FIX: blink annotations eyetracking/pupilometry

[schekroud]

Reference issue

Fixes #12408

What does this implement/fix?

properly adjusts blink onsets/offsets to account for the start time of the signal. This allows you to crop the signal and still have an accurate description of blink onsets

[schekroud]

@scott-huberty @larsoner sorry if i have completely screwed up how you guys normally do this - i closed the previous PR (i dont think i could edit the code once the PR was made) as i noticed it didn't import the annotations function needed (i incorrectly assumed it would be there by default, but then tested and found i was wrong).

This should work!

Again, sorry if i have messed up the normal workflow 😆

[larsoner]

@schekroud you can just edit the code in your schekroud:main branch on GitHub and those changes will be reflected in the PR. No need to close and open a new one

[scott-huberty]

No worries @schekroud there can be a learning curve for PR's. Have you read the contributing guide? I still use it from time to time to remind myself.

One comment (@larsoner can correct me if it isn't a big deal in this case), usually it's best to open a PR from a development branch (not your main branch). This should be covered in the contributing guide (let us know if it isn't).

[scott-huberty]

I just took a closer look at this PR. It looks like most of the failing tests are unrelated, and I think all of them should have been fixed by recently merged PR's (i.e. #12417 ).

@schekroud if you do want to work on this PR from a development branch here is what I would do:

git commands

(Assuming you are in the mne-python github respoitory directory, and on your main branch):

# note I have edited the commands below since initially posting this comment

# checkout new branch, bringing over commits from y9ou rmain branch
git checkout -b fix_interpolate_blinks

# add a link to the mne-python github repo, we'll call it "upstream"
git remote add upstream https://github.com/mne-tools/mne-python.git

# bring in the latest changes that have been merged into mne-python
git fetch upstream main
git merge upstream/main --ff-only

# push your new local development branch to your remote fork
 git push --set-upstream origin fix_interpolate_blinks

Then you could open another PR and close this one.

resetting your main branch to be in line with mne-pythons main branch

if you create a new branch with the changes from this PR, you'll want to reset your main branch:

git checkout main

git reset --hard upstream/main

Either way (you create a new dev branch or just continue this PR from your main branch), There a couple things to do.

1. add a new rst file to doc/changes/devel that describe the changes made by this PR. See https://mne.tools/dev/development/contributing.html#describe-your-changes-in-the-changelog
2. @larsoner should we amend test_interpolate_blinks to include a test with a cropped raw object?

[scott-huberty]

Hi @schekroud do you still have time to work on this? I think you just need to merge in the updates to mne since your last commit, and add an entry to the changelog (see point 1 in my previous message). Let me know if you need any support from us!

[mscheltienne]

I merged main. A test should be added to cover the previous failure.