Metadata-Version: 2.4
Name: pyVertexModel
Version: 1.0.7
Summary: A versatile 3D vertex model for modeling tissue and cell mechanics, particularly for tissue repair simulations.
Author-email: Pablo Vicente-Munuera <p.munuera@ucl.ac.uk>
License: MIT
Project-URL: Bug Tracker, https://github.com/Pablo1990/pyVertexModel/issues
Project-URL: Homepage, https://github.com/Pablo1990/pyVertexModel
Project-URL: Source, https://github.com/Pablo1990/pyVertexModel
Keywords: biophysics,cell mechanics,computational biology,tissue mechanics,tissue repair,vertex model
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: cython
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: pillow
Requires-Dist: scikit-image
Requires-Dist: cython
Requires-Dist: vtk
Requires-Dist: pandas
Requires-Dist: networkx
Requires-Dist: pyvista
Requires-Dist: scikit-learn
Requires-Dist: matplotlib
Requires-Dist: seaborn
Dynamic: license-file

![logo.png](logo.png)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17649952.svg)](https://doi.org/10.5281/zenodo.17649952)
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[![PyPI](https://img.shields.io/pypi/v/pyvertexmodel.svg?color=green)](https://pypi.org/project/pyvertexmodel)
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[![tests](https://github.com/Pablo1990/pyVertexModel/actions/workflows/tests.yaml/badge.svg)](https://github.com/Pablo1990/pyVertexModel/actions/workflows/tests.yaml)
[![codecov](https://codecov.io/gh/Pablo1990/pyVertexModel/graph/badge.svg?token=AKGWS79Z61)](https://codecov.io/gh/Pablo1990/pyVertexModel)

pyVertexModel is versatile 3D vertex model to model tissue and cell mechanics, in particular, regarding tissue repair.

Please, to ensure you use a polished version, use the 'paper' version/branch: https://github.com/Pablo1990/pyVertexModel/tree/paper 

## Environment

```bash
conda create -n pyVertexModel python=3.9
conda activate pyVertexModel
pip install -r requirements.txt
```

## Usage
The first time you run the code, you need to compile the cython code. To do so, run the following commands:
```bash
python setup.py build_ext --inplace
```

To run the code, you can use the following command:
```bash
python main.py
```

To run the tests, we use 'tox':
```bash
tox
```

## Changing the parameters
You can change the parameters of the model in the `parameters/set.py` file. At the moment, you should change it under 
the 'wing_disc()' function.

Each simulation will be saved in a different folder in the `results` directory. The name of the folder will be the date and time of the simulation.

## Help

For any issues with the code, you can put an issue in the repository.
For other matters, you can contact Pablo Vicente Munuera (p.munuera@ucl.ac.uk).

