Background Components for Caiman

[pauladkisson]

Fixes #782

Follow-up from ROIExtractors #291

[CodyCBakerPhD]

pauladkisson requested review from CodyCBakerPhD and alessandratrapani 13 minutes ago

@pauladkisson Tests are failing at installation - can you update the pin?

[pauladkisson]

@CodyCBakerPhD It's ready now

[CodyCBakerPhD]

LGTM but Alessio was requesting a quick rerelease following some bug fixes to the backend configuration and we wouldn't be able to do that until the ROIExtractors pin is released

So I guess question is, how soon can we get an ROIExtractors release?

[pauladkisson]

I think we can cut a release of ROIExtractors right away, but I'd like @EricThomson to take a look before we merge as well.

[pauladkisson]

No response from Eric Thompson, but I don't want to leave this hanging forever, so I think we should go ahead with this and he can raise an issue if he runs into any problems with it.

[CodyCBakerPhD]

@pauladkisson Does look like one test case broke a while ago

[pauladkisson]

Yeah, it looks like the conversion_options_schema doesn't like None for mask_type...

I tracked it down to src/neuroconv/utils/json_schema.py,

annotation_json_type_map = dict(
        bool="boolean",
        str="string",
        int="number",
        float="number",
        dict="object",
        list="array",
        tuple="array",
        FilePathType="string",
        FolderPathType="string",
    )

Apparently None isn't a valid type? I don't understand why we would annotate add_to_nwbfile as if you can provide none, if the schema doesn't actually let you do it. @CodyCBakerPhD, can you shed some light on this?

It does seem a bit outside of the scope of this PR tho.

[CodyCBakerPhD]

This has been known since #530 and would be resolved with the Pydantic integration for handling all schema validations and signature parsing - for now I'd just comment out that one test case since we're already aware of it

[EricThomson]

Sorry I was away last month when that @ came in. I'm back and can look things over now (early next week) if it would help?

[pauladkisson]

Sorry I was away last month when that @ came in. I'm back and can look things over now (early next week) if it would help?

Sure! That would be great! Just raise an issue and @ me if you run into any problems.

[codecov]

Codecov Report

Attention: Patch coverage is 93.10345% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 91.72%. Comparing base (a7b684a) to head (bbae94f).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #783      +/-   ##
==========================================
- Coverage   91.72%   91.72%   -0.01%     
==========================================
  Files         122      122              
  Lines        6682     6728      +46     
==========================================
+ Hits         6129     6171      +42     
- Misses        553      557       +4     

Flag	Coverage Δ
unittests	91.72% <93.10%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
...rfaces/ophys/basesegmentationextractorinterface.py	100.00% <ø> (ø)
src/neuroconv/tools/roiextractors/__init__.py	100.00% <ø> (ø)
src/neuroconv/tools/roiextractors/roiextractors.py	88.02% <93.10%> (+0.39%)	⬆️