Remove Cellpose ROI overlap check

[jluethi]

Closes #779

I decided against a detailed further review of this performance. Given that it is often a bottleneck in performance and its only value is a warning, I suggest we remove the check completely. We can reintroduce more relevant checks later if needed.

Checklist before merging

• I added an appropriate entry to CHANGELOG.md

[github-actions]

Coverage report

This PR does not seem to contain any modification to coverable code.

[jluethi]

@tcompa 2 brief CI questions:

1. It looks like we aren't testing the get_overlapping_pairs_3D anywhere else. I'm a bit hesitant to remove it, but it's not worth the trouble of adding specific tests for a function we aren't using. Opinions?
2. Any idea why our CI now thinks we only have a 30% coverage rate? Is it looking for 7k lines of something we aren't supposed to be testing? Would be useful to fix

[tcompa]

Any idea why our CI now thinks we only have a 30% coverage rate? Is it looking for 7k lines of something we aren't supposed to be testing? Would be useful to fix

This is the issue which hit us during the ngio-task PR: coverage is counting a bunch of internal modules, see https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-tasks-core/blob/python-coverage-comment-action-data/htmlcov/index.html:

It's the same as #881. I'll have to debug it again, cause the first round was not successful.

[tcompa]

It looks like we aren't testing the get_overlapping_pairs_3D anywhere else. I'm a bit hesitant to remove it, but it's not worth the trouble of adding specific tests for a function we aren't using. Opinions?

It is used in https://github.com/fmi-basel/gliberal-scMultipleX/blob/1413c909588508d0a2d9bf3d423a5e4d3c3cb8f2/src/scmultiplex/fractal/surface_mesh_multiscale.py#L27, thus we cannot remove it.

I can quickly add a test, if it's useful.

[tcompa]

It is used in https://github.com/fmi-basel/gliberal-scMultipleX/blob/1413c909588508d0a2d9bf3d423a5e4d3c3cb8f2/src/scmultiplex/fractal/surface_mesh_multiscale.py#L27, thus we cannot remove it.

This obviously change if we plan to also propose a PR that removes that feature from scmultiplex (and if we think nobody else is using it).

[jluethi]

Hmm, multiple tasks use Cellpose as a template. Besides scmultiplex, it's also the private rdcnet task that is also using this function.

I think we should not remove the function before the fractal-tasks-core 2.0 update, as it would break multiple other packages. But we should stop using it ourselves in the cellpose task.

[jluethi]

I can quickly add a test, if it's useful.

If we have a good setup to add a basic test, nothing against that. But given that we may deprecate it anyway later, let's not spend too much time on that

[tcompa]

The test is now in-place.

The coverage message is obviously wrong, but this is due to my other activities (outside this PR).

In principle you can already merge this PR, since I only added a (passing) test to the previous PR state. I'm still working on fixing the coverage issue, but that's unrelated.

[jluethi]

Thanks a lot @tcompa !