Installing TopoStats

NB - The package is currently undergoing heavy revision and these installation instructions apply to installing and workin on the the dev branch.

Currently TopoStats should be installed from the git repository, ideally under a Python Virtual Environment (e.g. Miniconda).

git clone git@github.com:AFM-SPM/TopoStats.git
cd TopoStats
git checkout dev
pip install .

If you wish to make changes to the code then install in editable mode, i.e. pip install -e ..

If you wish to develop features or address an existing issue then you should create a branch from dev and work on that before committing your changes and creating a pull request. The suggested nomenclature for branches is your GitHub username followed by a slash, then the issue number and a short description, e.g. ns-rse/90-refactor-topostats.

Tests

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 develop and making 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]"
pytest