nature-figure

Name: nature-figure
Author: Yuan1z0825

5.9kinstalls1.8kforks

How to install nature-figure?

yuan1z0825/nature-skills/nature-figure

$npx -y skills add Yuan1z0825/nature-skills --skill nature-figure

Installs into the current project.

Summary

Create, revise, audit, and export submission-grade scientific figures for Nature-family and other high-impact venues in Python (matplotlib/seaborn) or R (ggplot2/patchwork/ComplexHeatmap), including multi-panel plots, figures4papers-style work, and journal-ready SVG/PDF/TIFF outp

Files · 1

View on GitHub

SKILL.md

1	# Nature Figure Making — Router
2
3	This skill is split into two layers:
4
5	- A static layer under `static/` that holds versioned, reusable content fragments (the figure contract and default stance, plus a per-backend quick-start for Python and R).
6	- A dynamic layer (this file plus `manifest.yaml`) that detects the plotting backend and loads only the fragment needed for the current job. The large design, API, pattern, and QA material lives in on-demand references.
7
8	Do not try to apply the figure logic from memory or from this router. Always load fragments from disk as described below.
9
10	## Routing protocol
11
12	Follow these steps every time the skill is invoked.
13
14	### 0. Check for the OpenRouter AI-schematic route
15
16	If the user explicitly asks to generate a manuscript schematic, graphical abstract, mechanism diagram, concept illustration, or paper schematic with OpenRouter, GPT Image 2, an image-generation API, or similar wording, do not ask "Python or R?". This is a non-plotting AI-schematic route.
17
18	For this route:
19
20	1. Read [manifest.yaml](manifest.yaml) and the `always_load` files.
21	2. Read [references/openrouter-image-generation.md](references/openrouter-image-generation.md).
22	3. Use [scripts/generate_openrouter_schematic.py](scripts/generate_openrouter_schematic.py) when the user wants a real API call or a reproducible payload.
23	4. Treat output as a draft schematic / graphical abstract, not as a quantitative data panel. Do not invent experimental values, author logos, institutional marks, or unsupported mechanisms.
24
25	Only continue to the Python/R backend gate for plotting, charting, data visualization, or manuscript figure assembly tasks that are not explicit OpenRouter AI image-generation requests.
26
27	### 1. Load the manifest and the core layer
28
29	Read [manifest.yaml](manifest.yaml). It declares the `backend` axis, the allowed values, and the file paths each value maps to.
30
31	Also read every file listed under `always_load` (`static/core/contract.md` and `static/core/stance.md`). These hold the figure contract, the backend gate, the missing-runtime rule, the privacy rule, and the default operating stance that apply to every figure job.
32
33	### 2. Resolve the backend — a blocking gate
34
35	Backend selection blocks plotting tasks, but it should not annoy the same user forever. Decide the `backend` value in this order:
36
37	1. If the current request explicitly chooses Python or R, use that backend and save it with `scripts/nature_figure_backend.py set python` or `scripts/nature_figure_backend.py set r`.
38	2. If the request provides a clearly language-specific input file/workflow, use that backend and save it.
39	3. Otherwise run `scripts/nature_figure_backend.py get`. If it returns `python` or `r`, use the saved preference.
40	4. If no saved preference exists, ask exactly one concise question — Python or R? I will remember this as your default. — and stop. After the user answers, save the answer before proceeding.
41
42	- `python` — matplotlib / seaborn.
43	- `r` — ggplot2 / patchwork / ComplexHeatmap.
44
45	Do not guess or choose a backend by aesthetics alone. Only recommend a backend when the user explicitly asks you to choose; then use `references/backend-selection.md`, state the reason, save the selected backend, and proceed. Once selected, the backend is exclusive for all drawing, previewing, exporting, and visual QA (see `core/contract.md`). This gate does not apply to the explicit OpenRouter AI-schematic route above.
46
47	### 3. Load the matching backend fragment
48
49	After the backend is resolved, Read the mapped fragment (`static/fragments/backend/python.md` or `static/fragments/backend/r.md`). It carries the backend-only execution rule and the publication quick-start (rcParams/theme and export helper). Do not load the other backend's fragment.
50
51	### 4. Build the figure using the loaded material
52
53	Apply the loaded material in this order:
54
55	1. Figure contract (`core/contract.md`) — write the core conclusion, map the e

People who liked this also viewed

6 picks

Type

nature-figure

5.9kinstalls1.8kforks

View on GitHub

How to install nature-figure?

yuan1z0825/nature-skills/nature-figure

$npx -y skills add Yuan1z0825/nature-skills --skill nature-figure

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Nature Figure Making — Router
2
3	This skill is split into two layers:
4
5	- A static layer under `static/` that holds versioned, reusable content fragments (the figure contract and default stance, plus a per-backend quick-start for Python and R).
6	- A dynamic layer (this file plus `manifest.yaml`) that detects the plotting backend and loads only the fragment needed for the current job. The large design, API, pattern, and QA material lives in on-demand references.
7
8	Do not try to apply the figure logic from memory or from this router. Always load fragments from disk as described below.
9
10	## Routing protocol
11
12	Follow these steps every time the skill is invoked.
13
14	### 0. Check for the OpenRouter AI-schematic route
15
16	If the user explicitly asks to generate a manuscript schematic, graphical abstract, mechanism diagram, concept illustration, or paper schematic with OpenRouter, GPT Image 2, an image-generation API, or similar wording, do not ask "Python or R?". This is a non-plotting AI-schematic route.
17
18	For this route:
19
20	1. Read [manifest.yaml](manifest.yaml) and the `always_load` files.
21	2. Read [references/openrouter-image-generation.md](references/openrouter-image-generation.md).
22	3. Use [scripts/generate_openrouter_schematic.py](scripts/generate_openrouter_schematic.py) when the user wants a real API call or a reproducible payload.
23	4. Treat output as a draft schematic / graphical abstract, not as a quantitative data panel. Do not invent experimental values, author logos, institutional marks, or unsupported mechanisms.
24
25	Only continue to the Python/R backend gate for plotting, charting, data visualization, or manuscript figure assembly tasks that are not explicit OpenRouter AI image-generation requests.
26
27	### 1. Load the manifest and the core layer
28
29	Read [manifest.yaml](manifest.yaml). It declares the `backend` axis, the allowed values, and the file paths each value maps to.
30
31	Also read every file listed under `always_load` (`static/core/contract.md` and `static/core/stance.md`). These hold the figure contract, the backend gate, the missing-runtime rule, the privacy rule, and the default operating stance that apply to every figure job.
32
33	### 2. Resolve the backend — a blocking gate
34
35	Backend selection blocks plotting tasks, but it should not annoy the same user forever. Decide the `backend` value in this order:
36
37	1. If the current request explicitly chooses Python or R, use that backend and save it with `scripts/nature_figure_backend.py set python` or `scripts/nature_figure_backend.py set r`.
38	2. If the request provides a clearly language-specific input file/workflow, use that backend and save it.
39	3. Otherwise run `scripts/nature_figure_backend.py get`. If it returns `python` or `r`, use the saved preference.
40	4. If no saved preference exists, ask exactly one concise question — Python or R? I will remember this as your default. — and stop. After the user answers, save the answer before proceeding.
41
42	- `python` — matplotlib / seaborn.
43	- `r` — ggplot2 / patchwork / ComplexHeatmap.
44
45	Do not guess or choose a backend by aesthetics alone. Only recommend a backend when the user explicitly asks you to choose; then use `references/backend-selection.md`, state the reason, save the selected backend, and proceed. Once selected, the backend is exclusive for all drawing, previewing, exporting, and visual QA (see `core/contract.md`). This gate does not apply to the explicit OpenRouter AI-schematic route above.
46
47	### 3. Load the matching backend fragment
48
49	After the backend is resolved, Read the mapped fragment (`static/fragments/backend/python.md` or `static/fragments/backend/r.md`). It carries the backend-only execution rule and the publication quick-start (rcParams/theme and export helper). Do not load the other backend's fragment.
50
51	### 4. Build the figure using the loaded material
52
53	Apply the loaded material in this order:
54
55	1. Figure contract (`core/contract.md`) — write the core conclusion, map the e

People who liked this also viewed

6 picks

Type