CONTRIBUTING.md

Contributing to AFQ-Insight

Welcome to the AFQ-Insight repository! We're excited you're here and want to contribute.

Imposter's syndrome disclaimer¹: We want your help. No, really.

There may be a little voice inside your head that is telling you that you're not ready to be an open-source contributor; that your skills aren't nearly good enough to contribute. What could you possibly offer a project like this one?

We assure you - the little voice in your head is wrong. If you can write code at all, you can contribute code to open-source. Contributing to open-source projects is a fantastic way to advance one's coding skills. Writing perfect code isn't the measure of a good developer (that would disqualify all of us!); it's trying to create something, making mistakes, and learning from those mistakes. That's how we all improve, and we are happy to help others learn.

Being an open-source contributor doesn't just mean writing code, either. You can help out by writing documentation, tests, or even giving feedback about the project (and yes - that includes giving feedback about the contribution process). Some of these contributions may be the most valuable to the project as a whole, because you're coming to the project with fresh eyes, so you can see the errors and assumptions that seasoned contributors have glossed over.

Practical guide to submitting your contribution

These guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know by opening an issue!

Before you start, you'll need to set up a free GitHub account and sign in. Here are some instructions.

Already know what you're looking for in this guide? Jump to the following sections:

• Joining the conversation
• Contributing through Github
• Understanding issues
• Making a change
• Structuring contributions
• Licensing
• Recognizing contributors

Joining the conversation

AFQ-Insight is primarily maintained by a collaborative research group. But we maintain this software as an open project. This means that we welcome contributions from people outside our group and we make sure to give contributors from outside our group credit in presentations of the work. In other words, we're excited to have you join! Most of our discussions will take place on open issues. We actively monitor this space and look forward to hearing from you!

Contributing through GitHub

git is a really useful tool for version control. GitHub sits on top of git and supports collaborative and distributed working.

If you're not yet familiar with git, there are lots of great resources to help you git started! Some of our favorites include the git Handbook and the Software Carpentry introduction to git.

On GitHub, You'll use Markdown to chat in issues and pull requests. You can think of Markdown as a few little symbols around your text that will allow GitHub to render the text with a little bit of formatting. For example, you could write words as bold (**bold**), or in italics (*italics*), or as a link ([link](https://youtu.be/dQw4w9WgXcQ)) to another webpage.

GitHub has a really helpful page for getting started with writing and formatting Markdown on GitHub.

Understanding issues

Every project on GitHub uses issues slightly differently.

The following outlines how the AFQ-Insight developers think about these tools.

• Issues are individual pieces of work that need to be completed to move the project forward. A general guideline: if you find yourself tempted to write a great big issue that is difficult to be described as one unit of work, please consider splitting it into two or more issues.

  Issues are assigned [labels](#issue-labels) which explain how they relate to the overall project's
  goals and immediate next steps.
  

Issue Labels

The current list of issue labels are here and include:

• These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.

  If you feel that you can contribute to one of these issues, we especially encourage you to do so!

• These issues point to problems in the project.

  If you find new a bug, please give as much detail as possible in your issue, including steps to recreate the error. If you experience the same bug as one already listed, please add any additional information that you have as a comment.

• These issues are asking for new features and improvements to be considered by the project.

  Please try to make sure that your requested feature is distinct from any others that have already been requested or implemented. If you find one that's similar but there are subtle differences, please reference the other request in your issue.

In order to define priorities and directions in the development roadmap, we have two sets of special labels:

Label	Description
	Estimation of the downstream impact the proposed feature/bugfix will have.
	Estimation of effort required to implement the requested feature or fix the reported bug.

These labels help triage and set priorities to the development tasks. For instance, one bug regression that has been reported to affect most of the users after a release with an easy fix because it is a known old problem that came back. Such an issue will typically be assigned the following labels , and its priority will be maximal since addressing low-effort high-impact issues delivers the maximum turnout without increasing the churn by much.

Of course, the implementation of long-term goals may include the scheduling of . Finally, issues are less likely to be addressed.

Making a change

We appreciate all contributions to AFQ-Insight, but those accepted fastest will follow a workflow similar to the following:

1. Comment on an existing issue or open a new issue referencing your addition.
   This allows other members of the AFQ-Insight development team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
   This blog is a nice explanation of why putting this work in up front is so useful to everyone involved.

2. Fork the AFQ-Insight repository to your profile.
   This is now your own unique copy of AFQ-Insight. Changes here won't effect anyone else's work, so it's a safe space to explore edits to the code! On your own fork of the repository, select Settings -> Actions-> "Disable Actions for this repository" to avoid flooding your inbox with warnings from our continuous integration suite.

3. Clone your forked AFQ-Insight repository to your machine/computer.
   While you can edit files directly on github, sometimes the changes you want to make will be complex and you will want to use a text editor that you have installed on your local machine/computer. (One great text editor is vscode).
   In order to work on the code locally, you must clone your forked repository.
   To keep up with changes in the AFQ-Insight repository, add the "upstream" AFQ-Insight repository as a remote to your locally cloned repository.

   git remote add upstream https://github.com/richford/AFQ-Insight.git

   Make sure to keep your fork up to date with the upstream repository.
   For example, to update your main branch on your local cloned repository:

   git fetch upstream
   git checkout main
   git merge upstream/main

4. Install a development version of AFQ-Insight so that your local changes are reflected in your local tests
   You can install a development version of AFQ-Insight by navigating to the root of your AFQ-Insight repository and then typing

   pip install -e .[dev]

   or better still

   python -m pip install -e .[dev]

5. Create a new branch to develop and maintain the proposed code changes.
   For example:

   git fetch upstream  # Always start with an updated upstream
   git checkout -b fix/bug-1222 upstream/main

   Please consider using appropriate branch names as those listed below:

   Branch name	Use case
   fix/<some-identifier>	for bugfixes
   enh/<feature-name>	for new features
   doc/<some-identifier>	for documentation improvements

   You should name all your documentation branches with the prefix doc/ as that will preempt triggering the full battery of continuous integration tests.

6. Make the changes you've discussed, following the AFQ-Insight coding style guide.
   Try to keep the changes focused: it is generally easy to review changes that address one feature or bug at a time. Assuming you installed a development environment above, you can test your local changes using

   make lint
   make test

   Once you are satisfied with your local changes, add/commit/push them to the branch on your forked repository.

7. Submit a pull request.
   A member of the development team will review your changes to confirm that they can be merged into the main code base.
   Pull request titles should begin with a descriptive prefix (for example, ENH: Adding another estimator class):

   • ENH: enhancements or new features (example)
   • FIX: bug fixes (example)
   • TST: new or updated tests (example)
   • DOC: new or updated documentation (example)
   • STY: style changes (example)
   • REF: refactoring existing code ([example][ex_ref])
   • CI: updates to continous integration infrastructure (example)
   • MAINT: general maintenance (example)
   • For works-in-progress, add the WIP tag in addition to the descriptive prefix. Pull-requests tagged with WIP: will not be merged until the tag is removed.

8. Have your PR reviewed by the development team, and update your changes accordingly in your branch.
   The reviewers will take special care in assisting you to address their comments, as well as dealing with conflicts and other tricky situations that could emerge from distributed development. And if you don't make the requested changes, we might ask @bedevere-bot to poke you with soft cushions!

AFQ-Insight coding style guide

We use the Black code formatter for format our code contributions to a common style. All pull requests will automatically be checked for compliance using flake8 and the Black code formatter. We recommend you activate the pre-commit formatting hook by typing

pre-commit install

Afterward, all of your local changes will be automatically formatted before you commit them. This is the easiest way to ensure that your much appreciated contribution is not delayed due to formatting or style compliance.

Documentation

We use Sphinx to generate documentation from files stored in the docs/source folder. To generate proper documentation of functions, we use the numpy docstring standard when documenting code inline in docstrings.

Licensing

AFQ-Insight is licensed under the BSD license. By contributing to AFQ-Insight, you acknowledge that any contributions will be licensed under the same terms.

Reminder note for maintainers

AFQ-Insight pushes a development version to Test-PyPI on every pull request merged into the main branch. To release a new version of AFQ-Insight, use the publish_release.sh script from the root directory, i.e.:

.maintenance/publish_release.sh <version_number>

For releases, use the following format for <version*number>: "v..". When executed, this will ask you if you want to customize the CHANGES.rst document or the release notes. After that, *AFQ-Insight*'s GitHub actions will take care of publishing the new release on PyPI and creating a release on GitHub.

Footnotes

1. The imposter syndrome disclaimer was originally written by Adrienne Lowe for a PyCon talk, and was adapted based on its use in the README file for the MetPy project. ↩