GSoC 2021 - Refactoring mne.connectivity into mne-connectivity repository

This issue is meant to track the progress of refactoring existing functionality inside mne-python’s “connectivity” sub-module into an entirely new repository.

• Create new repository, mne-connectivity, inside mne.tools (I think I have access)
• Get CI and basic GH action tools setup, based on mne-bids and mne-python CI
• Refactor existing code into the mne-connectivity repo and include a validation notebook that validates that code in this refactored setting matches what is here

To track detailed progress inside mne-connectivity, such as getting CI up and running, I’ll point to issues in that specific repository.

Higher level goals

I think @agramfort spoke about this a bit with me and I agree: there is really no “great way” of saying which algorithm or model is better in certain instances. There are many “proposed connectivity algorithms”, whether they are time-domain, or free-domain based. So the metric moving forward in this new repo is to at least standardize what you should expect on a dataset.

Given 1-3 datasets, running a specific algorithm, one should expect certain performance or values. The current goal is to leverage openneuro and pull datasets for doing this in CI.

Reference Issues

#9060 #9030 #8729

[larsoner]

@adam2392 I read this only after making my comment in the other repo, which seems to echo almost 1:1 what you wrote here – so sounds good to me 😃

The current goal is to leverage openneuro and pull datasets for doing this in CI.

I would start smaller and try using toy or simulated datasets – preferably there are some of these in the reference papers. Once that works, examples that build on CircleCI to give outputs for real-data inputs are great, but I wouldn’t start from these if possible because debugging them will be harder both in terms of eyeballing errors and in terms of CI time (they are going to require a big download and a long processing time compared to a toy example).

[wmvanvliet]

This sounds like something I could merge the conpy module into.