Our review
Generates matplotlib code for publication-ready TDA figures following the conventions of a specific codebase.
Strengths
- Ensures stylistic consistency with predefined publication constants (size, DPI, colors).
- Automates common figure types (persistence diagrams, null histograms, etc.).
- Enforces standardized color rules and annotation practices for publications.
Limitations
- Requires familiarity with the trajectory_tda codebase and its conventions.
- Not flexible for non-standard figure layouts or domains outside TDA.
- Temporary figures must be saved separately from production output, which can be confusing.
Use this skill when you need to quickly produce publication-quality figures for a TDA paper while adhering to the trajectory_tda codebase conventions.
Avoid this skill when working on exploratory figures without style constraints or outside the TDA domain.
Security analysis
SafeThe skill provides declarative style and path guidance for generating matplotlib figure code. It does not instruct or invoke any execution of commands, network calls, file deletions, or unsafe operations. It only suggests code patterns and directory conventions.
No concerns found
Examples
/tda-figure-spec persistence-diagram P01-B/tda-figure-spec null-histogram P01-A/tda-figure-spec/tda-figure-spec — Generate Publication-Ready TDA Figures
Scaffold matplotlib figure code following the established trajectory_tda/viz/ conventions.
Uses PUBLICATION_RC, DPI, FIGSIZE_*, STATE_COLORS, and _save_figure from the
codebase — never ad-hoc sizes or colours.
Usage
/tda-figure-spec [figure-type] [paper-number]
Example: /tda-figure-spec persistence-diagram P01-B
Example: /tda-figure-spec null-histogram P01-A
Example: /tda-figure-spec (interactive)
Style constants (always import from trajectory_tda/viz/constants.py)
from trajectory_tda.viz.constants import (
DPI, FIGSIZE_FULL, FIGSIZE_WIDE, FIGSIZE_HALF, FIGSIZE_SQUARE,
PUBLICATION_RC, STATE_COLORS, STATES, STATE_LABELS, REGIME_LABELS,
)
import matplotlib.pyplot as plt
plt.rcParams.update(PUBLICATION_RC)
Figure size guide
| Use case | Constant | Size |
|---|---|---|
| Single full-width plot | FIGSIZE_FULL | 190mm × 120mm |
| Wide two-panel | FIGSIZE_WIDE | 190mm × 104mm |
| Half-width single panel | FIGSIZE_HALF | 90mm × 120mm |
| Square heatmap | FIGSIZE_SQUARE | 90mm × 90mm |
Save function (always use this pattern)
def _save_figure(fig, output_dir: Path, name: str) -> None:
output_dir.mkdir(parents=True, exist_ok=True)
fig.savefig(output_dir / f"{name}.pdf", format="pdf")
fig.savefig(output_dir / f"{name}.png", format="png", dpi=DPI)
Colour rules
- State space: always
STATE_COLORSdict — nevertab10or default cycle - Observations:
#2d6a2e(green); Null:steelblue; Dim 0: green; Dim 1:#1a237e - Regimes:
plt.cm.tab10withREGIME_LABELSorder - Sequential/diverging:
viridis,plasma,RdBu_r— neverjet
Annotation standards
- p-values: write
p=0.003, notp<0.01 - Axes: remove top and right spines; keep bottom and left
- Legends:
frameon=False - Subplot labels:
ax.text(0.02, 0.97, "(a)", transform=ax.transAxes, ...)
Figure templates available
| Template | When to use |
|---|---|
| plot_persistence_diagram(diagram, dim, ax) | Scatter birth-death pairs |
| plot_barcode(diagram, dim, ax) | Feature lifetimes sorted by persistence |
| plot_null_histogram(observed, null_dist, p_value, dim, ax) | Permutation test result |
| plot_landscape_comparison(obs, null, grid, ax) | L² landscape distance (mandatory) |
Output paths
| Context | Path | Naming |
|---|---|---|
| Production paper figure | papers/PXX/figures/ | fig{N}_{desc}.{pdf\|png} |
| Supplement | papers/PXX/figures/ | figS{N}_{desc}.{pdf\|png} |
| Working / exploratory | figures/{domain}/ | YYYYMMDD_{desc}.png |
Working figures must not be saved to papers/PXX/figures/ — that is for production only.
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