This section explains the basics for developers who wish to contribute to the TomoPy project.
The project is maintained on GitHub, which is a version control and a collaboration platform for software developers. To start first register on GitHub and fork the TomoPy repository by clicking the Fork button in the header of the TomoPy repository:
This creates a copy of the project in your personal GitHub space. The next thing you want to do is to clone it to your local machine. You can do this by clicking the Clone in Desktop button in the bottom of the right hand side bar:
This will launch the GitHub desktop application (available for both Mac and Win) and ask you where you want to save it. Select a location in your computer and feel comfortable with making modifications in the code.
To build and run TomoPy, you will need to install at least the dependencies
env/requirements-all.txt plus additional dependencies based
on your build environment. For example, installing requirements for building
the Python 2.7 version on Unix can be accomplished as follows:
$ conda install --file requirements-all.txt --file requirements-27.txt --file requirements-unix-build.txt
After navigating to inside the tomopy directory, you can install TomoPy by running the install script in the typical Python way:
$ python setup.py install
TomoPy has a suite of Python unit tests that live in the
where they follow the same tree structure as the packages under
These are automatically run by TravisCI when you make a pull request
(See below for how to do that). You can run them manually using pytest,
or whichever python test runner you prefer. To make it easier to run tests
on the changes you make to the code, it is recommended that you install TomoPy
in development mode. (python setup.py develop)
The pytest test runner, is available through pip or anaconda.
To run the tests open a terminal, navigate to your project folder,
To run sections of tests, pass py.test a
directory or filepath, as in
py.test test/test_recon or
When writing tests, at minimum we try to check all function returns with synthetic data, together with some dimension, type, etc. Writing tests is highly encouraged!
We try to keep our code consistent and readable. So, please keep in mind the following style and syntax guidance before you start coding.
First of all the code should be well documented, easy to understand, and integrate well into the rest of the project. For example, when you are writing a new function always describe the purpose and the parameters:
def my_awesome_func(a, b): """ Adds two numbers. Parameters ---------- a : scalar (float) First number to add b : scalar (float) Second number to add Returns ------- output : scalar (float) Added value """ return a+b
We follow the X.Y.Z (Major.Minor.Patch) semantic for package versioning. The version should be updated before each pull request accordingly. The patch number is incremented for minor changes and bug fixes which do not change the software’s API. The minor version is incremented for releases which add new, but backward-compatible, API features, and the major version is incremented for API changes which are not backward-compatible. For example, software which relies on version 2.1.5 of an API is compatible with version 2.2.3, but not necessarily with 3.2.4.
After making some changes in the code, you may want to take a snapshot of the edits you made. That’s when you make a commit. To do this, launch the GitHub desktop application and it should provide you all the changes in your code since your last commit. Write a brief Summary and Description about the changes you made and click the Commit button:
You can continue to make changes, add modules, write your own functions, and take more Commit snapshots of your code writing process.
Once you feel that the functionality you added would benefit the community, then you should consider contributing back to the TomoPy project. You will need to push your local commits to GitHub, then go to your online GitHub repository of the project and click on the green button to compare, review, and create a pull request.
After clicking on this button, you are presented with a review page where you can get a high-level overview of what exactly has changed between your forked branch and the original TomoPy repository. When you’re ready to submit your pull request, click Create pull request:
Clicking on Create pull request sends you to a discussion page, where you can enter a title and optional description. It’s important to provide as much useful information and a rationale for why you’re making this Pull Request in the first place.
When you’re ready typing out your heartfelt argument, click on Send pull request. You’re done!