Cellfinder merge

[willGraham01]

Experimental merging of cellfinder-core and cellfinder-napari, preserving both repository histories whilst also keeping things compatible and the transition as smooth as possible.

Some things still on the to-do list:

• We might just want this to be a new repository and archive this one
• Incorporate the cellfinder CLI things into here too. Also means that we don't need an extra step for the CI tests

[deprecated-napari-hub-preview-bot[bot]]

Preview page for your plugin is ready here: https://preview.napari-hub.org/brainglobe/cellfinder-core/218 Updated: 2023-08-29T10:52:44.049974

[willGraham01]

Throwing in a comment here that this commit marks a successful merge-point. Still cellfinder to merge in though.

[adamltyson]

Should cellfinder be merged in? There's stuff in cellfinder that has nothing to do with cell detection and should probably live elsewhere.

[willGraham01]

Should cellfinder be merged in? There's stuff in cellfinder that has nothing to do with cell detection and should probably live elsewhere

Has anyone done an audit of sorts regarding this recently? We eventually want to remove/rename the package currently called cellfinder, so it's probably a good time to do this.

[adamltyson]

Only in my head :roll_eyes:. The tools in cellfinder basically combine brainreg & cellfinder-core to create a streamlined pipeline for one type of data. We could just rename cellfinder to something else. However, cellfinder in it's current form is used a lot, so I would rather we had a clear plan for rolling out the metapackage, along with docs & advertising before we started.

[willGraham01]

The tools in cellfinder basically combine brainreg & cellfinder-core

Kind of sounds like we almost want what is currently cellfinder to be put into brainglobe-meta, and then to turn cellfinder-core + cellfinder-napari => cellfinder?

[adamltyson]

Yes, although does brainglobe-meta contain any actual functionality? I know we're meant to be consolidating repos, but maybe we should create brainglobe-scripts or better yet brainglobe-workflows to contain this type of stuff? The cellfinder (to be renamed) command-line tool could live in there.

[willGraham01]

Yeah we can certainly do that - if anything it might be easier as then we just rename (current) cellfinder to brainglobe-workflows & make the necessary code changes, and can then immediately rename/put out our new cellfinder.

Will add this to the dev meeting notes for Thursday as it's probably a good idea we give this a dedicated discussion!

[adamltyson]

Will add this to the dev meeting notes for Thursday as it's probably a good idea we give this a dedicated discussion!

:+1:

can then immediately rename/put out our new cellfinder.

We need to make sure the docs are sorted before anything is released. This would be a major breaking change for BrainGlobe.

[willGraham01]

Closing in favour of the strategy in https://github.com/brainglobe/BrainGlobe/issues/46