[DOC] Example comparing spectral connectivity computed over time or over trials

[Avoide]

PR Description

This PR adds an example comparing spectral connectivity over time or trials and closes #70

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>"

[Avoide]

Hi @adam2392, here is a draft for an example comparing spectral connectivity computed over time or over trials on simulated data and sample EEG data.

[adam2392]

Thanks for the PR @Avoide ! I left some preliminary review comments to re-organize the code and notes a bit better.

There are also some style failures on the CI. Do you mind fixing those? You can run make pep to check these locally.

[Avoide]

@adam2392 I should have fixed the code style errors and have updated the places you mentioned in the review in the new commit

[adam2392]

There are some errors on the CI still: https://github.com/mne-tools/mne-connectivity/actions/runs/4322408221/jobs/7573270726. You can check these locally running make pep.

Hmm... for some reason the CI build docs is not working. Can you investigate? Does it build properly on your local?

[Avoide]

There are some errors on the CI still: https://github.com/mne-tools/mne-connectivity/actions/runs/4322408221/jobs/7573270726. You can check these locally running make pep.

Hmm... for some reason the CI build docs is not working. Can you investigate? Does it build properly on your local?

hmm I didn't see those spelling errors when I ran make pep locally. But I just fixed them according to the error on the CI job in the newest commit. Hopefully that should work.

[adam2392]

Looking good! Leaving some more in-depth review comments now.

For now, the cirlceCI is failing due to some upstream issues in mne-python. Can you add mne-qt-browser to the requirements_doc.txt file for the circleCI to correctly build the documentation?

So I'm leaving some additional comments based on rendering the docs locally. Is it possible to add colorbars to the plots?

[Avoide]

I updated the example, and also added circleci to the requirement_doc.txt.
There was also a small typo in contributing.md (requirement_doc.text, which I fixed to requirement_doc.txt).

[adam2392]

https://output.circle-artifacts.com/output/job/21c46aa5-0fb7-4326-8cdf-bb256e43ca8a/artifacts/0/dev/auto_examples/compare_connectivity_over_time_over_trial.html#sphx-glr-auto-examples-compare-connectivity-over-time-over-trial-py

• can you add a label to the colorbars?
• looks like high connectivity at 0.15-0.2 seconds after the visual task. Are there any references for this?

[adam2392]

Rendered docs: https://output.circle-artifacts.com/output/job/03472a75-4383-47d6-923f-9364a9a1b443/artifacts/0/dev/index.html

Very cool! It looks a lot better now. I'll take a closer look later.

[adam2392]

So it seems that circleCI always blocks your docs build because perhaps you haven't connected your GH account to there :(. Any chance you can just create an account and then the docs build should proceed without someone in the future explicitly running it? (Annoying feature, but I guess there for security) Xref: https://support.circleci.com/hc/en-us/articles/360037744473-What-is-an-Unregistered-User-

Can you also add the colorbar title?

[Avoide]

Sure, I just registered my GH at circleCI. Let's see if it works.

I also added the label "Connectivity" for the colorbars.

Edit: It seems to work automatically now
https://output.circle-artifacts.com/output/job/1a786059-dccd-46c5-a7c2-01a0526d6f42/artifacts/0/dev/auto_examples/compare_connectivity_over_time_over_trial.html

[adam2392]

Some final nitpicks and then this LGTM for merge.

Some open-ended comments, so lmk if you disagree.

[adam2392]

If a comment is resolved/addressed, you can feel free to click the "Resolve conversation"

[Avoide]

Thanks for the all comments. And the practical instructions are also useful to know, as this is my first PR.

I have incorporated all your newest comments in the latest commit.

[adam2392]

LGTM

[adam2392]

Thanks @Avoide!