scifig

name	scifig
description	Agent-only skill that turns experimental data (CSV/Excel/matrix) into publication-grade scientific figures. Auto-detects structure, infers scientific domain, recommends charts, generates Nature/Cell/Science-aligned matplotlib code, and exports vector graphics with statistical reports. Does not require the scifig Python package. Triggers on "generate figure", "plot data", "sci figure", "科研图", "画图", "多 panel".
allowed-tools	Agent, AskUserQuestion, TodoWrite, Read, Write, Edit, Bash, Glob, Grep

SciFig Generate

End-to-end workflow for turning experimental data into submission-ready scientific figures. Journal-token driven, domain-aware, narrative-first.

Quick Start

preference gates → Phase 1 dataProfile → Phase 2 chartPlan → Phase 3 styledCode → Phase 4 outputBundle

Each phase owns one artifact. Blocking findings route back to the owning phase.

COMPACT DIRECTIVE: The phase marked in_progress in TodoWrite is active — keep it uncompressed. If a sentinel survives without the full protocol, Read("phases/0N-xxx.md") before continuing.

Directory Map

See reference/structure.md for the full layout.

Folder	Role
phases/	Phase 1–5 execution protocols
specs/	Chart catalog, journal profiles, policies
runtime/	Python generators, finalizer, registry
knowledge/	94-case visual grammar (modules + techniques)
resources/	Palette/layout/zorder JSON registries
reference/	Coordinator details (gates, finalizer, checklist)

Runtime Self-Containment

Agent-only — do not import the external pip install scifig package.

All behavior lives in this folder:

• runtime/helpers.py — finalizer, layout audit
• runtime/template_mining_helpers.py — journal kernel, palettes, idioms
• runtime/generators_*.py — chart generators
• runtime/registry.py — 121-chart registry

Generated scripts must embed and execute helper source inline.

Design Principles

1. Journal-token driven — explicit style profiles, not ad-hoc choices
2. Domain-aware charting — bias recommendations toward field conventions
3. Narrative multi-panel — hero/support/validation story, not unrelated grids
4. Palette governance — colorblind-safe, consistent semantic mappings
5. Statistical honesty — no inferential claims without replicate meaning
6. Template-grounded — rcParams, zorder, palettes trace to knowledge/ corpus

Details: reference/coordinator.md

Knowledge Base

Before Phase 2/3, load knowledge/INDEX.md. Consult modules and techniques instead of inventing patterns.

Loading protocol, bootstrap code, maintenance: reference/knowledge-base.md

Finalizer rules: reference/finalizer.md

Preference Gates

Complete before any phase dispatch. Full card flow: specs/preference-collection.md

Gate summary: reference/coordinator.md

Never scan workspace for data files. Never Read/Bash paths before file-path and mode gates.

Phase Dispatch

Phase	Document	Purpose
1	phases/01-data-detect.md	Ingest, semantic roles, domain inference
2	phases/02-recommend-stats.md	Chart taxonomy, stats, panel blueprint
3	phases/03-code-gen-style.md	Journal styling, code generation
4	phases/04-export-report.md	Export bundle, source data, QA
5*	phases/05-template-distill.md	Optional article-code promotion

Reference Specs (on demand)

Kind	Document
Journal	specs/journal-profiles.md
Charts	specs/chart-catalog.md
Domains	specs/domain-playbooks.md
Policies	specs/workflow-policies.md
Motifs	specs/template-visual-motifs.md
Distill	specs/template-distillation-contract.md
Layouts	resources/panel-layout-recipes.md
Palettes	resources/palette-presets.md

Input Format

FILE: /path/to/data.csv
EXTRAS: optional figure request
DOMAIN_OVERRIDE: optional domain hint
MUST_HAVE: optional chart requirements

TodoWrite Pattern

One active phase at a time. Expand into sub-tasks while in_progress; collapse to summary when completed.

Related Commands

• /spec-add learning ... — record plotting edge cases
• /spec-add arch ... — new runtime helpers or generator APIs