Contributing to shimming-toolbox


First off, thanks for taking the time to contribute to our project! πŸŽ‰

When contributing to this repository, please first discuss the change you wish to make by opening a new GitHub issue with one of the templates.

Contributions relating to content of the Github repository can be submitted through GitHub pull requests (PR).

PR for bug fixes or new features should be based on the master branch.

The following GitHub documentation may be useful:

For external contributors: Please fork this repository, make the desired changes, and then open a Pull request to have your code reviewed and merged.

For internal contributor: You can open a branch (see Opening a branch) directly in this repository. If you don't have the rights, contact the team leader.

Opening an issue

Issues (bugs, enhancement requests, or feature requests) can be submitted on our project's issue page. Please select the appropriate template when creating a new issue.

Before Submitting a New Issue

Please take a few seconds to search the issue database in case the issue has already been raised.

When reporting an issue, make sure your installation has not been tampered with (and if you can, update to the latest release in case the problem has already been fixed).

Submitting an Issue

Go through the checklist of the issue template to ensure you've met all our issue formatting requirements. This will help us to quickly address the issue ticket.

Issue Examples

Some good real-life examples:

Opening a Branch

If you are part of the core developer team, you can open a branch directly in this repository. Prefix the branch name with a personal identifier (e.g. your initials) and a forward slash; If the branch you are working on is in response to an issue, provide the issue number; Add some text that make the branch name meaningful.


  • ol/100-fixup-lr-scheduler

  • ab/loader-pep8


Pre-commit checks

We use pre-commit to enforce conventions like file sizes, correct Python syntax, and no merge conflict strings in the changeset. After you've installed shimming-toolbox, install the hooks by running pre-commit install at the root of the repo clone.


Make sure the PR changes are not in conflict with the master branch.

Code style

Please review your changes for styling issues, clarity, according to the PEP8 convention. Correct any code style suggested by an analyzer on your changes. PyCharm has a code analyser integrated or you can use pyflakes.

Do not address your functional changes in the same commits as any styling clean-up you may be doing on existing code.

Documentation and docstrings

If you are implementing a new feature, update the documentation to describe the feature, and comment the code (things that are not trivially understandable from the code) to improve its maintainability.

Make sure to cite any papers, algorithms or articles that can help understand the implementation of the feature. If you are implementing an algorithm described in a paper, add pointers to the section / steps.

Please use the Google style docstrings.


Please add tests, especially with new code. As of now, we have unit tests (in /test). They are straightforward to augment, but we understand it's the extra mile; it would still be appreciated if you provide something lighter (eg. in the commit messages or in the PR or issue text) that demonstrates that an issue was fixed, or a feature is functional.

Consider that if you add test cases, they will ensure that your feature still works in the future.


Ensure that you are the original author of your changes, and if that is not the case, ensure that the borrowed/adapted code is compatible with the project's license.


Commit Titles

Provide a concise and self-descriptive title (avoid > 80 characters). You may "scope" the title using the applicable command name(s), folder or other "module" as a prefix. If a commit is responsible for fixing an issue, post-fix the description with (fixes #ISSUE_NUMBER).


testing: add testing function for validation metrics
loader: add timer
documentation: add slice_axis to the config files

Commit Sequences

Update your branch to be baseline on the latest master if new developments were merged while you were developing. Please prefer rebasing to merging, as explained in this tutorial. Note that if you do rebases after review have started, they will be cancelled, so at this point it may be more appropriate to do a pull.

Clean-up your commit sequence. If your are not familiar with git, this good tutorial on the subject may help you.

Focus on committing 1 logical change at a time. See this article on the subject.

Submitting a Pull Request

Please go through the checklist in the PR template to ensure you've met all our PR formatting requirements. This will help us to easily review your PR so it can be quickly merged when ready.

PR Labels

You must add labels to your PRs, as these are used to automatically generate Changelog:

  • Category: Choose one label that describes the category.

  • Cross-compatibility: If your PR breaks cross-compatibility with a previous stable release of SCT, you should add the label compatibility (orange label).

Work in progress

If your PR is not ready for review yet, you can convert it to a "Draft", so the team is informed.

A draft pull request is styled differently to clearly indicate that it’s in a draft state. Merging is blocked in draft pull requests. Change the status to "Ready for review" near the bottom of your pull request to remove the draft state and allow merging according to your project’s settings.

Continuous Integration

The PR can't be merged if GitHub Actions "Run tests" hasn't succeeded. If you are familiar with it, consult the test results to fix the problem.


Any changes submitted for inclusion to the master branch will have to go through a review.

Only request a review when you deem the PR as "good to go". If the PR is not ready for review, convert it to a "Draft".

GitHub may suggest you to add particular reviewers to your PR. If that's the case and you don't know better, add all of these suggestions. The reviewers will be notified when you add them.

Merging your PR

When your PR has been approved by the reviewers you requested, you can merge it yourself using the rebase method.


Versioning uses the following convention: MAJOR.MINOR.PATCH, where:

PATCH version when there are backwards-compatible bug fixes or enhancements, without alteration to Python's modules or data/binaries. MINOR version when there are minor API changes or new functionality in a backwards-compatible manner, or when there are alteration to Python's modules or data/binaries (which requires to re-run installer for people working on the dev version), MAJOR version when there are major incompatible API changes, Beta releases follow the following convention:

MAJOR.MINOR.PATCH-beta.x (with x = 0, 1, 2, etc.) Stable version is indicated in the file version.txt. For development version (on master), the version is "dev".