Installation

Installation with mamba

gufe is available through conda-forge and can be installed with mamba (or conda):

$ mamba install -c conda-forge gufe

Optional Visualization Dependencies

gufe has optional software dependences which can be installed to visualize atom mappings. This dependences are optional to keep gufe lightweight when used purely for compute.

py3Dmol is used to create three dimensional views of atom mappings and can be installed with:

$ mamba install -c conda-forge py3dmol

ipywidgets is used to create a widget in a jupyter notebook to view atom mappings and can be installed with:

$ mamba install -c conda-forge ipywidgets

For an optimal installation experience we recommend installing the optional packages at the same time you install gufe:

$ mamba install -c conda-forge gufe py3dmol ipywidgets

While they can be installed after gufe is installed, we find that mamba has an easier time solving the environment when everything is installed at the same time.

Developer Installation

If you’re a developer, you will likely want to create a local editable installation.

  1. clone the repository:

$ git clone https://github.com/OpenFreeEnergy/gufe.git
$ cd gufe

  1. create and activate a new environment:

$ mamba create -f environment.yml
$ mamba activate gufe

  1. build an editable installation:

$ python -m pip install --no-deps -e .