generate_publication_figures

Skill: Generate Publication-Quality Figures

Purpose

Create matplotlib figures that meet journal submission standards: correct fonts, compact sizes, consistent styling, readable labels, and high DPI. Based on lessons learned from the CPA and TPflash papers (Fluid Phase Equilibria 2026).

SI Units (MANDATORY)

All figure axis labels MUST use SI units. See PAPER_WRITING_GUIDELINES.md "SI Units (MANDATORY)" for the full reference.

Axis label examples (GOOD)	NEVER use
Temperature (K) or $T$ (K)	Temperature (°F)
Pressure (kPa) or $P$ (MPa)	Pressure (psi) or Pressure (atm)
Density (kg/m³) or $\rho$ (kg/m$^3$)	Density (lb/ft³)
Viscosity (mPa·s)	Viscosity (cP) — numerically equal but use SI name
Flow rate (kg/s)	Flow rate (lb/h)
Energy (kJ/mol)	Energy (BTU/lbmol)

"bar" is acceptable for pressure axes in engineering contexts (1 bar = 100 kPa).

When to Use

• Creating figures for any scientific paper in the paperlab
• Regenerating figures after data or style revisions
• Setting up a new 02_generate_figures.py for a paper project

Core Setup (Copy-Paste Starter)

Every figure script should start with this rc configuration:

import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import numpy as np
import json
from pathlib import Path

# ── Publication-quality defaults ──────────────────────────────────
plt.rcParams.update({
    "font.family": "serif",
    "font.serif": ["Times New Roman", "DejaVu Serif"],
    "font.size": 9,
    "axes.titlesize": 10,
    "axes.labelsize": 9,
    "xtick.labelsize": 8,
    "ytick.labelsize": 8,
    "legend.fontsize": 8,
    "figure.dpi": 300,
    "savefig.dpi": 300,
    "savefig.bbox_inches": "tight",
    "axes.linewidth": 0.6,
    "xtick.direction": "in",
    "ytick.direction": "in",
    "xtick.major.size": 3,
    "ytick.major.size": 3,
    "xtick.minor.size": 1.5,
    "ytick.minor.size": 1.5,
    "grid.linewidth": 0.3,
    "grid.alpha": 0.4,
    "lines.linewidth": 1.0,
    "lines.markersize": 4,
})

# Consistent color palette
BLUE = "#2171b5"
ORANGE = "#e6550d"
GREEN = "#31a354"
GREY = "#636363"
PALETTE = [BLUE, ORANGE, GREEN, "#756bb1", "#e7298a", "#66a61e"]

# Output directory
FIGURES_DIR = Path(__file__).parent.parent / "figures"
FIGURES_DIR.mkdir(exist_ok=True)