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Expand Up @@ -7,111 +7,6 @@ _We're so excited you're here and want to contribute._
If you have any questions that aren't discussed below, please let us know by
[opening an issue](#understanding-issues).

## Table of contents

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

- [Contributing to BIDS-MATLAB](#contributing-to-bids-matlab)
- [Table of contents](#table-of-contents)
- [Joining the community](#joining-the-community)
- [Contributing through GitHub](#contributing-through-github)
- [Understanding issues](#understanding-issues)
- [Issue labels](#issue-labels)
- [Style guide](#style-guide)
- [Writing in markdown](#writing-in-markdown)
- [Matlab code style guide and quality](#matlab-code-style-guide-and-quality)
- [pre-commit hook: reformatting your code when committing](#pre-commit-hook-reformatting-your-code-when-committing)
- [Running tests on the code](#running-tests-on-the-code)
- [Making a change with a pull request](#making-a-change-with-a-pull-request)
- [1. Comment on an existing issue or open a new issue referencing your addition](#1-comment-on-an-existing-issue-or-open-a-new-issue-referencing-your-addition)
- [2. Fork [this repository](https://github.com/bids-standard/BIDS-MATLAB) to your profile](#2-fork-this-repository-to-your-profile)
- [3. Make the changes you've discussed](#3-make-the-changes-youve-discussed)
- [4. Submit a pull request](#4-submit-a-pull-request)
- [Example pull request](#example-pull-request)
- [Commenting on a pull request](#commenting-on-a-pull-request)
- [Navigating to open pull requests](#navigating-to-open-pull-requests)
- [Pull request description](#pull-request-description)
- [Generally commenting on a pull request](#generally-commenting-on-a-pull-request)
- [Specific comments on a pull request](#specific-comments-on-a-pull-request)
- [Suggesting text](#suggesting-text)
- [Accepting suggestion from a review](#accepting-suggestion-from-a-review)
- [How the decision to merge a pull request is made?](#how-the-decision-to-merge-a-pull-request-is-made)
- [Recognizing contributions](#recognizing-contributions)
- [Updating the bids-schema](#updating-the-bids-schema)

<!--
TODO: sections to add
- examples
- setting up an octave jupyter notebook
- binder
- continuous integration
- github actions
-->

## Joining the community

BIDS - the [Brain Imaging Data Structure](https://bids.neuroimaging.io/) - is a
growing community of neuroimaging enthusiasts, and we want to make our resources
accessible to and engaging for as many researchers as possible.

Most of our discussions take place here in
[GitHub issues](#understanding-issues).

To keep on top of new posts, please see this guide for setting your
[topic notifications](https://meta.discourse.org/t/discourse-new-user-guide/96331#heading--topic-notifications).

As a reminder, we expect that all contributions adhere to our
[Code of Conduct](./CODE_OF_CONDUCT.md).

## Contributing through GitHub

[Git](https://git-scm.com/) is a really useful tool for version control.
[GitHub](https://github.com/) sits on top of Git and supports collaborative and
distributed working.

We know that it can be daunting to start using Git and GitHub if you haven't
worked with them in the past, but the BIDS-MATLAB maintainers are here to help
you figure out any of the jargon or confusing instructions you encounter!

In order to contribute via GitHub you'll need to set up a free account and sign
in. Here are some
[instructions](https://help.github.com/articles/signing-up-for-a-new-github-account/)
to help you get going. Remember that you can ask us any questions you need to
along the way.

## Understanding issues

Every project on GitHub uses
[issues](https://github.com/bids-standard/bids-matlab/issues) slightly
differently.

The following outlines how BIDS developers think about communicating through
issues.

**Issues** are individual pieces of work that need to be completed or decisions
that need to be made to move the project forwards. A general guideline: if you
find yourself tempted to write a great big issue that is difficult to describe
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 labels are
[here](https://github.com/bids-standard/bids-matlab/labels) and include:

- [![Opinions wanted](https://img.shields.io/badge/-opinions%20wanted-84b6eb.svg)](https://github.com/bids-standard/bids-matlab/labels/opinions%20wanted)
_These issues hold discussions where we're especially eager for feedback._

Ongoing discussions benefit from broad feedback. This label is used to
highlight issues where decisions are being considered, so please join the
conversation!

<!-- TODO:
- add more issue labels description -->

## Style guide

### Writing in markdown
Expand Down Expand Up @@ -180,25 +75,6 @@ The code style and quality is also checked during the continuous integration.
For more information about MISS_HIT see its
[documentation](https://florianschanda.github.io/miss_hit/).

#### pre-commit hook: reformatting your code when committing

There is a [pre-commit hook](https://pre-commit.com/) that you can use to
reformat files as you commit them.

Install pre-commit by using our `requirements.txt` file

```bash
pip install -r requirements.txt
```

Install the hook

```bash
pre-commit install
```

You're done. `mh_style --fix` will now be run every time you commit.

### Running tests on the code

The unit and integration tests we have are in the [`tests` folder]'(./tests/)
Expand All @@ -209,176 +85,6 @@ If you are not sure what unit and integration tests are, check the chapter about
that in the
[Turing way](https://the-turing-way.netlify.app/reproducible-research/testing.html).

## Making a change with a pull request

We appreciate all contributions to BIDS-MATLAB. **THANK YOU** for helping us
build this useful resource.

#### 1. Comment on an existing issue or open a new issue referencing your addition

This allows other members of the BIDS-MATLAB 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.

#### 2. [Fork](https://help.github.com/articles/fork-a-repo/) [this repository](https://github.com/bids-standard/BIDS-MATLAB) to your profile

This is now your own unique copy of BIDS-MATLAB. Changes here won't affect
anyone else's work, so it's a safe space to explore edits to the code!

Make sure to
[keep your fork up to date](https://help.github.com/articles/syncing-a-fork/)
with the parent repository, otherwise you can end up with lots of dreaded
[merge conflicts](https://help.github.com/articles/about-merge-conflicts/).

#### 3. Make the changes you've discussed

Try to keep the changes focused. If you submit a large amount of work in all in
one go it will be much more work for whomever is reviewing your pull request.
Please detail the changes you are attempting to make.

#### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)

Please keep the title of your pull request short but informative.

Use one of the following prefixes in the title of your pull request:

- `[ENH]` - enhancement of the software that adds a new feature or support for
a new data type
- `[FIX]` - fix of a bug or documentation error
- `[INFRA]` - changes to the infrastructure automating the project release
(for example, testing in continuous integration, building HTML docs)
- `[MISC]` - everything else including changes to the file listing
contributors

If you are opening a pull request to obtain early feedback, but the changes are
not ready to be merged (also known as a "work in progress" pull request,
sometimes abbreviated by `WIP`), please use a
[draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).

If your pull request include:

- some new features in the code base
- or if it changes the expected behavior of the code that is already in place,

you may be asked to provide tests to describe the new expected behavior of the
code.

A member of the BIDS-MATLAB team will review your changes to confirm that they
can be merged into the main codebase.

A [review](https://help.github.com/articles/about-pull-request-reviews/) will
usually consist of a few questions to help clarify the work you've done. Keep an
eye on your GitHub notifications and be prepared to join in that conversation.

You can update your [fork](https://help.github.com/articles/about-forks/) of
BIDS-MATLAB and the pull request will automatically update with those commits.
You don't need to submit a new pull request when you make a change in response
to a review.

GitHub has a [nice introduction](https://help.github.com/articles/github-flow/)
to the pull request workflow, but please [get in touch](#get-in-touch) if you
have any questions.

## Example pull request

<img align="center" src="https://i.imgur.com/s8yELfK.png" alt="Example-Contribution" width="800"/>

## Commenting on a pull request

Our primary method of adding to or enhancing BIDS-MATLAB occurs in the form of
[pull requests](https://help.github.com/articles/about-pull-requests/).

This section outlines how to comment on a pull request.

### Navigating to open pull requests

The list of pull requests can be found by clicking on the "Pull requests" tab in
the [BIDS-MATLAB repository](https://github.com/bids-standard/BIDS-MATLAB).

### Pull request description

Upon opening the pull request we see a detailed description of what this pull
request is seeking to address. Descriptions are important for reviewers and the
community to gain context into what the pull request is achieving.

![BIDS-pr](docs/commenting_images/BIDS_pr.png "BIDS_pr")

### Generally commenting on a pull request

At the bottom of the pull request page, a comment box is provided for general
comments and questions.

![BIDS-comment](docs/commenting_images/BIDS_comment.png "BIDS-comment")

### Specific comments on a pull request

The proposed changes to the software can be seen in the "Files changed" tab.
Proposed additions are displayed on a green background with a `+` before each
added line. Proposed deletions are displayed on a red background with a `-`
before each removed line. To comment on a specific line, hover over it, and
click the blue plus sign (pictured below). Multiple lines can be selected by
clicking and dragging the plus sign.

![BIDS-specific-comment](docs/commenting_images/BIDS_file_comment.png "BIDS-specific-comment")

#### Suggesting text

Comments on lines can contain "suggestions", which allow you to propose specific
wording for consideration. To make a suggestion, click the plus/minus (±) icon
in the comment box (pictured below).

![BIDS-suggest-box](docs/commenting_images/BIDS_suggest.png "BIDS-suggest")

Once the button is clicked the highlighted text will be copied into the comment
box and formatted as a
[Markdown code block](https://help.github.com/en/github/writing-on-github/creating-and-highlighting-code-blocks).

![BIDS-suggest-text](docs/commenting_images/BIDS_suggest_text.png "BIDS-suggest-box")

The "Preview" tab in the comment box will show your suggestion as it will be
rendered. The "Suggested change" box will highlight the differences between the
original text and your suggestion.

![BIDS-suggest-change](docs/commenting_images/BIDS_suggest_change.png "BIDS-suggest-change")

A comment may be submitted on its own by clicking "Add single comment". Several
comments may be grouped by clicking "Start a review". As more comments are
written, accept them with "Add review comment", and submit your review comments
as a batch by clicking the "Finish your review" button.

## Accepting suggestion from a review

When others are making [suggestions to your pull request](#suggesting-text), you
have the possibility to accept directly the changes suggested during the review
through the GitHub interface. This can often be faster and more convenient than
make the changes locally and then pushing those changes to update your pull
request. Moreover it gives the opportunity to give credit to the reviewers for
their contribution.

To do this, you must click on the `Files changed` tab at the top of the page of
a pull request.

![BIDS_pr_files_changed](docs/commenting_images/BIDS_pr_files_changed.png "BIDS_pr_files_changed")

From there you can browse the different files changed and the 'diff' for each of
them (what line was changed and what the change consist of). You can also see
comments and directly change suggestions made by reviewers.

You can add each suggestion one by one or group them together in a batch.

![BIDS_pr_accept_comment](docs/commenting_images/BIDS_pr_accept_comment.png "BIDS_pr_accept_comment")

If you decide to batch the suggestions to add several of them at once, you must
scroll back to the top of the 'Files changed' page and the `commit suggestions`
button will let you add all those suggestions as a single commit.

![BIDS_pr_commit_batch](docs/commenting_images/BIDS_pr_commit_batch.png "BIDS_pr_commit_batch")

Once those suggestions are committed the commit information should mention the
reviewer as a co-author.

![BIDS_pr_reviewer_credit](docs/commenting_images/BIDS_pr_reviewer_credit.png "BIDS_pr_reviewer_credit")

## How the decision to merge a pull request is made?

The decision-making rules are outlined in
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