Install with pip

Before installing simcardems with pip you need to install the legacy version of FEniCS.

Installing FEniCS

FEniCS provides prebuilt high-performance Docker images, usable on most OS:

docker run -ti -v $(pwd):/home/fenics/shared -w /home/fenics/shared quay.io/fenicsproject/stable:latest

Linux

Ubuntu users can also use the dedicated Ubuntu package:

sudo apt-get install software-properties-common
sudo add-apt-repository ppa:fenics-packages/fenics
sudo apt-get update
sudo apt-get install fenics`

or the prebuilt Anaconda package:

conda create -n fenicsproject -c conda-forge fenics
source activate fenicsproject

Mac

On Mac with Intel CPUs, both Docker and Anaconda installation are possible. On Mac with Apple Silicon Chip, the Docker installation is recommended.

Windows

We recommend Windows users to use Windows Subsystem for Linux and follow the (Linux users)[#linux] instructions, or use Docker

Alternatively, FEniCS can also be built from source (only recommended for installation on HPC clusters), following the installation instructions from the (possibly not up-to-date) FEniCS Reference Manual.

Install simcardems

Once you have FEniCS installed, you can install simcardems with pip using the command

python3 -m pip install simcardems

If you want the latest version or you want to contribute to simcardems, you can install the code directly from the GitHub repo

python3 -m pip install git+https://github.com/ComputationalPhysiology/simcardems.git

or clone the repository and install it from there

git clone git@github.com:ComputationalPhysiology/simcardems.git
cd simcardems
python3 -m pip install .

Development installation

Developers should use editable install, adding the appropriate option -e to the previous pip install commands:

python -m pip install -e ".[dev]"

You should also install the pre-commit hook that comes with the package

pre-commit install

which will run a set of tests on the code that you commit to the repo. Note that linters and formatters will run in the CI system.