Figure Standardize

Documents

figure-standardize

Figure Standardize is an Agent Skill for documents published in the tsingyuai/scientify repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

Use this when the user wants to improve chart quality, standardize plotting style, regenerate release figures, or add captions/protocol notes. Normalizes fonts, colors, legends, units, and scope notes across Scientify figures.

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QUICK START

How to use this skill

Bring this guide into your coding agent with a prompt tailored to the tool you use.

Open your project in Codex.
Copy and paste the prompt below.
Review files and risks before approving any action.

Prompt to paste

Inspect the Agent Skill at https://github.com/tsingyuai/scientify/blob/HEAD/skills/figure-standardize/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/figure-standardize, but wait for my approval before writing files or running scripts.

Copying this prompt does not install or run the skill. Review third-party files before use.

Figure Standardization

Don't ask permission. Just do it.

Use this skill to turn one-off Scientify charts into release-ready figures.

Do not run new experiments here. Work from existing results, plotting scripts, and figure bundles. If the source data is missing or inconsistent, report that explicitly instead of smoothing it over.

Required Outputs

Updated plotting script(s) or a shared style helper
Regenerated .png and .pdf files when the pipeline supports both
A figure spec file:
- prefer reports/figures/figure_spec.md
- otherwise project/figures/figure_spec.md
paper/figures_manifest.md when the figure family is paper-facing or a paper/ workspace already exists

Workflow

Step 1: Inspect Inputs

Read:

existing figures
the generator script(s)
the result tables / JSON / Markdown that feed the figures
any surrounding README or release notes that explain the figure family

Prefer improving an existing generator over creating a second one-off script.

Step 2: Standardize the Figure Family

Normalize the full family, not just one chart:

font family and title hierarchy
semantic color mapping
axis labels and units
legend order and naming
decimal precision and tick formatting
line widths / marker sizes
caption structure
protocol note wording
callout wording
paper placement intent

Use:

references/figure-style-guide.md
references/caption-template.md
references/figure-placement-template.md

Step 3: Write the Figure Spec

Create or update figure_spec.md with one section per figure:

figure filename
source files
metrics shown
baseline or comparison family
quality guard / evaluation constraint
simulator/runtime note
intended takeaway

If the figure is used in a paper or paper-facing report, also create or update the matching entry in paper/figures_manifest.md with:

figure_id
file_path
latex_label
section
placement_hint
caption_short
caption_long
takeaway_sentence
callout_sentence
baseline
evidence_type
source_metrics
source_files
supports_claim_ids
must_appear_before_claim_ids

Keep figure_spec.md and paper/figures_manifest.md aligned. The spec is the release-facing summary; the manifest is the paper-facing contract.

Step 4: Re-render and Verify

Re-render the figures after script updates.

Keep filenames stable unless the user explicitly asked for a new release bundle.

Figure Rules

Keep metric semantics identical across a figure family.
Always show units explicitly.
If a result comes from simulator or proxy evaluation, state that in the caption or protocol note.
Do not hide failing or quality-guard-breaking baselines; mark them clearly.
Do not change the scientific claim. This skill improves packaging, not evidence.
If a figure is paper-facing, produce both a long caption and a first-use callout sentence.
If a figure supports a claim, the manifest must name that claim in supports_claim_ids.