bbrc-pyxnat 1.6.4.post2

XNAT in Python

Where to get it

The source code is currently hosted on GitHub at: https://github.com/pyxnat/pyxnat

Binary installers for the latest released version are available at the Python package index. pyxnat can be installed using pip with the following command:

pip install pyxnat

Dependencies

• requests v2.20 or higher

• python-lxml v4.3.2 or higher recommended, earlier versions may work.

For development purposes:

• pytest v7.1 or higher

• coverage v3.6 or higher

See the full installation instructions for recommended and optional dependencies.

Installation from sources

To install pyxnat from source, from the pyxnat directory (same one where you found this file after cloning the git repo), execute:

python setup.py install

Documentation

The official documentation is hosted at: https://pyxnat.github.io/pyxnat

Running the test suite

Until v1.1 tests were exclusively performed on XNAT Central using a dedicated user account (nosetests). However, some tests could not run due to restricted permissions. In v1.1, tests were restructured to use two independent XNAT instances based on permission level.

A public XNAT instance (NITRC/IR) is used for most tests with read access, while tests requiring write permissions run against a local XNAT instance in a Docker container.

Running the test suite requires the following:

• pytest v7.1+

• coverage v3.6+

• docker v18+

A local Docker-powered XNAT instance can be set up using docker-compose and any available recipe. We recommend the one maintained by the XNAT team (xnat-docker-compose). Once the repository is cloned, run:

docker-compose up -d

After a couple of minutes, the XNAT instance should be up and running locally at http://localhost.

Finally run the tests from the root of the project:

pytest --cov pyxnat

See .github/workflows/ci.yml (used for CI) for the full test setup.

Building the documentation

Building the docs requires to have setuptools and sphinx (v2.0+) installed. Then run the command:

python setup.py build_sphinx

The docs are built in the build/sphinx/html folder.

Contribute to pyxnat

To contribute to pyxnat, first create an account on GitHub. Once this is done, fork the pyxnat repository to have you own repository, clone it using git clone on the computers where you want to work. Make changes in your clone, push them to your GitHub fork, test them on several computers and when you are happy with them, send a pull request to the main repository.

License

BSD 3