Contributing Guide

Code of Conduct

This project and everyone participating in it is governed by our code of conduct guidelines. By participating, you are expected to uphold this code. Please report unacceptable behavior.

Types of Contributions

Did you find a bug? or Do you intend to add a new feature or change an existing one?

  • Submit issues and requests using our issue tracker

  • Ensure the feature or change was not already reported by searching on GitHub under HDMF Issues

  • If you are unable to find an open issue addressing the problem then open a new issue on the respective repository. Be sure to use our issue templates and include:

    • brief and descriptive title

    • clear description of the problem you are trying to solve. Describing the use case is often more important than proposing a specific solution. By describing the use case and problem you are trying to solve gives the development team community a better understanding for the reasons of changes and enables others to suggest solutions.

    • context providing as much relevant information as possible and if available a code sample or an executable test case demonstrating the expected behavior and/or problem.

  • Be sure to select the appropriate label (bug report or feature request) for your tickets so that they can be processed accordingly.

  • HDMF is currently being developed primarily by staff at scientific research institutions and industry, most of which work on many different research projects. Please be patient, if our development team is not able to respond immediately to your issues. In particular issues that belong to later project milestones may not be reviewed or processed until work on that milestone begins.

Did you write a patch that fixes a bug or implements a new feature?

See the Contributing Patches and Changes section below for details.

Did you fix whitespace, format code, or make a purely cosmetic patch in source code?

Source code changes that are purely cosmetic in nature and do not add anything substantial to the stability, functionality, or testability will generally not be accepted unless they have been approved beforehand. One of the main reasons is that there are a lot of hidden costs in addition to writing the code itself, and with the limited resources of the project, we need to optimize developer time. E.g,. someone needs to test and review PRs, backporting of bug fixes gets harder, it creates noise and pollutes the git repo and many other cost factors.

Do you have questions about HDMF?

See our hdmf-dev.github.io website for details.

Informal discussions between developers and users?

The https://nwb-users.slack.com slack is currently used for informal discussions between developers and users.

Contributing Patches and Changes

To contribute to HDMF you must submit your changes to the dev branch via a Pull Request.

From your local copy directory, use the following commands.

  1. First create a new branch to work on

$ git checkout -b <new_branch>

  1. Make your changes.

  2. Push your feature branch to origin (i.e. GitHub)

$ git push origin <new_branch>

  1. Once you have tested and finalized your changes, create a pull request targeting dev as the base branch. Be sure to use our pull request template and:

    • Ensure the PR description clearly describes the problem and solution.

    • Include the relevant issue number if applicable.

    • Before submitting, please ensure that: * The proposed changes include an addition to CHANGELOG.md describing your changes. To label the change with the PR number, you will have to first create the PR, then edit the CHANGELOG.md with the PR number, and push that change. * The code follows our coding style. This can be checked running ruff from the source directory.

    • NOTE: Contributed branches will be removed by the development team after the merge is complete and should, hence, not be used after the pull request is complete.

Style Guides

Python Code Style Guide

Before you create a Pull Request, make sure you are following the HDMF style guide. To check whether your code conforms to the HDMF style guide, simply run the ruff tool in the project’s root directory. ruff will also sort imports automatically and check against additional code style rules.

We also use ruff to sort python imports automatically and double-check that the codebase conforms to PEP8 standards, while using the codespell tool to check spelling.

ruff and codespell are installed when you follow the developer installation instructions. See Installing HDMF for Developers.

$ ruff check .
$ codespell

Pre-Commit

We encourage developers to use pre-commit tool to automatically process the codebase to follow the style guide, as well as identify issues before making a commit. See installation and operation instructions in the pre-commit documentation.

Git Commit Message Styleguide

  • Use the present tense (“Add feature” not “Added feature”)

  • The first should be short and descriptive.

  • Additional details may be included in further paragraphs.

  • If a commit fixes an issue, then include “Fix #X” where X is the number of the issue.

  • Reference relevant issues and pull requests liberally after the first line.

Documentation Styleguide

All documentations is written in reStructuredText (RST) using Sphinx.

Endorsement

Please do not take working with an organization (e.g., during a hackathon or via GitHub) as an endorsement of your work or your organization. It’s okay to say e.g., “We worked with XXXXX to advance science” but not e.g., “XXXXX supports our work on HDMF”.”