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.. _dev_testing_nipype:
==============
Testing nipype
==============
In order to ensure the stability of each release of Nipype, the project uses two
continuous integration services: `CircleCI <https://circleci.com/gh/nipy/nipype/tree/master>`_
and `Travis CI <https://travis-ci.org/nipy/nipype>`_.
If both batteries of tests are passing, the following badges should be shown in green color:
.. image:: https://travis-ci.org/nipy/nipype.png?branch=master
:target: https://travis-ci.org/nipy/nipype
.. image:: https://circleci.com/gh/nipy/nipype/tree/master.svg?style=svg
:target: https://circleci.com/gh/nipy/nipype/tree/master
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 <http://doc.pytest.org/en/latest/>`_.
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
<http://github.com/nipy/nipype/issues>`_.
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
<http://fsl.fmrib.ox.ac.uk/fslcourse/>`_. This reduced version of the package can be downloaded `here
<https://files.osf.io/v1/resources/nefdp/providers/osfstorage/57f472cf9ad5a101f977ecfe>`_.
To enable the tests depending on these data, just unpack the targz file and set the :code:`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 <https://docs.docker.com/engine/installation/>`_.
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.
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