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bioinformatics workspace by Annoroad","maintainers":[{"name":"seqyuan","email":"yfinddream@foxmail.com"}],"readme":"# annodex\n\nAI-native bioinformatics workspace by Annoroad, backed by Codex app-server. Browser workspace for project-scoped agent chat, file preview, extensions, and multi-provider models.\n\nVersion: `0.1.67`  \nRepository: [seqyuan/annodex](https://github.com/seqyuan/annodex)  \nDocs site: see [`site/`](site/) (Fumadocs)\n\n## Quick Start\n\n```bash\nnpm install -g @openai/codex @seqyuan/annodex\ncodex          # Ctrl+C at login prompt (one-time init)\nannodex\n```\n\nOpen [http://localhost:30121/workspace](http://localhost:30121/workspace). On first start, annodex can optionally set a web password (similar to Jupyter).\n\n**Before first use:** ensure your home directory is writable. Annodex and Codex both persist data under `$HOME` (see [Data & storage](#data--storage)). On Linux servers with small or read-only home quotas, set `ANNODEX_CONFIG_DIR` to a writable path (see below).\n\n## Features\n\n- **Project workspace** — pick a project directory; chats, files, and uploads stay scoped to that cwd.\n- **Project switcher** — pinned projects appear as sidebar folders with chat history; unpinned projects list in the top dropdown; the active unpinned project shows as a temporary folder.\n- **Codex threads** — create, resume, fork, and branch conversations via `codex app-server`.\n- **Any LLM provider** — DeepSeek, OpenAI, Anthropic, and OpenAI-compatible APIs through `~/.config/annodex/providers.json` (Settings → Models).\n- **Streaming UI** — live thinking, tool calls, waiting status, and SSE reconnect.\n- **Native `/goal`** — Codex thread goals with in-app panel and slash command.\n- **Images** — pasted images save to `{project}/.annodex-uploads/` and reload after refresh.\n- **Project memory** — working memory (retain / recall / reflect via MCP) with promote to `MEMORY.md` / `CONTEXT.md`.\n- **Project IM (WeCom)** — optional one bot per project cwd; configure in **Settings → Project → WeCom IM**; run `annodex-im-gateway` as a sidecar (auto-started by `annodex start`).\n- **Extensions** — MCP / plugin definitions (Settings → Extensions); global config in `~/.config/annodex/extensions.json`.\n- **Skills, tools, sandbox** — per-session tool presets and thinking level from the chat bar.\n- **Files panel** — browse, preview, and edit project files alongside chat.\n- **Optional password** — `annodex passwd` / `web-auth.json`.\n\n## CLI\n\n```bash\nannodex                      # start managed background server\nannodex start                # start if not already running\nannodex restart              # stop then start\nannodex stop                 # stop background server\nannodex status               # show server status\nannodex logs                 # show recent logs\nannodex logs -f              # follow logs\nannodex doctor               # diagnose codex path, config dir, transport\nannodex --port 8080          # custom port\nannodex --hostname 127.0.0.1 # bind host (use 0.0.0.0 on Linux servers)\nannodex --version            # print version\nannodex --help               # print help\nannodex update               # update global package\nannodex passwd               # set/change password\nannodex passwd --reset       # remove password\n\nPORT=8080 annodex\nANNODEX_PASSWORD=xxx annodex\nANNODEX_CONFIG_DIR=/data/you/annodex-config annodex\n```\n\nManaged servers auto-restart after package updates once active agent sessions are idle. Set `ANNODEX_AUTO_RESTART=0` to disable. Legacy `ANNOVIBE_*` and `PIDEX_*` environment variables are still accepted for migration.\n\n## Data & storage\n\nAnnodex reads Codex thread history from Codex storage and writes its own config under the user home (or `ANNODEX_CONFIG_DIR`).\n\n### Requires a writable home (or override)\n\nBoth annodex and Codex need to **create and update files** under the effective user home:\n\n| Location | Purpose |\n|---|---|\n| `~/.config/annodex/` | annodex config, runtime state, logs |\n| `~/.codex/` | Codex CLI config and chat/session storage (`CODEX_HOME`) |\n| `{project}/.annodex-uploads/` | pasted chat images (per project cwd) |\n| `{project}/.codex/` | optional project-scoped Codex extensions |\n\n**Linux notes**\n\n- Confirm `echo $HOME` points to a directory you own and can write to (`touch \"$HOME/.annodex-write-test\"`).\n- Common failures: home on **NFS with quota full**, **read-only** root/home, **container** users without a writable `$HOME`, or **batch/HPC** accounts with tiny home limits.\n- Fix: export a writable config root before starting:\n  ```bash\n  export ANNODEX_CONFIG_DIR=/scratch/$USER/annodex-config\n  mkdir -p \"$ANNODEX_CONFIG_DIR\"\n  # Codex sessions still use ~/.codex unless you set CODEX_HOME similarly:\n  export CODEX_HOME=/scratch/$USER/codex-home\n  mkdir -p \"$CODEX_HOME\"\n  annodex --hostname 0.0.0.0\n  ```\n- Server logs: `~/.config/annodex/annodex.log` (or under `ANNODEX_CONFIG_DIR`).\n\n### annodex config files (`~/.config/annodex/`)\n\n| File | Purpose |\n|---|---|\n| `providers.json` | LLM providers and models |\n| `annodex-projects.json` | pinned projects, sort order, registry |\n| `extensions.json` | global MCP / extension definitions |\n| `settings.json` | app preferences (e.g. auto-restart) |\n| `web-auth.json` | optional web UI password hash |\n| `SOUL.md`, `HARNESS.md` | optional global persona / harness text (seeded on first start if missing) |\n| `annodex.json` | runtime supervisor state while server is running |\n| `annodex.log` | background server log |\n\nLegacy filenames (`annovibe-*`, `pidex-*`) are read for migration; new writes use `annodex-*`.\n\n## Development\n\n```bash\nnpm install\nnpm run dev   # port 30121\n```\n\nTypecheck: `node_modules/.bin/tsc --noEmit`  \nLint: `npm run lint`\n\nDo not run `next build` during dev; it pollutes `.next/` and can break `npm run dev`.\n\nSee [AGENTS.md](AGENTS.md) for architecture and release workflow.\n","readmeFilename":"README.md"}