Cellxgene-census

Changes
* Fix r-universe build

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.11.0...v1.11.1

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.