Installing PyChaste

There are a variety of methods 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.

Installing in a new environment is recommended. To create an environment named <env-name>:

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

To activate the newly created environment:

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 Chaste Docker image comes with PyChaste and Jupyter pre-installed. If you do not already have Docker installed, please follow the instructions in the Docker documentation.

With Docker installed, you can pull the Chaste Docker image and launch a PyChaste container:

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

You can open a Jupyter notebook by launching a web browser to http://localhost:8888.

Build from Source#

To build PyChaste from source, we first need to install Chaste dependencies. See the Chaste Install Guides for step-by-step instructions on how to do this.

PyChaste requires additional pre-installed dependencies: castxml, clang, matplotlib, mpi4py, numpy, petsc4py, xvfb, xvfbwrapper, and Python bindings for vtk.

To install these additional dependencies on Ubuntu 24.04, for example:

sudo apt-get install -y castxml clang python3-matplotlib python3-mpi4py \
  python3-numpy python3-petsc4py-real python3-vtk7 python3-xvfbwrapper xvfb

Optionally, activate a virtual environment for installing PyChaste (recommended). Use --system-site-packages for access to Python dependencies installed via apt in Ubuntu as above.

python3 -m venv --system-site-packages venv
source venv/bin/activate

Clone the Chaste repository.

git clone https://github.com/Chaste/Chaste.git
cd Chaste

Create a build folder and configure Chaste with the Chaste_ENABLE_PYCHASTE flag switched on:

mkdir build && cd build
cmake -DChaste_ENABLE_PYCHASTE=ON ..

Build PyChaste:

make -j4 pychaste

Finally, pip install the built package:

python3 -m pip install pychaste/package