[Feature] `cellfinder` migration to `workflows` for BG-v1

[willGraham01]

Subtask of #33.

Migration of cellfinder to brainglobe-workflows.

The next stage in our migration to BrainGlobe version 1 will be to move the functionality of the cellfinder command-line tool into the workflows repository, and allow it to be installed by users.

The following tasks need to be completed:

cellfinder

• [x] Fix outstanding bugs
• [x] Open "repository has moved PR": https://github.com/brainglobe/cellfinder/pull/261
  • [x] Update README to point to workflows
  • [x] Merge in and tag cellfinder version <1. Tagged v0.8.1.
  • [x] PUSH TO PYPI
  • [x] DO NOT archive repository. We need it open for when we replace the functionality with a merge of cellfinder-core and cellfinder-napari.
  • [x] Migrate issues to workflows, and tag with "old cellfinder" so context is not lost.

workflows

• [x] Merge in cellfinder history, and reconcile with existing changes https://github.com/brainglobe/brainglobe-workflows/pull/29
  • [x] Update package metadata
  • [x] CLI workflow cellfinder to be given a new name - @adamltyson any suggestions?
  • [x] Give this workflow a temporary cellfinder alias to allow a grace period for migrating users.
  • [x] Ensure that manifest does not package our internal benchmarking tests!
  • [x] Update README to incorporate the cellfinder CLI function
• [x] Merge and tag a version 1 release
• [x] Push to PyPI

Dev branch: https://github.com/brainglobe/brainglobe-workflows/pull/29

website | https://github.com/brainglobe/brainglobe.github.io/pull/101

• [x] Blog post ready with cellfinder migration changes
• [x] Update v1 changelog
• [x] Update cellfinder docs page with redirect to workflows
• [x] Update workflows page (or create it if it does not exist!) with user-facing functionality
  • [x] Update developer docs if necessary with the benchmarking role of workflows.

[adamltyson]

CLI workflow cellfinder to be given a new name - @adamltyson any suggestions?

Nothing good. brainglobe-wholebrain-detection? Can we also keep cellfinder, maybe with a deprecation warning?

[willGraham01]

For now we can keep cellfinder as the name - I can mention in the blog that a name change is on the way but keep cellfinder for the time being

[willGraham01]

Closed as successfully deployed :partying_face: