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CONTRIBUTING.md

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Contributing

(adopted from graspologic)

This project welcomes contributions and suggestions and has adopted the Neurodata Code of Conduct.

Issue Submission (Bug or Feature)

We use GitHub issues to track all bugs and feature requests; feel free to open an issue if you have found a bug or wish to see a feature implemented. Please also feel free to tag one of the core contributors (see our Roles page).

In case you experience issues using this package, do not hesitate to submit a ticket to our Issue Tracker. You are also welcome to post feature requests or pull requests.

It is recommended to check that your issue complies with the following rules before submitting:

How to create an actionable bug report

When you submit an issue to Github, please do your best to follow these guidelines! This will make it a lot faster for us to respond to your issue.

  • The ideal bug report contains a short reproducible code snippet, this way anyone can try to reproduce the bug easily (see this for more details). If your snippet is longer than around 50 lines, please link to a gist or a github repo.

  • If not feasible to include a reproducible snippet, please be specific about what tests and/or functions are involved and the shape of the data.

  • If an exception is raised, please provide the full traceback.

  • Please include your operating system type and version number, as well as your Python and hyppo versions. This information can be found by running the following code snippet:

    import platform; print(platform.platform())
import sys; print(f"Python {sys.version}")
import hyppo; print(f"hyppo {hyppo.__version__}")

  • Please ensure all code snippets and error messages are formatted in appropriate code blocks. See Creating and highlighting code blocks for more details.

Contributing Code

Git workflow

The preferred workflow for contributing to hyppo is to fork the main repository on GitHub, clone, and develop on a branch. Steps:

  1. Fork the project repository by clicking on the ‘Fork’ button near the top right of the page. This creates a copy of the code under your GitHub user account. For more details on how to fork a repository see this guide.

  2. Clone your fork of the hyppo repo from your GitHub account to your local disk:

    git clone [email protected]:YourGithubAccount/hyppo.git
cd hyppo

  3. Create a feature branch to hold your development changes:

    git checkout -b my-feature

    Always use a feature branch. Pull requests directly to either dev or main will be rejected until you create a feature branch based on dev.

  4. Develop the feature on your feature branch. Add changed files using git add and then git commit files:

    git add modified_files
git commit

    After making all local changes, you will want to push your changes to your fork:

    git push -u origin my-feature

Pull Request Checklist

We recommended that your contribution complies with the following rules before you submit a pull request:

  • Follow the coding-guidelines.

  • Give your pull request a helpful title that summarizes what your contribution does.

  • Link your pull request to the issue (see: closing keywords for an easy way of linking your issue)

  • All public methods should have informative docstrings with sample usage presented as doctests when appropriate.

  • At least one paragraph of narrative documentation with links to references in the literature (with PDF links when possible) and the example.

  • If your feature is complex enough that a doctest is insufficient to fully showcase the utility, consider creating a Jupyter notebook to illustrate use instead

  • All functions and classes must have unit tests. These should include, at the very least, type checking and ensuring correct computation/outputs.

  • All code should be automatically formatted by black. You can run this formatter by calling:

    pip install black
black path/to/your_module.py

  • Ensure all tests are passing locally using pytest. Install the necessary packages by:

    pip install pytest pytest-cov
pytest

  • If you are proposing adding a new module, make sure you are inheriting from the appropriate base class. See the documentation for the appropriate class.

Guidelines

Coding Guidelines

Uniformly formatted code makes it easier to share code ownership. hyppo package closely follows the official Python guidelines detailed in PEP8 that detail how code should be formatted and indented. Please read it and follow it.

Docstring Guidelines

Properly formatted docstrings are required for documentation generation by Sphinx. The hyppo package closely follows the numpydoc guidelines. Please read and follow the numpydoc guidelines. Refer to the example.py provided by numpydoc.