[BPT-155] Spatial Data Refactor

[dylanclam12]

Refactoring Bento with SpatialData

• [x] change all file permissions back to 755
• [x] add summary list of changes
• [ ] datasets module refactor
• [x] signatures module refactor
• [x] defer to native SpatialData API for query
• [x] change bento.geo.get_points astype parameter options to lowercase
• [x] change bento.geo.sindex_points unindexed points from "None" to empty string
• [x] in bento.tl.lp pull out gene expression array into variable so it is not queried twice
• [x] cleanup unused @ track, batch, copy
• [x] in bento.tl.fe make getting sparse matrix in csr format more readable
• [x] resolve SpatialData as dependency
• [x] validate cell raster points and fluxmap shapes using spatialdata parse functions.
• [x] convert flux and flux_embed in cell raster points to individual columns so they can be saved
• [x] unit tests

[notion-workspace[bot]]

Port spatial features

[dylanclam12]

• [ ] change all file permissions back to 755
• [ ] cleanup commented out imports and decorators (track)
• [ ] add summary list of changes
• [ ] unit tests

Moved to PR Summary

[LucaMarconato]

🥳