Installation

The latest release can be installed from PyPi using:

$ pip install topsbm

Install the development version from GitHub using:

$ pip install https://github.com/TopSBM/topsbm/archive/master.zip

or by cloning the source code:

$ git clone https://github.com/TopSBM/topsbm
$ cd topsbm
$ pip install .

Installing dependencies

topsbm requires graph-tool to already be installed, as it cannot be installed with pip.

A simple way to install graph-tool and its dependencies is to use conda:

$ conda install -c conda-forge -c flyem-forge scikit-learn graph-tool pygobject cairo gtk3

or simply:

$ git clone https://github.com/TopSBM/topsbm
$ cd topsbm
$ conda env create

Check your installation

Check the installation has worked with:

$ python -m topsbm.check_install

or run the full test suite:

$ pip install pytest
$ pytest --pyargs topsbm