Installing pyAFQ#
The pyAFQ software works (at least) on Python 3.9 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,afqbrowser,plot]
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.
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: orgs/nrdg 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