v1.0.0

[1.0.0] - 2025-08-09

Pre-publication release (for Zenodo DOI creation).

Added

• Support multimodality (H&E + spatial omics). See this tutorial.
• Support multi-references in fine_tune and zero-shot modes
• Added novae.plot.loss_curve for minimal monitoring when not using Weight & Biases

Changed

• fine_tune method: use lr = 5e-4 and max_epochs = 20 as new default values
• Use reference="all" instead of "largest" by default
• Move novae.utils.load_dataset to novae.load_dataset (the old import is deprecated, it will be removed in future versions)
• Move novae.utils.quantile_scaling to novae.quantile_scaling (deprecated, as above)
• Move novae.utils.toy_dataset to novae.toy_dataset (deprecated, as above)
• Migrate to uv as a package manager, and ruff for formatting/linting

Fixed

• Slide-id passed correctly to dataloader for one-adata multi-slide mode
• Auto-detect change in n_hops_{local,view} to re-build graph
• Move representations to numpy when torch is not needed anymore (#19)