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

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