Cellxgene-census

Fixes/changes:
* Documentation and docsite improvements
* Fix issue 622, inconsistent default `census_version` used in various API endpoints

What's Changed
* pin builder dependencies by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/594
* pytorch eager fetch follow-up by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/592
* Adds sparse iter reference docs to doc-site by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/597
* docs: Add newsletter banner by tihuan in https://github.com/chanzuckerberg/cellxgene-census/pull/605
* change error handling for /curation REST errors by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/608
* Add R acceptance tests, update Python acceptance tests by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/576
* Expand doc-site section "Census data releases" and add data erratum by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/600
* [r] get_seurat: allow selection of Seurat `counts` or `data` slot by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/607
* fixes minor documentation issues by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/619
* Complete docstrings for PyTorch ExperimentDataPipe API by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/613
* consistently set default census version to stable by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/623
* add missing census_version param by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/624
* hard error if the builder receives an unsupported CXG schema version by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/625
* add do_not_delete flag to release.json format by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/628

New Contributors
* tihuan made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/605

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.3.0...v1.3.1

Breaking changes

* Remove Python 3.7 support

Additions

* New sparse iterator added to experimental package (591)

Fixes / changes

* Pytorch loader performance improvements and bug fixes
* Update dependency pins for multiple packages
* Documentation updates

What's Changed
* fix incorrect pytorch obs soma_joinids by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/555
* Fix MacOS failing tests by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/557
* remove pytorch_lr_classifier.py by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/556
* Fix doc-site link in README.md by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/571
* Correct pytorch notebook header by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/570
* Avoid unnecessary re-initialization of ExperimentDataPipe in mp mode by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/566
* census cell dup check by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/569
* require s3fs>=2021.06.1 where cache_regions kwarg is added by RemyLau in https://github.com/chanzuckerberg/cellxgene-census/pull/572
* Notebook reformatting by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/579
* [r] install tiledbsoma from github by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/589
* Remove python 3.7 support by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/582
* use less mem for hvg tests by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/590
* Add eager fetching of SOMA batches to ExperimentDataPipe by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/575
* add sparse iterator to experimental.utils by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/591

New Contributors
* RemyLau made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/572

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.2.1...v1.3.0

Additions
* Python 3.11 support
* add notebooks to demonstrate new experimental APIs

Fixes
* Pytorch loader multi-process issues [522, 516]
* Doc site improvements

What's Changed
* fix: pytorch unit test hangs by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/522
* Add support for Python 3.11 by martinkim0 in https://github.com/chanzuckerberg/cellxgene-census/pull/528
* update notebook guidelines by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/534
* Add docs for experimental modules by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/537
* demo notebook for HVG experimental API by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/536
* Add experimental notebooks to docsite + fix headers by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/541
* fix OOM on pytorch unit test by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/542
* Add pytorch notebook by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/551

New Contributors
* martinkim0 made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/528

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.2.0...v1.2.1

Add experimental API `cellxgene_census.experimental.pp.get_highly_variable_genes`

What's Changed
* minor clarifications for the pypi.org release process by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/512
* [r] cache most R dependencies to speed up r-check CI by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/517
* [r] Add comp_bio_census_info.Rmd by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/407
* fix pytorch multiprocessing result by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/516
* Update release_process.md by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/520
* highly variable gene annotation by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/511


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.1.0...v1.2.0

tiledbsoma` upgraded to `1.2.5`. Added an experimental PyTorch data loader.

What's Changed

* [docs] Add autosummary by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/492
* Add Databricks install instructions to FAQ by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/488
* [docs] Fix the Census link in navbar by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/491
* PyTorch DataLoader by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/499
* chore: update lifecycle tags by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/509
* bump python api tiledbsoma version by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/510

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.0.2...v1.1.0

What's Changed

Update to `tiledbsoma=1.2.4`, which adds support for MacOS ARM64.

Change log summary:
* Bump static census version in R tests by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/472
* [r] update `get_presence_matrix()` and vignette to use zero-based matrix view by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/475
* add acceptance test run by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/485
* rerun notebooks for census build 2023-05-15 by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/484
* Updated gget cellxgene tutorial to reflect workflow updates [formatting corrected] by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/490
* Add docsite version number from the library version by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/481
* pin tiledbsoma==1.2.4 by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/493


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.0.1...v1.0.2