fig-atlas¶
A tool that draws paper figures from a config, checks them before print, records where they came from, and manages them through a paper's life (exploration → paper figure → retirement). A field-neutral core is used together with domain packs (omics and others).
- You adjust a figure in its config. Colours, sizes, thresholds and layout are all in a commented YAML file, so you can change them without reading Python.
- Figures are drawn at their printed size. They are drawn 1:1 on the A4 text width, and
--preflightchecks for overlapping or clipped text, minimum sizes, colours that colour-blind readers cannot tell apart, and fonts. - Every figure keeps a record of its sources. The hashes of its input data, code and parameters are recorded, and when data change you are told which figures are now stale.
- Procedures are commands. Creating a project, bringing in data, promoting and retiring figures are
facommands, and AI agents call the same commands as MCP tools.
Where to start¶
| I want to | Read |
|---|---|
| understand what this tool is and how to use it (for researchers, no programming needed) | Guide for researchers |
| try it for the first time | Tutorial: first figure (15 min) |
| make a figure from my data | Data bundle contracts → fa ingest bundle |
| make a figure of microscope or blot images | Tutorial: a microscopy figure |
| use it with an AI agent | Connect AI agents |
| use it in another field | Write a domain pack |
| assemble paper figures | A figure's life |
| know why it is designed this way | Design decisions (ADR) |
fa --help lists every command. The repository's rules, for people and AI alike, are in AGENTS.md.