Installing PyChaste

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

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


Trying to install in an existing environment may fail if it already has conflicting dependencies installed!

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

Clone the PyChaste repository into the Chaste projects directory:

git clone --recursive /path/to/Chaste/projects/PyChaste


--recursive is important for retrieving git submodules. The build will fail without it!

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 .