Tiledbsoma

New features added

* [r] SOMA Experiment query API by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1030
* [r] Implement `PlatformConfig` and `SOMATileDBContext` for R by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1026
* [python] Allow all operations on a collection to share a timestamp by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1001
* [python] Explicit shaping for `DataFrame` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1027
* [python] Add `result_order` support to sparse NDArray reads by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1047
* [c++] Update C++ sandbox-build instructions by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1025

Breaking changes

* [python] Improve spec/impl consistency on `cls`/`type`/`kind` parameters by atolopko-czi in https://github.com/single-cell-data/TileDB-SOMA/pull/1045

Minor changes

* [python] Unmark experiment_query xfailures since they pass now by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1018
* [python] Pin stub versions used in type checking by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1024
* [python] Lifecycle maturity tags by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1028
* [r] Fix test for X-layer assertions by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1033
* [r] Revert 1026 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1037
* [python] Start adding errors to docstrings by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1036
* [python] Adding more docstring info on error handling by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1039
* [python] Depend on somacore 1.0.0rc4 by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1048

Bug fixes

* [c++/python] Correctly handle all four timestamp types by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1029
* [python] Return False on various `.exists()` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1040

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0rc2...1.0.0rc3

Bug fixes

* [python] Make the default timestamp in `SOMATileDBContext` be `None` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/998

Minor changes

* Don't run R CI jobs on pre-commit changes by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/993
* [python] Remove an extraneous print statement by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/996
* [python] Raise `TypeError` on unsupported index type `bool` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1002
* Note: this is a non-breaking change since this was already unsupported
* [r] Make `SparseNDArray$write` arg name match Python/spec by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1004
* [python] Depend on somacore 1.0.0rc3 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1012

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0rc1...1.0.0rc2

New features added

* [python] Handle `DataFrame` index types beyond int/string -- except timestamps and bools by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/968
* [python] Handle timestamp index types for `DataFrame` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/985
* [python] Include key–value pairs in metadata `repr` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/987

Breaking changes

* [python] Use the same timestamp across read and write operations by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/981

Minor changes

* [python] Depend upon somacore v1.0.0rc0 by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/982
* [python] Depend on `somacore` 1.0.0rc2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/992
* [python] Move `options` implementations modules to private by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/979
* [python] Add regression test for bug 919 by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/983
* [c++] Improved bounds-detection for Arrow array data by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/986
* [python] A few minor readthedocs-related neatens by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/980

Bug fixes

* [c++] Support `nnz` when `allow_duplicates=True` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/989

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0rc0...1.0.0rc1

New features

* [r] Return schema information as an Arrow schema by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/978

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a13...1.0rc0

As mentioned in the [0.0.5 release notes](https://github.com/single-cell-data/TileDB-SingleCell/releases/tag/0.0.5) there was one known issue in a dependent library to be addressed. This release pulls in that fix.

As well, AnnData `bool` fields in `obs`/`var` are now stored as `TILEDB_BOOL`.

Details

* Use bool attrs from tiledb-py 0.16.0 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/190
* Use logging.info for ingest/outgest prints by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/186
* Update to tiledb-py 0.16.1 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/195


**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.0.5...0.0.6

Status

There is a known issue which will be addressed in an upcoming 0.16.1.

Key changes

* `or` queries -- see 191 for an example
* Validation of I/O on `tiledb://` URIs -- see 189

Details

* Add isort & flake8 to CI by gsakkis in https://github.com/single-cell-data/TileDB-SingleCell/pull/185
* More flake8 findings by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/187
* Fix populate-soco --relative by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/188
* tiledb-cloud testing results by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/189
* Lint tools by gsakkis in https://github.com/single-cell-data/TileDB-SingleCell/pull/192
* Update to tiledb-py 0.16.0 by johnkerl in https://github.com/single-cell-data/TileDB-SingleCell/pull/191


**Full Changelog**: https://github.com/single-cell-data/TileDB-SingleCell/compare/0.0.4...0.0.5