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PyAFV

pyafv_pbc

PyPi Conda Version Docker License Tests on all platforms pytest Codecov Documentation arXiv:2604.15481 Open In Colab

PyAFV is a Python package for simulating cellular tissues based on the 2D active finite Voronoi (AFV) model. It provides a computational framework for investigating collective cell behaviors such as motility, adhesion, jamming, and tissue fracture in active matter and biophysical systems. In contrast to standard vertex or Voronoi models, the AFV model incorporates finite interaction ranges and cell-medium interfaces, allowing for detachment, free boundaries, and fragmentation. The package includes tools for geometry handling, time evolution, and analysis of cell configurations. The AFV formalism was introduced and further developed in, for example, Refs. [1–3].

See an interactive simulation demo using PyAFV on Prof. Dapeng (Max) Bi's homepage!

Installation

PyAFV is available on PyPI and can be installed using pip directly:

pip install pyafv

The package supports Python ≥ 3.10 and < 3.15, including Python 3.14t (the free-threaded, no-GIL build). To verify that the installation was successful and that the correct version is installed, run the following in Python:

import pyafv
print(pyafv.__version__)

As an alternative, you can install PyAFV via conda from the conda-forge channel:

conda install -c conda-forge pyafv

If you go this route, note that for Python 3.14 the conda-forge distribution currently provides only the GIL-enabled build.

See the documentation for instructions on installing the package from source or in offline environments.

Install using Docker 🐳

PyAFV can also be installed via containerized environments. Pull the Docker image from Docker Hub:

docker pull wwang721/pyafv:latest

The image is also available via the GitHub Container Registry (GHCR) under GitHub Packages; use ghcr.io/wwang721/pyafv to pull from GHCR instead.

Usage

Open In Colab

Here is a simple example to get you started, demonstrating how to construct a finite Voronoi diagram (click the Google Colab badge above to run the notebook directly):

import numpy as np
import pyafv as afv

N = 100                                          # number of cells
pts = np.random.rand(N, 2) * 10                  # initial positions
params = afv.PhysicalParams(r=1.0)               # use default parameter values
sim = afv.FiniteVoronoiSimulator(pts, params)    # initialize the simulator
sim.plot_2d(show=True)                           # visualize the Voronoi diagram

To compute the conservative forces and extract detailed geometric information (e.g., cell areas, vertices, and edges), call:

diag = sim.build()

The returned object diag is a Python dict containing these quantities. Refer to the documentation for more detailed usage.

Simulation previews

Below are representative simulation snapshots generated using the code:

Model illustration Periodic boundary conditions
Initial configuration After relaxation Active dynamics enabled

More information

Citing the package

To cite PyAFV, please refer to the associated paper available on arXiv. Here is a ready-made BibTeX entry:

@article{wang2026divergence,
  title   = {{Divergence of detachment forces in the finite Voronoi model}},
  author  = {Wang, Wei and Camley, Brian A},
  journal = {arXiv preprint arXiv:2604.15481},
  year    = {2026},
  doi     = {10.48550/arXiv.2604.15481}
}

References

[1] J. Huang, H. Levine, and D. Bi, Bridging the gap between collective motility and epithelial-mesenchymal transitions through the active finite Voronoi model, Soft Matter 19, 9389 (2023).
[2] E. Teomy, D. A. Kessler, and H. Levine, Confluent and nonconfluent phases in a model of cell tissue, Phys. Rev. E 98, 042418 (2018).
[3] W. Wang (汪巍) and B. A. Camley, Divergence of detachment forces in the finite Voronoi model arXiv:2604.15481 [cond-mat.soft] (2026).

Metadata

Release files for pyafv 0.4.16

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pyafv 0.4.16
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pyafv-0.4.16.tar.gz 72.8 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for pyafv 0.4.16
File
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Total release size: 69.3 MB

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This release

0.4.16 This release

55 release files

0.4.9

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0.4.7

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0.4.6

55 release files

0.4.3

55 release files

0.4.2

55 release files

0.4.0

55 release files

0.3.9

55 release files

0.3.6

46 release files

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