dsh-omicos

@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 (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.

Commands

/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.

UI

The client bundle adds two surfaces to the web profile:

• an OmicOS tab next to the conversation — a small console: sign-in state,
  plan and expiry with links to subscribe or manage; which kernels are attached,
  where, at what version, and what is bound in them right now; and a search box
  over the installed capability catalog;
• 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        # 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