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# GENOME.md — the-nexus
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# GENOME.md — Timmy_Foundation/timmy-home
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Generated by `pipelines/codebase_genome.py`.
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## Project Overview
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`the-nexus` is a hybrid repo that combines three layers in one codebase:
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Timmy Foundation's home repository for development operations and configurations.
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1. A browser-facing world shell rooted in `index.html`, `boot.js`, `bootstrap.mjs`, `app.js`, `style.css`, `portals.json`, `vision.json`, `manifest.json`, and `gofai_worker.js`
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2. A Python realtime bridge centered on `server.py` plus harness code under `nexus/`
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3. A memory / fleet / operator layer spanning `mempalace/`, `mcp_servers/`, `multi_user_bridge.py`, and supporting scripts
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- Text files indexed: 3133
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- Source and script files: 219
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- Test files: 73
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- Documentation files: 743
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The repo is not a clean single-purpose frontend and not just a backend harness. It is a mixed world/runtime/ops repository where browser rendering, WebSocket telemetry, MCP-driven game harnesses, and fleet memory tooling coexist.
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Grounded repo facts from this checkout:
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- Browser shell files exist at repo root: `index.html`, `app.js`, `style.css`, `manifest.json`, `gofai_worker.js`
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- Data/config files also live at repo root: `portals.json`, `vision.json`
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- Realtime bridge exists in `server.py`
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- Game harnesses exist in `nexus/morrowind_harness.py` and `nexus/bannerlord_harness.py`
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- Memory/fleet sync exists in `mempalace/tunnel_sync.py`
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- Desktop/game automation MCP servers exist in `mcp_servers/desktop_control_server.py` and `mcp_servers/steam_info_server.py`
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- Validation exists in `tests/test_browser_smoke.py`, `tests/test_portals_json.py`, `tests/test_index_html_integrity.py`, and `tests/test_repo_truth.py`
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The current architecture is best understood as a sovereign world shell plus operator/game harness backend, with accumulated documentation drift from multiple restoration and migration efforts.
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## Architecture Diagram
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## Architecture
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```mermaid
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graph TD
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browser[Index HTML Shell\nindex.html -> boot.js -> bootstrap.mjs -> app.js]
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assets[Root Assets\nstyle.css\nmanifest.json\ngofai_worker.js]
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data[World Data\nportals.json\nvision.json]
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ws[Realtime Bridge\nserver.py\nWebSocket broadcast hub]
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gofai[In-browser GOFAI\nSymbolicEngine\nNeuroSymbolicBridge\nsetupGOFAI/updateGOFAI]
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harnesses[Python Harnesses\nnexus/morrowind_harness.py\nnexus/bannerlord_harness.py]
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mcp[MCP Adapters\nmcp_servers/desktop_control_server.py\nmcp_servers/steam_info_server.py]
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memory[Memory + Fleet\nmempalace/tunnel_sync.py\nmempalace.js]
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bridge[Operator / MUD Bridge\nmulti_user_bridge.py\ncommands/timmy_commands.py]
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tests[Verification\ntests/test_browser_smoke.py\ntests/test_portals_json.py\ntests/test_repo_truth.py]
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docs[Contracts + Drift Docs\nBROWSER_CONTRACT.md\nREADME.md\nCLAUDE.md\nINVESTIGATION_ISSUE_1145.md]
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browser --> assets
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browser --> data
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browser --> gofai
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browser --> ws
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harnesses --> mcp
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harnesses --> ws
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bridge --> ws
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memory --> ws
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tests --> browser
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tests --> data
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tests --> docs
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docs --> browser
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repo_root["repo"]
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angband["angband"]
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ansible["ansible"]
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briefings["briefings"]
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codebase_genome["codebase_genome"]
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config["config"]
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configs["configs"]
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conftest["conftest"]
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dns_records["dns-records"]
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evennia["evennia"]
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evennia_tools["evennia_tools"]
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repo_root --> angband
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repo_root --> ansible
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repo_root --> briefings
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repo_root --> codebase_genome
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repo_root --> config
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repo_root --> configs
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```
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## Entry Points and Data Flow
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## Entry Points
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### Primary entry points
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- `codebase_genome.py` — python main guard (`python3 codebase_genome.py`)
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- `gemini-fallback-setup.sh` — operational script (`bash gemini-fallback-setup.sh`)
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- `morrowind/hud.sh` — operational script (`bash morrowind/hud.sh`)
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- `pipelines/codebase_genome.py` — python main guard (`python3 pipelines/codebase_genome.py`)
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- `scripts/agent_pr_gate.py` — operational script (`python3 scripts/agent_pr_gate.py`)
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- `scripts/auto_restart_agent.sh` — operational script (`bash scripts/auto_restart_agent.sh`)
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- `scripts/autonomous_issue_creator.py` — operational script (`python3 scripts/autonomous_issue_creator.py`)
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- `scripts/backlog_cleanup.py` — operational script (`python3 scripts/backlog_cleanup.py`)
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- `scripts/backlog_triage.py` — operational script (`python3 scripts/backlog_triage.py`)
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- `scripts/backlog_triage_cron.sh` — operational script (`bash scripts/backlog_triage_cron.sh`)
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- `scripts/backup_pipeline.sh` — operational script (`bash scripts/backup_pipeline.sh`)
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- `scripts/bezalel_gemma4_vps.py` — operational script (`python3 scripts/bezalel_gemma4_vps.py`)
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- `index.html` — root browser entry point
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- `boot.js` — startup selector; `tests/boot.test.js` shows it chooses file-mode vs HTTP/module-mode and injects `bootstrap.mjs` when served over HTTP
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- `bootstrap.mjs` — module bootstrap for the browser shell
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- `app.js` — main browser runtime; owns world state, GOFAI wiring, metrics polling, and portal/UI logic
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- `server.py` — WebSocket broadcast bridge on `ws://0.0.0.0:8765`
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- `nexus/morrowind_harness.py` — GamePortal/MCP harness for OpenMW Morrowind
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- `nexus/bannerlord_harness.py` — GamePortal/MCP harness for Bannerlord
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- `mempalace/tunnel_sync.py` — pulls remote fleet closets into the local palace over HTTP
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- `multi_user_bridge.py` — HTTP bridge for multi-user chat/session integration
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- `mcp_servers/desktop_control_server.py` — stdio MCP server exposing screenshots/mouse/keyboard control
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## Data Flow
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### Data flow
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1. Browser startup begins at `index.html`
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2. `boot.js` decides whether the page is being served correctly; in HTTP mode it injects `bootstrap.mjs`
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3. `bootstrap.mjs` hands off to `app.js`
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4. `app.js` loads world configuration from `portals.json` and `vision.json`
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5. `app.js` constructs the Three.js scene and in-browser reasoning components, including `SymbolicEngine`, `NeuroSymbolicBridge`, `setupGOFAI()`, and `updateGOFAI()`
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6. Browser state and external runtimes connect through `server.py`, which broadcasts messages between connected clients
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7. Python harnesses (`nexus/morrowind_harness.py`, `nexus/bannerlord_harness.py`) spawn MCP subprocesses for desktop control / Steam metadata, capture state, execute actions, and feed telemetry into the Nexus bridge
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8. Memory/fleet tools like `mempalace/tunnel_sync.py` import remote palace data into local closets, extending what the operator/runtime layers can inspect
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9. Tests validate both the static browser contract and the higher-level repo-truth/memory contracts
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### Important repo-specific runtime facts
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- `portals.json` is a JSON array of portal/world/operator entries; examples in this checkout include `morrowind`, `bannerlord`, `workshop`, `archive`, `chapel`, and `courtyard`
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- `server.py` is a plain broadcast hub: clients send messages, the server forwards them to other connected clients
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- `nexus/morrowind_harness.py` and `nexus/bannerlord_harness.py` both implement a GamePortal pattern with MCP subprocess clients over stdio and WebSocket telemetry uplink
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- `mempalace/tunnel_sync.py` is not speculative; it is a real client that discovers remote wings, searches remote rooms, and writes `.closet.json` payloads locally
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1. Operators enter through `codebase_genome.py`, `gemini-fallback-setup.sh`, `morrowind/hud.sh`.
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2. Core logic fans into top-level components: `angband`, `ansible`, `briefings`, `codebase_genome`, `config`, `configs`.
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3. Validation is incomplete around `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py`, `timmy-local/cache/agent_cache.py`, `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py`, so changes there carry regression risk.
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4. Final artifacts land as repository files, docs, or runtime side effects depending on the selected entry point.
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## Key Abstractions
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### Browser runtime
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- `app.js`
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- Defines in-browser reasoning/state machinery, including `class SymbolicEngine`, `class NeuroSymbolicBridge`, `setupGOFAI()`, and `updateGOFAI()`
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- Couples rendering, local symbolic reasoning, metrics polling, and portal/UI logic in one very large root module
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- `BROWSER_CONTRACT.md`
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- Acts like an executable architecture contract for the browser surface
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- Declares required files, DOM IDs, Three.js expectations, provenance rules, and WebSocket expectations
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### Realtime bridge
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- `server.py`
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- Single hub abstraction: a WebSocket broadcast server maintaining a `clients` set and forwarding messages from one client to the others
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- This is the seam between browser shell, harnesses, and external telemetry producers
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### GamePortal harness layer
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- `nexus/morrowind_harness.py`
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- `nexus/bannerlord_harness.py`
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- Both define MCP client wrappers, `GameState` / `ActionResult`-style data classes, and an Observe-Decide-Act telemetry loop
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- The harnesses are symmetric enough to be understood as reusable portal adapters with game-specific context injected on top
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### Memory / fleet layer
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- `mempalace/tunnel_sync.py`
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- Encodes the fleet-memory sync client contract: discover wings, pull broad room queries, write closet files, support dry-run
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- `mempalace.js`
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- Minimal browser/Electron bridge to MemPalace commands via `window.electronAPI.execPython(...)`
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- Important because it shows a second memory integration surface distinct from the Python fleet sync path
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### Operator / interaction bridge
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||||
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- `multi_user_bridge.py`
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- `commands/timmy_commands.py`
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- These bridge user-facing conversations or MUD/Evennia interactions back into Timmy/Nexus services
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- `codebase_genome.py` — classes `FunctionInfo`:19; functions `extract_functions()`:58, `generate_test()`:116, `scan_repo()`:191, `find_existing_tests()`:209, `main()`:231
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- `evennia/timmy_world/game.py` — classes `World`:91, `ActionSystem`:421, `TimmyAI`:539, `NPCAI`:550; functions `get_narrative_phase()`:55, `get_phase_transition_event()`:65
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- `evennia/timmy_world/world/game.py` — classes `World`:19, `ActionSystem`:326, `TimmyAI`:444, `NPCAI`:455; functions none detected
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||||
- `timmy-world/game.py` — classes `World`:19, `ActionSystem`:349, `TimmyAI`:467, `NPCAI`:478; functions none detected
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||||
- `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — classes none detected; functions none detected
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||||
- `uniwizard/self_grader.py` — classes `SessionGrade`:23, `WeeklyReport`:55, `SelfGrader`:74; functions `main()`:713
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||||
- `uni-wizard/v3/intelligence_engine.py` — classes `ExecutionPattern`:27, `ModelPerformance`:44, `AdaptationEvent`:58, `PatternDatabase`:69; functions none detected
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||||
- `scripts/know_thy_father/crossref_audit.py` — classes `ThemeCategory`:30, `Principle`:160, `MeaningKernel`:169, `CrossRefFinding`:178; functions `extract_themes_from_text()`:192, `parse_soul_md()`:206, `parse_kernels()`:264, `cross_reference()`:296, `generate_report()`:440, `main()`:561
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|
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## API Surface
|
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|
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### Browser / static surface
|
||||
- CLI: `python3 codebase_genome.py` — python main guard (`codebase_genome.py`)
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- CLI: `bash gemini-fallback-setup.sh` — operational script (`gemini-fallback-setup.sh`)
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- CLI: `bash morrowind/hud.sh` — operational script (`morrowind/hud.sh`)
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- CLI: `python3 pipelines/codebase_genome.py` — python main guard (`pipelines/codebase_genome.py`)
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||||
- CLI: `python3 scripts/agent_pr_gate.py` — operational script (`scripts/agent_pr_gate.py`)
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||||
- CLI: `bash scripts/auto_restart_agent.sh` — operational script (`scripts/auto_restart_agent.sh`)
|
||||
- CLI: `python3 scripts/autonomous_issue_creator.py` — operational script (`scripts/autonomous_issue_creator.py`)
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- CLI: `python3 scripts/backlog_cleanup.py` — operational script (`scripts/backlog_cleanup.py`)
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- Python: `extract_functions()` from `codebase_genome.py:58`
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- Python: `generate_test()` from `codebase_genome.py:116`
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- Python: `scan_repo()` from `codebase_genome.py:191`
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- Python: `find_existing_tests()` from `codebase_genome.py:209`
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- Python: `main()` from `codebase_genome.py:231`
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- Python: `get_narrative_phase()` from `evennia/timmy_world/game.py:55`
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|
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- `index.html` served over HTTP
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- `boot.js` exports `bootPage()`; verified by `node --test tests/boot.test.js`
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- Data APIs are file-based inside the repo: `portals.json`, `vision.json`, `manifest.json`
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## Test Coverage Report
|
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|
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### Network/runtime surface
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- Source and script files inspected: 219
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- Test files inspected: 73
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- Coverage gaps:
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- `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — no matching test reference detected
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- `timmy-local/cache/agent_cache.py` — no matching test reference detected
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- `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py` — no matching test reference detected
|
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- `wizards/allegro/home/skills/red-teaming/godmode/scripts/godmode_race.py` — no matching test reference detected
|
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- `skills/productivity/google-workspace/scripts/google_api.py` — no matching test reference detected
|
||||
- `wizards/allegro/home/skills/productivity/google-workspace/scripts/google_api.py` — no matching test reference detected
|
||||
- `morrowind/pilot.py` — no matching test reference detected
|
||||
- `skills/research/domain-intel/scripts/domain_intel.py` — no matching test reference detected
|
||||
- `wizards/allegro/home/skills/research/domain-intel/scripts/domain_intel.py` — no matching test reference detected
|
||||
- `timmy-local/scripts/ingest.py` — no matching test reference detected
|
||||
- `uni-wizard/scripts/generate_scorecard.py` — no matching test reference detected
|
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- `morrowind/local_brain.py` — no matching test reference detected
|
||||
|
||||
- `python3 server.py`
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- Starts the WebSocket bridge on port `8765`
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- `python3 l402_server.py`
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- Local HTTP microservice for cost-estimate style responses
|
||||
- `python3 multi_user_bridge.py`
|
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- Multi-user HTTP/chat bridge
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## Security Audit Findings
|
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|
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### Harness / operator CLI surfaces
|
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- [medium] `briefings/briefing_20260325.json:37` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"gitea_error": "Gitea 404: {\"errors\":null,\"message\":\"not found\",\"url\":\"http://143.198.27.163:3000/api/swagger\"}\n [http://143.198.27.163:3000/api/v1/repos/Timmy_Foundation/sovereign-orchestration/issues?state=open&type=issues&sort=created&direction=desc&limit=1&page=1]",`
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||||
- [medium] `briefings/briefing_20260328.json:11` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"provider_base_url": "http://localhost:8081/v1",`
|
||||
- [medium] `briefings/briefing_20260329.json:11` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"provider_base_url": "http://localhost:8081/v1",`
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||||
- [medium] `config.yaml:37` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `summary_base_url: http://localhost:11434/v1`
|
||||
- [medium] `config.yaml:47` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:52` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:57` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:62` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:67` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:77` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:82` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
|
||||
- [medium] `config.yaml:174` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: http://localhost:11434/v1`
|
||||
|
||||
- `python3 nexus/morrowind_harness.py`
|
||||
- `python3 nexus/bannerlord_harness.py`
|
||||
- `python3 mempalace/tunnel_sync.py --peer <url> [--dry-run] [--n N]`
|
||||
- `python3 mcp_servers/desktop_control_server.py`
|
||||
- `python3 mcp_servers/steam_info_server.py`
|
||||
## Dead Code Candidates
|
||||
|
||||
### Validation surface
|
||||
- `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `timmy-local/cache/agent_cache.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `wizards/allegro/home/skills/red-teaming/godmode/scripts/godmode_race.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `skills/productivity/google-workspace/scripts/google_api.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `wizards/allegro/home/skills/productivity/google-workspace/scripts/google_api.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `morrowind/pilot.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `skills/research/domain-intel/scripts/domain_intel.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `wizards/allegro/home/skills/research/domain-intel/scripts/domain_intel.py` — not imported by indexed Python modules and not referenced by tests
|
||||
- `timmy-local/scripts/ingest.py` — not imported by indexed Python modules and not referenced by tests
|
||||
|
||||
- `python3 -m pytest tests/test_portals_json.py tests/test_index_html_integrity.py tests/test_repo_truth.py -q`
|
||||
- `node --test tests/boot.test.js`
|
||||
- `python3 -m py_compile server.py nexus/morrowind_harness.py nexus/bannerlord_harness.py mempalace/tunnel_sync.py mcp_servers/desktop_control_server.py`
|
||||
- `tests/test_browser_smoke.py` defines the higher-cost Playwright smoke contract for the world shell
|
||||
## Performance Bottleneck Analysis
|
||||
|
||||
## Test Coverage Gaps
|
||||
|
||||
Strongly covered in this checkout:
|
||||
- `tests/test_portals_json.py` validates `portals.json`
|
||||
- `tests/test_index_html_integrity.py` checks merge-marker/DOM-integrity regressions in `index.html`
|
||||
- `tests/boot.test.js` verifies `boot.js` startup behavior
|
||||
- `tests/test_repo_truth.py` validates the repo-truth documents
|
||||
- Multiple `tests/test_mempalace_*.py` files cover the palace layer
|
||||
- `tests/test_bannerlord_harness.py` exists for the Bannerlord harness
|
||||
|
||||
Notable gaps or weak seams:
|
||||
- `nexus/morrowind_harness.py` is large and operationally critical, but the generated baseline still flags it as a gap relative to its size/complexity
|
||||
- `mcp_servers/desktop_control_server.py` exposes high-power automation but has no obvious dedicated test file in the root `tests/` suite
|
||||
- `app.js` is the dominant browser runtime file and mixes rendering, GOFAI, metrics, and integration logic in one place; browser smoke exists, but there is limited unit-level decomposition around those subsystems
|
||||
- `mempalace.js` appears minimally bridged and stale relative to the richer Python MemPalace layer
|
||||
- `multi_user_bridge.py` is a large integration surface and should be treated as high regression risk even though it is central to operator/chat flow
|
||||
|
||||
## Security Considerations
|
||||
|
||||
- `server.py` binds `HOST = "0.0.0.0"`, exposing the broadcast bridge beyond localhost unless network controls limit it
|
||||
- The WebSocket bridge is a broadcast hub without visible authentication in `server.py`; connected clients are trusted to send messages into the bus
|
||||
- `mcp_servers/desktop_control_server.py` exposes mouse/keyboard/screenshot control through a stdio MCP server. In any non-local or poorly isolated runtime, this is a privileged automation surface
|
||||
- `app.js` contains hardcoded local/network endpoints such as `http://localhost:${L402_PORT}/api/cost-estimate` and `http://localhost:8082/metrics`; these are convenient for local development but create environment drift and deployment assumptions
|
||||
- `app.js` also embeds explicit endpoint/status references like `ws://143.198.27.163:8765`, which is operationally brittle and the kind of hardcoded location data that drifts across environments
|
||||
- `mempalace.js` shells out through `window.electronAPI.execPython(...)`; this is powerful and useful, but it is a clear trust boundary between UI and host execution
|
||||
- `INVESTIGATION_ISSUE_1145.md` documents an earlier integrity hazard: agents writing to `public/nexus/` instead of canonical root paths. That path confusion is both an operational and security concern because it makes provenance harder to reason about
|
||||
|
||||
## Runtime Truth and Docs Drift
|
||||
|
||||
The most important architecture finding in this repo is not a class or subsystem. It is a truth mismatch.
|
||||
|
||||
- README.md says current `main` does not ship a browser 3D world
|
||||
- CLAUDE.md declares root `app.js` and `index.html` as canonical frontend paths
|
||||
- tests and browser contract now assume the root frontend exists
|
||||
|
||||
All three statements are simultaneously present in this checkout.
|
||||
|
||||
Grounded evidence:
|
||||
- `README.md` still says the repo does not contain an active root frontend such as `index.html`, `app.js`, or `style.css`
|
||||
- the current checkout does contain `index.html`, `app.js`, `style.css`, `manifest.json`, and `gofai_worker.js`
|
||||
- `BROWSER_CONTRACT.md` explicitly treats those root files as required browser assets
|
||||
- `tests/test_browser_smoke.py` serves those exact files and validates DOM/WebGL contracts against them
|
||||
- `tests/test_index_html_integrity.py` assumes `index.html` is canonical and production-relevant
|
||||
- `CLAUDE.md` says frontend code lives at repo root and explicitly warns against `public/nexus/`
|
||||
- `INVESTIGATION_ISSUE_1145.md` explains why `public/nexus/` is a bad/corrupt duplicate path and confirms the real classical AI code lives in root `app.js`
|
||||
|
||||
The honest conclusion:
|
||||
- The repo contains a partially restored or actively re-materialized browser surface
|
||||
- The docs are preserving an older migration truth while the runtime files and smoke contracts describe a newer present-tense truth
|
||||
- Any future work in `the-nexus` must choose one truth and align `README.md`, `CLAUDE.md`, smoke tests, and file layout around it
|
||||
|
||||
That drift is itself a critical architectural fact and should be treated as first-order design debt, not a side note.
|
||||
- `angband/mcp_server.py` — large module (353 lines) likely hides multiple responsibilities
|
||||
- `evennia/timmy_world/game.py` — large module (1541 lines) likely hides multiple responsibilities
|
||||
- `evennia/timmy_world/world/game.py` — large module (1345 lines) likely hides multiple responsibilities
|
||||
- `morrowind/mcp_server.py` — large module (451 lines) likely hides multiple responsibilities
|
||||
- `morrowind/pilot.py` — large module (459 lines) likely hides multiple responsibilities
|
||||
- `pipelines/codebase_genome.py` — large module (557 lines) likely hides multiple responsibilities
|
||||
- `scripts/know_thy_father/crossref_audit.py` — large module (657 lines) likely hides multiple responsibilities
|
||||
- `scripts/know_thy_father/index_media.py` — large module (405 lines) likely hides multiple responsibilities
|
||||
- `scripts/know_thy_father/synthesize_kernels.py` — large module (416 lines) likely hides multiple responsibilities
|
||||
- `scripts/predictive_resource_allocator.py` — large module (410 lines) likely hides multiple responsibilities
|
||||
|
||||
@@ -8,6 +8,7 @@ This pipeline gives Timmy a repeatable way to generate a deterministic `GENOME.m
|
||||
|
||||
- `pipelines/codebase_genome.py` — static analyzer that writes `GENOME.md`
|
||||
- `pipelines/codebase-genome.py` — thin CLI wrapper matching the expected pipeline-style entrypoint
|
||||
- `templates/GENOME-template.md` — reusable review scaffold with the exact sections the generator emits
|
||||
- `scripts/codebase_genome_nightly.py` — org-aware nightly runner that selects the next repo, updates a local checkout, and writes the genome artifact
|
||||
- `GENOME.md` — generated analysis for `timmy-home` itself
|
||||
|
||||
@@ -40,6 +41,14 @@ The hyphenated wrapper also works:
|
||||
python3 pipelines/codebase-genome.py --repo-root /path/to/repo --repo Timmy_Foundation/some-repo
|
||||
```
|
||||
|
||||
If an agent or human wants to review or hand-edit the artifact before publishing it, start from:
|
||||
|
||||
```text
|
||||
templates/GENOME-template.md
|
||||
```
|
||||
|
||||
The template uses the same section names as the generator output, so issue-specific verification can lock the structure without depending on one repo's exact contents.
|
||||
|
||||
## Nightly org rotation
|
||||
|
||||
Dry-run the next selection:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
# Burn Lane Empty Audit — timmy-home #662
|
||||
|
||||
Generated: 2026-04-17T03:42:50Z
|
||||
Generated: 2026-04-16T01:22:37Z
|
||||
Source issue: `[ops] Burn lane empty — all open issues triaged (2026-04-14)`
|
||||
|
||||
## Source Snapshot
|
||||
@@ -11,9 +11,9 @@ Issue #662 is an operational status note, not a normal feature request. Its body
|
||||
|
||||
- Referenced issues audited: 42
|
||||
- Already closed: 30
|
||||
- Open but likely closure candidates (merged PR found): 1
|
||||
- Open with active PRs: 0
|
||||
- Open / needs manual review: 11
|
||||
- Open but likely closure candidates (merged PR found): 0
|
||||
- Open with active PRs: 12
|
||||
- Open / needs manual review: 0
|
||||
|
||||
## Issue Body Drift
|
||||
|
||||
@@ -21,56 +21,56 @@ The body of #662 is not current truth. It mixes closed issues, open issues, rang
|
||||
|
||||
| Issue | State | Classification | PR Summary |
|
||||
|---|---|---|---|
|
||||
| #579 | closed | already closed | closed PR #644, closed PR #643, closed PR #640, closed PR #635, closed PR #620 |
|
||||
| #648 | open | needs manual review | closed PR #731 |
|
||||
| #579 | closed | already closed | closed PR #644, closed PR #640, closed PR #635, closed PR #620 |
|
||||
| #648 | open | active pr | open PR #731 |
|
||||
| #647 | closed | already closed | issue already closed |
|
||||
| #619 | closed | already closed | issue already closed |
|
||||
| #616 | closed | already closed | issue already closed |
|
||||
| #614 | closed | already closed | issue already closed |
|
||||
| #613 | closed | already closed | issue already closed |
|
||||
| #660 | closed | already closed | issue already closed |
|
||||
| #659 | closed | already closed | closed PR #660 |
|
||||
| #659 | closed | already closed | issue already closed |
|
||||
| #658 | closed | already closed | issue already closed |
|
||||
| #657 | closed | already closed | issue already closed |
|
||||
| #656 | closed | already closed | closed PR #658 |
|
||||
| #655 | closed | already closed | issue already closed |
|
||||
| #654 | closed | already closed | closed PR #661 |
|
||||
| #653 | closed | already closed | closed PR #660, closed PR #655 |
|
||||
| #652 | closed | already closed | closed PR #660, merged PR #657, closed PR #655 |
|
||||
| #651 | closed | already closed | closed PR #655 |
|
||||
| #650 | closed | already closed | closed PR #661, closed PR #660, merged PR #654, closed PR #651 |
|
||||
| #649 | closed | already closed | closed PR #660, merged PR #657, closed PR #651 |
|
||||
| #646 | closed | already closed | closed PR #655, closed PR #651 |
|
||||
| #582 | open | closure candidate | merged PR #641, merged PR #639, merged PR #637, merged PR #631, merged PR #630 |
|
||||
| #653 | closed | already closed | issue already closed |
|
||||
| #652 | closed | already closed | merged PR #657 |
|
||||
| #651 | closed | already closed | issue already closed |
|
||||
| #650 | closed | already closed | merged PR #654 |
|
||||
| #649 | closed | already closed | issue already closed |
|
||||
| #646 | closed | already closed | issue already closed |
|
||||
| #582 | open | active pr | open PR #738 |
|
||||
| #627 | closed | already closed | issue already closed |
|
||||
| #631 | closed | already closed | issue already closed |
|
||||
| #632 | closed | already closed | issue already closed |
|
||||
| #634 | closed | already closed | issue already closed |
|
||||
| #639 | closed | already closed | issue already closed |
|
||||
| #641 | closed | already closed | issue already closed |
|
||||
| #575 | closed | already closed | closed PR #658, merged PR #656 |
|
||||
| #576 | closed | already closed | merged PR #664, closed PR #663, closed PR #660, closed PR #655, merged PR #654, closed PR #651, closed PR #646, closed PR #642, closed PR #633 |
|
||||
| #575 | closed | already closed | merged PR #656 |
|
||||
| #576 | closed | already closed | closed PR #663, closed PR #660, closed PR #655, closed PR #651, closed PR #646, closed PR #642, closed PR #633 |
|
||||
| #578 | closed | already closed | merged PR #638, closed PR #636 |
|
||||
| #636 | closed | already closed | issue already closed |
|
||||
| #638 | closed | already closed | issue already closed |
|
||||
| #547 | open | needs manual review | closed PR #730 |
|
||||
| #548 | open | needs manual review | closed PR #712 |
|
||||
| #549 | open | needs manual review | closed PR #729 |
|
||||
| #550 | open | needs manual review | closed PR #727 |
|
||||
| #551 | open | needs manual review | closed PR #725 |
|
||||
| #552 | open | needs manual review | closed PR #724 |
|
||||
| #553 | open | needs manual review | closed PR #722 |
|
||||
| #562 | open | needs manual review | closed PR #718 |
|
||||
| #544 | open | needs manual review | closed PR #732 |
|
||||
| #545 | open | needs manual review | closed PR #719 |
|
||||
| #547 | open | active pr | open PR #730 |
|
||||
| #548 | open | active pr | open PR #712 |
|
||||
| #549 | open | active pr | open PR #729 |
|
||||
| #550 | open | active pr | open PR #727 |
|
||||
| #551 | open | active pr | open PR #725 |
|
||||
| #552 | open | active pr | open PR #724 |
|
||||
| #553 | open | active pr | open PR #722 |
|
||||
| #562 | open | active pr | open PR #718 |
|
||||
| #544 | open | active pr | open PR #732 |
|
||||
| #545 | open | active pr | open PR #719 |
|
||||
|
||||
## Closure Candidates
|
||||
|
||||
These issues are still open but already have merged PR evidence in the forge and should be reviewed for bulk closure.
|
||||
|
||||
| Issue | State | Classification | PR Summary |
|
||||
|---|---|---|---|
|
||||
| #582 | open | closure candidate | merged PR #641, merged PR #639, merged PR #637, merged PR #631, merged PR #630 |
|
||||
| None |
|
||||
|---|
|
||||
| None |
|
||||
|
||||
## Still Open / Needs Manual Review
|
||||
|
||||
@@ -78,17 +78,18 @@ These issues either have no matching PR signal or still have an active PR / ambi
|
||||
|
||||
| Issue | State | Classification | PR Summary |
|
||||
|---|---|---|---|
|
||||
| #648 | open | needs manual review | closed PR #731 |
|
||||
| #547 | open | needs manual review | closed PR #730 |
|
||||
| #548 | open | needs manual review | closed PR #712 |
|
||||
| #549 | open | needs manual review | closed PR #729 |
|
||||
| #550 | open | needs manual review | closed PR #727 |
|
||||
| #551 | open | needs manual review | closed PR #725 |
|
||||
| #552 | open | needs manual review | closed PR #724 |
|
||||
| #553 | open | needs manual review | closed PR #722 |
|
||||
| #562 | open | needs manual review | closed PR #718 |
|
||||
| #544 | open | needs manual review | closed PR #732 |
|
||||
| #545 | open | needs manual review | closed PR #719 |
|
||||
| #648 | open | active pr | open PR #731 |
|
||||
| #582 | open | active pr | open PR #738 |
|
||||
| #547 | open | active pr | open PR #730 |
|
||||
| #548 | open | active pr | open PR #712 |
|
||||
| #549 | open | active pr | open PR #729 |
|
||||
| #550 | open | active pr | open PR #727 |
|
||||
| #551 | open | active pr | open PR #725 |
|
||||
| #552 | open | active pr | open PR #724 |
|
||||
| #553 | open | active pr | open PR #722 |
|
||||
| #562 | open | active pr | open PR #718 |
|
||||
| #544 | open | active pr | open PR #732 |
|
||||
| #545 | open | active pr | open PR #719 |
|
||||
|
||||
## Recommendation
|
||||
|
||||
|
||||
@@ -23,7 +23,6 @@ class PullSummary:
|
||||
state: str
|
||||
merged: bool
|
||||
head: str
|
||||
body: str
|
||||
url: str
|
||||
|
||||
|
||||
@@ -76,8 +75,7 @@ def api_get(path: str, token: str):
|
||||
def collect_pull_summaries(repo: str, token: str) -> list[PullSummary]:
|
||||
pulls: list[PullSummary] = []
|
||||
for state in ("open", "closed"):
|
||||
page = 1
|
||||
while True:
|
||||
for page in range(1, 6):
|
||||
batch = api_get(f"/repos/{ORG}/{repo}/pulls?state={state}&limit=100&page={page}", token)
|
||||
if not batch:
|
||||
break
|
||||
@@ -89,18 +87,18 @@ def collect_pull_summaries(repo: str, token: str) -> list[PullSummary]:
|
||||
state=pr.get("state") or state,
|
||||
merged=bool(pr.get("merged")),
|
||||
head=(pr.get("head") or {}).get("ref") or "",
|
||||
body=pr.get("body") or "",
|
||||
url=pr.get("html_url") or pr.get("url") or "",
|
||||
)
|
||||
)
|
||||
page += 1
|
||||
if len(batch) < 100:
|
||||
break
|
||||
return pulls
|
||||
|
||||
|
||||
def match_prs(issue_num: int, pulls: Iterable[PullSummary]) -> list[PullSummary]:
|
||||
matches: list[PullSummary] = []
|
||||
for pr in pulls:
|
||||
text = f"{pr.title} {pr.head} {pr.body}"
|
||||
text = f"{pr.title} {pr.head}"
|
||||
if f"#{issue_num}" in text or pr.head == f"fix/{issue_num}" or f"/{issue_num}" in pr.head or f"-{issue_num}" in pr.head:
|
||||
matches.append(pr)
|
||||
return matches
|
||||
@@ -118,16 +116,12 @@ def classify_issue(issue: dict, related_prs: list[PullSummary]) -> IssueAuditRow
|
||||
else:
|
||||
merged = [pr for pr in related_prs if pr.merged]
|
||||
open_prs = [pr for pr in related_prs if pr.state == "open"]
|
||||
closed_unmerged = [pr for pr in related_prs if pr.state != "open" and not pr.merged]
|
||||
if merged:
|
||||
classification = "closure_candidate"
|
||||
pr_summary = summarize_prs(merged)
|
||||
elif open_prs:
|
||||
classification = "active_pr"
|
||||
pr_summary = summarize_prs(open_prs)
|
||||
elif closed_unmerged:
|
||||
classification = "needs_manual_review"
|
||||
pr_summary = summarize_prs(closed_unmerged)
|
||||
else:
|
||||
classification = "needs_manual_review"
|
||||
pr_summary = "no matching PR found"
|
||||
|
||||
67
templates/GENOME-template.md
Normal file
67
templates/GENOME-template.md
Normal file
@@ -0,0 +1,67 @@
|
||||
# GENOME.md — [org/repo]
|
||||
|
||||
Generated by `pipelines/codebase_genome.py` or used as a manual review scaffold when a human is curating the final artifact.
|
||||
|
||||
## Project Overview
|
||||
|
||||
[One paragraph: what the repo does, why it exists, and what outcome it creates.]
|
||||
|
||||
- Text files indexed: [count]
|
||||
- Source and script files: [count]
|
||||
- Test files: [count]
|
||||
- Documentation files: [count]
|
||||
|
||||
## Architecture
|
||||
|
||||
```mermaid
|
||||
graph TD
|
||||
repo_root["repo"] --> component_a["component-a"]
|
||||
repo_root --> component_b["component-b"]
|
||||
component_a --> component_b
|
||||
```
|
||||
|
||||
## Entry Points
|
||||
|
||||
- `[path/to/entrypoint]` — [why it matters] (`python3 path/to/entrypoint.py`)
|
||||
- `[path/to/other-entrypoint]` — [why it matters] (`bash path/to/script.sh`)
|
||||
|
||||
## Data Flow
|
||||
|
||||
1. [How operators or callers enter the system.]
|
||||
2. [Which modules or directories fan out from the entrypoint.]
|
||||
3. [Where validation or test gaps create risk.]
|
||||
4. [What artifact, state change, or runtime side effect is produced.]
|
||||
|
||||
## Key Abstractions
|
||||
|
||||
- `[module.py]` — classes `[ClassName]:line`; functions `[function_name()]:line`
|
||||
- `[another_module.py]` — classes `[AnotherClass]:line`; functions `[run()]:line`
|
||||
|
||||
## API Surface
|
||||
|
||||
- CLI: `python3 [entrypoint] --help` — [what it exposes]
|
||||
- Python: `[public_function]()` from `[module.py:line]`
|
||||
- HTTP/WebSocket/other: `[surface]` — [contract summary]
|
||||
|
||||
## Test Coverage Report
|
||||
|
||||
- Source and script files inspected: [count]
|
||||
- Test files inspected: [count]
|
||||
- Coverage gaps:
|
||||
- `[path/to/file]` — [missing coverage detail]
|
||||
- `[path/to/other]` — [missing coverage detail]
|
||||
|
||||
## Security Audit Findings
|
||||
|
||||
- `[severity]` `[path:line]` — [risk category]: [detail]. Evidence: `[snippet]`
|
||||
- `[severity]` `[path:line]` — [risk category]: [detail]. Evidence: `[snippet]`
|
||||
|
||||
## Dead Code Candidates
|
||||
|
||||
- `[path/to/file]` — [why it appears unreferenced]
|
||||
- `[path/to/other]` — [why it appears unreferenced]
|
||||
|
||||
## Performance Bottleneck Analysis
|
||||
|
||||
- `[path/to/file]` — [why runtime or scale could degrade here]
|
||||
- `[path/to/other]` — [filesystem scan / network / large module / hot path detail]
|
||||
@@ -1,13 +1,6 @@
|
||||
from pathlib import Path
|
||||
|
||||
from scripts.burn_lane_issue_audit import (
|
||||
PullSummary,
|
||||
classify_issue,
|
||||
collect_pull_summaries,
|
||||
extract_issue_numbers,
|
||||
match_prs,
|
||||
render_report,
|
||||
)
|
||||
from scripts.burn_lane_issue_audit import extract_issue_numbers, render_report
|
||||
|
||||
|
||||
def test_extract_issue_numbers_handles_ranges_and_literals() -> None:
|
||||
@@ -21,99 +14,6 @@ def test_extract_issue_numbers_handles_ranges_and_literals() -> None:
|
||||
assert extract_issue_numbers(body) == [579, 660, 659, 658, 582, 627, 631, 547, 546, 545]
|
||||
|
||||
|
||||
def test_match_prs_detects_issue_ref_in_pr_body() -> None:
|
||||
pulls = [
|
||||
PullSummary(
|
||||
number=731,
|
||||
title="docs: verify session harvest report",
|
||||
state="open",
|
||||
merged=False,
|
||||
head="fix/session-harvest-report",
|
||||
body="Refs #648",
|
||||
url="https://forge.example/pr/731",
|
||||
),
|
||||
PullSummary(
|
||||
number=732,
|
||||
title="unrelated",
|
||||
state="open",
|
||||
merged=False,
|
||||
head="fix/unrelated",
|
||||
body="Refs #700",
|
||||
url="https://forge.example/pr/732",
|
||||
),
|
||||
]
|
||||
|
||||
assert [pr.number for pr in match_prs(648, pulls)] == [731]
|
||||
|
||||
|
||||
|
||||
def test_open_issue_with_closed_unmerged_pr_stays_manual_review_with_history() -> None:
|
||||
issue = {
|
||||
"number": 648,
|
||||
"title": "session harvest report",
|
||||
"state": "open",
|
||||
"html_url": "https://forge.example/issues/648",
|
||||
}
|
||||
row = classify_issue(
|
||||
issue,
|
||||
[
|
||||
PullSummary(
|
||||
number=731,
|
||||
title="docs: add session harvest report",
|
||||
state="closed",
|
||||
merged=False,
|
||||
head="fix/648",
|
||||
body="Closes #648",
|
||||
url="https://forge.example/pr/731",
|
||||
)
|
||||
],
|
||||
)
|
||||
|
||||
assert row.classification == "needs_manual_review"
|
||||
assert row.pr_summary == "closed PR #731"
|
||||
|
||||
|
||||
|
||||
def test_collect_pull_summaries_pages_until_empty(monkeypatch) -> None:
|
||||
def fake_api_get(path: str, token: str):
|
||||
if "state=open" in path:
|
||||
return []
|
||||
page = int(path.split("page=")[1])
|
||||
if page <= 5:
|
||||
return [
|
||||
{
|
||||
"number": page * 1000 + i,
|
||||
"title": f"page {page} pr {i}",
|
||||
"state": "closed",
|
||||
"merged": False,
|
||||
"head": {"ref": f"fix/{page}-{i}"},
|
||||
"body": f"Refs #{page * 1000 + i}",
|
||||
"html_url": f"https://forge.example/pr/{page * 1000 + i}",
|
||||
}
|
||||
for i in range(100)
|
||||
]
|
||||
if page == 6:
|
||||
return [
|
||||
{
|
||||
"number": 900,
|
||||
"title": "late page pr",
|
||||
"state": "closed",
|
||||
"merged": False,
|
||||
"head": {"ref": "fix/900"},
|
||||
"body": "Refs #900",
|
||||
"html_url": "https://forge.example/pr/900",
|
||||
}
|
||||
]
|
||||
return []
|
||||
|
||||
monkeypatch.setattr("scripts.burn_lane_issue_audit.api_get", fake_api_get)
|
||||
|
||||
pulls = collect_pull_summaries("timmy-home", "token")
|
||||
|
||||
assert any(pr.number == 900 for pr in pulls)
|
||||
|
||||
|
||||
|
||||
def test_render_report_calls_out_drift_and_candidates() -> None:
|
||||
rows = [
|
||||
{
|
||||
|
||||
37
tests/test_issue_666_genome_template.py
Normal file
37
tests/test_issue_666_genome_template.py
Normal file
@@ -0,0 +1,37 @@
|
||||
from __future__ import annotations
|
||||
|
||||
from pathlib import Path
|
||||
|
||||
|
||||
ROOT = Path(__file__).resolve().parents[1]
|
||||
TEMPLATE_PATH = ROOT / "templates" / "GENOME-template.md"
|
||||
DOC_PATH = ROOT / "docs" / "CODEBASE_GENOME_PIPELINE.md"
|
||||
|
||||
|
||||
REQUIRED_HEADINGS = (
|
||||
"# GENOME.md — [org/repo]",
|
||||
"## Project Overview",
|
||||
"## Architecture",
|
||||
"## Entry Points",
|
||||
"## Data Flow",
|
||||
"## Key Abstractions",
|
||||
"## API Surface",
|
||||
"## Test Coverage Report",
|
||||
"## Security Audit Findings",
|
||||
"## Dead Code Candidates",
|
||||
"## Performance Bottleneck Analysis",
|
||||
)
|
||||
|
||||
|
||||
def test_issue_666_template_exists_and_covers_required_sections() -> None:
|
||||
assert TEMPLATE_PATH.exists(), "missing templates/GENOME-template.md"
|
||||
text = TEMPLATE_PATH.read_text(encoding="utf-8")
|
||||
for heading in REQUIRED_HEADINGS:
|
||||
assert heading in text
|
||||
|
||||
|
||||
def test_issue_666_docs_reference_template_and_single_repo_entrypoint() -> None:
|
||||
text = DOC_PATH.read_text(encoding="utf-8")
|
||||
assert "templates/GENOME-template.md" in text
|
||||
assert "python3 pipelines/codebase_genome.py" in text
|
||||
assert "python3 pipelines/codebase-genome.py" in text
|
||||
Reference in New Issue
Block a user