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).