Installation#

The page has information for installing openfe, installing software packages that integrate with openfe, and testing that your openfe installation is working.

openfe currently only works on POSIX system (macOS and UNIX/Linux). It is tested against Python 3.9 and 3.10.

Installing `openfe`#

When you install openfe through any of the methods described below, you will install both the core library and the command line interface (CLI).

Installation with `conda` (recommended)#

We recommend installing openfe with conda, because it provides easy installation of other tools, including molecular dynamics tools such as OpenMM and ambertools, which are needed by openfe. Conda can be installed either with the full Anaconda distribution, or with the smaller-footprint miniconda.

You can get openfe from the conda-forge channel. To install the most recent release in its own environment, use the commands

$ conda create -n openfe -c conda-forge openfe
$ conda activate openfe

That creates a separate environment for openfe that won’t interfere with other things you have installed. You will need to activate the openfe environment before using it in a new shell.

With that, you should be ready to use openfe!

Single file installer#

[COMING SOON!]

Developer install#

If you’re going to be developing for openfe, you will want an installation where your changes to the code are immediately reflected in the functionality. This is called a “developer” or “editable” installation.

Getting a developer installation for openfe first installing the requirements, and then creating the editable installation. We recommend doing that with conda using the following procedure:

First, clone the openfe repository, and switch into its root directory:

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

Next create a conda environment containing the requirements from the specification in that directory:

$ conda env create -f environment.yml

Then activate the openfe environment with:

$ conda activate openfe

Finally, create the editable installation:

$ python -m pip install -e .

Note the . at the end of that command, which indicates the current directory.

Optional dependencies#

Certain functionalities are only available if you also install other, optional packages.

perses tools: To use perses, you need to install perses and OpenEye, and you need a valid OpenEye license. To install both packages, use:
```
$ conda install -c conda-forge -c openeye perses openeye-toolkits
```

Testing your installation#

openfe has a thorough test suite, and running the test suite is a good start to troubleshooting any installation problems. The test suite requires pytest to run. You can install pytest with:

$ conda install -c conda-forge  pytest

Then you can run the test suite (from any directory) with the command:

$ pytest --pyargs openfe openfecli

The test suite contains several hundred individual tests. This will take a few minutes, and all tests should complete with status either passed, skipped, or xfailed (expected fail).