This guide is intended to get new developers started with contributing to diffsims.
Many potential contributors will be scientists with much expert knowledge but potentially little experience with open-source code development. This guide is primarily aimed at this audience, helping to reduce the barrier to contribution.
We have a Code of Conduct that must be honoured by contributors.
Start using diffsims#
The best way to start understanding how diffsims works is to use it.
For developing the code the home of diffsims is on GitHub and you’ll see that a lot of this guide boils down to using that platform well. so visit the following link and poke around the code, issues, and pull requests (PRs): diffsims on GitHub.
It’s probably also worth visiting the GitHub guides to get a feel for the terminology.
In brief, to give you a hint on the terminology to search for, the contribution pattern is:
Setup git/GitHub if you don’t have it.
Fork diffsims on GitHub.
Checkout your fork on your local machine.
Create a new branch locally where you will make your changes.
Push the local changes to your own github fork.
Create a PR to the official diffsims repository.
Note: You cannot mess up the main diffsims project. So when you’re starting out be confident to play, get it wrong, and if it all goes wrong you can always get a fresh install of diffsims!
PS: If you choose to develop in Windows/Mac you may find the Github Desktop useful.
Open source projects are all about community - we put in much effort to make good tools available to all and most people are happy to help others start out. Everyone had to start at some point and the philosophy of these projects centers around the fact that we can do better by working together.
Much of the conversation happens in ‘public’ using the ‘issues’ pages on GitHub – doing things in public can be scary but it ensures that issues are identified and logged until dealt with. This is also a good place to make a proposal for some new feature or tool that you want to work on.
Good coding practice#
The most important aspects of good coding practice are: (1) to work in manageable branches, (2) develop a good code style, (3) write tests for new functions, and (4) document what the code does. Tips on these points are provided below.
Use git to work in manageable branches#
Git is an open source “version control” system that enables you to can separate out your modifications to the code into many versions (called branches) and switch between them easily. Later you can choose which version you want to have integrated into diffsims.
You can learn all about Git here!
The most important thing is to separate your contributions so that each branch is a small advancement on the “master” code or on another branch.
Get the style right#
diffsims closely follows the Style Guide for Python Code - these are just some rules for consistency that you can read all about in the Python Style Guide.
Please run the latest version of black on your newly added and modified files prior to each PR.
Run and write tests#
All functionality in diffsims is tested via the pytest
framework. The tests reside in the
diffsims.tests module. Tests are short functions
that call functions in diffsims and compare resulting output values with known answers.
Good tests should depend on as few other features as possible so that when they break we
know exactly what caused it.
Install necessary dependencies to run the tests:
pip install --editable .[tests]
Some useful fixtures are available
To run the tests:
pytest --cov --pyargs diffsims
--cov flag makes coverage.py
print a nice report in the terminal. For an even nicer presentation, you can use
Then, you can open the created
htmlcov/index.html in the browser and inspect the
coverage in more detail.
Useful hints on testing:
When comparing integers, it’s fine to use
==. When comparing floats use something like assert
np.allclose(shifts, shifts_expected, atol=0.2).
@pytest.mark.parametrize()is a convenient decorator to test several parameters of the same function without having to write to much repetitive code, which is often error-prone. See pytest documentation for more details.
Build and write documentation#
Docstrings – written at the start of a function – give essential information about how it should be used, such as which arguments can be passed to it and what the syntax should be. The docstrings follow the NumPy specification, as shown in this example.
We use Sphinx for documenting functionality. Install necessary dependencies to build the documentation:
pip install -e .[doc]
Then, build the documentation from the
cd doc make html
The documentation’s HTML pages are built in the
doc/build/html directory from files
in the reStructuredText (reST)
plaintext markup language. They should be accessible in the browser by typing
file:///your-absolute/path/to/diffsims/doc/build/html/index.html in the address bar.
Continuous integration (CI)#
We use GitHub Actions to ensure that diffsims can be installed on Windows, macOS and Linux. After a successful installation, the CI server runs the tests. After the tests return no errors, code coverage is reported to Coveralls.
The Python programming language, for beginners.