fenics-beat

Library for running cardiac electrophysiology simulations.

Source code: https://github.com/finsberg/fenics-beat
Documentation: https://finsberg.github.io/fenics-beat

Getting started

Check out the examples at https://finsberg.github.io/fenics-beat/

Install

Using docker (recommended)

The simplest way to use fenics-beat is to use the provided docker image. You can get this image by pulling it from the github registry

docker pull ghcr.io/finsberg/fenics-beat:latest

It is also possible to pull a specific version by changing the tag, e.g.

docker pull ghcr.io/finsberg/fenics-beat:v0.0.8

will use version 0.0.8.

In order to start a container you can use the docker run command. For example the command

docker run --rm -v $(pwd):/home/shared -w /home/shared -ti ghcr.io/finsberg/fenics-beat:latest

will run the latest version and share your current working directory with the container. The source code of fenics-beat is located at /repo in the docker container.

Using pip

fenics-beat is also available on pypi and can be installed with

python3 -m pip install fenics-beat

However this requires FEniCS to already be installed. Currently, FEniCS can be installed by building from source, using conda or use some of the pre-built docker images

Automated tests

Upon pushing new code to the repository, a number of tests run:

pre-commit tests.

Install pre-commit:

python3 -m pip install pre-commit

Run pre-commit hooks:

pre-commit run --all

unit and integration tests can be found in tests folder
- Install tests dependencies:
```
python3 -m pip install -e .[test]
```
- Run tests
```
python3 -m pytest
```
Examples: All examples are run as part of building the documentation

Contributing guidelines

Detailed contributing guidelines are given here.

License

MIT

Need help or having issues

Please submit an issue

finsberg / fenics-beat