Testing nipype

In order to ensure the stability of each release of Nipype, the project uses two continuous integration services: CircleCI and Travis CI. If both batteries of tests are passing, the following badges should be shown in green color:

https://travis-ci.org/nipy/nipype.png?branch=master https://circleci.com/gh/nipy/nipype/tree/master.svg?style=svg

Installation for developers

To check out the latest development version:

git clone https://github.com/nipy/nipype.git

After cloning:

cd nipype
pip install -r requirements.txt
pip install -e .[dev]

Test implementation

Nipype testing framework is built upon pytest.

After installation in developer mode, the tests can be run with the following command at the root folder of the project

pytest -v --doctest-modules nipype

A successful test run should complete in 10-30 minutes and end with something like:

2445 passed, 41 skipped, 7 xfailed in 1277.66 seconds

No test should fail (unless you’re missing a dependency). If the SUBJECTS_DIR` environment variable is not set, some FreeSurfer related tests will fail. If any of the tests failed, please report them on our bug tracker.

On Debian systems with a local copy of MATLAB installed, set the following environment variable before running tests:

export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB

where $pathtomatlabdir is the path to your matlab installation and $platform is the directory referring to x86 or x64 installations (typically glnxa64 on 64-bit installations).

Skipped tests

Nipype will skip some tests depending on the currently available software and data dependencies. Installing software dependencies and downloading the necessary data will reduce the number of skipped tests.

A few tests in Nipype make use of some images distributed within the FSL course data. This reduced version of the package can be downloaded here. To enable the tests depending on these data, just unpack the targz file and set the FSL_COURSE_DATA environment variable to point to that folder. Note, that the test execution time can increase significantly with these additional tests.

Xfailed tests

Some tests are expect to fail until the code will be changed or for other reasons.

Testing Nipype using Docker

Nipype is tested inside Docker containers and users can use nipype images to test local versions. First, install the Docker Engine. Nipype has one base docker image called nipype/nipype:base, that contains several useful tools (FreeSurfer, AFNI, FSL, ANTs, etc.), and an additional test image for Python 3.8:

Users can pull the nipype image for Python 3.8 as follows:

docker pull nipype/nipype:py38

In order to test a local version of nipype you can run test within container as follows:

docker run -it -v $PWD:/src/nipype --rm nipype/nipype:py38 py.test -v --doctest-modules /src/nipype/nipype

Additional comments

If the project is tested both on your local OS and within a Docker container, you might have to remove all __pycache__ directories before switching between your OS and a container.