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CONTRIBUTING.md

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Contributor guide

The source code for NiftyNet is released via GitHub.

Submitting bug reports and feature requests

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

Submitting merge requests

All merge requests should be submitted via GitHub pull request.

Please make sure you have read the following subsections before submitting a merge request.

1. 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.

2. 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/
sh run_test.sh

3. Creating GitHub pull requests

  1. [on GitHub] Sign up/in GitHub.com (The rest steps assume GitHub user id: nntestuser).

  2. [on GitHub] Go to https://github.com/NifTK/NiftyNet, click the 'Fork' button.

  3. Download the repo:

    • git clone https://github.com/nntestuser/NiftyNet.git

  4. Synchronise your repo with the dev branch of https://github.com/NifTK/NiftyNet:

    • git remote add upstream git@github.com:NifTK/NiftyNet.git
    • git pull upstream dev

  5. Make commits, test changes locally, and push to nntestuser's repo:

    • git push github dev

    (This step assumes github is a remote name pointing at git@github.com:nntestuser/NiftyNet.git;

    set this with command: git remote add github git@github.com:nntestuser/NiftyNet.git;

    confirm this with command: git remote -v)

  6. [on GitHub] Create a pull request by clicking the 'pull request' button.

Writing unit tests

This section describes steps to create unit tests for NiftyNet.

1. Determine which module to test

Go to Gitlab pipeline page, click on the latest successful testing pipeline and check the test coverage report at the bottom of the test 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]_test.py

Create a unit test Python script with file name ends with _test.py. 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]_test.py 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
    # https://www.tensorflow.org/versions/r0.12/api_docs/python/test/unit_tests

if __name__ == "__main__":
    # so that we can run this test independently
    tf.test.main()

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]_test.py

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):
        pass
    # preferably using self.assert* functions from tensorflow unit tests API
    # https://www.tensorflow.org/versions/r0.12/api_docs/python/test/unit_tests
...

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

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

Thanks for your contributions :)

NiftyNet admin tasks

Making a release

NiftyNet versions are numbered following Semantic Versioning (semver). After adding notes for the current release to the NiftyNet changelog, the current release should be tagged with a PEP440-compliant semver number preceded by the letter v (for "version").

Publishing a NiftyNet pip installer on PyPI

Making NiftyNet available to the world via a simple pip install niftynet requires publishing the created wheel on the Python Package Index (PyPI). BUT PLEASE TAKE YOUR TIME TO READ THE NOTES BELOW BEFORE PROCEEDING:

  • PyPI is very tightly coupled to package versions. That means, once a wheel tagged e.g. as version 1.0.1 has been published, it is final. In other words, you cannot change your source code, bundle it again using the same version and re-submit to PyPI as the "updated" version 1.0.1.
  • Please consider submitting the bundled wheel to the PyPI test site (see the NiftyNet test page) to assess the visual appearance of the PyPI page before publishing on the actual PyPI.

To actually publish the bundled wheel on PyPI, you will need to run the twine upload command e.g. twine upload dist/NiftyNet-0.2.0-py2.py3-none-any.whl - this will of course work only if you have set the corresponding PyPI account credentials.

Merging GitHub pull requests

Please follow the steps below for merging pull requests on GitHub:

  1. [on GitHub] Review the pull request, and ask for changes if needed.

  2. Create a new branch off dev of https://github.com/NifTK/NiftyNet with a name representative of the pull request. For instance, if the pull request on GitHub was numbered 7 (assuming upstream is set to git@github.com:NifTK/NiftyNet.git):

    • git checkout -b merging-github-pr-7 upstream/dev

  3. Download the contributing commits and merge to merging-pr-7. For instance, if the pull request is from nntestuser's bug-fixing-branch:

    • git pull https://github.com/nntestuser/NiftyNet bug-fixing-branch

  4. Review and test locally.

  5. Push the commits to branch merging-github-pr-7 of remote repository https://github.com/NifTK/NiftyNet:

    • git push upstream merging-github-pr-7

  6. [on GitHub] Check CI tests results (Gitlab.com; quick tests only).

  7. [on GitHub] Create a new pull request from merging-github-pr-7 to dev.

  8. [on GitHub] Accept the new pull request onto dev.

  9. [on GitHub] Check CI tests results (Gitlab.com; full tests for dev)

At the moment only pushes (instead of pull requests from forks) to GitHub trigger GitLab's CI runner, a feature request has been submitted -- will simplify the workflow once resolved (more info).

Enhancing the pip installer

Adding a new command callable from a pip-installed NiftyNet

This requires added a new console_scripts entry point in the setup.py file. For a practical example see how the net_segment CLI command is implemented.

Deprecated instructions

Bundling a pip installer

The NiftyNet pip installer gets bundled automatically for Git tags starting with a v (for "version") pushed to CMICLab. The wheel version is determined automatically as part of this process. To see how this is done in practice, please go to the pip-camera-ready section of .gitlab-ci.yml (and see the result in this build log - esp. the last few lines lines, which show where the pip installer can be found on the build server).

In particular, bundling a pip installer boils down to running the command python setup.py bdist_wheel in the top-level directory. This creates a wheel binary package in a newly created dist directory, e.g. dist/NiftyNet-0.2.0-py2.py3-none-any.whl.

If you have made changes to the pip installer, please test these. For instance if you have added a new CLI entry point (i.e. a new "command" - also see the respective section below), make sure you include the appropriate tests in the GitLab CI configuration. For an example how to do this please see lines 223 to 270 in the .gitlab-ci.yml file.