dsh-science

A Claude Science–style research workbench for DeepSeek Harness — for genomics / pathogens / human health / bioinformatics projects.

One-liner: dsh-science — Claude Science-style research workbench for DSH: ReAct research-loop engine (research* tools), versioned artifacts with provenance (artifact tools), an SSH remote-compute engine (remote_ tools, mirroring Claude Science's Computer / Remote compute clusters), and 11 science skills for genomics / pathogens / bioinformatics.

• ReAct research loop engine — research_init / research_state / research_hypothesis / research_experiment / research_findings / research_phase / research_review / research_report, persisted in a research-manifest.json state machine (Question → Hypothesis → Experiment → Observe → Analyze → Conclude → Next Question).
• Versioned artifacts with provenance — artifact_save / artifact_list / artifact_show / artifact_diff / artifact_verify / artifact_deprecate / artifact_reproduce: every result saved as artifacts/<name>/v<N>/ with per-file SHA-256, artifact.json provenance (command / inputs / environment / envFile) and an append-only provenance.md.
• Remote compute engine (SSH / HPC clusters) — 16 tools: remote_host_add / remote_host_probe / remote_host_notes / remote_run / remote_status / remote_logs / remote_pull / remote_cancel / remote_exec etc. Connect lab workstations or HPC clusters via ~/.ssh/config aliases (nothing installed on the host, zero third-party deps). Long bioinformatics jobs run as detached processes on workstations or via sbatch on SLURM — they survive connection loss; submission asks for approval by default; remote_status batch-monitors and auto-transitions state (running → succeeded/failed/killed); remote_pull fetches outputs back (files over the size threshold stay on the host with their paths recorded).
• Remote Hosts config UI (bundle/profile-level) — a Settings > 远程主机 page (the analog of Claude Science's Settings > Compute > SSH hosts): list/add/probe/edit/remove hosts, plus each project's access allowlist and job summary. Host-side REST API (webServer route /dsh-science/remote-hosts/*, engines/remote-hosts-ui.mjs) + client bundle (client/remote-hosts-ui/, built by scripts/build-client-bundle.mjs) sharing the same data files as the remote engine. Requires a web-process restart to activate (see docs/remote-hosts-ui.md).
• Model Tier router (tiered, cross-provider) — via the companion bundle dsh-model-tier: within one session, automatically routes auxiliary requests (session titles, compaction summaries) and subagent/background tasks to a light tier, keeps the main conversation on the default tier, and escalates complex work (deep subagent chains, very long inputs) to a strong tier — each tier may point at a different provider (e.g. strong GLM-5.3 / default deepseek-v4-flash / light minimax-M3), mirroring Claude Code's Opus/Sonnet/Haiku strategy. Built on DSH's native agent/request + llm/stream waterfall extension points; a no-op when the tier's provider is unregistered. Installed automatically with dsh-science, but also standalone-installable into any profile (dsh plugin add dsh-model-tier).
• 11 science skills — research-loop, science-project-setup, artifact-provenance, scientific-reviewer, literature-connector, parallel-delegation, manuscript-writing, bioinformatics-toolkit, conda-environments, data-inventory, remote-compute.

All in-repo engine plugins are zero-dependency (Node built-ins + the system OpenSSH binaries, sharing engines/core.mjs) and register plain cordis tools; the companion dsh-model-tier router is likewise zero-dependency. Installable either as a profile bundle (dsh plugin add) or as an agent preset (科学模式).

v0.2.0: Model Tier router (new, companion bundle)

Mirrors Claude Code's Opus/Sonnet/Haiku tiering: within one session, auxiliary requests (purpose ∈ {session-title, compaction}) and subagents (session.meta.origin === 'subagent') are routed to the light tier; the main conversation keeps its own per-session model selection (never overridden); deep subagent chains (delegationDepth ≥ subagentDepthStrong) and very long inputs (escalateOnChars, opt-in) escalate to the strong tier. An optional LLM pre-classifier (routing.classify) grades each user prompt / subtask dispatch by complexity (light / default / strong) before routing. Each tier is {provider, model, reasoningEffort?} and may span providers.

Ships as the standalone bundle dsh-model-tier — dsh-science depends on it and mounts it in its cordis.patch.yml, but it can equally be installed on its own into any profile (dsh plugin add dsh-model-tier):

- id: model-tier
  name: dsh-model-tier
  config:
    tiers:
      strong: { provider: zai-coding-cn, model: glm-5.3 }
      default: { provider: deepseek-official, model: deepseek-v4-flash }
      light: { provider: opencode-go, model: minimax-m2.7 }
    routing:
      auxiliary: [session-title, compaction]
      subagents: light
      subagentDepthStrong: 3

• Host plane — mounted in the profile bundle (cordis.patch.yml), not the agent preset, so it applies to every session and subagent on the profile.
• Safety rails — no tiers configured → inert no-op; target provider unregistered → no routing; a failing light-tier call automatically falls back to the original route (auxiliary features never break).
• Verified — node packages/dsh-model-tier/test/model-tier.test.mjs (zero-dependency unit matrix) + bash packages/dsh-model-tier/scripts/test-model-tier.sh (E2E: light tier pointed at a local mock LLM; asserts the title request is actually routed).

v0.2.0: Remote compute (new)

Mirrors Claude Science's Remote compute clusters / Computer capability, following its documented mechanism:

• Host registration + read-only probe — remote_host_add takes a ~/.ssh/config alias (or user@host; ProxyJump etc. handled by OpenSSH), with optional port/identityFile overrides; probing records CPUs, memory, GPUs, CUDA driver, conda/module/Apptainer presence, scratch dirs, sbatch and SLURM partitions (remote_host_probe re-runs it). Host registry: $DSH_HOME/remotes/hosts.json.
• Job submission — remote_run copies script + inputs into <scratch>/<jobId>/ (default ~/dsh-scratch); workstations run it as a detached nohup+setsid process (connection-loss safe), SLURM clusters get sbatch (with --time); default job timeout 30 min; submission asks for approval by default (the analog of Claude Science's "Run this job on ?" card).
• Monitoring & reaction — remote_status batch-probes (ps / squeue+sacct / done+exitcode markers) and auto-transitions state; remote_logs tails logs; remote_pull fetches outputs and writes pulled-manifest.json (files > 100 MB stay on the host with recorded paths); remote_cancel kills (process group / scancel). Job registry: <project>/.dsh/remotes/jobs.json, persists across sessions.
• Host Details document — remote_host_notes maintains per-host notes (environment activation, partitions/account, conventions) that the model reads before submitting jobs.
• Per-project access allowlist (allowed servers, isolated per project) — every host-connecting action (add/probe, remote_host_probe, remote_exec, remote_run) requires the host to be in the project's allowlist (.dsh/remotes/allowlist.json) by default; first use pops an approval dialog and, on approval, persists the grant at project scope (the analog of Claude Science's "This project" approval scope). The project root resolves by priority: research-manifest.json (research project) → .dsh (workspace) → .git → session cwd — multiple research projects in one workspace keep separate allowlists; grants never leak across projects (authorization paths fail closed when no session cwd is available). Review with remote_host_allowlist, revoke with remote_host_revoke, pre-grant with remote_host_allow (approval-gated); disable with requireHostAccess: false for unattended runs.

v0.1.1 hardening (robustness update)

• Concurrency-safe state: all manifest/artifact writes go through a lightweight file lock (O_EXCL + stale reclaim) and atomic tmp+rename — parallel subagents can no longer corrupt or lose updates on research-manifest.json / artifacts.json.
• Structured error codes (ERR_NOT_INIT / ERR_NOT_FOUND / ERR_VALIDATION / ERR_PATH / ERR_QUOTA / ERR_LOCK_TIMEOUT / ERR_IO) instead of opaque strings.
• Hypothesis state machine (proposed → testing → supported/refuted/inconclusive) and forward-only phase transitions (rewind requires config).
• manifest ↔ artifacts linked: research_state merges the artifact index; artifact_save writes back to the manifest.
• Manifest schema v1→v2 migration on load, persisted on next write.
• Artifact upgrades: streaming SHA-256 (big files), identical-content dedup via hardlink, artifact_diff / artifact_verify / artifact_deprecate, envFile + input hashes in provenance.
• Structured JSON outputs (research_report, artifact_diff, artifact_verify) and an audit log at <root>/.science.log.

Install

Option A — profile bundle (community standard)

dsh plugin --profile web add dsh-science            # after npm publish
# or straight from GitHub:
dsh plugin --profile web add "github:biociao/dsh-science"

Restart the profile (or refresh the Web GUI). The bundle inserts the three engines into the profile layer stack; the research_* / artifact_* / remote_* tools become available to every agent on that profile.

Option B — agent preset (full 科学模式 experience, per-agent)

git clone https://github.com/biociao/dsh-science ~/.dsh/.agent-presets/science
# or from a local checkout:
bash scripts/install.sh          # copy   (or: bash scripts/install.sh link)

Then create a session in the DSH Web GUI and pick the 科学模式 preset — the preset carries the research persona + engines with per-agent scoping.

Skills

The 11 skills are discovered automatically from a project's .dsh/skills/ (drop this repo's skills/ into your project), or install them machine-wide:

bash scripts/install-skills.sh          # -> ~/.dsh/skills (respects $DSH_HOME)

Quick start (first session)

1. research_init — create research-manifest.json + the project skeleton (experiments/ literature/ artifacts/ analyses/ figures/ manuscript/ reviews/ data/ envs/).
2. Read research_state at the start of every session; the loop state persists across sessions.
3. Run the loop: research_hypothesis (H1/H2/…) → research_experiment (E01/…, creates experiments/<id>/{design.md,log.md,code/,results/}) → run code → research_findings (appends to log.md, updates hypothesis status, advances the loop) → artifact_save for anything worth citing or reproducing.
4. When GPU/cluster/specialized environments are needed: remote_host_add the host → remote_run a background job (approval required) → poll remote_status / remote_logs → remote_pull outputs when done → artifact_save to archive. See docs/remote-compute.md and the remote-compute skill.
5. For key claims: extract the claim, have a review subagent check it against the execution records (see the scientific-reviewer skill), archive with research_review (writes reviews/R0n/report.md).

Repository layout

dsh-science/
├── package.json          # dsh.bundle.patch -> ./cordis.patch.yml (+ dsh.client + exports)
├── cordis.patch.yml      # bundle patch: inserts the engines by subpath export + mounts dsh-model-tier
├── packages/
│   └── dsh-model-tier/   # 配套独立 bundle：模型分档路由（可单独 dsh plugin add）
├── engines/              # canonical engine sources (bundle form)
│   ├── core.mjs          #   shared core: locks, atomic writes, error codes, streaming sha256, structured tools, audit
│   ├── research-loop.mjs
│   ├── artifact-registry.mjs
│   ├── remote-compute.mjs#   SSH/local transports, host registry + probe, job submit/monitor/pull/cancel
│   └── remote-hosts-ui.mjs#  Remote Hosts 设置页的宿主 REST API（webServer 路由）
├── client/               # client 插件（设置页 UI，bundle/profile 级）
│   └── remote-hosts-ui/  #   src/index.js 源码 · lib/client.js 打包产物（build-client-bundle.mjs）
├── preset/               # agent-preset form (mirrors engines/ via sync-engines.sh)
│   ├── agent.cordis.yml  #   references ./engines/*.mjs (relative, preset mount)
│   ├── preset.yml
│   └── engines/          #   mirror — keep in sync: bash scripts/sync-engines.sh
├── skills/               # 11 SKILL.md skills
├── scripts/
│   ├── install.sh        # install preset -> ~/.dsh/.agent-presets/science
│   ├── install-skills.sh # install skills -> ~/.dsh/skills
│   ├── sync-engines.sh   # mirror engines/ -> preset/engines/
│   ├── init-project.sh   # project skeleton without a science session
│   ├── build-client-bundle.mjs # wrap client src -> __ModuleLoader__ bundle (lib/client.js)
│   ├── smoke-test.mjs    # 125 checks against a temp workspace (node >= 18)
│   └── stability-test.mjs# 25 concurrency/atomicity/stress checks (locks, lost-update, soak, migration)
└── test/verify-bundle.sh # isolated end-to-end bundle install + boot + client scan check

Verification

node scripts/smoke-test.mjs       # engine logic + end-to-end loop + error codes + migration
node scripts/stability-test.mjs   # concurrency / atomicity / lock / stress stability checks
bash test/verify-bundle.sh        # pnpm pack -> isolated profile -> install -> boot check

All are part of the release checklist and are safe to run in CI (both test scripts write only to a temp workspace; the bundle test uses an isolated $DSH_HOME).

FAQ

Why subpath exports and not relative paths in the bundle? dsh plugin add installs the package into the profile and its cordis.patch.yml rows join the profile composition. The profile loader resolves a row name relative to the profile directory (not the package), so ./engines/x.mjs fails with ERR_MODULE_NOT_FOUND. Referencing dsh-science/engines/x.mjs (subpath export, exports in package.json) resolves from the profile's node_modules and works — verified experimentally on dsh 0.1.0-rc.6. The agent-preset mount, by contrast, resolves relative names from the preset directory, which is why preset/agent.cordis.yml can use ./engines/*.mjs.

Bundle or preset — which should I use?

• Bundle: tools available to every agent on the profile; one command to install.
• Preset: the full 科学模式 experience (research persona, per-agent scoping). The persona row in cordis.patch.yml is commented out because a profile-wide persona would apply to all agents — uncomment it before publishing if that is what you want.

Where do the skills come from? A project's .dsh/skills/ is auto-discovered; scripts/install-skills.sh puts them machine-wide in ~/.dsh/skills (respecting $DSH_HOME).

Development

Branching model & release workflow (main = release, dev = integration, feat/* = features, tag-triggered npm publish + GitHub Release via Actions): see docs/branching.md.

bash scripts/sync-engines.sh    # after editing engines/*.mjs — keeps preset/engines in sync
node scripts/smoke-test.mjs     # logic + static package checks
node scripts/stability-test.mjs # concurrency / atomicity / lock stability checks
bash test/verify-bundle.sh      # end-to-end bundle install + boot

Workspace-isolation patch — DSH's New Session used to fall back to the most recently used Workspace, letting automation spawn sessions into unrelated projects. scripts/patch-session-isolation.mjs applies the one-line guard (idempotent, backs up first; re-apply after every dsh upgrade). See docs/workspace-isolation.md.

node scripts/patch-session-isolation.mjs apply   # idempotent, backs up first
node scripts/patch-session-isolation.mjs status  # check current state
node scripts/patch-session-isolation.mjs revert  # restore pristine file

Community

• Topic: github.com/topics/dsh-plugin
• Curated lists: awesome-dsh-plugin · awesome-deepseek-harness

License

MIT — see LICENSE.