Tiledbsoma

What's Changed

API:

* Support quiet/info/debug levels for data ingest by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/211
* Support group member deletion by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/210
* Allow skip ingest if exists by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/212
* Correctly use __delitem__ and __delattr__ by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/215

Internals:

* Initial type checking with mypy on CI and fixes by gsakkis in https://github.com/single-cell-data/TileDB-SingleCell/pull/197
* Use keyword-only args by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/209
* Add C++ ManagedQuery by gspowley in https://github.com/single-cell-data/TileDB-SingleCell/pull/194

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.0.8...0.0.9

Performance improvement for reads

Includes 208 which is a fix for the issue mentioned in the [0.0.7 release notes](https://github.com/single-cell-data/TileDB-SingleCell/releases/tag/0.0.7).

Details

* Optimize queries for allow_duplicates=False by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/208
* Pre-commit hooks by gsakkis in https://github.com/single-cell-data/TileDB-SingleCell/pull/193

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.0.7...0.0.8

Notebook/UX updates

Note

The `allow_duplicates=False` change comes with a performance update to be made today in a 0.0.8 follow-on, using 208.

What's Changed

Features:

* Allow users to add new matrices to obsm,varm,obsp,varp by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/203
* Disallow duplicates by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/199

Documentation:

* Collection-slice with heterogeneous data by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/207
* Expressive cell-count queries by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/183
* Make example docs more notebook-centric, part 1 of 3 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/205
* Neaten batch-query example by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/206

Notebook UX:

* Make a simple default display for SOMA objects in notebooks by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/204
* Make soma.uns display by default in notebooks by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/200
* Make it easier to see progress indicators in notebook ingests by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/202
* Neaten logger-init code by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/196

Admin:

* SOMA-consolidator script by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/198

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.0.6...0.0.7

Slice-query/batch-query examples

What's Changed
* Note `soma.attribute_filter` is now `soma.query`
* Preliminary SOMA-collection slice/batch queries by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/173
* Trivial internal name-neaten by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/179
* Include doc info on pip-install by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/180
* Uniformization examples by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/161
* Refactor C++ code by gspowley in https://github.com/single-cell-data/TileDB-SingleCell/pull/182
* Documentation proofreads by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/181
* Lint findings by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/184


**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.0.3...0.0.4