TileDB-SOMA 1.13.0

Deprecation notices

As noted in #2407, there will be new shape support in the upcoming TileDB-SOMA 1.14, with some impact to user API in the append-to-experiment use-case.

As noted in #2843, TileDBCreateOptions may no longer be passed to write methods.

• [Backport release-1.13] [python] Implement scheduled removal of TileDBCreateOptions being passed to write methods by @github-actions in #2843
• [python] Deprecate tiledb_ctx usage in TileDBSOMAContext by @nguyenv in #2693
• [python] Deprecate tiledb.Filter getters in PlatformConfig by @nguyenv in #2720
• [r/python] Deprecation notices for used_shape by @johnkerl in #2834
• [r] Use .Deprecated for used_shape in R by @johnkerl in #2835

New features added

• [python] Optionally drop unused categories in ExperimentAxisQuery.to_anndata by @nguyenv in #2811
• [Backport release-1.13] [python] X-write performance improvement for the non-append case by @github-actions in #2848
• [Backport release-1.13] [python] Add CollectionBase.members by @github-actions in #2849
• [c++/python] Add reopen for SOMAArray and SOMAGroup by @nguyenv in #2802
• [r] Connect re-indexer to blockwise iterator by @mojaveazure in #2742
• [r] Add drop_levels to SOMAExperimentAxisQuery -> ecosystem outgestors by @mojaveazure in #2825

Bug fixes

• [Backport release-1.13] [python] Use original error message when re-raising with DoesNotExistError by @github-actions in #2844
• [python] Support tiledbsoma.io.update_obs with post-nullable non-string attributes by @johnkerl in #2719
• [python] Allow platform config to set both extent and filter by @johnkerl in #2808
• [python] Improve error message on non-constant query-condition RHS by @johnkerl in #2831
• [python] More gracefully handle invalid operators in query-condition parser by @johnkerl in #2830
• [python] Allow platform config to set extent and filter by @johnkerl in #2808
• [c++] Fix enum-of-bool leveling by @johnkerl in #2723

Minor changes

• Use core 2.25, TileDB-Py 0.31, TileDB-R 0.29 by @johnkerl in #2813
• [Backport release-1.13] [python] Debug CI mypy failures related to # type: ignore[misc] by @github-actions in #2845
• [Backport release-1.13] [python] Misc. ingest/outgest code-neaten improvements by @github-actions in #2847
• [Backport release-1.13] [python] Ingest/outgest round-trip improvements by @github-actions in #2850
• [r] Prep for TileDB-SOMA 1.13 (release-1.13 branch) by @johnkerl in #2837
• [python/r] Update lifecycle tags to "Maturing" by @johnkerl in #2807
• [python] Pin to numpy < 2.0 for 1.12 release by @johnkerl in #2745
• [python] Add pybind11 bindings for SOMAGroup 2/5 by @nguyenv in #2732
• [python] Use bindings for SOMAGroup 3/5 by @nguyenv in #2735
• [python] Replace TileDBObject with SOMAObject; Remove tiledb.TileDBError usage 4/5 by @nguyenv in #2736
• [python] Remove tiledb-py from top-level src (sans io and options) 5/5 by @nguyenv in #2740
• [python] Remove a debug statement by @johnkerl in #2766
• [python] Continue to use tiledb.Ctx's config until it is removed by @nguyenv in #2768
• [python] devtools/outgestor stats and neaten by @johnkerl in #2770
• [python] Update a confusing filename by @johnkerl in #2776
• [python] Bump the stack level of the tiledb_ctx deprecation warning by @ivirshup in #2788
• [python] Release GIL where necessary in pybind11 code by @nguyenv in #2733
• [python] Hold onto GIL for open methods by @nguyenv in #2800
• [python] Retain GIL for exist by @nguyenv in #2801
• [python] Replace py::none with py::tuple for column_names default arg by @nguyenv in #2806
• [python] Typo-fix some parameter names in some internal functions by @johnkerl in #2809
• [c++/python] Add tiledb_timestamp argument for reopen by @nguyenv in #2820
• [python] Remove reshape stub by @johnkerl in #2826
• [python] More reshape neatens by @johnkerl in #2828
• [python] pin codecov/uploader==0.7.3 in codecov-action by @ryan-williams in #2827
• [r] R versioning past release-1.12 branch by @johnkerl in #2716
• [r,c++] Support DenseNDArray write case by @eddelbuettel in #2730
• Compare core to tiledb-py/tiledb-r major+minor, main branch by @johnkerl in #2784
• [r] Add missing documentation for set_data_type by @eddelbuettel in #2818
• [r] Support SparseNDArray writes case by @eddelbuettel in #2755
• [r] Use exists() to check for (local or) remote arrays by @eddelbuettel in #2803
• [r] Remove default mode-flipping in $reopen() by @mojaveazure in #2817
• [r] Expose object-type getter by @eddelbuettel in #2833
• [c++] Fix a nightly-build issue by @johnkerl in #2718
• [c++] Add missing SOMACollection getters and setters by @nguyenv in #2508
• [c++] More SOMAGroup refinements 1/5 by @nguyenv in #2731
• [c++] Remap TileDBError to TileDBSOMAError by @nguyenv in #2753
• [c++] General CMake clean-up by @jp-dark in #2762
• [c++] Split nanoarrow into a separate object library by @jp-dark in #2763
• [c++] Improve exception-handling for query futures by @johnkerl in #2789
• [c++] Cast ArrowTable values in SOMAArray::write to match ArraySchema on-disk by @nguyenv in #2786
• Bump setuptools from 69.5.1 to 70.0.0 in /doc by @dependabot in #2796
• [c++] exists should take in SOMAContext by @nguyenv in #2794
• [c++] Add NDArray::soma_data_type by @nguyenv in #2810
• [c++] Do not call schema evolution for each column by @nguyenv in #2805
• [c++] Check index in enumeration casting before using by @nguyenv in #2816
• pre-commit update by @bkmartinjr in #2821

New Contributors

• @ivirshup made their first contribution in #2788

Full Changelog: 1.12.0rc0...1.13.0