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CONTRIBUTING.md

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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 -C doc 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
    • change from [unreleased] to the version number
    • remove unused sections (like security)
  • 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 github tagged release
  • build and push docker images if necessary
  • after release
    • set version in citation.cff to dev
    • update changelog
      • add an [unreleased] section