Contributing to Nipype
Welcome to the Nipype repository! We're excited you're here and want to contribute.
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. If you are not familiar with version control systems such as git, we recommend the VCS module available from ReproNim.
Already know what you're looking for in this guide? Jump to the following sections:
- Understanding issue labels
- Making a change
- How to tag pull requests
- Notes for new code
- Recognizing contributions
The current list of issue labels are here and include:
If you find a new bug, please provide as much information as possible to recreate the error. The issue template will automatically populate any new issue you open, and contains information we've found to be helpful in addressing bug reports. Please fill it out to the best of your ability!
If you experience the same bug as one already listed in an open issue, please add any additional information that you have as a comment.
If you feel that you can contribute to one of these issues, we especially encourage you to do so! Issues that are also labelled as good-first-issue are a great place to start if you're looking to make your first contribution.
Please try to make sure that your requested enhancement 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.
Before proposing a new pull request, browse through the "orphaned" pull requests. You may find that someone has already made significant progress toward your goal, and you can re-use their unfinished work. An adopted PR should be updated to merge or rebase the current master, and a new PR should be created (see below) that references the original PR.
Making a change
We appreciate all contributions to Nipype, 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 Nipype 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.
This is now your own unique copy of the Nipype repository. Changes here won't affect anyone else's work, so it's a safe space to explore edits to the code!
You can clone your Nipype repository in order to create a local copy of the code on your machine.
To install your version of Nipype, and the dependencies needed for development,
in your Python environment, run
pip install -e ".[dev]" from your local Nipype
3. Make the changes you've discussed.
If you're adding a new tool from an existing neuroimaging toolkit (e.g., 3dDeconvolve from AFNI), check out the guide for adding new interfaces to Nipype.
When you are working on your changes, test frequently to ensure you are not breaking the existing code. For more on testing, please see the testing section of Nipype documentation.
Before pushing your changes to GitHub, run
make check-before-commit. This will remove trailing spaces, create new auto tests,
test the entire package, and build the documentation.
If you get no errors, you're ready to submit your changes!
It's a good practice to create a new branch of the repository for a new set of changes.
For Python 2.7-compatible fixes, the branch should start from the
maint/1.3.x branch on the
4. Submit a pull request.
A new pull request for your changes should be created from your fork of the repository.
When opening a pull request, please use one of the following prefixes:
- [ENH] for enhancements
- [FIX] for bug fixes
- [TST] for new or updated tests
- [DOC] for new or updated documentation
- [STY] for stylistic changes
- [REF] for refactoring existing code
5. Install pre-commit.
pre-commit is a git hook for running operations at commit time. To use it in
your environment, do
pip install pre-commit following by
inside your source directory.
Pull requests should be submitted early and often (please don't mix too many unrelated changes within one PR)! If your pull request is not yet ready to be merged, please also include the **[WIP]** prefix (you can remove it once your PR is ready to be merged). This tells the development team that your pull request is a "work-in-progress", and that you plan to continue working on it.
Review and discussion on new code can begin well before the work is complete, and the more discussion the better! The development team may prefer a different path than you've outlined, so it's better to discuss it and get approval at the early stage of your work.
One your PR is ready a member of the development team will review your changes to confirm that they can be merged into the main codebase.
Notes for New Code
In general, do not catch exceptions without good reason. For non-fatal exceptions, log the exception as a warning and add more information about what may have caused the error.
If you do need to catch an exception, raise a new exception using
raise NewException("message") from oldException).
Do not log this, as it creates redundant/confusing logs.
New code should be tested, whenever feasible. Bug fixes should include an example that exposes the issue. Any new features should have tests that show at least a minimal example. If you're not sure what this means for your code, please ask in your pull request.
We welcome and recognize all contributions from documentation to testing to code development.
The development team member who accepts/merges your pull request will update the CHANGES file to reference your contribution.
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 there!
— Based on contributing guidelines from the STEMMRoleModels project.