Tiledbsoma

What's Changed

This is a significant release:

* The [Python implementation](https://github.com/single-cell-data/TileDB-SOMA/tree/main-old/apis/python) has been renamed from `tiledbsc` to `tiledbsoma`
* The [R implementation](https://github.com/single-cell-data/TileDB-SOMA/tree/main-old/apis/r) has been moved into this package from its prior location at https://github.com/TileDB-Inc/tiledbsc

Breaking changes

* Rename `tiledbsc` to `tiledbsoma` everywhere on the old branch by johnkerl in 287
* Import https://github.com/TileDB-Inc/tiledbsc (R package) by johnkerl in #285
* Update ASCII storage for dataframes by johnkerl in 273

New features added

* Depend on TileDB-Py 0.17.4 by johnkerl in 335
* Correctly ingest multiple AnnData X layers by johnkerl in 326
* Support non-standard dim names for dataframes by johnkerl in 280

Minor changes

* Bump R version by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/351
* Unbreak R CI by johnkerl in 349
* Update R CI logic by johnkerl in 292
* Late update from 292 by johnkerl in 296
* Rename `apis/R` to `apis/r` by johnkerl in 320
* Debugging R-CMD-check CI failures by johnkerl in 289
* Error-check types on from_anndata/from_h5ad by johnkerl in 293
* Suppress C++ build for old branch by johnkerl in 341
* README.md updates, main-old branch by johnkerl in 344

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.1.11...0.1.20

Support for more array-schema-config options

What's Changed

Major:

* Depend on TileDB-Py 0.17.3 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/278
* Support more tiledb-config options by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/279

Minor:

* Obtain correct obs/var attrsel even without ids specified by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/268
* Document/enforce direct-child relation for SOMA in collection with relative=True by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/270
* libtiledbsc build info by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/275
* Trivial formatting updates for docstring material by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/276
* Setup for readthedocs by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/277

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.1.10...0.1.11

Compatibility with 2.11.1 release

What's Changed

This bypasses 0.1.9 which was no-ship -- the changelist here is for 0.1.8 to 0.1.10.

Major:

* More protection for df indexing on pandas readback by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/264
* This is for compatibility with the core 2.11.1 release deploying to the TileDB-Cloud service today

Internal:

* Build and install libtiledbsc with pip install by gspowley in https://github.com/single-cell-data/TileDB-SingleCell/pull/261
* Unbreak PyPI release by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/265
* Continuing to try to fix PyPI CI with libtiledbsc by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/266

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.1.8...0.1.10

Compatibility with 2.11.1 releasex

What's Changed

Note: marked as pre-release due to PyPI <-> `libtiledbsc` conflicts

Major:

* More protection for df indexing on pandas readback by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/264
* This is for compatibility with the core 2.11.1 release deploying to the TileDB-Cloud service today

Internal:

* Build and install libtiledbsc with pip install by gspowley in https://github.com/single-cell-data/TileDB-SingleCell/pull/261
* Unbreak PyPI release by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/265
* Continuing to try to fix PyPI CI with libtiledbsc by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/266

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.1.8...0.1.9

tiledb-py 0.17.2, and default info logging level

What's Changed

Major:

* Make zstd-filter default level match tiledbsc-r by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/257
* Depend on tiledb-py 0.17.2 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/262
* tiledbsc.logging.info() by default for good uploader UX by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/259

Minor:

* Support return_arrow for various queries by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/256
* Query-syntax neaten in AnnotationDataFrame by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/263

Internal:

* Fix for MacOS localhost build by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/253

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.1.7...0.1.8

Update-writes and improved to/from anndata X-layer selection options

What's Changed

Major UX:

* Support update-write of SOMAs by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/249
* Allow from_anndata to select X layer by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/245
* Keystroke-saver method for add-X-layer by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/246
* Fix NaN issue on SOMA-slice concat by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/248

Minor UX:

* Depend on latest TileDB-Py, with core 2.11 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/237
* Set dataframe indices correctly on readback, if from R by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/247

Docs and copyright:

* Add SOMA spec by aaronwolen in https://github.com/single-cell-data/TileDB-SingleCell/pull/252
* Add copyright notice to all C++ files by Shelnutt2 in https://github.com/single-cell-data/TileDB-SingleCell/pull/251

Internals:

* Improvements to the C++ acceleration library by gspowley in https://github.com/single-cell-data/TileDB-SingleCell/pull/235
* Support fmt that is system installed with spdlog by Shelnutt2 in https://github.com/single-cell-data/TileDB-SingleCell/pull/250

**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.1.6...0.1.7