Novae

Added
- `load_dataset`: add `custom_filter` and `dry_run` arguments
- added `min_prototypes_ratio` argument in `fine_tune` to run `init_slide_queue`
- Added tutorials for proteins data + minor docs improvements

Fixed
- Ensure reset clustering if multiple zero-shot (9)

Changed
- Removed the docs formatting (better for autocompletion)
- Reorder parameters in Novae `__init__` (sorted by importance)

Added
- `novae.utils.quantile_scaling` for proteins expression

Fixed
- Fix autocompletion using `__new__` to trick hugging_face inheritance

Added

- `novae.plot.connectivities(...)` to show the cells neighbors
- `novae.settings.auto_processing = False` to enforce using your own preprocessing
- Tutorials update (more plots and more details)

Fixed

- Issue with `library_id` in `novae.plot.domains` (8)
- Set `pandas>=2.0.0` in the dependencies (5)

Breaking changes

- `novae.utils.spatial_neighbors` must always be run, to force the user having more control on it
- For multi-slide mode, the `slide_key` argument should now be used in `novae.utils.spatial_neighbors` (and only there)
- Drop python 3.9 support (because dropped in `anndata`)

First official `novae` release. Preprint coming soon.