Developer docs

Contributions in the form of bug reports or code are warmly welcomed. You can find the source code as well as an issue tracker on GitHub.

Development environment

Clone the source repository:

git clone git@github.com:psychoinformatics-de/inm-icf-utilities.git
cd inm-icf-utilities

Install development software requirements in a virtual environment:

# create and enter a new virtual environment (optional)
$ virtualenv --python=python3 ~/env/icf
$ . ~/env/icf/bin/activate
pip install -r requirements-devel.txt
pip install -r docs/requirements.txt

Running tests

This package uses pytest for integration testing, and a CI test suite runs in the source repository on GitHub automatically. As the tooling are meant to run on specific systems only, executing tests locally requires additional setup steps that likely make it infeasible unless your system are the ICF servers.

The requirements are local DICOM data (not distributed alongside this software) that matches the layout, naming scheme, and permission set that the ICF uses. In addition, it requires the icf-utils Singularity image (see Bundled utilities), which needs to be installed as icf-utils in /usr/bin. Code that achieves this setup can be found in .appveyor.yml.

If this is in place, set the environment variable INM_ICF_TEST_STUDIES to point to the directory with DICOM data, and execute integrations tests with:

pytest -s -v .

Bundled utilities

The INM-ICF utilities are distributed as a bundle in the form of a Singularity software container. This container is updated regularly and can be downloaded from ci.appveyor.com/api/projects/mih/inm-icf-utilities/artifacts/icf.sif. When testing changes to the INM-ICF-utilities, the Singularity image needs to be rebuilt with the changes included. Its recipe can be found under singularity/icf.def. The image can be rebuilt automatically using the Appveyor-based CI test suite. If only software dependencies change, an update is not triggered automatically but requires that the build cache is wiped.