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        "author": "Henrik Finsberg",
        "author_email": "henriknf@simula.no",
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        "description": "\n[![InstallConda](https://anaconda.org/finsberg/pulse/badges/installer/conda.svg)](https://anaconda.org/finsberg/pulse)\n[![CircleCI](https://circleci.com/gh/finsberg/pulse.svg?style=shield)](https://circleci.com/gh/finsberg/pulse)\n[![Platform](https://anaconda.org/finsberg/pulse/badges/platforms.svg)](https://anaconda.org/finsberg/pulse)\n[![Binder](https://binder.pangeo.io/badge_logo.svg)](https://binder.pangeo.io/v2/gh/finsberg/pulse/master?filepath=index.ipynb)\n[![status](http://joss.theoj.org/papers/9abee735e6abadabe9252d5fcc84fd40/status.svg)](http://joss.theoj.org/papers/9abee735e6abadabe9252d5fcc84fd40)\n\n# pulse\n\nA software for solving problems in cardiac mechanics.\nThe code in this repository used to be part of [pulse-adjoint](https://bitbucket.org/finsberg/pulse_adjoint), but now works as a standalone mechanics solver without the need for dolfin-adjoint.\n\n## Overview\n`pulse` is a software based on [FEniCS](https://fenicsproject.org) 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](https://www.duo.uio.no/handle/10852/62015), where most of the relevant background for the code can be found.\n\nWhile 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. \n\n## Installation instructions\n\n### Install with pip\n`pulse` can be installed directly from [PyPI](https://pypi.org/project/fenics-pulse/)\n```\npip install fenics-pulse\n```\nor you can install the most recent development version\n```\npip install git+https://github.com/finsberg/pulse.git\n```\n\n### Install with conda\nYou can also install the package using `conda`\n```\nconda install -c finsberg pulse\n```\n`pulse` is also available on conda-forge\n```\nconda install -c conda-forge pulse\n```\n\n### Docker\nIt is also possible to use Docker. There is a prebuilt docker image\nusing FEniCS 2017.2, python3.6 and pulse. You can get it by typing\n```\ndocker pull finsberg/pulse:latest\n```\n\n## Requirements\n* FEniCS version 2016 or newer\n\nNote that if you install FEniCS using anaconda then you will not get support for parallel HDF5\nsee e.g [this issue](https://github.com/conda-forge/hdf5-feedstock/issues/51).\n\n## Getting started\nCheck out the demos in the demo folder.\n\n## Automated test\nTest are provided in the folder [`tests`](tests). You can run the test\nwith `pytest`\n```\npython -m pytest tests -vv\n```\n\n\n## Documentation\nDocumentation can be found at [finsberg.github.io/pulse](https://finsberg.github.io/pulse)\nYou can create documentation yourselves by typing `make html` in the\nroot directory.\n\n## Citing\n\nIf you use `pulse` in your own research, please cite the [JOSS paper](https://joss.theoj.org/papers/10.21105/joss.01539)\n\n```\n@article{pulse,\n  doi = {10.21105/joss.01539},\n  url = {https://doi.org/10.21105/joss.01539},\n  year  = {2019},\n  month = {sept},\n  publisher = {The Open Journal},\n  volume = {4},\n  number = {41},\n  pages = {1539},\n  author = {Henrik Finsberg},\n  title = {pulse: A python package based on FEniCS for solving problems in cardiac mechanics},\n  journal = {The Journal of Open Source Software}\n}\n```\n\n## Known issues\n* If you encounter errors with `h5py` try to uninstall it (`pip uninstall h5py`) and then re-install it without installing any binary packages, i.e\n```\npip install h5py --no-binary=h5py\n```\n\n\n\n",
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