README

A library handling geometries for Fenics-based problems. Based geometry.py as part of 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, 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. We recommend installing FEniCS using Docker

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.

Documentation

The documentation is built using ReadTheDocs and can be found at 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: .. code-block:: guess

  pip uninstall h5py pip install h5py –no-binary=h5py

• If you installed FEniCS using conda and encouter a Fatal Python error: Aborted with <frozen importlib._bootstrap> messages you need to specify the build for FEniCS during installation for h5py to work: .. code-block:: guess

  conda install fenics=2019.1.0=py37_5