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https://github.com/finsberg/fenics-beat
Cardiac electrophysiology solver
https://github.com/finsberg/fenics-beat
Last synced: 3 days ago
JSON representation
Cardiac electrophysiology solver
- Host: GitHub
- URL: https://github.com/finsberg/fenics-beat
- Owner: finsberg
- License: mit
- Created: 2023-09-16T20:15:43.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-05-22T21:28:04.000Z (6 months ago)
- Last Synced: 2024-05-22T22:33:27.734Z (6 months ago)
- Language: Python
- Homepage: https://finsberg.github.io/fenics-beat/
- Size: 338 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/finsberg/fenics-beat/actions/workflows/pre-commit.yml)
[](https://github.com/finsberg/fenics-beat/pkgs/container/fenics-beat)
[](https://github.com/finsberg/fenics-beat/actions/workflows/build_docs.yml)
[](https://github.com/finsberg/fenics-beat/actions/workflows/main.yml)
[](https://badge.fury.io/py/fenics-beat)
[](https://doi.org/10.5281/zenodo.13323643)
---
# 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`](https://docs.docker.com/engine/reference/commandline/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](https://pypi.org/project/fenics-beat/) 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](https://bitbucket.org/fenics-project/dolfin/src/master/), using [conda](https://anaconda.org/conda-forge/fenics) or use some of the [pre-built docker images](https://github.com/orgs/scientificcomputing/packages?repo_name=packages)
## 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](https://finsberg.github.io/fenics-beat/CONTRIBUTING.html).
## License
MIT
## Need help or having issues
Please submit an [issue](https://github.com/finsberg/fenics-beat/issues)