v1.0.1

[1.0.1] - 2025-12-10

🎉 Novae is now published in Nature Methods!

Added

• Full dataset added to our Hugging Face Hub
• Official Docker images released - see here
• Support reference=None in fine_tune (random initialization) and use it as default
• Added fast argument in novae.plot.domains to have a quick (but less accurate) rendering of domains.
• Added novae.settings.scale_to_microns if the coordinates are not in microns
• Use fast-array-utils to support multiple backends in adata.X (e.g., dask or backed mode)

Breaking changes

• Remove support for python==3.10

Changed

• Update hf-hub to use xet for faster dataset download from Hugging Face Hub
• Update to spatialdata>=0.5.0 to avoid installation issue related to xarray-dataclasses
• Threshold to decide when to enable lazy loading: based on n_obs * n_vars (i.e., the array size) instead of n_obs

Fixed

• Retrieve mode=multimodal when saving the model and re-loading the model after H&E training (#24)
• Fix tests for recent AnnData versions only supporting CSR/CSC sparse matrices