TileDB-SOMA 0.5.0a3

Breaking changes

Major query improvement:

• [python] ExperimentAxisQuery by @bkmartinjr in #632

Improved names for read methods:

• [python] Fluent API changes for read methods by @bkmartinjr in #663

New features added

Minor query improvements:

• [c++] Support empty range query by @gspowley in #618
• [c++] Support empty range query and Arrow nullable fields by @gspowley in #622
• [python] Support indexing by [] -> empty results in Python by @johnkerl in #623
• [python] DataFrame count accessor by @johnkerl in #637
• [python] Add len(dataframe) by @johnkerl in #649

Ingestion-UX improvements:

• [python] Less-in-core ingest from H5AD [main] by @johnkerl in #640
• [python] Resume mode [main] by @johnkerl in #664
• [python] More memory-reduction for ingest [main] by @johnkerl in #682

Minor changes

• [r] Add SOMACollection class by @aaronwolen in #606
• [r] Rename NdArray -> NDArray by @johnkerl in #609
• [python] Shorten class constants using Final typing feature by @thetorpedodog in #616
• [c++] Add clang-format check to CI by @gspowley in #617
• Add wiki link to README.md by @johnkerl in #619
• [c++] Add SOMAReader reset for stateful API changes by @gspowley in #624
• [r/ci] Fix and re-enable CI macOS builds by @aaronwolen in #629
• [python] Update to setuptools 65.5.1 [main] by @johnkerl in #630
• [r] Adjust SparseNDArray test to renamed soma_data method by @eddelbuettel in #634
• Python 3.7 CI by @johnkerl in #620
• [r] Regularize test-file naming [main] by @johnkerl in #553
• [python] Add some docstrings by @johnkerl in #635
• [python] Deadstrip some old code by @johnkerl in #647
• [r] Correct handling of soma_joinid and soma_rowid by @aaronwolen in #642
• [r] Enhancements to SparseNDArray by @eddelbuettel in #645
• [python] Temp pin to TileDB-Py 0.19.0 by @johnkerl in #651
• [python] Typofix by @johnkerl in #648
• [python] Fixing typing_extensions dependency by @johnkerl in #650
• [python] setup.* typing-extensions vs import typing_extensions by @johnkerl in #655
• [python] Remove _indent by @johnkerl in #658
• [python] Trivial io-module function-reorder by @johnkerl in #662
• [python] Complete basic anndata I/O tests by @johnkerl in #667
• [python] Use RNA not mRNA in examples/tests by @johnkerl in #665
• [python] Simplify setup by @gsakkis in #674
• [python/ci] Fix setup.py to play well with cibuildwheel by @gsakkis in #677
• [python] Trivial comments for wheel-build by @johnkerl in #676
• [python] Prep for import somacore by @johnkerl in #673
• [python] Remove duplicate test_general_utilities.py file. by @thetorpedodog in #680
• [python] Add a few hints so mypy knows what type things are. by @thetorpedodog in #683
• Remove bdist_egg command & unused names from setup.py by @gsakkis in #691
• [python] Bump versions of precommit hooks by @gsakkis in #692
• [r] Additional sparse test code by @eddelbuettel in #690
• [ci] Use paths-ignore to avoid R CI for Python commits and vice versa by @johnkerl in #694

Bug fixes

• [python] Honor AWS_DEFAULT_REGION if no overriding ctx is specified by @johnkerl in #625
• [r] Fix storage of int64 values by SOMADataFrame by @aaronwolen in #639
• [python] Do not use extent 2048 on 8-bit index types by @johnkerl in #653
• [r] Fix creation of SOMADataFrames with non-int32 dimensions by @aaronwolen in #657
• [python] Unbreak editable install from clean by @johnkerl in #689

Upcoming deprecation notices

• Experiment-level open and close, including open-at-timestamp support
• ids in some methods vs coords in others to be aligned (#686)
• Add explicit context to the API (#644)

Full Changelog: 0.5.0a2...0.5.0a3