Developer Introduction¶

Contributions to ProbNum are very welcome. Before getting started make sure to read the following guidelines.

All contributions to ProbNum should be made via pull requests (PR) to the master branch on GitHub. Some suggestions for a good PR are:

implements or fixes one functionality;
includes tests and appropriate documentation; and
makes minimal changes to the interface and core codebase.

If you would like to contribute but are unsure how, then writing examples, documentation or working on open issues are a good way to start. See the developer guides for detailed instructions.

Getting Started¶

Begin by forking the repository on GitHub and cloning your fork to a local machine. Next, create a new branch in your forked repository describing the feature you would like to implement. You can now get started writing code in your new branch. Make sure to keep the following best practices regarding code quality in mind.

Code Quality¶

Code quality is an essential component in a collaborative open-source project.

Make sure to observe good coding practice.
Keep dependencies to a minimum.
All code should be covered by tests within the unittest framework.
Documentation of code is essential. ProbNum uses the NumPy docstring format.
Code should be formatted with *Black* and follow the internal style guide. For more thorough Python code style guides we refer to PEP 8 and to the *Black* code style.

For all of the above the existing ProbNum code is a good initial reference point.

Using Tox¶

Probnum uses tox in its continuous integration (CI) pipeline to run tests, build documentation, check code formatting and code quality. Under the hood, tox builds virtual environments following the specifications in ./tox.ini in order to run tests across multiple python versions, while making sure that all the necessary dependencies are installed. Using tox unifies the local development process with CI, such that local test results should match the outcomes of Travis’s builds more closely. This ensures that your pull request can be merged seamlessly into ProbNum’s codebase.

Install tox from the Python Package Index (PyPI) via

pip install -U tox

Once tox and the required external tools below are installed, you can run tests and build the documentation locally by simply calling

tox

Note, to reduce runtime tox caches and reuses the virtual environment it creates the first time you run the command. If you are frequently switching between branches or adjusting the build configuration make sure to force recreation of the virtual environment via tox -r, if you experience unexpected tox failures.

Word of caution: Running tox runs all environments as specified in tox.ini, thus potentially running tests across many different Python versions. To run the full test suite make sure that you have all specified Python versions installed. Alternatively, you can run a single specific environment through tox -e <env>, e.g. tox -e py36 to run tests with Python 3.6 or tox -e docs to just build the documentation.

External Tools¶

Building the documentation locally requires additional packages (e.g. for inheritance diagrams), which can be found in .travis.yml. These packages are currently:

pandoc: In Ubuntu, install via sudo apt install pandoc
graphviz: In Ubuntu, install via sudo apt install graphviz

Advanced Developer Setup¶

For regular contributors to ProbNum we provide a configuration file .pre-commit-config.yaml with useful pre-commit hooks. These allow the automatic identification of simple issues in a commit, e.g. inconsistent code formatting. They are executed automatically whenever git commit is executed. This way one can avoid common problems in a pull request which prevent an automatic merge into the master branch on GitHub. To set up ProbNum’s pre-commit hooks simply install pre-commit by executing

pip install pre-commit

and install the configuration script via

pre-commit install

in the probnum folder.

Testing¶

We use unittest for testing and aim to cover as much code with tests as possible. Make sure to always add tests for newly implemented code. To run the test suite on your machine you have multiple options:

Full test suite with tox: Run the full suite across different Python versions with
```
tox
```
Single environment with tox: Run tests for a single Python environment, e.g. for Python 3.6
```
tox -e py36
```
pytest: Run tests directly in your local environment by calling
```
pytest
```

Code coverage of the tests is reported via codecov.

Documentation¶

ProbNum’s documentation is created with Sphinx and automatically built and hosted by ReadTheDocs for stable releases and the latest (master branch) version.

You can build the documentation locally via

tox -e docs

This creates a static web page under ./docs/_build/html/ which you can view in your browser by opening ./docs/_build/html/intro.html.

Alternatively, if you want to build the docs in your current environment you can manually execute

cd docs
make clean
make html

Continuous Integration¶

ProbNum uses Travis CI for continuous integration. For every pull request and every commit Travis builds the project and runs the test suite (through tox), to make sure that no breaking changes are introduced by mistake. Travis also automatically triggers a build of ProbNum’s documentation. Changes to Travis can be made through the .travis.yml file, as well as through tox.ini since Travis relies on tox for both testing and building the documentation. ProbNum also uses GitHub Actions to verify that all pushes and pull requests are compliant with the *Black* code style.