Welcome to the BIDS-MATLAB repository!
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.
Been here before? Already know what you're looking for in this guide? Jump to the following sections:
- Contributing to BIDS-MATLAB
- Table of contents
- Joining the community
- Contributing through GitHub
- Understanding issues
- Style guide
- Making a change with a pull request
- 1. Comment on an existing issue or open a new issue referencing your addition
- [2. Fork this repository to your profile](#2-fork-this-repository-to-your-profile)
- 3. Make the changes you've discussed
- 4. Submit a pull request
- Example pull request
- Commenting on a pull request
- Accepting suggestion from a review
- How the decision to merge a pull request is made?
- Recognizing contributions
- Updating the bids-schema
BIDS - the Brain Imaging Data Structure - 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.
To keep on top of new posts, please see this guide for setting your topic notifications.
As a reminder, we expect that all contributions adhere to our Code of Conduct.
Git is a really useful tool for version control. GitHub 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 to help you get going. Remember that you can ask us any questions you need to along the way.
Every project on GitHub uses 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 which explain how they relate to the overall project's goals and immediate next steps.
The current list of labels are here and include:
-
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!
For anything that is in markdown we have a soft rule that aims to enforce "hardline wrapping" to make sure that lines wrap around at a certain line length. The main reason is that it makes it easier for reviewers to detect the changes so in a whole paragraph.
Some editors can automatically enforce hard-line wrapping with some linter like
Prettier so that you are always only a shortcut away from a tidy document. See
an example with visual-studio code
here.
We use the MISS_HIT linter to automatically enforce / fix some code style issues and check for code quality.
The linter is a Python package that can be installed with:
pip3 install -r requirements.txt
💻 Installing Python
If you do not have Python on your computer, we warmly recommend the install instruction from the datalad handbook.
The rules followed by MISS_HIT are in the MISS_HIT configuration file.
To check the code style of the whole repository, you can can simply type:
mh_style .Some styling issues can be automatically fixed by using the --fix flag. You
might need to rerun this command several times if there are a lot of issues.
mh_style . --fixCode quality can be checked with:
mh_metric .To see only the issues that "break" the code quality rules set in the configuration file, type:
mh_metric . --ciThe code style and quality is also checked during the continuous integration.
For more information about MISS_HIT see its documentation.
There is a pre-commit hook that you can use to reformat files as you commit them.
Install pre-commit by using our requirements.txt file
pip install -r requirements.txtInstall the hook
pre-commit installYou're done. mh_style --fix will now be run every time you commit.
The unit and integration tests we have are in the [tests folder]'(./tests/)
and should be run with MoxUnit. For more information on the set up for the test,
see the README in the tests folder.
If you are not sure what unit and integration tests are, check the chapter about that in the Turing way.
We appreciate all contributions to BIDS-MATLAB. THANK YOU for helping us build this useful resource.
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 this repository 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 with the parent repository, otherwise you can end up with lots of dreaded merge conflicts.
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
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.
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 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 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 to the pull request workflow, but please get in touch if you have any questions.
Our primary method of adding to or enhancing BIDS-MATLAB occurs in the form of pull requests.
This section outlines how to comment on a pull request.
The list of pull requests can be found by clicking on the "Pull requests" tab in the BIDS-MATLAB repository.
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.
At the bottom of the pull request page, a comment box is provided for general comments and questions.
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.
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).
Once the button is clicked the highlighted text will be copied into the comment box and formatted as a Markdown code block.
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.
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.
When others are making suggestions to your pull request, 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.
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.
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.
Once those suggestions are committed the commit information should mention the reviewer as a co-author.
The decision-making rules are outlined in DECISION-MAKING.md.
BIDS-MATLAB follows the all-contributors specification, so we welcome and recognize all contributions from documentation to testing to code development. You can see a list of current contributors in the README.
Also make sure you add your information to the CITATION.cff file.
If you have made any type of contributions to BIDS-MATLAB, our team will add you as a contributor (or ask to be added if we forgot).
The schema of the BIDS specification is available as a set of yaml files in the bids-standards repository.
A JSON version is also available here: https://bids-specification.readthedocs.io/en/latest/schema.json
The latest version can be obtained by running the following command:
make update_schemaA new version of the schema is fetched automatically regularly via continuous integration (see the github action) when pushing to the repo or opening a pull-request.