Installing PyChaste

There are three ways to get PyChaste running on your system:

• Using the Conda Package – supported on Linux.
• Using the Docker Image – supported on any platform.
• Building from Source – supported on Linux.

Conda Package#

The conda package installs several dependencies automatically. Please install mamba first, as dependency resolution can be quite slow with conda itself.

We recommend that you install in a new environment. To do this, run:

mamba create -n <env-name> -c pychaste -c conda-forge chaste

where <env-name> is the name of the new environment. To activate the environment, run:

conda activate <env-name>

Alternatively, you can install in an existing conda environment. With the environment activated, run:

mamba install -c pychaste -c conda-forge chaste

Optionally, you can install and launch a Jupyter notebook from the environment:

mamba install -c conda-forge jupyterlab
jupyter lab

Docker Image#

The docker image comes with PyChaste and Jupyter pre-installed. If you do not already have docker installed, please follow the instructions to get docker.

With docker installed, you can pull the image and launch a PyChaste container with the following command:

docker run -it --init --rm -p 8888:8888 chaste/pychaste

You can open a Jupyter notebook from the container by launching a web browser and going to the address http://localhost:8888.

Build from Source#

To build PyChaste from source, we first need to install Chaste. See the Chaste Install Guides for information on installing Chaste dependencies.

After installing the required dependencies, clone the Chaste repository:

git clone --recursive https://github.com/Chaste/Chaste.git

Clone the PyChaste repository into the Chaste projects directory:

git clone --recursive https://github.com/Chaste/PyChaste.git /path/to/Chaste/projects/PyChaste

From outside the source tree, create a build folder and generate the CMake configuration:

mkdir build && cd build
cmake /path/to/Chaste

To build PyChaste, run:

make -j4 chaste_project_PyChaste
make -j4 chaste_project_PyChaste_Python

Finally, pip install the built package with these commands:

cd /path/to/build/projects/PyChaste/python/chaste
pip install .