TileDB-SOMA 1.14.0

New features added

• [python] update_uns_by_uri, _update_uns by @ryan-williams in #2876
• [python] Remove pyarrow pin on MacOS by @johnkerl in #3004
• [python] Expose tiledbsoma stats as JSON string or Python-parsed by @johnkerl in #2958
• [r] Timestamp write and read of data frame and array objects by @eddelbuettel in #2926

Bug fixes

• [python] Utilize Arrow schema pa.field nullabilities in DataFrame.create by @johnkerl in #2868
• [python] Offer better guidance on attribute names with . by @johnkerl in #2864
• [python] X-write performance improvement for the non-append case by @johnkerl in #2846
• [c++] Fix ManagedQuery usage in SOMAArray write path by @nguyenv in #2989
• [c++] Only evolve schema when enumerations are extended by @nguyenv in #2851
• [c++] Corner-case bug in extend-enumeration logic by @johnkerl in #2897
• [c++] Remap indexes even if no new enums were added by @nguyenv in #2993

Breaking changes

• [python] Post-deprecation removal of consolidate_and_vacuum from TileDBCreateOptions by @johnkerl in #3000
• [python] Implement scheduled removal of TileDBCreateOptions being passed to write methods by @johnkerl in #2842

Upcoming deprecation notices

• [python/r] Update ETA for new-shape feature by @johnkerl in #2998
• Add tracking links for dense/new-shape support by @johnkerl in #2960

Minor changes

• [python] Ingest/outgest round-trip improvements by @ryan-williams in #2804
• [python] Add CollectionBase.members by @nguyenv in #2795
• [python] Use original error message when re-raising with DoesNotExistError by @nguyenv in #2814
• [python] Debug CI mypy failures related to # type: ignore[misc] by @ryan-williams in #2838
• [python] Misc. ingest/outgest code-neaten improvements by @ryan-williams in #2824
• [python] pin pandas-stubs>=2 during pre-commit mypy hook by @ryan-williams in #2854
• [python] actions{cache,checkout,setup-python} upgrades by @ryan-williams in #2856
• [python] Move _update_column into pybind11 by @nguyenv in #2862
• [python] test_registration_mappings.py::test_pandas_indexing reformat by @ryan-williams in #2853
• [python] Fix a comment by @johnkerl in #2875
• [python] Use somacore 1.0.14 by @johnkerl in #2878
• [python] More AnnData equality assertions in tests by @ryan-williams in #2872
• [python] Update comments, remove unused test params by @ryan-williams in #2873
• [python] Remove some dead code by @johnkerl in #2887
• [python] improve uns DataFrame I/O by @ryan-williams in #2874
• [python] Docstring typo, test-assertion msgs, maybe_raises improvement, verify_logs helper by @ryan-williams in #2892
• [python] Unit-test helper make_df -> make_pd_df by @johnkerl in #2898
• [python] Trivial rename within a unit-test file by @johnkerl in #2908
• [python] Fix ref to method in docstring example by @spencerseale in #2942
• [python/r] Expose shape-related accessors to Python/R bindings by @johnkerl in #2953
• [c++/python] Map core-to-soma domains correctly by @johnkerl in #2957
• [python] Fix nightly-build failure / pybind11 exception-mapping by @johnkerl in #2963
• [python] Minor name-neaten in internals for domain/maxdomain by @johnkerl in #2969
• [python] Trivial dead-strip by @johnkerl in #2968
• [python/r] Array-creation mods for new shape by @johnkerl in #2962
• [c++/python] More exception-mapping fixes by @johnkerl in #2980
• [python] Complete TileDB-Py 0.32.0 pin by @johnkerl in #2984
• [python] Use somacore 1.0.15 by @johnkerl in #2986
• [python/r] Implement resize and tiledbsoma_upgrade_shape by @johnkerl in #2950
• [python] Move temporary feature flag into a module by @johnkerl in #3005
• shellcheck scripts/bld by @ryan-williams in #2927
• Use core 2.26.0 by @johnkerl in #2976
• [r] R DESCRIPTION bump in prep for 1.13 (main branch) by @johnkerl in #2836
• [r] Metadata read/write support via libtiledbsoma by @eddelbuettel in #2819
• [ci] Update autocut rule for current ownership by @johnkerl in #2893
• [r] Small robustification for version comparison by @eddelbuettel in #2914
• [r] Expose timestamp ranges for libtiledbsoma by @mojaveazure in #2929
• [r] Use cached timestamp in $create() and $write() by @mojaveazure in #2930
• [r] Signal script failure to calling script, polish messages by @eddelbuettel in #2932
• [r] Fix bug in blockwise iterator by @mojaveazure in #2965
• [r/ci] Fix bug when installing tiledb-r by @mojaveazure in #2971
• [r] Fix DenseNDArray write after create by @johnkerl in #2970
• [r] Updated groups read/write support via libtiledbsoma by @eddelbuettel in #2973
• [r] Correct a test expression by @eddelbuettel in #2974
• [r] Use cached SOMA context rather than re-creating by @mojaveazure in #2988
• [r] Lower some logging from 'info' to 'debug' by @eddelbuettel in #2991
• [r] Documentation refresher by @eddelbuettel in #2996
• [r] Remove core version check by @johnkerl in #3006
• [r] Add axis checks when initializing a sparse blockwise read by @mojaveazure in #3007
• [r] 1.14 version for release-1.14 branch by @johnkerl in #3010
• [c++] Support option to set log level from environment by @johnkerl in #2972
• [c++] Add dataset_type into SOMAExperiment metadata by @nguyenv in #2884
• [c++] Fix typos in unit-test case by @johnkerl in #2888
• [c++] Remove a temporary gdb hook from #2888 by @johnkerl in #2891
• [c++] Apply ArraySchemaEvolution to specified timestamp by @johnkerl in #2895
• [c++] Final update for Python/R metadata typing by @johnkerl in #2900
• [c++] Trivial parameterizes in test/common.cc by @johnkerl in #2910
• [c++] Methodize timestamped-schema-evolution factory by @johnkerl in #2909
• [c++] Trivial name-neaten by @johnkerl in #2913
• [c++] Remove some dead unit-test code by @johnkerl in #2918
• [c++,r] Update vendored nanoarrow to release 0.5.0 by @eddelbuettel in #2923
• [c++] Revert #2895 by @ryan-williams in #2921
• [c++] Remove some dead code in int64-only shape accessor by @johnkerl in #2915
• [c++] Arrow utils with current-domain option by @johnkerl in #2911
• [c++] Minor function-extract in a unit-test helper by @johnkerl in #2919
• [c++] Pre-neatens before making unit-test helpers for variant-indexed dataframes by @johnkerl in #2936
• [c++] More use_current_domain unit-test parameterization by @johnkerl in #2938
• [c++] Parameterize schema-creation unit-test helpers by @johnkerl in #2939
• [c++] Unit-test resize for SparseNDArray and DenseNDArray by @johnkerl in #2947
• [c++] Make a Catch2 test fixture for dataframes by @johnkerl in #2945
• [c++] Unit-test variant-indexed dataframes by @johnkerl in #2944
• [c++] Performant DataFrame.shape by @johnkerl in #2916
• [c++] Resize for variant-indexed DataFrame by @johnkerl in #2917
• [c++] Implement upgrade_shape for SparseNDArray and DenseNDArray by @johnkerl in #2948
• [c++] Clarify dataframe-shaping test/access points by @johnkerl in #2951
• [c++] Also check for leading slash when checking for 'relative' URLs by @eddelbuettel in #2956
• [c++] Deconfuse a test name by @johnkerl in #2977
• [c++] Remove ArrayBuffers from SOMAArray by @nguyenv in #2979
• [c++] Create specialized templates for SOMAArray casting functions by @nguyenv in #2982
• [c++] Refine concurrency configuration (soma.compute_concurrency_level) by @bkmartinjr in #2978
• [c++] Support writes when attaching Query to ColumnBuffer by @nguyenv in #2983
• [c++] Move cast_bit_to_uint8 into util by @nguyenv in #2992
• [r,c++] Use SOMA Context object throughout by @eddelbuettel in #2997
• [c++] Centralize some nanoarrow helpers by @johnkerl in #2994
• [c++] Use core 2.26.1 by @johnkerl in #3002
• [c++/r] Fix pkgdown build errors by @johnkerl in #3003

New Contributors

• @spencerseale made their first contribution in #2942

Full Changelog: 1.13.1...1.14.0