Cellxgene-census

What's Changed
* Upgrade to `tiledbsoma` 1.11.4 ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1185
* [python] Make docs searchable by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1166
* [python] Progress bar for download_source_h5ad by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1153
* [docs] Add cell guide notebook for queries on cell type descendants by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1163
* [docs] Update links to gget website and author email by lauraluebbert in https://github.com/chanzuckerberg/cellxgene-census/pull/1171
* [docs] Remove newsletter banner by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1161
* [python] Use pyproject.toml for doc env by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1172
* [python] Fix wrong parameters in ExperimentDataPipe by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1178



**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.14.0...v1.14.1

Major changes
- Upgrade to `tiledbsoma` 1.11.3
- Add a [cellxgene_census.get_obs](https://github.com/chanzuckerberg/cellxgene-census/blob/main/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py#L175) utility function that can be used to return an obs dataframe in Pandas format more easily.

What's Changed
* [builder] Update list of accepted assays and bump schema to 2.0.1 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1117
* [docs] update scvi notebook to use latest model by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1137
* [docs] Update geneformer notebook to latest API changes by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1138
* [docs] Add development setup notes for Census API by prathapsridharan in https://github.com/chanzuckerberg/cellxgene-census/pull/1111
* [python] Add get_obs by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1151
* [python] share census objects in tests for faster test time by ivirshup in https://github.com/chanzuckerberg/cellxgene-census/pull/1156
* [builder] Bump requests from 2.31.0 to 2.32.0 in /tools/cellxgene_census_builder by dependabot in https://github.com/chanzuckerberg/cellxgene-census/pull/1154
* [builder] Add ClientResponseError to the builder managed exceptions by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1126
* [python] [R] Bump tiledbsoma to 1.11.3

New Contributors
* ivirshup made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/1151

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.13.1...v1.14.0

Changes
This release pins `pytorch` to 2.2.0 to work around an incompatibility with `torchdata` introduced by the latest `pytorch` release. Therefore, if you're using the Census pytorch loaders and you're seeing dependency issues, you should upgrade to this version.

What's Changed
* [docs] add news article for categoricals by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1086
* [docs] Add 2024 articles to docsite by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1088
* [misc] Remove MacOS support claim for census builder by prathapsridharan in https://github.com/chanzuckerberg/cellxgene-census/pull/1084
* [builder] cellxgene_ontology_guide integration by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1094
* [builder] Remove datasets from "HTAN VUMC" Collection from the blocklist by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1099
* [docs] Update embedding notebook by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/1124
* [ci] Fix torch dependency issue and pause tests on Mac/Python3.8 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1118
* [python] Fix pytorch imports by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1129


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.13.0...v1.13.1

New embeddings API
Census embeddings can now accessed using a new, simplified API. Check the notebooks for [collaboration](https://github.com/chanzuckerberg/cellxgene-census/blob/main/api/python/notebooks/api_demo/census_access_maintained_embeddings.ipynb) and [hosted](https://github.com/chanzuckerberg/cellxgene-census/blob/main/api/python/notebooks/api_demo/census_embedding.ipynb) models for more information.

obs columns are now categorical instead of strings
Starting from the `2024-04-01` Census build, a subset of the columns in the `obs` dataframe are now categorical instead of strings.

For **Python users**, note that Pandas will encode these columns as `pandas.Categorical` for which some downstream operations may need to be adapted. See [this link](https://pandas.pydata.org/docs/user_guide/categorical.html#operations) for more details. In particular:

> Series methods like Series.value_counts() will use all categories, even if some categories are not present in the data

and

> DataFrame methods like sum, groupby, pivot, value_counts also show “unused” categories when observed=False, which is the default.

For **R users**, note that these columns will be encoded as `factor` and similarly downstream operations may need to be adapted. See [this link](https://r4ds.had.co.nz/factors.html) for more details.

For **Python and R users** interfacing with `arrow`, these columns will be encoded as `dictionary`, see more details for R in [this link](https://arrow.apache.org/docs/r/reference/dictionary.html) and Python in [this link](https://arrow.apache.org/docs/python/generated/pyarrow.dictionary.html).

Additions
* [builder] enable Arrow Dictionary feature flag by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/1064
* [python] New embeddings API by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1023
* [docs] New embeddings API notebooks by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/1070


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.12.0...v1.13.0

Changes
* Fix r-universe build

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