Add BIDS reading support and prepare input loading for pydra workflow - Githubissues

physiopy / physutils

Common tools for the physiopy suite

Apache License 2.0

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Add BIDS reading support and prepare input loading for pydra workflow #7

Closed maestroque closed 1 month ago

maestroque commented 3 months ago

Closes #9

Proposed Changes

Add a transform_to_physio pydra task to be used in all worfklows

Change Type

[ ] bugfix (+0.0.1)
[x] minor (+0.1.0)
[ ] major (+1.0.0)
[ ] refactoring (no version update)
[ ] test (no version update)
[ ] infrastructure (no version update)
[ ] documentation (no version update)
[ ] other

Checklist before review

[ ] I added everything I wanted to add to this PR.
[ ] [Code or tests only] I wrote/updated the necessary docstrings.
[ ] [Code or tests only] I ran and passed tests locally.
[ ] [Documentation only] I built the docs locally.
[ ] My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
[ ] My code respects the adopted style, especially linting conventions.
[ ] The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
[ ] I added or indicated the right labels.
[ ] I added information regarding the timeline of completion for this PR.
[ ] Please, comment on my PR while it's a draft and give me feedback on the development!

me-pic commented 3 months ago

Other than the changes requested by Stef, LGTM !

maestroque commented 2 months ago

I also added an auto mode, as per https://github.com/physiopy/phys2denoise/pull/57#discussion_r1738173058 @smoia @me-pic @m-miedema

m-miedema commented 2 months ago

@maestroque do you need any help addressing @smoia's comments?

smoia commented 1 month ago

@maestroque any progress on this side?

maestroque commented 1 month ago

@smoia @m-miedema I didnt have in mind that there was something pending for this sorry. As far as i can tell only the dependencies issue opening

smoia commented 1 month ago

@maestroque @m-miedema @me-pic I opened a PR to @maestroque 's branch: ~https://github.com/maestroque/physutils/pull/1/files~ https://github.com/maestroque/physutils/pull/2/files

It should take care of most issues. Emphasis on should.

smoia commented 1 month ago

And I also made a mess out of it - sorry. I shoudl have fixed things now, but the PR is #2 not #1

smoia commented 1 month ago

The only thing is that logging is still a bit weird cause it uses logging on one side and loguru on the other. Maybe we should just use logging for the moment?

maestroque commented 1 month ago

@me-pic @smoia please check the comments, unfortunately I cannot look into this right now. Before the changes it was ready however.

smoia commented 1 month ago

:rocket: PR was released in 0.3.0 :rocket: