Appendix A. Glossary¶
In alphabetical order. In brackets: other names, or the names used in files and commands.
| Term | Meaning | More |
|---|---|---|
| AI assistant / agent | An AI such as Claude Code or Gemini CLI that runs tools for you when you ask in words | chapter 12 |
| archive / retire | Moving a project no longer used to archive/ instead of deleting it |
chapter 11 |
| build | One run that redraws the figure from its config, arranges, checks and records it | chapter 4 |
| bundle | The data folder for one panel: a table (data.csv) + a note (metadata.yaml) |
chapter 3 |
| Case A, B, C | The three entry points for a new figure. A = plotting code you wrote + data, B = a standard bundle, C = data + a capture, sketch or description of the figure you want | chapter 5 |
| CI | Checks that run automatically each time a change reaches the repository. They stop rule violations. | — |
| compendium | A PDF with all the storyline's Figures in order | chapter 11 |
| config | The file with every value of a figure, each with an explaining comment. Where the researcher changes a figure | chapter 6 |
| contract | The rule saying which columns a bundle needs for each kind of figure. The bundle check uses it. | chapter 3, the contracts |
| exploratory / paper / archive | The three stages of a project. Also the names of their folders. | chapters 2, 11 |
| figure spec | The file with a figure's title, a note per panel and the limits of what it claims. Under figure_specs/ |
chapters 2, 7 |
| fingerprint (hash, sha256) | A string computed from a file's content, unique to it. It changes if even one byte changes. | chapter 10 |
| live number (claim) | A result number in a legend that is not typed by hand but filled in from the analysis. Written {name} in the legend. |
chapter 9 |
| MCP | The common way for AI assistants to call outside tools. fig-atlas offers its tools this way. | Connect AI agents |
note (metadata.yaml) |
The file in a bundle that says "what figure this is" (plot_type) and its first settings (plot_params) |
chapter 3 |
| panel | One part of a figure (a, b, c, ...) | chapter 4 |
| panel tag | The letter a, b, c at a panel's upper left. Placed automatically on the panel's outer edge. | chapter 4 |
| preflight | The check for overlapping or clipped text, text size, colour and font problems in a figure. error / warn / info | chapter 8 |
| project | The unit that makes one figure: three files, the config, the analysis script and the figure spec | chapter 2 |
| promote | Moving an exploratory project to a paper Figure project and renaming it | chapter 11 |
| provenance record | The record, kept automatically, of which data, settings and software made a figure, and when | chapter 10 |
| pt (point) | The unit of text size and line width. 1 pt ≈ 0.35 mm | chapter 6 |
| renderer | The software component that draws one kind of figure (line with error band, scatter, heatmap, ...). Researchers rarely deal with it directly. | — |
| research unit (domain) | The unit that groups projects (a researcher or a study). E.g. lab, kim, screening |
chapter 2 |
| revision record | The numbered record written each time the storyline changes: what changed, why, and on which data | chapter 11 |
| snapshot | A saved state of the storyline at one point (assignment, figure provenance, numbers), used for later comparison | chapter 11 |
| Source Data | A table of the values actually plotted in a figure. Some journals ask for it. | chapter 9 |
| stale / fresh | Stale if the data, settings or software changed after the figure was made; fresh if not | chapter 10 |
| storyline | The document with the paper's figure assignment (which project is Figure what) and its story | chapter 11 |
| verify | The check that the results (figure files, README, statistics tables, ...) are complete and agree. PASS / WARN / FAIL | chapter 8 |
| YAML | The format of the config. name: value lines grouped by indentation. |
chapter 6 |
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