CONTRIBUTING.md

Contributing to EddyMotionCorrection

Welcome to the EddyMotionCorrection 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.

Driving principles

EddyMotionCorrection is very much influenced and envisioned as a translation of fMRIPrep to diffusion MRI data. That means EddyMotionCorrection shares with fMRIPrep (and more generally, other NIPreps [NeuroImaging Preprocessing pipelines]) the fundamental design principles:

1. The tool only and fully supports BIDS and BIDS-Derivatives for the input and output data.
2. The tool is packaged as a fully-compliant BIDS-App, not just in its user interface, but also in the continuous integration, testing and delivery.
3. The tool is rigorously restricted to diffusion MRI preprocessing tasks, including (but not limited to): input/output metadata assessment, head-motion correction, eddy-currents-derived artifact correction, susceptibility-distortion correction, denoising, B1-bias field correction, session-drift correction, co-registration with anatomical data, spatial normalization to neuroimaging templates, gradient non-linearity correction, Gibbs unringing, etc. In other words, the tool does not deal with modeling, tractography or connectivity extraction.
4. The tool is agnostic to subsequent analysis, i.e., any software supporting BIDS-Derivatives for its inputs should be amenable perform tractography and to analyze data preprocessed with the tool.
5. The tool is thoroughly and transparently documented (including the generation of individual reports that can be used as scaffolds for understanding the underpinnings and design decisions of the tool).
6. The tool is community-driven, with a very open concept of contribution that is always credited with authorship offers when writing relevant papers.

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

EddyMotionCorrection is maintained by a growing group of enthusiastic developers— and we're excited to have you join! Most of our discussions will take place on open issues.

We also encourage users to report any difficulties they encounter on NeuroStars, a community platform for discussing neuroimaging.

We actively monitor both spaces and look forward to hearing from you in either venue!

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 EddyMotionCorrection 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 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 deliver the maximum turnout without increasing the churn by much.

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

Making a change

We appreciate all contributions to EddyMotionCorrection, 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 EddyMotionCorrection 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 EddyMotionCorrection repository to your profile.
   This is now your own unique copy of EddyMotionCorrection. Changes here won't effect anyone else's work, so it's a safe space to explore edits to the code!

3. Clone your forked EddyMotionCorrection 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 EddyMotionCorrection repository, add the "upstream" EddyMotionCorrection repository as a remote to your locally cloned repository.

   git remote add upstream https://github.com/nipreps/EddyMotionCorrection.git

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

   git fetch upstream
   git checkout master
   git merge upstream/master

4. 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/master

   Please consider using appropriate branch names as those listed below, and mind that some of them are special (e.g., doc/ and docs/):

   • 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/ or docs/ as that will preempt triggering the full battery of continuous integration tests.

5. Make the changes you've discussed, following the EddyMotionCorrection 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. It can also be helpful to test your changes locally, using a EddyMotionCorrection development environment. Once you are satisfied with your local changes, add/commit/push them to the branch on your forked repository.

6. 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 Gibbs unringing step):

   • 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)
   • 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.

7. 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!

EddyMotionCorrection coding style guide

Whenever possible, instances of Nipype Nodes and Workflows should use the same names as the variables they are assigned to. This makes it easier to relate the content of the working directory to the code that generated it when debugging.

Workflow variables should end in _wf to indicate that they refer to Workflows and not Nodes. For instance, a workflow whose base-name is myworkflow might be defined as follows:

from nipype.pipeline import engine as pe

myworkflow_wf = pe.Workflow(name='myworkflow_wf')

If a workflow is generated by a function, the name of the function should take the form init_<basename>_wf:

def init_myworkflow_wf(name='myworkflow_wf):
    workflow = pe.Workflow(name=name)
    ...
    return workflow

myworkflow_wf = init_workflow_wf(name='myworkflow_wf')

If multiple instances of the same workflow might be instantiated in the same namespace, the workflow names and variables should include either a numeric identifier or a one-word description, such as:

myworkflow0_wf = init_workflow_wf(name='myworkflow0_wf')
myworkflow1_wf = init_workflow_wf(name='myworkflow1_wf')

# or

myworkflow_lh_wf = init_workflow_wf(name='myworkflow_lh_wf')
myworkflow_rh_wf = init_workflow_wf(name='myworkflow_rh_wf')

Licensing

EddyMotionCorrection is licensed under the Apache 2.0 license. By contributing to EddyMotionCorrection, you acknowledge that any contributions will be licensed under the same terms.

Recognizing contributions

We welcome and recognize all contributions from documentation to testing to code development. You can see a list of current contributors in our zenodo file. If you are new to the project, don't forget to add your name and affiliation to the list of contributors there! Before every release, the zenodo file will be checked for new contributors, who will be invited again to add their names to the file (just in case they missed the automated message from our Welcome Bot). The update script will also sort creators and contributors by the relative size of their contributions, as provided by the git-line-summary utility distributed with the git-extras package. Last positions in both the creators and contributors list will be reserved to the project leaders. These special positions can be revised to add names by punctual request and revised for removal and update of ordering in an scheduled manner every two years. All the authors enlisted as creators participate in the revision of modifications.

Creators

Creators are contributors who drive the project. Examples of steering activities that drive the project are: actively participating in the follow-up meetings, helping in the design of the tool and definition of the roadmap, providing resources (in the broad sense, including funding), code-review, etc.

Contributors

Contributors helped the project in any sense: writing code, writing documentation, benchmarking modules of the tool, proposing new features, helping improve the scientific rigor of implementations, giving out support on the different communication channels (mattermost, NeuroStars, GitHub issues, etc.).

Publications

Anyone listed as a creator or a contributor in the zenodo file can start the submission process of a manuscript as first author. To compose the author list, all the creators MUST be included (except for those people who opt to drop-out) and all the contributors MUST be invited to participate. First authorship(s) is (are) reserved for the authors that originated and kept the initiative of submission and wrote the manuscript. The ordering of the rest of the authors follows the ordering criteria of the zenodo file, with the difference that all the authors are pulled together in a unique list (i.e., creators and contributors are treated equivalently). EddyMotionCorrection and its community adheres to open science principles, such that a pre-print should be posted on an adequate archive service (e.g., ArXiv or BioRxiv) prior publication.

Thank you!

You're awesome. 👋😃

— Based on contributing guidelines from the STEMMRoleModels project.

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. ↩