pulse
pulse: A python package based on FEniCS for solving problems in cardiac mechanics - Published in JOSS (2019)
Science Score: 100.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org -
✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords from Contributors
Scientific Fields
Repository
A software for solving problems in cardiac mechanics
Basic Info
- Host: GitHub
- Owner: finsberg
- License: lgpl-3.0
- Language: Python
- Default Branch: main
- Homepage: http://finsberg.github.io/pulse
- Size: 449 MB
Statistics
- Stars: 16
- Watchers: 2
- Forks: 13
- Open Issues: 5
- Releases: 8
Metadata Files
README.md
pulse
A software for solving problems in cardiac mechanics.
Overview
pulse is a software based on FEniCS that aims to solve problems in cardiac mechanics (but is easily extended to solve more general problems in continuum mechanics). pulse is a results of the author's PhD thesis, where most of the relevant background for the code can be found.
While FEniCS offers a general framework for solving PDEs, pulse specifically targets problems in continuum mechanics. Therefore, most of the code for applying compatible boundary conditions, formulating the governing equations, choosing appropriate spaces for the solutions and applying iterative strategies etc. are already implemented, so that the user can focus on the actual problem he/she wants to solve rather than implementing all the necessary code for formulating and solving the underlying equations.
Installation instructions
Install with pip
pulse can be installed directly from PyPI
python3 -m pip install fenics-pulse
or you can install the most recent development version
python3 -m pip install git+https://github.com/finsberg/pulse.git
Install with conda
You can also install the package using conda
conda install -c conda-forge pulse
Docker
It is also possible to use Docker. There is a prebuilt docker image
using the development version of FEniCS, python3.10 and pulse. You can get it by typing
docker pull ghcr.io/finsberg/pulse:latest
Requirements
- FEniCS version 2019.1.0 or newer (older versions might work but is not tested against anymore)
Note that if you install FEniCS using anaconda then you will not get support for parallel HDF5 see e.g this issue.
Getting started
Check out the demos in the demo folder. These demos are currently in jupyter notebook format.
If you want to run them as python files you can convert the notebooks to .py files using e.g jupytext
If you have a question about how to use the software you can ask a question or start a new discussion in the discussion section
Automated test
Test are provided in the folder tests. You can run the test
with pytest
python3 -m pytest tests -vv
Documentation
Documentation can be found at finsberg.github.io/pulse
You can create documentation yourselves by typing make html in the
root directory.
Citing
If you use pulse in your own research, please cite the JOSS paper
@article{pulse,
doi = {10.21105/joss.01539},
url = {https://doi.org/10.21105/joss.01539},
year = {2019},
month = {sept},
publisher = {The Open Journal},
volume = {4},
number = {41},
pages = {1539},
author = {Henrik Finsberg},
title = {pulse: A python package based on FEniCS for solving problems in cardiac mechanics},
journal = {The Journal of Open Source Software}
}
Known issues
- If you encounter errors with
h5pytry to uninstall it (pip uninstall h5py) and then re-install it without installing any binary packages, i.epython3 -m pip install h5py --no-binary=h5py
Contributing
See CONTRIBUTING.md
Owner
- Name: Henrik Finsberg
- Login: finsberg
- Kind: user
- Location: Oslo, Norway
- Company: Simula Research Laboratoy
- Website: https://finsberg.github.io
- Repositories: 13
- Profile: https://github.com/finsberg
Senior Research Engineer working with Scientific Computing and Computational Physiology
JOSS Publication
pulse: A python package based on FEniCS for solving problems in cardiac mechanics
Authors
Simula Research Laboratory, Oslo, Norway
Editor
Tania Allard
Tags
FEniCS Cardiac Mechanics Finite Element Method Continuum MechanicsCitation (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: "pulse" version: 2022.1.3 doi: 10.21105/joss.01539 license: LGPL-3.0 date-released: 2019-09-24 url: "https://github.com/finsberg/pulse"
GitHub Events
Total
- Watch event: 2
- Push event: 37
- Pull request event: 3
- Fork event: 1
- Create event: 2
Last Year
- Watch event: 2
- Push event: 37
- Pull request event: 3
- Fork event: 1
- Create event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Henrik Finsberg | h****f@s****o | 422 |
| pre-commit-ci[bot] | 6****] | 82 |
| Alexandra Diem | a****m@g****m | 11 |
| zoraiz | r****2@y****m | 3 |
| Joakim Sundnes | s****s@s****o | 3 |
| mjsadeghinia | m****a@o****m | 2 |
| Daniel S. Katz | d****z@i****g | 2 |
| jvbrink | j****s@s****o | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 18
- Total pull requests: 105
- Average time to close issues: 3 months
- Average time to close pull requests: 7 days
- Total issue authors: 6
- Total pull request authors: 6
- Average comments per issue: 4.06
- Average comments per pull request: 0.06
- Merged pull requests: 102
- Bot issues: 0
- Bot pull requests: 78
Past Year
- Issues: 0
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 0
- Pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- finsberg (5)
- jingbinzhao415 (4)
- melund (4)
- wilburmao (3)
- Tao-Bath (1)
- ramayzoraiz (1)
Pull Request Authors
- pre-commit-ci[bot] (80)
- finsberg (19)
- mjsadeghinia (4)
- danielskatz (2)
- mansoryashka (1)
- jvbrink (1)
- ramayzoraiz (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 215 last-month
- Total docker downloads: 176
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Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 2
(may contain duplicates) - Total versions: 39
- Total maintainers: 1
pypi.org: fenics-pulse
A python library based on FEniCS that aims to solve problems in continuum mechanics, in particular cardiac mechanics
- Homepage: https://finsberg.github.io/pulse/
- Documentation: https://finsberg.github.io/pulse/
- License: GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. An "Application" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. A "Combined Work" is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the "Linked Version". The "Minimal Corresponding Source" for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. The "Corresponding Application Code" for a Combined Work means the object code and/or source code for the Application, including any data and utility programs needed for reproducing the Combined Work from the Application, but excluding the System Libraries of the Combined Work. 1. Exception to Section 3 of the GNU GPL. You may convey a covered work under sections 3 and 4 of this License without being bound by section 3 of the GNU GPL. 2. Conveying Modified Versions. If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following: a) Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the object code with a copy of the GNU GPL and this license document. 4. Combined Works. You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following: a) Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the Combined Work with a copy of the GNU GPL and this license document. c) For a Combined Work that displays copyright notices during execution, include the copyright notice for the Library among these notices, as well as a reference directing the user to the copies of the GNU GPL and this license document. d) Do one of the following: 0) Convey the Minimal Corresponding Source under the terms of this License, and the Corresponding Application Code in a form suitable for, and under terms that permit, the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work, in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source. 1) Use a suitable shared library mechanism for linking with the Library. A suitable mechanism is one that (a) uses at run time a copy of the Library already present on the user's computer system, and (b) will operate properly with a modified version of the Library that is interface-compatible with the Linked Version. e) Provide Installation Information, but only if you would otherwise be required to provide such information under section 6 of the GNU GPL, and only to the extent that such information is necessary to install and execute a modified version of the Combined Work produced by recombining or relinking the Application with a modified version of the Linked Version. (If you use option 4d0, the Installation Information must accompany the Minimal Corresponding Source and Corresponding Application Code. If you use option 4d1, you must provide the Installation Information in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source.) 5. Combined Libraries. 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Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library.
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Latest release: 2025.0.0
published 9 months ago
Rankings
Maintainers (1)
conda-forge.org: pulse
pulse is a python library based on FEniCS that aims to solve problems in continuum mechanics, in particular cardiac mechanics.
- Homepage: https://finsberg.github.io/pulse
- License: LGPL-3.0-or-later
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Latest release: 2021.2.2
published about 4 years ago
Rankings
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