v1.9.0

Changes

• R and Python package dependencies updated to use TileDB-SOMA version 1.6.0

Deprecations

• [python] cellxgene_census.experimental.util.X_sparse_iter is deprecated and will be removed in a future release. Please use the new SOMA blockwise iterators available on the SparseNDMatrix class.

What's Changed

• [misc] Bump aiohttp from 3.8.6 to 3.9.0 in /tools/cellxgene_census_builder by @dependabot in #868
• [builder] Absolute uris should use the default mirror by @ebezzi in #863
• [python] GeneformerTokenizer maintenance by @mlin in #861
• [python] migrate GeneformerTokenizer to blockwise iterator by @mlin in #866
• [python] [r] Fix tests that had the mirror name hardcoded by @ebezzi in #869
• [builder] Fix builder release manifest validation to not check for absolute uri by @ebezzi in #882
• [python] upgrade to tiledbsoma and add obsm to get_anndata by @ebezzi in #885
• [misc] Contrib embeddings by @bkmartinjr in #853
• [r] add obsm_layers to get_seurat() and get_single_cell_experiment() by @mlin in #887
• [python] Geneformer fine-tuning scripts by @mlin in #805
• [python] scVI pipeline by @ebezzi in #787

Full Changelog: v1.8.0...v1.9.0