Cellxgene-census

What's Changed
* Modify README.md to remove pre-release status by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/423
* Docsite GHA workflow by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/422
* Add Census link to docpage navbar by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/408
* Add missing docs dependency by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/425
* Incorporates comms edits and updates links to new landing site by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/421
* Fix docsite build by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/431
* [doc-site] Small formatting nit fixes, removes one R example in quick start by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/428
* Change plausible snippet to the new docsite by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/432
* Change plausible snippet to the new docsite for R by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/434
* open_soma() alias handling changes by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/435
* Updates cell number in docsite visual by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/437
* Move release.json location by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/443
* Docsite favicon by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/442


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.0.0rc1...v1.0.0rc2

What's Changed
* update python package name python demonstration notebooks by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/350
* rerun notebooks for census build 2023-04-04 by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/353
* Builder: additional workflow steps by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/351
* [r] use new SOMATileDBContext$context() accessor by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/357
* census_dataset_presence.ipynb typo fix by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/352
* readthedocs setup by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/335
* Miscellaneous R doc changes by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/338
* Miscellaneous docs updates by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/365
* Update documentation link in README.md by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/367
* Adds Census FAQ by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/362
* Add plausible to sphinx and pkgdown by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/366
* Update examples link in README.md by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/368
* Editorial changes to notebook `comp_bio_data_integration_scvi.ipynb` by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/370
* Editorial changes to notebook `census_axis_query.ipynb` by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/371
* Editorial changes to notebook `comp_bio_census_info.ipynb` by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/369
* Fix naming and links and small editorial changes of documentation. by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/373
* chore: fix link to tutorials in README by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/375
* refractor get_seurat, update docs and tests by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/381
* [r] add remaining API demo vignettes by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/358
* Use GET /datasets endpoint for builder by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/378
* New documentation pages by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/386
* Change template for docsite to look like cellxgene by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/385
* fix anchors in docs by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/387
* Audit notebook 4 by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/377
* Updates schema to 1.0 by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/374
* chore: pin uberon ontology version by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/388
* Make census builder adhere to census schema 1.0 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/394
* [r] revise census_query_extract.Rmd by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/393
* Stable route for release.json by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/409
* Miscellaneous doc fixes by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/413
* Fix for Mac OSX certificate issue by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/416
* bump tiledbsoma to 1.2.2 by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/419


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v0.13.0...v1.0.0rc1

What's Changed

**Breaking changes:**
* Python package name has changed to `cellxgene_census`.

**Fixes**:
* Fix Python package import error on Python 3.8

**Summary of commits:**
* acceptance test run by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/310
* Modify GHA to push builder Docker image by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/312
* Add requirements.txt for notebooks by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/308
* rename ECR repo by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/334
* clean up dependencies for cell_census by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/337
* Rename to CELLxGENE Discover Census in README.md by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/333
* Python API name changes by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/339
* Add builder sub-module for old build cleanup by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/331
* name migration for tools/builder by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/340
* package name changes in docstrings by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/343
* [r] rename CellCensus to cellxgene.census by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/344
* add old package name redirect by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/346
* Adds cell census release info and cleans up storage policy by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/314
* Add notebook guidelines by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/316
* update package metadata to tag maturity as beta by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/348
* update cell census name in docstrings/md files by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/347


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v0.12.0...v0.13.0

What's Changed

Update package dependencies to specify `tiledbsoma` version `1.2.1`.

* work-around and diagnostics for Ctx excess allocation bug by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/292
* [r] census_datasets vignette by mlin in https://github.com/chanzuckerberg/cell-census/pull/252
* miscellaneous builder fixes / cleanup by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/298
* adds bug issue template by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/303
* "acceptance" tests by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/305
* adds feature request template by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/302
* [r] add `get_seurat()` by mlin in https://github.com/chanzuckerberg/cell-census/pull/293


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.11.0...v0.12.0

What's Changed
This release updates the cell census package to use `tiledbsoma v1.1.1`

* open_anndata unit test by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/254
* Unit tests for staging datasets by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/258
* Add validation data checks by Bento007 in https://github.com/chanzuckerberg/cell-census/pull/243
* setup_module for multiprocessing tests (test_source_assets) by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/262
* assertion to confirm correct MP configuration by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/263
* [r] use SOMATileDBContext by mlin in https://github.com/chanzuckerberg/cell-census/pull/256
* Util unit tests by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/261
* Update lifecycle annotations to be consistent with tiledbsoma by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/264
* Dockerfile for census builder by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/267
* [r] add `get_presence_matrix` by mlin in https://github.com/chanzuckerberg/cell-census/pull/274
* Add note to tissue_mapper.py by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/276
* Adds text to README to indicate pre-release state by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/273
* fix email address in Python package metadata by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/281
* Update readmes by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/282
* improved build workflow by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/272
* Add nbqa to reformat notebooks by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/277
* update Python package dependency to tiledbsoma 1.1.1 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/287


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.10.0...v0.11.0

What's Changed

Updated package to use `tiledbsoma` version `1.0.0`. There should be no breaking API changes.

* add unit tests for python cell_census package by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/244
* [ci] fix paths-ignore in workflow YMLs by mlin in https://github.com/chanzuckerberg/cell-census/pull/251
* [r] add source h5ad accessor functions by mlin in https://github.com/chanzuckerberg/cell-census/pull/250
* Update to tiledbsoma 1.0.0 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/255


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.9.0...v0.10.0