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https://github.com/computationalphysiology/fenics-geometry

A library handling geometries for Fenics-based problems. Based on pulse.geometry by Henrik Finsberg
https://github.com/computationalphysiology/fenics-geometry

Last synced: 7 days ago
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A library handling geometries for Fenics-based problems. Based on pulse.geometry by Henrik Finsberg

Host: GitHub
URL: https://github.com/computationalphysiology/fenics-geometry
Owner: ComputationalPhysiology
License: lgpl-3.0
Created: 2019-10-09T12:16:50.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2020-02-26T10:15:51.000Z (almost 5 years ago)
Last Synced: 2024-12-01T19:23:45.355Z (2 months ago)
Language: Python
Size: 11.4 MB
Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

[![Build Status](https://travis-ci.org/ComputationalPhysiology/fenics-geometry.svg?branch=master)](https://travis-ci.org/ComputationalPhysiology/fenics-geometry) [![Documentation Status](https://readthedocs.org/projects/fenics-geometry/badge/?version=latest)](https://fenics-geometry.readthedocs.io/en/latest/?badge=latest)

# README

A library handling geometries for Fenics-based problems. Based geometry.py as part of [pulse](https://github.com/ComputationalPhysiology/pulse) by Henrik Finsberg, and adapted by Alexandra Diem to fit arbitrary geometries.

## Overview

`fenics-geometry` provides a conventient way to create meshes for [FEniCS](https://fenicsproject.org), including cardiac meshes.

## Installation instructions

### Install with pip

The development version of `fenics-geometry` can directly be installed from git using pip
```
pip install git+https://github.com/KVSLab/fenics-geometry.git
```

### Requirements

* FEniCS version 2019.1.0 or newer

Note that if you install FEniCS using anaconda then you will not get support for parallel HDF5
see e.g [this issue](https://github.com/conda-forge/hdf5-feedstock/issues/51). We recommend installing FEniCS using [Docker](https://fenicsproject.org/download/)

## Getting started

Check out the demos in the demo folder.

## Automated test

Test are provided in the folder [`tests`](tests). You can run the test
with `pytest`
```
pytest -xv tests/
```
The tests are automatically run on [TravisCI](https://travis-ci.org/ComputationalPhysiology/fenics-geometry).

## Documentation

The documentation is built using ReadTheDocs and can be found at [https://fenics-geometry.readthedocs.io](https://fenics-geometry.readthedocs.io).

## Known issues

* If you encounter errors with `h5py` it needs to be built from scratch instead of installed from the binaries in `pip`:
```
pip uninstall h5py
pip install h5py --no-binary=h5py
```
* If you installed FEniCS using `conda` and encouter a `Fatal Python error: Aborted` with `` messages you need to specify the build for FEniCS during installation for `h5py` to work:
```
conda install fenics=2019.1.0=py37_5
```