Installing pyAFQ

The pyAFQ software works (at least) on Python 3.7 and 3.8.

Installing the release version

The released version of the software is the one that is officially supported, and if you are getting started with pyAFQ, this is probably where you should get started

To install it, in a shell or command line, issue the following:

pip install pyAFQ

Installing the development version

The development version is probably less stable, but might include new features and fixes. There are two ways to install this version. The first uses pip:

pip install git+https://github.com/yeatmanlab/pyAFQ.git

The other requires that you clone the source code to your machine:

git clone https://github.com/yeatmanlab/pyAFQ.git

Then, change your working directory into the top-level directory of this repo and issue:

pip install -e .[dev,fury]

which will install pyAFQ locally in editible mode and include extensions.

Note

The project follows the standard github fork and pull request workflow. So if you plan on contributing to pyAFQ it is recommended that you fork the repository and issue pull requests.

See Contributing to pyAFQ

Note

It is also recommended that you utilize python virtual environment and package mangagement tools and begin with a clean environment.

Installing using Docker

pyAFQ automatically builds and pushes a Docker image with pyAFQ installed for every commit. The images can be found here: https://github.com/orgs/nrdg/packages/container/package/pyafq To pull an image, you can either pull the latest:

docker pull ghcr.io/nrdg/pyafq:latest

or specify the commit using its hash:

docker pull ghcr.io/nrdg/pyafq:41c03ce18fa2fd872ece9df72165e7d8d8f58baf

pyAFQ also automatically builds and pushes a Docker image with pyAFQ and QSIprep (https://qsiprep.readthedocs.io/en/latest/) installed for every commit to master. This image may be useful if you want an all-in-one image for pre-processing and tractometry. You can pull the latest of this image or use a specific commit as well:

docker pull ghcr.io/nrdg/afqsi:latest