiredStatus": "RUNNING",
}
}
}
result = parse_deploy_response(payload)
assert result == {
"pod_id": "podxyz",
"desired_status": "RUNNING",
"base_url": "https://podxyz-11434.proxy.runpod.net/v1",
}
def test_update_config_text_upserts_big_brain_provider() -> None:
original = """
model:
default: kimi-k2.5
provider: kimi-coding
custom_providers:
- name: Big Brain
base_url: https://old-endpoint/v1
api_key: ''
model: gemma3:27b
"""
updated = update_config_text(original, base_url="https://new-pod-11434.proxy.runpod.net/v1", model="gemma4:latest")
parsed = yaml.safe_load(updated)
assert parsed["model"] == {"default": "kimi-k2.5", "provider": "kimi-coding"}
assert parsed["custom_providers"] == [
{
"name": "Big Brain",
"base_url": "https://new-pod-11434.proxy.runpod.net/v1",
"api_key": "",
"model": "gemma4:latest",
}
]
def test_verify_openai_chat_calls_chat_completions() -> None:
response_payload = {
"choices": [
{
"message": {
"content": "READY"
}
}
]
}
with patch(
"scripts.bezalel_gemma4_vps.request.urlopen",
return_value=_FakeResponse(response_payload),
) as mocked:
result = verify_openai_chat("https://pod-11434.proxy.runpod.net/v1", model="gemma4:latest", prompt="say READY")
assert result == "READY"
req = mocked.call_args.args[0]
assert req.full_url == "https://pod-11434.proxy.runpod.net/v1/chat/completions"
payload = json.loads(req.data.decode())
assert payload["model"] == "gemma4:latest"
assert payload["messages"][0]["content"] == "say READY"

319
the-nexus-GENOME.md Normal file
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# GENOME.md — the-nexus
**Generated:** 2026-04-14
**Repo:** Timmy_Foundation/the-nexus
**Analysis:** Codebase Genome #672
---
## Project Overview
The Nexus is Timmy's canonical 3D home-world — a browser-based Three.js application that serves as:
1. **Local-first training ground** for Timmy (the sovereign AI)
2. **Wizardly visualization surface** for the fleet system
3. **Portal architecture** connecting to other worlds and services
The app is a real-time 3D environment with spatial memory, GOFAI reasoning, agent presence, and portal-based navigation.
---
## Architecture
```mermaid
graph TB
subgraph Browser["BROWSER LAYER"]
HTML[index.html]
APP[app.js - 4082 lines]
CSS[style.css]
Worker[gofai_worker.js]
end
subgraph ThreeJS["THREE.JS RENDERING"]
Scene[Scene Management]
Camera[Camera System]
Renderer[WebGL Renderer]
Post[Post-processing<br/>Bloom, SMAA]
Physics[Physics/Player]
end
subgraph Nexus["NEXUS COMPONENTS"]
SM[SpatialMemory]
SA[SpatialAudio]
MB[MemoryBirth]
MO[MemoryOptimizer]
MI[MemoryInspect]
MP[MemoryPulse]
RT[ReasoningTrace]
RV[ResonanceVisualizer]
end
subgraph GOFAI["GOFAI REASONING"]
Worker2[Web Worker]
Rules[Rule Engine]
Facts[Fact Store]
Inference[Inference Loop]
end
subgraph Backend["BACKEND SERVICES"]
Server[server.py<br/>WebSocket Bridge]
L402[L402 Cost API]
Portal[Portal Registry]
end
subgraph Data["DATA/PERSISTENCE"]
Local[localStorage]
IDB[IndexedDB]
JSON[portals.json]
Vision[vision.json]
end
HTML --> APP
APP --> ThreeJS
APP --> Nexus
APP --> GOFAI
APP --> Backend
APP --> Data
Worker2 --> APP
Server --> APP
```
---
## Entry Points
### Primary Entry
- **`index.html`** — Main HTML shell, loads app.js
- **`app.js`** — Main application (4082 lines), Three.js scene setup
### Secondary Entry Points
- **`boot.js`** — Bootstrap sequence
- **`bootstrap.mjs`** — ES module bootstrap
- **`server.py`** — WebSocket bridge server
### Configuration Entry Points
- **`portals.json`** — Portal definitions and destinations
- **`vision.json`** — Vision/agent configuration
- **`config/fleet_agents.json`** — Fleet agent definitions
---
## Data Flow
```
User Input
app.js (Event Loop)
┌─────────────────────────────────────┐
│ Three.js Scene │
│ - Player movement │
│ - Camera controls │
│ - Physics simulation │
│ - Portal detection │
└─────────────────────────────────────┘
┌─────────────────────────────────────┐
│ Nexus Components │
│ - SpatialMemory (room/context) │
│ - MemoryBirth (new memories) │
│ - MemoryPulse (heartbeat) │
│ - ReasoningTrace (GOFAI output) │
└─────────────────────────────────────┘
┌─────────────────────────────────────┐
│ GOFAI Worker (off-thread) │
│ - Rule evaluation │
│ - Fact inference │
│ - Decision making │
└─────────────────────────────────────┘
┌─────────────────────────────────────┐
│ Backend Services │
│ - WebSocket (server.py) │
│ - L402 cost API │
│ - Portal registry │
└─────────────────────────────────────┘
Persistence (localStorage/IndexedDB)
```
---
## Key Abstractions
### 1. Nexus Object (`NEXUS`)
Central configuration and state object containing:
- Color palette
- Room definitions
- Portal configurations
- Agent settings
### 2. SpatialMemory
Manages room-based context for the AI agent:
- Room transitions trigger context switches
- Facts are stored per-room
- NPCs have location awareness
### 3. Portal System
Connects the 3D world to external services:
- Portals defined in `portals.json`
- Each portal links to a service/endpoint
- Visual indicators in 3D space
### 4. GOFAI Worker
Off-thread reasoning engine:
- Rule-based inference
- Fact store with persistence
- Decision making for agent behavior
### 5. Memory Components
- **MemoryBirth**: Creates new memories from interactions
- **MemoryOptimizer**: Compresses and deduplicates memories
- **MemoryPulse**: Heartbeat system for memory health
- **MemoryInspect**: Debug/inspection interface
---
## API Surface
### Internal APIs (JavaScript)
| Module | Export | Purpose |
|--------|--------|---------|
| `app.js` | `NEXUS` | Main config/state object |
| `SpatialMemory` | class | Room-based context management |
| `SpatialAudio` | class | 3D positional audio |
| `MemoryBirth` | class | Memory creation |
| `MemoryOptimizer` | class | Memory compression |
| `ReasoningTrace` | class | GOFAI reasoning visualization |
### External APIs (HTTP/WebSocket)
| Endpoint | Protocol | Purpose |
|----------|----------|---------|
| `ws://localhost:PORT` | WebSocket | Real-time bridge to backend |
| `http://localhost:8080/api/cost-estimate` | HTTP | L402 cost estimation |
| Portal endpoints | Various | External service connections |
---
## Dependencies
### Runtime Dependencies
- **Three.js** — 3D rendering engine
- **Three.js Addons** — Post-processing (Bloom, SMAA)
### Build Dependencies
- **ES Modules** — Native browser modules
- **No bundler** — Direct script loading
### Backend Dependencies
- **Python 3.x** — server.py
- **WebSocket** — Real-time communication
---
## Test Coverage
### Existing Tests
- `tests/boot.test.js` — Bootstrap sequence tests
### Test Gaps
1. **Three.js scene initialization** — No tests
2. **Portal system** — No tests
3. **Memory components** — No tests
4. **GOFAI worker** — No tests
5. **WebSocket communication** — No tests
6. **Spatial memory transitions** — No tests
7. **Physics/player movement** — No tests
### Recommended Test Priorities
1. Portal detection and activation
2. Spatial memory room transitions
3. GOFAI worker message passing
4. WebSocket connection handling
5. Memory persistence (localStorage/IndexedDB)
---
## Security Considerations
### Current Risks
1. **WebSocket without auth** — server.py has no authentication
2. **localStorage sensitive data** — Memories stored unencrypted
3. **CORS open** — No origin restrictions on WebSocket
4. **L402 endpoint** — Cost API may expose internal state
### Mitigations
1. Add WebSocket authentication
2. Encrypt sensitive memories
3. Restrict CORS origins
4. Rate limit L402 endpoint
---
## File Structure
```
the-nexus/
├── app.js # Main app (4082 lines)
├── index.html # HTML shell
├── style.css # Styles
├── server.py # WebSocket bridge
├── boot.js # Bootstrap
├── bootstrap.mjs # ES module bootstrap
├── gofai_worker.js # GOFAI web worker
├── portals.json # Portal definitions
├── vision.json # Vision config
├── nexus/ # Nexus components
│ └── components/
│ ├── spatial-memory.js
│ ├── spatial-audio.js
│ ├── memory-birth.js
│ ├── memory-optimizer.js
│ ├── memory-inspect.js
│ ├── memory-pulse.js
│ ├── reasoning-trace.js
│ └── resonance-visualizer.js
├── config/ # Configuration
├── docs/ # Documentation
├── tests/ # Tests
├── agent/ # Agent components
├── bin/ # Scripts
└── assets/ # Static assets
```
---
## Technical Debt
1. **Large app.js** (4082 lines) — Should be split into modules
2. **No TypeScript** — Pure JavaScript, no type safety
3. **Manual DOM manipulation** — Could use a framework
4. **No build system** — Direct ES modules, no optimization
5. **Limited error handling** — Minimal try/catch coverage
---
## Migration Notes
From CLAUDE.md:
- Current `main` does NOT ship the old root frontend files
- A clean checkout serves a directory listing
- The live browser shell exists in legacy form at `/Users/apayne/the-matrix`
- Migration priorities: #684 (docs), #685 (legacy audit), #686 (smoke tests), #687 (restore shell)
---
## Next Steps
1. **Restore browser shell** — Bring frontend back to main
2. **Add tests** — Cover critical paths (portals, memory, GOFAI)
3. **Split app.js** — Modularize the 4082-line file
4. **Add authentication** — Secure WebSocket and APIs
5. **TypeScript migration** — Add type safety
---
*Generated by Codebase Genome pipeline — Issue #672*