scifig

What does scifig do?

Scientific figures for papers, theses and slides. You do the thinking: the brief, the plotting code, the checks, the legend. A figure that explains comes from your host's own image-generation tool; this skill calls no image API. The bundled scripts measure, compare and convert.

Pick the route

They want	Route	Read
A figure that explains: graphical abstract, mechanism, pathway, workflow, roadmap, framework, model or system architecture, labelled diagram, cover. From an idea, an abstract, a sketch, or an image to change	Your host's image tool, from a brief you write	references/illustration.md
A chart of numbers: CSV, Excel, a pasted table	Plotting code with scripts/scistyle.py	references/charts.md
One of the diagrams that must be code (below)	Drawing code with scripts/scistyle.py	references/diagrams.md
A submission file, a larger file, one multi-panel figure, or editable labels and shapes, from a finished figure	scripts/export_figure.py, scripts/enlarge.py, scripts/panels.py, scripts/editable.py	references/export-and-checks.md
A pre-submission check, or a legend	scripts/check_figure.py	references/export-and-checks.md

Image tool or code. Boxes, arrows and text are no reason to draw in code. An architecture, a roadmap or a framework goes to the image tool too, and comes back with a designed finish. Image tools write dozens of labels correctly, Chinese and formulas included; scripts/check_text.py reads them back. Draw in code only when:

• it is a chart of data: an image model invents bars, axes and values;
• every count must be auditable: PRISMA and CONSORT flow diagrams;
• it is a formal notation: circuit, plasmid map, phylogenetic tree;
• your host has no image tool, the destination does not accept AI-generated images, or the user asks for vector artwork.

Every figure

1. Destination first. Journal, thesis, slide or poster decides the width, fonts, resolution and file type. For a generated figure it also decides whether the figure may be used at all: references/ai-image-policies.md (dated; several publishers restrict them).
2. Journal rules: bundled presets before the web. Column widths, fonts, minimum dpi and accepted formats of ten publishers are bundled; scripts/scistyle.py --list nature prints one with its verification date, --list all. Use them and pass that date on. Look online only for rules they lack: an unlisted journal, or a size rule of its own (graphical abstract, cover).
3. Look at what you made. Open every output image and compare it with the request before you call it done.
4. Hand over facts. File paths; pixel size and print size; what you checked; what you could not check; what you assumed. You cannot vouch for the science: the user must.

Running the scripts

uv run <skill-dir>/scripts/<name>.py --help

<skill-dir> is the folder that holds this file. uv installs each script's Python packages on first use, which needs network access and its cache folder: if your sandbox blocks either, ask for that permission instead of rewriting the script. Without uv, tell the user to install it (https://docs.astral.sh/uv/).