[Feature] BG-V1: cellfinder-core and napari merge

[willGraham01]

cellfinder-core and cellfinder-napari merge

Subtask of #33 | Depends on #45

A complete list of changes that need to be staged for the merging of cellfinder-core and cellfinder-napari into the existing cellfinder repository.

The existing cellfinder repo will have been migrated to workflows by #45, so we will be rm-ing the history of main with this update!

cellfinder-core

• Update with "final version" release. Stage as a PR against main. Prepare for retirement cellfinder-core#226
  • Point users to cellfinder repository as replacement
  • Point users to the blog post for more information
  • Tagged version should be =v1.0.0 so that users can revert to old version easily, if they wish
  • Push to PyPI
• Depreciate package on PyPI
• Migrate issues to cellfinder repo
• Archive repository

cellfinder-napari

• Update with "final version" release. Stage as a PR against main. Prepare for retirement cellfinder-napari#177
  • Point users to cellfinder repository as replacement
  • Point users to the blog post for more information
  • Tagged version should be =v1.0.0 so that users can revert to old version easily, if they wish
  • Push to PyPI
• Depreciate package on PyPI
• Migrate issues to cellfinder repo
• Archive repository

cellfinder

• Create dev branch for pulling-in of cellfinder-core and cellfinder-napari: https://github.com/brainglobe/cellfinder/tree/dev-bg-v2 is the branch with the merged versions of cellfinder-core and cellfinder-napari.
  • Add a CLI alias for "cellfinder" that tells users to install BG-workflows and use the updated name.
  • Ensure headless display fix is incorporated into dev branch
  • This will need to be a clean branch, with no related history to main
    • It should be this branch which will need to be pulled from cellfinder-core
    • There will be two submodules, core and napari, that perform analogous functions to the previous separate repositories
    • napari-hub preview workflow to be binned: Remove napari plugin preview workflow cellfinder#251
  • Package metadata needs updating
    • The two READMEs from cellfinder-napari and cellfinder-core need to be reconciled
    • The badges and pins should update to point to the cellfinder repo on PyPI
    • Move appropriate README content to the documentation website
• Move current main branch to cellfinder-pre-brainglobe-v1. Lock the branch if possible, and no longer make it default.
• Move dev branch to main, and setup the appropriate CI checks and protection rules. Adjust the workflows if not done automatically.
• Publish v1.0 release to PyPI ASAP, from the "new main" branch
• Reinstate brainmapper ci check cellfinder#347
• Re-in CI checks once brainglobe-workflows update goes in

brainglobe/website

• Merge in when ready: cellfinder-core and cellfinder-napari merge update brainglobe.github.io#104
• Accomodate cellfinder CLI renaming to brainmapper as per Zulip chat.
• Blog post
• Update v1 release changelog
• Update install guidelines
  • Recommended install is pip into a clean venv/conda env etc.
  • MacOS M1 users have issues with napari, which will require some additional instructions
• Update developer / contributing docs
• Update tool documentation - will need to move core and napari info into a single place

brainglobe-workflows

• cellfinder-core/napari text in README to be updated
• Package to depend on cellfinder version >=1 again
• API needs to switch from cellfinder-core to cellfinder.core etc
• Accomodate cellfinder CLI renaming to brainmapper as per Zulip chat.
• Prepare for cellfinder merge brainglobe-workflows#54 <- merge when cellfinder new version is released and CI passes!
• Release new version v1.1.0 to PyPI

[willGraham01]

Closing as completed with the migration on 2024-01-03.