NB - If you have trouble installing TopoStats please do checkout the discussion for possible solutions. If your problem isn’t covered then please do not hesitate to ask a question.

TopoStats is a Python package designed to run at the command line. If you are using Microsoft Windows you should use Powershell. You may have Python installed on your system but should use a Python Virtual Environment such as Miniconda and install and use TopoStats under the Virtual Environment. The versions of Python supported are Python >=3.8 and so when creating your virtual environment you should specify this 3.8 as the minimum.

Setting up Conda#

Once you have downloaded and installed Miniconda you can create a virtual environment for installing TopoStats for installing and running TopoStats. We will call this environment topostats (specified with the --name topostats option) and use Python 3.10 (the option python=3.10). After creating it we can, as per the instructions printed out, activate the environment.

conda create --name topostats python=3.10
conda activate topostats

You are now ready to install TopoStats.

NB If you are using an Apple M1 Macbook then you need to install Anaconda >= 2022.05.

Installing TopoStats#

There are two options for installing TopoStats depending on your usage

  1. Python Package Index - appropriate if you are just using TopoStats and don’t need to dig into the code.

  2. Cloning the GitHub Repository - if you want to look at the code, contribute to it, debug errors or perhaps test a new feature before a release.

PyPI Installation#

After activating your topostats Conda environment you can install TopoStats from PyPI using the following command.

pip install topostats

This will install TopoStats under your virtual environment and the command topostats will be available at the command line. It has a number of sub-commands which can be displayed by invoking it without any options. You can upgrade topostats by using the --upgrade flag…

pip install --upgrade topostats

You can always install a specific version from PyPI

pip install topostats==2.0.0

For more information on using pip to install and manage packages please refer to the pip documentation.

Installing from GitHub#

You may wish to consider cloning and installing TopoStats from GitHub if…

  • You wish to try out new features that have been developed since the last release (if you find problems please create an issue).

  • If you have found an issue in a released version and want to see if it has been fixed in the unreleased version.

  • If you wish to develop and extend TopoStats with new features yourself.

There are two options to install from GitHub, which you use will depend on what you want to do.

  1. Using PyPI to install directly.

  2. Clone the repository and install from there.

If all you want to do is use the development version of TopoStats then you can use option 1. If you wish to change the underlying code you should use option 2.

Installing from GitHub using PyPI#

pip supports installing packages from GitHub. To install the main branch of TopoStats use the following in your Virtual Environment.

pip install git+

You can install any branch on GitHub by modifying the last argument (@main) to the branch you wish to install, e.g. @another_branch would install the another_branch (if it existed).

Cloning the Repository and installing#

If you do not have Git already installed please see Git. If you intend to contribute to the development of TopoStats please read through the contributing section.

If you are familiar with the command line then you can clone and install TopoStats with the following after activating your virtual environment. By installing in editable mode (with the -e flag) switching branches will make the branch available.

cd ~/where/to/clone
git clone
cd TopoStats
pip install -e .

If you plan to contribute to development by adding features or address an existing issue please refer to the contributing section and pay particular attention to the section about installing additional dependencies.

We include notebooks which show how to use different aspects of TopoStats. If you wish to try these out the Jupyter Noteooks then you can install the dependencies that are required from the cloned TopoStats repository using…

pip install ".[notebooks]"

Cloning Using GitKraken#

If you are using GitKraken you can clone the repository by selecting “Clone” and then “” and typing TopoStats into the box next to “Repository to Clone” and you should be presented with the option of selecting “TopoStats” from the AFM-SPM organisation. Once cloned follow the above instructions to install with pip under your virtual environment.


One of the major changes in the refactoring is the introduction of unit tests. These require certain packages to be installed which are not installed to your virtual environment by setuptools in the above steps. If you are intending to modify or contribute to the development of TopoStats or make changes to the code base you will likely want to be able to run the tests. Install the necessary dependencies to do so with…

cd TopoStats
git checkout dev
pip install ".[tests]"


Git is a version control system for managing software development and is required to be installed on your computer in order to clone the TopoStats repository. Instructions on installing Git can be found at Git Guides - install git.

A nice Graphical User Interface for working with Git is GitKraken which includes everything you need.