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https://github.com/computationalphysiology/fenics-geometry

A library handling geometries for Fenics-based problems. Based on pulse.geometry by Henrik Finsberg

https://github.com/computationalphysiology/fenics-geometry

Science Score: 13.0%

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Last synced: 9 months ago · JSON representation

Repository

A library handling geometries for Fenics-based problems. Based on pulse.geometry by Henrik Finsberg

Basic Info
  • Host: GitHub
  • Owner: ComputationalPhysiology
  • License: lgpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 11.4 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 6 years ago · Last pushed over 6 years ago
Metadata Files
Readme License

README.md

Build Status Documentation Status

README

A library handling geometries for Fenics-based problems. Based geometry.py as part of pulse by Henrik Finsberg, and adapted by Alexandra Diem to fit arbitrary geometries.

Overview

fenics-geometry provides a conventient way to create meshes for FEniCS, including cardiac meshes.

Installation instructions

Install with pip

The development version of fenics-geometry can directly be installed from git using pip pip install git+https://github.com/KVSLab/fenics-geometry.git

Requirements

  • FEniCS version 2019.1.0 or newer

Note that if you install FEniCS using anaconda then you will not get support for parallel HDF5 see e.g this issue. We recommend installing FEniCS using Docker

Getting started

Check out the demos in the demo folder.

Automated test

Test are provided in the folder tests. You can run the test with pytest pytest -xv tests/ The tests are automatically run on TravisCI.

Documentation

The documentation is built using ReadTheDocs and can be found at https://fenics-geometry.readthedocs.io.

Known issues

  • If you encounter errors with h5py it needs to be built from scratch instead of installed from the binaries in pip: pip uninstall h5py pip install h5py --no-binary=h5py
  • If you installed FEniCS using conda and encouter a Fatal Python error: Aborted with <frozen importlib._bootstrap> messages you need to specify the build for FEniCS during installation for h5py to work: conda install fenics=2019.1.0=py37_5

Owner

  • Name: Computational Physiology at Simula Research Laboratory
  • Login: ComputationalPhysiology
  • Kind: organization
  • Location: Fornebu, Norway

GitHub organization for the computational physiology department at Simula Research Laboratory

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  • Total pull requests: 22
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  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 22
  • Bot issues: 0
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Top Authors
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  • alexdiem (21)
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Dependencies

docs/requirements.txt pypi
  • m2r *
  • sphinx *
  • sphinx_rtd_theme *
requirements.txt pypi
  • fenics *
  • h5py *
  • pytest *
setup.py pypi
  • fenics *
  • pytest *