Contributing#

Feel free to open issues to report a bug and ask for improvements.

If you want to contribute, have a look at our contributing guidelines that are meant to guide you and help you get started. If something is not clear or you get stuck: it is more likely we did not do good enough a job at explaining things. So do not hesitate to open an issue, just to ask for clarification.

Installation#

To install bidspm and make changes to it, it is recommend to install the python package in editable mode with all its development dependencies.

pip install -e .[dev]

Initialisation#

To facilitate running tests, make sure you initialize bidspm in dev mode, from the MATLAB command line:

bidspm dev

You can also run all the tests with:

bidspm run_tests

Style guidelines#

We use camelCase to name functions and variables for the vast majority of the code in this repository.

Scripts names in general and as well functions related to the demos use a snake_case.

Constant are written in UPPERCASE.

Input arguments ordering#

From more general to more specific

BIDS > opt > subject > session > run

  • BIDS (output from getData or bids.layout) restrict the set of possible analysis one can run to this BIDS data set

  • opt restricts this set even further

  • subject / session / run even more

% OK
varargout = getInfo(BIDS, opt, subLabel, info, varargin)

% not OK
varargout = getInfo(subLabel, BIDS, opt, info, varargin)

Output arguments ordering#

Try to return them in order of importance first and in order of appearance otherwise.

Exceptions#

If function creates or modifies a batch then matlabbatch is the first argin and first argout.

If a function performs an “action” to be chosen from a one of several strings (with a switch statement), this string comes as first argin or second if matlabbatch is first.

% OK
varargout = getInfo('filename', BIDS, opt, subID, varargin)
[matlabbatch, voxDim] = setBatchRealign(matlabbatch, [action = 'realign',] BIDS, opt, subID)

% not OK
% 'filename' is the name of the "action" or the info to get in this case
% batch and action should go first
varargout = getInfo(BIDS, opt, subID, 'filename', varargin)
[matlabbatch, voxDim] = setBatchRealign(BIDS, opt, subID, matlabbatch, [action = 'realign'])

Updating the FAQ#

The FAQ is rendered with FAQtory.

New questions must be added to docs/questions and the main FAQ.md can be created with:

make update_faq

release protocol#

  • [ ] create a dedicated branch for the release candidate

  • [ ] update version in citation.cff

  • [ ] documentation related

    • [ ] ensure the documentation is up to date

    • [ ] make sure the doc builds correctly and fix any error

  • [ ] update jupyter books

  • [ ] update binder

  • [ ] update docker recipes

  • [ ] update changelog

  • [ ] run make release

  • [ ] open a pull request (PR) from this release candidate branch targeting the default branch

  • [ ] fix any remaining failing continuous integration (test, markdown and code linting…)

  • [ ] merge to default branch

  • [ ] create a tagged release

  • [ ] build and push docker images if necessary

  • [ ] after release

    • [ ] set version in citation.cff to dev

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