@omicverse/dsh-omicos

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

Tools

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 (269 skills + 97 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.

Commands

/omicos-login (device-code pairing — sign in with phone or email in the browser), /omicos-status, /omicos-account, /omicos-logout, /omicos-stop-kernel.

UI

The client bundle adds two surfaces to the web profile:

• an OmicOS tab next to the conversation — sign-in state, plan, expiry, and links to subscribe or manage the account;
• a live tool view on 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.

Requirements

• omicos-core comes with the install. @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.
• An OmicOS account for cloud-backed models and the higher plan tiers. Sign in with /omicos-login; no token is ever persisted by this plugin — the approved login is handed to the local core, which keeps it.
• dsh 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.

Configuration

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

Security posture

• Tools run in core with 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.
• Catalog search projects before it answers: the skill 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.
• The plugin's HTTP routes are pinned to loopback.

Development

pnpm install
pnpm build       # tsc + the client bundle
pnpm typecheck
pnpm test        # 88 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