Cellxgene-census

Breaking Changes
* cell_census Python package updated to utilize `tiledbsoma` 1.0.0rc1, which includes a small breaking change to `SOMATileDBContext` timestamp handling.

Known issues
* there is an errant debugging message which will be printed upon calling `cell_census.open_soma()`. It can be safely ignored.

What's Changed
* docs: Clarifies text for Feature Dataset Presence Matrix, rename schema file by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/211
* Docsite by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/199
* feature: update builder tiledbsoma release by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/154
* Add SOMA page and links by ebezzi in https://github.com/chanzuckerberg/cell-census/pull/217
* docs: fix header level of notebooks by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/224
* add tests for builder arg parser by Bento007 in https://github.com/chanzuckerberg/cell-census/pull/200
* Python package: update tiledbsoma dep to 1.0.0rc1 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/225


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.6.0...v0.7.0

Breaking Changes
* Updated to `tiledbsoma` version 1.0rc0

Improvements
* Fixed performance regression in `open_soma`

What's Changed
* Add codecov github action by Bento007 in https://github.com/chanzuckerberg/cell-census/pull/178
* API cleanup by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/180
* Add validate to builder unit-test by Bento007 in https://github.com/chanzuckerberg/cell-census/pull/147
* Allow default context to be use in open_soma by Bento007 in https://github.com/chanzuckerberg/cell-census/pull/203
* update python package to tiledbsoma 1.0rc0 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/209


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.5.0...v0.6.0

What's Changed
No major changes. Update SOMA dependency to `tiledbsoma==0.5.0a11`.

* feature: builder census summary tweaks by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/171
* remove workaround for portal API gateway error bug by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/167
* update to mypy 1.0 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/169
* lint in census_summary by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/175
* update cell_census python package dependency tiledbsoma 0.5.0a11 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/176


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.4.0...v0.5.0

Breaking Changes
* `open_soma` returns a handle which must be closed upon completion of census use. It is also a context operator, allowing the use of the `with` statement.
* `get_anndata` coords arguments take a single coordinate point list, slice or int, rather than a per-dimension tuple, as these dataframes are always one-dimensional, and indexed by their `soma_joinid`
* package now imports `tiledbsoma==0.5.0a10` which has several breaking API changes.

Enhancements
* Python 3.7 support

What's Changed
* chore: Update license copyright year by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/118
* API cleanup by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/117
* Coords param change for get_anndata by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/122
* Add Python 3.7 support by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/121
* update installation docs to reflect publication of package on PyPi by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/153
* Port cell_census and notebooks to tiledbsoma 0.5.0a10 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/132

New Contributors
* ebezzi made their first contribution in https://github.com/chanzuckerberg/cell-census/pull/76
* Bento007 made their first contribution in https://github.com/chanzuckerberg/cell-census/pull/115
* metakuni made their first contribution in https://github.com/chanzuckerberg/cell-census/pull/127

**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.3.0...v0.4.0

Update to latest SOMA API, v0.5.0a8, including on-disk format change from TileDB v2.14. Includes breaking API changes from 0.2.0.

What's Changed
* update to tilebsoma 0.5.0a4 by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/77
* update to tiledbsoma 0.5.0a6 by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/82
* re-run comp_bio_explore_and_load_lung_data notebook by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/83
* builder fixes by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/84
* fix notebook import by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/90
* Improve notebook `comp_bio_explore_and_load_lung_data.ipynb` by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/91
* Improve notebook `comp_bio_data_integration_scvi.ipynb` by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/92
* tiledb version dependency fixes by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/95
* prep for 0.3.0 release by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/96


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.2.0...v0.3.0

Support v0.2.0 of the Cell Census schema, which moves the location of the dataset presence matrix.

What's Changed
* feat: builder schema changes by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/66
* presence matrix location change in schema 0.2.0 by bkmartinjr in https://github.com/chanzuckerberg/cell-census/pull/70
* fix cmd line example for builder by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/68
* docs: schema update presence matrix by pablo-gar in https://github.com/chanzuckerberg/cell-census/pull/69
* atol/bump builder census schema version by atolopko-czi in https://github.com/chanzuckerberg/cell-census/pull/71


**Full Changelog**: https://github.com/chanzuckerberg/cell-census/compare/v0.1.0...v0.2.0