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RevBayes Forge 0.1.0

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@ZengZichao ZengZichao released this 23 Oct 08:29
v0.1.0
11e1bd7

DeepSeek Harness (DSH) plugin that turns RevBayes script writing into a checkable pipeline: structured spec → block assembly → static validation → dry-run/smoke → diagnostics with fix suggestions.

Highlights

  • One plugin, 13 model packs — FBD, divergence dating, coalescent demography, diversification/SSE, continuous traits, biogeography (DEC/GeoSSE/FIG), advanced morphology, chromosome evolution, molecular selection (codon/PoMo), host repertoire, posterior predictive simulation, model selection (stepping-stone/path sampling), and total-evidence dating.
  • 4 core tools — revbayes_generate, revbayes_validate, revbayes_lookup, revbayes_environment; each enabled pack registers its own generation tool.
  • Settings page — overview, per-pack toggles with dependency handling, environment detection, JSON-spec generation and static/dry/smoke validation; pack selection persists to $DSH_HOME/revbayes-forge/state.json and survives restarts.
  • Function catalog — derived from the official RevBayes help database: 611 entries, 654 signatures, 451 methods, plus 18 legacy functions and 27 generic methods.
  • Official-corpus coverage register — all 52 tutorial directories on revbayes.github.io are accounted for: 43 with 304 Rev scripts mapped into 18 analysis families, fig_intro served by the biogeo pack, and 8 directories excluded with documented reasons (see docs/zh/coverage.md / docs/en/coverage.md, enforced by the coverage gate).
  • Bilingual documentation — complete reference set in docs/zh (Chinese) and docs/en (English): installation, configuration, architecture, tool reference, model packs, validation rules, settings page, verification, coverage.

Install

npm install
dsh plugin --profile desktop add file:"$PWD/packages/core"

Fully quit and restart DeepSeek Harness afterwards. See docs/en/installation.md for verification and uninstall.

Requirements

  • DeepSeek Harness (DSH) >= 0.2.1-rc.2 (@deepseek-ai/dsh-tools is provided by the host as a peer)
  • Node.js >= 20
  • RevBayes 1.4.1 (optional; static validation works without it, dry-run/smoke need a real rb binary)

License

GPL-3.0, consistent with RevBayes. Fixture data are synthetic and distributed under the same license.

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