simcardems
simcardems: A FEniCS-based cardiac electro-mechanics solver - Published in JOSS (2023)
Science Score: 95.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
1 of 11 committers (9.1%) from academic institutions -
○Institutional organization owner
-
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords from Contributors
Scientific Fields
Repository
Simula Cardiac ElectroMechanics Solver
Basic Info
- Host: GitHub
- Owner: ComputationalPhysiology
- License: lgpl-2.1
- Language: Python
- Default Branch: main
- Homepage: http://computationalphysiology.github.io/simcardems
- Size: 63.9 MB
Statistics
- Stars: 11
- Watchers: 6
- Forks: 11
- Open Issues: 15
- Releases: 7
Metadata Files
README.md
Simula Cardiac Electro-Mechanics Solver
simcardems is a FEniCS-based cardiac electro-mechanics solver and is developed as a part of the SimCardio Test project. The solver depends on pulse and cbcbeat.
Installation
Getting started
See the demos
Documentation
Documentation is hosted at http://computationalphysiology.github.io/simcardems.
Automated test
Tests are provided in the folder tests. You can run the tests with pytest
python3 -m pytest tests -vv
Contributing
Citing
If you use simcardems in your research, please cite it as follows
@article{Finsberg2023,
doi = {10.21105/joss.04753},
url = {https://doi.org/10.21105/joss.04753},
year = {2023},
publisher = {The Open Journal},
volume = {8},
number = {81},
pages = {4753},
author = {Henrik Nicolay Topnes Finsberg and Ilsbeth Gerarda Maria van Herck and Cécile Daversin-Catty and Hermenegild Arevalo and Samuel Wall},
title = {simcardems: A FEniCS-based cardiac electro-mechanics solver},
journal = {Journal of Open Source Software}
}
Known issues
- Issue with h5py, see https://github.com/ComputationalPhysiology/pulse#known-issues
Authors
- Henrik Finsberg (henriknf@simula.no)
- Ilsbeth van Herck (ilse@simula.no)
- Cécile Daversin-Catty (cecile@simula.no)
Owner
- Name: Computational Physiology at Simula Research Laboratory
- Login: ComputationalPhysiology
- Kind: organization
- Location: Fornebu, Norway
- Website: https://computationalphysiology.github.io
- Repositories: 51
- Profile: https://github.com/ComputationalPhysiology
GitHub organization for the computational physiology department at Simula Research Laboratory
JOSS Publication
simcardems: A FEniCS-based cardiac electro-mechanics solver
Authors
Simula Research Laboratory, Oslo, Norway
Simula Research Laboratory, Oslo, Norway
Simula Research Laboratory, Oslo, Norway
Simula Research Laboratory, Oslo, Norway
Simula Research Laboratory, Oslo, Norway
Editor
Aoife Hughes
Tags
FEniCS Cardiac Electro-Mechanics Finite Element Method Computational BiologyGitHub Events
Total
- Delete event: 20
- Issue comment event: 3
- Push event: 94
- Pull request event: 70
- Create event: 13
Last Year
- Delete event: 20
- Issue comment event: 3
- Push event: 94
- Pull request event: 70
- Create event: 13
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Henrik Finsberg | h****f@s****o | 456 |
| pre-commit-ci[bot] | 6****] | 115 |
| IlsevanHerck | i****e@s****o | 105 |
| Continuous Integration | u****e | 100 |
| Cécile | c****e@s****o | 34 |
| Jørgen S. Dokken | d****n@s****o | 14 |
| dependabot[bot] | 4****] | 11 |
| Ilse van Herck | i****h@l****a | 3 |
| samwall | s****l@s****o | 2 |
| Daniel S. Katz | d****z@i****g | 2 |
| Ilse van Herck | i****h@l****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 17
- Total pull requests: 225
- Average time to close issues: 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 7
- Total pull request authors: 7
- Average comments per issue: 1.41
- Average comments per pull request: 0.15
- Merged pull requests: 184
- Bot issues: 1
- Bot pull requests: 132
Past Year
- Issues: 1
- Pull requests: 74
- Average time to close issues: N/A
- Average time to close pull requests: 7 days
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.07
- Merged pull requests: 56
- Bot issues: 1
- Bot pull requests: 68
Top Authors
Issue Authors
- finsberg (5)
- mbarzegary (4)
- IlsevanHerck (3)
- jorgensd (2)
- ramayzoraiz (1)
- ndermul (1)
- pre-commit-ci[bot] (1)
Pull Request Authors
- pre-commit-ci[bot] (105)
- finsberg (71)
- dependabot[bot] (27)
- cdaversin (10)
- IlsevanHerck (10)
- jorgensd (1)
- danielskatz (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 40 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 35
- Total maintainers: 1
pypi.org: simcardems
Simula Cardiac electromechanics solver
- Homepage: https://github.com/ComputationalPhysiology/simcardems
- Documentation: https://simcardems.readthedocs.io/
- License: LGPL-2.1
-
Latest release: 2023.7.1
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- docker/build-push-action v3 composite
- docker/login-action v2 composite
- docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
- docker/setup-buildx-action v2 composite
- docker/setup-qemu-action v2 composite
- actions/checkout v2 composite
- peaceiris/actions-gh-pages v3 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- pypa/gh-action-pypi-publish master composite
- schneegans/dynamic-badges-action v1.6.0 composite
- finsberg/fenics latest build
- actions/checkout v3 composite
- actions/download-artifact v3 composite
- actions/setup-python v4 composite
- actions/upload-artifact v2 composite
- actions/checkout v3 composite
- ap-features *
- cardiac-geometries *
- cbcbeat *
- click *
- fenics-pulse *
- h5py *
- matplotlib *
- numpy *
- scipy *
- tqdm *
- typing-extensions *