Contributor guide

Bug reports and feature requests

Bug reports and feature requests should be submitted by creating an issue on CMICLab or GitHub.

Merge requests

All merge requests should be submitted via CMICLab or GitHub’s new pull request. Please make sure you have read the following subsections before submitting a merge request.

Python style guide

Please follow the PEP8 Style Guide for Python Code. In particular (from the guide):

Please be consistent. If you’re editing code, take a few minutes to look at the code around you and determine its style. If they use spaces around all their arithmetic operators, you should too. If their comments have little boxes of hash marks around them, make your comments have little boxes of hash marks around them too.

Testing your changes

Please submit merge requests from your branch to the dev branch.

Before submitting a merge request, please make sure your branch passes all unit tests, by running:

cd NiftyNet/

Writing unit tests

This section describes steps to create unit tests for NiftyNet.

1. Which module to test

Go to Cmiclab pipeline page, click on the latest successful testing pipeline and check the test coverage report at the bottom of the test log, e.g. a coverage report is available at the last part of this log. The coverage report lists all untested files (with line numbers of specific statements) in the project.

2. File an issue

Create a new issue indicating that you’ll be working on the tests of a particular module.

To avoid duplicated effort, please check the issue list and make sure nobody is implementing the unit tests for that module at the moment. Also make sure the issue description is concise and has specific tasks.

3. Create [name]

Clone NiftyNet and create a dedicated branch (from dev) for the unit tests.

For Cmiclab users:

git clone
git checkout -b unit-test-for-xxx dev

For GitHub users, please fork the project to your workspace and create a branch.

Create a unit test Python script with file name ends with This file should be added to NiftyNet/tests/ directory. (CI runner will automatically pick up the script and run it with Python 2.7&3)

A minimal working template for [name] is:

# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function

import tensorflow as tf

class ModuleNameTest(tf.test.TestCase):
    def test_my_function(self):
        x = tf.constant(1.0)
        self.assertEqual(x.eval(), 1.0)
    # preferably using self.assert* functions from TensorFlow unit tests API

if __name__ == "__main__":
    # so that we can run this test independently

If the unit tests write files locally, please ensure it’s writing to NiftyNet/testing_data folder.

4. Run tests locally

In NiftyNet source code folder, run:

python -m tests.[name]

make sure the test works locally. The test should finish in a few seconds (using CPU). If it takes significantly longer, please set it as slow test in the file:

@unittest.skipIf(os.environ.get('QUICKTEST', "").lower() == "true", 'Skipping slow tests')
class ModuleNameTest(tf.test.TestCase):
    def test_my_function(self):
    # preferably using self.assert* functions from tensorflow unit tests API

5. Run all tests locally

Normally the newly created unit test should not depend on the outcome of the other unit tests. A Bash script is defined for running all quick tests to confirm this.

(In, wget and tar are used to automatically download and unzip testing data. This can be done manually.)

6. Send a merge request

After finishing the local tests, git-push the changes to a Cmiclab branch. This will trigger CI tests, which will run the unit tests on our test server with Ubuntu Linux + Python 2&3).

Please send a merge request with only relevant changes to a particular unit tests.

Thanks for your contributions :)