vizopt 0.0.5

Mathematical optimization for data visualization

vizopt

Mathematical optimization for data visualization, specifically designed for graph layouts with hierarchical inclusion constraints ("bubble layouts").

Uses JAX for automatic differentiation and JIT compilation to efficiently optimize layouts via gradient descent.

Read the documentation https://spectalizer.github.io/vizopt/.

Installation

pip install vizopt

To use Optuna-based schedule search (e.g. the star_curriculum notebook):

uv sync --group hyperoptim

Quick Start

import numpy as np
from vizopt.templates import circle_packing

# Define circle radii
rng = np.random.default_rng(0)
radii = rng.uniform(0.1, 1.0, size=20).tolist()

# Pack circles to minimize overlap and bounding box size
positions = circle_packing.optimize_circle_packing(
    radii=radii,
    weight_total_size=10.0,
    collision_offset=0.05,
    optim_kwargs={"n_iters": 3000, "learning_rate": 0.01},
)
# positions is a list of (x, y) tuples, one per circle

Features

• Multi-objective optimization (edge lengths, compactness, collision avoidance, inclusion constraints)
• Efficient JAX-based gradient descent with JIT compilation
• Handles arbitrary hierarchical inclusion relationships
• Automatic per-variable normalization so optimizer performance is independent of input coordinate scale
• NetworkX integration with a consistent DiGraph convention: parent → child edges ((u, v) means v ⊂ u)

Examples

See examples/examples_with_bubbles.ipynb for detailed usage.

License

MIT

For developers

Quality assurance

Tests run automatically on every push and pull request via GitHub Actions:

uv run pytest

Type-check all notebooks locally (not in CI):

uv run python scripts/convert_all_notebooks_to_py.py

This converts each notebook to a temporary .py file, runs pyright across all of them, then deletes the generated files. Pass --no-cleanup to keep them for inspection.

Documentation

Using Zensical.

uv run zensical serve

uv run python scripts/nb_to_md.py --execute examples/circle_packing.ipynb docs/examples/from-notebook-circle-packing.md