Contributing

Contributing to GRiD

First off, thanks for taking the time to contribute! ❤️

All types of contributions are encouraged and valued. See the Table of Contents for different ways to help and details about how this project handles them. Please make sure to read the relevant section before making your contribution. It will make it a lot easier for us maintainers and smooth out the experience for all involved. The community looks forward to your contributions. 🎉

And if you like the project, but just don’t have time to contribute, that’s fine. There are other easy ways to support the project and show your appreciation, which we would also be very happy about:

  • Star the project

  • Tweet about it

  • Refer this project in your project’s readme

  • Mention the project at local meetups and tell your friends/colleagues

Table of Contents

Code of Conduct

This project and everyone participating in it is governed by the GRiD Code of Conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to Zachary Caterer.

I Have a Question

If you want to ask a question, we assume that you have read the available Documentation.

Before you ask a question, it is best to search for existing Issues that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first.

If you then still feel the need to ask a question and need clarification, we recommend the following:

  • Open an Issue.

  • Provide as much context as you can about what you’re running into.

  • Provide project and platform versions (nodejs, npm, etc), depending on what seems relevant.

We will then take care of the issue as soon as possible.

I Want To Contribute

When contributing to this project, you must agree that you have authored 100% of the content, that you have the necessary rights to the content and that the content you contribute may be provided under the project licence.

Reporting Bugs

Before Submitting a Bug Report

A good bug report shouldn’t leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible.

  • Make sure that you are using the latest version.

  • Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the documentation. If you are looking for support, you might want to check this section).

  • To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the bug tracker.

  • Also make sure to search the internet (including Stack Overflow) to see if users outside of the GitHub community have discussed the issue.

  • Collect information about the bug:

  • Stack trace (Traceback)

  • OS, Platform and Version (Windows, Linux, macOS, x86, ARM)

  • Version of the interpreter, compiler, SDK, runtime environment, package manager, depending on what seems relevant.

  • Possibly your input and the output

  • Can you reliably reproduce the issue? And can you also reproduce it with older versions?

How Do I Submit a Good Bug Report?

You must never report security related issues, vulnerabilities or bugs including sensitive information to the issue tracker, or elsewhere in public. Instead sensitive bugs must be sent by email to Zachary Caterer.

We use GitHub issues to track bugs and errors. If you run into an issue with the project:

  • Open an Issue. (Since we can’t be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.)

  • Explain the behavior you would expect and the actual behavior.

  • Please provide as much context as possible and describe the reproduction steps that someone else can follow to recreate the issue on their own. This usually includes your code. For good bug reports you should isolate the problem and create a reduced test case.

  • Provide the information you collected in the previous section.

Once it’s filed:

  • The project team will label the issue accordingly.

  • A team member will try to reproduce the issue with your provided steps. If there are no reproduction steps or no obvious way to reproduce the issue, the team will ask you for those steps and mark the issue as needs-repro. Bugs with the needs-repro tag will not be addressed until they are reproduced.

  • If the team is able to reproduce the issue, it will be marked needs-fix, as well as possibly other tags (such as critical), and the issue will be left to be implemented by someone.

Suggesting Enhancements

This section guides you through submitting an enhancement suggestion for GRiD, including completely new features and minor improvements to existing functionality. Following these guidelines will help maintainers and the community to understand your suggestion and find related suggestions.

Before Submitting an Enhancement

  • Make sure that you are using the latest version.

  • Read the documentation carefully and find out if the functionality is already covered, maybe by an individual configuration.

  • Perform a search to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one.

  • Find out whether your idea fits with the scope and aims of the project. It’s up to you to make a strong case to convince the project’s developers of the merits of this feature. Keep in mind that we want features that will be useful to the majority of our users and not just a small subset. If you’re just targeting a minority of users, consider writing an add-on/plugin library.

How Do I Submit a Good Enhancement Suggestion?

Enhancement suggestions are tracked as GitHub issues.

  • Use a clear and descriptive title for the issue to identify the suggestion.

  • Provide a step-by-step description of the suggested enhancement in as many details as possible.

  • Describe the current behavior and explain which behavior you expected to see instead and why. At this point you can also tell which alternatives do not work for you.

  • You may want to include screenshots or screen recordings which help you demonstrate the steps or point out the part which the suggestion is related to. You can use LICEcap to record GIFs on macOS and Windows, and the built-in screen recorder in GNOME or SimpleScreenRecorder on Linux.

  • Explain why this enhancement would be useful to most GRiD users. You may also want to point out the other projects that solved it better and which could serve as inspiration.

Your First Code Contribution

We’re thrilled you’re interested in contributing to GRiD 🎉

If this is your first contribution, here’s how to get started:

1. Set up your local environment
git clone https://github.com/caterer-z-t/GRiD.git
cd GRiD
conda create -n grid-dev python=3.11
conda activate grid-dev
pip install -e ".[dev]"

This installs GRiD in editable mode with development dependencies (testing, linting, docs).

2. Explore the project structure

The grid/ directory contains all source code. Each module corresponds to a pipeline component. Docs are under docs/, and tests are under tests/.

3. Run the test suite

Before making any code changes, confirm your setup works:

pytest --maxfail=1 --disable-warnings -q
4. Create a new branch
git checkout -b feat/your-feature-name
5. Implement your change

Follow the Styleguides below for consistency.

6. Commit and push
git add .
git commit -m "feat: add normalization helper for mosdepth"
git push origin feat/your-feature-name
7. Submit a Pull Request (PR)

Once your code is ready, open a PR to the main branch. Include:

  • A clear summary of the change

  • Tests (if applicable)

  • Updates to docs if functionality changed

A maintainer will review your PR and suggest revisions if needed.

Improving The Documentation

Good documentation is key to GRiD’s usability! 🧠

You can contribute by:

  • Fixing typos or improving clarity

  • Adding docstrings to functions or CLI commands

  • Expanding tutorials or examples

  • Adding usage screenshots or visualizations

To build the documentation locally:

cd GRiD
make -C docs html

Then open docs/build/html/index.html in your browser to preview.

To add a new page:

  • Create a .md file in docs/source/

  • Add it to index.rst or the relevant toctree

  • Use MyST markdown syntax (compatible with Sphinx)

Example page header:

(my-new-page)=
# My New Page Title

Styleguides

We maintain a consistent, readable, and clean codebase. Follow these guidelines when writing code or docs.

Python Code Style

  • Follow PEP 8

  • Use 4 spaces per indent, no tabs

  • Prefer descriptive variable names (sample_id, not sid)

  • Functions should be short and focused on one task

Use pre-commit hooks:

pre-commit install
pre-commit run --all-files

Lint and format:

black grid/
isort grid/
flake8 grid/
mypy grid/

Docstring Style

Use Google-style or NumPy-style docstrings.

Example:

def normalize_depth(values: list[float], min_depth: int = 10) -> list[float]:
    """Normalize coverage depth values.

    Args:
        values (list[float]): Coverage depth values.
        min_depth (int): Minimum threshold for normalization.

    Returns:
        list[float]: Normalized depth values.
    """

Commit Messages

We follow the Conventional Commits convention:

Format:
<type>(optional-scope): <description>
Examples:

  • feat(cli): add –dry-run option

  • fix(normalization): handle zero-coverage edge case

  • docs(readme): update installation section

Types:

  • feat: new feature

  • fix: bug fix

  • docs: documentation only

  • style: formatting or linting

  • refactor: code change that neither fixes a bug nor adds a feature

  • test: adding or updating tests

  • chore: maintenance tasks

Join The Project Team

We’re always excited to collaborate with others interested in genomics, pipelines, or bioinformatics tooling!

Ways to get involved:

  • Contribute code regularly → become a core contributor

  • Help triage GitHub issues

  • Review pull requests

  • Write or maintain documentation

  • Improve CI/CD or tests

If you’d like to join the core team:

  • Contribute consistently for a few PRs

  • Reach out via a GitHub discussion or issue

  • A maintainer will schedule a quick chat to discuss access and responsibilities

Attribution

This guide is based on the contributing.md!