Cellxgene-census

The Census builder is now using [Census schema 2.0.0](https://github.com/chanzuckerberg/cellxgene-census/blob/main/docs/cellxgene_census_schema.md) which in turn uses [CELLxGENE dataset schema version 5.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.0.0/schema.md). All [Census data releases](https://github.com/chanzuckerberg/cellxgene-census/blob/main/docs/cellxgene_census_docsite_data_release_info.md) starting on 2024-03-26 will adhere to this schema.

* Update to require [CELLxGENE schema version 5.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.0.0/schema.md). **Includes breaking changes**.
* Expanded list of assays included in the Census.
* Expanded the list of assays defined as full-gene sequencing assays, which have special normalized layer handling.
* Clarified handling of datasets which are multi-species on the obs or var axis.

Additions
* [builder] CxG schema 5 / Census schema 2 by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/1024

What's Changed
* [misc] 'native cell' -> 'unknown' on geneformer label_blocklist by danieljhegeman in https://github.com/chanzuckerberg/cellxgene-census/pull/999
* [misc] Prepare for 1.12.0 release by prathapsridharan in https://github.com/chanzuckerberg/cellxgene-census/pull/1061

New Contributors
* danieljhegeman made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/999

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.11.1...v1.12.0

The Census is now using [CELLxGENE schema version 4.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md).

Additions

* [docs] Adds biological demonstration notebooks by atarashansky in https://github.com/chanzuckerberg/cellxgene-census/pull/875
* [docs] Add citation notebooks by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/916
* [builder] schema 4.0 by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/872

Breaking changes

* [python] remove deprecated X_sparse_iter API by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/962

What’s Changed

* [python] [R] upgrade tiledbsoma to 1.7.0 by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/969
* [docs] add `no-sign-request` flag to model download in tutorials by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/956
* [builder] remove unused H5AD files from build by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/946
* [python] Syntactic sugar for specifying tiledb_config options by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/902
* [python] Make default soma context available for customization by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/895

New Contributors
* atarashansky made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/875
* seve made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/846

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.9.1...v1.10.0

What's Changed

* [python] Fix vector search import by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1287
* [python] Pin against tiledbsoma 1.14.1 by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1290
* [docs]: Add banner and newsletter signup (SCE-29) by kaloster in https://github.com/chanzuckerberg/cellxgene-census/pull/1286
* [python] Correct docs on default behaviour for DataLoader no longer including soma_joinid by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1292

New Contributors
* kaloster made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/1286

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.16.1...v1.16.2

What's Changed

* [python] Fix `predict_obs_metadata` when number of neighbors isn't `10` by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1277

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.16.0...v1.16.1

What's Changed

* [python] Embeddings search experimental API by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/1164
* [python] Add comp_bio_embedding_search notebook by mlin pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1241 https://github.com/chanzuckerberg/cellxgene-census/pull/1270
* Add FAQ on access from behind a proxy by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1266
* [docs] Update landing page with latest LTS data and API release. "Adds Release notes" link by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1239
* [python] Update minimum versions of dependencies + python versions following [SPEC-0](https://scientific-python.org/specs/spec-0000/) by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1189
* [python] Bump minimum tiledbsoma version to 1.12.3 by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1235
* [docs] Fix model names in metrics article by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1248
* [docs] Fix date on `cellxgene_census_docsite_data_release_info.md` by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1259

* Add Boroni collection to blocklist by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1262
* feat: Update navbar to include Differential Expression by tihuan in https://github.com/chanzuckerberg/cellxgene-census/pull/1264

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.15.0...v1.16.0

What's Changed

* [python] Shuffle multiple SOMA chunks by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/1103
* [python] Relax pin: `tiledbsoma~=1.11.4` by ryan-williams in https://github.com/chanzuckerberg/cellxgene-census/pull/1187
* [pytorch] Set shuffle as default in pytorch, use new algorithm by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1188
* [python] Remove pytorch pin by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1190
* [builder] Vector indexing pipeline for Census embeddings by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/1122
* [builder] Add collection_doi_label to the datasets dataframe by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1200
* [python] Require scikit-misc < 0.4 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1213
* [builder] Upgrade to CELLxGENE schema 5.1 by Bento007 in https://github.com/chanzuckerberg/cellxgene-census/pull/1192
* [docs] Update schema doc for version 2.1.0 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1211
* [python] Update scvi pipeline for the June LTS training by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1173
* [python] Check census version for get_all_available_embeddings by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1207
* [python] Move to {obs/var} specific arguments for get_anndata by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1149
* [python] Stop including `"do_not_delete"` key in result of `get_census_version_directory` by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1215
* [python] Add package specific user-agent by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1193
* [python] Update docs for `get_obs`, `get_var` by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1170
* [python] Geneformer updates for July 2024 LTS by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/961
* [python] Support custom obs encoders by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1191
* [python] Fix ExperimentDataPipe length by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1221
* [python] dataloader optimization (picking up 1169) by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1224
* [docs] Update census data release page with upcoming LTS information by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1210
* [docs] Add PyTorch loaders article release by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1214
* [python] Geneformer CLS embeddings by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/1225
* [docs] Update the Logistic Regression pytorch notebook by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1230
* [docs] Add metrics article for LTS 2024-12-15 by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1233


New Contributors

* ryan-williams made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/1187

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.14.1...v1.15.0