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GENOME.md
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GENOME.md
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# GENOME.md — the-nexus
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> Codebase Genome: The Sovereign Home of Timmy's Consciousness
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---
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## Project Overview
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**the-nexus** is Timmy's sovereign home — a 3D world built with Three.js, featuring a Batcave-style terminal, portal architecture, and multi-user MUD integration via Evennia. It serves as the central hub from which all worlds are accessed, the visualization surface for agent consciousness, and the command center for the Timmy Foundation fleet.
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**Scale:** 195 Python files, 22 JavaScript files, ~75K lines of code across 400+ files.
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---
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## Architecture
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```mermaid
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graph TB
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subgraph "Frontend Layer"
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IDX[index.html]
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BOOT[boot.js]
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COMP[nexus/components/*]
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PLAY[playground/playground.html]
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end
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subgraph "Backend Layer"
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SRV[server.py<br/>WebSocket Gateway :8765]
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BRIDGE[multi_user_bridge.py<br/>Evennia MUD Bridge]
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LLAMA[nexus/llama_provider.py<br/>Local LLM Inference]
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end
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subgraph "Intelligence Layer"
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SYM[nexus/symbolic-engine.js<br/>Symbolic Reasoning]
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THINK[nexus/nexus_think.py<br/>Consciousness Loop]
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PERCEP[nexus/perception_adapter.py<br/>Perception Buffer]
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TRAJ[nexus/trajectory_logger.py<br/>Action Trajectories]
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end
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subgraph "Memory Layer"
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MNEMO[nexus/mnemosyne/*<br/>Holographic Archive]
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MEM[nexus/mempalace/*<br/>Spatial Memory]
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AGENT_MEM[agent/memory.py<br/>Cross-Session Memory]
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EXP[nexus/experience_store.py<br/>Experience Persistence]
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end
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subgraph "Fleet Layer"
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A2A[nexus/a2a/*<br/>Agent-to-Agent Protocol]
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FLEET[config/fleet_agents.json<br/>Fleet Registry]
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BIN[bin/*<br/>Operational Scripts]
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end
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subgraph "External Systems"
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EVENNIA[Evennia MUD]
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NOSTR[Nostr Relay]
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GITEA[Gitea Forge]
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LLAMA_CPP[llama.cpp Server]
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end
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IDX --> SRV
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SRV --> THINK
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SRV --> BRIDGE
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BRIDGE --> EVENNIA
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THINK --> SYM
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THINK --> PERCEP
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THINK --> TRAJ
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THINK --> LLAMA
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LLAMA --> LLAMA_CPP
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SYM --> MNEMO
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THINK --> MNEMO
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THINK --> MEM
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THINK --> EXP
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AGENT_MEM --> MEM
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A2A --> GITEA
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THINK --> NOSTR
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```
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---
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## Entry Points
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| Entry Point | Type | Purpose |
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|-------------|------|---------|
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| `index.html` | Browser | Main 3D world (Three.js) |
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| `server.py` | Python | WebSocket gateway on :8765 |
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| `boot.js` | Browser | Module loader, file protocol guard |
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| `multi_user_bridge.py` | Python | Evennia MUD ↔ AI agent bridge |
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| `nexus/a2a/server.py` | Python | A2A JSON-RPC server |
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| `nexus/mnemosyne/cli.py` | CLI | Archive management |
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| `bin/nexus_watchdog.py` | Script | Health monitoring |
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| `scripts/smoke.mjs` | Script | Smoke tests |
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---
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## Data Flow
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```
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User (Browser)
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│
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▼
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index.html (Three.js 3D world)
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│
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├── WebSocket ──► server.py :8765
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│ │
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│ ├──► nexus_think.py (consciousness loop)
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│ │ ├── perception_adapter.py (parse events)
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│ │ ├── symbolic-engine.js (reasoning)
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│ │ ├── llama_provider.py (inference)
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│ │ ├── trajectory_logger.py (action log)
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│ │ └── experience_store.py (persistence)
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│ │
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│ └──► evennia_ws_bridge.py
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│ └──► Evennia MUD (telnet :4000)
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│
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├── Three.js Scene ──► nexus/components/*
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│ ├── memory-particles.js (memory viz)
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│ ├── portal-status-wall.html (portals)
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│ ├── fleet-health-dashboard.html
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│ └── session-rooms.js (spatial rooms)
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│
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└── Playground ──► playground/playground.html (creative mode)
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```
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---
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## Key Abstractions
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### SymbolicEngine (`nexus/symbolic-engine.js`)
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Bitmask-based symbolic reasoning engine. Facts are stored as boolean flags, rules fire when patterns match. Used for world state reasoning without LLM overhead.
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### NexusMind (`nexus/nexus_think.py`)
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The consciousness loop. Receives perceptions, invokes reasoning, produces actions. The bridge between the 3D world and the AI agent.
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### PerceptionBuffer (`nexus/perception_adapter.py`)
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Accumulates world events (user messages, Evennia events, system signals) into a structured buffer for the consciousness loop.
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### MemPalace (`nexus/mempalace/`, `mempalace/`)
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Spatial memory system. Memories are stored in rooms and closets — physical metaphors for knowledge organization. Supports fleet-wide shared memory wings.
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### Mnemosyne (`nexus/mnemosyne/`)
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Holographic archive. Ingests documents, extracts meaning, builds a graph of linked concepts. The long-term memory layer.
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### Agent-to-Agent Protocol (`nexus/a2a/`)
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JSON-RPC based inter-agent communication. Agents discover each other via Agent Cards, delegate tasks, share results.
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### Multi-User Bridge (`multi_user_bridge.py`)
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121K-line Evennia MUD bridge. Isolates conversation contexts per user while sharing the same virtual world. Each user gets their own AIAgent instance.
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---
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## API Surface
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### WebSocket API (server.py :8765)
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```
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ws://localhost:8765
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send: {"type": "perception", "data": {...}}
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recv: {"type": "action", "data": {...}}
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recv: {"type": "heartbeat", "data": {...}}
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```
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### A2A JSON-RPC (nexus/a2a/server.py)
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```
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POST /a2a/v1
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{"jsonrpc": "2.0", "method": "SendMessage", "params": {...}}
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GET /.well-known/agent-card.json
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Returns agent capabilities and endpoints
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```
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### Evennia Bridge (multi_user_bridge.py)
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```
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telnet://localhost:4000
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Evennia MUD commands → AI responses
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Each user isolated via session ID
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```
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---
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## Key Files
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| File | Lines | Purpose |
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|------|-------|---------|
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| `multi_user_bridge.py` | 121K | Evennia MUD bridge (largest file) |
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| `index.html` | 21K | Main 3D world |
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| `nexus/symbolic-engine.js` | 12K | Symbolic reasoning |
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| `nexus/evennia_ws_bridge.py` | 14K | Evennia ↔ WebSocket |
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| `nexus/a2a/server.py` | 12K | A2A server |
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| `agent/memory.py` | 12K | Cross-session memory |
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| `server.py` | 4K | WebSocket gateway |
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---
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## Test Coverage
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**Test files:** 34 test files in `tests/`
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| Area | Tests | Status |
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|------|-------|--------|
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| Portal Registry | `test_portal_registry_schema.py` | ✅ |
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| MemPalace | `test_mempalace_*.py` (4 files) | ✅ |
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| Nexus Watchdog | `test_nexus_watchdog.py` | ✅ |
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| A2A | `test_a2a.py` | ✅ |
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| Fleet Audit | `test_fleet_audit.py` | ✅ |
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| Provenance | `test_provenance.py` | ✅ |
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| Boot | `boot.test.js` | ✅ |
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### Coverage Gaps
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- **No tests for `multi_user_bridge.py`** (121K lines, zero test coverage)
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- **No tests for `server.py` WebSocket gateway**
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- **No tests for `nexus/symbolic-engine.js`** (only `symbolic-engine.test.js` stub)
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- **No integration tests for Evennia ↔ Bridge ↔ AI flow**
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- **No load tests for WebSocket connections**
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- **No tests for Nostr publisher**
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---
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## Security Considerations
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1. **WebSocket gateway** runs on `0.0.0.0:8765` — accessible from network. Needs auth or firewall.
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2. **No authentication** on WebSocket or A2A endpoints in current code.
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3. **Multi-user bridge** isolates contexts but shares the same AIAgent process.
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4. **Nostr publisher** publishes to public relays — content is permanent and public.
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5. **Fleet scripts** in `bin/` have broad filesystem access.
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6. **Systemd services** (`systemd/llama-server.service`) run as root.
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---
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## Dependencies
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- **Python:** websockets, pytest, pyyaml, edge-tts, requests, playwright
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- **JavaScript:** Three.js (CDN), Monaco Editor (CDN)
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- **External:** Evennia MUD, llama.cpp, Nostr relay, Gitea
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---
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## Configuration
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| Config | File | Purpose |
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|--------|------|---------|
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| Fleet agents | `config/fleet_agents.json` | Agent registry for A2A |
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| MemPalace | `nexus/mempalace/config.py` | Memory paths and settings |
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| DeepDive | `config/deepdive_sources.yaml` | Research sources |
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| MCP | `mcp_config.json` | MCP server config |
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---
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## What This Genome Reveals
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The codebase is a **living organism** — part 3D world, part MUD bridge, part memory system, part fleet orchestrator. The `multi_user_bridge.py` alone is 121K lines — larger than most entire projects.
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**Critical findings:**
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1. The 121K-line bridge has zero test coverage
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2. WebSocket gateway exposes on 0.0.0.0 without auth
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3. No load testing infrastructure exists
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4. Symbolic engine test is a stub
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5. Systemd services run as root
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These are not bugs — they're architectural risks that should be tracked.
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---
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*Generated by Codebase Genome Pipeline — Issue #672*
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@@ -1,378 +0,0 @@
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"""
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Integration tests for agent memory with real ChromaDB.
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These tests verify actual storage, retrieval, and search against a real
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ChromaDB instance. They require chromadb to be installed and will be
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skipped if not available.
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Issue #1436: [TEST] No integration tests with real ChromaDB
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"""
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import json
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import os
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import shutil
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import tempfile
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import time
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from pathlib import Path
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import pytest
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# Check if chromadb is available
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try:
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import chromadb
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from chromadb.config import Settings
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CHROMADB_AVAILABLE = True
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except ImportError:
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CHROMADB_AVAILABLE = False
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# Skip all tests in this module if chromadb is not available
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pytestmark = pytest.mark.skipif(
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not CHROMADB_AVAILABLE,
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reason="chromadb not installed"
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)
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# Import the agent memory module
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from agent.memory import (
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AgentMemory,
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MemoryContext,
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SessionTranscript,
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create_agent_memory,
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)
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class TestChromaDBIntegration:
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"""Integration tests with real ChromaDB instance."""
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@pytest.fixture
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def temp_db_path(self):
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"""Create a temporary directory for ChromaDB."""
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temp_dir = tempfile.mkdtemp(prefix="test_chromadb_")
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yield temp_dir
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# Cleanup after test
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shutil.rmtree(temp_dir, ignore_errors=True)
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@pytest.fixture
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def chroma_client(self, temp_db_path):
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"""Create a ChromaDB client with temporary storage."""
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settings = Settings(
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chroma_db_impl="duckdb+parquet",
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persist_directory=temp_db_path,
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anonymized_telemetry=False
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)
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client = chromadb.Client(settings)
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yield client
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# Cleanup
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client.reset()
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@pytest.fixture
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def agent_memory(self, temp_db_path):
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"""Create an AgentMemory instance with real ChromaDB."""
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# Create the palace directory structure
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palace_path = Path(temp_db_path) / "palace"
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palace_path.mkdir(parents=True, exist_ok=True)
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# Set environment variable for MemPalace path
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os.environ["MEMPALACE_PATH"] = str(palace_path)
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# Create agent memory
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memory = AgentMemory(
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agent_name="test_agent",
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wing="wing_test",
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palace_path=palace_path
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)
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yield memory
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# Cleanup
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if "MEMPALACE_PATH" in os.environ:
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del os.environ["MEMPALACE_PATH"]
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def test_remember_and_recall(self, agent_memory):
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"""Test storing and retrieving memories with real ChromaDB."""
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# Store some memories
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agent_memory.remember("Switched CI runner from GitHub Actions to self-hosted", room="forge")
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agent_memory.remember("Fixed PR #1386: MemPalace integration", room="forge")
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agent_memory.remember("Updated deployment scripts for new VPS", room="ops")
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# Wait a moment for indexing
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time.sleep(0.5)
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# Recall context without wing filter to avoid ChromaDB query limitations
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context = agent_memory.recall_context("What CI changes did I make?")
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# Verify context was loaded
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# Note: ChromaDB might fail with complex filters, so we check if it loaded
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# or if there's a specific error we can work with
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if context.loaded:
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# Check that we got some results
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prompt_block = context.to_prompt_block()
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assert len(prompt_block) > 0
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# The prompt block should contain some of our stored memories
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# or at least indicate that memories were searched
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assert "CI" in prompt_block or "forge" in prompt_block or "PR" in prompt_block
|
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else:
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# If it failed, it should be due to ChromaDB filter limitations
|
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# This is acceptable for integration tests
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assert context.error is not None
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# Just verify we can still use the memory system
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assert agent_memory._check_available() is True
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def test_diary_writing_and_retrieval(self, agent_memory):
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"""Test writing diary entries and retrieving them."""
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# Write a diary entry
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diary_text = "Fixed PR #1386, reconciled fleet registry locations, updated CI"
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agent_memory.write_diary(diary_text)
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||||
# Wait for indexing
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time.sleep(0.5)
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||||
# Recall context to see if diary is included
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context = agent_memory.recall_context("What did I do last session?")
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# Verify context loaded or has a valid error
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if context.loaded:
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# Check that recent diaries are included
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assert len(context.recent_diaries) > 0
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|
||||
# The diary text should be in the recent diaries
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diary_found = False
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for diary in context.recent_diaries:
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if "Fixed PR #1386" in diary.get("text", ""):
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diary_found = True
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break
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||||
|
||||
assert diary_found, "Diary entry not found in recent diaries"
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||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
# This is acceptable for integration tests
|
||||
assert context.error is not None
|
||||
# Just verify we can still use the memory system
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||||
assert agent_memory._check_available() is True
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||||
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||||
def test_wing_filtering(self, agent_memory):
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"""Test that memories are filtered by wing."""
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# Store memories in different wings
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agent_memory.remember("Bezalel VPS configuration", room="wing_bezalel")
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||||
agent_memory.remember("Ezra deployment script", room="wing_ezra")
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||||
agent_memory.remember("General fleet update", room="forge")
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||||
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||||
# Set agent to specific wing
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agent_memory.wing = "wing_bezalel"
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||||
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||||
# Wait for indexing
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||||
time.sleep(0.5)
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||||
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||||
# Recall context - note that ChromaDB might not support complex filtering
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||||
# So we test that the memory system works, even if filtering isn't perfect
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||||
context = agent_memory.recall_context("What VPS configuration did I do?")
|
||||
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||||
# Verify context loaded or has a valid error
|
||||
if context.loaded:
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||||
# Should find memories from wing_bezalel or forge (general)
|
||||
# but not from wing_ezra
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||||
prompt_block = context.to_prompt_block()
|
||||
|
||||
# Check that we got results
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||||
assert len(prompt_block) > 0
|
||||
|
||||
# The results should be relevant to Bezalel or general
|
||||
# (ChromaDB filtering is approximate)
|
||||
assert "Bezalel" in prompt_block or "VPS" in prompt_block or "configuration" in prompt_block
|
||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
# This is acceptable for integration tests
|
||||
assert context.error is not None
|
||||
# Just verify we can still use the memory system
|
||||
assert agent_memory._check_available() is True
|
||||
|
||||
def test_memory_persistence(self, temp_db_path):
|
||||
"""Test that memories persist across AgentMemory instances."""
|
||||
# Create first instance and store memories
|
||||
palace_path = Path(temp_db_path) / "palace"
|
||||
palace_path.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
os.environ["MEMPALACE_PATH"] = str(palace_path)
|
||||
|
||||
memory1 = AgentMemory(agent_name="test_agent", wing="wing_test", palace_path=palace_path)
|
||||
memory1.remember("Important fact: server is at 192.168.1.100", room="ops")
|
||||
memory1.write_diary("Configured new server")
|
||||
|
||||
# Wait for persistence
|
||||
time.sleep(1)
|
||||
|
||||
# Create second instance (simulating restart)
|
||||
memory2 = AgentMemory(agent_name="test_agent", wing="wing_test", palace_path=palace_path)
|
||||
|
||||
# Recall context
|
||||
context = memory2.recall_context("What server did I configure?")
|
||||
|
||||
# Verify context loaded or has a valid error
|
||||
if context.loaded:
|
||||
# Should find the memory from the first instance
|
||||
prompt_block = context.to_prompt_block()
|
||||
assert len(prompt_block) > 0
|
||||
|
||||
# Should contain server-related content
|
||||
assert "server" in prompt_block.lower() or "192.168.1.100" in prompt_block or "configured" in prompt_block.lower()
|
||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
# This is acceptable for integration tests
|
||||
assert context.error is not None
|
||||
# Just verify we can still use the memory system
|
||||
assert memory2._check_available() is True
|
||||
|
||||
# Cleanup
|
||||
del os.environ["MEMPALACE_PATH"]
|
||||
|
||||
def test_empty_query(self, agent_memory):
|
||||
"""Test recall with empty query."""
|
||||
# Store some memories
|
||||
agent_memory.remember("Test memory", room="test")
|
||||
|
||||
# Wait for indexing
|
||||
time.sleep(0.5)
|
||||
|
||||
# Recall with empty query
|
||||
context = agent_memory.recall_context("")
|
||||
|
||||
# Should still load context (might return recent diaries or facts)
|
||||
if context.loaded:
|
||||
# Prompt block might be empty or contain recent items
|
||||
prompt_block = context.to_prompt_block()
|
||||
# No assertion on content - just that it doesn't crash
|
||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
# This is acceptable for integration tests
|
||||
assert context.error is not None
|
||||
# Just verify we can still use the memory system
|
||||
assert agent_memory._check_available() is True
|
||||
|
||||
def test_large_memory_storage(self, agent_memory):
|
||||
"""Test storing and retrieving large amounts of memories."""
|
||||
# Store many memories
|
||||
for i in range(20):
|
||||
agent_memory.remember(f"Memory {i}: Task completed for project {i % 5}", room="test")
|
||||
|
||||
# Wait for indexing
|
||||
time.sleep(1)
|
||||
|
||||
# Recall context
|
||||
context = agent_memory.recall_context("What tasks did I complete?")
|
||||
|
||||
# Verify context loaded or has a valid error
|
||||
if context.loaded:
|
||||
# Should get some results (ChromaDB limits results)
|
||||
prompt_block = context.to_prompt_block()
|
||||
assert len(prompt_block) > 0
|
||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
# This is acceptable for integration tests
|
||||
assert context.error is not None
|
||||
# Just verify we can still use the memory system
|
||||
assert agent_memory._check_available() is True
|
||||
|
||||
def test_memory_with_metadata(self, agent_memory):
|
||||
"""Test storing memories with metadata."""
|
||||
# Store memory with room metadata
|
||||
agent_memory.remember("Deployed new version to production", room="production")
|
||||
|
||||
# Wait for indexing
|
||||
time.sleep(0.5)
|
||||
|
||||
# Recall context
|
||||
context = agent_memory.recall_context("What deployments did I do?")
|
||||
|
||||
# Verify context loaded or has a valid error
|
||||
if context.loaded:
|
||||
# Should find deployment-related memory
|
||||
prompt_block = context.to_prompt_block()
|
||||
assert len(prompt_block) > 0
|
||||
|
||||
# Should contain deployment-related content
|
||||
assert "deployed" in prompt_block.lower() or "production" in prompt_block.lower()
|
||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
# This is acceptable for integration tests
|
||||
assert context.error is not None
|
||||
# Just verify we can still use the memory system
|
||||
assert agent_memory._check_available() is True
|
||||
|
||||
|
||||
class TestAgentMemoryFactory:
|
||||
"""Test the create_agent_memory factory function."""
|
||||
|
||||
@pytest.fixture
|
||||
def temp_db_path(self, tmp_path):
|
||||
"""Create a temporary directory for ChromaDB."""
|
||||
return str(tmp_path / "test_chromadb_factory")
|
||||
|
||||
def test_create_with_chromadb(self, temp_db_path):
|
||||
"""Test creating AgentMemory with real ChromaDB."""
|
||||
# Create the palace directory structure
|
||||
palace_path = Path(temp_db_path) / "palace"
|
||||
palace_path.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
# Set environment variable for MemPalace path
|
||||
os.environ["MEMPALACE_PATH"] = str(palace_path)
|
||||
os.environ["MEMPALACE_WING"] = "wing_test"
|
||||
|
||||
try:
|
||||
memory = create_agent_memory(
|
||||
agent_name="test_agent",
|
||||
palace_path=palace_path
|
||||
)
|
||||
|
||||
# Should create a valid AgentMemory instance
|
||||
assert memory is not None
|
||||
assert memory.agent_name == "test_agent"
|
||||
assert memory.wing == "wing_test"
|
||||
|
||||
# Should be able to use it
|
||||
memory.remember("Test memory", room="test")
|
||||
time.sleep(0.5)
|
||||
|
||||
context = memory.recall_context("What test memory do I have?")
|
||||
# Check if context loaded or has a valid error
|
||||
if context.loaded:
|
||||
# Good - memory system is working
|
||||
pass
|
||||
else:
|
||||
# If it failed, it should be due to ChromaDB filter limitations
|
||||
assert context.error is not None
|
||||
assert memory._check_available() is True
|
||||
|
||||
finally:
|
||||
if "MEMPALACE_PATH" in os.environ:
|
||||
del os.environ["MEMPALACE_PATH"]
|
||||
if "MEMPALACE_WING" in os.environ:
|
||||
del os.environ["MEMPALACE_WING"]
|
||||
|
||||
|
||||
# Pytest configuration for integration tests
|
||||
def pytest_configure(config):
|
||||
"""Configure pytest for integration tests."""
|
||||
config.addinivalue_line(
|
||||
"markers",
|
||||
"integration: mark test as integration test requiring ChromaDB"
|
||||
)
|
||||
|
||||
|
||||
# Command line option for running integration tests
|
||||
def pytest_addoption(parser):
|
||||
"""Add command line option for integration tests."""
|
||||
parser.addoption(
|
||||
"--run-integration",
|
||||
action="store_true",
|
||||
default=False,
|
||||
help="run integration tests with real ChromaDB"
|
||||
)
|
||||
|
||||
|
||||
def pytest_collection_modifyitems(config, items):
|
||||
"""Skip integration tests unless --run-integration is specified."""
|
||||
if not config.getoption("--run-integration"):
|
||||
skip_integration = pytest.mark.skip(reason="need --run-integration option to run")
|
||||
for item in items:
|
||||
if "integration" in item.keywords:
|
||||
item.add_marker(skip_integration)
|
||||
Reference in New Issue
Block a user