[ENH] Multiple improvements to spectral_connectivity_time: ciPLV, and efficient computation of multiple metrics

[ruuskas]

PR Description

This PR addresses improvements mentioned in #104. I'm reposting this with the Git log now cleaned up.

• Add ciPLV metric.
• Compute all connectivity measures at once, avoiding the repeated computation of the cross-spectral density.
• Reinstitute the option to specify frequencies of interest also when using the multitaper method. The reasoning is that users should have control over the sparsity of the frequency grid.
• Add the option to use parts of each epoch as padding. This allows for the mitigation of edge effects in the time-frequency decomposition. The edges are removed after time-frequency decomposition, but before connectivity computation.
• Improve the function description to better describe the objective.

Merge checklist

Maintainer, please confirm the following before merging:

• [ ] All comments resolved
• [ ] This is not your own PR
• [ ] All CIs are happy
• [ ] PR title starts with [MRG]
• [ ] whats_new.rst is updated
• [ ] PR description includes phrase "closes <#issue-number>"

[ruuskas]

It looks like the CIs are not happy about the docs and loading the Matplotlib Qt backend fails with Python 3.7.

I can't check what's wrong with the docs it seems. Building locally, it complains about 'secondary_sidebar_items': ['page-toc'] added here.

[adam2392]

It looks like the CIs are not happy about the docs and loading the Matplotlib Qt backend fails with Python 3.7.

I can't check what's wrong with the docs it seems. Building locally, it complains about 'secondary_sidebar_items': ['page-toc'] added here.

Should be fixed now on main.

[adam2392]

Feel free to ping me whenever you need me to take a look again!

[adam2392]

Happy new years @ruuskas ! Just wanted to check in on this. It would be great to get this in and make a new release w/ all your cool improvements!

[ruuskas]

Happy new year @adam2392 ! I have been focusing on other things so this has been lagging. I'll try to get the necessary changes done this week (maybe today if there are no blockers).

[ruuskas]

Hi @adam2392 ! This should now be ready for review again. The freqs parameter is now required and I added a test for padding. It was a good idea since there was a bug hiding indeed.

Sphinx is not happy as there seems to be an issue with indentation in the docstring, which I couldn't figure out without changing config.

[drammock]

Sphinx is not happy as there seems to be an issue with indentation in the docstring, which I couldn't figure out without changing config.

The sphinx error:

sphinx.errors.ThemeError: An error happened in rendering the page api.
Reason: UndefinedError("'logo' is undefined")

is due to a change in sphinx 6.0 and is currently being addressed upstream in the website theme. Temporary workaround is to pin sphinx to <6.0

[ruuskas]

The Sphinx error I get locally is different. I can copy it verbatim tomorrow, but essentially "unexpected indentation" in the docstring. Indentation looks fine where it points to though.

[adam2392]

@ruuskas I fixed the indentation error and other sphinx issue. You have to git pull to sync changes.

[ruuskas]

Hi @adam2392! I addressed all the things you pointed out and pushed changes. WDYT?

[adam2392]

Thanks @ruuskas! Great addition and contribution.

[ruuskas]

Thanks @adam2392!