Cellxgene-census

Changes
R and Python package dependencies updated to use TileDB-SOMA version 1.8.0

What's Changed
* [misc] Fix CL_0002494 in geneformer pipeline by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1000
* [docs] Add embeddings API to docs by martinkim0 in https://github.com/chanzuckerberg/cellxgene-census/pull/1005
* [docs] Fix docstrings for various functions by martinkim0 in https://github.com/chanzuckerberg/cellxgene-census/pull/1002
* [builder] fix incorrect filtering of tissue type by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/1010
* [misc] add support for var embeddings to contrib curation tool by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/995
* [builder] add explicit validation check for primary tissue cells by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/1015
* [builder] update uberon and tissue_general mapping to schema 4 standard by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/1018
* [docs] Update copyright notice by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/978
* [docs] misc docsite adjustments by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1020
* [profiler] Early version of profiler harness by beroy in https://github.com/chanzuckerberg/cellxgene-census/pull/959
* [docs] Geneformer docs errata by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/1003
* [python] [r] Upgrade to tiledbsoma 1.8.0 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1046

New Contributors
* beroy made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/959

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.10.2...v1.11.0

What's Changed
* [python] use new indexer in highly variable genes algorithm by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/973
* [python] updates to the SCVI model training pipeline by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/939
* [python] remove upper bound on numpy version dependency by martinkim0 in https://github.com/chanzuckerberg/cellxgene-census/pull/980
* [builder] use tiledbsoma indexer for builder validation pass by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/988
* [python] update to use tiledbsoma indexer for get_embedding by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/991


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.10.1...v1.10.2

What's Changed
Fixed an issue where the Python package name showed up as `cellxgene_census` instead of the intended `cellxgene-census`.


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.10.0...v1.10.1

Census S3 H5AD bucket now is limited to data present in Census

Beginning with the 2024-01-29 Census weekly build, the Census build will only include H5AD files contributing data to companion SOMA objects. Previously, Census builds included all H5ADs in the CELLxGENE corpus. Put another way, if a dataset fails to contribute a cell to the Census, the dataset H5AD will not be present in the Census build h5ad directory.

Changes

Minor updates in preparation for releasing December LTS Census and contributed embeddings.

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
* [builder] Update release cleanup code to support relative URIs by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/888
* [python] Geneformer WDL: pin TileDB and Census versions by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/889
* [misc] contrib embedding curation fixes by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/890
* [r] Update R docs in preparation for API release 1.9.1 by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/893


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.9.0...v1.9.1

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 https://github.com/chanzuckerberg/cellxgene-census/pull/868
* [builder] Absolute uris should use the default mirror by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/863
* [python] GeneformerTokenizer maintenance by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/861
* [python] migrate GeneformerTokenizer to blockwise iterator by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/866
* [python] [r] Fix tests that had the mirror name hardcoded by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/869
* [builder] Fix builder release manifest validation to not check for absolute uri by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/882
* [python] upgrade to tiledbsoma and add obsm to get_anndata by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/885
* [misc] Contrib embeddings by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/853
* [r] add obsm_layers to get_seurat() and get_single_cell_experiment() by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/887
* [python] Geneformer fine-tuning scripts by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/805
* [python] scVI pipeline by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/787


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.8.0...v1.9.0