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