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fenics-beat

Cardiac electrophysiology solver

https://github.com/finsberg/fenics-beat

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Cardiac electrophysiology solver

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 3
  • Open Issues: 4
  • Releases: 3
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.md

pre-commit Create and publish a Docker image Build docs Test package PyPI version DOI

fenics-beat

Library for running cardiac electrophysiology simulations.

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

[!NOTE] This library are using the legacy version of FEnICS. New users are encourage to use fenicsx-beat which is based on FEniCSx

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

Owner

  • Name: Henrik Finsberg
  • Login: finsberg
  • Kind: user
  • Location: Oslo, Norway
  • Company: Simula Research Laboratoy

Senior Research Engineer working with Scientific Computing and Computational Physiology

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Finsberg"
  given-names: "Henrik"
  orcid: "https://orcid.org/0000-0003-3766-2393"
title: "fenics-beat"
version: "0.1.1"
doi: 10.5281/zenodo.13323643
date-released: "2024-08-17"
url: "https://github.com/finsberg/fenics-beat"

GitHub Events

Total
  • Issues event: 2
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 60
  • Pull request event: 56
  • Fork event: 3
  • Create event: 2
Last Year
  • Issues event: 2
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 60
  • Pull request event: 56
  • Fork event: 3
  • Create event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 93
  • Average time to close issues: 5 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.43
  • Average comments per pull request: 0.04
  • Merged pull requests: 88
  • Bot issues: 0
  • Bot pull requests: 66
Past Year
  • Issues: 1
  • Pull requests: 52
  • Average time to close issues: about 23 hours
  • Average time to close pull requests: 6 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 48
  • Bot issues: 0
  • Bot pull requests: 52
View more stats
Top Authors
Issue Authors
  • finsberg (4)
  • marie-cloet2000 (1)
  • andreerhardt (1)
  • jyk816108 (1)
Pull Request Authors
  • pre-commit-ci[bot] (78)
  • finsberg (46)
  • dependabot[bot] (14)
Top Labels
Issue Labels
Pull Request Labels
dependencies (14) github_actions (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 26 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 10
  • Total maintainers: 1
pypi.org: fenics-beat

Library to run cardiac EP simulations

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 26 Last month
Rankings
Dependent packages count: 9.3%
Average: 38.7%
Dependent repos count: 68.2%
Maintainers (1)
finsberg
Last synced: 6 months ago

Dependencies

pyproject.toml pypi
  • numpy *
  • scipy *