Installation

Prerequisites

Make sure you have at least Python 3.7 installed. Spateo does not officially support earlier Python versions.

Installation

Spateo can be installed either by downloading a release uploaded to the Python Package Index (PyPI), or the most up-to-date version directly from our GitHub repository.

PyPI

The following command will download and install the most recent release of Spateo.

pip install spateo-release

MPI

The cell-cell interaction modeling framework is dependent on the mpi4py package and a working MPI implementation. This is not automatically installed on install of the package. conda can be used to install both. Within the same environment where spateo is installed (or where spateo will be installed),

conda install mpi4py

This will simultaneously install an MPI implementation based on your computer system (OpenMPI for MacOS or Linux systems, MPICH/MS-MPI for Windows). To check whether the MPI implementation is successfully installed and on your path, run the mpiexec command.

GitHub

To have access to the most up-to-date version (which may include features not yet in the PyPI version), Spateo can be installed directly from the main branch of our GitHub repository.

pip install git+https://github.com/aristoteleo/spateo-release

To install Spateo from a specific GitHub branch,

pip install git+https://github.com/aristoteleo/spateo-release@{branch}

where {branch} is the branch name.

Known Issues and Fixes

There sometimes may be issues reading datasets from AnnData objects. To remedy this, manually install the following package versions into the environment that Spateo is contained in (if these versions are not already installed):

pip install h5py==3.7.0
pip install anndata==0.8.0

Development

If you are interested in contributing to Spateo, please read Contributing.