@omicverse/dsh-omicos
OmicOS 作为 deepseek-harness (dsh) 插件 — 模式 A：为 dsh 代理提供 omicos 生物信息学工具、后台任务和登录命令 (DSH-PLUGIN.md)。
插件会安装到这里；不确定时保持 web。
npx -y @deepseek-ai/dsh plugin --profile web add @omicverse/dsh-omicos@0.2.1Omicos 以 @omicverse/dsh-omicos 发布，当前版本为 0.2.1。Plugin Hub 会校验它的 manifest，并保存精确安装来源，便于复现安装结果。
Run OmicVerse/OmicOS bioinformatics analyses from inside DeepSeek Harness. The dsh agent keeps the wheel; this plugin gives it a persistent Python kernel (scanpy / omicverse / R) plus the catalog of analysis skills that OmicOS ships.
中文简介：把 OmicOS 的生信分析能力接进 dsh。DeepSeek 负责对话与规划， OmicOS 负责跑分析——持久 Python 内核，
adata等状态跨轮累积； 另带账号/订阅标签页与实时执行过程可视化。
dsh plugin --profile web add @omicverse/dsh-omicos
One tool runs an analysis; the rest are direct reads of the local kernel that cost neither a turn nor a token.
| Tool | What it does |
|---|---|
omicos_analyze | Runs a full OmicOS turn in a persistent kernel bound to the workspace. Repeated calls in one dsh session land on the same OmicOS conversation, so state accumulates. background: true hands it to ctx.jobs with live tqdm progress. |
omicos_capabilities | Searches the installed skill/agent catalog (several hundred skills and ~100 agents on a full install) and returns a ranked, bounded projection. Use it to decide whether a task is worth delegating. Omit the query for a category overview. |
omicos_list_variables | What currently lives in the kernel — name, type, shape, size. |
omicos_query_variable | One variable in detail. For an AnnData this includes the preprocessing state (is_int / is_normalized / is_log1p / is_scaled), which is what decides whether the next step is legal. |
omicos_list_generated_files | Every file the analyses of this conversation produced. |
/omicos-help (what the plugin adds, and where to look), /omicos-login
(device-code pairing — sign in with phone or email in the browser),
/omicos-status, /omicos-account, /omicos-logout, /omicos-stop-kernel.
Deliberately short: commands are for what the agent cannot do for you. Listing variables, browsing capabilities or finding outputs is better asked of the agent, which has tools for exactly that.
The client bundle adds two surfaces to the web profile:
omicos_analyze calls — the steps, tool calls and
stdout tail as the analysis runs, instead of a spinner that ends in a wall of
text. Generated figures render in the settled card.If dsh-better-sidebar is installed, an "OmicOS 产物" tab is registered there too; the integration is optional and detected at runtime.
@omicverse/omicos is a dependency,
so the ~21 MB platform binary lands in node_modules alongside the plugin
rather than being fetched by npx in the middle of your first tool call.
At run time the plugin still attaches to a kernel you already have running
(desktop app or terminal) if there is one, spawns the bundled binary only
when there is not, and only ever stops a kernel it started itself./omicos-login; no token is ever persisted by this plugin — the
approved login is handed to the local core, which keeps it.0.1.0-rc.6. Note that some @deepseek-ai/dsh-* packages have a stale
latest dist-tag pointing at 0.0.1-rc.x, so every dsh dependency here is
pinned exactly.Override in your profile's own cordis.patch.yml. A patch replaces the
row's whole config — there is no deep merge — so restate every key you care
about:
- id: omicos
config:
workspace: /path/to/project # '' = follow each dsh session's own cwd
autoStart: true # spawn a kernel when none is attachable
upstreamBaseUrl: https://auth.omicos.cn
npmRegistry: '' # mirror knob for the kernel spawn
permission_mode: "full". A single-shot tool result
has no room for a mid-flight approval prompt, and blocking on one deadlocks
the turn; bridging dsh's approval UI into an OmicOS turn is planned, not done.source_path (an
absolute local path) and the verbatim use_when routing text are indexed but
never returned, so they do not travel to the model.pnpm install
pnpm build # tsc + the client bundle
pnpm typecheck
pnpm test # 89 tests against the real dsh defineTool and a mock core
This package publishes as ONE dependency-light artifact: the @omicverse/omicos-*
SDK is inlined by esbuild.host.mjs and kept as devDependencies, while
@deepseek-ai/* stays external (the harness supplies it, and a second copy of
Schema would fail config validation) and @omicverse/omicos stays a real
dependency (it is spawned as a child process, never imported).
src/host/dsh-compat.ts is the only module allowed to import @deepseek-ai/*.
bridge.ts / kernel.ts / runner.ts / auth.ts have no dsh dependency at
all, so a dsh API change is absorbed in the compat layer plus tools.ts,
commands.ts and index.ts.
GPL-3.0-only